From be62b033634e78a6800be4a480372651182aa26e Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Sat, 18 May 2024 20:13:08 +1000
Subject: [PATCH 01/23] fixed up fileformats deps

---
 related-packages/fileformats/pyproject.toml | 34 +++++----------------
 1 file changed, 8 insertions(+), 26 deletions(-)

diff --git a/related-packages/fileformats/pyproject.toml b/related-packages/fileformats/pyproject.toml
index d26d786..d148dc1 100644
--- a/related-packages/fileformats/pyproject.toml
+++ b/related-packages/fileformats/pyproject.toml
@@ -7,21 +7,11 @@ name = "fileformats-medimage-afni"
 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",
-    "fileformats-medimage >= 0.2"
-]
-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",
-]
+dependencies = ["fileformats >= 0.4", "fileformats-medimage >= 0.2"]
+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",
@@ -39,19 +29,13 @@ classifiers = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
-dev = [
-    "black",
-    "pre-commit",
-    "codespell",
-    "flake8",
-    "flake8-pyproject",
-]
+dev = ["black", "pre-commit", "codespell", "flake8", "flake8-pyproject"]
 test = [
     "pytest >=6.2.5",
     "pytest-env>=0.6.2",
     "pytest-cov>=2.12.1",
     "codecov",
-    "fileformats-medimage-CHANGME-extras",
+    "fileformats-medimage-afni-extras",
 ]
 
 [project.urls]
@@ -76,9 +60,7 @@ ignore-words = ".codespell-ignorewords"
 
 [tool.flake8]
 doctests = true
-per-file-ignores = [
-    "__init__.py:F401"
-]
+per-file-ignores = ["__init__.py:F401"]
 max-line-length = 88
 select = "C,E,F,W,B,B950"
 extend-ignore = ['E203', 'E501', 'E129']

From a01349510967e73fb27f64635e82747501a7e71a Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Sat, 18 May 2024 22:26:36 +1000
Subject: [PATCH 02/23] added version imports to fileformats

---
 .../fileformats/extras/medimage_afni/__init__.py                | 2 ++
 .../fileformats/fileformats/medimage_afni/__init__.py           | 1 +
 2 files changed, 3 insertions(+)

diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
index 38f073f..1d9732a 100644
--- a/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
+++ b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
@@ -15,6 +15,8 @@
     Unit errts+tlrc,
     Gii,
 )
+from ._version import __version__
+
 
 
 
diff --git a/related-packages/fileformats/fileformats/medimage_afni/__init__.py b/related-packages/fileformats/fileformats/medimage_afni/__init__.py
index 87e2dfe..5515d4a 100644
--- a/related-packages/fileformats/fileformats/medimage_afni/__init__.py
+++ b/related-packages/fileformats/fileformats/medimage_afni/__init__.py
@@ -1,4 +1,5 @@
 from fileformats.generic import File
+from ._version import __version__
 
 class OneD(File):
     ext = ".1D"

From ee3741c7b327d2f8b77438b47bb00c588f0e85a4 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Sat, 18 May 2024 22:35:25 +1000
Subject: [PATCH 03/23] fixed up fileformats

---
 .../extras/medimage_afni/__init__.py          | 32 ++++---------------
 .../fileformats/medimage_afni/__init__.py     |  2 +-
 2 files changed, 8 insertions(+), 26 deletions(-)

diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
index 1d9732a..66c7315 100644
--- a/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
+++ b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
@@ -3,17 +3,13 @@
 from random import Random
 from fileformats.core import FileSet
 from fileformats.medimage_afni import (
-    Oned,
+    OneD,
     Dset,
-    Nii[0],
-    Threed,
+    ThreeD,
     Head,
-    Ncorr,
+    NCorr,
     R1,
     All1,
-    Oned,
-    Unit errts+tlrc,
-    Gii,
 )
 from ._version import __version__
 
@@ -21,7 +17,7 @@
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_oned_data(oned: Oned, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+def gen_sample_oned_data(oned: OneD, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
     raise NotImplementedError
 
