Merge pull request #5 from mirpedrol/use-nfcore-dev

Use nfcore dev

.github/.coveragerc

@@ -0,0 +1,4 @@
+[run]
+omit = nf_class/*-template/*
+source = nf_class
+relative_files = True

.github/workflows/lint-code.yml

@@ -0,0 +1,33 @@
+name: Lint code formatting
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  Pre-commit:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files

.github/workflows/pytest.yml

@@ -0,0 +1,174 @@
+name: Python tests
+# This workflow is triggered on pushes and PRs to the repository.
+# Only run if we changed a Python file
+on:
+  push:
+    branches:
+      - dev
+    paths-ignore:
+      - "CHANGELOG.md"
+  pull_request:
+    paths-ignore:
+      - "CHANGELOG.md"
+      # ignore github workflows except for the current one
+      - ".github/**"
+      - "!.github/workflows/pytest.yml"
+  release:
+    types: [published]
+  workflow_dispatch:
+
+# Cancel if a newer run with the same workflow name is queued
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  setup:
+    runs-on: "ubuntu-latest"
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.12"]
+        runner: ["ubuntu-latest"]
+        include:
+          - python-version: "3.8"
+            runner: "ubuntu-20.04"
+
+    steps:
+      - name: Check conditions
+        id: conditions
+        run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> "$GITHUB_OUTPUT"
+
+    outputs:
+      python-version: ${{ matrix.python-version }}
+      runner: ${{ matrix.runner }}
+      run-tests: ${{ steps.conditions.outputs.run-tests }}
+
+  # create a test matrix based on all python files in /tests
+  list_tests:
+    name: Get test file matrix
+    runs-on: "ubuntu-latest"
+    steps:
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        name: Check out source-code repository
+
+      - name: List tests
+        id: list_tests
+        run: |
+          echo "tests=$(find tests -type f -name "test_*.py" | tac | sed 's/tests\///g'  | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
+    outputs:
+      tests: ${{ steps.list_tests.outputs.tests }}
+
+  test:
+    name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
+    needs: [setup, list_tests]
+    if: ${{ needs.setup.outputs.run-tests }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
+      fail-fast: false # run all tests even if one fails
+    steps:
+      - name: go to subdirectory and change nextflow workdir
+        run: |
+          mkdir -p pytest
+          cd pytest
+          export NXF_WORK=$(pwd)
+
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        name: Check out source-code repository
+
+      - name: Set up Python ${{ needs.setup.outputs.python-version }}
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: ${{ needs.setup.outputs.python-version }}
+          cache: "pip"
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
+
+      - name: Install dev version of nf-core
+        # reinstall the dev version of nf-core until v3.0.0 is released
+        run: |
+          pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Downgrade git to the Ubuntu official repository's version
+        if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }}
+        run: |
+          sudo apt update
+          sudo apt remove -y git git-man
+          sudo add-apt-repository --remove ppa:git-core/ppa
+          sudo apt install -y git
+
+      - name: Set up Singularity
+        if: ${{ matrix.test == 'test_download.py'}}
+        uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Get current date
+        id: date
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+
+      - name: move coveragerc file up
+        run: |
+          mv .github/.coveragerc .
+
+      - name: Test with pytest
+        run: |
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$?
+
+      - name: remove slashes from test name
+        run: |
+          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
+          echo "test=${test}" >> $GITHUB_ENV
+
+      - name: Upload coverage
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        with:
+          name: coverage_${{ env.test }}
+          path: .coverage
+
+  coverage:
+    needs: test
+    # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
+    runs-on: ubuntu-latest
+    steps:
+      - name: go to subdirectory
+        run: |
+          mkdir -p pytest
+          cd pytest
+
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
+
+      - name: move coveragerc file up
+        run: |
+          mv .github/.coveragerc .
+
+      - name: Download all artifacts
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4
+      - name: Run coverage
+        run: |
+          coverage combine --keep coverage*/.coverage*
+          coverage report
+          coverage xml

CHANGELOG.md

@@ -3,4 +3,6 @@
 ## v1.0.0dev
 
 - Initial creation of the package
-- Add command `nf-class modules create-from-class` command [#1](https://github.com/mirpedrol/nf-class/pull/1)
+- Add command `nf-class modules create-from-class` [#1](https://github.com/mirpedrol/nf-class/pull/1)
+- Add command `nf-class subworkflows expand-class` [#2](https://github.com/mirpedrol/nf-class/pull/2)
+- Add pytests [#5](https://github.com/mirpedrol/nf-class/pull/5)

nf_class/__main__.py

@@ -249,14 +249,15 @@ def command_modules_create_from_class(
 
     try:
         create_obj = ModuleCreateFromClass(
-            ctx,
             classname,
             toolname,
             dir,
             author,
             force,
             conda_name,
             conda_package_version,
+            ctx.obj["modules_repo_url"],
+            ctx.obj["modules_repo_branch"],
         )
         create_obj.create_from_class()
     except UserWarning as e:
@@ -369,21 +370,20 @@ def command_subworkflows_expand_class(
 
