Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

update sleepwaste #21

Open
wants to merge 5 commits into
base: main
Choose a base branch
from
Open

update sleepwaste #21

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
e5d9c82
update sleepwaste
bernt-matthias Mar 15, 2024
ff9260b
update CI
bernt-matthias Mar 15, 2024
9629d86
add shed.yaml
bernt-matthias Mar 15, 2024
05a949a
tool update
bernt-matthias Mar 15, 2024
3428ce5
comment bash tests
bernt-matthias Mar 15, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
38 changes: 19 additions & 19 deletions .github/workflows/ci.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ on:
types: [run-all-tool-tests-command]
env:
GALAXY_FORK: galaxyproject
GALAXY_BRANCH: release_23.2
GALAXY_BRANCH: release_24.0
MAX_CHUNKS: 40
jobs:
setup:
Expand All @@ -27,7 +27,7 @@ jobs:
steps:
- name: Add reaction
if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
uses: peter-evans/create-or-update-comment@v2
uses: peter-evans/create-or-update-comment@v4
with:
token: ${{ secrets.PAT }}
repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
Expand All @@ -43,11 +43,11 @@ jobs:
- name: Determine latest commit in the Galaxy repo
id: get-galaxy-sha
run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
Expand All @@ -56,7 +56,7 @@ jobs:
# are not available as wheels, pip will build a wheel for them, which can be cached.
- name: Install wheel
run: pip install wheel
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 1
- name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
Expand Down Expand Up @@ -84,14 +84,14 @@ jobs:
matrix:
python-version: ['3.11']
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 1
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
Expand All @@ -104,7 +104,7 @@ jobs:
repository-list: ${{ needs.setup.outputs.repository-list }}
tool-list: ${{ needs.setup.outputs.tool-list }}
additional-planemo-options: --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
if: ${{ failure() }}
with:
name: 'Tool linting output'
Expand Down Expand Up @@ -133,20 +133,20 @@ jobs:
steps:
# checkout the repository
# and use it as the current working directory
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 1
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
- name: Get number of CPU cores
uses: SimenB/github-actions-cpu-cores@v1
uses: SimenB/github-actions-cpu-cores@v2
id: cpu-cores
- name: Clean dotnet folder for space
run: rm -Rf /usr/share/dotnet
Expand All @@ -163,7 +163,7 @@ jobs:
galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
# Limit each test to 15 minutes
test_timeout: 900
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
with:
name: 'Tool test output ${{ matrix.chunk }}'
path: upload
Expand All @@ -182,14 +182,14 @@ jobs:
# This job runs on Linux
runs-on: ubuntu-latest
steps:
- uses: actions/download-artifact@v3
- uses: actions/download-artifact@v4
with:
path: artifacts
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
Expand All @@ -200,7 +200,7 @@ jobs:
with:
mode: combine
html-report: true
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
with:
name: 'All tool test results'
path: upload
Expand All @@ -211,7 +211,7 @@ jobs:

- name: Create comment
if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
uses: peter-evans/create-or-update-comment@v2
uses: peter-evans/create-or-update-comment@v4
with:
token: ${{ secrets.PAT }}
repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
Expand Down
68 changes: 33 additions & 35 deletions .github/workflows/pr.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ name: Galaxy Tool Linting and Tests for push and PR
on:
pull_request:
paths-ignore:
- '.github/**'
- 'deprecated/**'
- 'docs/**'
- '*'
Expand All @@ -11,13 +10,12 @@ on:
- main
- master
paths-ignore:
- '.github/**'
- 'deprecated/**'
- 'docs/**'
- '*'
env:
GALAXY_FORK: galaxyproject
GALAXY_BRANCH: release_23.2
GALAXY_BRANCH: release_24.0
MAX_CHUNKS: 4
MAX_FILE_SIZE: 1M
concurrency:
Expand Down Expand Up @@ -59,17 +57,17 @@ jobs:
- name: Determine latest commit in the Galaxy repo
id: get-galaxy-sha
run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
- name: Cache .planemo
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-planemo
with:
path: ~/.planemo
Expand All @@ -80,7 +78,7 @@ jobs:
run: pip install wheel
- name: Install flake8
run: pip install flake8 flake8-import-order
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
Expand Down Expand Up @@ -113,14 +111,14 @@ jobs:
matrix:
python-version: ['3.11']
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 1
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
Expand All @@ -142,7 +140,7 @@ jobs:
fail-level: ${{ env.FAIL_LEVEL }}
repository-list: ${{ needs.setup.outputs.repository-list }}
tool-list: ${{ needs.setup.outputs.tool-list }}
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
if: ${{ failure() }}
with:
name: 'Tool linting output'
Expand All @@ -159,14 +157,14 @@ jobs:
matrix:
python-version: ['3.11']
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 1
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
Expand All @@ -175,7 +173,7 @@ jobs:
run: pip install flake8 flake8-import-order
- name: Flake8
run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
if: ${{ failure() }}
with:
name: 'Python linting output'
Expand All @@ -184,21 +182,21 @@ jobs:
lintr:
name: Lint R scripts
needs: setup
if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
if: ${{ needs.setup.outputs.repository-list != '' }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-20.04]
r-version: ['release']
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 1
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.r-version }}
- name: Cache R packages
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ${{ env.R_LIBS_USER }}
key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
Expand All @@ -214,7 +212,7 @@ jobs:
echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off
git status
git diff --exit-code | tee rlint_report.txt
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
if: ${{ failure() }}
with:
name: 'R linting output'
Expand All @@ -226,7 +224,7 @@ jobs:
if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Check file sizes
Expand All @@ -241,7 +239,7 @@ jobs:
cat file_size_report.txt
exit 1
fi
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
if: ${{ failure() }}
with:
name: 'File size report'
Expand Down Expand Up @@ -269,26 +267,26 @@ jobs:
ports:
- 5432:5432
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 1
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
- name: Cache .planemo
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-planemo
with:
path: ~/.planemo
key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
- name: Get number of CPU cores
uses: SimenB/github-actions-cpu-cores@v1
uses: SimenB/github-actions-cpu-cores@v2
id: cpu-cores
- name: Clean dotnet folder for space
run: rm -Rf /usr/share/dotnet
Expand Down Expand Up @@ -319,7 +317,7 @@ jobs:
galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
# Limit each test to 15 minutes
test_timeout: 1800
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
with:
name: 'Tool test output ${{ matrix.chunk }}'
path: upload
Expand All @@ -338,14 +336,14 @@ jobs:
matrix:
python-version: ['3.11']
steps:
- uses: actions/download-artifact@v3
- uses: actions/download-artifact@v4
with:
path: artifacts
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
Expand All @@ -357,7 +355,7 @@ jobs:
mode: combine
html-report: true
markdown-report: true
- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
with:
name: 'All tool test results'
path: upload
Expand All @@ -384,14 +382,14 @@ jobs:
matrix:
python-version: ['3.11']
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 1
- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
uses: actions/cache@v4
id: cache-pip
with:
path: ~/.cache/pip
Expand Down Expand Up @@ -425,7 +423,7 @@ jobs:
with:
sha: ${{ github.event.after }}
- name: Create comment
uses: peter-evans/create-or-update-comment@v2
uses: peter-evans/create-or-update-comment@v4
with:
token: ${{ secrets.PAT }}
issue-number: ${{ steps.getpr.outputs.number }}
Expand Down
Loading
Loading