Merge pull request #18 from AllenInstitute/feature/DT-6858-make-packa…

…ge-public

Adding License, docs and placeholder workflows to make package public

.github/workflows/release.yml

@@ -1,37 +1,139 @@
-name: Create Release
+name: Publish to PyPI
 
 on:
-  # push:
-  #   tags:
-  #     - 'v*'
-
   workflow_dispatch:
     inputs:
-      tag:
-        description: 'Target Tag for Release'
-        type: string
+      part:
+        description: "Semver part to bump (major, minor, patch)"
+        type: choice
         required: true
-      force:
-        description: 'Force Release?'
+        default: "patch"
+        options: ["major", "minor", "patch"]
+      dry-run:
+        description: "Dry run"
         type: boolean
-        required: false
-        default: false
+        required: true
+        default: true
+      python-version:
+        description: "Python version used to build the distribution"
+        type: choice
+        required: true
+        default: "3.11"
+        options: ["3.9", "3.10", "3.11", "3.12"]
 
 jobs:
-  create-release:
+  bump:
+    name: Bump version
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      id-token: write
+    outputs:
+      VERSION: ${{ steps.get-version-and-commit-sha.outputs.VERSION }}
+      SHORT_VERSION: ${{ steps.get-version-and-commit-sha.outputs.SHORT_VERSION }}
+      MAJOR_VERSION: ${{ steps.get-version-and-commit-sha.outputs.MAJOR_VERSION }}
+      MINOR_VERSION: ${{ steps.get-version-and-commit-sha.outputs.MINOR_VERSION }}
+      PATCH_VERSION: ${{ steps.get-version-and-commit-sha.outputs.PATCH_VERSION }}
+      COMMIT_SHA: ${{ steps.get-version-and-commit-sha.outputs.COMMIT_SHA }}
     steps:
-      - name: Checkout code
+      - name: Checkout
         uses: actions/checkout@v4
+      - name: Set up Python ${{ github.event.inputs.python-version }}
+        uses: actions/setup-python@v4        
+        with:
+          python-version: ${{ github.event.inputs.python-version }}
+          cache: 'pip'
+      - name: Set up AllenInstitute Repo Authorization
+        uses: ./.github/actions/configure-org-repo-authorization
+        with:
+          token: ${{ secrets.AI_PACKAGES_TOKEN }}
+      - name: Get tags
+        run: git fetch --tags origin
+      - name: Configure git for github-actions[bot]
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+      - name: Run Install
+        run: |
+          make install-release
+        shell: bash
+      - name: Bump version with bumpversion
+        run: |
+          source .venv/bin/activate  
+          bump-my-version bump ${{ github.event.inputs.part }}
+      - name: Commit and push with tags
+        if: ${{ github.event.inputs.dry-run == 'false' }}
+        run: |
+          git push --follow-tags
+      - name: Get version and commit SHA
+        id: get-version-and-commit-sha
+        run: |
+          latest_tag=$(git describe --tags `git rev-list --tags --max-count=1`)
+          # remove the leading v from tag
+          version="${latest_tag:1}"
+          echo "VERSION=$version" >> $GITHUB_OUTPUT
+          major_version="$(cut -d '.' -f 1 <<< $version)"
+          echo "MAJOR_VERSION=$major_version" >> $GITHUB_OUTPUT
+          minor_version="$(cut -d '.' -f 2 <<< $version)"
+          echo "MINOR_VERSION=$minor_version" >> $GITHUB_OUTPUT
+          patch_version="$(cut -d '.' -f 3 <<< $version)"
+          echo "PATCH_VERSION=$patch_version" >> $GITHUB_OUTPUT
+          short_version="$major_version.$minor_version"
+          echo "SHORT_VERSION=$short_version" >> $GITHUB_OUTPUT
+          commit_sha=$(git rev-parse $latest_tag)
+          echo "COMMIT_SHA=$commit_sha" >> $GITHUB_OUTPUT
+      - name: Show version
+        run: |
+          echo VERSION: ${{ steps.get-version-and-commit-sha.outputs.VERSION }}
+          echo SHORT_VERSION: ${{ steps.get-version-and-commit-sha.outputs.SHORT_VERSION }}
+          echo MAJOR_VERSION: ${{ steps.get-version-and-commit-sha.outputs.MAJOR_VERSION }}
+          echo MINOR_VERSION: ${{ steps.get-version-and-commit-sha.outputs.MINOR_VERSION }}
+          echo PATCH_VERSION: ${{ steps.get-version-and-commit-sha.outputs.PATCH_VERSION }}
+          echo COMMIT_SHA: ${{ steps.get-version-and-commit-sha.outputs.COMMIT_SHA }}
+
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    needs: bump
+    if: ${{ github.event.inputs.dry-run == 'false' }}
+    steps:
+      - uses: actions/checkout@v4
         with:
-          ref: ${{ github.event.inputs.tag || github.ref }}
-      - name: Create Release with Changelog
-        id: create_release
-        uses: softprops/action-gh-release@v1
+          ref: ${{ needs.bump.outputs.COMMIT_SHA }}
+      - name: Set up Python ${{ github.event.inputs.python-version }}
+        uses: actions/setup-python@v4        
+        with:
+          python-version: ${{ github.event.inputs.python-version }}
+          cache: 'pip'
+      - name: Set up AllenInstitute Repo Authorization
+        uses: ./.github/actions/setup-ai-github-urls
+        with:
+          token: ${{ secrets.AI_PACKAGES_TOKEN }}
+      - name: Run Release
+        run: |
+          make dist
+        shell: bash
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: build
+    if: ${{ github.event.inputs.dry-run == 'false' }}
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/aibs-informatics-core
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
         with:
-          tag_name: ${{ github.event.inputs.tag || github.ref_name }}
-          name: Release ${{ github.event.inputs.tag || github.ref_name }}
-          draft: false
-          prerelease: false
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

