Reqs in pyproject

Author: benjeffery

.circleci/config.yml

@@ -27,8 +27,9 @@ jobs:
           command: |
             sudo apt-get update
             sudo apt-get install libgsl0-dev libcunit1-dev libconfig-dev ninja-build valgrind clang
-            pip install --user -r requirements/CI-complete/requirements.txt
-            pip install --user build twine meson
+            pip install uv
+            uv venv
+            uv pip install -r pyproject.toml --extra test
             # way to set path persistently https://circleci.com/docs/2.0/env-vars/#setting-path
             echo 'export PATH=/home/circleci/.local/bin:$PATH' >> $BASH_ENV
       - save_cache:
@@ -39,12 +40,14 @@ jobs:
       - run:
           name: Compile Python
           command: |
+            source .venv/bin/activate
             make allchecks
 
       - run:
           name: Run highlevel tests
           # Run tests without background threads
           command: |
+            source .venv/bin/activate
             pytest --cov=msprime --cov-report=xml --cov-branch -n 0 tests
 
       - codecov/upload:
@@ -59,11 +62,13 @@ jobs:
       - run:
           name: Compile C with gcc
           command: |
+            source .venv/bin/activate
             CFLAGS=--coverage meson lib/ build-gcc && ninja -C build-gcc
 
       - run:
           name: Run the low-level tests.
           command: |
+            source .venv/bin/activate
             ninja -C build-gcc test
 
       - run:
@@ -100,7 +105,7 @@ jobs:
       - run:
           name: Make sure we can build a distribution.
           command: |
-            python -m pip install build
+            source .venv/bin/activate
             python -m build --sdist
             python -m build --wheel
             python -m twine check dist/*.tar.gz --strict

.github/workflows/docs.yml

@@ -8,8 +8,7 @@ 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
     with:
-      requirements-path: requirements/CI-docs/requirements.txt
       additional-setup: sudo apt-get install -y libgsl0-dev
       make-command: make cmodule

.github/workflows/tests.yml

@@ -43,16 +43,8 @@ jobs:
         with:
           submodules: true
 
-      - name: Cache conda and dependencies
-        id: cache
-        uses: actions/cache@v4.2.2
-        with:
-          path: ${{ env.CONDA }}/envs
-          key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v2-${{ hashFiles('requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('requirements/CI-tests-pip/requirements.txt') }}
-
-      - name: Install Conda
+      - name: Install Conda (needed for GSL)
         uses: conda-incubator/setup-miniconda@v3.1.1
-        if: steps.cache.outputs.cache-hit != 'true'
         with:
           activate-environment: anaconda-client-env
           python-version: ${{ matrix.python }}
@@ -72,17 +64,20 @@ jobs:
         run: |
           cp ~/.bash_profile ~/.profile
 
-      - name: Install conda deps
+      - name: Install GSL
         if: steps.cache.outputs.cache-hit != 'true'
         shell: bash -l {0} #We need a login shell to get conda
-        run: conda install --yes --file=requirements/CI-tests-conda/requirements.txt
+        run: conda install gsl
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          version: "0.8.15"
+      
       - name: Install pip deps
-        if: steps.cache.outputs.cache-hit != 'true'
         shell: bash -l {0}
         run: | 
-          pip install -r requirements/CI-tests-pip/requirements.txt
-          pip uninstall -y msprime
+          uv pip install -r pyproject.toml --extra test
 
       - name: Build module
         env:

docs/development.md

@@ -64,17 +64,18 @@ on the documentation because it requires a locally built version of the
 
 ### Python requirements
 
-The list of packages needed for development are listed in
-``requirements/development.txt``. Install these 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
+$ python -m pip install -e ".[dev]"
 ```
-or
+
+For conda users, you may need to install GSL first:
 ```
-$ python -m pip install -r requirements/development.txt
+conda install gsl
+pip install -e ".[dev]"
 ```
-depending on whether you are a conda or pip user.
 
 ## Overview
 
@@ -734,9 +735,13 @@ new simulation functionality, as subtle statistical bugs can easily slip in
 unnoticed.
 
 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`. Run
-this script using:
+The script has some extra dependencies, which can be installed using:
+
+```
+pip install -e ".[verification]"
+```
+
+Run this script using:
 
 ```{code-block} bash
 

pyproject.toml

@@ -69,6 +69,92 @@ include-package-data = true
 [tool.setuptools_scm]
 write_to = "msprime/_version.py"
 
+[project.optional-dependencies]
+test = [
+    "bintrees==2.2.0",
+    "build==1.3.0",
+    "daiquiri==3.2.5.1; python_version<='3.9'",
+    "daiquiri==3.3.0; python_version>'3.9'",
+    "demes==0.2.3",
+    "kastore==0.3.3",
+    "meson==1.9.0",
+    "newick==1.10.0",
+    "pytest==8.4.1",
+    "pytest-cov==6.2.1",
+    "pytest-xdist==3.8.0",
+    "python_jsonschema_objects==0.5.7",
+    "setuptools==80.9.0",
+    "scipy==1.13.1; python_version<='3.10'",
+    "scipy==1.16.1; python_version>'3.10'",
+    "tskit==0.6.4",
+    "twine==6.2.0"
+]
+
+docs = [
+    "daiquiri==3.3.0",
+    "demes==0.2.3",
+    "demesdraw==0.4.0",
+    "jupyter-book==1.0.4.post1",
+    "networkx==3.5",
+    "matplotlib==3.10.3",
+    "newick==1.10.0",
+    "setuptools==80.9.0",
+    "sphinx-argparse==0.5.2",
+    "sphinx-book-theme",
+    "sphinx-issues==5.0.1",
+    "tskit==0.6.4",
+    "scipy==1.16.1"
+]
+
+dev = [
+    "docutils==0.21.2",
+    "asv==0.6.1",
+    "bintrees",
+    "coverage",
+    "daiquiri",
+    "demes>=0.2.0",
+    "demesdraw",
+    "flake8",
+    "matplotlib>=3.4.0",
+    "meson>=0.61.0",
+    "mock",
+    "mypy",
+    "ninja",
+    "numpy",
+    "pre-commit",
+    "pytest",
+    "pytest-cov",
+    "pytest-xdist",
+    "tskit>=0.5.2",
+    "kastore",
+    "sphinx-book-theme",
+    "scipy",
+    "setuptools_scm",
+    "sphinx>=4.4",
+    "sphinx-argparse",
+    "sphinx-issues",
+    "jupyter-book",
+    "networkx",
+    "newick>=1.3.0",
+    "python_jsonschema_objects"
+]
+
+verification = [
+    "dendropy",
+    "matplotlib",
+    "numpy",
+    "pandas",
+    "pyvolve",
+    "scipy==1.2",
+    "scikit-allel",
+    "statsmodels",
+    "seaborn",
+    "tqdm",
+    "argparse",
+    "daiquiri",
+    "pyslim>=1.0"
+]
+
 [tool.pytest.ini_options]
 addopts = "-n 4"
 testpaths = ["tests"]