 
@@ -31,12 +27,7 @@ def gen_sample_dset_data(dset: Dset, dest_dir: Path, seed: ty.Union[int, Random]
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_nii[0]_data(nii[0]: Nii[0], dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
-    raise NotImplementedError
-
-
-@FileSet.generate_sample_data.register
-def gen_sample_threed_data(threed: Threed, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+def gen_sample_threed_data(threed: ThreeD, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
     raise NotImplementedError
 
 
@@ -46,7 +37,7 @@ def gen_sample_head_data(head: Head, dest_dir: Path, seed: ty.Union[int, Random]
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_ncorr_data(ncorr: Ncorr, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+def gen_sample_ncorr_data(ncorr: NCorr, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
     raise NotImplementedError
 
 
@@ -61,15 +52,6 @@ def gen_sample_all1_data(all1: All1, dest_dir: Path, seed: ty.Union[int, Random]
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_oned_data(oned: Oned, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+def gen_sample_oned_data(oned: OneD, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
     raise NotImplementedError
 
-
-@FileSet.generate_sample_data.register
-def gen_sample_unit errts+tlrc_data(unit errts+tlrc: Unit errts+tlrc, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
-    raise NotImplementedError
-
-
-@FileSet.generate_sample_data.register
-def gen_sample_gii_data(gii: Gii, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
-    raise NotImplementedError
diff --git a/related-packages/fileformats/fileformats/medimage_afni/__init__.py b/related-packages/fileformats/fileformats/medimage_afni/__init__.py
index 5515d4a..cfc3154 100644
--- a/related-packages/fileformats/fileformats/medimage_afni/__init__.py
+++ b/related-packages/fileformats/fileformats/medimage_afni/__init__.py
@@ -22,7 +22,7 @@ class Head(File):
     binary = True
 
 
-class Ncorr(File):
+class NCorr(File):
     ext = ".ncorr"
     binary = True
 

From abd140e2e73e248f876f22d55275a308ca7216aa Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Sat, 18 May 2024 22:40:58 +1000
Subject: [PATCH 04/23] fixed up fileformats again

---
 nipype-auto-conv/specs/interfaces/net_corr.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype-auto-conv/specs/interfaces/net_corr.yaml b/nipype-auto-conv/specs/interfaces/net_corr.yaml
index 5b04d5e..5cfbbc4 100644
--- a/nipype-auto-conv/specs/interfaces/net_corr.yaml
+++ b/nipype-auto-conv/specs/interfaces/net_corr.yaml
@@ -49,7 +49,7 @@ inputs:
     # type=file|default=<undefined>: can include a whole brain mask within which to calculate correlation. Otherwise, data should be masked already
     weight_ts: generic/file
     # type=file|default=<undefined>: input a 1D file WTS of weights that will be applied multiplicatively to each ROI's average time series. WTS can be a column- or row-file of values, but it must have the same length as the input time series volume. If the initial average time series was A[n] for n=0,..,(N-1) time points, then applying a set of weights W[n] of the same length from WTS would produce a new time series:  B[n] = A[n] * W[n]
-    out_file: medimage-afni/ncorr
+    out_file: medimage-afni/n-corr
     # type=file|default=<undefined>: output file name part
   metadata:
   # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)

From 33b60cb0c7fe669143538e295bd73e08870fb7f7 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Sat, 18 May 2024 22:43:43 +1000
Subject: [PATCH 05/23] fixed up fileformats

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

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index c00af6b..4cfc58b 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -107,7 +107,7 @@ jobs:
         python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
     - name: Test fileformats with pytest
       run: |
-        cd ./fileformats
+        cd ./related-packages/fileformats
         pytest -sv --cov fileformats.medimage_afni --cov fileformats.extras.medimage_afni --cov-report xml .
 
   test:

From 1d798badbac0981e1a24fbe4ae37c6a9be3c558b Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Sat, 18 May 2024 22:50:21 +1000
Subject: [PATCH 06/23] touched up ci-cd

