Update pyproject.toml

Fixup packaging to use pyproject.toml

Update

update

Author: jeromekelleher

.github/workflows/ci.yml

@@ -7,15 +7,15 @@ on:
       - main
 
 jobs:
-  pre-commit:
-    name: Lint
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-      - uses: pre-commit/[email protected]
+  # pre-commit:
+  #   name: Lint
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - uses: actions/setup-python@v5
+  #       with:
+  #         python-version: '3.11'
+  #     - uses: pre-commit/[email protected]
   test:
     name: Test
     runs-on: ubuntu-latest
@@ -29,7 +29,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install '.[dev]'
+          python -m pip install '.[dev,analysis]'
 
       - name: Run tests
         run: |
@@ -42,3 +42,22 @@ jobs:
       #     # This is a quick workaround for doing a proper "parallel" setup:
       #     # https://github.com/coverallsapp/github-action
       #     fail-on-error: false
+
+  packaging:
+    name: Packaging
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build twine validate-pyproject[all]
+      - name: Check and install package
+        run: |
+          validate-pyproject pyproject.toml
+          python -m build
+          python -m twine check --strict dist/*
+          python -m pip install dist/*.whl

pyproject.toml

@@ -1,29 +1,51 @@
-[build-system]
-requires = [
-    "setuptools>=42",
-    "setuptools_scm",
-    "wheel",
-]
-build-backend = "setuptools.build_meta"
-
 [project]
 name = "sc2ts"
-description = "Infer ARGs in tskit format for SARS-Cov2"
+description = "Infer ARGs for SARS-Cov2 in tskit format"
 readme = "README.md"
 license = {file = "LICENSE"}
 authors = [
-  {name = "FIXME", email = "FIXME"},
+  {name = "Jerome Kelleher", email = "[email protected]"},
 ]
+requires-python = ">=3.9"
 dependencies = [
   "tsinfer",
   "pyfaidx",
+  "tskit>=0.5.3",
+  "tszip",
+  "tsinfer>=0.3.0",
+  "pandas",
+  "numba",
+  "tqdm",
+  "scipy",
+  "click",
+  "zarr<2.18",
 ]
+dynamic = ["version"]
 
 [project.optional-dependencies]
 dev = [
+  "msprime",
   "pytest",
   "pytest-coverage",
 ]
+analysis = [
+  "matplotlib",
+  "scikit-learn",
+  "pandas",
+  "IPython",
+  "networkx",
+]
+
+[build-system]
+requires = [
+    "setuptools>=42",
+    "setuptools_scm",
+    "wheel",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+packages = ["sc2ts"]
 
 [tool.setuptools_scm]
 write_to = "sc2ts/_version.py"