From b727c5219c2d724ddbd2e5915ee31419921c3699 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 25 Aug 2021 11:11:38 -0500 Subject: [PATCH 001/137] Add nextflow Github token --- dot_nextflow/scm.tmpl | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 dot_nextflow/scm.tmpl diff --git a/dot_nextflow/scm.tmpl b/dot_nextflow/scm.tmpl new file mode 100644 index 0000000..8332f2c --- /dev/null +++ b/dot_nextflow/scm.tmpl @@ -0,0 +1,6 @@ +providers { + github { + user = '{{ .githubuser }}' + password = '{{ (bitwarden "item" "3e123829-7167-4dd2-8f3f-ad8f01081fee").login.password }}' + } +} From ab434bc04eb2f8e494ccdeadd040c0243ef554bb Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 25 Aug 2021 11:15:41 -0500 Subject: [PATCH 002/137] Update executable_dot_zshrc --- executable_dot_zshrc | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/executable_dot_zshrc b/executable_dot_zshrc index e1f5bd9..5cca1d3 100644 --- a/executable_dot_zshrc +++ b/executable_dot_zshrc @@ -5,6 +5,10 @@ if [[ -r "${XDG_CACHE_HOME:-$HOME/.cache}/p10k-instant-prompt-${(%):-%n}.zsh" ]] source "${XDG_CACHE_HOME:-$HOME/.cache}/p10k-instant-prompt-${(%):-%n}.zsh" fi +if [ -f "$HOME/.modules" ]; then + source $HOME/.modules +fi + # Load the antigen library if [[ ! -f "$HOME/.antigen.zsh" ]]; then curl -L git.io/antigen > $HOME/.antigen.zsh From 22e423f0e8b578b9eb940bb9ea0da83b58914dec Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 25 Aug 2021 15:31:11 -0500 Subject: [PATCH 003/137] Update dot_envvar Update executable_dot_bashrc --- dot_envvar | 3 +++ executable_dot_bashrc | 4 ++++ 2 files changed, 7 insertions(+) diff --git a/dot_envvar b/dot_envvar index 37e1a33..43f58b7 100644 --- a/dot_envvar +++ b/dot_envvar @@ -44,3 +44,6 @@ export NXF_HOME="$HOME/.nextflow" export NXF_CONDA_CACHEDIR="$NXF_HOME/conda" export NXF_SINGULARITY_CACHEDIR="$NXF_HOME/singularity" export NXF_CHARLIECLOUD_CACHEDIR="$NXF_HOME/charlie" + +# Give Julia full CPU access +export JULIA_NUM_THREADS=$(nproc) diff --git a/executable_dot_bashrc b/executable_dot_bashrc index 7e8104c..9490478 100644 --- a/executable_dot_bashrc +++ b/executable_dot_bashrc @@ -5,6 +5,10 @@ if [ -f /etc/bashrc ]; then . /etc/bashrc fi +if [ -f "$HOME/.modules" ]; then + source $HOME/.modules +fi + # Hook virtual environment modifers source $HOME/.hooks From e1f5ca6e9254eef45dd23632bd29ac74a1f2f3cc Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 25 Aug 2021 16:14:53 -0500 Subject: [PATCH 004/137] Update dot_nextflow/config.tmpl --- dot_nextflow/config.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_nextflow/config.tmpl b/dot_nextflow/config.tmpl index 722e129..90f1412 100644 --- a/dot_nextflow/config.tmpl +++ b/dot_nextflow/config.tmpl @@ -1,4 +1,4 @@ tower { enabled = true - accessToken = {{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }} + accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}' } From d50cabb9c78ebcc4878727baeedb944abc4de096 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 25 Aug 2021 22:48:51 -0400 Subject: [PATCH 005/137] Update executable_dot_Renviron --- executable_dot_Renviron | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/executable_dot_Renviron b/executable_dot_Renviron index e1c55e5..60890ef 100644 --- a/executable_dot_Renviron +++ b/executable_dot_Renviron @@ -1,2 +1,2 @@ ## Change library to constant location for all R 4.x versions -R_LIBS_SITE=~/R/library +R_LIBS_SITE=~/.R/library From d1013db98b40bce499cfb46b37757184b658e620 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 26 Aug 2021 07:52:02 -0500 Subject: [PATCH 006/137] Update dot_profile --- dot_profile | 3 --- 1 file changed, 3 deletions(-) diff --git a/dot_profile b/dot_profile index 34f15a1..40ccadf 100644 --- a/dot_profile +++ b/dot_profile @@ -12,8 +12,5 @@ elif [ -d $HOME/.linuxbrew ]; then fi if [ -n "$BREWPATH" ]; then - if [[ "$SHELL" =~ "zsh" ]]; then - export fpath+=($BREWPATH/share/zsh/site-functions) - fi eval "$($BREWPATH/bin/brew shellenv)" fi From 412e05e9befb485370eef8ac1c6ca3b90391bb85 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 26 Aug 2021 07:52:09 -0500 Subject: [PATCH 007/137] Add dot_zshenv --- dot_zshenv | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 dot_zshenv diff --git a/dot_zshenv b/dot_zshenv new file mode 100644 index 0000000..975f0d1 --- /dev/null +++ b/dot_zshenv @@ -0,0 +1,10 @@ +# Linuxbrew setup +if [ -d $HOME/../linuxbrew/.linuxbrew ]; then + BREWPATH=$HOME/../linuxbrew/.linuxbrew +elif [ -d $HOME/.linuxbrew ]; then + BREWPATH=$HOME/.linuxbrew +fi + +if [ -n "$BREWPATH" ]; then + export fpath+=($BREWPATH/share/zsh/site-functions) +fi From 52ea6d75be31cdbb42ab58cce0d9bb24dc835129 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 26 Aug 2021 07:53:37 -0500 Subject: [PATCH 008/137] Update dot_zshenv --- dot_zshenv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dot_zshenv b/dot_zshenv index 975f0d1..056994c 100644 --- a/dot_zshenv +++ b/dot_zshenv @@ -6,5 +6,6 @@ elif [ -d $HOME/.linuxbrew ]; then fi if [ -n "$BREWPATH" ]; then - export fpath+=($BREWPATH/share/zsh/site-functions) + fpath+=($BREWPATH/share/zsh/site-functions) + export fpath fi From ebfe4fb98174c62174eb53addd302675d8d80ca5 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 1 Sep 2021 12:16:17 -0500 Subject: [PATCH 009/137] Update executable_dot_bashrc --- executable_dot_bashrc | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/executable_dot_bashrc b/executable_dot_bashrc index 9490478..ca58cfd 100644 --- a/executable_dot_bashrc +++ b/executable_dot_bashrc @@ -32,7 +32,9 @@ conda config --set changeps1 true # <<< conda initialize <<< # >>> direnv initalize >>> -eval "$(direnv hook bash)" +if [ $(command -v direnv) ]; then + eval "$(direnv hook bash)" +fi # <<< direnv initalize <<< source $HOME/.envvar From cbf864e60187e0558f35d9867f08ad603089bf44 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 1 Sep 2021 12:16:59 -0500 Subject: [PATCH 010/137] Update executable_dot_zshrc --- executable_dot_zshrc | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/executable_dot_zshrc b/executable_dot_zshrc index 5cca1d3..622f5f0 100644 --- a/executable_dot_zshrc +++ b/executable_dot_zshrc @@ -81,7 +81,9 @@ unset __conda_setup # <<< conda initialize <<< # >>> direnv initalize >>> -eval "$(direnv hook zsh)" +if [ $(command -v direnv) ]; then + eval "$(direnv hook zsh)" +fi # <<< direnv initalize <<< # Tell Antigen that you're done From 56db205f7d1959966834eb89fb89976893172698 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 1 Sep 2021 12:27:15 -0500 Subject: [PATCH 011/137] Update dot_envvar --- dot_envvar | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dot_envvar b/dot_envvar index 43f58b7..ecb93c7 100644 --- a/dot_envvar +++ b/dot_envvar @@ -21,20 +21,20 @@ elif [ $(command -v emacs) ]; then fi # Set a cool new pager with color support -if [[ $(command -v most) ]]; then +if [ $(command -v most) ]; then export PAGER=most fi # Replace cat with bat -if [[ $(command -v bat) ]]; then +if [ $(command -v bat) ]; then export BAT_PAGER="less -RF" export MANPAGER="sh -c 'col -bx | bat -l man -p'" export MANROFFOPT="-c" fi # Add notification support for long-running processes -if [[ $(command -v ntfy) ]]; then +if [ $(command -v ntfy) ]; then eval "$(ntfy shell-integration --longer-than 30)" export AUTO_NTFY_DONE_IGNORE="vim nano emacs kate zshconfig screen tmux ssh top htop less more most nethogs 'singularity shell' julia man" fi From a9f8e40cfd73a0e69f3136d62bd3b0d4f0385045 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 1 Sep 2021 12:35:54 -0500 Subject: [PATCH 012/137] Update executable_dot_zshrc --- executable_dot_zshrc | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/executable_dot_zshrc b/executable_dot_zshrc index 622f5f0..0fb64d3 100644 --- a/executable_dot_zshrc +++ b/executable_dot_zshrc @@ -9,6 +9,12 @@ if [ -f "$HOME/.modules" ]; then source $HOME/.modules fi +# User specific environment +if ! [[ "$PATH" =~ "$HOME/.local/bin:$HOME/bin:" ]] +then + export PATH="$HOME/.local/bin:$HOME/bin:$PATH" +fi + # Load the antigen library if [[ ! -f "$HOME/.antigen.zsh" ]]; then curl -L git.io/antigen > $HOME/.antigen.zsh From 722416e43b3c1105be490e80afa1d93053b43612 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Mon, 11 Oct 2021 09:40:23 -0500 Subject: [PATCH 013/137] Add env_parallel support to zsh --- executable_dot_zshrc | 3 +++ 1 file changed, 3 insertions(+) diff --git a/executable_dot_zshrc b/executable_dot_zshrc index 0fb64d3..ecfb666 100644 --- a/executable_dot_zshrc +++ b/executable_dot_zshrc @@ -106,5 +106,8 @@ source $HOME/.envvar alias zshconfig="$EDITOR ~/.zshrc" source $HOME/.aliases +# Import GNU parallel +source $(which env_parallel.zsh) + # To customize prompt, run `p10k configure` or edit ~/.p10k.zsh. [[ ! -f ~/.p10k.zsh ]] || source ~/.p10k.zsh From 4f2e31565e36082b1675754684c3944b8980886a Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Mon, 11 Oct 2021 09:47:50 -0500 Subject: [PATCH 014/137] Add env_parallel support to bash --- executable_dot_bashrc | 2 ++ 1 file changed, 2 insertions(+) diff --git a/executable_dot_bashrc b/executable_dot_bashrc index ca58cfd..4533693 100644 --- a/executable_dot_bashrc +++ b/executable_dot_bashrc @@ -39,5 +39,7 @@ fi source $HOME/.envvar +source $(which env_parallel.bash) + # Make the prompt pretty, just in case we're stuck in bash land export PS1="[\[\e[32m\]\u\[\e[m\]@\[\e[33m\]\h\[\e[m\] \[\e[34m\]\W\[\e[m\]] \\$ " From 21a28dd90b3409d5c94e3c01b299877561550a8d Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 15:18:38 -0500 Subject: [PATCH 015/137] Update executable_dot_zshrc --- executable_dot_zshrc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/executable_dot_zshrc b/executable_dot_zshrc index ecfb666..1c9e3dc 100644 --- a/executable_dot_zshrc +++ b/executable_dot_zshrc @@ -17,7 +17,7 @@ fi # Load the antigen library if [[ ! -f "$HOME/.antigen.zsh" ]]; then - curl -L git.io/antigen > $HOME/.antigen.zsh + curl -L git.io/antigen > $HOME/antigen.zsh fi source "$HOME/.antigen.zsh" From addb5618085aa896b3cb50c71661ae39536cbe13 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 15:23:33 -0500 Subject: [PATCH 016/137] Update executable_dot_zshrc --- executable_dot_zshrc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/executable_dot_zshrc b/executable_dot_zshrc index 1c9e3dc..b081566 100644 --- a/executable_dot_zshrc +++ b/executable_dot_zshrc @@ -16,7 +16,7 @@ then fi # Load the antigen library -if [[ ! -f "$HOME/.antigen.zsh" ]]; then +if [[ ! -f "$HOME/antigen.zsh" ]]; then curl -L git.io/antigen > $HOME/antigen.zsh fi source "$HOME/.antigen.zsh" From 1368bf11a71971484ececcd370f8cb8c048fa95f Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 16:05:10 -0500 Subject: [PATCH 017/137] Rename executable_dot_bashrc to executable_dot_bashrc.tmpl --- executable_dot_bashrc => executable_dot_bashrc.tmpl | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename executable_dot_bashrc => executable_dot_bashrc.tmpl (100%) diff --git a/executable_dot_bashrc b/executable_dot_bashrc.tmpl similarity index 100% rename from executable_dot_bashrc rename to executable_dot_bashrc.tmpl From f06d6797c5abc8aecb15015b32e98159ffec625c Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 16:17:03 -0500 Subject: [PATCH 018/137] Update executable_dot_bashrc.tmpl --- executable_dot_bashrc.tmpl | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index 4533693..bc44116 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -5,6 +5,16 @@ if [ -f /etc/bashrc ]; then . /etc/bashrc fi +{{ if (eq .chezmoi.osRelease.id "centos") }} +{{ if (eq .chezmoi.osRelease.versionID "7") }} +# Switch to zsh if interactive, and we haven't been told not to +if [[ ($- == *i*) && ($SSH_TTY) && (-z $NO_ZSH) ]]; then + export SHELL=$(which zsh) + exec $SHELL -l +fi +{{ end }} +{{ end }} + if [ -f "$HOME/.modules" ]; then source $HOME/.modules fi From 08aba126fccb8de99ebcce3eee24d6f876d67c7c Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 16:27:58 -0500 Subject: [PATCH 019/137] Update executable_dot_Renviron --- executable_dot_Renviron | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/executable_dot_Renviron b/executable_dot_Renviron index e1c55e5..60890ef 100644 --- a/executable_dot_Renviron +++ b/executable_dot_Renviron @@ -1,2 +1,2 @@ ## Change library to constant location for all R 4.x versions -R_LIBS_SITE=~/R/library +R_LIBS_SITE=~/.R/library From 8e2ff856c047f2d9e788d6ad8b4f8ef8a1513ab2 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 16:30:54 -0500 Subject: [PATCH 020/137] Update dot_profile --- dot_profile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dot_profile b/dot_profile index 40ccadf..183c491 100644 --- a/dot_profile +++ b/dot_profile @@ -13,4 +13,6 @@ fi if [ -n "$BREWPATH" ]; then eval "$($BREWPATH/bin/brew shellenv)" + export HOMEBREW_MAKE_JOBS=1 + export HOMEBREW_NO_ANALYTICS=1 fi From 9ca0192356cd252b0fce409fba6fded03296668b Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 16:34:21 -0500 Subject: [PATCH 021/137] Rename dot_envvar to dot_envvar.tmpl --- dot_envvar => dot_envvar.tmpl | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename dot_envvar => dot_envvar.tmpl (100%) diff --git a/dot_envvar b/dot_envvar.tmpl similarity index 100% rename from dot_envvar rename to dot_envvar.tmpl From a96168062754151cb04112291d972a20013143de Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 16:54:31 -0500 Subject: [PATCH 022/137] Update dot_envvar.tmpl --- dot_envvar.tmpl | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/dot_envvar.tmpl b/dot_envvar.tmpl index ecb93c7..40b802b 100644 --- a/dot_envvar.tmpl +++ b/dot_envvar.tmpl @@ -41,9 +41,19 @@ fi # Set the Nextflow enviroment caches export NXF_HOME="$HOME/.nextflow" -export NXF_CONDA_CACHEDIR="$NXF_HOME/conda" -export NXF_SINGULARITY_CACHEDIR="$NXF_HOME/singularity" -export NXF_CHARLIECLOUD_CACHEDIR="$NXF_HOME/charlie" +{{ if (eq .cluster "scinet") }} +NXF_CACHE=/90daydata/shared/$USER/.nextflow +{{ else }} +NXF_CACHE=$NXF_HOME +{{ end }} +export NXF_CONDA_CACHEDIR="$NXF_CACHE/conda" +export NXF_SINGULARITY_CACHEDIR="$NXF_CACHE/singularity" +export NXF_CHARLIECLOUD_CACHEDIR="$NXF_CACHE/charlie" + +{{ if (eq .cluster "scinet") }} +# Set the Singularity image cache +NXF_CACHE=/90daydata/share/$USER/.singularity +{{ end }} # Give Julia full CPU access export JULIA_NUM_THREADS=$(nproc) From 3fd743908ce2a79b2c1ff8c737422ffbc442e446 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 16:57:31 -0500 Subject: [PATCH 023/137] Update dot_screenrc --- dot_screenrc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_screenrc b/dot_screenrc index 8c2d2ae..b1bcd37 100644 --- a/dot_screenrc +++ b/dot_screenrc @@ -1,4 +1,4 @@ -shell /usr/bin/zsh +shell zsh startup_message off hardstatus alwayslastline hardstatus string "%{= KW} %H %{= Kw}|%{-} %-Lw%{= bW}%n%f %t%{-}%+Lw %=%C%a %Y-%M-%d" From 58344c1e301312b761b7eb9febc41c014e3dbea4 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 17:02:27 -0500 Subject: [PATCH 024/137] Update dot_envvar.tmpl --- dot_envvar.tmpl | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dot_envvar.tmpl b/dot_envvar.tmpl index 40b802b..f43e86c 100644 --- a/dot_envvar.tmpl +++ b/dot_envvar.tmpl @@ -57,3 +57,6 @@ NXF_CACHE=/90daydata/share/$USER/.singularity # Give Julia full CPU access export JULIA_NUM_THREADS=$(nproc) + +# Make NCBI happy +export NCBI_API_KEY='{{ (bitwarden "item" "7d42eba0-c256-4d3b-8d0e-adbf016a08f8").login.password }}' From 72857ec29143b1e76f49287df5ca612261e6bdb3 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 17:22:28 -0500 Subject: [PATCH 025/137] Update executable_dot_zshrc --- executable_dot_zshrc | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/executable_dot_zshrc b/executable_dot_zshrc index b081566..843da68 100644 --- a/executable_dot_zshrc +++ b/executable_dot_zshrc @@ -107,7 +107,9 @@ alias zshconfig="$EDITOR ~/.zshrc" source $HOME/.aliases # Import GNU parallel -source $(which env_parallel.zsh) +if [ $(command -v env_parallel.zsh) ]; then + source $(which env_parallel.zsh) +fi # To customize prompt, run `p10k configure` or edit ~/.p10k.zsh. [[ ! -f ~/.p10k.zsh ]] || source ~/.p10k.zsh From 1a1a4cf05ec4192acbc6c0a2714d6cc9a4832f16 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 17:23:04 -0500 Subject: [PATCH 026/137] Update executable_dot_bashrc.tmpl --- executable_dot_bashrc.tmpl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index bc44116..8b74bbc 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -49,7 +49,9 @@ fi source $HOME/.envvar -source $(which env_parallel.bash) +if [ $(command -v env_parallel.bash) ]; then + source $(which env_parallel.bash) +fi # Make the prompt pretty, just in case we're stuck in bash land export PS1="[\[\e[32m\]\u\[\e[m\]@\[\e[33m\]\h\[\e[m\] \[\e[34m\]\W\[\e[m\]] \\$ " From 506830ab9bee4680a7564568760588442aeec654 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 12 Oct 2021 17:26:38 -0500 Subject: [PATCH 027/137] Update dot_envvar.tmpl --- dot_envvar.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_envvar.tmpl b/dot_envvar.tmpl index f43e86c..c31bfb9 100644 --- a/dot_envvar.tmpl +++ b/dot_envvar.tmpl @@ -52,7 +52,7 @@ export NXF_CHARLIECLOUD_CACHEDIR="$NXF_CACHE/charlie" {{ if (eq .cluster "scinet") }} # Set the Singularity image cache -NXF_CACHE=/90daydata/share/$USER/.singularity +SINGULARITY_CACHEDIR=/90daydata/share/$USER/.singularity {{ end }} # Give Julia full CPU access From d508b92efd2d065cd6af621265264269c9c15ad9 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 07:24:24 -0500 Subject: [PATCH 028/137] Make profile POSIX compliant Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_profile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dot_profile b/dot_profile index 183c491..0a184df 100644 --- a/dot_profile +++ b/dot_profile @@ -1,7 +1,7 @@ +# shellcheck shell=sh # User specific environment -if ! [[ "$PATH" =~ "$HOME/.local/bin:$HOME/bin:" ]] -then - export PATH="$HOME/.local/bin:$HOME/bin:$PATH" +if ! [ "$(expr "$PATH" : "$HOME/.local/bin:$HOME/bin:")" ];then + export PATH="$HOME/.local/bin:$HOME/bin:$PATH" fi # Linuxbrew setup From 363a93030eac39c99c6b6f5b18c94653c77ad7bd Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 07:27:45 -0500 Subject: [PATCH 029/137] Make .bash_profile shellcheck compliant Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- executable_dot_bash_profile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/executable_dot_bash_profile b/executable_dot_bash_profile index 70bd631..9433f6e 100644 --- a/executable_dot_bash_profile +++ b/executable_dot_bash_profile @@ -1 +1,3 @@ -source $HOME/.profile +# shellcheck shell=bash +# shellcheck source=dot_profile +source "${HOME}/.profile" From 2dabcd4e1140d2248ff0ba01d6c7aafd59813f12 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 07:46:01 -0500 Subject: [PATCH 030/137] Try to bring the profile PATH into bash Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- executable_dot_bashrc.tmpl | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index 8b74bbc..2dda122 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -1,10 +1,15 @@ +# shellcheck shell=bash # .bashrc +# Source login shell +source "${HOME}/.bash_profile" + # Source global definitions if [ -f /etc/bashrc ]; then - . /etc/bashrc + source /etc/bashrc fi +# shellcheck disable=1054,1073,1050,1072,1009 {{ if (eq .chezmoi.osRelease.id "centos") }} {{ if (eq .chezmoi.osRelease.versionID "7") }} # Switch to zsh if interactive, and we haven't been told not to From 0f2023f99925bc25095803fd32bceb59e9a4b270 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 07:56:22 -0500 Subject: [PATCH 031/137] Switch to more portable zsh switching Older versions of `which` apparantly are more verbose and list extra text in addition to the path. Get rid of that nonsense Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_profile | 4 +--- executable_dot_bashrc.tmpl | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/dot_profile b/dot_profile index 0a184df..036b64b 100644 --- a/dot_profile +++ b/dot_profile @@ -1,8 +1,6 @@ # shellcheck shell=sh # User specific environment -if ! [ "$(expr "$PATH" : "$HOME/.local/bin:$HOME/bin:")" ];then - export PATH="$HOME/.local/bin:$HOME/bin:$PATH" -fi +export PATH="$HOME/.local/bin:$HOME/bin:$PATH" # Linuxbrew setup if [ -d $HOME/../linuxbrew/.linuxbrew ]; then diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index 2dda122..d6ae9c4 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -14,7 +14,7 @@ fi {{ if (eq .chezmoi.osRelease.versionID "7") }} # Switch to zsh if interactive, and we haven't been told not to if [[ ($- == *i*) && ($SSH_TTY) && (-z $NO_ZSH) ]]; then - export SHELL=$(which zsh) + export SHELL=$(command -v zsh) exec $SHELL -l fi {{ end }} From 734240b1cb5953aee6148779aef0db43ef6f5bdf Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 08:00:47 -0500 Subject: [PATCH 032/137] Quit sourcing global definitions Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- executable_dot_bashrc.tmpl | 5 ----- 1 file changed, 5 deletions(-) diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index d6ae9c4..d1a40b5 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -4,11 +4,6 @@ # Source login shell source "${HOME}/.bash_profile" -# Source global definitions -if [ -f /etc/bashrc ]; then - source /etc/bashrc -fi - # shellcheck disable=1054,1073,1050,1072,1009 {{ if (eq .chezmoi.osRelease.id "centos") }} {{ if (eq .chezmoi.osRelease.versionID "7") }} From 