renamed references to pydra-* to pydra-tasks-*

tclose · tclose · commit 734630812369 · 2025-09-17T23:20:10.000+10:00
diff --git a/nipype2pydra/cli/pkg_gen.py b/nipype2pydra/cli/pkg_gen.py
@@ -308,7 +308,7 @@ def pkg_gen(
             for example_pkg_name in example_pkg_names:
                 specs_dir = (
                     output_dir
-                    / ("pydra-" + example_pkg_name)
+                    / ("pydra-tasks-" + example_pkg_name)
                     / "nipype-auto-conv"
                     / "specs"
                 )
diff --git a/nipype2pydra/package.py b/nipype2pydra/package.py
@@ -1162,7 +1162,7 @@ def write_pkg_inits(
     from ._version import __version__
 except ImportError:
     raise RuntimeError(
-        "pydra-{pkg} has not been properly installed, please run "
+        "pydra-tasks-{pkg} has not been properly installed, please run "
         f"`pip install -e {str(pkg_path)}` to install a development version"
     )
 if "nipype" not in __version__:
diff --git a/nipype2pydra/pkg_gen/__init__.py b/nipype2pydra/pkg_gen/__init__.py
@@ -611,7 +611,7 @@ def _fields_stub(cls, name, category_class, values=None):
 
 
 def download_tasks_template(output_path: Path):
-    """Downloads the latest pydra-template to the output path"""
+    """Downloads the latest pydra-tasks-template to the output path"""
     output_path.parent.mkdir(parents=True, exist_ok=True)
 
     release_url = (
diff --git a/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-interface.yaml b/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-interface.yaml
@@ -183,7 +183,7 @@ jobs:
       if: ${{ always() }}
       with:
         files: coverage.xml
-        name: pydra-CHANGEME
+        name: pydra-tasks-CHANGEME
 
 
   deploy-fileformats:
@@ -391,7 +391,7 @@ jobs:
         if: github.event_name == 'release' || github.event_name == 'repository_dispatch'
         run: >-
           curl -XPOST -u "${{ env.POST_RELEASE_PAT }}" -H "Accept: application/vnd.github.everest-preview+json"
-          "https://api.github.com/repos/nipype/pydra-CHANGEME/dispatches"
+          "https://api.github.com/repos/nipype/pydra-tasks-CHANGEME/dispatches"
           -d '{
             "event_type": "progress-report",
             "client_payload": ${{ steps.generate-report.output.progress_report }}
diff --git a/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-workflow.yaml b/nipype2pydra/pkg_gen/resources/templates/gh_workflows/ci-cd-workflow.yaml
@@ -174,7 +174,7 @@ jobs:
       if: ${{ always() }}
       with:
         files: coverage.xml
-        name: pydra-CHANGEME
+        name: pydra-tasks-CHANGEME
 
 
   deploy:
diff --git a/nipype2pydra/pkg_gen/resources/templates/init.py b/nipype2pydra/pkg_gen/resources/templates/init.py
@@ -14,7 +14,7 @@
     from ._version import __version__
 except ImportError:
     raise RuntimeError(
-        "pydra-CHANGEME has not been properly installed, please run "
+        "pydra-tasks-CHANGEME has not been properly installed, please run "
         f"`pip install -e {str(pkg_path)}` to install a development version"
     )
 if "post" not in __version__:
diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/pyproject.toml b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats-extras/pyproject.toml
@@ -58,7 +58,7 @@ converters = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-CHANGEME"
+repository = "https://github.com/nipype/pydra-tasks-CHANGEME"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/pyproject.toml b/nipype2pydra/pkg_gen/resources/templates/related-packages/fileformats/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-CHANGEME"
+repository = "https://github.com/nipype/pydra-tasks-CHANGEME"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/nipype2pydra/tests/test_package.py b/nipype2pydra/tests/test_package.py
@@ -12,23 +12,23 @@
     "niworkflows": [
         "bids",
         "templateflow",
-        "pydra-ants",
-        "pydra-afni",
+        "pydra-tasks-ants",
+        "pydra-tasks-afni",
     ],
     "mriqc": [
         "nipype2pydra",
-        "pydra-ants",
-        "pydra-afni",
-        "pydra-fsl",
-        "pydra-mrtrix3 >=3.0.3a0",
+        "pydra-tasks-ants",
+        "pydra-tasks-afni",
+        "pydra-tasks-fsl",
+        "pydra-tasks-mrtrix3 >=3.1.0a1",
         "fileformats-medimage-afni-extras",
         "fileformats-medimage-mrtrix3-extras",
         "fileformats-medimage-fsl-extras",
         "statsmodels",
         "dipy",
         "bids",
-        "pydra-niworkflows",
-        "pydra-nireports",
+        "pydra-tasks-niworkflows",
+        "pydra-tasks-nireports",
         "matplotlib",
         "seaborn",
         "templateflow",
@@ -67,7 +67,7 @@ def test_package_complete(package_spec, cli_runner, tmp_path, tasks_template_arg
         + tasks_template_args,
     )
     assert result.exit_code == 0, show_cli_trace(result)
-    pkg_root = repo_output / f"pydra-{pkg_name}"
+    pkg_root = repo_output / f"pydra-tasks-{pkg_name}"
     assert pkg_root.exists()
 