---
 .github/workflows/ci-cd.yaml | 52 ++++++++++++++++++------------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index 4cfc58b..1f959a6 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -84,34 +84,34 @@ jobs:
         python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.extras.medimage_afni 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 "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
-        python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-    - name: Test fileformats with pytest
-      run: |
-        cd ./related-packages/fileformats
-        pytest -sv --cov fileformats.medimage_afni --cov fileformats.extras.medimage_afni --cov-report xml .
+  # 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 "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
+  #       python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+  #   - name: Test fileformats with pytest
+  #     run: |
+  #       cd ./related-packages/fileformats
+  #       pytest -sv --cov fileformats.medimage_afni --cov fileformats.extras.medimage_afni --cov-report xml .
 
   test:
-    needs: [nipype-conv, fileformats-test]
+    needs: [nipype-conv]
     runs-on: ubuntu-22.04
     strategy:
       matrix:

From 08ff445258caabe30f01e9fb3f032d63756dedc7 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Sat, 18 May 2024 23:17:57 +1000
Subject: [PATCH 07/23] fixed up fileset generators

---
 .../extras/medimage_afni/__init__.py          | 27 ++++++-------------
 .../fileformats/medimage_afni/__init__.py     |  6 ++---
 2 files changed, 11 insertions(+), 22 deletions(-)

diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
index 66c7315..204d50e 100644
--- a/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
+++ b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
@@ -1,7 +1,4 @@
-from pathlib import Path
-import typing as ty
-from random import Random
-from fileformats.core import FileSet
+from fileformats.core import FileSet, SampleFileGenerator
 from fileformats.medimage_afni import (
     OneD,
     Dset,
@@ -14,44 +11,36 @@
 from ._version import __version__
 
 
-
-
 @FileSet.generate_sample_data.register
-def gen_sample_oned_data(oned: OneD, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+def gen_sample_oned_data(oned: OneD, generator: SampleFileGenerator):
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_dset_data(dset: Dset, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+def gen_sample_dset_data(dset: Dset, generator: SampleFileGenerator):
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_threed_data(threed: ThreeD, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+def gen_sample_threed_data(threed: ThreeD, generator: SampleFileGenerator):
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_head_data(head: Head, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+def gen_sample_head_data(head: Head, generator: SampleFileGenerator):
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_ncorr_data(ncorr: NCorr, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+def gen_sample_ncorr_data(ncorr: NCorr, generator: SampleFileGenerator):
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_r1_data(r1: R1, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+def gen_sample_r1_data(r1: R1, generator: SampleFileGenerator):
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_all1_data(all1: All1, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+def gen_sample_all1_data(all1: All1, generator: SampleFileGenerator):
     raise NotImplementedError
-
-
-@FileSet.generate_sample_data.register
-def gen_sample_oned_data(oned: OneD, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
-    raise NotImplementedError
-
diff --git a/related-packages/fileformats/fileformats/medimage_afni/__init__.py b/related-packages/fileformats/fileformats/medimage_afni/__init__.py
index cfc3154..1741f42 100644
--- a/related-packages/fileformats/fileformats/medimage_afni/__init__.py
+++ b/related-packages/fileformats/fileformats/medimage_afni/__init__.py
@@ -1,5 +1,6 @@
 from fileformats.generic import File
-from ._version import __version__
+from ._version import __version__  # noqa
+
 
 class OneD(File):
     ext = ".1D"
@@ -17,6 +18,7 @@ class ThreeD(File):
     binary = True
     alternate_exts = (".3d",)
 
+
 class Head(File):
     ext = ".HEAD"
     binary = True
@@ -35,5 +37,3 @@ class R1(File):
 class All1(File):
     ext = ".all1"
     binary = True
-
-

From a1d6657fb0ac5d6b175297cdd74de86e88e8a4a2 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Sat, 18 May 2024 23:27:53 +1000
Subject: [PATCH 08/23] deleted freesurfer install from ci-cd