0e971860ad4edf8636de6706e562506732d6a2f7 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 08:06:01 -0500 Subject: [PATCH 033/137] Rename dot_zshenv to dot_zshenv.tmpl --- dot_zshenv => dot_zshenv.tmpl | 1 + 1 file changed, 1 insertion(+) rename dot_zshenv => dot_zshenv.tmpl (91%) diff --git a/dot_zshenv b/dot_zshenv.tmpl similarity index 91% rename from dot_zshenv rename to dot_zshenv.tmpl index 056994c..08c5694 100644 --- a/dot_zshenv +++ b/dot_zshenv.tmpl @@ -1,3 +1,4 @@ +# shellcheck shell=zsh # Linuxbrew setup if [ -d $HOME/../linuxbrew/.linuxbrew ]; then BREWPATH=$HOME/../linuxbrew/.linuxbrew From 219c25e0f0b4f7a36a51b97b4ed220bb35fc5c3c Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 08:27:30 -0500 Subject: [PATCH 034/137] Add in workaround for fpath Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_zshenv.tmpl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/dot_zshenv.tmpl b/dot_zshenv.tmpl index 08c5694..8efe7b4 100644 --- a/dot_zshenv.tmpl +++ b/dot_zshenv.tmpl @@ -1,4 +1,19 @@ # shellcheck shell=zsh + +{{- if (eq .cluster "scinet") -}} +# Workaround for SCINet admins clobbering fpath +ZEXECDIR=$(dirname $(command -v zsh)) +if [ -d $ZEXECDIR/../share/zsh/functions ]; then + fpath+=$(realpath $ZEXECDIR/../share/zsh/functions) +else + for ZSHAREDIR in $ZEXECDIR/../share/zsh/*; do + if [ -d $ZSHAREDIR/functions ]; then + fpath+=$(realpath $ZSHAREDIR/functions) + fi + done +fi +{{- end -}} + # Linuxbrew setup if [ -d $HOME/../linuxbrew/.linuxbrew ]; then BREWPATH=$HOME/../linuxbrew/.linuxbrew From 397a2f9ac8a9e8f9b17c571cef33077ec8c1ced0 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 08:37:38 -0500 Subject: [PATCH 035/137] Simplify fpath workaround Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_zshenv.tmpl | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/dot_zshenv.tmpl b/dot_zshenv.tmpl index 8efe7b4..2a79f32 100644 --- a/dot_zshenv.tmpl +++ b/dot_zshenv.tmpl @@ -1,18 +1,9 @@ -# shellcheck shell=zsh +# shellcheck shell=bash -{{- if (eq .cluster "scinet") -}} +{{ if (or (eq .chezmoi.hostname "Atlas-login-1") (eq .chezmoi.hostname "Atlas-login-2")) -}} # Workaround for SCINet admins clobbering fpath -ZEXECDIR=$(dirname $(command -v zsh)) -if [ -d $ZEXECDIR/../share/zsh/functions ]; then - fpath+=$(realpath $ZEXECDIR/../share/zsh/functions) -else - for ZSHAREDIR in $ZEXECDIR/../share/zsh/*; do - if [ -d $ZSHAREDIR/functions ]; then - fpath+=$(realpath $ZSHAREDIR/functions) - fi - done -fi -{{- end -}} +fpath+=($HOME/.local/share/zsh/5.8/functions) +{{- end }} # Linuxbrew setup if [ -d $HOME/../linuxbrew/.linuxbrew ]; then From b4d29be2b4155143d65d93dd3eb96868c93ff058 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 08:42:17 -0500 Subject: [PATCH 036/137] Rename executable_dot_zshrc to executable_dot_zshrc.tmpl --- executable_dot_zshrc => executable_dot_zshrc.tmpl | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename executable_dot_zshrc => executable_dot_zshrc.tmpl (100%) diff --git a/executable_dot_zshrc b/executable_dot_zshrc.tmpl similarity index 100% rename from executable_dot_zshrc rename to executable_dot_zshrc.tmpl From 03f75b29c31582cfdb28929445202744a5780fde Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 08:44:01 -0500 Subject: [PATCH 037/137] Disable instant prompt for SCINet Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- executable_dot_zshrc.tmpl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index 843da68..c038b4f 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -1,9 +1,11 @@ +{{- if (not (eq .cluster "scinet")) -}} # Enable Powerlevel10k instant prompt. Should stay close to the top of ~/.zshrc. # Initialization code that may require console input (password prompts, [y/n] # confirmations, etc.) must go above this block; everything else may go below. if [[ -r "${XDG_CACHE_HOME:-$HOME/.cache}/p10k-instant-prompt-${(%):-%n}.zsh" ]]; then source "${XDG_CACHE_HOME:-$HOME/.cache}/p10k-instant-prompt-${(%):-%n}.zsh" fi +{{- end }} if [ -f "$HOME/.modules" ]; then source $HOME/.modules From e394d9a0265015032e39ea4452f00e00ae04236b Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 08:49:52 -0500 Subject: [PATCH 038/137] Switch execution order of profile and rc Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- executable_dot_bash_profile | 1 + executable_dot_bashrc.tmpl | 3 --- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/executable_dot_bash_profile b/executable_dot_bash_profile index 9433f6e..9ede22c 100644 --- a/executable_dot_bash_profile +++ b/executable_dot_bash_profile @@ -1,3 +1,4 @@ # shellcheck shell=bash # shellcheck source=dot_profile source "${HOME}/.profile" +source "${HOME}/.bashrc" diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index d1a40b5..7b85a14 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -1,9 +1,6 @@ # shellcheck shell=bash # .bashrc -# Source login shell -source "${HOME}/.bash_profile" - # shellcheck disable=1054,1073,1050,1072,1009 {{ if (eq .chezmoi.osRelease.id "centos") }} {{ if (eq .chezmoi.osRelease.versionID "7") }} From 494d813dec9ef114df43b8953252c0441ccbca91 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Oct 2021 09:07:44 -0500 Subject: [PATCH 039/137] Fix exporting the Singularity cache directory Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_envvar.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_envvar.tmpl b/dot_envvar.tmpl index c31bfb9..cc7e6b4 100644 --- a/dot_envvar.tmpl +++ b/dot_envvar.tmpl @@ -52,7 +52,7 @@ export NXF_CHARLIECLOUD_CACHEDIR="$NXF_CACHE/charlie" {{ if (eq .cluster "scinet") }} # Set the Singularity image cache -SINGULARITY_CACHEDIR=/90daydata/share/$USER/.singularity +export SINGULARITY_CACHEDIR=/90daydata/share/$USER/.singularity {{ end }} # Give Julia full CPU access From 4f64e9f1a3eb1608b1db518f64a81f6f2e9cf05c Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 10 Nov 2021 14:19:32 -0600 Subject: [PATCH 040/137] Add private_dot_git-credentials.tmpl --- private_dot_git-credentials.tmpl | 1 + 1 file changed, 1 insertion(+) create mode 100644 private_dot_git-credentials.tmpl diff --git a/private_dot_git-credentials.tmpl b/private_dot_git-credentials.tmpl new file mode 100644 index 0000000..a500198 --- /dev/null +++ b/private_dot_git-credentials.tmpl @@ -0,0 +1 @@ +https://millironx: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@github.com From b0a0a4a9fbe74cbe678585dc228dc4478e2e50ea Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 10 Nov 2021 14:21:55 -0600 Subject: [PATCH 041/137] Update private_dot_git-credentials.tmpl --- private_dot_git-credentials.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/private_dot_git-credentials.tmpl b/private_dot_git-credentials.tmpl index a500198..7ca97ad 100644 --- a/private_dot_git-credentials.tmpl +++ b/private_dot_git-credentials.tmpl @@ -1 +1 @@ -https://millironx: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@github.com +https://{{ .githubuser }}:{{ (bitwarden "item" "3e123829-7167-4dd2-8f3f-ad8f01081fee").login.password }}@github.com From fbb0dc81ea339aca6c8808e991434d742ac11197 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 17 Nov 2021 12:45:06 -0600 Subject: [PATCH 042/137] Fix incorrect path for Singularity cache --- dot_envvar.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_envvar.tmpl b/dot_envvar.tmpl index cc7e6b4..c5b649d 100644 --- a/dot_envvar.tmpl +++ b/dot_envvar.tmpl @@ -52,7 +52,7 @@ export NXF_CHARLIECLOUD_CACHEDIR="$NXF_CACHE/charlie" {{ if (eq .cluster "scinet") }} # Set the Singularity image cache -export SINGULARITY_CACHEDIR=/90daydata/share/$USER/.singularity +export SINGULARITY_CACHEDIR=/90daydata/shared/$USER/.singularity {{ end }} # Give Julia full CPU access From 6057729c590c0e4b0d443af895ff7c4c945facc8 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Dec 2021 10:59:25 -0600 Subject: [PATCH 043/137] Add Nextflow configuration options for SCINet Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_nextflow/config.tmpl | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/dot_nextflow/config.tmpl b/dot_nextflow/config.tmpl index 90f1412..557be40 100644 --- a/dot_nextflow/config.tmpl +++ b/dot_nextflow/config.tmpl @@ -2,3 +2,22 @@ tower { enabled = true accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}' } +{{ if (eq .cluster "scinet") }} +process { + executor = 'slurm' + clusterOptions = '--account=fabadru' + {{ if (or (eq .chezmoi.hostname "Atlas-login-1") (eq .chezmoi.hostname "Atlas-login-2")) }} + withLabel: process_high_memory { + queue = 'bigmem' + } + {{ end }} + {{ if (eq .chezmoi.hostname "ceres") }} + withLabel: process_high_memory { + queue = 'mem' + } + withLabel: process_long { + queue = 'long' + } + {{ end }} +} +{{ end }} From 1371471497fe39f87542135a190d5e5d3b247666 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Dec 2021 11:28:09 -0600 Subject: [PATCH 044/137] Use scratch spaces when using SCINet Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_nextflow/config.tmpl | 1 + 1 file changed, 1 insertion(+) diff --git a/dot_nextflow/config.tmpl b/dot_nextflow/config.tmpl index 557be40..1715f6b 100644 --- a/dot_nextflow/config.tmpl +++ b/dot_nextflow/config.tmpl @@ -4,6 +4,7 @@ tower { } {{ if (eq .cluster "scinet") }} process { + scratch = true executor = 'slurm' clusterOptions = '--account=fabadru' {{ if (or (eq .chezmoi.hostname "Atlas-login-1") (eq .chezmoi.hostname "Atlas-login-2")) }} From 0043e59068a554fcc496cb48375b44134aba1401 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 15 Dec 2021 10:15:04 -0600 Subject: [PATCH 045/137] Add default merge mode to gitconfig Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- executable_dot_gitconfig.tmpl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/executable_dot_gitconfig.tmpl b/executable_dot_gitconfig.tmpl index b79eb05..885e01b 100644 --- a/executable_dot_gitconfig.tmpl +++ b/executable_dot_gitconfig.tmpl @@ -12,6 +12,8 @@ defaultBranch = master [github] user = MillironX +[pull] + rebase = false {{- if eq .chezmoi.osRelease.id "fedora" }} [diff] tool = kdiff3 From 838a9741a903c36cbd5bfde7ee06ecac749ee957 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 15 Dec 2021 10:15:48 -0600 Subject: [PATCH 046/137] Disable line wrap in bat by default Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_envvar.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_envvar.tmpl b/dot_envvar.tmpl index c5b649d..43373a2 100644 --- a/dot_envvar.tmpl +++ b/dot_envvar.tmpl @@ -28,7 +28,7 @@ fi # Replace cat with bat if [ $(command -v bat) ]; then - export BAT_PAGER="less -RF" + export BAT_PAGER="less -SRF" export MANPAGER="sh -c 'col -bx | bat -l man -p'" export MANROFFOPT="-c" fi From 1526bf85d6c5b32f614ad55717032792386e52ac Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 30 Dec 2021 12:41:28 -0600 Subject: [PATCH 047/137] Add lots more options for Nextflow+SCINet Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_nextflow/config.tmpl | 74 ++++++++++++++++++++++++++++++++++------ 1 file changed, 63 insertions(+), 11 deletions(-) diff --git a/dot_nextflow/config.tmpl b/dot_nextflow/config.tmpl index 1715f6b..3dd22a5 100644 --- a/dot_nextflow/config.tmpl +++ b/dot_nextflow/config.tmpl @@ -2,23 +2,75 @@ tower { enabled = true accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}' } -{{ if (eq .cluster "scinet") }} +{{- if (eq .cluster "scinet") -}} +params { + {{ if (eq .chezmoi.hostname "ceres") }} + max_memory = 768.GB + max_cpus = 40 + max_time = 1000.h + {{ end }} + {{ if (or (eq .chezmoi.hostname "Atlas-login-1") (eq .chezmoi.hostname "Atlas-login-2")) }} + max_memory = 1539.GB + max_cpus = 24 + max_time = 14.d + {{ end }} +} + process { scratch = true executor = 'slurm' clusterOptions = '--account=fabadru' {{ if (or (eq .chezmoi.hostname "Atlas-login-1") (eq .chezmoi.hostname "Atlas-login-2")) }} - withLabel: process_high_memory { - queue = 'bigmem' - } + cpus = 12 + memory = 192.GB + time = 7.d + withLabel: process_high_memory { + queue = 'bigmem' + memory = 1536.GB + } + withLabel: process_long { + time = 14.d + } + withLabel: process_medium { + cpus = 12 + memory = 192.GB + time = 7.d + } + withLabel: process_high { + cpus = 24 + memory = 384.GB + time = 14.d + } {{ end }} {{ if (eq .chezmoi.hostname "ceres") }} - withLabel: process_high_memory { - queue = 'mem' - } - withLabel: process_long { - queue = 'long' - } + queue = 'short' + cpus = 18 + memory = 54.GB + time = 24.h + withLabel: process_high_memory { + queue = 'mem' + memory = 640.GB + } + withLabel: process_long { + queue = 'long' + time = 21.d + } + withLabel: process_medium { + queue = 'medium' + cpus = 36 + time = 7.d + } + withLabel: process_high { + queue = 'long' + cpus = 36 + time = 21.d + } {{ end }} + withLabel: process_low { + cpus = 2 + memory = 4.GB + time = 1.h + {{ if (eq .chezmoi.hostname "ceres") }}queue = 'short'{{ end }} + } } -{{ end }} +{{- end -}} From 3d373a25b5dfd06a71e6d0416b4b25b96d547780 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 30 Dec 2021 12:46:02 -0600 Subject: [PATCH 048/137] Remove whitespace changes from Nextflow config Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_nextflow/config.tmpl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dot_nextflow/config.tmpl b/dot_nextflow/config.tmpl index 3dd22a5..75af6c1 100644 --- a/dot_nextflow/config.tmpl +++ b/dot_nextflow/config.tmpl @@ -2,7 +2,7 @@ tower { enabled = true accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}' } -{{- if (eq .cluster "scinet") -}} +{{ if (eq .cluster "scinet") }} params { {{ if (eq .chezmoi.hostname "ceres") }} max_memory = 768.GB @@ -73,4 +73,4 @@ process { {{ if (eq .chezmoi.hostname "ceres") }}queue = 'short'{{ end }} } } -{{- end -}} +{{ end }} From aae9718f59ff9015cabb27163b80b9c248fabfca Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 8 Mar 2022 09:36:52 -0600 Subject: [PATCH 049/137] Refactor Nextflow config to profiles Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_nextflow/config.tmpl | 156 ++++++++++++++++++++++----------------- 1 file changed, 90 insertions(+), 66 deletions(-) diff --git a/dot_nextflow/config.tmpl b/dot_nextflow/config.tmpl index 75af6c1..f76e329 100644 --- a/dot_nextflow/config.tmpl +++ b/dot_nextflow/config.tmpl @@ -2,75 +2,99 @@ tower { enabled = true accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}' } -{{ if (eq .cluster "scinet") }} -params { - {{ if (eq .chezmoi.hostname "ceres") }} - max_memory = 768.GB - max_cpus = 40 - max_time = 1000.h - {{ end }} - {{ if (or (eq .chezmoi.hostname "Atlas-login-1") (eq .chezmoi.hostname "Atlas-login-2")) }} - max_memory = 1539.GB - max_cpus = 24 - max_time = 14.d - {{ end }} -} +profiles { + aahz { + params { + config_profile_description = 'KSU VDL Molecular NGS Big Server profile' + config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>' + config_profile_url = null -process { - scratch = true - executor = 'slurm' - clusterOptions = '--account=fabadru' - {{ if (or (eq .chezmoi.hostname "Atlas-login-1") (eq .chezmoi.hostname "Atlas-login-2")) }} - cpus = 12 - memory = 192.GB - time = 7.d - withLabel: process_high_memory { - queue = 'bigmem' - memory = 1536.GB + max_memory = 745.GB + max_cpus = 78 + max_time = 7.d + } + singularity { + enabled = true + autoMounts = true + envWhitelist = 'NCBI_API_KEY' + } + process { + executor = 'local' + } } - withLabel: process_long { - time = 14.d + atlas { + params { + config_profile_description = 'Mississippi State University Atlas Cluster profile' + config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>' + config_profile_url = 'https://www.hpc.msstate.edu/computing/atlas/' + + max_memory = 1539.GB + max_cpus = 24 + max_time = 14.d + } + singularity { + enabled = true + autoMounts = true + envWhitelist = 'NCBI_API_KEY' + } + process { + scratch = true + executor = 'slurm' + clusterOptions = '--account=fabadru' + + withLabel: process_high_memory { + queue = 'bigmem' + } + } } - withLabel: process_medium { - cpus = 12 - memory = 192.GB - time = 7.d + ceres { + params { + config_profile_description = 'USDA ARS SCInet Ceres Cluster profile' + config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>' + config_profile_url = 'https://scinet.usda.gov/guide/ceres/#partitions-or-queues' + + max_memory = 768.GB + max_cpus = 40 + max_time = 1000.h + } + singularity { + enabled = true + autoMounts = true + envWhitelist = 'NCBI_API_KEY' + } + process { + scratch = true + executor = 'slurm' + queue = 'short' + + withLabel: process_high_memory { + queue = 'mem' + } + withLabel: process_long { + queue = 'long' + } + withLabel: process_medium { + queue = 'medium' + } + } } - withLabel: process_high { - cpus = 24 - memory = 384.GB - time = 14.d - } - {{ end }} - {{ if (eq .chezmoi.hostname "ceres") }} - queue = 'short' - cpus = 18 - memory = 54.GB - time = 24.h - withLabel: process_high_memory { - queue = 'mem' - memory = 640.GB - } - withLabel: process_long { - queue = 'long' - time = 21.d - } - withLabel: process_medium { - queue = 'medium' - cpus = 36 - time = 7.d - } - withLabel: process_high { - queue = 'long' - cpus = 36 - time = 21.d - } - {{ end }} - withLabel: process_low { - cpus = 2 - memory = 4.GB - time = 1.h - {{ if (eq .chezmoi.hostname "ceres") }}queue = 'short'{{ end }} + tananda { + params { + config_profile_description = 'KSU VDL Molecular NGS Desktop profile' + config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>' + config_profile_url = null + + max_memory = 14.GB + max_cpus = 12 + max_time = 4.h + } + docker { + enabled = true + userEmulation = true + envWhitelist = 'NCBI_API_KEY' + } + process { + executor = 'local' + } } } -{{ end }} From 03075ed5025cbd8bfbf6ecaac01a696d930821b6 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 23 Mar 2022 17:24:11 -0500 Subject: [PATCH 050/137] Remove switching to zsh Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- executable_dot_bashrc.tmpl | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index 7b85a14..7782a56 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -1,17 +1,6 @@ # shellcheck shell=bash # .bashrc -# shellcheck disable=1054,1073,1050,1072,1009 -{{ if (eq .chezmoi.osRelease.id "centos") }} -{{ if (eq .chezmoi.osRelease.versionID "7") }} -# Switch to zsh if interactive, and we haven't been told not to -if [[ ($- == *i*) && ($SSH_TTY) && (-z $NO_ZSH) ]]; then - export SHELL=$(command -v zsh) - exec $SHELL -l -fi -{{ end }} -{{ end }} - if [ -f "$HOME/.modules" ]; then source $HOME/.modules fi From 724e4068e301e706ac60fb1bc34c7b51adca765c Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 23 Mar 2022 17:27:07 -0500 Subject: [PATCH 051/137] Remove zsh directive from screen config Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_screenrc | 1 - 1 file changed, 1 deletion(-) diff --git a/dot_screenrc b/dot_screenrc index b1bcd37..5528458 100644 --- a/dot_screenrc +++ b/dot_screenrc @@ -1,4 +1,3 @@ -shell zsh startup_message off hardstatus alwayslastline hardstatus string "%{= KW} %H %{= Kw}|%{-} %-Lw%{= bW}%n%f %t%{-}%+Lw %=%C%a %Y-%M-%d" From 62f65a6e07c46346075669a82a99fd7814844ed3 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Apr 2022 08:49:13 -0500 Subject: [PATCH 052/137] Add nano syntax files as submodule Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- .gitmodules | 3 +++ .nano | 1 + 2 files changed, 4 insertions(+) create mode 100644 .gitmodules create mode 160000 .nano diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..3f51f66 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule ".nano"] + path = .nano + url = git@github.com:scopatz/nanorc.git diff --git a/.nano b/.nano new file mode 160000 index 0000000..1aa64a8 --- /dev/null +++ b/.nano @@ -0,0 +1 @@ +Subproject commit 1aa64a86cf4c750e4d4788ef1a19d7a71ab641dd From 46d1473b5e7b997193a25adcb762636034c9121e Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Apr 2022 08:49:32 -0500 Subject: [PATCH 053/137] Add .nanorc Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_nanorc.tmpl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 dot_nanorc.tmpl diff --git a/dot_nanorc.tmpl b/dot_nanorc.tmpl new file mode 100644 index 0000000..d0fbae7 --- /dev/null +++ b/dot_nanorc.tmpl @@ -0,0 +1,15 @@ +{{- if eq .chezmoi.osRelease.id "fedora" }} +set linenumbers +set titlecolor bold,lightwhite,blue +set promptcolor lightwhite,lightblack +set statuscolor bold,lightwhite,green +set errorcolor bold,lightwhite,red +set spotlightcolor black,lime +set selectedcolor lightwhite,magenta +set stripecolor ,yellow +set scrollercolor cyan +set numbercolor lightwhite,lightblack +set keycolor cyan +set functioncolor green +{{- end }} +include ~/.nano/*.nanorc From 5032413bdafda3be7225eb31a8b0292449d67c6f Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Apr 2022 08:51:40 -0500 Subject: [PATCH 054/137] Only include nano syntax on modern systems Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_nanorc.