     pyproject_fspath = pkg_root / "pyproject.toml"
@@ -104,10 +104,10 @@ def test_package_complete(package_spec, cli_runner, tmp_path, tasks_template_arg
     pip_output = pip_output.decode("utf-8")
     assert (
         not p.returncode
-    ), f"Failed to install package pydra-{pkg_name} with command:\n{' '.join(pip_cmd)}:\n\n{pip_output}"
+    ), f"Failed to install package pydra-tasks-{pkg_name} with command:\n{' '.join(pip_cmd)}:\n\n{pip_output}"
     p = sp.Popen([venv_pytest, str(pkg_root)], stderr=sp.PIPE, stdout=sp.STDOUT)
     pytest_output, _ = p.communicate()
     pytest_output = pytest_output.decode("utf-8")
     assert (
         p.returncode
-    ), f"Tests for pydra-{pkg_name} package (\n{' '.join(pip_cmd)}) failed:\n\n{pytest_output}"
+    ), f"Tests for pydra-tasks-{pkg_name} package (\n{' '.join(pip_cmd)}) failed:\n\n{pytest_output}"
diff --git a/required-fileformats/afni/pyproject.toml b/required-fileformats/afni/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-afni"
+repository = "https://github.com/nipype/pydra-tasks-afni"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/ants/pyproject.toml b/required-fileformats/ants/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-ants"
+repository = "https://github.com/nipype/pydra-tasks-ants"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/brainsuite/pyproject.toml b/required-fileformats/brainsuite/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-brainsuite"
+repository = "https://github.com/nipype/pydra-tasks-brainsuite"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/bru2nii/pyproject.toml b/required-fileformats/bru2nii/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-bru2nii"
+repository = "https://github.com/nipype/pydra-tasks-bru2nii"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/c3/pyproject.toml b/required-fileformats/c3/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-c3"
+repository = "https://github.com/nipype/pydra-tasks-c3"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/camino/pyproject.toml b/required-fileformats/camino/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-camino"
+repository = "https://github.com/nipype/pydra-tasks-camino"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/camino2trackvis/pyproject.toml b/required-fileformats/camino2trackvis/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-camino2trackvis"
+repository = "https://github.com/nipype/pydra-tasks-camino2trackvis"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/cat12/pyproject.toml b/required-fileformats/cat12/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-cat12"
+repository = "https://github.com/nipype/pydra-tasks-cat12"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/cmtk/pyproject.toml b/required-fileformats/cmtk/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-cmtk"
+repository = "https://github.com/nipype/pydra-tasks-cmtk"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/dcmstack/pyproject.toml b/required-fileformats/dcmstack/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-dcmstack"
+repository = "https://github.com/nipype/pydra-tasks-dcmstack"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/diffusion_toolkit/pyproject.toml b/required-fileformats/diffusion_toolkit/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-diffusion_toolkit"
+repository = "https://github.com/nipype/pydra-tasks-diffusion_toolkit"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/dipy/pyproject.toml b/required-fileformats/dipy/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-dipy"
+repository = "https://github.com/nipype/pydra-tasks-dipy"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/dtitk/pyproject.toml b/required-fileformats/dtitk/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-dtitk"
+repository = "https://github.com/nipype/pydra-tasks-dtitk"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/dynamic_slicer/pyproject.toml b/required-fileformats/dynamic_slicer/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-dynamic_slicer"
+repository = "https://github.com/nipype/pydra-tasks-dynamic_slicer"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/elastix/pyproject.toml b/required-fileformats/elastix/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-elastix"
+repository = "https://github.com/nipype/pydra-tasks-elastix"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/freesurfer/pyproject.toml b/required-fileformats/freesurfer/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-freesurfer"
+repository = "https://github.com/nipype/pydra-tasks-freesurfer"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/fsl/pyproject.toml b/required-fileformats/fsl/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-fsl"
+repository = "https://github.com/nipype/pydra-tasks-fsl"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/meshfix/pyproject.toml b/required-fileformats/meshfix/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-meshfix"
+repository = "https://github.com/nipype/pydra-tasks-meshfix"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/minc/pyproject.toml b/required-fileformats/minc/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-minc"
+repository = "https://github.com/nipype/pydra-tasks-minc"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/mipav/pyproject.toml b/required-fileformats/mipav/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-mipav"
+repository = "https://github.com/nipype/pydra-tasks-mipav"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/niftyfit/pyproject.toml b/required-fileformats/niftyfit/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-niftyfit"
+repository = "https://github.com/nipype/pydra-tasks-niftyfit"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/niftyreg/pyproject.toml b/required-fileformats/niftyreg/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-niftyreg"
+repository = "https://github.com/nipype/pydra-tasks-niftyreg"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/niftyseg/pyproject.toml b/required-fileformats/niftyseg/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-niftyseg"
+repository = "https://github.com/nipype/pydra-tasks-niftyseg"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/nilearn/pyproject.toml b/required-fileformats/nilearn/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-nilearn"
+repository = "https://github.com/nipype/pydra-tasks-nilearn"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/nitime/pyproject.toml b/required-fileformats/nitime/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-nitime"
+repository = "https://github.com/nipype/pydra-tasks-nitime"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/petpvc/pyproject.toml b/required-fileformats/petpvc/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-petpvc"
+repository = "https://github.com/nipype/pydra-tasks-petpvc"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/quickshear/pyproject.toml b/required-fileformats/quickshear/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-quickshear"
+repository = "https://github.com/nipype/pydra-tasks-quickshear"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/robex/pyproject.toml b/required-fileformats/robex/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-robex"
+repository = "https://github.com/nipype/pydra-tasks-robex"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/semtools/pyproject.toml b/required-fileformats/semtools/pyproject.toml
@@ -55,7 +55,7 @@ test = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-semtools"
+repository = "https://github.com/nipype/pydra-tasks-semtools"
 
