Merge pull request #1 from AllenInstitute/feature/DT-6858-make-packag…

…e-public

Adding License, docs and placeholder workflows to make package public

.github/workflows/release.yml

@@ -0,0 +1,65 @@
+name: Publish to PyPI
+
+on:
+  workflow_dispatch:
+    inputs:
+      part:
+        description: "Semver part to bump (major, minor, patch)"
+        type: choice
+        required: true
+        default: "patch"
+        options: ["major", "minor", "patch"]
+      dry-run:
+        description: "Dry run"
+        type: boolean
+        required: true
+        default: true
+
+jobs:
+
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4        
+        with:
+          python-version: ${{ matrix.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
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/aibs-informatics-test-resources
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution to PyPI
+        if: ${{ github.event.inputs.dry-run == 'false' }}
+        uses: pypa/gh-action-pypi-publish@release/v1

CONTRIBUTING.md

@@ -0,0 +1,29 @@
+# Contributing to `aibs-informatics-test-resources`
+
+Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
+
+## Types of Contributions
+
+### Reporting Bugs
+
+Report bugs to our [issues page](https://github.com/aibs-informatics-test-resources/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-test-resources/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

@@ -166,6 +166,11 @@ coverage-server: $(INSTALL_STAMP) ## Run coverage server
 ##@ Release Commands
 #####################
 
+dist: $(PYTHON) $(DEP_FILES) ## Build source and wheel package
+	@. $(VENV_BIN)/activate;\
+	$(PIP) install .[release];\
+	$(PYTHON) -m build;
+
 reinstall: obliterate install ## Recreate environment and install
 
 pre-build: obliterate ## Removes existing build environment

README.md

@@ -4,4 +4,61 @@
 
 ---
 
-Python test utility package
+## Overview
+
+This package provides a collection of utilities and resources to facilitate testing in various AIBS Informatics projects. It includes base test classes, mock utilities, and other helpful tools.
+
+## Available Modules
+
+### Base Test Class
+
+The [`BaseTest`](./src/aibs_informatics_test_resources/base.py) class provides a base class for creating unit tests with common setup and teardown functionality. It includes the following features:
+
+- **Environment Management**:
+  - `set_env_vars(*key_values_pairs: Tuple[str, Optional[str]])`: Set environment variables for the duration of the test.
+  - `reset_environ`: Class variable to reset environment variables after each test.
+
+- **Temporary Files and Directories**:
+  - `tmp_path(basename: Optional[str] = None) -> Path`: Create a temporary directory.
+  - `tmp_file(basename: Optional[str] = None, dirname: Optional[str] = None, content: Optional[str] = None) -> Path`: Create a temporary file with optional content.
+
+- **Assertions**:
+  - `assertStringPattern(pattern: str, actual: str)`: Assert that a string matches a given regex pattern.
+  - `assertJsonEqual(first: Union[dict, str, int, list], second: Union[dict, str, int, list])`: Assert that two JSON objects are equal.
+  - `assertListEqual(list1: List[Any], list2: List[Any], msg: Any = None, presort: bool = False, **presort_kwargs) -> None`: Assert that two lists are equal, with an option to sort them before comparison.
+
+- **Mocking**:
+  - `create_patch(name: str, **kwargs) -> MagicMock`: Create a patch for a given name and add it to the cleanup list.
+
+- **Context Managers**:
+  - `chdir(destination: Union[str, Path])`: Context manager to change the current working directory temporarily.
+
+
+### Mock Utilities
+
+- `does_not_raise`: A context manager for assertions that no exceptions are raised.
+- [`reset_environ_after_test`](./src/aibs_informatics_test_resources/utils.py): A decorator to reset environment variables after a test.
+
+### Example Usage
+
+Here is an example of how to use the `BaseTest` class in your tests:
+
+```python
+from aibs_informatics_test_resources import BaseTest
+
+class MyTest(BaseTest):
+    def test_example(self):
+        self.assertEqual(1 + 1, 2)
+
+    def test_use_temp_file(self):
+        with self.tmp_file(content="Hello, World!") as tmp_file:
+            self.assertTrue(tmp_file.exists())
+            self.assertEqual(tmp_file.read_text(), "Hello, World!")
+
+```
+
+## Contributing
+Any and all PRs are welcome. Please see [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
+
+## Licensing
+This software is licensed under the Allen Institute Software License, which is the 2-clause BSD license plus a third clause that prohibits redistribution and use for commercial purposes without further permission. For more information, please visit [Allen Institute Terms of Use](https://alleninstitute.org/terms-of-use/).

pyproject.toml

@@ -3,38 +3,49 @@
 #   https://setuptools.pypa.io/en/latest/setuptools.html#building-and-distributing-packages-with-setuptools
 # -----------------------------------------------------------------------------
 
-# [build-system]
-# requires = ["setuptools>=61", "setuptools_scm[toml]>=6.2", "wheel"]
-# build-backend = "setuptools.build_meta"
-# [tool.setuptools_scm]
-
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 # -----------------------------------------------------------------------------
 [project]
 name = "aibs-informatics-test-resources"
-description = "unit test resources for informatics packages"
+authors = [{ name = "AIBS Informatics Group"}]
+maintainers = [{ name = "AIBS Informatics Group", email = "[email protected]"}]
+description = "unit test resources for AIBS informatics packages"
+license = { file = "LICENSE" }
 dynamic = ["version"]
 
 requires-python = ">=3.9"
 dependencies = [
     "black==23.11.0",
-    "coverage[toml]~=7.3.2",
+    "coverage[toml]~=7.3",
     "flake8~=6.1.0",
     "isort~=5.10",
-    "mypy~=1.6.1",
-    "pytest~=7.4.3",
+    "mypy~=1.6",
+    "pytest~=7.4",
     "pytest-cov",
 ]
 
+[project.optional-dependencies]
+
+release = [
+    "build",
+    "twine",
+    "wheel",
+]
+
 [tool.setuptools.packages.find]
 where = ["src"]
 
 [tool.hatch.version]
 path = "src/aibs_informatics_test_resources/__version__.py"
 
+[project.urls]
+Documentation = "https://.github.io/aibs-informatics-test-resources/"
+Homepage = "https://github.com/AllenInstitute/aibs-informatics-test-resources/"
+Issues = "https://github.com/AllenInstitute/aibs-informatics-test-resources/issues"
+Repository = "https://github.com/AllenInstitute/aibs-informatics-test-resources/"
 
 # -----------------------------------------------------------------------------
 ##  Pyright Configurations