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Update CI and documentation for the general registry

- Update documentation workflow.
- Update CompatHelper workflow.
- Update TagBot workflow.
- Update unit test workflow.
- Update codecov.
This commit is contained in:
Ciarán O'Mara 2020-05-25 14:08:07 +10:00 committed by Ciarán O'Mara
parent 81dbf41798
commit eaf5c73eb5
10 changed files with 62 additions and 102 deletions

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@ -2,37 +2,16 @@ name: CompatHelper
on:
schedule:
- cron: '00 * * * *'
- cron: '0 0 * * *'
jobs:
CompatHelper:
runs-on: ${{ matrix.os }}
strategy:
matrix:
julia-version: [1.3.0]
julia-arch: [x86]
os: [ubuntu-latest]
runs-on: 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")'
- name: CompatHelper.main
run: julia --color=yes -e 'using Pkg; Pkg.add("CompatHelper")'
- name: Run CompatHelper
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: julia -e '
using CompatHelper, Pkg;
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");'
COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
run: julia --color=yes -e 'using CompatHelper; CompatHelper.main(master_branch = "master")'

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@ -1,34 +1,26 @@
name: Documentation
name: Build Documentation
on:
push:
branches:
- 'master'
- 'develop'
- 'release/.*'
tags: '*'
pull_request:
push:
branches:
- master
- develop
- release/*
tags: '*'
pull_request:
jobs:
build:
runs-on: ${{ matrix.os }}
strategy:
matrix:
julia-version: [1.3.0]
julia-arch: [x86]
os: [ubuntu-latest]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1.0.0
- uses: julia-actions/setup-julia@latest
- uses: actions/checkout@v2
- uses: julia-actions/setup-julia@v1
with:
version: ${{ matrix.julia-version }}
- name: Install dependencies
run: |
julia ci_prep.jl;
julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
- name: Build and deploy
version: '1'
- name: Install Dependencies
run: julia --color=yes --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

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@ -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

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@ -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-arch: [x64]
julia-version:
- '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
- uses: julia-actions/setup-julia@v1
- name: Checkout Repository
uses: actions/checkout@v2
- name: Setup Julia
uses: julia-actions/setup-julia@v1
with:
version: ${{ matrix.julia-version }}
arch: ${{ matrix.julia-arch }}
- name: Install dependencies
run: julia ci_prep.jl
- uses: julia-actions/julia-runtest@master
- name: Run Tests
uses: julia-actions/julia-runtest@latest
- name: Create CodeCov
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 }}

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@ -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"

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@ -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.
By default, Julia's package manager only includes the "General" package registry.
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:
You can install the XAM package 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
add XAM
```

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@ -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"))

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

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@ -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

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@ -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
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.
By default, Julia's package manager only includes the "General" package registry.
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:
You can install the XAM package 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
add XAM
```