From c4971610bf12fd6384f89a3e07eb6657d064b7e0 Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Tue, 13 Jun 2023 13:40:57 +0200 Subject: [PATCH] First version from cookiecutter --- .bumpversion.cfg | 20 ++ .github/workflows/omero_plugin.yml | 34 +++ .github/workflows/publish_pypi.yml | 20 ++ .gitignore | 9 + .isort.cfg | 2 + .omeroci/README | 2 + .omeroci/release | 13 + .pre-commit-config.yaml | 76 ++++++ CHANGES.txt | 7 + LICENSE.txt | 339 ++++++++++++++++++++++++ MANIFEST.in | 4 + README.rst | 58 ++++ setup.cfg | 15 ++ setup.py | 65 +++++ src/omero/plugins/mkngff.py | 32 +++ src/omero_mkngff/__init__.py | 55 ++++ test/integration/clitest/test_mkngff.py | 42 +++ 17 files changed, 793 insertions(+) create mode 100644 .bumpversion.cfg create mode 100644 .github/workflows/omero_plugin.yml create mode 100644 .github/workflows/publish_pypi.yml create mode 100644 .gitignore create mode 100644 .isort.cfg create mode 100644 .omeroci/README create mode 100755 .omeroci/release create mode 100644 .pre-commit-config.yaml create mode 100644 CHANGES.txt create mode 100644 LICENSE.txt create mode 100644 MANIFEST.in create mode 100644 README.rst create mode 100644 setup.cfg create mode 100755 setup.py create mode 100644 src/omero/plugins/mkngff.py create mode 100644 src/omero_mkngff/__init__.py create mode 100644 test/integration/clitest/test_mkngff.py diff --git a/.bumpversion.cfg b/.bumpversion.cfg new file mode 100644 index 0000000..e6f9fac --- /dev/null +++ b/.bumpversion.cfg @@ -0,0 +1,20 @@ +[bumpversion] +current_version = 0.1.0.dev0 +commit = True +tag = True +sign_tags = True +parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\.(?P[a-z]+)(?P\d+))? +serialize = + {major}.{minor}.{patch}.{release}{build} + {major}.{minor}.{patch} + +[bumpversion:part:release] +optional_value = prod +first_value = dev +values = + dev + prod + +[bumpversion:part:build] + +[bumpversion:file:setup.py] diff --git a/.github/workflows/omero_plugin.yml b/.github/workflows/omero_plugin.yml new file mode 100644 index 0000000..f90e1ea --- /dev/null +++ b/.github/workflows/omero_plugin.yml @@ -0,0 +1,34 @@ +# Install and test and OMERO plugin e.g. a Web app, a CLI plugin or a library +# +# This workflow will install omero-test-infra, start an OMERO environment +# including database, server and web deployment, configure the OMERO plugin +# and run integration tests. +# +# 1. Set up the stage variable depending on the plugin. Supported stages +# are: app, cli, scripts, lib, srv +# +# 2. Adjust the cron schedule as necessary + +name: OMERO +on: + push: + pull_request: + schedule: + - cron: '0 0 * * 0' + +jobs: + test: + name: Run integration tests against OMERO + runs-on: ubuntu-latest + env: + STAGE: cli + steps: + - uses: actions/checkout@v3 + - name: Checkout omero-test-infra + uses: actions/checkout@master + with: + repository: ome/omero-test-infra + path: .omero + ref: ${{ secrets.OMERO_TEST_INFRA_REF }} + - name: Build and run OMERO tests + run: .omero/docker $STAGE diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml new file mode 100644 index 0000000..81eccda --- /dev/null +++ b/.github/workflows/publish_pypi.yml @@ -0,0 +1,20 @@ +--- +name: PyPI +on: push + +jobs: + build-n-publish: + name: Build and publish Python distribution to PyPI + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + - name: Build a binary wheel and a source tarball + run: | + python -mpip install wheel + python setup.py sdist bdist_wheel + - name: Publish distribution to PyPI + if: startsWith(github.ref, 'refs/tags') + uses: pypa/gh-action-pypi-publish@v1.3.0 + with: + password: ${{ secrets.PYPI_PASSWORD }} diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..33f3d50 --- /dev/null +++ b/.gitignore @@ -0,0 +1,9 @@ +build +dist +omero-mkngff-* +*.egg* +.cache +*.DS_Store +.*un~ +*.pyc +.omero diff --git a/.isort.cfg b/.isort.cfg new file mode 100644 index 0000000..f26b789 --- /dev/null +++ b/.isort.cfg @@ -0,0 +1,2 @@ +[settings] +known_third_party = omero,omero_mkngff,setuptools diff --git a/.omeroci/README b/.omeroci/README new file mode 100644 index 0000000..6f24a00 --- /dev/null +++ b/.omeroci/README @@ -0,0 +1,2 @@ +This directory implements scripts to unify +build and release actions across repos. diff --git a/.omeroci/release b/.omeroci/release new file mode 100755 index 0000000..1610d3f --- /dev/null +++ b/.omeroci/release @@ -0,0 +1,13 @@ +#!