 [tool.hatch.version]
 source = "vcs"
diff --git a/required-fileformats/slicer/pyproject.toml b/required-fileformats/slicer/pyproject.toml
diff --git a/required-fileformats/spm/pyproject.toml b/required-fileformats/spm/pyproject.toml
diff --git a/required-fileformats/vista/pyproject.toml b/required-fileformats/vista/pyproject.toml
diff --git a/required-fileformats/workbench/pyproject.toml b/required-fileformats/workbench/pyproject.toml

Original file line number	Diff line number	Diff line change
`@@ -308,7 +308,7 @@ def pkg_gen(`
`308`	`308`	`for example_pkg_name in example_pkg_names:`
`309`	`309`	`specs_dir = (`
`310`	`310`	`output_dir`
`311`		`- / ("pydra-" + example_pkg_name)`
	`311`	`+ / ("pydra-tasks-" + example_pkg_name)`
`312`	`312`	`/ "nipype-auto-conv"`
`313`	`313`	`/ "specs"`
`314`	`314`	`)`
Original file line number	Diff line number	Diff line change
`@@ -1162,7 +1162,7 @@ def write_pkg_inits(`
`1162`	`1162`	`from ._version import __version__`
`1163`	`1163`	`except ImportError:`
`1164`	`1164`	`raise RuntimeError(`
`1165`		`- "pydra-{pkg} has not been properly installed, please run "`
	`1165`	`+ "pydra-tasks-{pkg} has not been properly installed, please run "`
`1166`	`1166`	f"`pip install -e {str(pkg_path)}` to install a development version"
`1167`	`1167`	`)`
`1168`	`1168`	`if "nipype" not in __version__:`
Original file line number	Diff line number	Diff line change
`@@ -14,7 +14,7 @@`
`14`	`14`	`from ._version import __version__`
`15`	`15`	`except ImportError:`
`16`	`16`	`raise RuntimeError(`
`17`		`- "pydra-CHANGEME has not been properly installed, please run "`
	`17`	`+ "pydra-tasks-CHANGEME has not been properly installed, please run "`
`18`	`18`	f"`pip install -e {str(pkg_path)}` to install a development version"
`19`	`19`	`)`
`20`	`20`	`if "post" not in __version__:`
Original file line number	Diff line number	Diff line change
`@@ -58,7 +58,7 @@ converters = [`
`58`	`58`	`]`
`59`	`59`
`60`	`60`	`[project.urls]`
`61`		`-repository = "https://github.com/nipype/pydra-CHANGEME"`
	`61`	`+repository = "https://github.com/nipype/pydra-tasks-CHANGEME"`
`62`	`62`
`63`	`63`	`[tool.hatch.version]`
`64`	`64`	`source = "vcs"`
Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@ test = [`
`55`	`55`	`]`
`56`	`56`
`57`	`57`	`[project.urls]`
`58`		`-repository = "https://github.com/nipype/pydra-CHANGEME"`
	`58`	`+repository = "https://github.com/nipype/pydra-tasks-CHANGEME"`
`59`	`59`
`60`	`60`	`[tool.hatch.version]`
`61`	`61`	`source = "vcs"`