diff --git a/.data-template-new.png b/.data-template-new.png new file mode 100644 index 0000000..d7c462d Binary files /dev/null and b/.data-template-new.png differ diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 0000000..1c3780d --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,50 @@ +name: Publish + +on: + # publish from the Releases page: + release: + types: [published] + # test building only on PRs + pull_request: + +env: + VERSION_NUMBER: ${{ github.event.release.tag_name }} + +jobs: + publish: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Set up Python + uses: actions/setup-python@v1 + - name: Build tools + run: | + python -m pip install --upgrade pip + pip install build + - name: Replace dummy values in `setup.py` (only for `data-template`) + if: ${{ github.event.repository.name }} == "data-template" + run: perl -pi -e 's/\${dataset_name}/template/' setup.py + - name: Replace version string in `setup.py` + run: perl -pi -e 's/version="dev"/version="${{ env.VERSION_NUMBER }}"/' setup.py + - name: Build + run: | + python -m build --wheel --sdist + - name: Publish to Github + if: startsWith(github.ref, 'refs/tags/') + uses: softprops/action-gh-release@v1 + with: + files: 'dist/*' + fail_on_unmatched_files: true + tag_name: ${{ env.VERSION_NUMBER }} + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + - name: Publish to PyPI + if: startsWith(github.ref, 'refs/tags/') + uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + # TODO: Replace this personal API token with one that: + # - Points at pypi.org, not test.pypi.org + # - Is generated by the NeuroPoly PyPI account (https://github.com/neuropoly/onboarding/issues/140) + password: ${{ secrets.TEST_PYPI_API_TOKEN_JOSHUACWNEWTON }} + repository_url: https://test.pypi.org/legacy/ diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..92148bd --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +dist/ +build/ + +*.whl +*.egg-info +__pycache__ diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..49ce653 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,317 @@ +Creative Commons Attribution 4.0 International Public License + +By exercising the Licensed Rights (defined below), You accept and agree +to be bound by the terms and conditions of this Creative Commons +Attribution 4.0 International Public License ("Public License"). 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If the provision + cannot be reformed, it shall be severed from this Public License + without affecting the enforceability of the remaining terms and + conditions. + + c. No term or condition of this Public License will be waived and no + failure to comply consented to unless expressly agreed to by the + Licensor. + + d. Nothing in this Public License constitutes or may be interpreted + as a limitation upon, or waiver of, any privileges and immunities + that apply to the Licensor or You, including from the legal + processes of any jurisdiction or authority. diff --git a/README.md b/README.md index e69de29..0396b23 100644 --- a/README.md +++ b/README.md @@ -0,0 +1,105 @@ +# `data-${dataset_name}` + +Part of [`spinalcordtoolbox`](https://github.com/spinalcordtoolbox). + + +## Using the Template + +1. Make a [new repo](https://github.com/new) using this as its template. + + Name it `spinalcordtoolbox/data-${dataset_name}` where `${dataset_name}` is something usefully descriptive: + + ![data-template-new](./.data-template-new.png) + +2. Download the new repo + + ```bash + git clone git@github.com:spinalcordtoolbox/data-${dataset_name}.git + cd data-${dataset_name} + ``` + +3. Fill with initial metadata + + ```bash + # 1. Find and replace ${dataset-name} with the name you picked (e.g. `supercats`) + perl -pi -e 's/\${dataset_name}/supercats/' README.md + perl -pi -e 's/\${dataset_name}/supercats/' setup.py + + # 2. Rename the repo's `dataset` folder to match the repo name + git mv src/spinalcordtoolbox/data/dataset src/spinalcordtoolbox/data/${dataset_name} + + # 3. Commit the changes + git add -u + git commit -m "Setting data-${dataset_name} package metadata" + git push + ``` + +4. Fill with initial data and upload + + ```bash + # 1. Copy over the data files to the dataset folder in this repo + cp ${data_files} src/spinalcordtoolbox/data/${dataset_name} + + # 2. Add, commit, and push the newly-added