From affd37e11244b0f1277bae1a2b80a1ba18911017 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 11:04:20 +1100
Subject: [PATCH 01/18] changed a few things to hopefully get the auto package
 to import

---
 .github/workflows/pythonpackage.yaml | 2 +-
 nipype-auto-conv/generate            | 8 +++++---
 pydra/tasks/freesurfer/__init__.py   | 4 ++--
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index 33c5b35..2b17a7a 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -106,7 +106,7 @@ jobs:
         python -m pip install --upgrade pip
     - name: Install task package
       run: |
-        pip install ".[test]"
+        pip install -e ".[test]"
         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__}')"
     - name: Test with pytest
diff --git a/nipype-auto-conv/generate b/nipype-auto-conv/generate
index 2e27fd1..dca1fb9 100755
--- a/nipype-auto-conv/generate
+++ b/nipype-auto-conv/generate
@@ -7,7 +7,7 @@ import shutil
 from importlib import import_module
 import yaml
 import nipype
-import nipype2pydra
+import nipype2pydra.utils
 from nipype2pydra.task import TaskConverter
 
 
@@ -47,13 +47,15 @@ for fspath in sorted(SPECS_DIR.glob("**/*.yaml")):
 
     callables = import_module(rel_pkg_path + "_callables")
 
+    module_name = nipype2pydra.utils.to_snake_case(spec["task_name"])
+
     converter = TaskConverter(
-        output_module=f"pydra.tasks.{PKG_NAME}.auto.{spec['task_name']}",
+        output_module=f"pydra.tasks.{PKG_NAME}.auto.{module_name}",
         callables_module=callables,  # type: ignore
         **spec,
     )
     converter.generate(PKG_ROOT)
-    auto_init += f"from .{spec['task_name']} import {converter.task_name}\n"
+    auto_init += f"from .{module_name} import {converter.task_name}\n"
 
 
 with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "_version.py", "w") as f:
diff --git a/pydra/tasks/freesurfer/__init__.py b/pydra/tasks/freesurfer/__init__.py
index 0185301..179c1f8 100644
--- a/pydra/tasks/freesurfer/__init__.py
+++ b/pydra/tasks/freesurfer/__init__.py
@@ -20,8 +20,8 @@
 if "nipype" not in __version__:
     try:
         from .auto._version import nipype_version, nipype2pydra_version
-    except ImportError:
-        if "No module named pydra.tasks.freesurfer.auto._version":
+    except ModuleNotFoundError as e:
+        if "No module named 'pydra.tasks.freesurfer.auto._version'" in str(e):
             warn(
                 "Nipype interfaces haven't been automatically converted from their specs in "
                 f"`nipype-auto-conv`. Please run `{str(pkg_path / 'nipype-auto-conv' / 'generate')}` "

From 3934416a4b99f016a56bf4b8fbf36e1d649cc628 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 11:09:59 +1100
Subject: [PATCH 02/18] explicitly add `auto` package to pyproject.toml so it
 isn't excluded

---
 .github/workflows/pythonpackage.yaml | 2 +-
 pyproject.toml                       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index 2b17a7a..33c5b35 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -106,7 +106,7 @@ jobs:
         python -m pip install --upgrade pip
     - name: Install task package
       run: |
-        pip install -e ".[test]"
+        pip install ".[test]"
         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__}')"
     - name: Test with pytest
diff --git a/pyproject.toml b/pyproject.toml
index 1a2bdf7..c4f330a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,7 +60,7 @@ source = "vcs"
 version-file = "pydra/tasks/freesurfer/_version.py"
 
 [tool.hatch.build.targets.wheel]
-packages = ["pydra"]
+packages = ["pydra", "pydra.tasks.freesurfer.auto"]
 include-only = ["pydra/tasks/freesurfer"]
 
 [tool.black]

From 93fae081f1f15bbbaba623bb8de9b1573753325d Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 11:45:17 +1100
Subject: [PATCH 03/18] strip auto package from gitignore when building package
 on github

---
 .github/workflows/pythonpackage.yaml | 11 ++++++++---
 .gitignore                           |  2 +-
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index 33c5b35..725bad6 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -59,6 +59,9 @@ jobs:
       with:
         name: converted-nipype
         path: pydra/tasks/freesurfer/auto
+    - name: Strip auto package from gitignore so it is included in package
+      run: |
+        sed -i '/\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
@@ -93,10 +96,9 @@ jobs:
       with:
         name: converted-nipype
         path: pydra/tasks/freesurfer/auto
-    - name: Check directory structure
+    - name: Strip auto package from gitignore so it is included in package
       run: |
-        sudo apt install tree
-        tree .
+        sed -i '/\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
@@ -147,6 +149,9 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install build tools
       run: python -m pip install build twine
+    - name: Strip auto package from gitignore so it is included in package
+      run: |
+        sed -i '/\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
     - name: Build source and wheel distributions
       run: python -m build
     - name: Check distributions
diff --git a/.gitignore b/.gitignore
index b160ce2..dc819e3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -137,5 +137,5 @@ dmypy.json
 # Mac garbarge
 .DS_store
 
-/pydra/tasks/freesurfer/auto
 /pydra/tasks/freesurfer/_version.py
+/pydra/tasks/freesurfer/auto

From c81816a062b5cf86a988089f454939641f669d86 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 12:47:50 +1100
Subject: [PATCH 04/18] add freesurfer installation to test jobs

---
 .github/workflows/pythonpackage.yaml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index 725bad6..654cabe 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -81,12 +81,16 @@ jobs:
 
   test:
     needs: [nipype-conv]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         python-version: ['3.8', '3.11']
 
     steps:
+    - name: Install Freesurfer
+      run: |
+        wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.0/freesurfer_ubuntu22-7.4.0_amd64.deb ~/freesurfer-install.deb
+        sudo apt install ~/freesurfer-install.deb
     - uses: actions/checkout@v3
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'