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_nanorc.tmpl b/dot_nanorc.tmpl index d0fbae7..c5191ad 100644 --- a/dot_nanorc.tmpl +++ b/dot_nanorc.tmpl @@ -11,5 +11,5 @@ set scrollercolor cyan set numbercolor lightwhite,lightblack set keycolor cyan set functioncolor green -{{- end }} include ~/.nano/*.nanorc +{{- end }} From 58898fba47ae89e51051e7568e9ef3b0ecc4eee9 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Apr 2022 15:17:26 -0500 Subject: [PATCH 055/137] Add private_dot_librewolf/.keep Add private_dot_librewolf/native-messaging-hosts/.keep Add private_dot_librewolf/native-messaging-hosts/org.kde.plasma.browser_integration.json --- private_dot_librewolf/.keep | 0 private_dot_librewolf/native-messaging-hosts/.keep | 0 .../org.kde.plasma.browser_integration.json | 7 +++++++ 3 files changed, 7 insertions(+) create mode 100644 private_dot_librewolf/.keep create mode 100644 private_dot_librewolf/native-messaging-hosts/.keep create mode 100644 private_dot_librewolf/native-messaging-hosts/org.kde.plasma.browser_integration.json diff --git a/private_dot_librewolf/.keep b/private_dot_librewolf/.keep new file mode 100644 index 0000000..e69de29 diff --git a/private_dot_librewolf/native-messaging-hosts/.keep b/private_dot_librewolf/native-messaging-hosts/.keep new file mode 100644 index 0000000..e69de29 diff --git a/private_dot_librewolf/native-messaging-hosts/org.kde.plasma.browser_integration.json b/private_dot_librewolf/native-messaging-hosts/org.kde.plasma.browser_integration.json new file mode 100644 index 0000000..e316dcb --- /dev/null +++ b/private_dot_librewolf/native-messaging-hosts/org.kde.plasma.browser_integration.json @@ -0,0 +1,7 @@ +{ + "name": "org.kde.plasma.browser_integration", + "description": "Native connector for KDE Plasma", + "path": "/usr/bin/plasma-browser-integration-host", + "type": "stdio", + "allowed_extensions": ["plasma-browser-integration@kde.org"] +} From 779e7c5d32b96a1a1da55bf92091f1372fe99b28 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Mon, 16 May 2022 08:35:20 -0500 Subject: [PATCH 056/137] Add default GPG signing to gitconfig Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- executable_dot_gitconfig.tmpl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/executable_dot_gitconfig.tmpl b/executable_dot_gitconfig.tmpl index 885e01b..78279d0 100644 --- a/executable_dot_gitconfig.tmpl +++ b/executable_dot_gitconfig.tmpl @@ -14,6 +14,8 @@ user = MillironX [pull] rebase = false +[commit] + gpgsign = true {{- if eq .chezmoi.osRelease.id "fedora" }} [diff] tool = kdiff3 From 56bb301c2e2504cb22c01b7bd394d55e242bd458 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Mon, 16 May 2022 08:37:40 -0500 Subject: [PATCH 057/137] Use tmux-256color terminal in tmux Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- dot_tmux.conf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_tmux.conf b/dot_tmux.conf index 542c418..029f1db 100644 --- a/dot_tmux.conf +++ b/dot_tmux.conf @@ -1,2 +1,2 @@ -set -g default-terminal "xterm-256color" +set -g default-terminal "tmux-256color" source "/usr/share/tmux/powerline.conf" From 7b53be4a946cd4d717de2aa08e96783469fa7c8e Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 18 May 2022 07:14:57 -0500 Subject: [PATCH 058/137] Add dot_local/.keep Add dot_local/share/.keep Add dot_local/share/konsole/.keep Add dot_local/share/konsole/private_My Default.profile --- dot_local/.keep | 0 dot_local/share/.keep | 0 dot_local/share/konsole/.keep | 0 .../share/konsole/private_My Default.profile | 20 +++++++++++++++++++ 4 files changed, 20 insertions(+) create mode 100644 dot_local/.keep create mode 100644 dot_local/share/.keep create mode 100644 dot_local/share/konsole/.keep create mode 100644 dot_local/share/konsole/private_My Default.profile diff --git a/dot_local/.keep b/dot_local/.keep new file mode 100644 index 0000000..e69de29 diff --git a/dot_local/share/.keep b/dot_local/share/.keep new file mode 100644 index 0000000..e69de29 diff --git a/dot_local/share/konsole/.keep b/dot_local/share/konsole/.keep new file mode 100644 index 0000000..e69de29 diff --git a/dot_local/share/konsole/private_My Default.profile b/dot_local/share/konsole/private_My Default.profile new file mode 100644 index 0000000..68254a0 --- /dev/null +++ b/dot_local/share/konsole/private_My Default.profile @@ -0,0 +1,20 @@ +[Appearance] +ColorScheme=Breeze +Font=MesloLGS NF,10,-1,5,50,0,0,0,0,0 +TabColor=255,255,255 + +[Cursor Options] +CursorShape=1 + +[General] +Name=My Default +Parent=FALLBACK/ +RemoteTabTitleFormat=[SSH] %H + +[Interaction Options] +CopyTextAsHTML=false +MouseWheelZoomEnabled=false +UnderlineFilesEnabled=true + +[Terminal Features] +BlinkingCursorEnabled=true From 69033f78f9149e9c667f6053cbb78934657b7535 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 18 May 2022 07:15:27 -0500 Subject: [PATCH 059/137] Add dot_config/.keep Add dot_config/private_yakuakerc --- dot_config/.keep | 0 dot_config/private_yakuakerc | 16 ++++++++++++++++ 2 files changed, 16 insertions(+) create mode 100644 dot_config/.keep create mode 100644 dot_config/private_yakuakerc diff --git a/dot_config/.keep b/dot_config/.keep new file mode 100644 index 0000000..e69de29 diff --git a/dot_config/private_yakuakerc b/dot_config/private_yakuakerc new file mode 100644 index 0000000..6bdff87 --- /dev/null +++ b/dot_config/private_yakuakerc @@ -0,0 +1,16 @@ +[Desktop Entry] +DefaultProfile=My Default.profile + +[Dialogs] +FirstRun=false + +[Shortcuts] +next-session=Shift+Right; Ctrl+Shift+Tab +previous-terminal=none + +[Window] +DynamicTabTitles=true +Height=60 +Screen=1 +ShowSystrayIcon=false +Width=60 From b8a9d9138c461f66674d138d9abc171c1c0841e2 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 18 May 2022 07:15:41 -0500 Subject: [PATCH 060/137] Add dot_config/private_konsolerc --- dot_config/private_konsolerc | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 dot_config/private_konsolerc diff --git a/dot_config/private_konsolerc b/dot_config/private_konsolerc new file mode 100644 index 0000000..77ef34a --- /dev/null +++ b/dot_config/private_konsolerc @@ -0,0 +1,17 @@ +[Desktop Entry] +DefaultProfile=My Default.profile + +[MainWindow] +DP-1 DP-2 Height 1920x1080=955 +DP-1 DP-2 Width 1920x1080=1607 +DP-1 DP-2 Window-Maximized 1920x1080=true +DisplayPort-0 DisplayPort-1 Height 1920x1080=634 +DisplayPort-0 DisplayPort-1 Width 1920x1080=1108 +DisplayPort-0 DisplayPort-1 XPosition 1920x1080=2468 +DisplayPort-0 DisplayPort-1 YPosition 1920x1080=276 +State=AAAA/wAAAAD9AAAAAQAAAAAAAAAAAAAAAPwCAAAAAfsAAAAcAFMAUwBIAE0AYQBuAGEAZwBlAHIARABvAGMAawAAAAAA/////wAAANUBAAADAAAHgAAAA6sAAAAEAAAABAAAAAgAAAAI/AAAAAEAAAACAAAAAgAAABYAbQBhAGkAbgBUAG8AbwBsAEIAYQByAQAAAAD/////AAAAAAAAAAAAAAAcAHMAZQBzAHMAaQBvAG4AVABvAG8AbABiAGEAcgEAAADf/////wAAAAAAAAAA +StatusBar=Disabled +ToolBarsMovable=Disabled + +[UiSettings] +ColorScheme=Default From bc71aff24d2bc7a7413fad948d358661a3037f8e Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 19 May 2022 13:35:20 -0500 Subject: [PATCH 061/137] Update dot_nextflow/config.tmpl --- dot_nextflow/config.tmpl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/dot_nextflow/config.tmpl b/dot_nextflow/config.tmpl index f76e329..b47f405 100644 --- a/dot_nextflow/config.tmpl +++ b/dot_nextflow/config.tmpl @@ -1,7 +1,9 @@ +{{ if eq .machinetype "workstation" }} tower { enabled = true accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}' } +{{ end }} profiles { aahz { params { From 98eda3571d0b8c36bb2aacc8db53c62c51ecfc68 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Mon, 6 Jun 2022 17:45:22 -0500 Subject: [PATCH 062/137] Switch nf tower off for workstations --- dot_nextflow/config.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_nextflow/config.tmpl b/dot_nextflow/config.tmpl index b47f405..f4bc612 100644 --- a/dot_nextflow/config.tmpl +++ b/dot_nextflow/config.tmpl @@ -1,4 +1,4 @@ -{{ if eq .machinetype "workstation" }} +{{ if ne .machinetype "workstation" }} tower { enabled = true accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}' From 90184e54cd2a86a213763a898a63f7566d63466a Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 14 Jun 2022 12:32:49 -0500 Subject: [PATCH 063/137] Update dot_envvar.tmpl --- dot_envvar.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_envvar.tmpl b/dot_envvar.tmpl index 43373a2..72517aa 100644 --- a/dot_envvar.tmpl +++ b/dot_envvar.tmpl @@ -36,7 +36,7 @@ fi # Add notification support for long-running processes if [ $(command -v ntfy) ]; then eval "$(ntfy shell-integration --longer-than 30)" - export AUTO_NTFY_DONE_IGNORE="vim nano emacs kate zshconfig screen tmux ssh top htop less more most nethogs 'singularity shell' julia man" + export AUTO_NTFY_DONE_IGNORE="vim nano emacs kate zshconfig screen tmux ssh top htop less more most nethogs 'singularity shell' julia man glances" fi # Set the Nextflow enviroment caches From 207a965fc2d4c1a7b3108034c5a641c12ae46e6c Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 08:56:29 -0500 Subject: [PATCH 064/137] Remove nano submodule --- .gitmodules | 3 --- .nano | 1 - 2 files changed, 4 deletions(-) delete mode 100644 .gitmodules delete mode 160000 .nano diff --git a/.gitmodules b/.gitmodules deleted file mode 100644 index 3f51f66..0000000 --- a/.gitmodules +++ /dev/null @@ -1,3 +0,0 @@ -[submodule ".nano"] - path = .nano - url = git@github.com:scopatz/nanorc.git diff --git a/.nano b/.nano deleted file mode 160000 index 1aa64a8..0000000 --- a/.nano +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 1aa64a86cf4c750e4d4788ef1a19d7a71ab641dd From 6c4f85d7f910176c36ce6f144d9f2d078b5a6e32 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 10:17:44 -0500 Subject: [PATCH 065/137] Add .nano as chezmoi external --- .chezmoiexternal.toml | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 .chezmoiexternal.toml diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml new file mode 100644 index 0000000..20fb0a6 --- /dev/null +++ b/.chezmoiexternal.toml @@ -0,0 +1,4 @@ +[".nano"] + type = "archive" + url = "https://github.com/scopatz/nanorc/archive/master.zip" + refreshPeriod = "30d" From ad1defed09bf490e0a0cf126e3bba9bea29cd82f Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 10:19:26 -0500 Subject: [PATCH 066/137] Fix refreshperiod --- .chezmoiexternal.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml index 20fb0a6..4ba4b10 100644 --- a/.chezmoiexternal.toml +++ b/.chezmoiexternal.toml @@ -1,4 +1,4 @@ [".nano"] type = "archive" url = "https://github.com/scopatz/nanorc/archive/master.zip" - refreshPeriod = "30d" + refreshPeriod = "720h" From ee09f4241aafd565a91d38a9157484d54de1bbd2 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 10:35:37 -0500 Subject: [PATCH 067/137] Add 'grim' alias --- dot_aliases | 1 + 1 file changed, 1 insertion(+) diff --git a/dot_aliases b/dot_aliases index 9951889..a2a14ab 100644 --- a/dot_aliases +++ b/dot_aliases @@ -22,6 +22,7 @@ alias_if_exists ls lsd alias config='git --git-dir=$HOME/.cfg/ --work-tree=$HOME' alias please='sudo $(fc -ln -1)' alias nrun='__NV_PRIME_RENDER_OFFLOAD=1 __GLX_VENDOR_LIBRARY_NAME=nvidia __VK_LAYER_NV_optimus="NVIDIA_only"' +alias grim='git rebase -i --autosquash $(git_main_branch)' # Alias-like functions nd () { From 332cd9590024abc4791c10fb24ab22d248594aac Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 10:36:39 -0500 Subject: [PATCH 068/137] Add 'grid' alias --- dot_aliases | 1 + 1 file changed, 1 insertion(+) diff --git a/dot_aliases b/dot_aliases index a2a14ab..e21d69f 100644 --- a/dot_aliases +++ b/dot_aliases @@ -23,6 +23,7 @@ alias config='git --git-dir=$HOME/.cfg/ --work-tree=$HOME' alias please='sudo $(fc -ln -1)' alias nrun='__NV_PRIME_RENDER_OFFLOAD=1 __GLX_VENDOR_LIBRARY_NAME=nvidia __VK_LAYER_NV_optimus="NVIDIA_only"' alias grim='git rebase -i --autosquash $(git_main_branch)' +alias grid='git rebase -i --autosquash $(git_develop_branch)' # Alias-like functions nd () { From 82a9c55817a5d50d7f4a6c080d9a8538d8aed190 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 16:07:30 -0500 Subject: [PATCH 069/137] Add Powerlevel10k fonts --- .chezmoiexternal.toml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml index 4ba4b10..269b594 100644 --- a/.chezmoiexternal.toml +++ b/.chezmoiexternal.toml @@ -2,3 +2,23 @@ type = "archive" url = "https://github.com/scopatz/nanorc/archive/master.zip" refreshPeriod = "720h" + +[".local/share/fonts/meslolgs-nf-regular.ttf"] + type = "file" + url = "https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Regular.ttf" + refreshPeriod = "168h" + +[".local/share/fonts/meslolgs-nf-bold.ttf"] + type = "file" + url = "https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Bold.ttf" + refreshPeriod = "168h" + +[".local/share/fonts/meslolgs-nf-italic.ttf"] + type = "file" + url = "https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Italic.ttf" + refreshPeriod = "168h" + +[".local/share/fonts/meslolgs-nf-bold-italic.ttf"] + type = "file" + url = "https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Bold%20Italic.ttf" + refreshPeriod = "168h" From adeb1811c5978cd56fb16421f692721a3f1fe0b0 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 16:40:17 -0500 Subject: [PATCH 070/137] Only include nanorc files from nano --- .chezmoiexternal.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml index 269b594..9117ea0 100644 --- a/.chezmoiexternal.toml +++ b/.chezmoiexternal.toml @@ -2,6 +2,8 @@ type = "archive" url = "https://github.com/scopatz/nanorc/archive/master.zip" refreshPeriod = "720h" + stripComponents = 1 + include = ["*.nanorc"] [".local/share/fonts/meslolgs-nf-regular.ttf"] type = "file" From 1c37c5ab4be45d8c0f5941a0be5daa8050607807 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 16:40:31 -0500 Subject: [PATCH 071/137] Add Fira Code external files --- .chezmoiexternal.toml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml index 9117ea0..8ceb458 100644 --- a/.chezmoiexternal.toml +++ b/.chezmoiexternal.toml @@ -24,3 +24,24 @@ type = "file" url = "https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Bold%20Italic.ttf" refreshPeriod = "168h" + +[".local/share/fonts/fira-code-bold.ttf"] + type = "file" + url = "https://github.com/tonsky/FiraCode/releases/download/6.2/Fira_Code_v6.2.zip" + [".local/share/fonts/fira-code-bold.ttf".filter] + command = "unzip" + args = ["-p", "/dev/stdin", "ttf/FiraCode-Bold.ttf"] + +[".local/share/fonts/fira-code-medium.ttf"] + type = "file" + url = "https://github.com/tonsky/FiraCode/releases/download/6.2/Fira_Code_v6.2.zip" + [".local/share/fonts/fira-code-medium.ttf".filter] + command = "unzip" + args = ["-p", "/dev/stdin", "ttf/FiraCode-Medium.ttf"] + +[".local/share/fonts/fira-code-regular.ttf"] + type = "file" + url = "https://github.com/tonsky/FiraCode/releases/download/6.2/Fira_Code_v6.2.zip" + [".local/share/fonts/fira-code-regular.ttf".filter] + command = "unzip" + args = ["-p", "/dev/stdin", "ttf/FiraCode-Regular.ttf"] From c9824a0b75f561f80e32892bd277d8ddf9fb93b0 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 16:43:26 -0500 Subject: [PATCH 072/137] Add installer for n --- .chezmoiexternal.toml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml index 8ceb458..4aa7120 100644 --- a/.chezmoiexternal.toml +++ b/.chezmoiexternal.toml @@ -5,6 +5,12 @@ stripComponents = 1 include = ["*.nanorc"] +[".local/bin/n"] + type = "file" + url = "https://raw.githubusercontent.com/tj/n/master/bin/n" + executable = true + refreshPeriod = "168h" + [".local/share/fonts/meslolgs-nf-regular.ttf"] type = "file" url = "https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Regular.ttf" From a20ed92869d8c51eee629db23056b3f85bf010bd Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 18:10:38 -0500 Subject: [PATCH 073/137] Add VSCode settings to chezmoi --- .chezmoiignore | 1 + .../symlink_settings.json.tmpl | 1 + settings.json | 222 ++++++++++++++++++ 3 files changed, 224 insertions(+) create mode 100644 .chezmoiignore create mode 100644 dot_config/private_VSCodium/symlink_settings.json.tmpl create mode 100644 settings.json diff --git a/.chezmoiignore b/.chezmoiignore new file mode 100644 index 0000000..e38da20 --- /dev/null +++ b/.chezmoiignore @@ -0,0 +1 @@ +settings.json diff --git a/dot_config/private_VSCodium/symlink_settings.json.tmpl b/dot_config/private_VSCodium/symlink_settings.json.tmpl new file mode 100644 index 0000000..1127a87 --- /dev/null +++ b/dot_config/private_VSCodium/symlink_settings.json.tmpl @@ -0,0 +1 @@ +{{ .chezmoi.sourceDir }}/settings.json diff --git a/settings.json b/settings.json new file mode 100644 index 0000000..c4303ed --- /dev/null +++ b/settings.json @@ -0,0 +1,222 @@ +{ + "breadcrumbs.enabled": true, + "editor.bracketPairColorization.enabled": true, + "editor.defaultFormatter": "esbenp.prettier-vscode", + "editor.guides.bracketPairs": "active", + "editor.inlineSuggest.enabled": true, + "editor.linkedEditing": true, + "editor.minimap.enabled": false, + "editor.quickSuggestions": { + "comments": false + }, + "editor.renderWhitespace": "boundary", + "editor.rulers": [80, 120], + "editor.tabCompletion": "on", + "editor.wrappingIndent": "deepIndent", + "editor.unicodeHighlight.ambiguousCharacters": false, + "extensions.ignoreRecommendations": true, + "files.trimFinalNewlines": true, + "files.trimTrailingWhitespace": true, + "prettier.resolveGlobalModules": true, + "workbench.editor.closeOnFileDelete": true, + "workbench.editor.enablePreview": false, + "workbench.editor.enablePreviewFromQuickOpen": false, + "workbench.startupEditor": "none", + + "telemetry.telemetryLevel": "off", + "update.mode": "none", + "workbench.enableExperiments": false, + + "diffEditor.ignoreTrimWhitespace": false, + "git.autofetch": true, + "git.confirmSync": false, + "git.enableCommitSigning": true, + "git.enableSmartCommit": true, + "git.inputValidation": "always", + "git.inputValidationLength": 75, + "git.inputValidationSubjectLength": null, + + "explorer.confirmDelete": false, + "explorer.confirmDragAndDrop": false, + "files.exclude": { + "**/tmp/**": true, + "**/node_modules/**": true, + "**/.sif": true, + "**/.sif.**/**": true, + "**/.git/objects/**": true, + "**/.git": true, + "**/.svn": true, + "**/.hg": true, + "**/CVS": true, + "**/.DS_Store": true + }, + "files.insertFinalNewline": true, + "search.smartCase": true, + "search.followSymlinks": false, + "search.exclude": { + "**/node_modules": true, + "**/bower_components": true, + "**/*.code-search": true, + "**/tmp/**": true, + "**/dist/**": true, + "**/*.sif/**": true, + "**/.git/objects/**": true, + "**/.git/subtree-cache/**": true + }, + "security.workspace.trust.enabled": false, + "files.watcherExclude": { + "**/.git/objects/**": true, + "**/.git/subtree-cache/**": true, + "**/node_modules/*/**": true, + "**/.hg/store/**": true, + "**/.nextflow/**": true, + "**/work/**": true + }, + + "editor.fontFamily": "Fira Code", + "editor.fontLigatures": true, + "window.menuBarVisibility": "visible", + "window.zoomLevel": -1, + "workbench.colorTheme": "Default Dark+", + "workbench.iconTheme": "vscode-great-icons", + + "terminal.integrated.allowChords": false, + "terminal.integrated.cursorBlinking": true, + "terminal.integrated.cursorStyle": "line", + "terminal.integrated.defaultProfile.windows": "Cmder", + "terminal.integrated.fontFamily": "'MesloLGS NF'", + "terminal.integrated.persistentSessionReviveProcess": "never", + "terminal.integrated.gpuAcceleration": "off", + "terminal.integrated.profiles.windows": { + "Cmder": { + "path": [ + "${env:windir}\\Sysnative\\cmd.exe", + "${env:windir}\\System32\\cmd.exe" + ], + "env": { + "CMDER_ROOT": "C:\\tools\\Cmder" + }, + "args": ["/k", "%CMDER_ROOT%\\vendor\\bin\\vscode_init.cmd"] + }, + "PowerShell": { + "source": "PowerShell", + "icon": "terminal-powershell" + }, + "Command Prompt": { + "path": [ + "${env:windir}\\Sysnative\\cmd.exe", + "${env:windir}\\System32\\cmd.exe" + ], + "args": [], + "icon": "terminal-cmd" + }, + "Git Bash": { + "source": "Git Bash" + } + }, + "terminal.integrated.defaultProfile.linux": "zsh", + "terminal.integrated.profiles.linux": { + "bash": { + "path": "bash" + }, + "zsh": { + "path": "zsh" + }, + "fish": { + "path": "fish" + }, + "tmux": { + "path": "tmux", + "icon": "terminal-tmux" + }, + "screen": { + "path": "screen", + "icon": "terminal-tmux" + }, + "pwsh": { + "path": "pwsh", + "icon": "terminal-powershell" + } + }, + "terminal.external.windowsExec": "C:\\Tools\\Cmder\\cmder.exe", + "terminal.external.linuxExec": "yakuake", + + "[shellscript]": { + "files.eol": "\n", + "editor.tabSize": 2, + "files.insertFinalNewline": true, + "files.trimFinalNewlines": true, + "files.trimTrailingWhitespace": true, + "editor.rulers": [80, 92, 120] + }, + "shellcheck.customArgs": ["-x"], + + "[html]": { + "editor.tabSize": 2 + }, + + "[javascript]": { + "editor.tabSize": 2 + }, + + "[json]": { + "editor.tabSize": 2 + }, + + "[julia]": { + "editor.detectIndentation": false, + "editor.insertSpaces": true, + "editor.tabSize": 4, + "files.insertFinalNewline": true, + "files.trimFinalNewlines": true, + "files.trimTrailingWhitespace": true, + "editor.rulers": [92], + "editor.defaultFormatter": "julialang.language-julia" + }, + "julia.enableCrashReporter": false, + "julia.enableTelemetry": false, + "julia.NumThreads": 8, + "julia.symbolCacheDownload": true, + "terminal.integrated.commandsToSkipShell": ["language-julia.interrupt"], + + "latex-workshop.view.pdf.viewer": "tab", + + "[markdown]": { + "editor.tabSize": 2 + }, + "files.associations": { + "README": "markdown" + }, + "markdown-preview-github-styles.colorTheme": "light", + + "[nextflow]": { + "editor.rulers": [80, 84, 120] + }, + + "[python]": { + "editor.rulers": [72, 79, 99] + }, + "python.formatting.provider": "black", + "python.formatting.blackPath": "black", + + "[r]": { + "editor.defaultFormatter": "Ikuyadeu.r" + }, + + "[typescript]": { + "editor.tabSize": 2 + }, + + "[yaml]": { + "editor.tabSize": 2 + }, + "redhat.telemetry.enabled": false, + + "sync.autoDownload": true, + "sync.gist": "ac23d90cbe13499f59ed319c101b4b13", + "sync.quietSync": true, + "workbench.editorAssociations": { + "*.pdf": "latex-workshop-pdf-hook" + }, + "terminal.integrated.tabs.title": "${cwdFolder}${separator}${process}" +} From e860b3a50246be0d8611f6457d463219e1ba8185 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 14 Jul 2022 18:11:04 -0500 Subject: [PATCH 074/137] Comment out the Fira code installer --- .chezmoiexternal.toml | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml index 4aa7120..4442216 100644 --- a/.chezmoiexternal.toml +++ b/.chezmoiexternal.toml @@ -31,23 +31,23 @@ url = "https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Bold%20Italic.ttf" refreshPeriod = "168h" -[".local/share/fonts/fira-code-bold.ttf"] - type = "file" - url = "https://github.com/tonsky/FiraCode/releases/download/6.2/Fira_Code_v6.2.zip" - [".local/share/fonts/fira-code-bold.ttf".filter] - command = "unzip" - args = ["-p", "/dev/stdin", "ttf/FiraCode-Bold.ttf"] +# [".local/share/fonts/fira-code-bold.ttf"] +# type = "file" +# url = "https://github.com/tonsky/FiraCode/releases/download/6.2/Fira_Code_v6.2.zip" +# [".local/share/fonts/fira-code-bold.ttf".filter] +# command = "unzip" +# args = ["-p", "/dev/stdin", "ttf/FiraCode-Bold.ttf"] -[".local/share/fonts/fira-code-medium.ttf"] - type = "file" - url = "https://github.com/tonsky/FiraCode/releases/download/6.2/Fira_Code_v6.2.zip" - [".local/share/fonts/fira-code-medium.ttf".filter] - command = "unzip" - args = ["-p", "/dev/stdin", "ttf/FiraCode-Medium.ttf"] +# [".local/share/fonts/fira-code-medium.ttf"] +# type = "file" +# url = "https://github.com/tonsky/FiraCode/releases/download/6.2/Fira_Code_v6.2.zip" +# [".local/share/fonts/fira-code-medium.ttf".filter] +# command = "unzip" +# args = ["-p", "/dev/stdin", "ttf/FiraCode-Medium.ttf"] -[".local/share/fonts/fira-code-regular.ttf"] - type = "file" - url = "https://github.com/tonsky/FiraCode/releases/download/6.2/Fira_Code_v6.2.zip" - [".local/share/fonts/fira-code-regular.ttf".filter] - command = "unzip" - args = ["-p", "/dev/stdin", "ttf/FiraCode-Regular.ttf"] +# [".local/share/fonts/fira-code-regular.ttf"] +# type = "file" +# url = "https://github.com/tonsky/FiraCode/releases/download/6.2/Fira_Code_v6.2.zip" +# [".local/share/fonts/fira-code-regular.ttf".filter] +# command = "unzip" +# args = ["-p", "/dev/stdin", "ttf/FiraCode-Regular.ttf"] From 2a0fbb5419a06c8e82646a64b9778ad0bcd2c424 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 19 Jul 2022 09:53:04 -0500 Subject: [PATCH 075/137] Update nanorc archive location --- .chezmoiexternal.