---
 .github/workflows/ci-cd.yaml | 31 ++-----------------------------
 1 file changed, 2 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index 1f959a6..5b6f90d 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -121,35 +121,8 @@ jobs:
       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::afni-linux-ubuntu22_amd64-7.4.1"
-    - name: Cache FreeSurfer
-      uses: actions/cache@v2
-      with:
-        path: $HOME/downloads/afni
-        key: ${{ steps.cache-key.outputs.key }}
-        restore-keys: |
-          afni-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/afni
-        curl -s -o $HOME/downloads/afni/afni-linux-ubuntu22_amd64-7.4.1.tar.gz https://surfer.nmr.mgh.harvard.edu/pub/dist/afni/7.4.1/afni-linux-ubuntu22_amd64-7.4.1.tar.gz
-      shell: bash
-    - name: Install Freesurfer
-      env:
-        FREESURFER_LICENCE: ${{ secrets.FREESURFER_LICENCE }}
-      run: |
-        pushd $HOME/downloads/afni
-        tar -zxpf afni-linux-ubuntu22_amd64-7.4.1.tar.gz
-        mv afni $HOME/
-        popd
-        export FREESURFER_HOME=$HOME/afni
-        source $FREESURFER_HOME/SetUpFreeSurfer.sh
-        echo $FREESURFER_LICENCE > $FREESURFER_HOME/license.txt
-        export PATH=$FREESURFER_HOME/bin:$PATH
-    - uses: actions/checkout@v3
+
+    - uses: actions/checkout@v4
     - 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}')

From 2bc73d6474434dffd16205f448e5e455b90e5d45 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Sat, 18 May 2024 23:29:42 +1000
Subject: [PATCH 09/23] more touch ups of fileformats

---
 .../extras/medimage_afni/__init__.py          | 28 ++++++++++++++-----
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
index 204d50e..8deca1e 100644
--- a/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
+++ b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/__init__.py
@@ -1,3 +1,5 @@
+import typing as ty
+from pathlib import Path
 from fileformats.core import FileSet, SampleFileGenerator
 from fileformats.medimage_afni import (
     OneD,
@@ -12,35 +14,47 @@
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_oned_data(oned: OneD, generator: SampleFileGenerator):
+def gen_sample_oned_data(
+    oned: OneD, generator: SampleFileGenerator
+) -> ty.Iterable[Path]:
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_dset_data(dset: Dset, generator: SampleFileGenerator):
+def gen_sample_dset_data(
+    dset: Dset, generator: SampleFileGenerator
+) -> ty.Iterable[Path]:
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_threed_data(threed: ThreeD, generator: SampleFileGenerator):
+def gen_sample_threed_data(
+    threed: ThreeD, generator: SampleFileGenerator
+) -> ty.Iterable[Path]:
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_head_data(head: Head, generator: SampleFileGenerator):
+def gen_sample_head_data(
+    head: Head, generator: SampleFileGenerator
+) -> ty.Iterable[Path]:
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_ncorr_data(ncorr: NCorr, generator: SampleFileGenerator):
+def gen_sample_ncorr_data(
+    ncorr: NCorr, generator: SampleFileGenerator
+) -> ty.Iterable[Path]:
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_r1_data(r1: R1, generator: SampleFileGenerator):
+def gen_sample_r1_data(r1: R1, generator: SampleFileGenerator) -> ty.Iterable[Path]:
     raise NotImplementedError
 
 
 @FileSet.generate_sample_data.register
-def gen_sample_all1_data(all1: All1, generator: SampleFileGenerator):
+def gen_sample_all1_data(
+    all1: All1, generator: SampleFileGenerator
+) -> ty.Iterable[Path]:
     raise NotImplementedError

From be431c4dd165e2df088d70b6988d16dd7deaef99 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Sat, 18 May 2024 23:50:03 +1000
Subject: [PATCH 10/23] fixed up dependencies

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 4b96265..6f0f3e3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,6 +44,7 @@ doc = [
     "sphinxcontrib-versioning",
 ]
 test = [
+    "nipype2pydra",
     "pytest >= 4.4.0",
     "pytest-cov",
     "pytest-env",

From 10289d1a7c5eebc2b890944bc9f22cd7faf0974f Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Sat, 18 May 2024 23:50:54 +1000
Subject: [PATCH 11/23] more deps

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6f0f3e3..f42078c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,8 @@ dependencies = [
     "fileformats >=0.8.3",
     "fileformats-datascience >=0.1",
     "fileformats-medimage >=0.4.1",
-    "fileformats-medimage-afni"
+    "fileformats-medimage-afni",
+    "looseversion"
 ]
 license = {file = "LICENSE"}
 authors = [{name = "Nipype developers", email = "neuroimaging@python.org"}]