From 82975e2616128013f8bf4ba78de62cdbd309f24a Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 14:09:43 +1100
Subject: [PATCH 05/18] added fileformats packages into repository

---
 .github/workflows/pythonpackage.yaml          | 83 +++++++++++++++---
 .gitignore                                    |  6 +-
 docs/index.rst                                |  2 +-
 .../conftest.py                               | 37 ++++++++
 .../extras/medimage_freesurfer/__init__.py    |  1 +
 .../extras/medimage_freesurfer/_version.py    | 16 ++++
 .../pyproject.toml                            | 87 +++++++++++++++++++
 fileformats-medimage-freesurfer/conftest.py   | 37 ++++++++
 .../medimage_freesurfer/__init__.py           |  1 +
 .../medimage_freesurfer/_version.py           | 16 ++++
 .../pyproject.toml                            | 82 +++++++++++++++++
 src/conftest.py                               | 27 ++++++
 .../pydra}/tasks/freesurfer/__init__.py       |  0
 .../pydra}/tasks/freesurfer/latest.py         |  0
 .../pydra}/tasks/freesurfer/v1/__init__.py    |  0
 pyproject.toml => src/pyproject.toml          |  8 +-
 16 files changed, 385 insertions(+), 18 deletions(-)
 create mode 100644 fileformats-medimage-freesurfer-extras/conftest.py
 create mode 100644 fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/__init__.py
 create mode 100644 fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/_version.py
 create mode 100644 fileformats-medimage-freesurfer-extras/pyproject.toml
 create mode 100644 fileformats-medimage-freesurfer/conftest.py
 create mode 100644 fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/__init__.py
 create mode 100644 fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/_version.py
 create mode 100644 fileformats-medimage-freesurfer/pyproject.toml
 create mode 100644 src/conftest.py
 rename {pydra => src/pydra}/tasks/freesurfer/__init__.py (100%)
 rename {pydra => src/pydra}/tasks/freesurfer/latest.py (100%)
 rename {pydra => src/pydra}/tasks/freesurfer/v1/__init__.py (100%)
 rename pyproject.toml => src/pyproject.toml (92%)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index 654cabe..f18fad5 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -61,7 +61,7 @@ jobs:
         path: pydra/tasks/freesurfer/auto
     - name: Strip auto package from gitignore so it is included in package
       run: |
-        sed -i '/\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
+        sed -i '/\/src\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
@@ -75,22 +75,74 @@ 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 }} ".[dev]"
+        pip install ${{ matrix.pip-flags }} "./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__}')"
 
+  fileformats-test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.11']
+    steps:
+    - uses: actions/checkout@v3
+    - name: Revert version to most recent tag on upstream update
+      if: github.event_name == 'repository_dispatch'
+      run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+    - name: Install task package
+      run: |
+        pip install "./fileformats-medimage-freesurfer[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
+
+  fileformats-extras-test:
+    needs: ["fileformats-test"]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.11']
+    steps:
+    - uses: actions/checkout@v3
+    - name: Revert version to most recent tag on upstream update
+      if: github.event_name == 'repository_dispatch'
+      run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+    - name: Install task package
+      run: |
+        pip install "./fileformats-medimage-freesurfer-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  
+
   test:
-    needs: [nipype-conv]
+    needs: [nipype-conv, fileformats-test, fileformats-extras-test]
     runs-on: ubuntu-22.04
     strategy:
       matrix:
         python-version: ['3.8', '3.11']
-
     steps:
     - name: Install Freesurfer
       run: |
-        wget https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.0/freesurfer_ubuntu22-7.4.0_amd64.deb ~/freesurfer-install.deb
-        sudo apt install ~/freesurfer-install.deb
+        wget -q https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.0/freesurfer_ubuntu22-7.4.0_amd64.deb ~/freesurfer-install.deb
+        sudo apt install -y ~/freesurfer-install.deb
     - uses: actions/checkout@v3
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'
@@ -102,7 +154,7 @@ jobs:
         path: pydra/tasks/freesurfer/auto
     - name: Strip auto package from gitignore so it is included in package
       run: |
-        sed -i '/\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
+        sed -i '/\/src\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
@@ -112,15 +164,18 @@ jobs:
         python -m pip install --upgrade pip
     - name: Install task package
       run: |
-        pip install ".[test]"
+        pip install "./src[test]"
         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__}')"
     - name: Test with pytest
       run: |
-        pytest -sv --doctest-modules pydra/tasks/freesurfer \
+        pytest -sv --doctest-modules ./src/pydra/tasks/freesurfer \
             --cov pydra.tasks.freesurfer --cov-report xml
     - uses: codecov/codecov-action@v3
       if: ${{ always() }}
+      with:
+        files: .src/coverage.xml,./fileformats-medimage-freesurfer/coverage.xml,./fileformats-medimage-freesurfer-extras/coverage.xml
+        name: pydra-freesurfer
 
   deploy:
     needs: [devcheck, test]
@@ -155,9 +210,13 @@ jobs:
       run: python -m pip install build twine
     - name: Strip auto package from gitignore so it is included in package
       run: |
-        sed -i '/\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
-    - name: Build source and wheel distributions
-      run: python -m build
+        sed -i '/\/src\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
+    - name: Build Pydra tasks source and wheel distributions
+      run: python -m build ./src
+    - name: Build fileformats source and wheel distributions
+      run: python -m build ./fileformats-medimage-freesurfer
+    - name: Build fileformats extras source and wheel distributions
+      run: python -m build ./fileformats-medimage-freesurfer-extras
     - name: Check distributions
       run: twine check dist/*
     - uses: actions/upload-artifact@v3
diff --git a/.gitignore b/.gitignore
index dc819e3..74c6a7e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -137,5 +137,7 @@ dmypy.json
 # Mac garbarge
 .DS_store
 