files + git add . + git commit -m "Copy over data files to dataset folder" + git push + ``` + +5. Remove the "Using this template" section from `README.md`, since it is now no longer needed. + + ```bash + # Delete the 'Using the Template' section from `README.md` + vi README.md + + # Add, commit, and push the changes + git add README.md + git commit -m "Removing template section from README.md" + git push + ``` + + +## How to update this dataset + +1. Edit and commit the files in `src/spinalcordtoolbox/data/` +2. Go to https://github.com/spinalcordtoolbox/data-${dataset_name}/releases +3. Click "Draft Release" +4. Fill in a version tag. We recommend using date-based releases (e.g. `2020.1.1`, `2022.5.18`, etc.). + + **Note**: The version must be formatted in a way that complies with [PEP 440](https://peps.python.org/pep-0440/). The easiest way to do this is to use a numerical version number in the form of X.Y.Z, but there is [some flexibility](https://peps.python.org/pep-0440/#final-releases) here. + +5. Click "Publish Release" +6. Wait a few minutes; +7. Monitor the progress at https://github.com/spinalcordtoolbox/data-${dataset_name}/actions/workflows/release.yml +8. The release should appear on https://github.com/spinalcordtoolbox/data-${dataset_name}/releases + with the .tar.gz (sdist) and .whl (wheel) formats attached momentarily. + + +## How to test this repo locally + +If you've encountered an error during the GitHub Actions workflow, you can use the following steps to test the repo locally: + +```bash +# Create a virtual environment +python -m venv venv +source venv/bin/activate + +# Install the `build` package (which is necessary to build pip packages) +pip install build + +# Build the pip package, which will generate: +# 1. A build folder (containing a copy of the files to be packaged) +# 2. A packaged wheel (stored in ./dist/${package-name}.whl) +# 3. A packaged source distribution (stored in ./dist/${package-name}.tar.gz) +# 4. Package metadata (stored in ./src/${package-name}.egg-info +python -m build --wheel --sdist + +# Install the generated wheel. +# As a result, the contents of ./src/ will be installed to: +# ./venv/lib/python3.7/site-packages/spinalcordtoolbox/data/${dataset_name} +# This means that the installed data package will coexist alongside the +# installed `spinalcordtoolbox` pip package. +pip install dist/*.whl +``` + +This should give you enough clues to hopefully to track down any problems. diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..1ce1d64 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,3 @@ +# this ensures builds are done reliably +[build-system] +requires = ["setuptools>=40.8.0", "setuptools_scm[toml]", "wheel"] diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..1578777 --- /dev/null +++ b/setup.py @@ -0,0 +1,40 @@ +from setuptools import setup, find_namespace_packages +import pathlib + +here = pathlib.Path(__file__).parent.resolve() + +# workaround a bug introduced by pyproject.toml +# https://github.com/pypa/pip/issues/7953#issuecomment-645133255 +import site; site.ENABLE_USER_SITE = True + +setup( + name='spinalcordtoolbox-data-${dataset_name}', + version="dev", + description='Part of https://github.com/neuropoly/spinalcordtoolbox', + long_description=(here / 'README.md').read_text(encoding='utf-8'), + long_description_content_type='text/markdown', + author='Neuropoly', + author_email='pip@neuropoly.org', + url='https://spinalcordtoolbox.com/', + project_urls={ + 'Source': 'https://github.com/spinalcordtoolbox/data-${dataset_name}', + 'Documentation': 'https://spinalcordtoolbox.com/', + }, + license='CC-BY-4.0', + license_files=[ 'LICENSE.txt' ], # TODO? + + packages=find_namespace_packages('src/'), + package_dir={"":"src/"}, + + # with setuptools_scm, means it includes non-python files if they're under git + include_package_data=True, + + # pyproject.toml::build-system.requires is supposed to supersede this, but it's still very new so we duplicate it. + setup_requires=[ + 'setuptools', + 'wheel', + ], + + zip_safe=False, # guarantees that importlib.resources.path() is safe +) + diff --git a/src/spinalcordtoolbox/data/dataset/__init__.py b/src/spinalcordtoolbox/data/dataset/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/data/dataset/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO >