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Merge pull request #35 from nipype/src-dir
Adds fileformats sub-packages and refactors pyproject and github actions
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‎.github/workflows/pythonpackage.yaml renamed to ‎.github/workflows/ci-cd.yaml

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# For deployment, it will be necessary to create a PyPI API token and store it as a secret
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# https://docs.github.com/en/actions/reference/encrypted-secrets
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name: Python package
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name: CI/CD
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on:
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push:

‎.gitignore

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.Python
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build/
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develop-eggs/
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_version.py
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dist/
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downloads/
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eggs/

‎README.md

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@@ -10,16 +10,18 @@ All tasks will be inserted into the `pydra.tasks.<yourtaskpackagename>` namespac
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1. Give your repo a name.
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1. Once the repo is created and cloned, search for CHANGEME (`grep -rn CHANGEME . `) and
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replace with appropriate name.
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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. Rename the following folders to replace `CHANGEME` with the name of the package:
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* `src/pydra/tasks/CHANGEME`
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* `fileformats/fileformats/medimage_CHANGEME`
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* `fileformats/fileformats/extras/medimage_CHANGEME`
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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.
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twine upload dist/*
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```
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Note that uploading to PyPI is done via [Continuous integration](#continuous-integration)) when
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Note that uploading to PyPI is done via [Continuous integration](#continuous-integration) when
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a tag is pushed to the repository, so only the first step needs to be donne manually.
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Note also that we assume tags will be version numbers and not be prefixed with `v` or some other

‎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]

‎related-packages/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)

‎related-packages/fileformats-extras/LICENSE

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Copyright 2021 Nipype developers
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.

‎related-packages/fileformats-extras/README.rst

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FileFormats-CHANGEME Extras
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======================================
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.. image:: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml/badge.svg
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:target: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml
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This is a extras module for the `fileformats-CHANGEME <https://github.com/nipype/pydra-freesurfer/>`__
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fileformats extension package, which provides additional functionality to format classes (i.e. aside
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from basic identification and validation), such as conversion tools, metadata parsers, test data generators, etc...
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Quick Installation
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------------------
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This extension can be installed for Python 3 using *pip*::
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$ pip3 install fileformats-CHANGEME-extras
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This will install the core package and any other dependencies
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License
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-------
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This work is licensed under a
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`Creative Commons Attribution 4.0 International License <http://creativecommons.org/licenses/by/4.0/>`_
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.. image:: https://i.creativecommons.org/l/by/4.0/88x31.png
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:target: http://creativecommons.org/licenses/by/4.0/
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:alt: Creative Commons Attribution 4.0 International License

‎related-packages/fileformats-extras/fileformats/extras/medimage_CHANGEME/__init__.py

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from ._version import __version__

‎related-packages/fileformats-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 = "Extensions to add functionality to tool-specific *fileformats* classes"
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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",
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"fileformats-medimage-CHANGEME",
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"pydra >= 0.23.0a"
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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-CHANGEME"
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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_CHANGEME/_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_CHANGEME/_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']

‎related-packages/fileformats/LICENSE

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Copyright 2021 Nipype developers
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.

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