-/pydra/tasks/freesurfer/_version.py
-/pydra/tasks/freesurfer/auto
+/src/pydra/tasks/freesurfer/_version.py
+/fileformts-medimage-freesurfer/fileformats/medimage_freesurfer/_version.py
+/fileformts-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/_version.py
+/src/pydra/tasks/freesurfer/auto
diff --git a/docs/index.rst b/docs/index.rst
index bc1ee5e..2f809eb 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -1,5 +1,5 @@
 Welcome to pydra-freesurfer's documentation!
-=========================================
+============================================
 
 .. toctree::
    :maxdepth: 2
diff --git a/fileformats-medimage-freesurfer-extras/conftest.py b/fileformats-medimage-freesurfer-extras/conftest.py
new file mode 100644
index 0000000..2a703c0
--- /dev/null
+++ b/fileformats-medimage-freesurfer-extras/conftest.py
@@ -0,0 +1,37 @@
+import os
+import logging
+from pathlib import Path
+import tempfile
+import pytest
+
+# Set DEBUG logging for unittests
+
+log_level = logging.WARNING
+
+logger = logging.getLogger("fileformats")
+logger.setLevel(log_level)
+
+sch = logging.StreamHandler()
+sch.setLevel(log_level)
+formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
+sch.setFormatter(formatter)
+logger.addHandler(sch)
+
+
+# For debugging in IDE's don't catch raised exceptions and let the IDE
+# break at it
+if os.getenv("_PYTEST_RAISE", "0") != "0":
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_exception_interact(call):
+        raise call.excinfo.value
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_internalerror(excinfo):
+        raise excinfo.value
+
+
+@pytest.fixture
+def work_dir():
+    work_dir = tempfile.mkdtemp()
+    return Path(work_dir)
diff --git a/fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/__init__.py b/fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/__init__.py
new file mode 100644
index 0000000..8dee4bf
--- /dev/null
+++ b/fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/__init__.py
@@ -0,0 +1 @@
+from ._version import __version__
diff --git a/fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/_version.py b/fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/_version.py
new file mode 100644
index 0000000..4b004e0
--- /dev/null
+++ b/fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/_version.py
@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.1.dev19+g7f136b2.d20231103'
+__version_tuple__ = version_tuple = (0, 1, 'dev19', 'g7f136b2.d20231103')
diff --git a/fileformats-medimage-freesurfer-extras/pyproject.toml b/fileformats-medimage-freesurfer-extras/pyproject.toml
new file mode 100644
index 0000000..1c28130
--- /dev/null
+++ b/fileformats-medimage-freesurfer-extras/pyproject.toml
@@ -0,0 +1,87 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+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"
+requires-python = ">=3.8"
+dependencies = [
+    "fileformats >= 0.7",
+    "fileformats-medimage-freesurfer",
+    "pydra >= 0.22.0"
+]
+license = {file = "../LICENSE"}
+authors = [
+    {name = "Thomas G. Close", email = "tom.g.close@gmail.com"},
+]
+maintainers = [
+    {name = "Thomas G. Close", email = "tom.g.close@gmail.com"},
+]
+keywords = [
+    "file formats",
+    "data",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+dev = [
+    "black",
+    "pre-commit",
+    "codespell",
+    "flake8",
+    "flake8-pyproject",
+]
+test = [
+    "pytest >=6.2.5",
+    "pytest-env>=0.6.2",
+    "pytest-cov>=2.12.1",
+    "codecov",
+]
+
+converters = [
+]
+
+[project.urls]
+repository = "https://github.com/nipype/pydra-freesurfer"
+
+[tool.hatch.version]
+source = "vcs"
+raw-options = { root = ".." }
+
+[tool.hatch.build.hooks.vcs]
+version-file = "fileformats/extras/medimage_freesurfer/_version.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["fileformats"]
+
+[tool.black]
+target-version = ['py38']
+exclude = "fileformats/extras/medimage_freesurfer/_version.py"
+
+[tool.codespell]
+ignore-words = ".codespell-ignorewords"
+
+[tool.flake8]
+doctests = true
+per-file-ignores = [
+    "__init__.py:F401"
+]
+max-line-length = 88
+select = "C,E,F,W,B,B950"
+extend-ignore = ['E203', 'E501', 'E129']
diff --git a/fileformats-medimage-freesurfer/conftest.py b/fileformats-medimage-freesurfer/conftest.py
new file mode 100644
index 0000000..2a703c0
--- /dev/null
+++ b/fileformats-medimage-freesurfer/conftest.py
@@ -0,0 +1,37 @@
+import os
+import logging
+from pathlib import Path
+import tempfile
+import pytest
+
+# Set DEBUG logging for unittests
+
+log_level = logging.WARNING
+
+logger = logging.getLogger("fileformats")
+logger.setLevel(log_level)
+
+sch = logging.StreamHandler()
+sch.setLevel(log_level)
+formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
+sch.setFormatter(formatter)
+logger.addHandler(sch)
+
+
+# For debugging in IDE's don't catch raised exceptions and let the IDE
+# break at it
+if os.getenv("_PYTEST_RAISE", "0") != "0":
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_exception_interact(call):
+        raise call.excinfo.value
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_internalerror(excinfo):
+        raise excinfo.value
+
+
+@pytest.fixture
+def work_dir():
+    work_dir = tempfile.mkdtemp()
+    return Path(work_dir)
diff --git a/fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/__init__.py b/fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/__init__.py
new file mode 100644
index 0000000..8dee4bf
--- /dev/null
+++ b/fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/__init__.py
@@ -0,0 +1 @@
+from ._version import __version__
diff --git a/fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/_version.py b/fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/_version.py
new file mode 100644
index 0000000..4b004e0
--- /dev/null
+++ b/fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/_version.py
@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.1.dev19+g7f136b2.d20231103'
+__version_tuple__ = version_tuple = (0, 1, 'dev19', 'g7f136b2.d20231103')
diff --git a/fileformats-medimage-freesurfer/pyproject.toml b/fileformats-medimage-freesurfer/pyproject.toml
new file mode 100644
index 0000000..2cd17d0
--- /dev/null
+++ b/fileformats-medimage-freesurfer/pyproject.toml
@@ -0,0 +1,82 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+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"
+requires-python = ">=3.8"
+dependencies = [
+    "fileformats >= 0.4"
+]
+license = {file = "../LICENSE"}
+authors = [
+    {name = "Thomas G. Close", email = "tom.g.close@gmail.com"},
+]
+maintainers = [
+    {name = "Thomas G. Close", email = "tom.g.close@gmail.com"},
+]
+keywords = [
+    "file formats",
+    "data",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Topic :: Scientific/Engineering",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+dev = [
+    "black",
+    "pre-commit",
+    "codespell",
+    "flake8",
+    "flake8-pyproject",
+]
+test = [
+    "pytest >=6.2.5",
+    "pytest-env>=0.6.2",
+    "pytest-cov>=2.12.1",
+    "codecov",
+]
+
+[project.urls]
+repository = "https://github.com/nipype/pydra-freesurfer"
+
+[tool.hatch.version]
+source = "vcs"
+raw-options = { root = ".." }
+
+[tool.hatch.build.hooks.vcs]
+version-file = "fileformats/medimage_freesurfer/_version.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["fileformats"]
+
+[tool.black]
+target-version = ['py38']
+exclude = "fileformats/medimage_freesurfer/_version.py"
+
+[tool.codespell]
+ignore-words = ".codespell-ignorewords"
+
+[tool.flake8]
+doctests = true
+per-file-ignores = [
+    "__init__.py:F401"
+]
+max-line-length = 88
+select = "C,E,F,W,B,B950"
+extend-ignore = ['E203', 'E501', 'E129']
diff --git a/src/conftest.py b/src/conftest.py
new file mode 100644
index 0000000..97cd9d0
--- /dev/null
+++ b/src/conftest.py
@@ -0,0 +1,27 @@
+import os
+import pytest
+import logging
+
+log_level = logging.WARNING
+
+logger = logging.getLogger("fileformats")
+logger.setLevel(log_level)
+
+sch = logging.StreamHandler()
+sch.setLevel(log_level)
+formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
+sch.setFormatter(formatter)
+logger.addHandler(sch)
+
+
+# For debugging in IDE's don't catch raised exceptions and let the IDE
+# break at it
+if os.getenv("_PYTEST_RAISE", "0") != "0":
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_exception_interact(call):
+        raise call.excinfo.value
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_internalerror(excinfo):
+        raise excinfo.value
diff --git a/pydra/tasks/freesurfer/__init__.py b/src/pydra/tasks/freesurfer/__init__.py
similarity index 100%
rename from pydra/tasks/freesurfer/__init__.py
rename to src/pydra/tasks/freesurfer/__init__.py
diff --git a/pydra/tasks/freesurfer/latest.py b/src/pydra/tasks/freesurfer/latest.py
similarity index 100%
rename from pydra/tasks/freesurfer/latest.py
rename to src/pydra/tasks/freesurfer/latest.py
diff --git a/pydra/tasks/freesurfer/v1/__init__.py b/src/pydra/tasks/freesurfer/v1/__init__.py
similarity index 100%
rename from pydra/tasks/freesurfer/v1/__init__.py
rename to src/pydra/tasks/freesurfer/v1/__init__.py
diff --git a/pyproject.toml b/src/pyproject.toml
similarity index 92%
rename from pyproject.toml
rename to src/pyproject.toml
index c4f330a..090208e 100644
--- a/pyproject.toml
+++ b/src/pyproject.toml
@@ -5,14 +5,15 @@ build-backend = "hatchling.build"
 [project]
 name = "pydra-tasks-freesurfer"
 description = "Pydra tasks package for freesurfer"
-readme = "README.rst"
+readme = "../README.rst"
 requires-python = ">=3.8"
 dependencies = [
     "pydra >=0.22",
     "fileformats >=0.8.3",
     "fileformats-datascience >=0.1",
-    "fileformats-medimage >=0.4.1"]
-license = {file = "LICENSE"}
+    "fileformats-medimage >=0.4.1",
+    "fileformats-medimage-freesurfer"]
+license = {file = "../LICENSE"}
 authors = [{name = "Nipype developers", email = "neuroimaging@python.org"}]
 maintainers = [{name = "Nipype developers", email = "neuroimaging@python.org"}]
 keywords = ["pydra"]
@@ -55,6 +56,7 @@ test = [
 
