Merge pull request #18 from nipype/workflow-src-conv

Workflow converter

Author: tclose

.github/workflows/ci-cd.yml

@@ -49,19 +49,19 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Update build tools
-      run: python3 -m pip install --upgrade pip setuptools wheel
+      run: python3 -m pip install --break-system-packages --upgrade pip setuptools wheel
 
     - name: Install required file-formats packages
       run: |
         pushd required-fileformats
-        python3 -m pip install -r requirements.txt
+        python3 -m pip install --break-system-packages -r requirements.txt
         popd
 
     - name: Install Dipy separately as it was causing trouble
-      run: python3 -m pip install dipy
+      run: python3 -m pip install --break-system-packages dipy
 
     - name: Install Package
-      run: python3 -m pip install .[test]
+      run: python3 -m pip install --break-system-packages .[test]
 
     - name: Pytest
       run: pytest -vvs --cov nipype2pydra --cov-config .coveragerc --cov-report xml
@@ -92,7 +92,7 @@ jobs:
         python-version: '3.11'
 
     - name: Install build tools
-      run: python3 -m pip install build twine
+      run: python3 -m pip install --break-system-packagesbuild twine
 
     - name: Build source and wheel distributions
       run: python3 -m build .

conftest.py

@@ -1,27 +1,22 @@
 import os
 from pathlib import Path
-import traceback
 import tempfile
 import pytest
 from click.testing import CliRunner
 
 
 PKG_DIR = Path(__file__).parent
 EXAMPLE_SPECS_DIR = PKG_DIR / "example-specs"
-EXAMPLE_TASKS_DIR = EXAMPLE_SPECS_DIR / "task" / "nipype"
+EXAMPLE_INTERFACES_DIR = EXAMPLE_SPECS_DIR / "interface" / "nipype"
 EXAMPLE_WORKFLOWS_DIR = EXAMPLE_SPECS_DIR / "workflow"
+EXAMPLE_PKG_GEN_DIR = EXAMPLE_SPECS_DIR / "pkg-gen"
 
 
 @pytest.fixture
 def gen_test_conftest():
     return PKG_DIR / "scripts" / "pkg_gen" / "resources" / "conftest.py"
 
 
-@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")
-
-
 @pytest.fixture
 def work_dir():
     work_dir = tempfile.mkdtemp()