CONTRIBUTING.md

@@ -0,0 +1,29 @@
+# Contributing to `aibs-informatics-core`
+
+Contributions are welcome and appreciated!
+
+## Types of Contributions
+
+### Reporting Bugs
+
+Report bugs to our [issues page](https://github.com/aibs-informatics-core/issues).
+
+If you are reporting a bug, please include:
+
+- Your operating system name and version.
+- Any details about your local setup that might be helpful in troubleshooting.
+- Detailed steps to reproduce the bug, in the form of a [minimal reproducible example](https://stackoverflow.com/help/minimal-reproducible-example).
+
+### Making Changes
+
+Look through the GitHub issues for bugs, features, and other requests. Most issues will have a label that can help you identify the type of issue.  
+
+### Submitting Feedback
+
+The best way to send feedback is to [create an issue](https://github.com/aibs-informatics-core/issues/new) on GitHub.
+
+If you are proposing a feature:
+
+- Explain in detail how it would work.
+- Keep the scope as narrow as possible, to make it easier to implement.
+- Remember that while contributions are welcome, developer/maintainer time is limited.

LICENSE

@@ -0,0 +1,33 @@
+Allen Institute Software License – This software license is the 2-clause BSD 
+license plus a third clause that prohibits redistribution and use for 
+commercial purposes without further permission. 
+
+Copyright © 2024. Allen Institute.  All rights reserved.
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this 
+list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+3. Redistributions and use for commercial purposes are not permitted without 
+the Allen Institute’s written permission. For purposes of this license, 
+commercial purposes are the incorporation of the Allen Institute's software 
+into anything for which you will charge fees or other compensation or use of 
+the software to perform a commercial service for a third party. Contact 
+[email protected] for commercial licensing opportunities.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Makefile

@@ -76,6 +76,10 @@ $(INSTALL_STAMP): $(PYTHON) $(DEP_FILES)
 	$(PIP) install -e .[dev]; 
 	@touch $(INSTALL_STAMP)
 
+install-release: clean-install-stamp $(PYTHON) $(DEP_FILES) ## Installs package for release
+	@. $(VENV_BIN)/activate;\
+	$(PIP) install .[release]
+
 install-force: clean-install-stamp install ## Force install package dependencies
 
 link-packages: ## Link local packages to virtualenv  
@@ -174,6 +178,10 @@ package: $(INSTALL_STAMP)  ## Build package distribution
 ##@ Release Commands
 #####################
 
+dist: install-release ## Build source and wheel package
+	@. $(VENV_BIN)/activate;\
+	$(PYTHON) -m build;
+
 reinstall: obliterate install ## Recreate environment and install
 
 pre-build: obliterate ## Removes existing build environment