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moved fileformats packages again and fixed up freesurfer install
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tclose committed Nov 6, 2023

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1 parent 7eb31de commit e7e30f3
Showing 9 changed files with 18 additions and 15 deletions.
21 changes: 12 additions & 9 deletions .github/workflows/pythonpackage.yaml
Original file line number Diff line number Diff line change
@@ -77,9 +77,12 @@ jobs:
python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
- name: Install task package
run: |
pip install ${{ matrix.pip-flags }} "./fileformats-medimage-freesurfer" "./src[dev]"
pip install ${{ matrix.pip-flags }} "./fileformats[dev]" "./fileformats-extras[dev]" "./src[dev]"
python -c "import pydra.tasks.freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
python -c "import fileformats.freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
python -c "import fileformats.extras.freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
fileformats-test:
runs-on: ubuntu-latest
@@ -100,12 +103,12 @@ jobs:
python -m pip install --upgrade pip
- name: Install task package
run: |
pip install "./fileformats/medimage-freesurfer[test]"
pip install "./fileformats[test]"
python -c "import fileformats.medimage_freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
# - name: Test fileformats with pytest
# run: |
# pytest -sv --doctest-modules ./fileformats-medimage-freesurfer/fileformats/medimage_freesurfer \
# --cov fileformats/medimage_freesurfer --cov-report xml
# pytest -sv --doctest-modules ./fileformats/fileformats/medimage_freesurfer \
# --cov fileformats.medimage_freesurfer --cov-report xml

fileformats-extras-test:
needs: ["fileformats-test"]
@@ -127,12 +130,12 @@ jobs:
python -m pip install --upgrade pip
- name: Install task package
run: |
pip install "./fileformats/medimage-freesurfer" "./fileformats/medimage-freesurfer-extras[test]"
pip install "./fileformats" "./fileformats-extras[test]"
python -c "import fileformats.extras.medimage_freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
# - name: Test fileformats extras with pytest
# run: |
# pytest -sv --doctest-modules ./fileformats-medimage-freesurfer-extras/fileformats/medimage_freesurfer \
# --cov fileformats/medimage_freesurfer --cov-report xml
# pytest -sv --doctest-modules ./fileformats-extras/fileformats/medimage_freesurfer \
# --cov fileformats.extras.medimage_freesurfer --cov-report xml

test:
needs: [nipype-conv, fileformats-test, fileformats-extras-test]
@@ -167,7 +170,7 @@ jobs:
run: |
pushd $HOME/downloads/freesurfer
tar -zxpf freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz
mv freesurfer-linux-ubuntu22_amd64-7.4.1 $HOME/freesurfer
mv freesurfer $HOME/
popd
export FREESURFER_HOME=$HOME/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
@@ -213,7 +216,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
pkg-dir: [".", "./fileformats/medimage-freesurfer", "./fileformats/medimage-freesurfer-extras"]
pkg-dir: [".", "./fileformats", "./fileformats-extras"]
steps:
- uses: actions/checkout@v3
with:
File renamed without changes.
Original file line number Diff line number Diff line change
@@ -5,14 +5,14 @@ build-backend = "hatchling.build"
[project]
name = "fileformats-medimage-freesurfer-extras"
description = "Classes for representing file formats used exclusively by the Freesurfer tool in Python classes for use in type hinting in data workflows"
readme = "../../README.rst"
readme = "../README.rst"
requires-python = ">=3.8"
dependencies = [
"fileformats >= 0.7",
"fileformats-medimage-freesurfer",
"pydra >= 0.22.0"
]
license = {file = "../../LICENSE"}
license = {file = "../LICENSE"}
authors = [
{name = "Thomas G. Close", email = "[email protected]"},
]
@@ -62,7 +62,7 @@ repository = "https://github.com/nipype/pydra-freesurfer"

[tool.hatch.version]
source = "vcs"
raw-options = { root = "../.." }
raw-options = { root = ".." }

[tool.hatch.build.hooks.vcs]
version-file = "fileformats/extras/medimage_freesurfer/_version.py"
File renamed without changes.
Original file line number Diff line number Diff line change
@@ -5,12 +5,12 @@ build-backend = "hatchling.build"
[project]
name = "fileformats-medimage-freesurfer"
description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows"
readme = "../../README.rst"
readme = "../README.rst"
requires-python = ">=3.8"
dependencies = [
"fileformats >= 0.4"
]
license = {file = "../../LICENSE"}
license = {file = "../LICENSE"}
authors = [
{name = "Thomas G. Close", email = "[email protected]"},
]
@@ -57,7 +57,7 @@ repository = "https://github.com/nipype/pydra-freesurfer"

[tool.hatch.version]
source = "vcs"
raw-options = { root = "../.." }
raw-options = { root = ".." }

[tool.hatch.build.hooks.vcs]
version-file = "fileformats/medimage_freesurfer/_version.py"

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