Move reqs into pyproject, remove setup.py

.github/workflows/docs.yml

@@ -36,7 +36,7 @@ jobs:
             /usr/share/miniconda/envs/anaconda-client-env
             ~/osx-conda
             ~/.profile
-          key: conda-v${{ env.CACHE_NUM }}-${{ hashFiles('requirements/CI-docs/requirements.txt') }}
+          key: conda-v${{ env.CACHE_NUM }}-${{ hashFiles('pyproject.toml') }}
 
       - name: Install Conda
         uses: conda-incubator/[email protected]
@@ -54,11 +54,14 @@ jobs:
         run: |
           conda install --yes slim
 
-      - name: Install pip deps
+      - name: Install uv and pip deps
         if: steps.cache.outputs.cache-hit != 'true'
         shell: bash -l {0}
         run: |
-          pip install -r requirements/CI-docs/requirements.txt
+          pip install uv
+          uv pip install --system -r pyproject.toml --extra docs
+          # Install current pyslim as editable to ensure we get the latest version
+          uv pip install --system -e .
 
       # # Retaining commented block for next devel cycle
       # - name: Build SLiM

.github/workflows/tests.yml

@@ -50,7 +50,6 @@ jobs:
         uses: mamba-org/[email protected]
         with:
           environment-name: anaconda-client-env
-          environment-file: requirements/CI-conda/ci-environment.yml
           cache-environment: true
           create-args: |
             python=${{ matrix.python }}
@@ -92,6 +91,12 @@ jobs:
           cmake -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release ..
           make -j 2
 
+      - name: Install uv and dependencies
+        shell: bash -l {0}
+        run: |
+          pip install uv
+          uv pip install --system -r pyproject.toml --extra test
+
       - name: Install SLiM macos / linux
         if: (matrix.os == 'macos-latest' || matrix.os == 'ubuntu-24.04')
         run: |

docs/development.md

@@ -21,7 +21,7 @@ To install a particular version of ``pyslim`` from source, e.g., to obtain a rec
 ```bash
 git clone https://github.com/tskit-dev/pyslim.git
 cd pyslim
-python setup.py install --user
+python -m pip install -e ".[dev]"
 ```
 
 
@@ -48,7 +48,7 @@ git clone [email protected]:YOUR_GITHUB/pyslim.git
 ```
 
 - Install the development requirements using
-  ``python3 -m pip install -r requirements/development.txt``.
+  ``python3 -m pip install -e ".[dev]"``.
 - Run the tests to ensure everything has worked: ``python3 -m pytest tests``. These should
   all pass.
 - Make your changes in a local branch, and open a pull request on GitHub when you

pyproject.toml

@@ -0,0 +1,91 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyslim"
+dynamic = ["version"]
+description = "Manipulate tree sequences produced by SLiM."
+readme = "README.md"
+license = {text = "MIT"}
+authors = [
+    {name = "Peter Ralph", email = "[email protected]"},
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: POSIX",
+    "Operating System :: Microsoft :: Windows",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+keywords = ["tree sequences", "tskit"]
+requires-python = ">=3.9"
+dependencies = [
+    "msprime>=1.0.1",
+    "tskit",
+    "numpy",
+]
+
+[project.urls]
+homepage = "https://github.com/tskit-dev/pyslim"
+repository = "https://github.com/tskit-dev/pyslim"
+"Bug Reports" = "https://github.com/tskit-dev/pyslim/issues"
+
+[tool.setuptools]
+packages = ["pyslim"]
+include-package-data = true
+
+[tool.setuptools.dynamic]
+version = {attr = "pyslim._version.pyslim_version"}
+
+[project.optional-dependencies]
+test = [
+    "flake8==7.1.2",
+    "pytest==8.3.5", 
+    "pytest-cov==6.1.1",
+    "pytest-xdist==3.6.1",
+    "filelock==3.19.1",
+    "tskit==0.6.4",
+    "msprime>=1.2.0",
+    "matplotlib==3.9.4",
+    "pandas==2.3.2",
+]
+
+docs = [
+    "jupyter-book==1.0.4.post1",
+    "matplotlib==3.10.3",
+    "msprime==1.3.4",
+    "pandas==2.2.3",
+    "PyGithub==2.6.1",
+    "setuptools-scm==8.2.1",
+    "sphinx-argparse==0.5.2",
+    "sphinx-issues==5.0.0",
+    "tskit==0.6.3",
+]
+
+dev = [
+    "flake8>=7.0",
+    "pytest>=8.0", 
+    "pytest-cov>=6.0",
+    "pytest-xdist>=3.0",
+    "numpy",
+    "filelock",
+    "tskit>=0.6.3",
+    "msprime>=1.2.0",
+    "matplotlib>=3.0",
+    "pandas>=2.0",
+    "jupyter-book>=1.0",
+    "setuptools-scm>=8.0",
+    "sphinx-argparse>=0.5",
+    "sphinx-issues>=5.0",
+]