moved fileformats packages again and fixed up freesurfer install

.github/workflows/pythonpackage.yaml

@@ -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:

fileformats/medimage-freesurfer-extras/pyproject.toml → fileformats-extras/pyproject.toml

@@ -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"

fileformats/medimage-freesurfer/pyproject.toml → fileformats/pyproject.toml

@@ -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"