 [tool.hatch.version]
 source = "vcs"
+raw-options = { root = ".." }
 
 [tool.hatch.build.hooks.vcs]
 version-file = "pydra/tasks/freesurfer/_version.py"

From 7f2bfbb45501ae087bc06d59948698c8c6071cbf Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 14:47:01 +1100
Subject: [PATCH 06/18] commented out fileformats tests as they are currently
 empty

---
 .github/workflows/pythonpackage.yaml | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index f18fad5..3fea0b2 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -100,10 +100,10 @@ jobs:
       run: |
         pip install "./fileformats-medimage-freesurfer[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
+    # - name: Test fileformats with pytest
+    #   run: |
+    #     pytest -sv --doctest-modules ./fileformats-medimage-freesurfer/fileformats/medimage_freesurfer \
+    #         --cov fileformats/medimage_freesurfer --cov-report xml
 
   fileformats-extras-test:
     needs: ["fileformats-test"]
@@ -127,10 +127,10 @@ jobs:
       run: |
         pip install "./fileformats-medimage-freesurfer-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  
+    # - 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  
 
   test:
     needs: [nipype-conv, fileformats-test, fileformats-extras-test]
@@ -174,7 +174,8 @@ jobs:
     - uses: codecov/codecov-action@v3
       if: ${{ always() }}
       with:
-        files: .src/coverage.xml,./fileformats-medimage-freesurfer/coverage.xml,./fileformats-medimage-freesurfer-extras/coverage.xml
+        files: .src/coverage.xml
+        # ,./fileformats-medimage-freesurfer/coverage.xml,./fileformats-medimage-freesurfer-extras/coverage.xml
         name: pydra-freesurfer
 
   deploy:

