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Merged
merged 6 commits into from
Mar 16, 2024
Merged

Add package generation test #14

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9bef9fc
added and started to debug pkg gen
tclose Mar 16, 2024
9d705be
touch up test for package generation
tclose Mar 16, 2024
5b338ce
updated location of to_mime within fileformats package
tclose Mar 16, 2024
d35efd8
added check for isclass before checking for sub-classes
tclose Mar 16, 2024
04a2c60
configure git in GH action
tclose Mar 16, 2024
0694d7b
stripped out examples dir
tclose Mar 16, 2024
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6 changes: 5 additions & 1 deletion .github/workflows/ci-cd.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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 "[email protected]"
git config --global user.name "Dummy User"

- name: Fetch tags
run: git fetch --prune --unshallow
Expand Down
11 changes: 7 additions & 4 deletions nipype2pydra/pkg_gen/__init__.py
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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"
Expand Down
17 changes: 17 additions & 0 deletions nipype2pydra/tests/test_pkg_gen.py
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Original file line number Diff line number Diff line change
@@ -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)