Move reqs to pyproject

.github/workflows/docs.yml

@@ -8,4 +8,4 @@ on:
   merge_group:
 jobs:
   Docs:
-    uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@main
+    uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1

.github/workflows/tests.yml

@@ -18,33 +18,38 @@ jobs:
       - uses: actions/checkout@v4.2.2
       - uses: actions/setup-python@v5.3.0
         with:
-          python-version: '3.10'
+          python-version: '3.12'
       - uses: pre-commit/action@v3.0.1
 
   test:
     name: Python
-    runs-on: ubuntu-24.04
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-
+        python: [ "3.10", 3.13 ]
+        os:  [ macos-latest, ubuntu-24.04, windows-latest ]
+    defaults:
+      run:
+        shell: bash
     steps:
       - name: Cancel Previous Runs
         uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
       - uses: actions/checkout@v4.2.2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5.3.0
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.python }}
+          version: "0.8.15"
+
       - name: Install dependencies
         run: |
-          python3 -m pip install --upgrade pip
-          python3 -m pip install -r requirements/CI-tests-pip/requirements.txt
+          uv venv
+          uv pip install -r pyproject.toml --extra test
       - name: Test with pytest
         run: |
-          python3 -m pytest --cov=tstrait --cov-report=xml --cov-branch -n 0 tests
+          uv run --no-sync python -m pytest --cov=tstrait --cov-report=xml --cov-branch -n 0 tests
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v5.1.1
         env:
@@ -64,7 +69,7 @@ jobs:
       - uses: actions/checkout@v4.2.2
       - uses: actions/setup-python@v5.3.0
         with:
-          python-version: '3.10'
+          python-version: '3.12'
       - name: Install dependencies
         run: |
           python3 -m pip install --upgrade pip

.github/workflows/wheels.yml

@@ -18,7 +18,7 @@ jobs:
       - uses: actions/checkout@v4.2.2
       - uses: actions/setup-python@v5.3.0
         with:
-          python-version: '3.10'
+          python-version: '3.12'
       - name: Install dependencies
         run: |
           python3 -m pip install --upgrade pip
@@ -40,7 +40,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", "3.11"]
+        python: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - name: Download wheels
         uses: actions/download-artifact@v4.1.8
@@ -62,7 +62,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", "3.11"]
+        python: ["3.10", "3.11", "3.12", "3.13"]
         wordsize: [64]
     steps:
       - name: Download wheels
@@ -86,7 +86,7 @@ jobs:
     needs: ['distbuild']
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", "3.11"]
+        python: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - name: Download wheels
         uses: actions/download-artifact@v4.1.8

docs/contributing.md

@@ -51,17 +51,21 @@ Afterwards, go to Github and open a pull request by pressing a green Pull Reques
 
 ## Requirements
 
-The list of packages needed for development are listed in `requirements.development.txt`.
-Install these by using either:
+The packages needed for development are specified as optional dependencies
+in the ``pyproject.toml`` file. Install these using:
 
 ```
-conda install --file requirements/development.txt
+python3 -m venv env
+source env/bin/activate
+python3 -m pip install -e ".[dev]"
 ```
 
-or
+Alternatively, you can use uv for faster dependency management:
 
 ```
-python -m pip install -r requirements/development.txt
+uv venv
+source .venv/bin/activate
+uv pip install -e ".[dev]"
 ```
 
 ## Documentation
@@ -111,8 +115,8 @@ the desired statistical properties. Since these tests are quite expensive to run
 validate, they are not run as part of continuous integration (CI) but instead as a pre-release sanity check.
 
 The statistical tests are all run via the `verification.py` script in the project root. The script has some
-extra dependencies listed in the `requirements/verification.txt`, which can be installed using
-`pip install -r` or `conda install --file`. You should also need to install [R](https://www.r-project.org/)
+extra dependencies specified in the `verification` optional dependencies in `pyproject.toml`, which can be installed using
+`pip install -e ".[verification]"` or `uv pip install -e ".[verification]"`. You should also need to install [R](https://www.r-project.org/)
 into your environment. Run this script using:
 
 ```

docs/install.md

@@ -7,7 +7,7 @@ We recommend using `conda` for most users.
 
 ## System requirements
 
-tstrait requires Python 3.8+. Python dependencies are installed automatically by `pip` or `conda`.
+tstrait requires Python 3.10+. Python dependencies are installed automatically by `pip` or `conda`.
 
 ## Via conda
 

pyproject.toml

@@ -1,3 +1,126 @@
 [build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
+requires = [
+    "setuptools>=64",
+    "setuptools-scm>=8",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "tstrait"
+dynamic = [
+    "version",
+]
+description = "Quantitative trait simulation of tree sequence data"
+readme = "README.md"
+maintainers = [
+    { name = "Tskit Developers", email = "admin@tskit.dev" },
+]
+authors = [
+    { name = "Daiki Tagami et al." },
+]
+keywords = [
+    "gwas",
+    "population genetics",
+    "quantitative trait",
+    "simulation",
+    "statistical genetics",
+    "tree sequence",
+    "tskit",
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: MacOS",
+]
+requires-python = ">=3.10"
+dependencies = [
+    "numpy>=1.20.3",
+    "numba>=0.57.0",
+    "pandas>=1.0",
+    "tskit>=0.5.5",
+]
+
+[project.license]
+text = "MIT"
+
+[project.urls]
+Homepage = "https://tskit.dev/tstrait/"
+"Bug Tracker" = "https://github.com/tskit-dev/tstrait/issues"
+Documentation = "https://tskit.dev/tstrait/docs/"
+"Source Code" = "https://github.com/tskit-dev/tstrait"
+
+[project.optional-dependencies]
+test = [
+    "msprime==1.3.4",
+    "numba==0.61.2",
+    "pandas==2.3.2",
+    "tskit==0.6.4",
+    "pytest==8.4.2",
+    "pytest-cov==6.3.0",
+    "pytest-xdist==3.8.0",
+    "scipy==1.15.3",
+]
+docs = [
+    "jupyter-book==1.0.4.post1",
+    "matplotlib==3.10.6",
+    "msprime==1.3.4",
+    "numba==0.61.2",
+    "numpydoc==1.9.0",
+    "pandas==2.3.2",
+    "sphinx-issues==5.0.1",
+    "tskit==0.6.4",
+]
+dev = [
+    "jupyter-book",
+    "matplotlib",
+    "msprime",
+    "numba",
+    "numpy",
+    "numpydoc",
+    "pandas",
+    "pre-commit",
+    "pytest",
+    "scipy",
+    "sphinx",
+    "sphinx-issues",
+    "tskit",
+    "pytest-cov",
+    "pytest-xdist",
+]
+verification = [
+    "matplotlib",
+    "numpy",
+    "pandas",
+    "scipy",
+    "statsmodels",
+    "seaborn",
+    "tqdm",
+    "argparse",
+    "daiquiri",
+    "msprime",
+]
+
+[tool.setuptools]
+packages = [
+    "tstrait",
+]
+
+[tool.setuptools_scm]
+
+[tool.pytest.ini_options]
+testpaths = [
+    "tests",
+]