From 6646979f60b8bc4d1b105f7a670e3302f29afc48 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 10:33:35 +1000
Subject: [PATCH 12/23] fixed up version handling in package __init__

---
 pydra/tasks/afni/__init__.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/pydra/tasks/afni/__init__.py b/pydra/tasks/afni/__init__.py
index 993f5b2..b209d29 100644
--- a/pydra/tasks/afni/__init__.py
+++ b/pydra/tasks/afni/__init__.py
@@ -19,15 +19,16 @@
     )
 if "nipype" not in __version__:
     try:
-        from .auto._version import nipype_version, nipype2pydra_version
-    except ImportError:
+        from .auto._post_release import src_pkg_version, nipype2pydra_version
+    except ImportError as e:
+        raise 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')}` "
             "to generated the converted Nipype interfaces in pydra.tasks.afni.auto"
         )
     else:
-        n_ver = nipype_version.replace(".", "_")
+        n_ver = src_pkg_version.replace(".", "_")
         n2p_ver = nipype2pydra_version.replace(".", "_")
         __version__ += (
             "_" if "+" in __version__ else "+"

From bbf417508312cca2631cac56e06e777b4f375964 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 10:41:56 +1000
Subject: [PATCH 13/23] touching up ci-cd and version handling

---
 .github/workflows/ci-cd.yaml | 56 +++++++++++++++++++-----------------
 pydra/tasks/afni/__init__.py |  4 +--
 2 files changed, 31 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index 5b6f90d..c3568ea 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -43,7 +43,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.11']  # Check oldest and newest versions
+        python-version: ['3.8', '3.12']  # Check oldest and newest versions
         pip-flags: ['', '--editable']
         pydra:
         - 'pydra'
@@ -84,38 +84,38 @@ jobs:
         python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.extras.medimage_afni 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 "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
-  #       python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-  #   - name: Test fileformats with pytest
-  #     run: |
-  #       cd ./related-packages/fileformats
-  #       pytest -sv --cov fileformats.medimage_afni --cov fileformats.extras.medimage_afni --cov-report xml .
+  fileformats-test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.12']
+    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 "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
+        python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+    - name: Test fileformats with pytest
+      run: >-
+        pytest ./related-packages/fileformats -sv --cov fileformats.medimage_afni
+        --cov fileformats.extras.medimage_afni --cov-report xml .
 
   test:
     needs: [nipype-conv]
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ['3.8']  # '3.11'
+        python-version: ['3.8', '3.12']
     steps:
     - name: Removed unnecessary tools to free space
       run: |
@@ -131,6 +131,8 @@ jobs:
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
+    - name: Show package contents
+      run: tree ./pydra
     - name: Strip auto package from gitignore so it is included in package
       run: |
         sed -i '/\/src\/pydra\/tasks\/afni\/auto/d' .gitignore
diff --git a/pydra/tasks/afni/__init__.py b/pydra/tasks/afni/__init__.py
index b209d29..89ab108 100644
--- a/pydra/tasks/afni/__init__.py
+++ b/pydra/tasks/afni/__init__.py
@@ -5,6 +5,7 @@
 >>> import pydra.engine
 >>> import pydra.tasks.afni
 """
+
 from warnings import warn
 from pathlib import Path
 
@@ -20,8 +21,7 @@
 if "nipype" not in __version__:
     try:
         from .auto._post_release import src_pkg_version, nipype2pydra_version
-    except ImportError as e:
-        raise e
+    except ImportError:
         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 2be7805718c55c0dcdad2286b8d44665fbf4e2fa Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 10:47:49 +1000
Subject: [PATCH 14/23] touched up ci-cd

---
 .github/workflows/ci-cd.yaml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index c3568ea..728f165 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -107,7 +107,7 @@ jobs:
         python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
     - name: Test fileformats with pytest
       run: >-
-        pytest ./related-packages/fileformats -sv --cov fileformats.medimage_afni
+        pytest ./related-packages -sv --cov fileformats.medimage_afni
         --cov fileformats.extras.medimage_afni --cov-report xml .
 