From d225f06075ffe4cbae5710606c5a0c7a63326b3b Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 14:50:58 +1100
Subject: [PATCH 07/18] added fileformats-medimage-freesurfer to extras test

---
 .github/workflows/pythonpackage.yaml | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index 3fea0b2..2600f1d 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -71,7 +71,9 @@ jobs:
         python -m pip install --upgrade pip
     - name: Install Pydra
       run: |
+        pushd $HOME
         pip install ${{ matrix.pydra }}
+        popd
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
     - name: Install task package
       run: |
@@ -125,7 +127,7 @@ jobs:
         python -m pip install --upgrade pip
     - name: Install task package
       run: |
-        pip install "./fileformats-medimage-freesurfer-extras[test]"
+        pip install "./fileformats-medimage-freesurfer" "./fileformats-medimage-freesurfer-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: |
@@ -141,8 +143,13 @@ jobs:
     steps:
     - name: Install Freesurfer
       run: |
-        wget -q https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.0/freesurfer_ubuntu22-7.4.0_amd64.deb ~/freesurfer-install.deb
-        sudo apt install -y ~/freesurfer-install.deb
+        curl -s -o $HOME/freesurfer.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz
+        df -h
+        pushd $HOME
+        tar -zxpf freesurfer.tar.gz
+        popd
+        export FREESURFER_HOME=$HOME/freesurfer
+        source $FREESURFER_HOME/SetUpFreeSurfer.sh
     - uses: actions/checkout@v3
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'

From f39531c231fa9c0724ffabb523eb53c6c75f52df Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 18:13:08 +1100
Subject: [PATCH 08/18] added fileformats-medimage-freesurfer to dev check
 install

---
 .github/workflows/pythonpackage.yaml | 4 ++--
 src/pyproject.toml                   | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index 2600f1d..fe62537 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -77,7 +77,7 @@ 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 }} "./src[dev]"
+        pip install ${{ matrix.pip-flags }} "./fileformats-medimage-freesurfer" "./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__}')"
 
@@ -171,7 +171,7 @@ jobs:
         python -m pip install --upgrade pip
     - name: Install task package
       run: |
-        pip install "./src[test]"
+        pip install "./fileformats-medimage-freesurfer" "./src[test]"
         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__}')"
     - name: Test with pytest
diff --git a/src/pyproject.toml b/src/pyproject.toml
index 090208e..21fd253 100644
--- a/src/pyproject.toml
+++ b/src/pyproject.toml
@@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"]
 build-backend = "hatchling.build"
 
 [project]
-name = "pydra-tasks-freesurfer"
+name = "pydra-freesurfer"
 description = "Pydra tasks package for freesurfer"
 readme = "../README.rst"
 requires-python = ">=3.8"

From fc31fdd660779a1235d048f1df414ac6932a84a7 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 18:20:43 +1100
Subject: [PATCH 09/18] changed message to check for when seeing if auto
 packages have been generated

---
 src/pydra/tasks/freesurfer/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pydra/tasks/freesurfer/__init__.py b/src/pydra/tasks/freesurfer/__init__.py
index 179c1f8..a61327e 100644
--- a/src/pydra/tasks/freesurfer/__init__.py
+++ b/src/pydra/tasks/freesurfer/__init__.py
@@ -21,7 +21,7 @@
     try:
         from .auto._version import nipype_version, nipype2pydra_version
     except ModuleNotFoundError as e:
-        if "No module named 'pydra.tasks.freesurfer.auto._version'" in str(e):
+        if "No module named 'pydra.tasks.freesurfer.auto'" in str(e):
             warn(
                 "Nipype interfaces haven't been automatically converted from their specs in "
                 f"`nipype-auto-conv`. Please run `{str(pkg_path / 'nipype-auto-conv' / 'generate')}` "

From 0acff99bcbf8bff85a774560f09bcc3c142c045b Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 18:27:27 +1100
Subject: [PATCH 10/18] add freesurfer license key to test gha job

---
 .github/workflows/pythonpackage.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index fe62537..0fe3386 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -142,6 +142,8 @@ jobs:
         python-version: ['3.8', '3.11']
     steps:
     - name: Install Freesurfer
+      env:
+        FREESURFER_LICENCE: ${{ secrets.FREESURFER_LICENCE }}
       run: |
         curl -s -o $HOME/freesurfer.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz
         df -h
@@ -150,6 +152,7 @@ jobs:
         popd
         export FREESURFER_HOME=$HOME/freesurfer
         source $FREESURFER_HOME/SetUpFreeSurfer.sh
+        echo $FREESURFER_LICENCE > $FREESURFER_HOME/license.txt
     - uses: actions/checkout@v3
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'

From 27d326a43339e424c55597879973353086cc6b1f Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 18:30:10 +1100
Subject: [PATCH 11/18] removed matrix from deploy node

---
 .github/workflows/pythonpackage.yaml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index 0fe3386..a2ab450 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -191,9 +191,6 @@ jobs:
   deploy:
     needs: [devcheck, test]
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.11']
     steps:
     - uses: actions/checkout@v3
       with:
@@ -213,10 +210,10 @@ jobs:
         git add -f pydra/tasks/freesurfer/auto/_version.py
         git commit -am"added auto-generated version to make new tag for package version"
         git tag ${TAG}post${POST}    
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: '3.11'
     - name: Install build tools
       run: python -m pip install build twine
     - name: Strip auto package from gitignore so it is included in package

From 41044f9b38e1b589b246953d94f8f5f2a6cf1ec1 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Fri, 3 Nov 2023 18:38:17 +1100
Subject: [PATCH 12/18] dropped 3.11 from test matrix

---
 .github/workflows/pythonpackage.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index a2ab450..994e1f5 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -139,7 +139,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8']  # '3.11'
     steps:
     - name: Install Freesurfer
       env:

From 9f6653c7b5371baec61c566aa75321c78d37fe6f Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 6 Nov 2023 11:09:12 +1100
Subject: [PATCH 13/18] trying to get freesurfer gha install to work

---
 .github/workflows/pythonpackage.yaml | 24 +++++++++++++++++++-----
 src/pyproject.toml                   |  1 +
 2 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index 994e1f5..2735128 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -141,14 +141,28 @@ jobs:
       matrix:
         python-version: ['3.8']  # '3.11'
     steps:
+    - name: Get Download cache Key
+      id: cache-key
+      run: echo "::set-output name=key::freesurfer-linux-ubuntu22_amd64-7.4.1"
+    - name: Cache FreeSurfer
+      uses: actions/cache@v2
+      with:
+        path: $HOME/downloads/freesurfer
+        key: ${{ steps.cache-key.outputs.key }}
+        restore-keys: |
+          freesurfer-linux-ubuntu22_amd64-7.4.1
+    - name: Download FreeSurfer
+      if: steps.cache-key.outputs.key != steps.cache-hit.outputs.key
+      run: |
+        mkdir -p $HOME/downloads/freesurfer
+        curl -s -o $HOME/downloads/freesurfer/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz
+      shell: bash
     - name: Install Freesurfer
       env:
         FREESURFER_LICENCE: ${{ secrets.FREESURFER_LICENCE }}
       run: |
-        curl -s -o $HOME/freesurfer.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz
-        df -h
-        pushd $HOME
-        tar -zxpf freesurfer.tar.gz
+        pushd $HOME/downloads/freesurfer
+        tar -zxpf freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz
         popd
         export FREESURFER_HOME=$HOME/freesurfer
         source $FREESURFER_HOME/SetUpFreeSurfer.sh
@@ -174,7 +188,7 @@ jobs:
         python -m pip install --upgrade pip
     - name: Install task package
       run: |
-        pip install "./fileformats-medimage-freesurfer" "./src[test]"
+        pip install "./fileformats-medimage-freesurfer" "./fileformats-medimage-freesurfer-extras" "./src[test]"
         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__}')"
     - name: Test with pytest
diff --git a/src/pyproject.toml b/src/pyproject.toml
index 21fd253..4224d18 100644
--- a/src/pyproject.toml
+++ b/src/pyproject.toml
@@ -52,6 +52,7 @@ test = [
     "fileformats-extras",
     "fileformats-datascience-extras",
     "fileformats-medimage-extras",
+    "fileformats-medimage-freesurfer-extras",
 ]
 
 [tool.hatch.version]

From 594cd0a040494bc818e96cbb4f6d4db3817805bd Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 6 Nov 2023 11:27:26 +1100
Subject: [PATCH 14/18] remove unneccessary tools to free space in image

---
 .github/workflows/pythonpackage.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index 2735128..8319038 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -141,6 +141,10 @@ jobs:
       matrix:
         python-version: ['3.8']  # '3.11'
     steps:
+    - name: Removed unnecessary tools to free space
+      run: |
+        sudo rm -rf /usr/share/dotnet
+        sudo rm -rf "$AGENT_TOOLSDIRECTORY"      
     - name: Get Download cache Key
       id: cache-key
       run: echo "::set-output name=key::freesurfer-linux-ubuntu22_amd64-7.4.1"

From df363d5cb2ad3e739f8cfb92b33f66d6b3d5a8bd Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 6 Nov 2023 11:30:02 +1100
Subject: [PATCH 15/18] add freesurfer bin to path

---
 .github/workflows/pythonpackage.yaml | 27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index 8319038..c7c95ad 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -36,7 +36,7 @@ jobs:
     - uses: actions/upload-artifact@v3
       with:
         name: converted-nipype
-        path: pydra/tasks/freesurfer/auto
+        path: src/pydra/tasks/freesurfer/auto
 