/usr/bin/env make -f +release: +ifndef VERSION + $(error VERSION is undefined) +endif + git describe --exact + python setup.py sdist + echo twine upload dist/omero-mkngff-$(VERSION).tar.gz + +clean: + rm -rf build dist omero-mkngff.egg-info *.pyc + +.PHONY: release clean diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..99acf94 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,76 @@ +--- +repos: + + - repo: https://github.com/asottile/seed-isort-config + rev: v2.2.0 + hooks: + - id: seed-isort-config + + - repo: https://github.com/PyCQA/isort + rev: 5.10.1 + hooks: + - id: isort + args: ["--profile", "black"] + + - repo: https://github.com/psf/black + rev: 23.3.0 + hooks: + - id: black + args: [--target-version=py36] + + - repo: https://github.com/asottile/pyupgrade + rev: v2.29.1 + hooks: + - id: pyupgrade + args: + - --py36-plus + + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.0.1 + hooks: + - id: trailing-whitespace + exclude: .bumpversion.cfg + - id: end-of-file-fixer + - id: check-json + files: \.(json)$ + - id: check-yaml + - id: fix-encoding-pragma + args: + - --remove + - id: check-case-conflict + - id: check-merge-conflict + - id: check-symlinks + - id: pretty-format-json + args: + - --autofix + + - repo: https://github.com/PyCQA/flake8 + rev: 4.0.1 + hooks: + - id: flake8 + additional_dependencies: [ + flake8-blind-except, + flake8-builtins, + flake8-rst-docstrings, + flake8-logging-format, + ] + args: [ + # default black line length is 88 + "--max-line-length=88", + # Conflicts with black: E203 whitespace before ':' + "--extend-ignore=E203", + "--rst-roles=class,func,ref,module,const", + ] + + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v0.971 + hooks: + - id: mypy + language_version: python3 + + - repo: https://github.com/adrienverge/yamllint.git + rev: v1.26.3 + hooks: + - id: yamllint + # args: [--config-data=relaxed] + # diff --git a/CHANGES.txt b/CHANGES.txt new file mode 100644 index 0000000..3d533cf --- /dev/null +++ b/CHANGES.txt @@ -0,0 +1,7 @@ +======= +Changes +======= + +0.1 - 2023-06-13 +================== +* Initial release. Based on https://github.com/ome/cookiecutter-omero-cli-plugin diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..d511905 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,339 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. 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It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..131793c --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,4 @@ +include *.txt +include *.rst +prune dist +prune build diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..2e1fdf7 --- /dev/null +++ b/README.rst @@ -0,0 +1,58 @@ +.. image:: https://github.com/ome/omero-mkngff/workflows/OMERO/badge.svg + :target: https://github.com/ome/omero-mkngff + +.. image:: https://badge.fury.io/py/omero-mkngff.svg + :target: https://badge.fury.io/py/omero-mkngff + +omero-mkngff +================================== + +Plugin to swap OMERO filesets with NGFF + + +Requirements +============ + +* OMERO 5.6.0 or newer +* Python 3.6 or newer + + +Installing from PyPI +==================== + +This section assumes that an OMERO.py is already installed. + +Install the command-line tool using `pip `_: + +:: + + $ pip install -U omero-mkngff + +Release process +--------------- + +This repository uses `bump2version `_ to manage version numbers. +To tag a release run:: + + $ bumpversion release + +This will remove the ``.dev0`` suffix from the current version, commit, and tag the release. + +To switch back to a development version run:: + + $ bumpversion --no-tag [major|minor|patch] + +specifying ``major``, ``minor`` or ``patch`` depending on whether the development branch will be a `major, minor or patch release `_. This will also add the ``.dev0`` suffix. + +Remember to ``git push`` all commits and tags. + +License +------- + +This project, similar to many Open Microscopy Environment (OME) projects, is +licensed under the terms of the GNU General Public License (GPL) v2 or later. + +Copyright +--------- + +2017-2020, The Open Microscopy Environment diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..5873c0f --- /dev/null +++ b/setup.cfg @@ -0,0 +1,15 @@ +[metadata] +description-file = README.rst + +[mypy] +check_untyped_defs = true +disallow_any_generics = true +disallow_incomplete_defs = true +disallow_untyped_defs = true +no_implicit_optional = true + +[mypy-setup] +disallow_untyped_defs = false + +[mypy-test_rdf] +disallow_untyped_defs = false diff --git a/setup.py b/setup.py new file mode 100755 index 0000000..df70176 --- /dev/null +++ b/setup.py @@ -0,0 +1,65 @@ +#!