     try:
         create_obj = SubworkflowExpandClass(
-            ctx,
             classname,
             dir,
             author,
             force,
             expand_modules,
             prefix,
             suffix,
+            ctx.obj["modules_repo_url"],
+            ctx.obj["modules_repo_branch"],
         )
         create_obj.expand_class()
     except UserWarning as e:
-        raise
         log.error(e)
         sys.exit(1)
     except LookupError as e:
-        raise
         log.error(e)
         sys.exit(1)

nf_class/components/create.py

@@ -12,11 +12,12 @@
 
 # import nf_core.components.components_utils
 import nf_core.components.create
+import nf_core.modules.modules_repo
 
 # TODO: include this once new version of nf-core is released
 # import nf_core.pipelines.lint_utils
-import nf_core.lint_utils
-import nf_core.modules.modules_repo
+import nf_core.pipelines.lint_utils
+from nf_class.utils import NF_CLASS_MODULES_REMOTE
 from nf_core.utils import nfcore_question_style
 
 log = logging.getLogger(__name__)
@@ -27,7 +28,6 @@ class ComponentCreateFromClass(nf_core.components.create.ComponentCreate):
     Create a new module or subworkflow from a class.
 
     Args:
-        ctx (dict): Click context object.
         component_type (str): Type of component to create. [modules|subworkflows]
         directory (str): Directory to create the component in. [default: <current directory>]
         classname (str): Name of the class to create the component from.
@@ -54,7 +54,6 @@ class ComponentCreateFromClass(nf_core.components.create.ComponentCreate):
 
     def __init__(
         self,
-        ctx,
         component_type: str,
         directory: str = ".",
         classname: str = "",
@@ -63,6 +62,8 @@ def __init__(
         force: bool = False,
         conda_name: Optional[str] = None,
         conda_version: Optional[str] = None,
+        modules_repo_url: Optional[str] = NF_CLASS_MODULES_REMOTE,
+        modules_repo_branch: Optional[str] = "main",
     ):
         super().__init__(
             component_type=component_type,
@@ -77,9 +78,7 @@ def __init__(
             empty_template=False,
             migrate_pytest=False,
         )
-        self.modules_repo = nf_core.modules.modules_repo.ModulesRepo(
-            ctx.obj["modules_repo_url"], ctx.obj["modules_repo_branch"]
-        )
+        self.modules_repo = nf_core.modules.modules_repo.ModulesRepo(modules_repo_url, modules_repo_branch)
         self.classname = classname
 
     def create_from_class(self) -> None:
@@ -109,8 +108,6 @@ def create_from_class(self) -> None:
 
         # Check existence of directories early for fast-fail
         self.file_paths = self._get_component_dirs()
-        # TODO: remove this lines once the new version of nf-core/tools is released
-        self.file_paths.pop("tests/tags.yml")
 
         if self.component_type == "modules":
             # Try to find a bioconda package for 'component'
@@ -254,9 +251,7 @@ def _render_template(self) -> None:
             with open(dest_fn, "w") as fh:
                 log.debug(f"Writing output to: '{dest_fn}'")
                 fh.write(rendered_output)
-            # TODO: change line once new version of nf-core is released
-            # nf_core.pipelines.lint_utils.run_prettier_on_file(dest_fn)
-            nf_core.lint_utils.run_prettier_on_file(dest_fn)
+            nf_core.pipelines.lint_utils.run_prettier_on_file(dest_fn)
 
             # Mirror file permissions
             template_stat = (Path(nf_class.__file__).parent / f"{self.component_type}-template" / template_fn).stat()

nf_class/modules/create.py

@@ -8,29 +8,30 @@ class ModuleCreateFromClass(ComponentCreateFromClass):
     Create a new module from a class.
 
     Args:
-        ctx (dict): Click context object.
         classname (str): Name of the class to create the module from.
         component (str): Name of the module to create.
         dir (str): Directory to create the module in. [default: <current directory>]
         author (str): Author of the module.
         force (bool): Overwrite existing files.
         conda_name (str): Name of the conda environment.
         conda_version (str): Version of the conda environment.
+        modules_repo_url (str): URL of the modules repository.
+        modules_repo_branch (str): Branch of the modules repository.
     """
 
     def __init__(
         self,
-        ctx,
         classname: str = "",
         component: str = "",
         dir: str = ".",
         author: Optional[str] = None,
         force: bool = False,
         conda_name: Optional[str] = None,
         conda_version: Optional[str] = None,
+        modules_repo_url: Optional[str] = None,
+        modules_repo_branch: Optional[str] = None,
     ):
         super().__init__(
-            ctx,
             "modules",
             dir,
             classname,
@@ -39,4 +40,6 @@ def __init__(
             force,
             conda_name,
             conda_version,
+            modules_repo_url,
+            modules_repo_branch,
         )