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml index 4442216..c47b9ca 100644 --- a/.chezmoiexternal.toml +++ b/.chezmoiexternal.toml @@ -1,7 +1,6 @@ [".nano"] type = "archive" - url = "https://github.com/scopatz/nanorc/archive/master.zip" - refreshPeriod = "720h" + url = "https://github.com/scopatz/nanorc/releases/download/2020.10.10/nanorc-2020.10.10.tar.gz" stripComponents = 1 include = ["*.nanorc"] From 0c81dcaff90cb73b78c911e788190f4945a794d4 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 19 Jul 2022 10:01:46 -0500 Subject: [PATCH 076/137] Fix include flag in nanorc --- .chezmoiexternal.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml index c47b9ca..c6b3783 100644 --- a/.chezmoiexternal.toml +++ b/.chezmoiexternal.toml @@ -2,7 +2,7 @@ type = "archive" url = "https://github.com/scopatz/nanorc/releases/download/2020.10.10/nanorc-2020.10.10.tar.gz" stripComponents = 1 - include = ["*.nanorc"] + include = ["*/*.nanorc"] [".local/bin/n"] type = "file" From e349d9968f11af098f1f9c32ee0df2fcef525dbf Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 21 Jul 2022 11:05:57 -0500 Subject: [PATCH 077/137] Add mamba to Nextflow config --- dot_nextflow/config.tmpl | 96 +--------------------------------------- 1 file changed, 2 insertions(+), 94 deletions(-) diff --git a/dot_nextflow/config.tmpl b/dot_nextflow/config.tmpl index f4bc612..12db9cf 100644 --- a/dot_nextflow/config.tmpl +++ b/dot_nextflow/config.tmpl @@ -4,99 +4,7 @@ tower { accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}' } {{ end }} -profiles { - aahz { - params { - config_profile_description = 'KSU VDL Molecular NGS Big Server profile' - config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>' - config_profile_url = null - max_memory = 745.GB - max_cpus = 78 - max_time = 7.d - } - singularity { - enabled = true - autoMounts = true - envWhitelist = 'NCBI_API_KEY' - } - process { - executor = 'local' - } - } - atlas { - params { - config_profile_description = 'Mississippi State University Atlas Cluster profile' - config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>' - config_profile_url = 'https://www.hpc.msstate.edu/computing/atlas/' - - max_memory = 1539.GB - max_cpus = 24 - max_time = 14.d - } - singularity { - enabled = true - autoMounts = true - envWhitelist = 'NCBI_API_KEY' - } - process { - scratch = true - executor = 'slurm' - clusterOptions = '--account=fabadru' - - withLabel: process_high_memory { - queue = 'bigmem' - } - } - } - ceres { - params { - config_profile_description = 'USDA ARS SCInet Ceres Cluster profile' - config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>' - config_profile_url = 'https://scinet.usda.gov/guide/ceres/#partitions-or-queues' - - max_memory = 768.GB - max_cpus = 40 - max_time = 1000.h - } - singularity { - enabled = true - autoMounts = true - envWhitelist = 'NCBI_API_KEY' - } - process { - scratch = true - executor = 'slurm' - queue = 'short' - - withLabel: process_high_memory { - queue = 'mem' - } - withLabel: process_long { - queue = 'long' - } - withLabel: process_medium { - queue = 'medium' - } - } - } - tananda { - params { - config_profile_description = 'KSU VDL Molecular NGS Desktop profile' - config_profile_contact = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>' - config_profile_url = null - - max_memory = 14.GB - max_cpus = 12 - max_time = 4.h - } - docker { - enabled = true - userEmulation = true - envWhitelist = 'NCBI_API_KEY' - } - process { - executor = 'local' - } - } +conda { + useMamba = true } From d771de2741755fe073273f7b07ea91439cfb6721 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 21 Jul 2022 11:11:32 -0500 Subject: [PATCH 078/137] Convert konsolerc to symlink --- .chezmoiignore | 1 + dot_config/symlink_private_konsolerc.tmpl | 1 + dot_config/private_konsolerc => symlinks/dot_config/konsolerc | 4 ++-- 3 files changed, 4 insertions(+), 2 deletions(-) create mode 100644 dot_config/symlink_private_konsolerc.tmpl rename dot_config/private_konsolerc => symlinks/dot_config/konsolerc (53%) diff --git a/.chezmoiignore b/.chezmoiignore index e38da20..aa15e92 100644 --- a/.chezmoiignore +++ b/.chezmoiignore @@ -1 +1,2 @@ settings.json +symlinks diff --git a/dot_config/symlink_private_konsolerc.tmpl b/dot_config/symlink_private_konsolerc.tmpl new file mode 100644 index 0000000..2dcbab9 --- /dev/null +++ b/dot_config/symlink_private_konsolerc.tmpl @@ -0,0 +1 @@ +{{ .chezmoi.sourceDir }}/symlinks/dot_config/konsolerc diff --git a/dot_config/private_konsolerc b/symlinks/dot_config/konsolerc similarity index 53% rename from dot_config/private_konsolerc rename to symlinks/dot_config/konsolerc index 77ef34a..6e6b4ce 100644 --- a/dot_config/private_konsolerc +++ b/symlinks/dot_config/konsolerc @@ -9,9 +9,9 @@ DisplayPort-0 DisplayPort-1 Height 1920x1080=634 DisplayPort-0 DisplayPort-1 Width 1920x1080=1108 DisplayPort-0 DisplayPort-1 XPosition 1920x1080=2468 DisplayPort-0 DisplayPort-1 YPosition 1920x1080=276 -State=AAAA/wAAAAD9AAAAAQAAAAAAAAAAAAAAAPwCAAAAAfsAAAAcAFMAUwBIAE0AYQBuAGEAZwBlAHIARABvAGMAawAAAAAA/////wAAANUBAAADAAAHgAAAA6sAAAAEAAAABAAAAAgAAAAI/AAAAAEAAAACAAAAAgAAABYAbQBhAGkAbgBUAG8AbwBsAEIAYQByAQAAAAD/////AAAAAAAAAAAAAAAcAHMAZQBzAHMAaQBvAG4AVABvAG8AbABiAGEAcgEAAADf/////wAAAAAAAAAA +State=AAAA/wAAAAD9AAAAAQAAAAAAAAAAAAAAAPwCAAAAAvsAAAAcAFMAUwBIAE0AYQBuAGEAZwBlAHIARABvAGMAawAAAAAA/////wAAANMBAAAD+wAAACIAUQB1AGkAYwBrAEMAbwBtAG0AYQBuAGQAcwBEAG8AYwBrAAAAAAD/////AAAArQEAAAMAAAeAAAADowAAAAQAAAAEAAAACAAAAAj8AAAAAQAAAAIAAAACAAAAFgBtAGEAaQBuAFQAbwBvAGwAQgBhAHIBAAAAAP////8AAAAAAAAAAAAAABwAcwBlAHMAcwBpAG8AbgBUAG8AbwBsAGIAYQByAQAAAN//////AAAAAAAAAAA= StatusBar=Disabled ToolBarsMovable=Disabled [UiSettings] -ColorScheme=Default +ColorScheme= From 7f622ac439ac9aac93cd2c2fd1fb17ad2cd00e97 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 21 Jul 2022 11:17:09 -0500 Subject: [PATCH 079/137] Add juliaup support --- dot_profile | 5 +++++ dot_zshenv.tmpl | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/dot_profile b/dot_profile index 036b64b..af1c378 100644 --- a/dot_profile +++ b/dot_profile @@ -2,6 +2,11 @@ # User specific environment export PATH="$HOME/.local/bin:$HOME/bin:$PATH" +# juliaup setup +if [ -d $HOME/.julia/juliaup/bin ]; then + export PATH="$HOME/.julia/juliaup/bin:$PATH" +fi + # Linuxbrew setup if [ -d $HOME/../linuxbrew/.linuxbrew ]; then BREWPATH=$HOME/../linuxbrew/.linuxbrew diff --git a/dot_zshenv.tmpl b/dot_zshenv.tmpl index 2a79f32..b03aab1 100644 --- a/dot_zshenv.tmpl +++ b/dot_zshenv.tmpl @@ -5,6 +5,11 @@ fpath+=($HOME/.local/share/zsh/5.8/functions) {{- end }} +# juliaup setup +if [ -d $HOME/.julia/juliaup/bin ]; then + export PATH="$HOME/.julia/juliaup/bin:$PATH" +fi + # Linuxbrew setup if [ -d $HOME/../linuxbrew/.linuxbrew ]; then BREWPATH=$HOME/../linuxbrew/.linuxbrew From 1754e2bbcdc3177568cc74a296e7051f4dd675f5 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 21 Jul 2022 12:01:22 -0500 Subject: [PATCH 080/137] Switch to chezmoi deciding my zsh theme --- executable_dot_zshrc.tmpl | 51 +++++++++++++++------------------------ 1 file changed, 20 insertions(+), 31 deletions(-) diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index c038b4f..7a0a3cb 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -1,4 +1,8 @@ -{{- if (not (eq .cluster "scinet")) -}} +{{- if or + (eq .machinetype "workstation") + (eq .chezmoi.osRelease.id "fedora") + (and (eq .chezmoi.osRelease.id "almalinux" "centos" "rhel") (gt (atoi .chezmoi.osRelease.versionID) 7)) + (and (eq .chezmoi.osRelease.id "debian") (gt (atoi .chezmoi.osRelease.versionID) 9 )) -}} # Enable Powerlevel10k instant prompt. Should stay close to the top of ~/.zshrc. # Initialization code that may require console input (password prompts, [y/n] # confirmations, etc.) must go above this block; everything else may go below. @@ -7,10 +11,6 @@ if [[ -r "${XDG_CACHE_HOME:-$HOME/.cache}/p10k-instant-prompt-${(%):-%n}.zsh" ]] fi {{- end }} -if [ -f "$HOME/.modules" ]; then - source $HOME/.modules -fi - # User specific environment if ! [[ "$PATH" =~ "$HOME/.local/bin:$HOME/bin:" ]] then @@ -28,12 +28,7 @@ antigen use oh-my-zsh # Default bundles antigen bundle git -antigen bundle gitignore -antigen bundle colored-man-pages -antigen bundle cp antigen bundle screen -antigen bundle npm -antigen bundle bundler antigen bundle extract # Custom bundles @@ -41,30 +36,18 @@ antigen bundle zsh-users/zsh-syntax-highlighting antigen bundle zsh-users/zsh-autosuggestions antigen bundle zsh-users/zsh-completions antigen bundle esc/conda-zsh-completion -antigen bundle RobSis/zsh-completion-generator antigen bundle kloetzl/biozsh antigen bundle millironx/cowsay-cows -DEFAULT_USER="$USER" - -# Theming: if I have a nerd fond, use it to the fullest extent possible -# If not, check for basic powerline, then fall back to text-based -# The presence of nerd fonts and/or powerline fonts will be designated -# by the presence of a ".nf" and ".powerline" file in the home directory, -# respectively -source /etc/os-release -if [[ -f "$HOME/.nf" ]]; then - # Nerd font config flag set - antigen theme romkatv/powerlevel10k -else - if [[ -f "$HOME/.powerline" ]]; then - # Powerline config flag set - antigen theme https://gist.github.com/e95df0a0aa6d1721e85b905399971515.git believer - else - # Powerline config flag not set - antigen theme https://gist.github.com/efde5e8d507bd3e1e046198b69d579f8.git gianu-improved - fi -fi +{{ if or + (eq .machinetype "workstation") + (eq .chezmoi.osRelease.id "fedora") + (and (eq .chezmoi.osRelease.id "almalinux" "centos" "rhel") (gt (atoi .chezmoi.osRelease.versionID) 7)) + (and (eq .chezmoi.osRelease.id "debian") (gt (atoi .chezmoi.osRelease.versionID) 9 )) -}} +antigen theme romkatv/powerlevel10k +{{- else -}} +antigen theme https://gist.github.com/efde5e8d507bd3e1e046198b69d579f8.git gianu-improved +{{- end }} # oh-my-zsh configuration settings HYPHEN_INSENSITIVE="true" @@ -113,5 +96,11 @@ if [ $(command -v env_parallel.zsh) ]; then source $(which env_parallel.zsh) fi +{{ if or + (eq .machinetype "workstation") + (eq .chezmoi.osRelease.id "fedora") + (and (eq .chezmoi.osRelease.id "almalinux" "centos" "rhel") (gt (atoi .chezmoi.osRelease.versionID) 7)) + (and (eq .chezmoi.osRelease.id "debian") (gt (atoi .chezmoi.osRelease.versionID) 9 )) -}} # To customize prompt, run `p10k configure` or edit ~/.p10k.zsh. [[ ! -f ~/.p10k.zsh ]] || source ~/.p10k.zsh +{{- end }} From 4e24dfb645ff09f77757ef99c19bb81f511ade5a Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 19 Nov 2022 15:57:55 -0600 Subject: [PATCH 081/137] Add Julia/Git variable to environment --- dot_envvar.tmpl | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dot_envvar.tmpl b/dot_envvar.tmpl index 72517aa..620d511 100644 --- a/dot_envvar.tmpl +++ b/dot_envvar.tmpl @@ -58,5 +58,8 @@ export SINGULARITY_CACHEDIR=/90daydata/shared/$USER/.singularity # Give Julia full CPU access export JULIA_NUM_THREADS=$(nproc) +# Make Julia use preinstalled Git +JULIA_PKG_USE_CLI_GIT=true + # Make NCBI happy export NCBI_API_KEY='{{ (bitwarden "item" "7d42eba0-c256-4d3b-8d0e-adbf016a08f8").login.password }}' From 31caced2fd23cf57c864531425b63dd7d538b531 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 19 Nov 2022 15:58:07 -0600 Subject: [PATCH 082/137] Remove Git credentials file --- private_dot_git-credentials.tmpl | 1 - 1 file changed, 1 deletion(-) delete mode 100644 private_dot_git-credentials.tmpl diff --git a/private_dot_git-credentials.tmpl b/private_dot_git-credentials.tmpl deleted file mode 100644 index 7ca97ad..0000000 --- a/private_dot_git-credentials.tmpl +++ /dev/null @@ -1 +0,0 @@ -https://{{ .githubuser }}:{{ (bitwarden "item" "3e123829-7167-4dd2-8f3f-ad8f01081fee").login.password }}@github.com From f9c55ce334070a758cc6b36fe00e8eae14a348ff Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 20 Jul 2022 08:47:16 -0500 Subject: [PATCH 083/137] Move VSCode settings into correct folder --- dot_config/private_VSCodium/{ => User}/symlink_settings.json.tmpl | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename dot_config/private_VSCodium/{ => User}/symlink_settings.json.tmpl (100%) diff --git a/dot_config/private_VSCodium/symlink_settings.json.tmpl b/dot_config/private_VSCodium/User/symlink_settings.json.tmpl similarity index 100% rename from dot_config/private_VSCodium/symlink_settings.json.tmpl rename to dot_config/private_VSCodium/User/symlink_settings.json.tmpl From f95cd261e44df8d7a38b1d29fefa84dafa8c728c Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 22 Nov 2022 14:31:57 -0600 Subject: [PATCH 084/137] Remove biozsh --- executable_dot_zshrc.tmpl | 1 - 1 file changed, 1 deletion(-) diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index 7a0a3cb..87f0427 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -36,7 +36,6 @@ antigen bundle zsh-users/zsh-syntax-highlighting antigen bundle zsh-users/zsh-autosuggestions antigen bundle zsh-users/zsh-completions antigen bundle esc/conda-zsh-completion -antigen bundle kloetzl/biozsh antigen bundle millironx/cowsay-cows {{ if or From 88248f447782a27cd311f501cd076bd84cca9773 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Tue, 29 Nov 2022 05:29:20 +0000 Subject: [PATCH 085/137] Update definition of "modern" for nanorc --- dot_nanorc.tmpl | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/dot_nanorc.tmpl b/dot_nanorc.tmpl index c5191ad..08ee2d0 100644 --- a/dot_nanorc.tmpl +++ b/dot_nanorc.tmpl @@ -1,4 +1,8 @@ -{{- if eq .chezmoi.osRelease.id "fedora" }} +{{- if or + (eq .machinetype "workstation") + (eq .chezmoi.osRelease.id "fedora") + (and (eq .chezmoi.osRelease.id "almalinux" "centos" "rhel") (gt (atoi .chezmoi.osRelease.versionID) 7)) + (and (eq .chezmoi.osRelease.id "debian") (gt (atoi .chezmoi.osRelease.versionID) 9 )) -}} set linenumbers set titlecolor bold,lightwhite,blue set promptcolor lightwhite,lightblack From 4e5552effdcbfa8510bb79aa2b69074678d94400 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 4 Feb 2023 21:34:04 -0600 Subject: [PATCH 086/137] Change prompt to rounded ends --- dot_p10k.zsh | 167 ++++++++++++++++++++++++++++++++++----------------- 1 file changed, 111 insertions(+), 56 deletions(-) diff --git a/dot_p10k.zsh b/dot_p10k.zsh index e06909b..66c9fa5 100644 --- a/dot_p10k.zsh +++ b/dot_p10k.zsh @@ -1,8 +1,8 @@ -# Generated by Powerlevel10k configuration wizard on 2021-04-21 at 10:28 MDT. -# Based on romkatv/powerlevel10k/config/p10k-rainbow.zsh, checksum 32822. +# Generated by Powerlevel10k configuration wizard on 2023-01-17 at 18:32 CST. +# Based on romkatv/powerlevel10k/config/p10k-rainbow.zsh, checksum 15312. # Wizard options: nerdfont-complete + powerline, small icons, rainbow, unicode, -# slanted separators, sharp heads, blurred tails, 1 line, compact, many icons, concise, -# instant_prompt=quiet. +# slanted separators, sharp heads, round tails, 1 line, compact, many icons, concise, +# transient_prompt, instant_prompt=quiet. # Type `p10k configure` to generate another config. # # Config for Powerlevel10k with powerline prompt style with colorful background. @@ -46,14 +46,14 @@ command_execution_time # duration of the last command background_jobs # presence of background jobs direnv # direnv status (https://direnv.net/) - # asdf # asdf version manager (https://github.com/asdf-vm/asdf) + asdf # asdf version manager (https://github.com/asdf-vm/asdf) virtualenv # python virtual environment (https://docs.python.org/3/library/venv.html) anaconda # conda environment (https://conda.io/) - # pyenv # python environment (https://github.com/pyenv/pyenv) - # goenv # go environment (https://github.com/syndbg/goenv) - # nodenv # node.js version from nodenv (https://github.com/nodenv/nodenv) - # nvm # node.js version from nvm (https://github.com/nvm-sh/nvm) - # nodeenv # node.js environment (https://github.com/ekalinin/nodeenv) + pyenv # python environment (https://github.com/pyenv/pyenv) + goenv # go environment (https://github.com/syndbg/goenv) + nodenv # node.js version from nodenv (https://github.com/nodenv/nodenv) + nvm # node.js version from nvm (https://github.com/nvm-sh/nvm) + nodeenv # node.js environment (https://github.com/ekalinin/nodeenv) node_version # node.js version # go_version # go version (https://golang.org) # rust_version # rustc version (https://www.rust-lang.org) @@ -63,28 +63,32 @@ # java_version # java version (https://www.java.com/) # package # name@version from package.json (https://docs.npmjs.com/files/package.json) rbenv # ruby version from rbenv (https://github.com/rbenv/rbenv) - # rvm # ruby version from rvm (https://rvm.io) - # fvm # flutter version management (https://github.com/leoafarias/fvm) - # luaenv # lua version from luaenv (https://github.com/cehoffman/luaenv) - # jenv # java version from jenv (https://github.com/jenv/jenv) - # plenv # perl version from plenv (https://github.com/tokuhirom/plenv) - # phpenv # php version from phpenv (https://github.com/phpenv/phpenv) - # scalaenv # scala version from scalaenv (https://github.com/scalaenv/scalaenv) - # haskell_stack # haskell version from stack (https://haskellstack.org/) - # kubecontext # current kubernetes context (https://kubernetes.io/) - # terraform # terraform workspace (https://www.terraform.io) - # aws # aws profile (https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-profiles.html) - # aws_eb_env # aws elastic beanstalk environment (https://aws.amazon.com/elasticbeanstalk/) - # azure # azure account name (https://docs.microsoft.com/en-us/cli/azure) - # gcloud # google cloud cli account and project (https://cloud.google.com/) - # google_app_cred # google application credentials (https://cloud.google.com/docs/authentication/production) + rvm # ruby version from rvm (https://rvm.io) + fvm # flutter version management (https://github.com/leoafarias/fvm) + luaenv # lua version from luaenv (https://github.com/cehoffman/luaenv) + jenv # java version from jenv (https://github.com/jenv/jenv) + plenv # perl version from plenv (https://github.com/tokuhirom/plenv) + perlbrew # perl version from perlbrew (https://github.com/gugod/App-perlbrew) + phpenv # php version from phpenv (https://github.com/phpenv/phpenv) + scalaenv # scala version from scalaenv (https://github.com/scalaenv/scalaenv) + haskell_stack # haskell version from stack (https://haskellstack.org/) + kubecontext # current kubernetes context (https://kubernetes.io/) + terraform # terraform workspace (https://www.terraform.io) + # terraform_version # terraform version (https://www.terraform.io) + aws # aws profile (https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-profiles.html) + aws_eb_env # aws elastic beanstalk environment (https://aws.amazon.com/elasticbeanstalk/) + azure # azure account name (https://docs.microsoft.com/en-us/cli/azure) + gcloud # google cloud cli account and project (https://cloud.google.com/) + google_app_cred # google application credentials (https://cloud.google.com/docs/authentication/production) + toolbox # toolbox name (https://github.com/containers/toolbox) context # user@hostname - # nordvpn # nordvpn connection status, linux only (https://nordvpn.com/) - # ranger # ranger shell (https://github.com/ranger/ranger) + nordvpn # nordvpn connection status, linux only (https://nordvpn.com/) + ranger # ranger shell (https://github.com/ranger/ranger) nnn # nnn shell (https://github.com/jarun/nnn) + xplr # xplr shell (https://github.com/sayanarijit/xplr) vim_shell # vim shell indicator (:sh) - # midnight_commander # midnight commander shell (https://midnight-commander.org/) - # nix_shell # nix shell (https://nixos.org/nixos/nix-pills/developing-with-nix-shell.html) + midnight_commander # midnight commander shell (https://midnight-commander.org/) + nix_shell # nix shell (https://nixos.org/nixos/nix-pills/developing-with-nix-shell.html) vi_mode # vi mode (you don't need this if you've enabled prompt_char) vpn_ip # virtual private network indicator # load # CPU load @@ -138,7 +142,7 @@ # Filler between left and right prompt on the first prompt line. You can set it to ' ', '·' or # '─'. The last two make it easier to see the alignment between left and right prompt and to # separate prompt from command output. You might want to set POWERLEVEL9K_PROMPT_ADD_NEWLINE=false - # for more compact prompt if using using this option. + # for more compact prompt if using this option. typeset -g POWERLEVEL9K_MULTILINE_FIRST_PROMPT_GAP_CHAR=' ' typeset -g POWERLEVEL9K_MULTILINE_FIRST_PROMPT_GAP_BACKGROUND= typeset -g POWERLEVEL9K_MULTILINE_NEWLINE_PROMPT_GAP_BACKGROUND= @@ -165,9 +169,9 @@ # The left end of right prompt. typeset -g POWERLEVEL9K_RIGHT_PROMPT_FIRST_SEGMENT_START_SYMBOL='\uE0B2' # The left end of left prompt. - typeset -g POWERLEVEL9K_LEFT_PROMPT_FIRST_SEGMENT_START_SYMBOL='░▒▓' + typeset -g POWERLEVEL9K_LEFT_PROMPT_FIRST_SEGMENT_START_SYMBOL='\uE0B6' # The right end of right prompt. - typeset -g POWERLEVEL9K_RIGHT_PROMPT_LAST_SEGMENT_END_SYMBOL='▓▒░' + typeset -g POWERLEVEL9K_RIGHT_PROMPT_LAST_SEGMENT_END_SYMBOL='\uE0B4' # Left prompt terminator for lines without any segments. typeset -g POWERLEVEL9K_EMPTY_LINE_LEFT_PROMPT_LAST_SEGMENT_END_SYMBOL= @@ -341,14 +345,14 @@ # typeset -g POWERLEVEL9K_DIR_PREFIX='in ' #####################################[ vcs: git status ]###################################### - # Version control system colors. + # Version control background colors. typeset -g POWERLEVEL9K_VCS_CLEAN_BACKGROUND=2 typeset -g POWERLEVEL9K_VCS_MODIFIED_BACKGROUND=3 typeset -g POWERLEVEL9K_VCS_UNTRACKED_BACKGROUND=2 typeset -g POWERLEVEL9K_VCS_CONFLICTED_BACKGROUND=3 typeset -g POWERLEVEL9K_VCS_LOADING_BACKGROUND=8 - # Branch icon. Set this parameter to '\uF126 ' for the popular Powerline branch icon. + # Branch icon. Set this parameter to '\UE0A0 ' for the popular Powerline branch icon. typeset -g POWERLEVEL9K_VCS_BRANCH_ICON='\uF126 ' # Untracked files icon. It's really a question mark, your font isn't broken. @@ -357,7 +361,7 @@ # Formatter for Git status. # - # Example output: master ⇣42⇡42 *42 merge ~42 +42 !42 ?42. + # Example output: master wip ⇣42⇡42 *42 merge ~42 +42 !42 ?42. # # You can edit the function to customize how Git status looks. # @@ -414,6 +418,11 @@ res+="${meta}:${clean}${(V)VCS_STATUS_REMOTE_BRANCH//\%/%%}" fi + # Display "wip" if the latest commit's summary contains "wip" or "WIP". + if [[ $VCS_STATUS_COMMIT_SUMMARY == (|*[^[:alnum:]])(wip|WIP)(|[^[:alnum:]]*) ]]; then + res+=" ${modified}wip" + fi + # ⇣42 if behind the remote. (( VCS_STATUS_COMMITS_BEHIND )) && res+=" ${clean}⇣${VCS_STATUS_COMMITS_BEHIND}" # ⇡42 if ahead of the remote; no leading space if also behind the remote: ⇣42⇡42. @@ -477,7 +486,7 @@ # Show status of repositories of these types. You can add svn and/or hg if you are # using them. If you do, your prompt may become slow even when your current directory - # isn't in an svn or hg reposotiry. + # isn't in an svn or hg repository. typeset -g POWERLEVEL9K_VCS_BACKENDS=(git) ##########################[ status: exit code of the last command ]########################### @@ -734,6 +743,13 @@ # Custom icon. # typeset -g POWERLEVEL9K_NNN_VISUAL_IDENTIFIER_EXPANSION='⭐' + ##################[ xplr: xplr shell (https://github.com/sayanarijit/xplr) ]################## + # xplr shell color. + typeset -g POWERLEVEL9K_XPLR_FOREGROUND=0 + typeset -g POWERLEVEL9K_XPLR_BACKGROUND=6 + # Custom icon. + # typeset -g POWERLEVEL9K_XPLR_VISUAL_IDENTIFIER_EXPANSION='⭐' + ###########################[ vim_shell: vim shell indicator (:sh) ]########################### # Vim shell indicator color. typeset -g POWERLEVEL9K_VIM_SHELL_FOREGROUND=0 @@ -974,10 +990,10 @@ # # The default format has the following logic: # - # 1. Display "$P9K_CONTENT $P9K_PYENV_PYTHON_VERSION" if $P9K_PYENV_PYTHON_VERSION is not - # empty and unequal to $P9K_CONTENT. - # 2. Otherwise display just "$P9K_CONTENT". - typeset -g POWERLEVEL9K_PYENV_CONTENT_EXPANSION='${P9K_CONTENT}${${P9K_PYENV_PYTHON_VERSION:#$P9K_CONTENT}:+ $P9K_PYENV_PYTHON_VERSION}' + # 1. Display just "$P9K_CONTENT" if it's equal to "$P9K_PYENV_PYTHON_VERSION" or + # starts with "$P9K_PYENV_PYTHON_VERSION/". + # 2. Otherwise display "$P9K_CONTENT $P9K_PYENV_PYTHON_VERSION". + typeset -g POWERLEVEL9K_PYENV_CONTENT_EXPANSION='${P9K_CONTENT}${${P9K_CONTENT:#$P9K_PYENV_PYTHON_VERSION(|/*)}:+ $P9K_PYENV_PYTHON_VERSION}' # Custom icon. # typeset -g POWERLEVEL9K_PYENV_VISUAL_IDENTIFIER_EXPANSION='⭐' @@ -1180,6 +1196,16 @@ # Custom icon. # typeset -g POWERLEVEL9K_PLENV_VISUAL_IDENTIFIER_EXPANSION='⭐' + ###########[ perlbrew: perl version from perlbrew (https://github.com/gugod/App-perlbrew) ]############ + # Perlbrew color. + typeset -g POWERLEVEL9K_PERLBREW_FOREGROUND=67 + # Show perlbrew version only when in a perl project subdirectory. + typeset -g POWERLEVEL9K_PERLBREW_PROJECT_ONLY=true + # Don't show "perl-" at the front. + typeset -g POWERLEVEL9K_PERLBREW_SHOW_PREFIX=false + # Custom icon. + # typeset -g POWERLEVEL9K_PERLBREW_VISUAL_IDENTIFIER_EXPANSION='⭐' + ############[ phpenv: php version from phpenv (https://github.com/phpenv/phpenv) ]############ # PHP color. typeset -g POWERLEVEL9K_PHPENV_FOREGROUND=0 @@ -1259,10 +1285,20 @@ typeset -g POWERLEVEL9K_TERRAFORM_OTHER_BACKGROUND=0 # typeset -g POWERLEVEL9K_TERRAFORM_OTHER_VISUAL_IDENTIFIER_EXPANSION='⭐' + #############[ terraform_version: terraform version (https://www.terraform.io) ]############## + # Terraform version color. + typeset -g POWERLEVEL9K_TERRAFORM_VERSION_FOREGROUND=4 + typeset -g POWERLEVEL9K_TERRAFORM_VERSION_BACKGROUND=0 + # Custom icon. + # typeset -g POWERLEVEL9K_TERRAFORM_VERSION_VISUAL_IDENTIFIER_EXPANSION='⭐' + + ################[ terraform_version: It shows active terraform version (https://www.terraform.io) ]################# + typeset -g POWERLEVEL9K_TERRAFORM_VERSION_SHOW_ON_COMMAND='terraform|tf' + #############[ kubecontext: current kubernetes context (https://kubernetes.io/) ]############# - # Show kubecontext only when the the command you are typing invokes one of these tools. + # Show kubecontext only when the command you are typing invokes one of these tools. # Tip: Remove the next line to always show kubecontext. - typeset -g POWERLEVEL9K_KUBECONTEXT_SHOW_ON_COMMAND='kubectl|helm|kubens|kubectx|oc|istioctl|kogito|k9s|helmfile|fluxctl|stern' + typeset -g POWERLEVEL9K_KUBECONTEXT_SHOW_ON_COMMAND='kubectl|helm|kubens|kubectx|oc|istioctl|kogito|k9s|helmfile|flux|fluxctl|stern|kubeseal|skaffold' # Kubernetes context classes for the purpose of using different colors, icons and expansions with # different contexts. @@ -1349,7 +1385,7 @@ # typeset -g POWERLEVEL9K_KUBECONTEXT_PREFIX='at ' #[ aws: aws profile (https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-profiles.html) ]# - # Show aws only when the the command you are typing invokes one of these tools. + # Show aws only when the command you are typing invokes one of these tools. # Tip: Remove the next line to always show aws. typeset -g POWERLEVEL9K_AWS_SHOW_ON_COMMAND='aws|awless|terraform|pulumi|terragrunt' @@ -1384,6 +1420,12 @@ typeset -g POWERLEVEL9K_AWS_DEFAULT_BACKGROUND=1 # typeset -g POWERLEVEL9K_AWS_DEFAULT_VISUAL_IDENTIFIER_EXPANSION='⭐' + # AWS segment format. The following parameters are available within the expansion. + # + # - P9K_AWS_PROFILE The name of the current AWS profile. + # - P9K_AWS_REGION The region associated with the current AWS profile. + typeset -g POWERLEVEL9K_AWS_CONTENT_EXPANSION='${P9K_AWS_PROFILE//\%/%%}${P9K_AWS_REGION:+ ${P9K_AWS_REGION//\%/%%}}' + #[ aws_eb_env: aws elastic beanstalk environment (https://aws.amazon.com/elasticbeanstalk/) ]# # AWS Elastic Beanstalk environment color. typeset -g POWERLEVEL9K_AWS_EB_ENV_FOREGROUND=2 @@ -1392,7 +1434,7 @@ # typeset -g POWERLEVEL9K_AWS_EB_ENV_VISUAL_IDENTIFIER_EXPANSION='⭐' ##########[ azure: azure account name (https://docs.microsoft.com/en-us/cli/azure) ]########## - # Show azure only when the the command you are typing invokes one of these tools. + # Show azure only when the command you are typing invokes one of these tools. # Tip: Remove the next line to always show azure. typeset -g POWERLEVEL9K_AZURE_SHOW_ON_COMMAND='az|terraform|pulumi|terragrunt' # Azure account name color. @@ -1402,9 +1444,9 @@ # typeset -g POWERLEVEL9K_AZURE_VISUAL_IDENTIFIER_EXPANSION='⭐' ##########[ gcloud: google cloud account and project (https://cloud.google.com/) ]########### - # Show gcloud only when the the command you are typing invokes one of these tools. + # Show gcloud only when the command you are typing invokes one of these tools. # Tip: Remove the next line to always show gcloud. - typeset -g POWERLEVEL9K_GCLOUD_SHOW_ON_COMMAND='gcloud|gcs' + typeset -g POWERLEVEL9K_GCLOUD_SHOW_ON_COMMAND='gcloud|gcs|gsutil' # Google cloud color. typeset -g POWERLEVEL9K_GCLOUD_FOREGROUND=7 typeset -g POWERLEVEL9K_GCLOUD_BACKGROUND=4 @@ -1444,7 +1486,7 @@ # typeset -g POWERLEVEL9K_GCLOUD_VISUAL_IDENTIFIER_EXPANSION='⭐' #[ google_app_cred: google application credentials (https://cloud.google.com/docs/authentication/production) ]# - # Show google_app_cred only when the the command you are typing invokes one of these tools. + # Show google_app_cred only when the command you are typing invokes one of these tools. # Tip: Remove the next line to always show google_app_cred. typeset -g POWERLEVEL9K_GOOGLE_APP_CRED_SHOW_ON_COMMAND='terraform|pulumi|terragrunt' @@ -1498,6 +1540,17 @@ # Note: ${VARIABLE//\%/%%} expands to ${VARIABLE} with all occurrences of '%' replaced by '%%'. typeset -g POWERLEVEL9K_GOOGLE_APP_CRED_DEFAULT_CONTENT_EXPANSION='${P9K_GOOGLE_APP_CRED_PROJECT_ID//\%/%%}' + ##############[ toolbox: toolbox name (https://github.com/containers/toolbox) ]############### + # Toolbox color. + typeset -g POWERLEVEL9K_TOOLBOX_FOREGROUND=0 + typeset -g POWERLEVEL9K_TOOLBOX_BACKGROUND=3 + # Don't display the name of the toolbox if it matches fedora-toolbox-*. + typeset -g POWERLEVEL9K_TOOLBOX_CONTENT_EXPANSION='${P9K_TOOLBOX_NAME:#fedora-toolbox-*}' + # Custom icon. + # typeset -g POWERLEVEL9K_TOOLBOX_VISUAL_IDENTIFIER_EXPANSION='⭐' + # Custom prefix. + # typeset -g POWERLEVEL9K_TOOLBOX_PREFIX='in ' + ###############################[ public_ip: public IP address ]############################### # Public IP color. typeset -g POWERLEVEL9K_PUBLIC_IP_FOREGROUND=7 @@ -1529,13 +1582,15 @@ # The following parameters are accessible within the expansion: # # Parameter | Meaning - # ----------------------+--------------- - # P9K_IP_IP | IP address - # P9K_IP_INTERFACE | network interface - # P9K_IP_RX_BYTES | total number of bytes received - # P9K_IP_TX_BYTES | total number of bytes sent - # P9K_IP_RX_RATE | receive rate (since last prompt) - # P9K_IP_TX_RATE | send rate (since last prompt) + # ----------------------+------------------------------------------- + # P9K_IP_IP | IP address + # P9K_IP_INTERFACE | network interface + # P9K_IP_RX_BYTES | total number of bytes received + # P9K_IP_TX_BYTES | total number of bytes sent + # P9K_IP_RX_BYTES_DELTA | number of bytes received since last prompt + # P9K_IP_TX_BYTES_DELTA | number of bytes sent since last prompt + # P9K_IP_RX_RATE | receive rate (since last prompt) + # P9K_IP_TX_RATE | send rate (since last prompt) typeset -g POWERLEVEL9K_IP_CONTENT_EXPANSION='${P9K_IP_RX_RATE:+⇣$P9K_IP_RX_RATE }${P9K_IP_TX_RATE:+⇡$P9K_IP_TX_RATE }$P9K_IP_IP' # Show information for the first network interface whose name matches this regular expression. # Run `ifconfig` or `ip -4 a show` to see the names of all network interfaces. @@ -1562,7 +1617,7 @@ typeset -g POWERLEVEL9K_BATTERY_STAGES='\uf58d\uf579\uf57a\uf57b\uf57c\uf57d\uf57e\uf57f\uf580\uf581\uf578' # Don't show the remaining time to charge/discharge. typeset -g POWERLEVEL9K_BATTERY_VERBOSE=false - typeset -g POWERLEVEL9K_BATTERY_BACKGROUND=237 + typeset -g POWERLEVEL9K_BATTERY_BACKGROUND=0 #####################################[ wifi: wifi speed ]##################################### # WiFi color. @@ -1647,7 +1702,7 @@ # - always: Trim down prompt when accepting a command line. # - same-dir: Trim down prompt when accepting a command line unless this is the first command # typed after changing current working directory. - typeset -g POWERLEVEL9K_TRANSIENT_PROMPT=off + typeset -g POWERLEVEL9K_TRANSIENT_PROMPT=always # Instant prompt mode. # From 65f0f12a29d710bee9d39bac8a956f4efbae30c4 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 15 Feb 2023 20:42:22 -0600 Subject: [PATCH 087/137] Add dot_local/share/applications/executable_org.kde.kate.desktop --- .../executable_org.kde.kate.desktop | 197 ++++++++++++++++++ 1 file changed, 197 insertions(+) create mode 100644 dot_local/share/applications/executable_org.kde.kate.desktop diff --git a/dot_local/share/applications/executable_org.kde.kate.desktop b/dot_local/share/applications/executable_org.kde.kate.desktop new file mode 100644 index 0000000..8bde499 --- /dev/null +++ b/dot_local/share/applications/executable_org.kde.kate.desktop @@ -0,0 +1,197 @@ +[Desktop Action Session eb0a191797624dd3a48fa681d3061212] +Exec=kate -s master +Name=master + +[Desktop Entry] +Actions=Session eb0a191797624dd3a48fa681d3061212; +Categories=Qt;KDE;Utility;TextEditor; +Comment[en_US]=KDE Advanced Text Editor +Comment=KDE Advanced Text Editor +Comment[ar]=كيت محرّر النّصوص المتقدّم +Comment[ast]=Editor avanzáu de testu de KDE +Comment[az]=Əlavə KDE mətn redaktoru +Comment[ca@valencia]=Editor avançat de text pel KDE +Comment[ca]=Editor avançat de text pel KDE +Comment[cs]=Pokročilý textový editor pro KDE +Comment[da]=KDE Avanceret Tekst Editor +Comment[de]=Erweiterter Texteditor für KDE +Comment[el]=Προχωρημένος επεξεργαστής κειμένου για το KDE +Comment[en_GB]=KDE Advanced Text Editor +Comment[es]=Editor de texto avanzado de KDE +Comment[et]=KDE täiustatud tekstiredaktor +Comment[eu]=KDE testu-editore aurreratua +Comment[fi]=KDE:n kehittynyt tekstimuokkain +Comment[fr]=Éditeur de texte avancé de KDE +Comment[gl]=Editor avanzado de textos de KDE +Comment[he]=עורך טקסט מתקדם של KDE +Comment[hu]=Speciális szövegszerkesztő +Comment[ia]=KDE Advanced Text Editor, i.e. Editor avantiate de texto de KDE +Comment[id]=Pengedit Teks KDE Tingkat Lanjut +Comment[it]=Editor di testi avanzato di KDE +Comment[ko]=KDE 고급 텍스트 편집기 +Comment[lt]=Sudėtingesnė KDE rašyklė +Comment[nb]=Avansert skriveprogram for KDE +Comment[nl]=KDE geavanceerde tekstbewerker +Comment[nn]=Avansert skriveprogram for KDE +Comment[pa]=KDE ਤਕਨੀਕੀ ਟੈਕਸਟ ਐਡੀਟਰ +Comment[pl]=Rozbudowany edytor tekstu KDE +Comment[pt]=Editor de Texto Avançado do KDE +Comment[pt_BR]=Editor de texto avançado do KDE +Comment[ro]=Redactor de text avansat KDE +Comment[ru]=Улучшенный текстовый редактор от KDE +Comment[sk]=KDE pokročilý textový editor +Comment[sl]=Napreden urejevalnik besedil za KDE +Comment[sr@ijekavian]=КДЕ‑ов напредни уређивач текста +Comment[sr@ijekavianlatin]=KDE‑ov napredni uređivač teksta +Comment[sr@latin]=KDE‑ov napredni uređivač teksta +Comment[sr]=КДЕ‑ов напредни уређивач текста +Comment[sv]=KDE avancerad texteditor +Comment[tg]=Муҳаррири матнии KDE (Васеъшуда) +Comment[tr]=KDE Gelişmiş Metin Düzenleyici +Comment[uk]=Потужний текстовий редактор KDE +Comment[vi]=Trình biên tập văn bản nâng cao của KDE +Comment[x-test]=xxKDE Advanced Text Editorxx +Comment[zh_CN]=KDE 高级文本编辑器 +Comment[zh_TW]=KDE 進階文字編輯器 +Exec=kate -s master %U +GenericName[en_US]=Advanced Text Editor +GenericName=Advanced Text Editor +GenericName[ar]=محرّر نصوص متقدّم +GenericName[ast]=Editor avanzáu de testu +GenericName[az]=Əlavə mətn redaktoru +GenericName[bg]=Усъвършенстван текстов редактор +GenericName[bs]=Napredni uređivač teksta +GenericName[ca@valencia]=Editor de text avançat +GenericName[ca]=Editor de text avançat +GenericName[cs]=Pokročilý textový editor +GenericName[da]=Avanceret teksteditor +GenericName[de]=Erweiterter Texteditor +GenericName[el]=Προχωρημένος επεξεργαστής κειμένου +GenericName[en_GB]=Advanced Text Editor +GenericName[es]=Editor de texto avanzado +GenericName[et]=Täiustatud tekstiredaktor +GenericName[eu]=Testu-editore aurreratua +GenericName[fi]=Kehittynyt tekstimuokkain +GenericName[fr]=Éditeur de texte avancé +GenericName[ga]=Ardeagarthóir Téacs +GenericName[gl]=Editor avanzado de textos +GenericName[he]=עורך טקסט מתקדם +GenericName[hr]=Napredni uređivač teksta +GenericName[hu]=Speciális szövegszerkesztő +GenericName[ia]=Editor avantiate de texto +GenericName[id]=Pengedit Teks Tingkat Lanjut +GenericName[is]=Þróaður textaritill +GenericName[it]=Editor di testi avanzato +GenericName[ja]=高度なテキストエディタ +GenericName[kk]=Үздік мәтін редакторы +GenericName[km]=កម្មវិធី​និពន្ធ​អត្ថបទ​កម្រិត​ខ្ពស់ +GenericName[ko]=고급 텍스트 편집기 +GenericName[lt]=Sudėtingesnis teksto redaktorius +GenericName[lv]=Jaudīgs teksta redaktors +GenericName[mr]=प्रगत पाठ्य संपादक +GenericName[nb]=Avansert skriveprogram +GenericName[nds]=Verwiedert Texteditor +GenericName[ne]=उन्नत पाठ सम्पादक +GenericName[nl]=Geavanceerde teksteditor +GenericName[nn]=Avansert skriveprogram +GenericName[pa]=ਤਕਨੀਕੀ ਟੈਕਸਟ ਐਡੀਟਰ +GenericName[pl]=Rozbudowany edytor tekstu +GenericName[pt]=Editor de Texto Avançado +GenericName[pt_BR]=Editor de textos avançado +GenericName[ro]=Redactor de text avansat +GenericName[ru]=Улучшенный текстовый редактор +GenericName[si]=උසස් පෙළ සකසනය +GenericName[sk]=Pokročilý textový editor +GenericName[sl]=Napreden urejevalnik besedil +GenericName[sr@ijekavian]=Напредни уређивач текста +GenericName[sr@ijekavianlatin]=Napredni uređivač teksta +GenericName[sr@latin]=Napredni uređivač teksta +GenericName[sr]=Напредни уређивач текста +GenericName[sv]=Avancerad texteditor +GenericName[tg]=Муҳаррири матнӣ (Васеъшуда) +GenericName[tr]=Gelişmiş Metin Düzenleyici +GenericName[ug]=ئالىي تېكىست تەھرىرلىگۈچ +GenericName[uk]=Потужний текстовий редактор +GenericName[vi]=Trình biên tập văn bản nâng cao +GenericName[x-test]=xxAdvanced Text Editorxx +GenericName[zh_CN]=高级文本编辑器 +GenericName[zh_TW]=進階文字編輯器 +Icon=kate +InitialPreference=9 +MimeType=text/plain; +Name[en_US]=Kate +Name=Kate +Name[ar]=كيت +Name[ast]=Kate +Name[az]=Kate +Name[be]=Kate +Name[bg]=Kate +Name[bs]=Kate +Name[ca@valencia]=Kate +Name[ca]=Kate +Name[cs]=Kate +Name[da]=Kate +Name[de]=Kate +Name[el]=Kate +Name[en_GB]=Kate +Name[eo]=Kate +Name[es]=Kate +Name[et]=Kate +Name[eu]=Kate +Name[fi]=Kate +Name[fr]=Kate +Name[ga]=Kate +Name[gl]=Kate +Name[he]=Kate +Name[hu]=Kate +Name[ia]=Kate +Name[id]=Kate +Name[it]=Kate +Name[ja]=Kate +Name[kk]=Kate +Name[km]=Kate +Name[ko]=Kate +Name[lt]=Kate +Name[lv]=Kate +Name[mr]=केट +Name[ms]=Kate +Name[nb]=Kate +Name[nds]=Kate +Name[ne]=केट +Name[nl]=Kate +Name[nn]=Kate +Name[pa]=ਕੇਟ +Name[pl]=Kate +Name[pt]=Kate +Name[pt_BR]=Kate +Name[ro]=Kate +Name[ru]=Kate +Name[si]=Kate +Name[sk]=Kate +Name[sl]=Kate +Name[sr@ijekavian]=Кејт +Name[sr@ijekavianlatin]=Kate +Name[sr@latin]=Kate +Name[sr]=Кејт +Name[sv]=Kate +Name[tg]=Кейт +Name[tr]=Kate +Name[ug]=Kate +Name[uk]=Kate +Name[vi]=Kate +Name[wa]=Kate +Name[x-test]=xxKatexx +Name[zh_CN]=Kate +Name[zh_TW]=Kate +Path= +StartupNotify=true +StartupWMClass=kate +Terminal=false +TerminalOptions= +Type=Application +X-DBUS-ServiceName=org.kde.kate +X-DBUS-StartupType=multi +X-DocPath=kate/index.html +X-KDE-HasTempFileOption=true +X-KDE-SubstituteUID=false +X-KDE-Username= From 48197dcaf724f4fe572634dbd540a306d5d72030 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 15 Feb 2023 20:43:30 -0600 Subject: [PATCH 088/137] Add dot_local/share/kservices5/ServiceMenus/kate.desktop Add dot_local/share/kservices5/ServiceMenus/vlc.desktop --- .../kservices5/ServiceMenus/kate.desktop | 12 ++++++++++ .../share/kservices5/ServiceMenus/vlc.desktop | 23 +++++++++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 dot_local/share/kservices5/ServiceMenus/kate.desktop create mode 100644 dot_local/share/kservices5/ServiceMenus/vlc.desktop diff --git a/dot_local/share/kservices5/ServiceMenus/kate.desktop b/dot_local/share/kservices5/ServiceMenus/kate.desktop new file mode 100644 index 0000000..0649c10 --- /dev/null +++ b/dot_local/share/kservices5/ServiceMenus/kate.desktop @@ -0,0 +1,12 @@ +[Desktop Entry] +Actions=OpenWithKate +Icon=kate +ServiceTypes=KonqPopupMenu/Plugin +MimeType=application/octet-stream; +Type=Service +X-KDE-Priority=TopLevel + +[Desktop Action OpenWithKate] +Exec=kate -s master %u +Icon=kate +Name=Edit with Kate diff --git a/dot_local/share/kservices5/ServiceMenus/vlc.desktop b/dot_local/share/kservices5/ServiceMenus/vlc.desktop new file mode 100644 index 0000000..c05a30f --- /dev/null +++ b/dot_local/share/kservices5/ServiceMenus/vlc.desktop @@ -0,0 +1,23 @@ +[Desktop Entry] +Actions=VLCPlayFolder +Icon=vlc +ServiceTypes=KonqPopupMenu/Plugin,inode/directory,inode/directory-locked +Type=Service +X-KDE-Priority=TopLevel + +[Desktop Entry] +Actions=AppendVLCPlaylist +Icon=vlc +MimeType=application/ogg;application/x-ogg;audio/ogg;audio/vorbis;audio/x-vorbis;audio/x-vorbis+ogg;video/ogg;video/x-ogm;video/x-ogm+ogg;video/x-theora+ogg;video/x-theora;audio/x-speex;audio/opus;application/x-flac;audio/flac;audio/x-flac;audio/x-ms-asf;audio/x-ms-asx;audio/x-ms-wax;audio/x-ms-wma;video/x-ms-asf;video/x-ms-asf-plugin;video/x-ms-asx;video/x-ms-wm;video/x-ms-wmv;video/x-ms-wmx;video/x-ms-wvx;video/x-msvideo;audio/x-pn-windows-acm;video/divx;video/msvideo;video/vnd.divx;video/avi;video/x-avi;application/vnd.rn-realmedia;application/vnd.rn-realmedia-vbr;audio/vnd.rn-realaudio;audio/x-pn-realaudio;audio/x-pn-realaudio-plugin;audio/x-real-audio;audio/x-realaudio;video/vnd.rn-realvideo;audio/mpeg;audio/mpg;audio/mp1;audio/mp2;audio/mp3;audio/x-mp1;audio/x-mp2;audio/x-mp3;audio/x-mpeg;audio/x-mpg;video/mp2t;video/mpeg;video/mpeg-system;video/x-mpeg;video/x-mpeg2;video/x-mpeg-system;application/mpeg4-iod;application/mpeg4-muxcodetable;application/x-extension-m4a;application/x-extension-mp4;audio/aac;audio/m4a;audio/mp4;audio/x-m4a;audio/x-aac;video/mp4;video/mp4v-es;video/x-m4v;application/x-quicktime-media-link;application/x-quicktimeplayer;video/quicktime;application/x-matroska;audio/x-matroska;video/x-matroska;video/webm;audio/webm;audio/3gpp;audio/3gpp2;audio/AMR;audio/AMR-WB;video/3gp;video/3gpp;video/3gpp2;x-scheme-handler/mms;x-scheme-handler/mmsh;x-scheme-handler/rtsp;x-scheme-handler/rtp;x-scheme-handler/rtmp;x-scheme-handler/icy;x-scheme-handler/icyx;application/x-cd-image;x-content/video-vcd;x-content/video-svcd;x-content/video-dvd;x-content/audio-cdda;x-content/audio-player;application/ram;application/xspf+xml;audio/mpegurl;audio/x-mpegurl;audio/scpls;audio/x-scpls;text/google-video-pointer;text/x-google-video-pointer;video/vnd.mpegurl;application/vnd.apple.mpegurl;application/vnd.ms-asf;application/vnd.ms-wpl;application/sdp;audio/dv;video/dv;audio/x-aiff;audio/x-pn-aiff;video/x-anim;video/x-nsv;video/fli;video/flv;video/x-flc;video/x-fli;video/x-flv;audio/wav;audio/x-pn-au;audio/x-pn-wav;audio/x-wav;audio/x-adpcm;audio/ac3;audio/eac3;audio/vnd.dts;audio/vnd.dts.hd;audio/vnd.dolby.heaac.1;audio/vnd.dolby.heaac.2;audio/vnd.dolby.mlp;audio/basic;audio/midi;audio/x-ape;audio/x-gsm;audio/x-musepack;audio/x-tta;audio/x-wavpack;audio/x-shorten;application/x-shockwave-flash;application/x-flash-video;misc/ultravox;image/vnd.rn-realpix;audio/x-it;audio/x-mod;audio/x-s3m;audio/x-xm;application/mxf; +Type=Service +ServiceTypes=KonqPopupMenu/Plugin + +[Desktop Action VLCPlayFolder] +Exec=vlc %f +Icon=vlc +Name=Play Folder with VLC + +[Desktop Action AppendVLCPlaylist] +Exec=vlc --one-instance --playlist-enqueue %U +Icon=vlc +Name=Append to VLC Playlist From c072544efbde062f20b85f08e423c2382f189845 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Mar 2023 12:04:36 -0600 Subject: [PATCH 089/137] Update executable_dot_zshrc.tmpl --- executable_dot_zshrc.