/usr/bin/env python +# +# Copyright (c) 2023 German BioImaging. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU Affero General Public License as +# published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see . +# +# +import os + +from setuptools import setup + + +def read(fname): + """ + Utility function to read the README file. + :rtype : String + """ + return open(os.path.join(os.path.dirname(__file__), fname)).read() + + +version = "0.1.0.dev0" +url = "https://github.com/ome/omero-mkngff" + +setup( + version=version, + packages=["omero_mkngff", "omero.plugins"], + package_dir={"": "src"}, + name="omero-mkngff", + description="Plugin to swap OMERO filesets with NGFF", + long_description=read("README.rst"), + classifiers=[ + "Development Status :: 2 - Pre-Alpha", + "Environment :: Plugins", + "Intended Audience :: Developers", + "Intended Audience :: End Users/Desktop", + "License :: OSI Approved :: GNU General Public License v2 " + "or later (GPLv2+)", # noqa + "Natural Language :: English", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Topic :: Software Development :: Libraries :: Python Modules", + ], # Get strings from + # http://pypi.python.org/pypi?%3Aaction=list_classifiers + author="OME Team", + author_email="ome-team@openmicroscopy.org", + license="GPL-2.0+", + url="%s" % url, + zip_safe=False, + download_url=f"{url}/v{version}.tar.gz", + install_requires=["omero-py>=5.8", "future"], + python_requires=">=3", + keywords=["OMERO.CLI", "plugin"], + tests_require=["pytest", "restview", "mox3"], +) diff --git a/src/omero/plugins/mkngff.py b/src/omero/plugins/mkngff.py new file mode 100644 index 0000000..6c96c42 --- /dev/null +++ b/src/omero/plugins/mkngff.py @@ -0,0 +1,32 @@ +#!/usr/bin/env python + +# +# Copyright (c) 2023 German BioImaging. +# All rights reserved. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +import sys + +from omero.cli import CLI +from omero_mkngff import HELP, MkngffControl + +try: + register("mkngff", MkngffControl, HELP) # type: ignore +except NameError: + if __name__ == "__main__": + cli = CLI() + cli.register("mkngff", MkngffControl, HELP) + cli.invoke(sys.argv[1:]) diff --git a/src/omero_mkngff/__init__.py b/src/omero_mkngff/__init__.py new file mode 100644 index 0000000..6894ea6 --- /dev/null +++ b/src/omero_mkngff/__init__.py @@ -0,0 +1,55 @@ +#!/usr/bin/env python + +# +# Copyright (c) 2023 German BioImaging. +# All rights reserved. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +from argparse import Namespace + +from omero.cli import BaseControl, Parser + +HELP = """Plugin to swap OMERO filesets with NGFF + +Add your documentation here. + +Examples: + + # Do something + omero mkngff ... + +""" + + +class MkngffControl(BaseControl): + def _configure(self, parser: Parser) -> None: + parser.add_login_arguments() + parser.add_argument( + "--force", + "-f", + default=False, + action="store_true", + help="Actually do something. Default: false.", + ) + parser.add_argument("fileset_id") + parser.add_argument("zarr_name") + parser.add_argument("symlink_target") + parser.set_defaults(func=self.action) + + def action(self, args: Namespace) -> None: + conn = self.ctx.conn(args) # noqa + print(conn) + self.ctx.out("done.") diff --git a/test/integration/clitest/test_mkngff.py b/test/integration/clitest/test_mkngff.py new file mode 100644 index 0000000..8ab80fc --- /dev/null +++ b/test/integration/clitest/test_mkngff.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python + +# +# Copyright (c) 2023 German BioImaging. +# All rights reserved. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 2 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +from omero.plugins.mkngff import MkngffControl +from omero.testlib.cli import CLITest + + +class TestMkngff(CLITest): + def setup_method(self, method): # type: ignore + super().setup_method(method) + self.cli.register("mkngff", MkngffControl, "TEST") + self.args += ["mkngff"] + + def mkngff(self, capfd): # type: ignore + self.cli.invoke(self.args, strict=True) + return capfd.readouterr()[0] + + def test_mkngff(self, capfd): # type: ignore + name = self.uuid() + object_type = "Project" + oid = self.create_object(object_type, name=f"{name}") + obj_arg = f"{object_type}:{oid}" + self.args += [obj_arg] + out = self.rdf(capfd) + assert out