WIP

Author: benjeffery

.circleci/config.yml

@@ -27,8 +27,10 @@ jobs:
           command: |
             sudo apt-get update
             sudo apt-get install libgsl0-dev libcunit1-dev libconfig-dev ninja-build valgrind clang
-            pip install --user build twine meson
-            pip install --user -e ".[test]"
+            pip install uv
+            uv venv
+            uv pip install build twine meson
+            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 +41,14 @@ 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:

.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 }}-${{ matrix.python}}-conda-v3-${{ hashFiles('requirements/conda-minimal.txt') }}-${{ hashFiles('pyproject.toml') }}
-
-      - 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 }}
@@ -72,18 +64,17 @@ 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 gsl
 
-      - name: Install a specific version of uv
+      - 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: | 
           uv pip install -r pyproject.toml --extra test

pyproject.toml

@@ -78,11 +78,12 @@ test = [
     "kastore==0.3.3",
     "newick==1.10.0",
     "pytest==8.4.1",
+    "pytest-cov",
     "pytest-xdist==3.8.0",
     "python_jsonschema_objects==0.5.7",
     "setuptools==80.9.0",
-    "scipy==1.13.1; python_version<='3.9'",
-    "scipy==1.16.1; python_version>'3.9'",
+    "scipy==1.13.1; python_version<='3.10'",
+    "scipy==1.16.1; python_version>'3.10'",
     "tskit==0.6.4"
 ]