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moved fileformats sub-packages into separate sub-directories
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‎README.md

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@@ -13,13 +13,13 @@ All tasks will be inserted into the `pydra.tasks.<yourtaskpackagename>` namespac
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1. One of the folders is called CHANGEME. This should also be renamed to your package
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name.
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1. Under the newly renamed package (i.e. formerly CHANGEME) there is a directory named "v1",
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`pydra/tasks/<package-name>/v1`, change this to valid Python package name starting with
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`src/pydra/tasks/<package-name>/v1`, change this to valid Python package name starting with
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'v' to indicate the version of the tool the Pydra interfaces will be designed for,
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e.g. FSL v6.0.2 could be `pydra/tasks/fsl/v6` or `pydra/tasks/fsl/v6_0` depending on
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e.g. FSL v6.0.2 could be `src/pydra/tasks/fsl/v6` or `src/pydra/tasks/fsl/v6_0` depending on
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how stable the CLI of the tool is between minor versions.
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1. Edit `pydra/tasks/<package-name>/latest.py` to update references to `v1` to the
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1. Edit `src/pydra/tasks/<package-name>/latest.py` to update references to `v1` to the
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tool target version
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1. Add tasks to the `pydra/tasks/<package-name>/v<package-version>` folder.
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1. Add tasks to the `src/pydra/tasks/<package-name>/v<package-version>` folder.
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1. You may want to initialize a [Sphinx] docs directory.
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1. Review the workflow in `.github/workflows/pythonpackage.yml`. Testing editable installations
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is probably not useful unless you are reconfiguring namespace packages.

‎fileformats/medimage-CHANGEME/conftest.py

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import os
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import logging
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from pathlib import Path
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import tempfile
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import pytest
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# Set DEBUG logging for unittests
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log_level = logging.WARNING
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logger = logging.getLogger("fileformats")
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logger.setLevel(log_level)
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sch = logging.StreamHandler()
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sch.setLevel(log_level)
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formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
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sch.setFormatter(formatter)
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logger.addHandler(sch)
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# For debugging in IDE's don't catch raised exceptions and let the IDE
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# break at it
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if os.getenv("_PYTEST_RAISE", "0") != "0":
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@pytest.hookimpl(tryfirst=True)
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def pytest_exception_interact(call):
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raise call.excinfo.value
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@pytest.hookimpl(tryfirst=True)
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def pytest_internalerror(excinfo):
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raise excinfo.value
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@pytest.fixture
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def work_dir():
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work_dir = tempfile.mkdtemp()
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return Path(work_dir)

‎fileformats/medimage-CHANGEME/fileformats/medimage_CHANGEME/__init__.py

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from ._version import __version__

‎fileformats/medimage-CHANGEME/pyproject.toml

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[build-system]
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requires = ["hatchling", "hatch-vcs"]
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build-backend = "hatchling.build"
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[project]
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name = "fileformats-medimage-CHANGEME"
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description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows"
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readme = "../README.rst"
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requires-python = ">=3.8"
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dependencies = [
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"fileformats >= 0.4",
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"fileformats-medimage > = 0.2"
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]
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license = {file = "../LICENSE"}
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authors = [
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{name = "Thomas G. Close", email = "[email protected]"},
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]
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maintainers = [
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{name = "Thomas G. Close", email = "[email protected]"},
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]
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keywords = [
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"file formats",
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"data",
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]
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classifiers = [
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"Development Status :: 3 - Alpha",
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"Environment :: Console",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: Apache Software License",
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"Operating System :: MacOS :: MacOS X",
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"Operating System :: Microsoft :: Windows",
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"Operating System :: POSIX :: Linux",
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Topic :: Scientific/Engineering",
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]
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dynamic = ["version"]
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[project.optional-dependencies]
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dev = [
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"black",
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"pre-commit",
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"codespell",
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"flake8",
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"flake8-pyproject",
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]
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test = [
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"pytest >=6.2.5",
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"pytest-env>=0.6.2",
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"pytest-cov>=2.12.1",
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"codecov",
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"fileformats-medimage-CHANGME",
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]
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[project.urls]
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repository = "https://github.com/nipype/pydra-freesurfer"
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[tool.hatch.version]
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source = "vcs"
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raw-options = { root = ".." }
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[tool.hatch.build.hooks.vcs]
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version-file = "fileformats/medimage_freesurfer/_version.py"
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[tool.hatch.build.targets.wheel]
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packages = ["fileformats"]
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[tool.black]
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target-version = ['py38']
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exclude = "fileformats/medimage_freesurfer/_version.py"
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[tool.codespell]
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ignore-words = ".codespell-ignorewords"
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[tool.flake8]
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doctests = true
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per-file-ignores = [
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"__init__.py:F401"
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]
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max-line-length = 88
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select = "C,E,F,W,B,B950"
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extend-ignore = ['E203', 'E501', 'E129']