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index 87f0427..a9f0d6e 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -21,7 +21,7 @@ fi if [[ ! -f "$HOME/antigen.zsh" ]]; then curl -L git.io/antigen > $HOME/antigen.zsh fi -source "$HOME/.antigen.zsh" +source "$HOME/antigen.zsh" # Load the oh-my-zsh library antigen use oh-my-zsh From 9df027d4a6f8d781a00901402d8d69750a116671 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Mar 2023 12:07:00 -0600 Subject: [PATCH 090/137] Update dot_envvar.tmpl --- dot_envvar.tmpl | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/dot_envvar.tmpl b/dot_envvar.tmpl index 620d511..42346d3 100644 --- a/dot_envvar.tmpl +++ b/dot_envvar.tmpl @@ -4,12 +4,14 @@ if [ $(command -v pipx) ]; then fi # Preferred editor for local and remote sessions -if [ $(command -v nano) ]; then +if [ $(command -v nvim) ]; then + export EDITOR=nvim +elif [ $(command -v nano) ]; then export EDITOR=nano -elif [ $(command -v emacs) ]; then - export EDITOR='emacs -nw' elif [ $(command -v vim) ]; then export EDITOR=vim +elif [ $(command -v emacs) ]; then + export EDITOR='emacs -nw' fi if [ $(command -v kate) ]; then From 446e991859bc890e8d9d24471956e017ac0574e8 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Mar 2023 12:25:10 -0600 Subject: [PATCH 091/137] Update executable_dot_gitconfig.tmpl --- executable_dot_gitconfig.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/executable_dot_gitconfig.tmpl b/executable_dot_gitconfig.tmpl index 78279d0..7c714c2 100644 --- a/executable_dot_gitconfig.tmpl +++ b/executable_dot_gitconfig.tmpl @@ -3,7 +3,7 @@ email = {{ .email }} signingkey = {{ .pubkey }} [core] - editor = nano + editor = nvim [credential] helper = store [color] From 8052c8f83be901ce8d2914de6d832ebaf164b319 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Mar 2023 12:28:57 -0600 Subject: [PATCH 092/137] Update executable_dot_gitconfig.tmpl --- executable_dot_gitconfig.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/executable_dot_gitconfig.tmpl b/executable_dot_gitconfig.tmpl index 7c714c2..c248c73 100644 --- a/executable_dot_gitconfig.tmpl +++ b/executable_dot_gitconfig.tmpl @@ -14,9 +14,9 @@ user = MillironX [pull] rebase = false +{{- if eq .machinetype "workstation" }} [commit] gpgsign = true -{{- if eq .chezmoi.osRelease.id "fedora" }} [diff] tool = kdiff3 [merge] From 826b6a5fe8a7e2afd7619396e4c04cfdf473265a Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Mar 2023 12:32:57 -0600 Subject: [PATCH 093/137] Change git credentials --- executable_dot_gitconfig.tmpl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/executable_dot_gitconfig.tmpl b/executable_dot_gitconfig.tmpl index c248c73..fec6ef4 100644 --- a/executable_dot_gitconfig.tmpl +++ b/executable_dot_gitconfig.tmpl @@ -1,7 +1,7 @@ [user] - name = {{ .name }} - email = {{ .email }} - signingkey = {{ .pubkey }} + name = "Thomas A. Christensen II" + email = "25492070+MillironX@users.noreply.github.com" + signingkey = 0xD5F50D10552A4BEC [core] editor = nvim [credential] From 01e5ae652b378ab7ef564fd8615914632f33a3d0 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Mar 2023 12:42:41 -0600 Subject: [PATCH 094/137] Update dot_hooks --- dot_hooks | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/dot_hooks b/dot_hooks index a7d3a2b..ffaa685 100644 --- a/dot_hooks +++ b/dot_hooks @@ -8,3 +8,9 @@ if [ $(command -v n) ]; then export N_PREFIX=$HOME/.n export PATH="$HOME/.n/bin:$PATH" fi + +{{- if eq .machinetype "workstation" }} +export GPG_TTY="$(tty)" +export SSH_AUTH_SOCK=$(gpgconf --list-dirs agent-ssh-socket) +gpgconf --launch gpg-agent +{{- end }} From 66d3a5c39051545805a255d6989b512e00bc684a Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Mar 2023 12:44:20 -0600 Subject: [PATCH 095/137] Update dot_hooks --- dot_hooks | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dot_hooks b/dot_hooks index ffaa685..ec49f4f 100644 --- a/dot_hooks +++ b/dot_hooks @@ -9,6 +9,11 @@ if [ $(command -v n) ]; then export PATH="$HOME/.n/bin:$PATH" fi +if [ -f $HOME/.ion/bin/ion ]; then + export PATH="$HOME/.ion/bin/ion:$PATH" + export FPATH=$HOME/.ion/completions:$FPATH" +fi + {{- if eq .machinetype "workstation" }} export GPG_TTY="$(tty)" export SSH_AUTH_SOCK=$(gpgconf --list-dirs agent-ssh-socket) From 5601bd7546e8847dc83eb0f375bfe7febf22128d Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Mar 2023 12:46:05 -0600 Subject: [PATCH 096/137] Update dot_hooks --- dot_hooks | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_hooks b/dot_hooks index ec49f4f..7af0c42 100644 --- a/dot_hooks +++ b/dot_hooks @@ -11,7 +11,7 @@ fi if [ -f $HOME/.ion/bin/ion ]; then export PATH="$HOME/.ion/bin/ion:$PATH" - export FPATH=$HOME/.ion/completions:$FPATH" + export FPATH="$HOME/.ion/completions:$FPATH" fi {{- if eq .machinetype "workstation" }} From 58d8801d7de5252a85e24d55ad22f73077c31b7c Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Mar 2023 12:47:17 -0600 Subject: [PATCH 097/137] Rename dot_hooks to dot_hooks.tmpl --- dot_hooks => dot_hooks.tmpl | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename dot_hooks => dot_hooks.tmpl (100%) diff --git a/dot_hooks b/dot_hooks.tmpl similarity index 100% rename from dot_hooks rename to dot_hooks.tmpl From 8369610a0edc1d699a0573d5cbc3d587e8c1dd2c Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Mar 2023 19:19:11 +0000 Subject: [PATCH 098/137] Add Docker directory to unsafe allowed directories --- executable_dot_gitconfig.tmpl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/executable_dot_gitconfig.tmpl b/executable_dot_gitconfig.tmpl index fec6ef4..35a2da7 100644 --- a/executable_dot_gitconfig.tmpl +++ b/executable_dot_gitconfig.tmpl @@ -14,6 +14,8 @@ user = MillironX [pull] rebase = false +[safe] + directory = /var/docker {{- if eq .machinetype "workstation" }} [commit] gpgsign = true From 455d5636a77e38260f0b867ee74734ba7af60690 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 2 Mar 2023 19:33:57 +0000 Subject: [PATCH 099/137] Update tmux.conf --- dot_profile | 13 +++++++++++++ dot_tmux.conf | 2 -- dot_tmux.conf.tmpl | 6 ++++++ 3 files changed, 19 insertions(+), 2 deletions(-) delete mode 100644 dot_tmux.conf create mode 100644 dot_tmux.conf.tmpl diff --git a/dot_profile b/dot_profile index af1c378..17df7a2 100644 --- a/dot_profile +++ b/dot_profile @@ -7,6 +7,19 @@ if [ -d $HOME/.julia/juliaup/bin ]; then export PATH="$HOME/.julia/juliaup/bin:$PATH" fi +# >>> juliaup initialize >>> + +# !! Contents within this block are managed by juliaup !! + +case ":$PATH:" in + *:/home/millironx/.juliaup/bin:*) + ;; + *) + export PATH=/home/millironx/.juliaup/bin${PATH:+:${PATH}} + ;; +esac +# <<< juliaup initialize <<< + # Linuxbrew setup if [ -d $HOME/../linuxbrew/.linuxbrew ]; then BREWPATH=$HOME/../linuxbrew/.linuxbrew diff --git a/dot_tmux.conf b/dot_tmux.conf deleted file mode 100644 index 029f1db..0000000 --- a/dot_tmux.conf +++ /dev/null @@ -1,2 +0,0 @@ -set -g default-terminal "tmux-256color" -source "/usr/share/tmux/powerline.conf" diff --git a/dot_tmux.conf.tmpl b/dot_tmux.conf.tmpl new file mode 100644 index 0000000..1c3c442 --- /dev/null +++ b/dot_tmux.conf.tmpl @@ -0,0 +1,6 @@ +set -g default-terminal "tmux-256color" +{{- if (eq .chezmoi.osRelease.id "debian") }} +source "/usr/share/powerline/bindings/tmux/powerline.conf" +{{- else -}} +source "/usr/share/tmux/powerline.conf" +{{- end }} From 1a200f6117a190fa9da78b6f9154e4e7ffc9ec8f Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 4 Mar 2023 22:48:00 -0600 Subject: [PATCH 100/137] Update executable_dot_zshrc.tmpl --- executable_dot_zshrc.tmpl | 1 - 1 file changed, 1 deletion(-) diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index a9f0d6e..5c42c92 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -50,7 +50,6 @@ antigen theme https://gist.github.com/efde5e8d507bd3e1e046198b69d579f8.git gianu # oh-my-zsh configuration settings HYPHEN_INSENSITIVE="true" -ENABLE_CORRECTION="true" COMPLETION_WAITING_DOTS="true" source $HOME/.hooks From 159ae1f4aae7fc1574c5c21390347317b37197c4 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 14 Apr 2023 12:13:36 -0500 Subject: [PATCH 101/137] Add private_dot_ssh/config.tmpl --- private_dot_ssh/config.tmpl | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 private_dot_ssh/config.tmpl diff --git a/private_dot_ssh/config.tmpl b/private_dot_ssh/config.tmpl new file mode 100644 index 0000000..ca7432b --- /dev/null +++ b/private_dot_ssh/config.tmpl @@ -0,0 +1,32 @@ +Host * + IdentitiesOnly yes + IdentityFile {{ if and (eq .machinetype "workstation") (ne .chezmoi.os "windows") }}~/.ssh/id_rsa_yubikey.pub{{ else }}~/.ssh/id_ed25519.pub{{ end }} + +Host aahz + HostName 129.130.108.37 + User tchristensen + +Host skeeve + HostName 129.130.108.157 + User tchristensen + +Host ceres + HostName ceres.scinet.usda.gov + User thomas.christensen + TCPKeepAlive yes + ServerAliveInterval 20 + ServerAliveCountMax 30 + IdentitiesOnly no + +Host atlas + HostName Atlas-login-1.hpc.msstate.edu + User thomas.christensen + TCPKeepAlive yes + ServerAliveInterval 20 + ServerAliveCountMax 30 + IdentitiesOnly no + +Host atlas-dtn + HostName Atlas-dtn.hpc.msstate.edu + User thomas.christensen + IdentitiesOnly no From 26ce08cab80d8232ab802293664d6d9bf919bc0e Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 14 Apr 2023 12:40:26 -0500 Subject: [PATCH 102/137] chore: Stop using symlinks for konsolerc --- dot_config/private_konsolerc | 9 +++++++++ dot_config/symlink_private_konsolerc.tmpl | 1 - symlinks/dot_config/konsolerc | 10 +--------- 3 files changed, 10 insertions(+), 10 deletions(-) create mode 100644 dot_config/private_konsolerc delete mode 100644 dot_config/symlink_private_konsolerc.tmpl diff --git a/dot_config/private_konsolerc b/dot_config/private_konsolerc new file mode 100644 index 0000000..7f417e8 --- /dev/null +++ b/dot_config/private_konsolerc @@ -0,0 +1,9 @@ +[Desktop Entry] +DefaultProfile=My Default.profile + +[MainWindow] +StatusBar=Disabled +ToolBarsMovable=Disabled + +[UiSettings] +ColorScheme=Default diff --git a/dot_config/symlink_private_konsolerc.tmpl b/dot_config/symlink_private_konsolerc.tmpl deleted file mode 100644 index 2dcbab9..0000000 --- a/dot_config/symlink_private_konsolerc.tmpl +++ /dev/null @@ -1 +0,0 @@ -{{ .chezmoi.sourceDir }}/symlinks/dot_config/konsolerc diff --git a/symlinks/dot_config/konsolerc b/symlinks/dot_config/konsolerc index 6e6b4ce..7f417e8 100644 --- a/symlinks/dot_config/konsolerc +++ b/symlinks/dot_config/konsolerc @@ -2,16 +2,8 @@ DefaultProfile=My Default.profile [MainWindow] -DP-1 DP-2 Height 1920x1080=955 -DP-1 DP-2 Width 1920x1080=1607 -DP-1 DP-2 Window-Maximized 1920x1080=true -DisplayPort-0 DisplayPort-1 Height 1920x1080=634 -DisplayPort-0 DisplayPort-1 Width 1920x1080=1108 -DisplayPort-0 DisplayPort-1 XPosition 1920x1080=2468 -DisplayPort-0 DisplayPort-1 YPosition 1920x1080=276 -State=AAAA/wAAAAD9AAAAAQAAAAAAAAAAAAAAAPwCAAAAAvsAAAAcAFMAUwBIAE0AYQBuAGEAZwBlAHIARABvAGMAawAAAAAA/////wAAANMBAAAD+wAAACIAUQB1AGkAYwBrAEMAbwBtAG0AYQBuAGQAcwBEAG8AYwBrAAAAAAD/////AAAArQEAAAMAAAeAAAADowAAAAQAAAAEAAAACAAAAAj8AAAAAQAAAAIAAAACAAAAFgBtAGEAaQBuAFQAbwBvAGwAQgBhAHIBAAAAAP////8AAAAAAAAAAAAAABwAcwBlAHMAcwBpAG8AbgBUAG8AbwBsAGIAYQByAQAAAN//////AAAAAAAAAAA= StatusBar=Disabled ToolBarsMovable=Disabled [UiSettings] -ColorScheme= +ColorScheme=Default From 262da4064775e9a8f614d06e5547d2c760269d69 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 14 Apr 2023 12:43:02 -0500 Subject: [PATCH 103/137] feat: Add Yubikey SSH key --- private_dot_ssh/private_id_rsa_yubikey.pub | 1 + 1 file changed, 1 insertion(+) create mode 100644 private_dot_ssh/private_id_rsa_yubikey.pub diff --git a/private_dot_ssh/private_id_rsa_yubikey.pub b/private_dot_ssh/private_id_rsa_yubikey.pub new file mode 100644 index 0000000..b381025 --- /dev/null +++ b/private_dot_ssh/private_id_rsa_yubikey.pub @@ -0,0 +1 @@ +ssh-rsa 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 cardno:18 319 764 From 341c97ef5cdc1b4897ba996ac7ef376bdf997f3e Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 14 Apr 2023 13:01:04 -0500 Subject: [PATCH 104/137] refactor: Stop using symlinks for VSCode settings --- .../private_VSCodium/User/settings.json | 222 ++++++++++++++++++ .../User/symlink_settings.json.tmpl | 1 - settings.json | 222 ------------------ 3 files changed, 222 insertions(+), 223 deletions(-) create mode 100644 dot_config/private_VSCodium/User/settings.json delete mode 100644 dot_config/private_VSCodium/User/symlink_settings.json.tmpl delete mode 100644 settings.json diff --git a/dot_config/private_VSCodium/User/settings.json b/dot_config/private_VSCodium/User/settings.json new file mode 100644 index 0000000..e536218 --- /dev/null +++ b/dot_config/private_VSCodium/User/settings.json @@ -0,0 +1,222 @@ +{ + "breadcrumbs.enabled": true, + "editor.bracketPairColorization.enabled": true, + "editor.defaultFormatter": "esbenp.prettier-vscode", + "editor.guides.bracketPairs": "active", + "editor.inlineSuggest.enabled": true, + "editor.linkedEditing": true, + "editor.minimap.enabled": false, + "editor.quickSuggestions": { + "comments": false + }, + "editor.renderWhitespace": "boundary", + "editor.rulers": [80, 120], + "editor.tabCompletion": "on", + "editor.wrappingIndent": "deepIndent", + "editor.unicodeHighlight.ambiguousCharacters": false, + "extensions.ignoreRecommendations": true, + "files.trimFinalNewlines": true, + "files.trimTrailingWhitespace": true, + "prettier.resolveGlobalModules": true, + "workbench.editor.closeOnFileDelete": true, + "workbench.editor.enablePreview": false, + "workbench.editor.enablePreviewFromQuickOpen": false, + "workbench.startupEditor": "none", + + "telemetry.telemetryLevel": "off", + "update.mode": "none", + "workbench.enableExperiments": false, + + "diffEditor.ignoreTrimWhitespace": false, + "git.autofetch": true, + "git.confirmSync": false, + "git.enableCommitSigning": true, + "git.enableSmartCommit": true, + "git.inputValidation": "always", + "git.inputValidationLength": 75, + "git.inputValidationSubjectLength": null, + + "explorer.confirmDelete": false, + "explorer.confirmDragAndDrop": false, + "files.exclude": { + "**/tmp/**": true, + "**/node_modules/**": true, + "**/.sif": true, + "**/.sif.**/**": true, + "**/.git/objects/**": true, + "**/.git": true, + "**/.svn": true, + "**/.hg": true, + "**/CVS": true, + "**/.DS_Store": true + }, + "files.insertFinalNewline": true, + "search.smartCase": true, + "search.followSymlinks": false, + "search.exclude": { + "**/node_modules": true, + "**/bower_components": true, + "**/*.code-search": true, + "**/tmp/**": true, + "**/dist/**": true, + "**/*.sif/**": true, + "**/.git/objects/**": true, + "**/.git/subtree-cache/**": true + }, + "security.workspace.trust.enabled": false, + "files.watcherExclude": { + "**/.git/objects/**": true, + "**/.git/subtree-cache/**": true, + "**/node_modules/*/**": true, + "**/.hg/store/**": true, + "**/.nextflow/**": true, + "**/work/**": true + }, + + "editor.fontFamily": "Fira Code", + "editor.fontLigatures": true, + "window.menuBarVisibility": "visible", + "window.zoomLevel": -1, + "workbench.colorTheme": "Default Dark+", + "workbench.iconTheme": "vscode-great-icons", + + "terminal.integrated.allowChords": false, + "terminal.integrated.cursorBlinking": true, + "terminal.integrated.cursorStyle": "line", + "terminal.integrated.defaultProfile.windows": "Cmder", + "terminal.integrated.fontFamily": "'MesloLGS NF'", + "terminal.integrated.persistentSessionReviveProcess": "never", + "terminal.integrated.gpuAcceleration": "off", + "terminal.integrated.profiles.windows": { + "Cmder": { + "path": [ + "${env:windir}\\Sysnative\\cmd.exe", + "${env:windir}\\System32\\cmd.exe" + ], + "env": { + "CMDER_ROOT": "C:\\tools\\Cmder" + }, + "args": ["/k", "%CMDER_ROOT%\\vendor\\bin\\vscode_init.cmd"] + }, + "PowerShell": { + "source": "PowerShell", + "icon": "terminal-powershell" + }, + "Command Prompt": { + "path": [ + "${env:windir}\\Sysnative\\cmd.exe", + "${env:windir}\\System32\\cmd.exe" + ], + "args": [], + "icon": "terminal-cmd" + }, + "Git Bash": { + "source": "Git Bash" + } + }, + "terminal.integrated.defaultProfile.linux": "zsh", + "terminal.integrated.profiles.linux": { + "bash": { + "path": "bash" + }, + "zsh": { + "path": "zsh" + }, + "fish": { + "path": "fish" + }, + "tmux": { + "path": "tmux", + "icon": "terminal-tmux" + }, + "screen": { + "path": "screen", + "icon": "terminal-tmux" + }, + "pwsh": { + "path": "pwsh", + "icon": "terminal-powershell" + } + }, + "terminal.external.windowsExec": "C:\\Tools\\Cmder\\cmder.exe", + "terminal.external.linuxExec": "yakuake", + + "[shellscript]": { + "files.eol": "\n", + "editor.tabSize": 2, + "files.insertFinalNewline": true, + "files.trimFinalNewlines": true, + "files.trimTrailingWhitespace": true, + "editor.rulers": [80, 92, 120] + }, + "shellcheck.customArgs": ["-x"], + + "[html]": { + "editor.tabSize": 2 + }, + + "[javascript]": { + "editor.tabSize": 2 + }, + + "[json]": { + "editor.tabSize": 2 + }, + + "[julia]": { + "editor.detectIndentation": false, + "editor.insertSpaces": true, + "editor.tabSize": 4, + "files.insertFinalNewline": true, + "files.trimFinalNewlines": true, + "files.trimTrailingWhitespace": true, + "editor.rulers": [92], + "editor.defaultFormatter": "julialang.language-julia" + }, + "julia.enableCrashReporter": false, + "julia.enableTelemetry": false, + "julia.NumThreads": 8, + "julia.symbolCacheDownload": true, + "terminal.integrated.commandsToSkipShell": ["language-julia.interrupt"], + + "latex-workshop.view.pdf.viewer": "tab", + + "[markdown]": { + "editor.tabSize": 2 + }, + "files.associations": { + "README": "markdown" + }, + "markdown-preview-github-styles.colorTheme": "light", + + "[nextflow]": { + "editor.rulers": [80, 84, 120] + }, + + "[python]": { + "editor.rulers": [72, 79, 99] + }, + "python.formatting.provider": "black", + "python.formatting.blackPath": "black", + + "[r]": { + "editor.defaultFormatter": "Ikuyadeu.r" + }, + + "[typescript]": { + "editor.tabSize": 2 + }, + + "[yaml]": { + "editor.tabSize": 2 + }, + "redhat.telemetry.enabled": false, + + "sync.autoDownload": true, + "sync.gist": "ac23d90cbe13499f59ed319c101b4b13", + "sync.quietSync": true, + "workbench.editorAssociations": { + "*.pdf": "latex-workshop-pdf-hook" + }, + "terminal.integrated.tabs.title": "${cwdFolder}${separator}${process}" + } diff --git a/dot_config/private_VSCodium/User/symlink_settings.json.tmpl b/dot_config/private_VSCodium/User/symlink_settings.json.tmpl deleted file mode 100644 index 1127a87..0000000 --- a/dot_config/private_VSCodium/User/symlink_settings.json.tmpl +++ /dev/null @@ -1 +0,0 @@ -{{ .chezmoi.sourceDir }}/settings.json diff --git a/settings.json b/settings.json deleted file mode 100644 index c4303ed..0000000 --- a/settings.json +++ /dev/null @@ -1,222 +0,0 @@ -{ - "breadcrumbs.enabled": true, - "editor.bracketPairColorization.enabled": true, - "editor.defaultFormatter": "esbenp.prettier-vscode", - "editor.guides.bracketPairs": "active", - "editor.inlineSuggest.enabled": true, - "editor.linkedEditing": true, - "editor.minimap.enabled": false, - "editor.quickSuggestions": { - "comments": false - }, - "editor.renderWhitespace": "boundary", - "editor.rulers": [80, 120], - "editor.tabCompletion": "on", - "editor.wrappingIndent": "deepIndent", - "editor.unicodeHighlight.ambiguousCharacters": false, - "extensions.ignoreRecommendations": true, - "files.trimFinalNewlines": true, - "files.trimTrailingWhitespace": true, - "prettier.resolveGlobalModules": true, - "workbench.editor.closeOnFileDelete": true, - "workbench.editor.enablePreview": false, - "workbench.editor.enablePreviewFromQuickOpen": false, - "workbench.startupEditor": "none", - - "telemetry.telemetryLevel": "off", - "update.mode": "none", - "workbench.enableExperiments": false, - - "diffEditor.ignoreTrimWhitespace": false, - "git.autofetch": true, - "git.confirmSync": false, - "git.enableCommitSigning": true, - "git.enableSmartCommit": true, - "git.inputValidation": "always", - "git.inputValidationLength": 75, - "git.inputValidationSubjectLength": null, - - "explorer.confirmDelete": false, - "explorer.confirmDragAndDrop": false, - "files.exclude": { - "**/tmp/**": true, - "**/node_modules/**": true, - "**/.sif": true, - "**/.sif.