   devcheck:
     needs: [nipype-conv]
@@ -58,7 +58,7 @@ jobs:
       uses: actions/download-artifact@v3
       with:
         name: converted-nipype
-        path: pydra/tasks/freesurfer/auto
+        path: src/pydra/tasks/freesurfer/auto
     - name: Strip auto package from gitignore so it is included in package
       run: |
         sed -i '/\/src\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
@@ -100,7 +100,7 @@ jobs:
         python -m pip install --upgrade pip
     - name: Install task package
       run: |
-        pip install "./fileformats-medimage-freesurfer[test]"
+        pip install "./fileformats/medimage-freesurfer[test]"
         python -c "import fileformats.medimage_freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
     # - name: Test fileformats with pytest
     #   run: |
@@ -127,7 +127,7 @@ 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/medimage-freesurfer" "./fileformats/medimage-freesurfer-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: |
@@ -167,10 +167,12 @@ 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 $HOME/freesurfer
         popd
         export FREESURFER_HOME=$HOME/freesurfer
         source $FREESURFER_HOME/SetUpFreeSurfer.sh
         echo $FREESURFER_LICENCE > $FREESURFER_HOME/license.txt
+        export PATH=$FREESURFER_HOME/bin:$PATH
     - uses: actions/checkout@v3
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'
@@ -179,7 +181,7 @@ jobs:
       uses: actions/download-artifact@v3
       with:
         name: converted-nipype
-        path: pydra/tasks/freesurfer/auto
+        path: src/pydra/tasks/freesurfer/auto
     - name: Strip auto package from gitignore so it is included in package
       run: |
         sed -i '/\/src\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
@@ -209,6 +211,9 @@ jobs:
   deploy:
     needs: [devcheck, test]
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        pkg-dir: [".", "./fileformats/medimage-freesurfer", "./fileformats/medimage-freesurfer-extras"]
     steps:
     - uses: actions/checkout@v3
       with:
@@ -218,14 +223,14 @@ jobs:
       uses: actions/download-artifact@v3
       with:
         name: converted-nipype
-        path: pydra/tasks/freesurfer/auto
+        path: src/pydra/tasks/freesurfer/auto
     - name: Tag release with a post-release based on Nipype and Nipype2Pydra versions
       if: github.event_name == 'repository_dispatch'
       run: |
         TAG=$(git tag -l | tail -n 1 | awk -F post '{print $1}')
         POST=$(python -c "from pydra.tasks.freesurfer.auto._version import *; print(post_release)")
         git checkout $TAG
-        git add -f pydra/tasks/freesurfer/auto/_version.py
+        git add -f src/pydra/tasks/freesurfer/auto/_version.py
         git commit -am"added auto-generated version to make new tag for package version"
         git tag ${TAG}post${POST}    
     - name: Set up Python
@@ -237,12 +242,8 @@ jobs:
     - name: Strip auto package from gitignore so it is included in package
       run: |
         sed -i '/\/src\/pydra\/tasks\/freesurfer\/auto/d' .gitignore
-    - name: Build Pydra tasks source and wheel distributions
-      run: python -m build ./src
-    - name: Build fileformats source and wheel distributions
-      run: python -m build ./fileformats-medimage-freesurfer
-    - name: Build fileformats extras source and wheel distributions
-      run: python -m build ./fileformats-medimage-freesurfer-extras
+    - name: Build source and wheel distributions
+      run: python -m build ${{ matrix.pkg-dir }}
     - name: Check distributions
       run: twine check dist/*
     - uses: actions/upload-artifact@v3

From 3cbcdefd4eeae60ff7d8ec76ea848442b8db8005 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 6 Nov 2023 14:36:30 +1100
Subject: [PATCH 16/18] moved fileformats inside `fileformats` directory

---
 .github/workflows/pythonpackage.yaml          | 25 +++++++++++--------
 .gitignore                                    |  7 ++++--
 .../extras/medimage_freesurfer/_version.py    | 16 ------------
 .../medimage_freesurfer/_version.py           | 16 ------------
 nipype-auto-conv/generate                     |  8 +++---
 .../conftest.py                               |  0
 .../extras/medimage_freesurfer/__init__.py    |  0
 .../pyproject.toml                            |  0
 .../conftest.py                               |  0
 .../medimage_freesurfer/__init__.py           |  0
 .../pyproject.toml                            |  0
 11 files changed, 23 insertions(+), 49 deletions(-)
 delete mode 100644 fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/_version.py
 delete mode 100644 fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/_version.py
 rename {fileformats-medimage-freesurfer-extras => src-fileformats-extras}/conftest.py (100%)
 rename {fileformats-medimage-freesurfer-extras => src-fileformats-extras}/fileformats/extras/medimage_freesurfer/__init__.py (100%)
 rename {fileformats-medimage-freesurfer-extras => src-fileformats-extras}/pyproject.toml (100%)
 rename {fileformats-medimage-freesurfer => src-fileformats}/conftest.py (100%)
 rename {fileformats-medimage-freesurfer => src-fileformats}/fileformats/medimage_freesurfer/__init__.py (100%)
 rename {fileformats-medimage-freesurfer => src-fileformats}/pyproject.toml (100%)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index c7c95ad..faf4e17 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.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 }} "./src-fileformats[dev]" "./src-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 "./src-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 ./src-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 "./src-fileformats" "./src-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 ./src-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
@@ -194,7 +197,7 @@ jobs:
         python -m pip install --upgrade pip
     - name: Install task package
       run: |
-        pip install "./fileformats-medimage-freesurfer" "./fileformats-medimage-freesurfer-extras" "./src[test]"
+        pip install "./src-fileformats" "./src-fileformats-extras" "./src[test]"
         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__}')"
     - name: Test with pytest
@@ -205,7 +208,7 @@ jobs:
       if: ${{ always() }}
       with:
         files: .src/coverage.xml
-        # ,./fileformats-medimage-freesurfer/coverage.xml,./fileformats-medimage-freesurfer-extras/coverage.xml
+        # ,./src-fileformats/coverage.xml,./src-fileformats-extras/coverage.xml
         name: pydra-freesurfer
 
   deploy:
@@ -213,7 +216,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        pkg-dir: [".", "./fileformats/medimage-freesurfer", "./fileformats/medimage-freesurfer-extras"]
+        pkg-dir: [".", "./src-fileformats", "./src-fileformats-extras"]
     steps:
     - uses: actions/checkout@v3
       with:
diff --git a/.gitignore b/.gitignore
index 74c6a7e..2d8ee4f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -137,7 +137,10 @@ dmypy.json
 # Mac garbarge
 .DS_store
 
