Deploy cladetime to test-pypi (#81)

* Update pyproject.toml for use with pypi

This changeset makes a few fixes and updates to pyproject.toml as
we work towards releasing Cladetime on pypi. Mostly adds and revises
metadata, and fixes a few directives that impact the build process.

* Add a workflow for building and publishing to test PyPI

Cladetime has been successfully published to test-pypi:
https://test.pypi.org/project/cladetime/

This commit adds a workflow to automate publishing to test-pypi. Once this
is hooked up, we can focus on what deployment to the real PyPI should look like
(presumably we'd want to use a similar process to what Zhian set up for our
R packages).

* Bump cladetime version

.github/workflows/publish-pypi-test.yaml

@@ -0,0 +1,61 @@
+# .github/workflows/publish-pypi-test.yaml
+# uses trusted publishing to publish the package to TestPyPI as described here:
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+name: Publish to Test PyPI
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Set up Python 🐍
+        uses: actions/setup-python@v5
+
+      - name: Install uv 🌟
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: ">=0.0.1"
+
+      - name: Build package for distribution 🛠️
+        run: |
+          uv build
+
+      - name: Upload distribution packages 📤
+        uses: actions/upload-artifact@v4
+        with:
+          name: cladetime-package-distribution
+          path: dist/
+
+  publish-to-testpypi:
+    name: Publish Python distribution to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi-test
+      url: https://test.pypi.org/p/cladetime
+    permissions:
+       id-token: write  # needed for trusted publishing (i.e., OIDC)
+
+    steps:
+    - name: Download distribution artifacts 📥
+      uses: actions/download-artifact@v4
+      with:
+        name: cladetime-package-distributions
+        path: dist/
+    - name: Publish distribution to TestPyPI 🚀
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/

pyproject.toml

@@ -1,21 +1,31 @@
 [project]
 name = "cladetime"
-version = "0.2.0"
-description = "Assign clades to viral genome sequences at a point in time."
+version = "0.2.3"
+description = "Assign clades to SARS-CoV-2 genome sequences at a point in time."
 authors = [
+    {name = "Reich Lab @ University of Massachusetts", email = "nick@umass.edu"},
+]
+maintainers = [
+    {name = "Becky Sweger", email = "rsweger@umass.edu"},
     {name = "Evan Ray", email="elray@umass.edu"},
     {name = "Ben Rogers", email = "bwrogers@umass.edu"},
-    {name = "Becky Sweger", email = "rsweger@umass.edu"},
 ]
-
-requires-python = ">=3.11"
-readme = "README.md"
+license = {text = "MIT License"}
+keywords = ["biostatistics", "clade", "covid", "epidemiology", "genome", "sequence"]
 
 classifiers = [
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "License :: OSI Approved :: MIT License",
+  "Natural Language :: English",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 
+requires-python = ">=3.11"
+readme = "README.md"
+
 dependencies = [
     "awscli>=1.32.92",
     "biopython",
@@ -59,7 +69,7 @@ docs = [
     "sphinx-github-style",
     "sphinxext-opengraph",
     "sphinx_toolbox",
-    ]
+]
 
 [project.urls]
 Repository = "https://github.com/reichlab/cladetime.git"
@@ -70,6 +80,10 @@ Issues = "https://github.com/reichlab/cladetime/issues"
 requires = ["setuptools>=64", "wheel"]
 build-backend = "setuptools.build_meta"
 
+[tool.setuptools.packages.find]
+namespaces = true
+where = ["src"]
+
 [tool.pytest.ini_options]
 tmp_path_retention_policy = "none"
 filterwarnings = [
@@ -89,9 +103,5 @@ lint.extend-select = ["I"]
 # Ignore import formatting rules in `__init__.py`
 "__init__.py" = ["I001"]
 
-[tools.setuptools]
-packages = ["cladetime"]
-
 [tool.mypy]
 ignore_missing_imports = true
-