**/**": true, - "**/.git/objects/**": true, - "**/.git": true, - "**/.svn": true, - "**/.hg": true, - "**/CVS": true, - "**/.DS_Store": true - }, - "files.insertFinalNewline": true, - "search.smartCase": true, - "search.followSymlinks": false, - "search.exclude": { - "**/node_modules": true, - "**/bower_components": true, - "**/*.code-search": true, - "**/tmp/**": true, - "**/dist/**": true, - "**/*.sif/**": true, - "**/.git/objects/**": true, - "**/.git/subtree-cache/**": true - }, - "security.workspace.trust.enabled": false, - "files.watcherExclude": { - "**/.git/objects/**": true, - "**/.git/subtree-cache/**": true, - "**/node_modules/*/**": true, - "**/.hg/store/**": true, - "**/.nextflow/**": true, - "**/work/**": true - }, - - "editor.fontFamily": "Fira Code", - "editor.fontLigatures": true, - "window.menuBarVisibility": "visible", - "window.zoomLevel": -1, - "workbench.colorTheme": "Default Dark+", - "workbench.iconTheme": "vscode-great-icons", - - "terminal.integrated.allowChords": false, - "terminal.integrated.cursorBlinking": true, - "terminal.integrated.cursorStyle": "line", - "terminal.integrated.defaultProfile.windows": "Cmder", - "terminal.integrated.fontFamily": "'MesloLGS NF'", - "terminal.integrated.persistentSessionReviveProcess": "never", - "terminal.integrated.gpuAcceleration": "off", - "terminal.integrated.profiles.windows": { - "Cmder": { - "path": [ - "${env:windir}\\Sysnative\\cmd.exe", - "${env:windir}\\System32\\cmd.exe" - ], - "env": { - "CMDER_ROOT": "C:\\tools\\Cmder" - }, - "args": ["/k", "%CMDER_ROOT%\\vendor\\bin\\vscode_init.cmd"] - }, - "PowerShell": { - "source": "PowerShell", - "icon": "terminal-powershell" - }, - "Command Prompt": { - "path": [ - "${env:windir}\\Sysnative\\cmd.exe", - "${env:windir}\\System32\\cmd.exe" - ], - "args": [], - "icon": "terminal-cmd" - }, - "Git Bash": { - "source": "Git Bash" - } - }, - "terminal.integrated.defaultProfile.linux": "zsh", - "terminal.integrated.profiles.linux": { - "bash": { - "path": "bash" - }, - "zsh": { - "path": "zsh" - }, - "fish": { - "path": "fish" - }, - "tmux": { - "path": "tmux", - "icon": "terminal-tmux" - }, - "screen": { - "path": "screen", - "icon": "terminal-tmux" - }, - "pwsh": { - "path": "pwsh", - "icon": "terminal-powershell" - } - }, - "terminal.external.windowsExec": "C:\\Tools\\Cmder\\cmder.exe", - "terminal.external.linuxExec": "yakuake", - - "[shellscript]": { - "files.eol": "\n", - "editor.tabSize": 2, - "files.insertFinalNewline": true, - "files.trimFinalNewlines": true, - "files.trimTrailingWhitespace": true, - "editor.rulers": [80, 92, 120] - }, - "shellcheck.customArgs": ["-x"], - - "[html]": { - "editor.tabSize": 2 - }, - - "[javascript]": { - "editor.tabSize": 2 - }, - - "[json]": { - "editor.tabSize": 2 - }, - - "[julia]": { - "editor.detectIndentation": false, - "editor.insertSpaces": true, - "editor.tabSize": 4, - "files.insertFinalNewline": true, - "files.trimFinalNewlines": true, - "files.trimTrailingWhitespace": true, - "editor.rulers": [92], - "editor.defaultFormatter": "julialang.language-julia" - }, - "julia.enableCrashReporter": false, - "julia.enableTelemetry": false, - "julia.NumThreads": 8, - "julia.symbolCacheDownload": true, - "terminal.integrated.commandsToSkipShell": ["language-julia.interrupt"], - - "latex-workshop.view.pdf.viewer": "tab", - - "[markdown]": { - "editor.tabSize": 2 - }, - "files.associations": { - "README": "markdown" - }, - "markdown-preview-github-styles.colorTheme": "light", - - "[nextflow]": { - "editor.rulers": [80, 84, 120] - }, - - "[python]": { - "editor.rulers": [72, 79, 99] - }, - "python.formatting.provider": "black", - "python.formatting.blackPath": "black", - - "[r]": { - "editor.defaultFormatter": "Ikuyadeu.r" - }, - - "[typescript]": { - "editor.tabSize": 2 - }, - - "[yaml]": { - "editor.tabSize": 2 - }, - "redhat.telemetry.enabled": false, - - "sync.autoDownload": true, - "sync.gist": "ac23d90cbe13499f59ed319c101b4b13", - "sync.quietSync": true, - "workbench.editorAssociations": { - "*.pdf": "latex-workshop-pdf-hook" - }, - "terminal.integrated.tabs.title": "${cwdFolder}${separator}${process}" -} From 36d30714bd62644546d424f74ef784b0e07e561e Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 14 Apr 2023 13:04:13 -0500 Subject: [PATCH 105/137] chore: Remove unused symlink stuff --- .chezmoiignore | 2 -- symlinks/dot_config/konsolerc | 9 --------- 2 files changed, 11 deletions(-) delete mode 100644 .chezmoiignore delete mode 100644 symlinks/dot_config/konsolerc diff --git a/.chezmoiignore b/.chezmoiignore deleted file mode 100644 index aa15e92..0000000 --- a/.chezmoiignore +++ /dev/null @@ -1,2 +0,0 @@ -settings.json -symlinks diff --git a/symlinks/dot_config/konsolerc b/symlinks/dot_config/konsolerc deleted file mode 100644 index 7f417e8..0000000 --- a/symlinks/dot_config/konsolerc +++ /dev/null @@ -1,9 +0,0 @@ -[Desktop Entry] -DefaultProfile=My Default.profile - -[MainWindow] -StatusBar=Disabled -ToolBarsMovable=Disabled - -[UiSettings] -ColorScheme=Default From 4c15e228ce7ff8e9904b50c7fc284f114c4dc41c Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 14 Apr 2023 13:05:35 -0500 Subject: [PATCH 106/137] feat!: Remove all GNU Nano config --- .chezmoiexternal.toml | 6 ------ dot_nanorc.tmpl | 19 ------------------- 2 files changed, 25 deletions(-) delete mode 100644 dot_nanorc.tmpl diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml index c6b3783..c58bdfc 100644 --- a/.chezmoiexternal.toml +++ b/.chezmoiexternal.toml @@ -1,9 +1,3 @@ -[".nano"] - type = "archive" - url = "https://github.com/scopatz/nanorc/releases/download/2020.10.10/nanorc-2020.10.10.tar.gz" - stripComponents = 1 - include = ["*/*.nanorc"] - [".local/bin/n"] type = "file" url = "https://raw.githubusercontent.com/tj/n/master/bin/n" diff --git a/dot_nanorc.tmpl b/dot_nanorc.tmpl deleted file mode 100644 index 08ee2d0..0000000 --- a/dot_nanorc.tmpl +++ /dev/null @@ -1,19 +0,0 @@ -{{- if or - (eq .machinetype "workstation") - (eq .chezmoi.osRelease.id "fedora") - (and (eq .chezmoi.osRelease.id "almalinux" "centos" "rhel") (gt (atoi .chezmoi.osRelease.versionID) 7)) - (and (eq .chezmoi.osRelease.id "debian") (gt (atoi .chezmoi.osRelease.versionID) 9 )) -}} -set linenumbers -set titlecolor bold,lightwhite,blue -set promptcolor lightwhite,lightblack -set statuscolor bold,lightwhite,green -set errorcolor bold,lightwhite,red -set spotlightcolor black,lime -set selectedcolor lightwhite,magenta -set stripecolor ,yellow -set scrollercolor cyan -set numbercolor lightwhite,lightblack -set keycolor cyan -set functioncolor green -include ~/.nano/*.nanorc -{{- end }} From d4e523271ee43855da6524943138234b56c3b3c9 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 15:54:11 -0500 Subject: [PATCH 107/137] fix: Add whitespace back into tmux.conf --- dot_tmux.conf.tmpl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/dot_tmux.conf.tmpl b/dot_tmux.conf.tmpl index 1c3c442..4f55050 100644 --- a/dot_tmux.conf.tmpl +++ b/dot_tmux.conf.tmpl @@ -1,6 +1,6 @@ set -g default-terminal "tmux-256color" -{{- if (eq .chezmoi.osRelease.id "debian") }} +{{ if (eq .chezmoi.osRelease.id "debian") }} source "/usr/share/powerline/bindings/tmux/powerline.conf" -{{- else -}} +{{ else }} source "/usr/share/tmux/powerline.conf" -{{- end }} +{{ end }} From 1c558abfa65114663c0e5dce183cfd30ec9e6e09 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 17:09:08 -0500 Subject: [PATCH 108/137] feat: Add gpub alias --- dot_aliases | 1 + 1 file changed, 1 insertion(+) diff --git a/dot_aliases b/dot_aliases index e21d69f..6448c8f 100644 --- a/dot_aliases +++ b/dot_aliases @@ -24,6 +24,7 @@ alias please='sudo $(fc -ln -1)' alias nrun='__NV_PRIME_RENDER_OFFLOAD=1 __GLX_VENDOR_LIBRARY_NAME=nvidia __VK_LAYER_NV_optimus="NVIDIA_only"' alias grim='git rebase -i --autosquash $(git_main_branch)' alias grid='git rebase -i --autosquash $(git_develop_branch)' +alias gpub='git push --set-upstream origin $(git rev-parse --abbrev-ref HEAD)' # Alias-like functions nd () { From 7319c7382024a0be3fc673bdb32e61cc1f2bc93c Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 17:11:41 -0500 Subject: [PATCH 109/137] chore: Convert .aliases to template --- dot_aliases => dot_aliases.tmpl | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename dot_aliases => dot_aliases.tmpl (100%) diff --git a/dot_aliases b/dot_aliases.tmpl similarity index 100% rename from dot_aliases rename to dot_aliases.tmpl From 1e8b917803e053e955628b4df02adec49b26ad0b Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 17:16:40 -0500 Subject: [PATCH 110/137] refactor: Replace shell path evaluation with Chezmoi evaluation --- dot_aliases.tmpl | 27 +++++++++------------------ 1 file changed, 9 insertions(+), 18 deletions(-) diff --git a/dot_aliases.tmpl b/dot_aliases.tmpl index 6448c8f..89e6d7e 100644 --- a/dot_aliases.tmpl +++ b/dot_aliases.tmpl @@ -1,22 +1,13 @@ -# Only create aliases if the underlying programs are available -# This allows portability between machines in different states -alias_if_exists () { - ALIAS=${1} - COMMAND=${2} - ARGS=${3} - if [ $(command -v $COMMAND) ]; then - if [ -n "$ARGS" ]; then - alias $ALIAS="$COMMAND $ARGS" - else - alias $ALIAS="$COMMAND" - fi - fi -} - # Context-sensitive aliases -alias_if_exists bat batcat -alias_if_exists cat bat -alias_if_exists ls lsd +{{- if lookPath "batcat" }} +alias bat=batcat +{{- end }} +{{- if or (lookPath "bat") (lookPath "batcat") }} +alias cat=bat +{{- end }} +{{- if lookPath "lsd" }} +alias ls=lsd +{{- end }} # Universal aliases alias config='git --git-dir=$HOME/.cfg/ --work-tree=$HOME' From 6f57123a63834c3ab3af2c38b85fd8490a0a21df Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 17:19:08 -0500 Subject: [PATCH 111/137] feat: Add alias for codium --- dot_aliases.tmpl | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dot_aliases.tmpl b/dot_aliases.tmpl index 89e6d7e..45b6949 100644 --- a/dot_aliases.tmpl +++ b/dot_aliases.tmpl @@ -8,6 +8,9 @@ alias cat=bat {{- if lookPath "lsd" }} alias ls=lsd {{- end }} +{{- if and (lookPath "codium") (not (lookPath "code")) }} +alias code=codium +{{- end }} # Universal aliases alias config='git --git-dir=$HOME/.cfg/ --work-tree=$HOME' From f89211ef87d2110a44ef90e65a98ec4673ca2fbd Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 17:45:11 -0500 Subject: [PATCH 112/137] feat!: Remove rbenv and n hooks I'll be using nix for those types of dependencies from now on --- dot_hooks.tmpl | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/dot_hooks.tmpl b/dot_hooks.tmpl index 7af0c42..69a2185 100644 --- a/dot_hooks.tmpl +++ b/dot_hooks.tmpl @@ -1,14 +1,3 @@ -if [ -f $HOME/.rbenv/bin/rbenv ]; then - export PATH="$HOME/.rbenv/bin:$PATH" - eval "$(rbenv init -)" - export PATH="$HOME/.rbenv/plugins/ruby-build/bin:$PATH" -fi - -if [ $(command -v n) ]; then - export N_PREFIX=$HOME/.n - export PATH="$HOME/.n/bin:$PATH" -fi - if [ -f $HOME/.ion/bin/ion ]; then export PATH="$HOME/.ion/bin/ion:$PATH" export FPATH="$HOME/.ion/completions:$FPATH" From 433c576a444b760bb27f12ad3b0e758153f79f0e Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 17:45:49 -0500 Subject: [PATCH 113/137] refactor: Replace all shell command searching with Chezmoi searching --- dot_envvar.tmpl | 57 ++++++++++++++++++++++--------------------------- 1 file changed, 25 insertions(+), 32 deletions(-) diff --git a/dot_envvar.tmpl b/dot_envvar.tmpl index 42346d3..206ff7b 100644 --- a/dot_envvar.tmpl +++ b/dot_envvar.tmpl @@ -1,45 +1,38 @@ +{{- if lookPath "pipx" }} # Enable pipx completions -if [ $(command -v pipx) ]; then - eval "$(register-python-argcomplete pipx)" -fi +eval "$(register-python-argcomplete pipx)" +{{- end }} +{{- if lookPath "nvim" }} # Preferred editor for local and remote sessions -if [ $(command -v nvim) ]; then - export EDITOR=nvim -elif [ $(command -v nano) ]; then - export EDITOR=nano -elif [ $(command -v vim) ]; then - export EDITOR=vim -elif [ $(command -v emacs) ]; then - export EDITOR='emacs -nw' -fi +export EDITOR=nvim +{{- end }} -if [ $(command -v kate) ]; then - export VISUAL=kate -elif [ $(command -v code) ]; then - export VISUAL=code -elif [ $(command -v emacs) ]; then - export VISUAL=emacs -fi +{{- if lookPath "kate" }} +export VISUAL=kate +{{- else if lookPath "codium" }} +export VISUAL=codium +{{- else if lookPath "code" }} +export VISUAL=code +{{- end }} +{{- if lookPath "most" }} # Set a cool new pager with color support -if [ $(command -v most) ]; then - export PAGER=most -fi - +export PAGER=most +{{- end }} +{{- if or (lookPath "bat") (lookPath "catbat") }} # Replace cat with bat -if [ $(command -v bat) ]; then - export BAT_PAGER="less -SRF" - export MANPAGER="sh -c 'col -bx | bat -l man -p'" - export MANROFFOPT="-c" -fi +export BAT_PAGER="less -SRF" +export MANPAGER="sh -c 'col -bx | bat -l man -p'" +export MANROFFOPT="-c" +{{- end }} # Add notification support for long-running processes -if [ $(command -v ntfy) ]; then - eval "$(ntfy shell-integration --longer-than 30)" - export AUTO_NTFY_DONE_IGNORE="vim nano emacs kate zshconfig screen tmux ssh top htop less more most nethogs 'singularity shell' julia man glances" -fi +{{- if lookPath "ntfy" }} +eval "$(ntfy shell-integration --longer-than 30)" +export AUTO_NTFY_DONE_IGNORE="vim nano emacs kate zshconfig screen tmux ssh top htop less more most nethogs 'singularity shell' julia man glances" +{{- end }} # Set the Nextflow enviroment caches export NXF_HOME="$HOME/.nextflow" From c416a5304be4a6cd723fd4c5036e9c5f1de172af Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 18:01:04 -0500 Subject: [PATCH 114/137] refactor: Move conda hooks to .hooks --- dot_hooks.tmpl | 15 +++++++++++++++ executable_dot_bashrc.tmpl | 16 ---------------- executable_dot_zshrc.tmpl | 15 --------------- 3 files changed, 15 insertions(+), 31 deletions(-) diff --git a/dot_hooks.tmpl b/dot_hooks.tmpl index 69a2185..ead7ebd 100644 --- a/dot_hooks.tmpl +++ b/dot_hooks.tmpl @@ -1,3 +1,18 @@ +# >>> conda initialize >>> +# !! Contents within this block are managed by 'conda init' !! +__conda_setup="$($HOME/miniconda3/bin/conda shell.$(basename $0) 'hook' 2> /dev/null)" +if [ $? -eq 0 ]; then + eval "$__conda_setup" +else + if [ -f "$HOME/miniconda3/etc/profile.d/conda.sh" ]; then + . "$HOME/miniconda3/etc/profile.d/conda.sh" + else + export PATH="$HOME/miniconda3/bin:$PATH" + fi +fi +unset __conda_setup +# <<< conda initialize <<< + if [ -f $HOME/.ion/bin/ion ]; then export PATH="$HOME/.ion/bin/ion:$PATH" export FPATH="$HOME/.ion/completions:$FPATH" diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index 7782a56..732a3b7 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -11,22 +11,6 @@ source $HOME/.hooks # User specific aliases and functions source $HOME/.aliases -# >>> conda initialize >>> -# !! Contents within this block are managed by 'conda init' !! -__conda_setup="$('$HOME/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" -if [ $? -eq 0 ]; then - eval "$__conda_setup" -else - if [ -f "$HOME/miniconda3/etc/profile.d/conda.sh" ]; then - . "$HOME/miniconda3/etc/profile.d/conda.sh" - else - export PATH="$HOME/miniconda3/bin:$PATH" - fi -fi -unset __conda_setup -conda config --set changeps1 true -# <<< conda initialize <<< - # >>> direnv initalize >>> if [ $(command -v direnv) ]; then eval "$(direnv hook bash)" diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index 5c42c92..bedc10e 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -54,21 +54,6 @@ COMPLETION_WAITING_DOTS="true" source $HOME/.hooks -# >>> conda initialize >>> -# !! Contents within this block are managed by 'conda init' !! -__conda_setup="$('$HOME/miniconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)" -if [ $? -eq 0 ]; then - eval "$__conda_setup" -else - if [ -f "$HOME/miniconda3/etc/profile.d/conda.sh" ]; then - . "$HOME/miniconda3/etc/profile.d/conda.sh" - else - export PATH="$HOME/miniconda3/bin:$PATH" - fi -fi -unset __conda_setup -# <<< conda initialize <<< - # >>> direnv initalize >>> if [ $(command -v direnv) ]; then eval "$(direnv hook zsh)" From 6caa4f13efe132f131e070c1a3239ee46a746fed Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 18:01:23 -0500 Subject: [PATCH 115/137] feat: Persist ps1 change for conda in bash --- dot_condarc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dot_condarc b/dot_condarc index fab3508..9a57598 100644 --- a/dot_condarc +++ b/dot_condarc @@ -1,2 +1,2 @@ auto_activate_base: false -changeps1: false +changeps1: true From 85b05d50f0558e46a91e33c3e9931002a125956f Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 18:01:42 -0500 Subject: [PATCH 116/137] feat: Add mamba hooks --- dot_hooks.tmpl | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/dot_hooks.tmpl b/dot_hooks.tmpl index ead7ebd..757e684 100644 --- a/dot_hooks.tmpl +++ b/dot_hooks.tmpl @@ -11,6 +11,10 @@ else fi fi unset __conda_setup + +if [ -f "$HOME/miniconda3/etc/profile.d/mamba.sh" ]; then + . "$HOME/miniconda3/etc/profile.d/mamba.sh" +fi # <<< conda initialize <<< if [ -f $HOME/.ion/bin/ion ]; then From ba3dfc5f52b61e23e851fabc94f446316648b463 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 18:03:24 -0500 Subject: [PATCH 117/137] refactor: Move direnv hooks to .hooks --- dot_hooks.tmpl | 4 ++++ executable_dot_bashrc.tmpl | 6 ------ executable_dot_zshrc.tmpl | 6 ------ 3 files changed, 4 insertions(+), 12 deletions(-) diff --git a/dot_hooks.tmpl b/dot_hooks.tmpl index 757e684..565dc5a 100644 --- a/dot_hooks.tmpl +++ b/dot_hooks.tmpl @@ -17,6 +17,10 @@ if [ -f "$HOME/miniconda3/etc/profile.d/mamba.sh" ]; then fi # <<< conda initialize <<< +{{- if lookPath "direnv" }} +eval "$(direnv hook $(basename $0))" +{{- end }} + if [ -f $HOME/.ion/bin/ion ]; then export PATH="$HOME/.ion/bin/ion:$PATH" export FPATH="$HOME/.ion/completions:$FPATH" diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index 732a3b7..aac0dde 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -11,12 +11,6 @@ source $HOME/.hooks # User specific aliases and functions source $HOME/.aliases -# >>> direnv initalize >>> -if [ $(command -v direnv) ]; then - eval "$(direnv hook bash)" -fi -# <<< direnv initalize <<< - source $HOME/.envvar if [ $(command -v env_parallel.bash) ]; then diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index bedc10e..734a0de 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -54,12 +54,6 @@ COMPLETION_WAITING_DOTS="true" source $HOME/.hooks -# >>> direnv initalize >>> -if [ $(command -v direnv) ]; then - eval "$(direnv hook zsh)" -fi -# <<< direnv initalize <<< - # Tell Antigen that you're done antigen apply From 99c8b6ec4b23161a39d0e8f7a82261c6280f3981 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 18:12:14 -0500 Subject: [PATCH 118/137] refactor: Move env_parallel hooks to .hooks --- dot_hooks.tmpl | 5 +++++ executable_dot_bashrc.tmpl | 4 ---- executable_dot_zshrc.tmpl | 5 ----- 3 files changed, 5 insertions(+), 9 deletions(-) diff --git a/dot_hooks.tmpl b/dot_hooks.tmpl index 565dc5a..29097e0 100644 --- a/dot_hooks.tmpl +++ b/dot_hooks.tmpl @@ -26,6 +26,11 @@ if [ -f $HOME/.ion/bin/ion ]; then export FPATH="$HOME/.ion/completions:$FPATH" fi +# Import GNU parallel +if [ $(command -v env_parallel.$(basename $0)) ]; then + source $(which env_parallel.