+# Auto-generated version files
 /src/pydra/tasks/freesurfer/_version.py
-/fileformts-medimage-freesurfer/fileformats/medimage_freesurfer/_version.py
-/fileformts-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/_version.py
+/src-fileformats/fileformats/medimage_freesurfer/_version.py
+/src-fileformts-extras/fileformats/extras/medimage_freesurfer/_version.py
+
+# Auto-converted (from Nipype) interfaces directory (needs to be stripped before packaging)
 /src/pydra/tasks/freesurfer/auto
diff --git a/fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/_version.py b/fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/_version.py
deleted file mode 100644
index 4b004e0..0000000
--- a/fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/_version.py
+++ /dev/null
@@ -1,16 +0,0 @@
-# file generated by setuptools_scm
-# don't change, don't track in version control
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple, Union
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-else:
-    VERSION_TUPLE = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-
-__version__ = version = '0.1.dev19+g7f136b2.d20231103'
-__version_tuple__ = version_tuple = (0, 1, 'dev19', 'g7f136b2.d20231103')
diff --git a/fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/_version.py b/fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/_version.py
deleted file mode 100644
index 4b004e0..0000000
--- a/fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/_version.py
+++ /dev/null
@@ -1,16 +0,0 @@
-# file generated by setuptools_scm
-# don't change, don't track in version control
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple, Union
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-else:
-    VERSION_TUPLE = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-
-__version__ = version = '0.1.dev19+g7f136b2.d20231103'
-__version_tuple__ = version_tuple = (0, 1, 'dev19', 'g7f136b2.d20231103')
diff --git a/nipype-auto-conv/generate b/nipype-auto-conv/generate
index dca1fb9..eadeaf1 100755
--- a/nipype-auto-conv/generate
+++ b/nipype-auto-conv/generate
@@ -31,7 +31,7 @@ sys.path.insert(0, str(SPECS_DIR))
 
 auto_init = f"# Auto-generated by {__file__}, do not edit as it will be overwritten\n\n"
 
-auto_dir = PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto"
+auto_dir = PKG_ROOT / "src" / "pydra" / "tasks" / PKG_NAME / "auto"
 if auto_dir.exists():
     shutil.rmtree(auto_dir)
 
@@ -54,11 +54,11 @@ for fspath in sorted(SPECS_DIR.glob("**/*.yaml")):
         callables_module=callables,  # type: ignore
         **spec,
     )
-    converter.generate(PKG_ROOT)
+    converter.generate(PKG_ROOT / "src")
     auto_init += f"from .{module_name} import {converter.task_name}\n"
 
 
-with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "_version.py", "w") as f:
+with open(auto_dir / "_version.py", "w") as f:
     f.write(
         f"""# Auto-generated by {__file__}, do not edit as it will be overwritten
 
@@ -68,5 +68,5 @@ post_release = (nipype_version + nipype2pydra_version).replace(".", "")
 """
     )
 
-with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "__init__.py", "w") as f:
+with open(auto_dir / "__init__.py", "w") as f:
     f.write(auto_init)
diff --git a/fileformats-medimage-freesurfer-extras/conftest.py b/src-fileformats-extras/conftest.py
similarity index 100%
rename from fileformats-medimage-freesurfer-extras/conftest.py
rename to src-fileformats-extras/conftest.py
diff --git a/fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/__init__.py b/src-fileformats-extras/fileformats/extras/medimage_freesurfer/__init__.py
similarity index 100%
rename from fileformats-medimage-freesurfer-extras/fileformats/extras/medimage_freesurfer/__init__.py
rename to src-fileformats-extras/fileformats/extras/medimage_freesurfer/__init__.py
diff --git a/fileformats-medimage-freesurfer-extras/pyproject.toml b/src-fileformats-extras/pyproject.toml
similarity index 100%
rename from fileformats-medimage-freesurfer-extras/pyproject.toml
rename to src-fileformats-extras/pyproject.toml
diff --git a/fileformats-medimage-freesurfer/conftest.py b/src-fileformats/conftest.py
similarity index 100%
rename from fileformats-medimage-freesurfer/conftest.py
rename to src-fileformats/conftest.py
diff --git a/fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/__init__.py b/src-fileformats/fileformats/medimage_freesurfer/__init__.py
similarity index 100%
rename from fileformats-medimage-freesurfer/fileformats/medimage_freesurfer/__init__.py
rename to src-fileformats/fileformats/medimage_freesurfer/__init__.py
diff --git a/fileformats-medimage-freesurfer/pyproject.toml b/src-fileformats/pyproject.toml
similarity index 100%
rename from fileformats-medimage-freesurfer/pyproject.toml
rename to src-fileformats/pyproject.toml

From 608d949b959d24c5d79873c198eabed462e64a55 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Tue, 7 Nov 2023 08:58:01 +1100
Subject: [PATCH 17/18] changed order of installation in devcheck

---
 .github/workflows/pythonpackage.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index faf4e17..c62e226 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -77,7 +77,7 @@ 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 }} "./src-fileformats[dev]" "./src-fileformats-extras[dev]" "./src[dev]"
+        pip install ${{ matrix.pip-flags }} "./src[dev]" "./src-fileformats[dev]" "./src-fileformats-extras[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__}')"

From 6617008b89578dd1a9cffeccfb24858bdd2da701 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Tue, 7 Nov 2023 09:02:47 +1100
Subject: [PATCH 18/18] moved install of fileformats into separate step

---
 .github/workflows/pythonpackage.yaml | 7 ++++---
 src-fileformats/pyproject.toml       | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
index c62e226..c0e8d94 100644
--- a/.github/workflows/pythonpackage.yaml
+++ b/.github/workflows/pythonpackage.yaml
@@ -77,11 +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 }} "./src[dev]" "./src-fileformats[dev]" "./src-fileformats-extras[dev]"
+        pip install "./src-fileformats[dev]" "./src-fileformats-extras[dev]"
+        pip install ${{ matrix.pip-flags }} "./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__}')"
+        python -c "import fileformats.medimage_freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        python -c "import fileformats.extras.medimage_freesurfer as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         
 
   fileformats-test:
diff --git a/src-fileformats/pyproject.toml b/src-fileformats/pyproject.toml
index 2cd17d0..167e292 100644
--- a/src-fileformats/pyproject.toml
+++ b/src-fileformats/pyproject.toml
@@ -4,7 +4,7 @@ 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"
+description = "Classes for representing different file formats solely used by the 'freesurfer' tool in Python classes for use in type hinting in data workflows"
 readme = "../README.rst"
 requires-python = ">=3.8"
 dependencies = [