Update CI and documentation for the general registry

- Update documentation workflow.
- Update CompatHelper workflow.
- Update TagBot workflow.
- Update unit test workflow.
- Update codecov.

.github/workflows/CompatHelper.yml

@@ -2,37 +2,16 @@ name: CompatHelper
 
 on:
   schedule:
-    - cron: '00 * * * *'
+    - cron: '0 0 * * *'
 
 jobs:
   CompatHelper:
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        julia-version: [1.3.0]
-        julia-arch: [x86]
-        os: [ubuntu-latest]
     steps:
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: ${{ matrix.julia-version }}
       - name: Add CompatHelper
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+        run: julia --color=yes -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main
+      - name: Run CompatHelper
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: julia -e '
+          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
-                using CompatHelper, Pkg;
+        run: julia --color=yes -e 'using CompatHelper; CompatHelper.main(master_branch = "master")'
-                my_registries = [
-                    Pkg.RegistrySpec(
-                        name = "BioJuliaRegistry",
-                        uuid = "ccbd2cc2-2954-11e9-1ccf-f3e7900901ca",
-                        url = "https://github.com/BioJulia/BioJuliaRegistry.git"
-                    ),
-                    Pkg.RegistrySpec(
-                        name = "General",
-                        uuid = "23338594-aafe-5451-b93e-139f81909106",
-                        url = "https://github.com/JuliaRegistries/General.git"
-                    )
-                ];
-                CompatHelper.main(; registries = my_registries, master_branch = "master");'

.github/workflows/Documentation.yml

@@ -1,34 +1,26 @@
-name: Documentation
+name: Build Documentation
 
 on:
-    push:
+  push:
-        branches:
+    branches:
-            - 'master'
+      - master
-            - 'develop'
+      - develop
-            - 'release/.*'
+      - release/*
-        tags: '*'
+    tags: '*'
-    pull_request:
+  pull_request:
 
 jobs:
   build:
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        julia-version: [1.3.0]
-        julia-arch: [x86]
-        os: [ubuntu-latest]
     steps:
-      - uses: actions/checkout@v1.0.0
+      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v1
         with:
-          version: ${{ matrix.julia-version }}
+          version: '1'
-      - name: Install dependencies
+      - name: Install Dependencies
-        run: |
+        run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-          julia ci_prep.jl;
+      - name: Build and Deploy
-          julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
         env:
-          # https://github.com/JuliaDocs/Documenter.jl/issues/1177
           # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-        run: julia --project=docs/ --color=yes docs/make.jl
+        run: julia --color=yes --project=docs/ docs/make.jl

.github/workflows/TagBot.yml

@@ -1,7 +1,7 @@
 name: TagBot
 on:
   schedule:
-    - cron: '0 * * * *'
+    - cron: '0 0 * * *'
 jobs:
   TagBot:
     runs-on: ubuntu-latest
@@ -10,4 +10,3 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           ssh: ${{ secrets.TAGBOT_KEY }}
-          registry: BioJulia/BioJuliaRegistry

.github/workflows/UnitTests.yml

@@ -1,22 +1,44 @@
-name: Unit tests
+name: Unit Tests
 
-on: [push, pull_request]
+on:
+  - push
+  - pull_request
 
 jobs:
   test:
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
     strategy:
+      fail-fast: false
       matrix:
-        julia-version: ['1.1', '1.2', '1.3']
+        julia-version:
-        julia-arch: [x64]
+          - '1.0' # LTS
+          - '1'
+        julia-arch: [x64, x86]
         os: [ubuntu-latest, windows-latest, macOS-latest]
+        experimental: [false]
+        include:
+          - julia-version: nightly
+            julia-arch: x64
+            os: ubuntu-latest
+            experimental: true
 
     steps:
-      - uses: actions/checkout@v1.0.0
+      - name: Checkout Repository
-      - uses: julia-actions/setup-julia@v1
+        uses: actions/checkout@v2
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia-version }}
-          arch: ${{ matrix.julia-arch }}
+      - name: Run Tests
-      - name: Install dependencies
+        uses: julia-actions/julia-runtest@latest
-        run: julia ci_prep.jl
+      - name: Create CodeCov
-      - uses: julia-actions/julia-runtest@master
+        uses: julia-actions/julia-processcoverage@v1
+      - name: Upload CodeCov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./lcov.info
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: false
+          token: ${{ secrets.CODECOV_TOKEN }}

Project.toml

@@ -23,7 +23,7 @@ BioSequences = "2"
 GenomicFeatures = "2"
 Indexes = "0.1"
 TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
-julia = "1.1"
+julia = "1"
 
 [extras]
 FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"

README.md

@@ -11,18 +11,11 @@
 blog post").
 
 ## Description
-XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
+The XAM package provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
 
 ## Installation
-The latest version of XAM is made available to install through BioJulia's package registry.
+You can install the XAM package from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
-By default, Julia's package manager only includes the "General" package registry.
+Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
-
-To add the BioJulia registry from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/), press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
-```julia
-registry add https://github.com/BioJulia/BioJuliaRegistry.git
-```
-
-Once the registry is added to your configuration, you can install XAM while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
 ```julia
 add XAM
 ```

ci_prep.jl

@@ -1,3 +0,0 @@
-using Pkg.Registry
-Registry.add(Registry.RegistrySpec(url = "https://github.com/BioJulia/BioJuliaRegistry.git"))
-Registry.add(Registry.RegistrySpec(url = "https://github.com/JuliaRegistries/General.git"))

coverage/Project.toml

@@ -1,2 +0,0 @@
-[deps]
-Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"

coverage/coverage.jl

@@ -1,11 +0,0 @@
-get(ENV, "TRAVIS_OS_NAME", "") == "linux" || exit()
-get(ENV, "TRAVIS_JULIA_VERSION", "") == "1.3" || exit()
-
-using Pkg
-Pkg.instantiate()
-
-using Coverage
-
-cd(joinpath(@__DIR__, "..")) do
-   Codecov.submit(Codecov.process_folder())
-end

docs/src/index.md

@@ -10,20 +10,11 @@
 > This project follows the [semver](http://semver.org) pro forma and uses the [git-flow branching model](https://nvie.com/posts/a-successful-git-branching-model/).
 
 ## Description
-
+The XAM package provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
-XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
-
 
 ## Installation
-The latest version of XAM is made available to install through BioJulia's package registry.
+You can install the XAM package from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
-By default, Julia's package manager only includes the "General" package registry.
+Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
-
-To add the BioJulia registry from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/), press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
-```julia
-registry add https://github.com/BioJulia/BioJuliaRegistry.git
-```
-
-Once the registry is added to your configuration, you can install XAM while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
 ```julia
 add XAM
 ```