   test:
@@ -150,8 +150,7 @@ jobs:
         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/afni \
-            --cov pydra.tasks.afni --cov-report xml
+        pytest -sv ./pydra/tasks/afni --cov pydra.tasks.afni --cov-report xml
     - uses: codecov/codecov-action@v3
       if: ${{ always() }}
       with:

From 62bf0fc10852c8862658026215c6f480c7785568 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 10:54:45 +1000
Subject: [PATCH 15/23] added fileformats tests

---
 .../tests/test_generate_sample_data.py        | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 related-packages/fileformats-extras/fileformats/extras/medimage_afni/tests/test_generate_sample_data.py

diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_afni/tests/test_generate_sample_data.py b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/tests/test_generate_sample_data.py
new file mode 100644
index 0000000..2264b1f
--- /dev/null
+++ b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/tests/test_generate_sample_data.py
@@ -0,0 +1,45 @@
+import pytest
+from fileformats.medimage_anfi import (
+    OneD,
+    Dset,
+    ThreeD,
+    Head,
+    NCorr,
+    R1,
+    All1,
+)
+
+
+@pytest.mark.xfail(reason="generate_sample_data not implemented")
+def test_generate_one_d_data():
+    assert isinstance(OneD.sample(), OneD)
+
+
+@pytest.mark.xfail(reason="generate_sample_data not implemented")
+def test_generate_three_d_data():
+    assert isinstance(ThreeD.sample(), ThreeD)
+
+
+@pytest.mark.xfail(reason="generate_sample_data not implemented")
+def test_generate_dset_data():
+    assert isinstance(Dset.sample(), Dset)
+
+
+@pytest.mark.xfail(reason="generate_sample_data not implemented")
+def test_generate_head_data():
+    assert isinstance(Head.sample(), Head)
+
+
+@pytest.mark.xfail(reason="generate_sample_data not implemented")
+def test_generate_ncorr_data():
+    assert isinstance(NCorr.sample(), NCorr)
+
+
+@pytest.mark.xfail(reason="generate_sample_data not implemented")
+def test_generate_r1_data():
+    assert isinstance(R1.sample(), R1)
+
+
+@pytest.mark.xfail(reason="generate_sample_data not implemented")
+def test_generate_all1_data():
+    assert isinstance(All1.sample(), All1)

From 198951366ca82303b4689ed06a389b54ba939fba Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 10:58:55 +1000
Subject: [PATCH 16/23] debugging ci-cd

---
 .github/workflows/ci-cd.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index 728f165..c6b5b23 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -80,6 +80,7 @@ jobs:
         pip install "./related-packages/fileformats[dev]" "related-packages/fileformats-extras[dev]"
         pip install ${{ matrix.pip-flags }} ".[dev]"
         python -c "import pydra.tasks.afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        python -c "import pydra.tasks.afni.auto as m; print(f'{m.__name__} @ {m.__file__}')"
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.extras.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
@@ -147,6 +148,7 @@ jobs:
       run: |
         pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]"
         python -c "import pydra.tasks.afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        python -c "import pydra.tasks.afni.auto as m; print(f'{m.__name__} @ {m.__file__}')"
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
     - name: Test with pytest
       run: |

From 0ed9c8311101d1cdc1d1e49312a4ee3ebb0f859e Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 11:07:53 +1000
Subject: [PATCH 17/23] fixed up fileformats afni import

---
 .../extras/medimage_afni/tests/test_generate_sample_data.py     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_afni/tests/test_generate_sample_data.py b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/tests/test_generate_sample_data.py
index 2264b1f..d436d21 100644
--- a/related-packages/fileformats-extras/fileformats/extras/medimage_afni/tests/test_generate_sample_data.py
+++ b/related-packages/fileformats-extras/fileformats/extras/medimage_afni/tests/test_generate_sample_data.py
@@ -1,5 +1,5 @@
 import pytest
-from fileformats.medimage_anfi import (
+from fileformats.medimage_afni import (
     OneD,
     Dset,
     ThreeD,

From c2d05ebca519955e3f78d3977dbc574e52cec293 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 11:20:45 +1000
Subject: [PATCH 18/23] copying across some updates to ci-cd from pydra-ants

