diff --git a/README.md b/README.md index e3d17bc..303ac2d 100644 --- a/README.md +++ b/README.md @@ -12,13 +12,6 @@ All tasks will be inserted into the `pydra.tasks.` namespac replace with appropriate name. 1. Rename the namespace package root directory to replace `CHANGEME` with the name of the package: * `src/pydra/tasks/CHANGEME` -1. If you are planning to define [fileformats](https://arcanaframework.github.io/fileformats/) classes specific - to the tools defined in the task package, then rename the base and "extras" packages using a - matching name to the package (if the tool is from in another field other than medical imaging, - also replace the `medimage` part). If you don't need to define and tool-specific fileformats you can delete - these packages and the .github/workflows/fileformats-ci-cd.yaml - * `related-packages/fileformats/fileformats/medimage_CHANGEME` - * `related-packages/fileformats-extras/fileformats/extras/medimage_CHANGEME` 1. Under the newly renamed package (i.e. formerly CHANGEME) there is a directory named "v1", `src/pydra/tasks//v1`, change this to valid Python package name starting with 'v' to indicate the version of the tool the Pydra interfaces will be designed for, diff --git a/related-packages/conftest.py b/related-packages/conftest.py deleted file mode 100644 index 2a703c0..0000000 --- a/related-packages/conftest.py +++ /dev/null @@ -1,37 +0,0 @@ -import os -import logging -from pathlib import Path -import tempfile -import pytest - -# Set DEBUG logging for unittests - -log_level = logging.WARNING - -logger = logging.getLogger("fileformats") -logger.setLevel(log_level) - -sch = logging.StreamHandler() -sch.setLevel(log_level) -formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s") -sch.setFormatter(formatter) -logger.addHandler(sch) - - -# For debugging in IDE's don't catch raised exceptions and let the IDE -# break at it -if os.getenv("_PYTEST_RAISE", "0") != "0": - - @pytest.hookimpl(tryfirst=True) - def pytest_exception_interact(call): - raise call.excinfo.value - - @pytest.hookimpl(tryfirst=True) - def pytest_internalerror(excinfo): - raise excinfo.value - - -@pytest.fixture -def work_dir(): - work_dir = tempfile.mkdtemp() - return Path(work_dir) diff --git a/related-packages/fileformats-extras/LICENSE b/related-packages/fileformats-extras/LICENSE deleted file mode 100644 index e00bcb3..0000000 --- a/related-packages/fileformats-extras/LICENSE +++ /dev/null @@ -1,13 +0,0 @@ - Copyright 2021 Nipype developers - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/related-packages/fileformats-extras/README.rst b/related-packages/fileformats-extras/README.rst deleted file mode 100644 index 4aa206c..0000000 --- a/related-packages/fileformats-extras/README.rst +++ /dev/null @@ -1,32 +0,0 @@ -FileFormats-medimage-CHANGEME Extras -==================================== - -.. image:: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml/badge.svg - :target: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml - - -This is a extras module for the `fileformats-medimage-CHANGEME `__ -fileformats extension package, which provides additional functionality to format classes (i.e. aside -from basic identification and validation), such as conversion tools, metadata parsers, -sample data generators, etc... - - -Quick Installation ------------------- - -This extension can be installed for Python 3 using *pip*:: - - $ pip3 install fileformats-medimage-CHANGEME-extras - -This will install the package, base packages, and any other dependencies required to -implement the extra functionality. - -License -------- - -This work is licensed under a -`Creative Commons Attribution 4.0 International License `_ - -.. image:: https://i.creativecommons.org/l/by/4.0/88x31.png - :target: http://creativecommons.org/licenses/by/4.0/ - :alt: Creative Commons Attribution 4.0 International License diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_CHANGEME/__init__.py b/related-packages/fileformats-extras/fileformats/extras/medimage_CHANGEME/__init__.py deleted file mode 100644 index 8dee4bf..0000000 --- a/related-packages/fileformats-extras/fileformats/extras/medimage_CHANGEME/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from ._version import __version__ diff --git a/related-packages/fileformats-extras/pyproject.toml b/related-packages/fileformats-extras/pyproject.toml deleted file mode 100644 index fbb1237..0000000 --- a/related-packages/fileformats-extras/pyproject.toml +++ /dev/null @@ -1,87 +0,0 @@ -[build-system] -requires = ["hatchling", "hatch-vcs"] -build-backend = "hatchling.build" - -[project] -name = "fileformats-medimage-CHANGEME-extras" -description = "Extensions to add functionality to tool-specific *fileformats* classes" -readme = "README.rst" -requires-python = ">=3.8" -dependencies = [ - "fileformats", - "fileformats-medimage-CHANGEME", - "pydra >= 0.23.0a" -] -license = {file = "LICENSE"} -authors = [ - {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, -] -maintainers = [ - {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, -] -keywords = [ - "file formats", - "data", -] -classifiers = [ - "Development Status :: 3 - Alpha", - "Environment :: Console", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: Apache Software License", - "Operating System :: MacOS :: MacOS X", - "Operating System :: Microsoft :: Windows", - "Operating System :: POSIX :: Linux", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Topic :: Scientific/Engineering", -] -dynamic = ["version"] - -[project.optional-dependencies] -dev = [ - "black", - "pre-commit", - "codespell", - "flake8", - "flake8-pyproject", -] -test = [ - "pytest >=6.2.5", - "pytest-env>=0.6.2", - "pytest-cov>=2.12.1", - "codecov", -] - -converters = [ -] - -[project.urls] -repository = "https://github.com/nipype/pydra-CHANGEME" - -[tool.hatch.version] -source = "vcs" -raw-options = { root = "../.." } - -[tool.hatch.build.hooks.vcs] -version-file = "fileformats/extras/medimage_CHANGEME/_version.py" - -[tool.hatch.build.targets.wheel] -packages = ["fileformats"] - -[tool.black] -target-version = ['py38'] -exclude = "fileformats/extras/medimage_CHANGEME/_version.py" - -[tool.codespell] -ignore-words = ".codespell-ignorewords" - -[tool.flake8] -doctests = true -per-file-ignores = [ - "__init__.py:F401" -] -max-line-length = 88 -select = "C,E,F,W,B,B950" -extend-ignore = ['E203', 'E501', 'E129'] diff --git a/related-packages/fileformats/LICENSE b/related-packages/fileformats/LICENSE deleted file mode 100644 index e00bcb3..0000000 --- a/related-packages/fileformats/LICENSE +++ /dev/null @@ -1,13 +0,0 @@ - Copyright 2021 Nipype developers - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/related-packages/fileformats/README.rst b/related-packages/fileformats/README.rst deleted file mode 100644 index 1d07e92..0000000 --- a/related-packages/fileformats/README.rst +++ /dev/null @@ -1,28 +0,0 @@ -FileFormats-medimage-CHANGEME -============================= - -.. image:: https://github.com/nipype/pydra-CHANGEME/actions/workflows/ci-cd.yml/badge.svg - :target: https://github.com/nipype/pydra-CHANGEME/actions/workflows/ci-cd.yml - -This is an extension module of the `fileformats `__ -package for defining file formats that are specific to the CHANGME software toolkit. - - -Quick Installation ------------------- - -This extension can be installed for Python 3 using *pip*:: - - $ pip3 install fileformats-medimage-CHANGEME - -This will install the format extensions and dependent base packages. - -License -------- - -This work is licensed under a -`Creative Commons Attribution 4.0 International License `_ - -.. image:: https://i.creativecommons.org/l/by/4.0/88x31.png - :target: http://creativecommons.org/licenses/by/4.0/ - :alt: Creative Commons Attribution 4.0 International License diff --git a/related-packages/fileformats/fileformats/medimage_CHANGEME/__init__.py b/related-packages/fileformats/fileformats/medimage_CHANGEME/__init__.py deleted file mode 100644 index 8dee4bf..0000000 --- a/related-packages/fileformats/fileformats/medimage_CHANGEME/__init__.py +++ /dev/null @@ -1 +0,0 @@ -from ._version import __version__ diff --git a/related-packages/fileformats/pyproject.toml b/related-packages/fileformats/pyproject.toml deleted file mode 100644 index b070d1f..0000000 --- a/related-packages/fileformats/pyproject.toml +++ /dev/null @@ -1,84 +0,0 @@ -[build-system] -requires = ["hatchling", "hatch-vcs"] -build-backend = "hatchling.build" - -[project] -name = "fileformats-medimage-CHANGEME" -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", - "fileformats-medimage" -] -license = {file = "LICENSE"} -authors = [ - {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, -] -maintainers = [ - {name = "Thomas G. Close", email = "tom.g.close@gmail.com"}, -] -keywords = [ - "file formats", - "data", -] -classifiers = [ - "Development Status :: 3 - Alpha", - "Environment :: Console", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: Apache Software License", - "Operating System :: MacOS :: MacOS X", - "Operating System :: Microsoft :: Windows", - "Operating System :: POSIX :: Linux", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Topic :: Scientific/Engineering", -] -dynamic = ["version"] - -[project.optional-dependencies] -dev = [ - "black", - "pre-commit", - "codespell", - "flake8", - "flake8-pyproject", -] -test = [ - "pytest >=6.2.5", - "pytest-env>=0.6.2", - "pytest-cov>=2.12.1", - "codecov", - "fileformats-medimage-CHANGME-extras", -] - -[project.urls] -repository = "https://github.com/nipype/pydra-CHANGEME" - -[tool.hatch.version] -source = "vcs" -raw-options = { root = "../.." } - -[tool.hatch.build.hooks.vcs] -version-file = "fileformats/medimage_CHANGEME/_version.py" - -[tool.hatch.build.targets.wheel] -packages = ["fileformats"] - -[tool.black] -target-version = ['py38'] -exclude = "fileformats/medimage_CHANGEME/_version.py" - -[tool.codespell] -ignore-words = ".codespell-ignorewords" - -[tool.flake8] -doctests = true -per-file-ignores = [ - "__init__.py:F401" -] -max-line-length = 88 -select = "C,E,F,W,B,B950" -extend-ignore = ['E203', 'E501', 'E129']