added NOTICE and other files to pkg-gen templatests

Author: tclose

nipype2pydra/pkg_gen/__init__.py

@@ -653,6 +653,11 @@ def copy_ignore(_, names):
     with open(pkg_dir / "README.rst", "w") as f:
         f.write(readme_rst)
 
+    with open(pkg_dir / "AUTHORS", "w") as f:
+        f.write("# Enter list of names and emails of contributors to this package")
+
+    shutil.copyfile(TEMPLATES_DIR / "NOTICE", pkg_dir / "NOTICE")
+
     fileformat_readme_path = related_pkgs_dir / "fileformats" / "README.rst"
     with open(fileformat_readme_path) as f:
         ff_readme_rst = f.read()
@@ -678,6 +683,9 @@ def copy_ignore(_, names):
     with open(pkg_dir / "pyproject.toml", "w") as f:
         f.write(pyproject_toml)
 
+    for tool_path in (TEMPLATES_DIR / "tools").iterdir():
+        shutil.copyfile(tool_path, pkg_dir / tool_path.name)
+
     # Add "pydra.tasks.<pkg>.auto to gitignore"
     with open(pkg_dir / ".gitignore", "a") as f:
         f.write(f"\n/pydra/tasks/{pkg}/auto" f"\n/pydra/tasks/{pkg}/_version.py\n")

nipype2pydra/pkg_gen/resources/templates/NOTICE

@@ -0,0 +1,6 @@
+Pydra-CHANGEME
+Copyright 2024 Pydra Development Team
+
+The bases for the task interfaces defined in this package were semi-automatically converted
+from Nipype interfaces (https://github.com/nipy/nipype) using the Nipype2Pydra tool
+(https://github.com/nipype/nipype2pydra).

nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd.yaml

@@ -16,6 +16,10 @@ on:
   repository_dispatch:
     types: [create-post-release]
 
+env:
+  CHANGEME_version: <set-CHANGEME-version-here>
+  CHANGEME_install_dir:  ${{ github.workspace }}/install
+
 jobs:
 
   nipype-conv:
@@ -103,7 +107,7 @@ jobs:
 
   test:
     needs: [nipype-conv]
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ['3.8', '3.11']
@@ -117,14 +121,23 @@ jobs:
     - name: Checkout repo
       uses: actions/checkout@v4
 
-    - name: Revert version to most recent version tag on upstream update
+    - name: Revert version to most recent version tag on Nipype or Nipype2Pydra update
       if: github.event_name == 'repository_dispatch'
       run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
 
+    - name: Cache CHANGEME Install
+      id: cache-install
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.CHANGEME_install_dir }}
+        key: CHANGEME-${{ env.CHANGEME_version }}-${{ runner.os }}
+
     - name: Install CHANGEME Package
+      if: steps.cache-install.outputs.cache-hit != 'true'
       run: |
-        echo "NOT IMPLEMENTED YET"
-        exit 1  # This is a placeholder for the actual install command
+        echo "NOT IMPLEMENTED YET (install at CHANGEME_install_dir: $CHANGEME_install_dir)"
+        exit 1  # This is a placeholder, replace this line and the one above with the installation procedure
+        echo "PATH=${{ env.CHANGEME_install_dir }}/bin:$PATH" >> $GITHUB_ENV
     
     - name: Download tasks converted from Nipype 
       uses: actions/download-artifact@v3
@@ -362,6 +375,31 @@ jobs:
         draft: false
         prerelease: false        
 
+
+  report_progress:
+    needs: [deploy]
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Generate progress report
+        id: generate-report
+        run: |
+          tools/report_progress.py outputs/progress-report.json
+          echo "progress_report=$(cat outputs/progress-report.json)" >> $GITHUB_OUTPUT
+
+      - name: Report progress to Nipype2Pydra repo
+        if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
+        run: >-
+          curl -XPOST -u "${{ env.POST_RELEASE_PAT }}" -H "Accept: application/vnd.github.everest-preview+json"
+          "https://api.github.com/repos/nipype/pydra-CHANGEME/dispatches"
+          -d '{
+            "event_type": "progress-report",
+            "client_payload": ${{ steps.generate-report.output.progress_report }}
+          }'
+        env:
+          PAT: ${{ env.PROGRESS_REPORT_PAT }}
+
+
 # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
 # Secrets are not accessible in the if: condition [0], so set an output variable [1]
 # [0] https://github.community/t/16928

nipype2pydra/pkg_gen/resources/templates/tools/report_progress.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python3
+from pathlib import Path
+import json
+import yaml
+import click
+
+
+@click.command
+@click.argument(
+    "out_json_path",
+    type=click.Path(path_type=Path),
+    help="The output path to save the report",
+)
+def report_progress(out_json_path: Path):
+
+    out_json_path.parent.mkdir(exist_ok=True, parents=True)
+
+    SPECS_DIR = Path(__file__).parent / "nipype-auto-conv" / "specs"
+
+    report = {}
+
+    for spec_path in SPECS_DIR.glob("*.yaml"):
+        with open(spec_path) as f:
+            spec = yaml.load(f, Loader=yaml.SafeLoader)
+
+        report[spec["task_name"]] = {
+            n: not s["xfail"] for n, s in spec["tests"].items()
+        }
+
+    with open(out_json_path, "w") as f:
+        json.dump(report, f)

nipype2pydra/task/tests/test_task.py

@@ -2,10 +2,16 @@
 import yaml
 import pytest
 import logging
-from nipype2pydra.utils import show_cli_trace
+import io
+import contextlib
 from traceback import format_exc
 from nipype2pydra.cli.task import task as task_cli
-from nipype2pydra.utils import add_to_sys_path, add_exc_note, INBUILT_NIPYPE_TRAIT_NAMES
+from nipype2pydra.utils import (
+    add_to_sys_path,
+    add_exc_note,
+    INBUILT_NIPYPE_TRAIT_NAMES,
+    show_cli_trace,
+)
 from conftest import EXAMPLE_TASKS_DIR
 
 
@@ -120,6 +126,23 @@ def test_task_conversion(task_spec_file, cli_runner, work_dir, gen_test_conftest
                 )
             )
 
+        # Run doctests
+        logging.info("Running doctests for %s", output_module_path)
+        with add_to_sys_path(pkg_root):
+            with contextlib.redirect_stdout(io.StringIO()) as f:
+                exit_code = pytest.main(
+                    [
+                        str(
+                            pkg_root.joinpath(
+                                *output_module_path.split(".")
+                            ).with_suffix(".py")
+                        ),
+                        "--doctest-modules",
+                        "--ignore-glob=test_*.py",
+                    ]
+                )
+
+        assert not exit_code, f.getvalue()
         # tests_fspath = pkg_root.joinpath(*output_module_path.split(".")).parent / "tests"
 
         # # logging.info("Running generated tests for %s", output_module_path)