---
 .github/workflows/ci-cd.yaml | 62 +++++++++++++++++++++++++-----------
 .gitignore                   |  1 -
 2 files changed, 43 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index c6b5b23..6a35b6e 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -9,31 +9,46 @@ name: CI/CD
 on:
   push:
     branches: [ main, develop ]
-    tags: [ '*' ]
   pull_request:
     branches: [ main, develop ]
+  release:
+    types: [published]
   repository_dispatch:
-    types: [create-release]
+    types: [create-post-release]
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
 
 jobs:
 
   nipype-conv:
     runs-on: ubuntu-latest
     steps:
+
     - name: Checkout
-      uses: actions/checkout@v3
-    - name: Revert version to most recent tag on upstream update
+      uses: actions/checkout@v4
+
+    - name: Revert version to most recent version 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
+      run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
     - name: Install build dependencies
       run: python -m pip install --upgrade pip
+
     - name: Install requirements
-      run: python -m pip install ./related-packages/fileformats -r ./nipype-auto-conv/requirements.txt
+      run: python -m pip install -r ./nipype-auto-conv/requirements.txt
+
     - name: Run automatic Nipype > Pydra conversion
       run: ./nipype-auto-conv/generate
-    - uses: actions/upload-artifact@v3
+
+    - uses: actions/upload-artifact@v4
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
@@ -50,31 +65,37 @@ jobs:
         - '--editable git+https://github.com/nipype/pydra.git#egg=pydra'
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
-    - name: Revert version to most recent tag on upstream update
+      uses: actions/checkout@v4
+
+    - name: Revert version to most recent version tag on Nipype or Nipype2Pydra update
       if: github.event_name == 'repository_dispatch'
-      run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')    
-    - name: Download tasks converted from Nipype 
-      uses: actions/download-artifact@v3
+      run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
+
+    - name: Download tasks converted from Nipype
+      uses: actions/download-artifact@v4
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
     - name: Strip auto package from gitignore so it is included in package
       run: |
         sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
+        sed -i '/^_version.py/d' .gitignore
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install build dependencies
       run: |
         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: |
         pip install "./related-packages/fileformats[dev]" "related-packages/fileformats-extras[dev]"
@@ -126,9 +147,10 @@ jobs:
     - uses: actions/checkout@v4
     - 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: Download tasks converted from Nipype 
-      uses: actions/download-artifact@v3
+      run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
+
+    - name: Download tasks converted from Nipype
+      uses: actions/download-artifact@v4
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
@@ -138,12 +160,14 @@ jobs:
       run: |
         sed -i '/\/src\/pydra\/tasks\/afni\/auto/d' .gitignore
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install build dependencies
       run: |
         python -m pip install --upgrade pip
+
     - name: Install task package
       run: |
         pip install "./related-packages/fileformats" "./related-packages/fileformats-extras" ".[test]"
diff --git a/.gitignore b/.gitignore
index 36ae412..7f12be7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -138,6 +138,5 @@ dmypy.json
 .DS_store
 
 /pydra/tasks/afni/auto
-/pydra/tasks/afni/nipype_ports
 /pydra/tasks/afni/_version.py
 /related-packages/**/_version.py
\ No newline at end of file

From fe34622a2922498154216ec3b6c81b08691b682a Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 11:23:37 +1000
Subject: [PATCH 19/23] added fileformats to nipype-conv ci

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

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index 6a35b6e..8302726 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -43,7 +43,7 @@ jobs:
       run: python -m pip install --upgrade pip
 
     - name: Install requirements
-      run: python -m pip install -r ./nipype-auto-conv/requirements.txt
+      run: python -m pip install -r ./nipype-auto-conv/requirements.txt ./related-packages/fileformats
 
     - name: Run automatic Nipype > Pydra conversion
       run: ./nipype-auto-conv/generate

From 5423234f023d1714d3a7fafcf3212e5c2638ca28 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 12:15:52 +1000
Subject: [PATCH 20/23] fixed up sed in ci-cd to unignore auto directory

