Rename to forest-analysis and migrate to pyproject.toml

.github/workflows/build.yml

@@ -30,10 +30,8 @@ jobs:
         if: ${{ startsWith(matrix.os, 'windows') }}
         uses: FedericoCarboni/setup-ffmpeg@v3
         id: setup-ffmpeg
-      - name: Install Forest
-        run: pip install -e .
-      - name: Install dev dependencies
-        run: pip install -r requirements.txt
+      - name: Install Forest and optional development dependencies
+        run: pip install -e ".[dev]"
       - name: Run code style checking
         run: flake8
       - name: Run static type checking

.gitignore

@@ -1,14 +1,15 @@
 __pycache__/
+dist/
+/forest_analysis.egg-info
+
+.vagrant/
 .venv/
 .DS_Store
 
 # IntelliJ, VsCode project files
 .idea
 .vscode
 
-# for installing Forest in editable mode when developing
-/forest.egg-info/
-
 #We don't want to add data to github
 /tutorials/data/
 /tutorials/comm_output/

docs/source/development.md

@@ -4,8 +4,7 @@ Information for contributors
 
 ## Quick start
 * Change current directory to the top level of your local Forest repository
-* Install Forest in editable mode: `pip install -e .`
-* Install development tools: `pip install -r requirements.txt`
+* Install Forest in editable mode along with development tools: `pip install -e ".[dev]"`
 * Run code style checks: `flake8`
 * Run type hint checks: `mypy -p forest`
 * Run test suite: `pytest`
@@ -44,6 +43,23 @@ Open `docs/_build/html/index.html` in a web browser to check the results
 * Use the [logging module](https://docs.python.org/3/library/logging.html) instead of `print()`
 * [Formatting log messages](http://reinout.vanrees.org/weblog/2015/06/05/logging-formatting.html): `logger.info("%s went %s wrong", 42, 'very')`
 * Continue writing code and comments all the way until the end of the line then indent appropriately
+* [Packaging Python Projects](https://packaging.python.org/en/latest/tutorials/packaging-projects)
+
+### Packaging and distribution
+
+#### Python Package Index
+* Use [TestPyPI](https://test.pypi.org/) for testing that your package can be uploaded, downloaded, and installed correctly
+* [Register an account](https://test.pypi.org/account/register/)
+* [Create an API token](https://test.pypi.org/manage/account/#api-tokens) (setting the "Scope" to "Entire account")
+* [Add API token](https://packaging.python.org/en/latest/specifications/pypirc/#using-a-pypi-token) to your `$HOME/.pypirc` file
+* Generate distribution archives: `python -m build`
+* Check the results: `twine check dist/*`
+* Upload distribution archives:
+  * TestPyPI: `twine upload --repository testpypi dist/*`
+  * PyPI: `twine upload dist/*`
+* Install from TestPyPI to verify:
+  * TestPyPI: `pip install --index-url https://test.pypi.org/simple/ --no-deps forest-analysis`
+  * PyPI: `pip install forest-analysis`
 
 ## GitHub
 

pyproject.toml

@@ -0,0 +1,53 @@
+[build-system]
+requires = ["setuptools>=64", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "forest-analysis"
+version = "0.1.1"
+description = "--add description here--"
+readme = "README.md"
+license = { file = "LICENSE.md" }
+authors = [
+    { name = "Onnela Lab", email = "[email protected]" }
+]
+dependencies = [
+    "holidays",  # poplar
+    "librosa",  # audio file durations in sycamore
+    "numpy",
+    "openrouteservice",
+    "pandas",
+    "pyproj",  # jasmine
+    "pytz",  # jasmine, poplar
+    "ratelimit",
+    "requests",  # bonsai
+    "scipy",
+    "shapely",  # jasmine
+    "ssqueezepy",  # oak
+    "timezonefinder",  # poplar, bonsai
+]
+requires-python = ">=3.11"
+
+[project.urls]
+Homepage = "https://github.com/onnela-lab/forest"
+
+[project.optional-dependencies]
+dev = [
+    "build",
+    "flake8==6.1.0",
+    "flake8-pytest-style==1.7.2",
+    "mypy==1.6.1",
+    "pytest==7.4.3",
+    "pytest-mock==3.12.0",
+    "twine",
+    "types-python-dateutil==2.8.19.14",
+    "types-pytz==2023.3.1.1",
+    "types-requests==2.31.0.10",
+    "types-setuptools==68.2.0.0"
+]
+
+[tool.setuptools.packages.find]
+include = ["forest*"]
+
+[tool.setuptools.package-data]
+"forest.poplar.raw" = ["noncode/*.csv", "noncode/*.json"]