ci: bump pysam and poetry to support py3.14

.github/workflows/release.yml

@@ -38,7 +38,7 @@ jobs:
       - name: Install Poetry
         if: ${{ steps.release.outputs.release_created }}
         run: |
-          pip install 'poetry==2.2.1'  # keep version synced with dev-env.yml
+          pip install 'poetry==2.3.4'  # keep version synced with dev-env.yml
           poetry --version
 
       - name: Bump version for developmental release
@@ -53,7 +53,7 @@ jobs:
         run: |
           poetry build --ansi
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v7
         if: ${{ steps.release.outputs.release_created }}
         with:
           name: dist
@@ -69,7 +69,7 @@ jobs:
       id-token: write
     steps:
       - name: Get artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           merge-multiple: true
           path: dist

.github/workflows/tests.yml

@@ -29,14 +29,14 @@ jobs:
 
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Setup Miniforge
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v4
         with:
           conda-remove-defaults: true
           activate-environment: panct
-          auto-activate-base: false
+          auto-activate: false
           miniforge-version: latest
           use-mamba: true
 
@@ -46,7 +46,7 @@ jobs:
         shell: bash
 
       - name: Cache Conda env
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: ${{ env.CONDA }}/envs
           key:
@@ -82,8 +82,9 @@ jobs:
           nox --verbose --python=${{ matrix.python }}
 
       - name: Upload coverage data
-        if: always() && matrix.session == 'tests'
-        uses: "actions/upload-artifact@v4"
+        # if: always() && matrix.session == 'tests'
+        if: false  # temporarily disable coverage upload for now
+        uses: actions/upload-artifact@v7
         with:
           name: coverage-data
           path: ".coverage.*"
@@ -93,7 +94,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Check for large files
         uses: ppremk/lfs-warning@v3.3

dev-env.yml

@@ -5,11 +5,11 @@ channels:
 dependencies:
   - conda-forge::python=3.10 # the lowest version of python that we formally support; keep in sync with release.yml, tests.yml, .readthedocs.yaml, and noxfile.py
   - conda-forge::pip==25.2
-  - aryarm::gbz-base==0.2.0
-  - conda-forge::poetry==2.2.1 # should keep this in sync with version in release.yml
+  - aryarm::gbz-base==0.4.0
+  - conda-forge::poetry==2.3.4 # should keep this in sync with version in release.yml
   - conda-forge::nox==2025.5.1
   - conda-forge::poetry-conda==0.1.4
   - conda-forge::poetry-plugin-export==1.9.0
   - pip:
     - nox-poetry==1.2.0
-    - poetry-plugin-shell==1.0.1
+    - poetry-plugin-shell==1.0.1