Merge pull request #14 from nipype/pkg-gen-test

tclose · web-flow · commit 7d6ff89acded · 2024-03-16T21:45:38.000+11:00
Add package generation test
diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml
@@ -31,7 +31,11 @@ jobs:
     - 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
+      run: |
+        git config --local --unset http.https://github.com/.extraheader
+        git config --global init.defaultBranch main
+        git config --global user.email "dummy@email.com"
+        git config --global user.name "Dummy User"
 
     - name: Fetch tags
       run: git fetch --prune --unshallow
diff --git a/nipype2pydra/pkg_gen/__init__.py b/nipype2pydra/pkg_gen/__init__.py
@@ -7,13 +7,14 @@
 import shutil
 import string
 from pathlib import Path
+import inspect
 import attrs
 from warnings import warn
 import requests
 from operator import itemgetter
 import yaml
 import black.parsing
-import fileformats.core.utils
+import fileformats.core
 import fileformats.core.mixin
 from fileformats.generic import File, Directory
 from fileformats.medimage import Nifti1, NiftiGz, Bval, Bvec
@@ -261,7 +262,7 @@ def generate_yaml_spec(self) -> str:
         def type2str(tp):
             if tp in non_mime:
                 return tp.__name__
-            return fileformats.core.utils.to_mime(tp, official=False)
+            return fileformats.core.to_mime(tp, official=False)
 
         tests, doctests = self._gen_tests(
             doctest_blocks, input_types, output_types, output_templates
@@ -481,9 +482,10 @@ def combine_types(type_, prev_type):
                     if ty.get_origin(type_) is list:
                         as_list = True
                         type_ = ty.get_args(type_)[0]
-                    if issubclass(type_, prev_type):
+                    both_classes = inspect.isclass(type_) and inspect.isclass(prev_type)
+                    if both_classes and issubclass(type_, prev_type):
                         combined = type_
-                    elif issubclass(prev_type, type_):
+                    elif both_classes and issubclass(prev_type, type_):
                         combined = prev_type
                     else:
                         if ty.get_origin(prev_type) is ty.Union:
@@ -563,6 +565,7 @@ def _fields_stub(cls, name, category_class, values=None):
 
 def download_tasks_template(output_path: Path):
     """Downloads the latest pydra-template to the output path"""
+    output_path.parent.mkdir(parents=True, exist_ok=True)
 
     release_url = (
         "https://api.github.com/repos/nipype/pydra-tasks-template/releases/latest"
diff --git a/nipype2pydra/tests/test_pkg_gen.py b/nipype2pydra/tests/test_pkg_gen.py
@@ -0,0 +1,17 @@
+from nipype2pydra.cli.pkg_gen import pkg_gen
+from conftest import show_cli_trace
+
+
+def test_pkg_gen(cli_runner, tmp_path):
+    outputs_dir = tmp_path / "output-dir"
+    outputs_dir.mkdir()
+
+    result = cli_runner(
+        pkg_gen,
+        [
+            str(outputs_dir),
+            "--work-dir",
+            str(tmp_path / "work-dir"),
+        ],
+    )
+    assert result.exit_code == 0, show_cli_trace(result)