‎fileformats/medimage-CHANGME-extras/conftest.py

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import os
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import logging
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from pathlib import Path
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import tempfile
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import pytest
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# Set DEBUG logging for unittests
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log_level = logging.WARNING
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logger = logging.getLogger("fileformats")
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logger.setLevel(log_level)
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sch = logging.StreamHandler()
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sch.setLevel(log_level)
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formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
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sch.setFormatter(formatter)
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logger.addHandler(sch)
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# For debugging in IDE's don't catch raised exceptions and let the IDE
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# break at it
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if os.getenv("_PYTEST_RAISE", "0") != "0":
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@pytest.hookimpl(tryfirst=True)
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def pytest_exception_interact(call):
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raise call.excinfo.value
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@pytest.hookimpl(tryfirst=True)
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def pytest_internalerror(excinfo):
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raise excinfo.value
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@pytest.fixture
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def work_dir():
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work_dir = tempfile.mkdtemp()
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return Path(work_dir)

‎fileformats/medimage-CHANGME-extras/fileformats/extras/medimage_CHANGEME/__init__.py

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from ._version import __version__

‎fileformats/medimage-CHANGME-extras/pyproject.toml

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[build-system]
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requires = ["hatchling", "hatch-vcs"]
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build-backend = "hatchling.build"
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[project]
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name = "fileformats-medimage-CHANGEME-extras"
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description = "Classes for representing file formats used exclusively by the Freesurfer tool in Python classes for use in type hinting in data workflows"
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readme = "../README.rst"
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requires-python = ">=3.8"
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dependencies = [
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"fileformats >= 0.7",
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"fileformats-medimage-freesurfer",
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"pydra >= 0.22.0"
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]
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license = {file = "../LICENSE"}
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authors = [
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{name = "Thomas G. Close", email = "[email protected]"},
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]
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maintainers = [
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{name = "Thomas G. Close", email = "[email protected]"},
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]
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keywords = [
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"file formats",
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"data",
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]
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classifiers = [
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"Development Status :: 3 - Alpha",
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"Environment :: Console",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: Apache Software License",
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"Operating System :: MacOS :: MacOS X",
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"Operating System :: Microsoft :: Windows",
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"Operating System :: POSIX :: Linux",
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Topic :: Scientific/Engineering",
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]
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dynamic = ["version"]
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[project.optional-dependencies]
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dev = [
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"black",
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"pre-commit",
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"codespell",
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"flake8",
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"flake8-pyproject",
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]
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test = [
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"pytest >=6.2.5",
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"pytest-env>=0.6.2",
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"pytest-cov>=2.12.1",
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"codecov",
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]
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converters = [
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]
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[project.urls]
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repository = "https://github.com/nipype/pydra-freesurfer"
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[tool.hatch.version]
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source = "vcs"
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raw-options = { root = ".." }
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[tool.hatch.build.hooks.vcs]
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version-file = "fileformats/extras/medimage_freesurfer/_version.py"
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[tool.hatch.build.targets.wheel]
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packages = ["fileformats"]
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[tool.black]
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target-version = ['py38']
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exclude = "fileformats/extras/medimage_freesurfer/_version.py"
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[tool.codespell]
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ignore-words = ".codespell-ignorewords"
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[tool.flake8]
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doctests = true
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per-file-ignores = [
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"__init__.py:F401"
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]
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max-line-length = 88
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select = "C,E,F,W,B,B950"
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extend-ignore = ['E203', 'E501', 'E129']

‎pyproject.toml

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@@ -3,15 +3,17 @@ requires = ["hatchling", "hatch-vcs"]
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build-backend = "hatchling.build"
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[project]
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name = "pydra-tasks-CHANGEME"
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name = "pydra-CHANGEME"
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description = "Pydra tasks package for CHANGEME"
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readme = "README.md"
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requires-python = ">=3.8"
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dependencies = [
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"pydra >=0.22",
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"fileformats >=0.8.3",
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"fileformats-datascience >=0.1",
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"fileformats-medimage >=0.4.1"]
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"fileformats-medimage >=0.4.1",
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"fileformats-medimage-CHANGEME"
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]
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license = {file = "LICENSE"}
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authors = [{name = "Nipype developers", email = "[email protected]"}]
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maintainers = [{name = "Nipype developers", email = "[email protected]"}]
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"fileformats-extras",
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"fileformats-datascience-extras",
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"fileformats-medimage-extras",
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"fileformats-medimage-CHANGEME-extras"
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]
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[tool.hatch.version]
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source = "vcs"
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[tool.hatch.build.hooks.vcs]
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version-file = "pydra/tasks/CHANGEME/_version.py"
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version-file = "src/pydra/tasks/CHANGEME/_version.py"
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[tool.hatch.build.targets.wheel]
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packages = ["pydra"]
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include-only = ["pydra/tasks/CHANGEME"]
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include-only = ["src/pydra/tasks/CHANGEME"]
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[tool.black]
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target-version = ["py38"]

‎pydra/tasks/CHANGEME/__init__.py renamed to ‎src/pydra/tasks/CHANGEME/__init__.py

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‎pydra/tasks/CHANGEME/latest.py renamed to ‎src/pydra/tasks/CHANGEME/latest.py

File renamed without changes.

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