Merge pull request #13 from nipype/function-task

Adds support for converting function tasks

Author: tclose

.github/workflows/ci-cd.yml

@@ -0,0 +1,111 @@
+name: CI/CD
+
+on:
+  push:
+    branches: [ main, develop ]
+  pull_request:
+    branches: [ main, develop ]
+  release:
+    types: [published]
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest]
+        python-version: ["3.8", "3.11"]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Unset header
+      # checkout@v2 adds a header that makes branch protection report errors
+      # because the Github action bot is not a collaborator on the repo
+      run: git config --local --unset http.https://github.com/.extraheader
+
+    - name: Fetch tags
+      run: git fetch --prune --unshallow
+
+    - name: Disable etelemetry
+      run:  echo "NO_ET=TRUE" >> $GITHUB_ENV
+
+    - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Update build tools
+      run: python3 -m pip install --upgrade pip setuptools wheel
+
+    - name: Install required file-formats packages
+      run: |
+        pushd required-fileformats
+        python3 -m pip install -r requirements.txt
+        popd
+
+    - name: Install Dipy separately as it was causing trouble
+      run: python3 -m pip install dipy
+
+    - name: Install Package
+      run: python3 -m pip install .[test]
+
+    - name: Pytest
+      run: pytest -vvs --cov nipype2pydra --cov-config .coveragerc --cov-report xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        fail_ci_if_error: true
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+  deploy:
+    needs: [test]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+        fetch-depth: 0
+
+    - name: Unset header
+      # checkout@v2 adds a header that makes branch protection report errors
+      # because the Github action bot is not a collaborator on the repo
+      run: git config --local --unset http.https://github.com/.extraheader
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Install build tools
+      run: python3 -m pip install build twine
+
+    - name: Build source and wheel distributions
+      run: python3 -m build .
+
+    - name: Check distributions
+      run: twine check dist/*
+
+    - name: Check for PyPI token on tag
+      id: deployable
+      if: github.event_name == 'release'
+      env:
+        PYPI_API_TOKEN: "${{ secrets.PYPI_API_TOKEN }}"
+      run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi
+
+    - name: Upload to PyPI
+      if: steps.deployable.outputs.DEPLOY
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/publish.yml

@@ -1,4 +1,4 @@
-.venv*
+*.venv*
 /.project
 /.pydevproject
 *.pyc
@@ -20,6 +20,6 @@ __pycache__
 *.egg-info
 ~*
 /outputs
-/Test.venv
 /test-data
-/nipype2pydra/_version.py
+/nipype2pydra/_version.py
+

.github/workflows/tests.yml

@@ -4,12 +4,11 @@
 import tempfile
 import pytest
 from click.testing import CliRunner
-from fileformats.generic import File
 
 
 PKG_DIR = Path(__file__).parent
 EXAMPLE_SPECS_DIR = PKG_DIR / "example-specs"
-EXAMPLE_TASKS_DIR = EXAMPLE_SPECS_DIR / "task"
+EXAMPLE_TASKS_DIR = EXAMPLE_SPECS_DIR / "task" / "nipype"
 EXAMPLE_WORKFLOWS_DIR = EXAMPLE_SPECS_DIR / "workflow"
 
 
@@ -18,11 +17,6 @@ def gen_test_conftest():
     return PKG_DIR / "scripts" / "pkg_gen" / "resources" / "conftest.py"
 
 
-@pytest.fixture(params=[str(p.stem) for p in (EXAMPLE_TASKS_DIR).glob("*.yaml")])
-def task_spec_file(request):
-    return (EXAMPLE_TASKS_DIR / request.param).with_suffix(".yaml")
-
-
 @pytest.fixture(params=[str(p.stem) for p in EXAMPLE_WORKFLOWS_DIR.glob("*.yaml")])
 def workflow_spec_file(request):
     return (EXAMPLE_WORKFLOWS_DIR / request.param).with_suffix(".yaml")
@@ -34,6 +28,13 @@ def work_dir():
     return Path(work_dir)
 
 
+@pytest.fixture
+def outputs_dir():
+    outputs_dir = PKG_DIR / "outputs" / "workflows"
+    outputs_dir.mkdir(parents=True, exist_ok=True)
+    return outputs_dir
+
+
 @pytest.fixture
 def cli_runner(catch_cli_exceptions):
     def invoke(*args, catch_exceptions=catch_cli_exceptions, **kwargs):
@@ -56,6 +57,11 @@ def pytest_exception_interact(call):
     def pytest_internalerror(excinfo):
         raise excinfo.value
 
+    def pytest_configure(config):
+        config.option.capture = 'no'  # allow print statements to show up in the console    
+        config.option.log_cli = True  # show log messages in the console
+        config.option.log_level = "INFO"  # set the log level to INFO
+
     CATCH_CLI_EXCEPTIONS = False
 else:
     CATCH_CLI_EXCEPTIONS = True