$(basename $0)) +fi + {{- if eq .machinetype "workstation" }} export GPG_TTY="$(tty)" export SSH_AUTH_SOCK=$(gpgconf --list-dirs agent-ssh-socket) diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index aac0dde..34b39c0 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -13,9 +13,5 @@ source $HOME/.aliases source $HOME/.envvar -if [ $(command -v env_parallel.bash) ]; then - source $(which env_parallel.bash) -fi - # Make the prompt pretty, just in case we're stuck in bash land export PS1="[\[\e[32m\]\u\[\e[m\]@\[\e[33m\]\h\[\e[m\] \[\e[34m\]\W\[\e[m\]] \\$ " diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index 734a0de..41cb7f8 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -68,11 +68,6 @@ source $HOME/.envvar alias zshconfig="$EDITOR ~/.zshrc" source $HOME/.aliases -# Import GNU parallel -if [ $(command -v env_parallel.zsh) ]; then - source $(which env_parallel.zsh) -fi - {{ if or (eq .machinetype "workstation") (eq .chezmoi.osRelease.id "fedora") From 9813078c5ee3f6fa514149d753f1be97228822cd Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 18:13:02 -0500 Subject: [PATCH 119/137] feat: Remove n external download --- .chezmoiexternal.toml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml index c58bdfc..6ddd71a 100644 --- a/.chezmoiexternal.toml +++ b/.chezmoiexternal.toml @@ -1,9 +1,3 @@ -[".local/bin/n"] - type = "file" - url = "https://raw.githubusercontent.com/tj/n/master/bin/n" - executable = true - refreshPeriod = "168h" - [".local/share/fonts/meslolgs-nf-regular.ttf"] type = "file" url = "https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Regular.ttf" From 597a4edb0f17cca1dc6a553aacee7de3ba5ca04b Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 18:15:03 -0500 Subject: [PATCH 120/137] refactor: Move antigen to chezmoiexternal --- .chezmoiexternal.toml | 5 +++++ executable_dot_zshrc.tmpl | 3 --- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.chezmoiexternal.toml b/.chezmoiexternal.toml index 6ddd71a..a107be7 100644 --- a/.chezmoiexternal.toml +++ b/.chezmoiexternal.toml @@ -1,3 +1,8 @@ +["antigen.zsh"] + type = "file" + url = "https://git.io/antigen" + refreshPeriod = "168h" + [".local/share/fonts/meslolgs-nf-regular.ttf"] type = "file" url = "https://github.com/romkatv/powerlevel10k-media/raw/master/MesloLGS%20NF%20Regular.ttf" diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index 41cb7f8..4bf3d42 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -18,9 +18,6 @@ then fi # Load the antigen library -if [[ ! -f "$HOME/antigen.zsh" ]]; then - curl -L git.io/antigen > $HOME/antigen.zsh -fi source "$HOME/antigen.zsh" # Load the oh-my-zsh library From 2bf7c0a80b92626fb788cd7df3ea2414e243fb3a Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 18:46:50 -0500 Subject: [PATCH 121/137] feat: Add mamba installer --- run_once_install_mamba.sh.tmpl | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 run_once_install_mamba.sh.tmpl diff --git a/run_once_install_mamba.sh.tmpl b/run_once_install_mamba.sh.tmpl new file mode 100644 index 0000000..a17e22f --- /dev/null +++ b/run_once_install_mamba.sh.tmpl @@ -0,0 +1,12 @@ +#!/bin/bash +{{ if eq .chezmoi.os "linux" }} +{{ $mambaURL := print "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-pypy3-Linux-x86_64.sh" }} +{{ if lookPath "wget" }} +wget -qO- "{{ $mambaURL }}" > mamba.sh +{{ else }} +curl -L "{{ $mambaURL }}" > mamba.sh +{{ end }} +chmod +x mamba.sh +./mamba.sh -b -u -p $HOME/miniconda3 +rm mamba.sh +{{ end }} From 774e277e9900b3d6fe92de5eff687503d9e08deb Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 18:57:04 -0500 Subject: [PATCH 122/137] refactor: Simplify juliaup support --- dot_profile | 18 ++---------------- 1 file changed, 2 insertions(+), 16 deletions(-) diff --git a/dot_profile b/dot_profile index 17df7a2..93f26fa 100644 --- a/dot_profile +++ b/dot_profile @@ -3,22 +3,8 @@ export PATH="$HOME/.local/bin:$HOME/bin:$PATH" # juliaup setup -if [ -d $HOME/.julia/juliaup/bin ]; then - export PATH="$HOME/.julia/juliaup/bin:$PATH" -fi - -# >>> juliaup initialize >>> - -# !! Contents within this block are managed by juliaup !! - -case ":$PATH:" in - *:/home/millironx/.juliaup/bin:*) - ;; - *) - export PATH=/home/millironx/.juliaup/bin${PATH:+:${PATH}} - ;; -esac -# <<< juliaup initialize <<< +export PATH="$HOME/.julia/juliaup/bin:$PATH" +export PATH="$HOME/.juliaup/bin:$PATH" # Linuxbrew setup if [ -d $HOME/../linuxbrew/.linuxbrew ]; then From 83f28d03f08c0203a602936d98473b2c950ad694 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 19:01:21 -0500 Subject: [PATCH 123/137] fix: Use private key to login on Windows --- private_dot_ssh/config.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/private_dot_ssh/config.tmpl b/private_dot_ssh/config.tmpl index ca7432b..1288e19 100644 --- a/private_dot_ssh/config.tmpl +++ b/private_dot_ssh/config.tmpl @@ -1,6 +1,6 @@ Host * IdentitiesOnly yes - IdentityFile {{ if and (eq .machinetype "workstation") (ne .chezmoi.os "windows") }}~/.ssh/id_rsa_yubikey.pub{{ else }}~/.ssh/id_ed25519.pub{{ end }} + IdentityFile {{ if and (eq .machinetype "workstation") (ne .chezmoi.os "windows") }}~/.ssh/id_rsa_yubikey.pub{{ else }}~/.ssh/id_ed25519{{ end }} Host aahz HostName 129.130.108.37 From bc153ee4d1652662687ef379d5acc09d27720748 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 19:11:11 -0500 Subject: [PATCH 124/137] feat: Add local nix install hook --- dot_profile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/dot_profile b/dot_profile index 93f26fa..9079577 100644 --- a/dot_profile +++ b/dot_profile @@ -18,3 +18,7 @@ if [ -n "$BREWPATH" ]; then export HOMEBREW_MAKE_JOBS=1 export HOMEBREW_NO_ANALYTICS=1 fi + +if [ -e "$HOME/.nix-profile/etc/profile.d/nix.sh" ]; then + . "$HOME/.nix-profile/etc/profile.d/nix.sh" +fi From 44b9b80d27441fed56f8cd9dfa18a81b3af44208 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 19:13:10 -0500 Subject: [PATCH 125/137] refactor: Update GPG conf to match Dr Duh's --- private_dot_gnupg/private_gpg-agent.conf | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/private_dot_gnupg/private_gpg-agent.conf b/private_dot_gnupg/private_gpg-agent.conf index 918e9f9..ca45c6f 100644 --- a/private_dot_gnupg/private_gpg-agent.conf +++ b/private_dot_gnupg/private_gpg-agent.conf @@ -1,2 +1,4 @@ -default-cache-ttl 10000 -max-cache-ttl 86400 +enable-ssh-support +ttyname $GPG_TTY +default-cache-ttl 60 +max-cache-ttl 120 From be48c89689b9a8d3abb8dd8fe0f7e35f64b5cf30 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 19:31:22 -0500 Subject: [PATCH 126/137] fix: Replace $0 with more robust shell checker --- dot_hooks.tmpl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/dot_hooks.tmpl b/dot_hooks.tmpl index 29097e0..a025c71 100644 --- a/dot_hooks.tmpl +++ b/dot_hooks.tmpl @@ -1,6 +1,6 @@ # >>> conda initialize >>> # !! Contents within this block are managed by 'conda init' !! -__conda_setup="$($HOME/miniconda3/bin/conda shell.$(basename $0) 'hook' 2> /dev/null)" +__conda_setup="$($HOME/miniconda3/bin/conda shell.$(basename $(readlink -f /proc/$$/exe)) 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else @@ -18,7 +18,7 @@ fi # <<< conda initialize <<< {{- if lookPath "direnv" }} -eval "$(direnv hook $(basename $0))" +eval "$(direnv hook $(basename $(readlink -f /proc/$$/exe)))" {{- end }} if [ -f $HOME/.ion/bin/ion ]; then @@ -27,8 +27,8 @@ if [ -f $HOME/.ion/bin/ion ]; then fi # Import GNU parallel -if [ $(command -v env_parallel.$(basename $0)) ]; then - source $(which env_parallel.$(basename $0)) +if [ $(command -v env_parallel.$(basename $(readlink -f /proc/$$/exe))) ]; then + source $(which env_parallel.$(basename $(readlink -f /proc/$$/exe))) fi {{- if eq .machinetype "workstation" }} From 24e09bc0840ec90bf348dfec938bff56eb27306a Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 15 Apr 2023 19:43:31 -0500 Subject: [PATCH 127/137] fix: Only evaluate distro if os is linux --- dot_tmux.conf.tmpl | 2 ++ executable_dot_zshrc.tmpl | 4 ++++ 2 files changed, 6 insertions(+) diff --git a/dot_tmux.conf.tmpl b/dot_tmux.conf.tmpl index 4f55050..28546d2 100644 --- a/dot_tmux.conf.tmpl +++ b/dot_tmux.conf.tmpl @@ -1,6 +1,8 @@ set -g default-terminal "tmux-256color" +{{- if eq .chezmoi.os "linux" }} {{ if (eq .chezmoi.osRelease.id "debian") }} source "/usr/share/powerline/bindings/tmux/powerline.conf" {{ else }} source "/usr/share/tmux/powerline.conf" {{ end }} +{{- end }} diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index 4bf3d42..4529d6f 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -1,3 +1,4 @@ +{{- if eq .chezmoi.os "linux" }} {{- if or (eq .machinetype "workstation") (eq .chezmoi.osRelease.id "fedora") @@ -10,6 +11,7 @@ if [[ -r "${XDG_CACHE_HOME:-$HOME/.cache}/p10k-instant-prompt-${(%):-%n}.zsh" ]] source "${XDG_CACHE_HOME:-$HOME/.cache}/p10k-instant-prompt-${(%):-%n}.zsh" fi {{- end }} +{{- end }} # User specific environment if ! [[ "$PATH" =~ "$HOME/.local/bin:$HOME/bin:" ]] @@ -65,6 +67,7 @@ source $HOME/.envvar alias zshconfig="$EDITOR ~/.zshrc" source $HOME/.aliases +{{- if eq .chezmoi.os "linux" }} {{ if or (eq .machinetype "workstation") (eq .chezmoi.osRelease.id "fedora") @@ -73,3 +76,4 @@ source $HOME/.aliases # To customize prompt, run `p10k configure` or edit ~/.p10k.zsh. [[ ! -f ~/.p10k.zsh ]] || source ~/.p10k.zsh {{- end }} +{{- end }} From b657e9e09d752295887eed614f686f444ddd708d Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sun, 16 Apr 2023 14:55:52 -0500 Subject: [PATCH 128/137] refactor: Use DNS name for aahz --- private_dot_ssh/config.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/private_dot_ssh/config.tmpl b/private_dot_ssh/config.tmpl index 1288e19..8e4b31b 100644 --- a/private_dot_ssh/config.tmpl +++ b/private_dot_ssh/config.tmpl @@ -3,7 +3,7 @@ Host * IdentityFile {{ if and (eq .machinetype "workstation") (ne .chezmoi.os "windows") }}~/.ssh/id_rsa_yubikey.pub{{ else }}~/.ssh/id_ed25519{{ end }} Host aahz - HostName 129.130.108.37 + HostName nistac-108-37.dhcp.ksu.edu User tchristensen Host skeeve From 8a4438cf425e0072aaa0ec1654992157c476a6f9 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 21 Apr 2023 20:27:32 -0500 Subject: [PATCH 129/137] feat: Add anderson alias to ssh config --- private_dot_ssh/config.tmpl | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/private_dot_ssh/config.tmpl b/private_dot_ssh/config.tmpl index 8e4b31b..cde6ce3 100644 --- a/private_dot_ssh/config.tmpl +++ b/private_dot_ssh/config.tmpl @@ -2,6 +2,10 @@ Host * IdentitiesOnly yes IdentityFile {{ if and (eq .machinetype "workstation") (ne .chezmoi.os "windows") }}~/.ssh/id_rsa_yubikey.pub{{ else }}~/.ssh/id_ed25519{{ end }} +Host anderson + HostName anderson.millironx.com + User millironx + Host aahz HostName nistac-108-37.dhcp.ksu.edu User tchristensen From dec84dc5c3dd3887dedc60aca758a179377a41fe Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 21 Apr 2023 20:44:38 -0500 Subject: [PATCH 130/137] refactor: Replace bw item ids with verbose names --- dot_envvar.tmpl | 2 +- dot_nextflow/config.tmpl | 2 +- dot_nextflow/scm.tmpl | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/dot_envvar.tmpl b/dot_envvar.tmpl index 206ff7b..b3a78b0 100644 --- a/dot_envvar.tmpl +++ b/dot_envvar.tmpl @@ -57,4 +57,4 @@ export JULIA_NUM_THREADS=$(nproc) JULIA_PKG_USE_CLI_GIT=true # Make NCBI happy -export NCBI_API_KEY='{{ (bitwarden "item" "7d42eba0-c256-4d3b-8d0e-adbf016a08f8").login.password }}' +export NCBI_API_KEY='{{ (bitwarden "item" "NCBI API Key").login.password }}' diff --git a/dot_nextflow/config.tmpl b/dot_nextflow/config.tmpl index 12db9cf..a4291d4 100644 --- a/dot_nextflow/config.tmpl +++ b/dot_nextflow/config.tmpl @@ -1,7 +1,7 @@ {{ if ne .machinetype "workstation" }} tower { enabled = true - accessToken = '{{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}' + accessToken = '{{ (bitwarden "item" "Nextflow Tower Access Token").login.password }}' } {{ end }} diff --git a/dot_nextflow/scm.tmpl b/dot_nextflow/scm.tmpl index 8332f2c..6f58cd0 100644 --- a/dot_nextflow/scm.tmpl +++ b/dot_nextflow/scm.tmpl @@ -1,6 +1,6 @@ providers { github { user = '{{ .githubuser }}' - password = '{{ (bitwarden "item" "3e123829-7167-4dd2-8f3f-ad8f01081fee").login.password }}' + password = '{{ (bitwarden "item" "GitHub Nextflow Token").login.password }}' } } From f61d3d225be474bb36605fe905be5127fb34896d Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sun, 30 Apr 2023 21:00:56 -0500 Subject: [PATCH 131/137] feat: Add folder-stable Breeze icon --- .../breeze-dark/places/16/folder-stable.svg | 40 ++++++ .../breeze-dark/places/22/folder-stable.svg | 41 ++++++ .../breeze-dark/places/32/folder-stable.svg | 122 ++++++++++++++++++ .../breeze-dark/places/48/folder-stable.svg | 122 ++++++++++++++++++ .../breeze-dark/places/64/folder-stable.svg | 122 ++++++++++++++++++ 5 files changed, 447 insertions(+) create mode 100644 dot_local/share/icons/breeze-dark/places/16/folder-stable.svg create mode 100644 dot_local/share/icons/breeze-dark/places/22/folder-stable.svg create mode 100644 dot_local/share/icons/breeze-dark/places/32/folder-stable.svg create mode 100644 dot_local/share/icons/breeze-dark/places/48/folder-stable.svg create mode 100644 dot_local/share/icons/breeze-dark/places/64/folder-stable.svg diff --git a/dot_local/share/icons/breeze-dark/places/16/folder-stable.svg b/dot_local/share/icons/breeze-dark/places/16/folder-stable.svg new file mode 100644 index 0000000..24084b6 --- /dev/null +++ b/dot_local/share/icons/breeze-dark/places/16/folder-stable.svg @@ -0,0 +1,40 @@ + + + + + + + + + + diff --git a/dot_local/share/icons/breeze-dark/places/22/folder-stable.svg b/dot_local/share/icons/breeze-dark/places/22/folder-stable.svg new file mode 100644 index 0000000..4b6599f --- /dev/null +++ b/dot_local/share/icons/breeze-dark/places/22/folder-stable.svg @@ -0,0 +1,41 @@ + + + + + + + + + + diff --git a/dot_local/share/icons/breeze-dark/places/32/folder-stable.svg b/dot_local/share/icons/breeze-dark/places/32/folder-stable.svg new file mode 100644 index 0000000..96f23aa --- /dev/null +++ b/dot_local/share/icons/breeze-dark/places/32/folder-stable.svg @@ -0,0 +1,122 @@ + + + + + + + + diff --git a/dot_local/share/icons/breeze-dark/places/48/folder-stable.svg b/dot_local/share/icons/breeze-dark/places/48/folder-stable.svg new file mode 100644 index 0000000..10ba115 --- /dev/null +++ b/dot_local/share/icons/breeze-dark/places/48/folder-stable.svg @@ -0,0 +1,122 @@ + + + + + + + + diff --git a/dot_local/share/icons/breeze-dark/places/64/folder-stable.svg b/dot_local/share/icons/breeze-dark/places/64/folder-stable.svg new file mode 100644 index 0000000..c6f1643 --- /dev/null +++ b/dot_local/share/icons/breeze-dark/places/64/folder-stable.svg @@ -0,0 +1,122 @@ + + + + + + + + From 6d1bd2012ef78162af0e43ee43ad745c80fe3c49 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 13 May 2023 17:05:20 -0500 Subject: [PATCH 132/137] Add Julia binaries to PATH --- dot_profile | 1 + dot_zshenv.tmpl | 7 ++++--- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/dot_profile b/dot_profile index 9079577..01f5e0d 100644 --- a/dot_profile +++ b/dot_profile @@ -3,6 +3,7 @@ export PATH="$HOME/.local/bin:$HOME/bin:$PATH" # juliaup setup +export PATH="$HOME/.julia/bin:$PATH" export PATH="$HOME/.julia/juliaup/bin:$PATH" export PATH="$HOME/.juliaup/bin:$PATH" diff --git a/dot_zshenv.tmpl b/dot_zshenv.tmpl index b03aab1..320c25b 100644 --- a/dot_zshenv.tmpl +++ b/dot_zshenv.tmpl @@ -6,9 +6,10 @@ fpath+=($HOME/.local/share/zsh/5.8/functions) {{- end }} # juliaup setup -if [ -d $HOME/.julia/juliaup/bin ]; then - export PATH="$HOME/.julia/juliaup/bin:$PATH" -fi +export PATH="$HOME/.julia/bin:$PATH" +export PATH="$HOME/.julia/juliaup/bin:$PATH" +export PATH="$HOME/.juliaup/bin:$PATH" +fpath+=($HOME/.julia/completions) # Linuxbrew setup if [ -d $HOME/../linuxbrew/.linuxbrew ]; then From 791f4ae7b7685d1bdbf5c3323d5585087701a4f8 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 6 Oct 2023 10:47:04 -0500 Subject: [PATCH 133/137] feat: Replace shell execution with shell variable --- dot_hooks.tmpl | 9 +++++---- executable_dot_bashrc.tmpl | 1 + executable_dot_zshrc.tmpl | 1 + 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/dot_hooks.tmpl b/dot_hooks.tmpl index a025c71..71a5e17 100644 --- a/dot_hooks.tmpl +++ b/dot_hooks.tmpl @@ -1,6 +1,7 @@ +# shellcheck shell=sh # >>> conda initialize >>> # !! Contents within this block are managed by 'conda init' !! -__conda_setup="$($HOME/miniconda3/bin/conda shell.$(basename $(readlink -f /proc/$$/exe)) 'hook' 2> /dev/null)" +__conda_setup="$($HOME/miniconda3/bin/conda shell.$SH 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else @@ -18,7 +19,7 @@ fi # <<< conda initialize <<< {{- if lookPath "direnv" }} -eval "$(direnv hook $(basename $(readlink -f /proc/$$/exe)))" +eval "$(direnv hook $SH)" {{- end }} if [ -f $HOME/.ion/bin/ion ]; then @@ -27,8 +28,8 @@ if [ -f $HOME/.ion/bin/ion ]; then fi # Import GNU parallel -if [ $(command -v env_parallel.$(basename $(readlink -f /proc/$$/exe))) ]; then - source $(which env_parallel.$(basename $(readlink -f /proc/$$/exe))) +if [ $(command -v env_parallel.$SH) ]; then + source $(which env_parallel.$SH) fi {{- if eq .machinetype "workstation" }} diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index 34b39c0..ceb87b1 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -1,5 +1,6 @@ # shellcheck shell=bash # .bashrc +export SH=bash if [ -f "$HOME/.modules" ]; then source $HOME/.modules diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index 4529d6f..3f80f0e 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -1,3 +1,4 @@ +export SH=zsh {{- if eq .chezmoi.os "linux" }} {{- if or (eq .machinetype "workstation") From ad7c7b7a4ec871f5f71bbd3e41768a98aaefda9b Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 6 Oct 2023 10:57:26 -0500 Subject: [PATCH 134/137] feat: Add nproc alias for osx --- dot_aliases.tmpl | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/dot_aliases.tmpl b/dot_aliases.tmpl index 45b6949..ec25204 100644 --- a/dot_aliases.tmpl +++ b/dot_aliases.tmpl @@ -12,6 +12,11 @@ alias ls=lsd alias code=codium {{- end }} +# Platform-specific aliases +{{- if eq .chezmoi.os "darwin" }} +alias nproc='sysctl -n hw.logicalcpu' +{{- end }} + # Universal aliases alias config='git --git-dir=$HOME/.cfg/ --work-tree=$HOME' alias please='sudo $(fc -ln -1)' From ceefb8697eed5eb02fecae59603daa4b7b1ecb76 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 6 Oct 2023 10:57:59 -0500 Subject: [PATCH 135/137] refactor: Rearrange aliases to be in place before hooks --- executable_dot_bashrc.tmpl | 6 +++--- executable_dot_zshrc.tmpl | 5 +++-- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/executable_dot_bashrc.tmpl b/executable_dot_bashrc.tmpl index ceb87b1..619df33 100644 --- a/executable_dot_bashrc.tmpl +++ b/executable_dot_bashrc.tmpl @@ -6,12 +6,12 @@ if [ -f "$HOME/.modules" ]; then source $HOME/.modules fi -# Hook virtual environment modifers -source $HOME/.hooks - # User specific aliases and functions source $HOME/.aliases +# Hook virtual environment modifers +source $HOME/.hooks + source $HOME/.envvar # Make the prompt pretty, just in case we're stuck in bash land diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index 3f80f0e..65f82b2 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -52,6 +52,9 @@ antigen theme https://gist.github.com/efde5e8d507bd3e1e046198b69d579f8.git gianu HYPHEN_INSENSITIVE="true" COMPLETION_WAITING_DOTS="true" +alias zshconfig="$EDITOR ~/.zshrc" +source $HOME/.aliases + source $HOME/.hooks # Tell Antigen that you're done @@ -65,8 +68,6 @@ bashcompinit source $HOME/.envvar -alias zshconfig="$EDITOR ~/.zshrc" -source $HOME/.aliases {{- if eq .chezmoi.os "linux" }} {{ if or From dc626c4ed9d07d731be86a640ca99a28fe0d0629 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:01:42 -0500 Subject: [PATCH 136/137] fix: Add p10k config for Darwin --- executable_dot_zshrc.tmpl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/executable_dot_zshrc.tmpl b/executable_dot_zshrc.tmpl index 65f82b2..210e161 100644 --- a/executable_dot_zshrc.tmpl +++ b/executable_dot_zshrc.tmpl @@ -1,5 +1,5 @@ export SH=zsh -{{- if eq .chezmoi.os "linux" }} +{{ if or (eq .chezmoi.os "linux") (eq .chezmoi.os "darwin") }} {{- if or (eq .machinetype "workstation") (eq .chezmoi.osRelease.id "fedora") @@ -69,7 +69,7 @@ bashcompinit source $HOME/.envvar -{{- if eq .chezmoi.os "linux" }} +{{ if or (eq .chezmoi.os "linux") (eq .chezmoi.os "darwin") }} {{ if or (eq .machinetype "workstation") (eq .chezmoi.osRelease.id "fedora") From 632f8edf4ddad9b049dd6d31427e6fae1243c273 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:07:36 -0500 Subject: [PATCH 137/137] feat: Replace linuxbrew hook with Homebrew hook --- dot_profile => dot_profile.tmpl | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) rename dot_profile => dot_profile.tmpl (52%) diff --git a/dot_profile b/dot_profile.tmpl similarity index 52% rename from dot_profile rename to dot_profile.tmpl index 01f5e0d..035d52a 100644 --- a/dot_profile +++ b/dot_profile.tmpl @@ -7,18 +7,10 @@ export PATH="$HOME/.julia/bin:$PATH" export PATH="$HOME/.julia/juliaup/bin:$PATH" export PATH="$HOME/.juliaup/bin:$PATH" -# Linuxbrew setup -if [ -d $HOME/../linuxbrew/.linuxbrew ]; then - BREWPATH=$HOME/../linuxbrew/.linuxbrew -elif [ -d $HOME/.linuxbrew ]; then - BREWPATH=$HOME/.linuxbrew -fi - -if [ -n "$BREWPATH" ]; then - eval "$($BREWPATH/bin/brew shellenv)" - export HOMEBREW_MAKE_JOBS=1 - export HOMEBREW_NO_ANALYTICS=1 -fi +{{ if eq .chezmoi.os "darwin" }} +# Homebrew setup +eval "$(/opt/homebrew/bin/brew shellenv)" +{{ end }} if [ -e "$HOME/.nix-profile/etc/profile.d/nix.sh" ]; then . "$HOME/.nix-profile/etc/profile.d/nix.sh"