update versions in CI

.github/workflows/docs.yml

@@ -15,18 +15,17 @@ jobs:
     # won't be valid. But to avoid confusion, we explicitly restrict the scope.
     # See https://github.com/popsim-consortium/stdpopsim/issues/662
     if: github.repository == 'popsim-consortium/stdpopsim'
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.10
 
       - name: Install deps
         run: |
           python -m pip install wheel
-          python -m pip install numpy==1.19.2  # for scikit-allel
           python -m pip install -r requirements/CI/requirements.txt
           # Install the local package so that stdpopsim is in the path,
           # which is needed for generating docs `command-output`.
@@ -37,7 +36,7 @@ jobs:
 
       - name: Checkout docs site
         if: (!github.event.pull_request)
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: popsim-consortium/stdpopsim-docs
           token: ${{ secrets.POPSIMBOT_STDPOPSIM_DOCS_TOKEN }}

.github/workflows/pre-commit.yml

@@ -8,10 +8,10 @@ on:
 
 jobs:
   pre-commit:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.8
-      - uses: pre-commit/action@v2.0.0
+          python-version: 3.12
+      - uses: pre-commit/action@v3.0.1

.github/workflows/tests.yml

@@ -17,62 +17,52 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macos-12, windows-latest]
-        python: ["3.8", "3.10"]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python: ["3.9", "3.10"]
     env:
       CONDA_ENV_NAME: stdpopsim
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python }}
     steps:
       - name: cancel previous runs
-        uses: styfle/cancel-workflow-action@0.6.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
 
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: find conda
         id: find-conda
         run: |
           echo "CONDA=$CONDA" >> $GITHUB_OUTPUT
 
-      - name: fix conda permissions
-        if: runner.os == 'macOS'
-        run: |
-          # Fix incorrect conda permissions on mac that prevent cache restore.
-          sudo chown -R $USER:staff ${{ steps.find-conda.outputs.CONDA }}
-
       - name: cache conda
         id: cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           # Increase this to reset the cache if the key hasn't changed.
-          CACHE_NUM: 9
+          CACHE_NUM: 11
         with:
           path: |
             ${{ steps.find-conda.outputs.CONDA }}/envs/${{ env.CONDA_ENV_NAME }}
             ~/.bash_profile
           key: ${{ runner.os }}-${{ matrix.python }}-conda-${{ hashFiles('requirements/CI/*') }}-${{ env.CACHE_NUM }}
 
       - name: install conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         if: steps.cache.outputs.cache-hit != 'true'
         with:
           activate-environment: ${{ env.CONDA_ENV_NAME }}
           python-version: ${{ matrix.python }}
           channels: conda-forge
           channel-priority: strict
           auto-update-conda: true
-          use-only-tar-bz2: true
 
-      - name: move profile
-        if: steps.cache.outputs.cache-hit != 'true' && runner.os != 'Windows'
+      - name: Fix windows .profile
+        if: steps.cache.outputs.cache-hit != 'true' && runner.os == 'Windows'
         run: |
-          # The setup-miniconda action leaves different shell init files for
-          # different OSes. Bash gives priority to ~/.bash_profile, so here we
-          # ensure that's used for all platforms.
-          mv ~/.profile ~/.bash_profile
+          cp ~/.bash_profile ~/.profile
 
       - name: install dependencies
         if: steps.cache.outputs.cache-hit != 'true'

requirements/CI/conda.txt

@@ -1,2 +1,2 @@
-msprime==1.2.0
-slim==4.0
+msprime==1.3.3
+slim==4.3

requirements/CI/requirements.txt

@@ -1,21 +1,20 @@
-coverage==6.3.3
+coverage==7.5.4
 flake8==5.0.4
-pytest==7.3.2
-pytest-cov==4.1.0
-pytest-xdist==3.3.1
-setuptools-scm==7.1.0
+pytest==8.2.2
+pytest-cov==5.0.0
+pytest-xdist==3.6.1
+setuptools-scm==8.1.0
 sphinx==5.0.2
 sphinx-argparse==0.4.0
 sphinx-issues==3.0.1
 sphinx_rtd_theme==1.2.0
 sphinxcontrib-programoutput==0.17
-msprime==1.2.0
-attrs==21.4.0
+attrs==24.2.0
 appdirs==1.4.4
-humanize==4.6.0
+humanize==4.10.0
 pyslim==1.0.4
-numpy==1.23.5
-scipy==1.10.1
+numpy==1.26.4
+scipy==1.13.1
 scikit-allel==1.3.6
 biopython==1.80
 demes==0.2.2