Skip to content

Commit

Permalink
Merge pull request #89 from Plant-Food-Research-Open/dev
Browse files Browse the repository at this point in the history
Candidate for 2.0.0
  • Loading branch information
GallVp authored Jun 5, 2024
2 parents 9dfb828 + 5474d3a commit 690e56b
Show file tree
Hide file tree
Showing 342 changed files with 16,633 additions and 2,846 deletions.
10 changes: 1 addition & 9 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
Expand Up @@ -10,15 +10,7 @@
"vscode": {
// Set *default* container specific settings.json values on container create.
"settings": {
"python.defaultInterpreterPath": "/opt/conda/bin/python",
"python.linting.enabled": true,
"python.linting.pylintEnabled": true,
"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
"python.formatting.yapfPath": "/opt/conda/bin/yapf",
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
"python.linting.pylintPath": "/opt/conda/bin/pylint"
"python.defaultInterpreterPath": "/opt/conda/bin/python"
},

// Add the IDs of extensions you want installed when the container is created.
Expand Down
29 changes: 22 additions & 7 deletions .editorconfig
Original file line number Diff line number Diff line change
Expand Up @@ -18,17 +18,32 @@ end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
indent_size = unset
[/subworkflows/nf-core/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset

# These files are edited and tested upstream in pfr/modules
[/modules/pfr/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
[/subworkflows/pfr/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset

[/assets/email*]
indent_size = unset

# ignore Readme
[README.md]
indent_style = unset

# ignore python
[*.{py}]
# ignore python and markdown
[*.{py,md}]
indent_style = unset

# ignore perl
Expand Down
9 changes: 6 additions & 3 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,11 @@ If you're not used to this workflow with git, you can start with some [docs from

## Tests

You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:

```bash
nf-test test --profile debug,test,docker --verbose
```

When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
Expand Down Expand Up @@ -81,7 +84,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.

Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.

The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.

### Naming schemes

Expand Down
2 changes: 1 addition & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/plant-food-r
- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/plant-food-research-open/assemblyqc/tree/master/.github/CONTRIBUTING.md)
- [ ] Make sure your code lints (`nf-core lint`) and (`pre-commit run --all`)
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/branch.yml
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ jobs:
# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
- name: Post PR comment
if: failure()
uses: mshick/add-pr-comment@v2
uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
with:
message: |
## This PR is against the `master` branch :x:
Expand Down
27 changes: 20 additions & 7 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -25,19 +25,32 @@ jobs:
matrix:
NXF_VER:
- "23.04.0"
RUN_CONFIG:
- "-profile test,docker"
- "-profile docker -c ./tests/stub/stub.config -stub"
- "-profile docker -params-file ./tests/invalid/params.json"
TEST_PARAMS:
- minimal
- invalid
- stub
include:
- OPTION_STUB: ""
- OPTION_STUB: "-stub"
TEST_PARAMS: stub
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2
with:
version: ${{ matrix.NXF_VER }}

- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} --outdir ./results ${{ matrix.RUN_CONFIG }}
nextflow run \
${GITHUB_WORKSPACE} \
--outdir ./results \
-profile docker \
-params-file \
./tests/${{ matrix.TEST_PARAMS }}/params.json \
${{ matrix.OPTION_STUB }}
2 changes: 1 addition & 1 deletion .github/workflows/clean-up.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ jobs:
issues: write
pull-requests: write
steps:
- uses: actions/stale@v9
- uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
with:
stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
Expand Down
35 changes: 27 additions & 8 deletions .github/workflows/download_pipeline.yml
Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,16 @@ name: Test successful pipeline download with 'nf-core download'
# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
on:
workflow_dispatch:
inputs:
testbranch:
description: "The specific branch you wish to utilize for the test execution of nf-core download."
required: true
default: "dev"
pull_request:
types:
- opened
- edited
- synchronize
branches:
- master
pull_request_target:
Expand All @@ -20,16 +27,19 @@ env:

jobs:
download:
runs-on: ["self-hosted"]
runs-on: ubuntu-latest
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2

- uses: actions/setup-python@v5
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: "3.11"
python-version: "3.12"
architecture: "x64"
- uses: eWaterCycle/setup-singularity@v7
- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
with:
singularity-version: 3.8.3

Expand All @@ -42,13 +52,13 @@ jobs:
run: |
echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
- name: Download the pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./
run: |
nf-core download ${{ env.REPO_LOWERCASE }} \
nf-core download ${{ env.REPO_LOWERCASE }} \
--revision ${{ env.REPO_BRANCH }} \
--outdir ./${{ env.REPOTITLE_LOWERCASE }} \
--compress "none" \
Expand All @@ -60,8 +70,17 @@ jobs:
- name: Inspect download
run: tree ./${{ env.REPOTITLE_LOWERCASE }}

- name: Run the downloaded pipeline
- name: Run the downloaded pipeline (stub)
id: stub_run_pipeline
continue-on-error: true
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
- name: Run the downloaded pipeline (stub run not supported)
id: run_pipeline
if: ${{ job.steps.stub_run_pipeline.status == failure() }}
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
59 changes: 50 additions & 9 deletions .github/workflows/fix-linting.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ on:
types: [created]

jobs:
deploy:
fix-linting:
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
if: >
contains(github.event.comment.html_url, '/pull/') &&
Expand All @@ -13,36 +13,77 @@ jobs:
runs-on: ubuntu-latest
steps:
# Use the @nf-core-bot token to check out so we can push later
- uses: actions/checkout@v4
- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
with:
token: ${{ secrets.nf_core_bot_auth_token }}

# indication that the linting is being fixed
- name: React on comment
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
with:
comment-id: ${{ github.event.comment.id }}
reactions: eyes

# Action runs on the issue comment, so we don't get the PR by default
# Use the gh cli to check out the PR
- name: Checkout Pull Request
run: gh pr checkout ${{ github.event.issue.number }}
env:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

- name: Set up Python 3.11
uses: actions/setup-python@v5
# Install and run pre-commit
- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: 3.11
cache: "pip"
python-version: "3.12"

- name: Install pre-commit
run: pip install pre-commit

- name: Run pre-commit
run: pre-commit run --all-files || echo "status=fail" >> $GITHUB_ENV
id: pre-commit
run: pre-commit run --all-files
continue-on-error: true

# indication that the linting has finished
- name: react if linting finished succesfully
if: steps.pre-commit.outcome == 'success'
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
with:
comment-id: ${{ github.event.comment.id }}
reactions: "+1"

- name: Commit & push changes
if: env.status == 'fail'
id: commit-and-push
if: steps.pre-commit.outcome == 'failure'
run: |
git config user.email "[email protected]"
git config user.name "nf-core-bot"
git config push.default upstream
git add .
git status
git commit -m "[automated] Fix linting with pre-commit"
git commit -m "[automated] Fix code linting"
git push
- name: react if linting errors were fixed
id: react-if-fixed
if: steps.commit-and-push.outcome == 'success'
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
with:
comment-id: ${{ github.event.comment.id }}
reactions: hooray

- name: react if linting errors were not fixed
if: steps.commit-and-push.outcome == 'failure'
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
with:
comment-id: ${{ github.event.comment.id }}
reactions: confused

- name: react if linting errors were not fixed
if: steps.commit-and-push.outcome == 'failure'
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
with:
issue-number: ${{ github.event.issue.number }}
body: |
@${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
See [CI log](https://github.com/plant-food-research-open/assemblyqc/actions/runs/${{ github.run_id }}) for more details.
Loading

0 comments on commit 690e56b

Please sign in to comment.