Test PR for nf-core modules lint (#414)

* Update functions.nf for publish_by_id

* Pass a list of publish_by_id instead of a string

* Remove NF version

* Rename code linting file

* Run separate workflow for nf-core modules lint

* Adjust nf-core update comment

* Comment out linting from pytest-workflow.yml

* Remove commented out linting code from pytest-workflow.yml

* Adjust spacing

* Adjust spacing again

* Move NF version to job level for linting

* Add CAPSULE_LOG none env when installing NF

* Remove NXF_ANSI_LOG env for linting

* Revert changes
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Harshil Patel 2021-04-09 07:58:43 +01:00 committed by GitHub
parent 63b3975292
commit f34892c1af
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3 changed files with 84 additions and 9 deletions

75
.github/workflows/nf-core-linting.yml vendored Normal file
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@ -0,0 +1,75 @@
name: nf-core linting
# This workflow is triggered on pushes and PRs to the repository.
# It runs the `nf-core lint` tests to ensure that the module code meets the nf-core guidelines
on: [push, pull_request]
jobs:
changes:
name: Check for changes
runs-on: ubuntu-latest
outputs:
# Expose matched filters as job 'modules' output variable
modules: ${{ steps.filter.outputs.changes }}
steps:
- uses: actions/checkout@v2
- uses: dorny/paths-filter@v2
id: filter
with:
filters: 'tests/config/pytest_software.yml'
lint:
runs-on: ubuntu-20.04
env:
NXF_VER: 21.03.0-edge
name: ${{ matrix.tags }}
needs: changes
if: needs.changes.outputs.modules != '[]'
strategy:
fail-fast: false
matrix:
tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
steps:
- uses: actions/checkout@v2
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- uses: actions/cache@v2
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install pip
run: python -m pip install --upgrade pip
# FIXME: Remove this when nf-core modules lint stabilizes and install stable release
- name: Install nf-core tools development version
run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
- name: Install Nextflow
env:
CAPSULE_LOG: none
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Lint ${{ matrix.tags }}
run: nf-core modules lint . -t ${{ matrix.tags }}
- uses: actions/cache@v2
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}
restore-keys: |
${{ runner.os }}

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@ -10,6 +10,7 @@ jobs:
modules: ${{ steps.filter.outputs.changes }} modules: ${{ steps.filter.outputs.changes }}
steps: steps:
- uses: actions/checkout@v2 - uses: actions/checkout@v2
- uses: dorny/paths-filter@v2 - uses: dorny/paths-filter@v2
id: filter id: filter
with: with:
@ -17,23 +18,26 @@ jobs:
test: test:
runs-on: ubuntu-20.04 runs-on: ubuntu-20.04
name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }} name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
needs: changes needs: changes
if: needs.changes.outputs.modules != '[]' if: needs.changes.outputs.modules != '[]'
strategy: strategy:
fail-fast: false fail-fast: false
matrix: matrix:
nxf_version: ['20.11.0-edge', '21.03.0-edge'] nxf_version: ['21.03.0-edge']
tags: ['${{ fromJson(needs.changes.outputs.modules) }}'] tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
profile: ['docker', 'singularity', 'conda'] profile: ['docker', 'singularity', 'conda']
env: env:
NXF_ANSI_LOG: false NXF_ANSI_LOG: false
steps: steps:
- uses: actions/checkout@v2 - uses: actions/checkout@v2
- name: Set up Python - name: Set up Python
uses: actions/setup-python@v2 uses: actions/setup-python@v2
with: with:
python-version: "3.x" python-version: "3.x"
- uses: actions/cache@v2 - uses: actions/cache@v2
with: with:
path: ~/.cache/pip path: ~/.cache/pip
@ -45,14 +49,9 @@ jobs:
uses: actions/setup-python@v2 uses: actions/setup-python@v2
with: with:
python-version: "3.x" python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# FIXME: Remove this when nf-core modules lint stabilizes
- name: Install nf-core tools development version
run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
- name: Lint ${{ matrix.tags }} - name: Install Python dependencies
run: nf-core modules lint . -t ${{ matrix.tags }} run: python -m pip install --upgrade pip pytest-workflow
- uses: actions/cache@v2 - uses: actions/cache@v2
with: with:
@ -64,11 +63,11 @@ jobs:
- name: Install Nextflow - name: Install Nextflow
env: env:
NXF_VER: ${{ matrix.nxf_version }} NXF_VER: ${{ matrix.nxf_version }}
CAPSULE_LOG: none
run: | run: |
wget -qO- get.nextflow.io | bash wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
- name: Set up Singularity - name: Set up Singularity
if: matrix.profile == 'singularity' if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-singularity@v5 uses: eWaterCycle/setup-singularity@v5
@ -82,6 +81,7 @@ jobs:
auto-update-conda: true auto-update-conda: true
channels: conda-forge,bioconda,defaults channels: conda-forge,bioconda,defaults
python-version: ${{ matrix.python-version }} python-version: ${{ matrix.python-version }}
- name: Conda clean - name: Conda clean
if: matrix.profile == 'conda' if: matrix.profile == 'conda'
run: conda clean -a run: conda clean -a