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

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index 8302726..c7da5f9 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -158,7 +158,7 @@ jobs:
       run: tree ./pydra
     - name: Strip auto package from gitignore so it is included in package
       run: |
-        sed -i '/\/src\/pydra\/tasks\/afni\/auto/d' .gitignore
+        sed -i '/\/pydra\/tasks\/afni\/auto/d' .gitignore
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:

From 02d9242a55980abf4765aec603f6f87aff4666d9 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 12:40:20 +1000
Subject: [PATCH 21/23] fixed up deploy download of artefacts

---
 .github/workflows/ci-cd.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index c7da5f9..111ca21 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -256,7 +256,7 @@ jobs:
         submodules: recursive
         fetch-depth: 0
     - name: Download tasks converted from Nipype 
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: converted-nipype
         path: pydra/tasks/afni/auto
@@ -282,7 +282,7 @@ jobs:
       run: python -m build .
     - name: Check distributions
       run: twine check dist/*
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: distributions
         path: dist/

From 6c104bfd291e6f64807edbfde07cfa20142a5903 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 12:53:58 +1000
Subject: [PATCH 22/23] cleaned up readme

---
 README.md  | 48 ------------------------------------------------
 README.rst |  4 ++--
 2 files changed, 2 insertions(+), 50 deletions(-)
 delete mode 100644 README.md

diff --git a/README.md b/README.md
deleted file mode 100644
index 5e96855..0000000
--- a/README.md
+++ /dev/null
@@ -1,48 +0,0 @@
-# Pydra task package for afni
-
-This package contains a collection of Pydra task interfaces for afni. The basis for
-which have been semi-automatically 
-boo
-
-## Tests
-
-This package comes with a default set of test modules, and we encourage users to use pytest.
-Tests can be discovered and run using:
-
-```
-pytest --doctest-modules pydra/tasks/*
-```
-
-## Continuous integration
-
-This template uses [GitHub Actions](https://docs.github.com/en/actions/) to run tests. To simulate
-several plausible development or installation environments, we test over all Python versions
-supported by Pydra, and install Pydra and the current package in both standard and
-[editable](https://pip.pypa.io/en/stable/reference/pip_install/#editable-installs) modes.
-
-The combination of standard/editable is in particular designed to ensure that namespace packaging
-does not break. We strongly recommend keeping these tests in place for this reason, as one
-non-compliant package can potentially affect Pydra or other task packages.
-
-In addition to verifying installations do not break or conflict, pytest is run on the package,
-including all tests found in `test/` directories and [doctests].
-
-Finally, packages are built and uploaded as artifacts for inspection. When a tag is pushed,
-the packages are uploaded to PyPI if a valid [API token](https://pypi.org/help/#apitoken) is placed
-in the [repository secrets](https://docs.github.com/en/actions/reference/encrypted-secrets).
-
-[doctests]: https://docs.python.org/3/library/doctest.html
-
-# Contributing to this package
-
-## For developers
-
-Install repo in developer mode from the source directory. It is also useful to
-install pre-commit to take care of styling via [black](https://black.readthedocs.io/):
-
-```
-pip install -e .[dev]
-pre-commit install
-```
-
-
diff --git a/README.rst b/README.rst
index f1d5683..90b9765 100644
--- a/README.rst
+++ b/README.rst
@@ -1,6 +1,6 @@
-===============================
+===========================
 Pydra task package for afni
-===============================
+===========================
 
 .. image:: https://github.com/nipype/pydra-afni/actions/workflows/pythonpackage.yaml/badge.svg
    :target: https://github.com/nipype/pydra-afni/actions/workflows/pythonpackage.yaml

From 5c231489ec766e5bf3bfa66bae10650b28a71bc7 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Mon, 20 May 2024 13:08:35 +1000
Subject: [PATCH 23/23] touched up readme

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 90b9765..7c8288c 100644
--- a/README.rst
+++ b/README.rst
@@ -78,7 +78,7 @@ ensure consistent code-style and quality.
 .. code-block::
 
    $ pip install -e .[test,dev]
-$ pre-commit install
+   $ pre-commit install
 
 Next install the requirements for running the auto-conversion script and generate the
 Pydra task interfaces from their Nipype counterparts