8000 moved download of task template into separate job to avoid issues wit… by tclose · Pull Request #19 · nipype/nipype2pydra · GitHub
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moved download of task template into separate job to avoid issues wit… #19

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Merged
merged 13 commits into from
May 17, 2024
Merged

moved download of task template into separate job to avoid issues wit… #19

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91cd4e5
moved download of task template into separate job to avoid issues wit…
tclose May 17, 2024
1ebc139
fixed ci-cd
tclose May 17, 2024
ad8f658
debugging ci-cd
tclose May 17, 2024
5a17c33
bugfixing github
tclose May 17, 2024
740c333
debugging gha
tclose May 17, 2024
bbf5373
gha debugging
tclose May 17, 2024
bfcf0cf
gha action debug
tclose May 17, 2024
8e1c0d1
task template debugging
tclose May 17, 2024
c9ad097
debugging
tclose May 17, 2024
1d6991e
debugging gha
tclose May 17, 2024
402df91
debugging gha
tclose May 17, 2024
a72f1e7
gh db
tclose May 17, 2024
c9c0fcf
ghdb
tclose May 17, 2024
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moved download of task template into separate job to avoid issues wit… 
…hin tests
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@tclose
tclose committed May 17, 2024
commit 91cd4e5682a6290d15f6d57ee4cc75fc0c4af8c9
27 changes: 26 additions & 1 deletion .github/workflows/ci-cd.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,23 @@ defaults:
shell: bash

jobs:

download-task-template:
runs-on: ubuntu-latest
steps:

- name: Download task template
run: |
LATEST=$(curl -s https://api.github.com/repos/nipype/pydra-tasks-template/releases/latest | grep tag_name | awk -F\" '{print $4}')
curl -Lo pydra-task-template.tar.gz https://github.com/nipype/pydra-tasks-template/archive/refs/tags/$LATEST.tar.gz
tar xzf pydra-task-template.tar.gz
mv pydra-tasks-template-* pydra-tasks-template

- uses: actions/upload-artifact@v4
with:
name: tasks-template
path: pydra-tasks-template

test:
strategy:
matrix:
Expand All @@ -28,6 +45,12 @@ jobs:
- name: Checkout
uses: actions/checkout@v2

- name: Download the pydra-tasks-template artefact
uses: actions/download-artifact@v4
with:
name: pydra-tasks-template
path: $HOME/pydra-tasks-template

- 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
Expand Down Expand Up @@ -64,7 +87,9 @@ jobs:
run: python3 -m pip install --break-system-packages .[test]

- name: Pytest
run: pytest -vvs --cov nipype2pydra --cov-config .coveragerc --cov-report xml
run: >-
NIPYPE2PYDRA_PYDRA_TASK_TEMPLATE=$HOME/pydra-tasks-template
pytest -vvs --cov nipype2pydra --cov-config .coveragerc --cov-report xml

- name: Upload coverage to Codecov
uses: codecov/codecov-action@v2
Expand Down
8 changes: 8 additions & 0 deletions conftest.py
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Expand Up @@ -40,6 +40,14 @@ def invoke(*args, catch_exceptions=catch_cli_exceptions, **kwargs):
return invoke


@pytest.fixture
def tasks_template_args():
template = os.environ.get("NIPYPE2PYDRA_PYDRA_TASK_TEMPLATE", None)
if template:
return ["--task-template", template]
return []


# For debugging in IDE's don't catch raised exceptions and let the IDE
# break at it
if os.getenv("_PYTEST_RAISE", "0") != "0":
Expand Down
5 changes: 3 additions & 2 deletions nipype2pydra/pkg_gen/tests/test_pkg_gen.py
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Expand Up @@ -15,7 +15,7 @@ def pkg_gen_spec_file(request):
return EXAMPLE_PKG_GEN_DIR.joinpath(*request.param.split("-")).with_suffix(".yaml")


def test_pkg_gen(pkg_gen_spec_file, cli_runner, tmp_path):
def test_pkg_gen(pkg_gen_spec_file, cli_runner, tmp_path, tasks_template_args):
outputs_dir = tmp_path / "output-dir"
outputs_dir.mkdir()

Expand All @@ -24,6 +24,7 @@ def test_pkg_gen(pkg_gen_spec_file, cli_runner, tmp_path):
[
str(pkg_gen_spec_file),
str(outputs_dir),
],
]
+ tasks_template_args,
)
assert result.exit_code == 0, show_cli_trace(result)
5 changes: 3 additions & 2 deletions nipype2pydra/tests/test_package.py
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Expand Up @@ -33,7 +33,7 @@ def package_spec(request):


@pytest.mark.xfail(reason="Fails due to missing dependencies on PyPI")
def test_package_complete(package_spec, cli_runner, tmp_path):
def test_package_complete(package_spec, cli_runner, tmp_path, tasks_template_args):
pkg_name = package_spec.stem
repo_output = tmp_path / "repo"
repo_output.mkdir()
Expand All @@ -43,7 +43,8 @@ def test_package_complete(package_spec, cli_runner, tmp_path):
[
str(package_spec),
str(repo_output),
],
]
+ tasks_template_args,
)
assert result.exit_code == 0, show_cli_trace(result)
pkg_root = repo_output / f"pydra-{pkg_name}"
Expand Down
0