Fix CI run on ubuntu-latest-py3.12

.github/workflows/pytest.yaml

@@ -19,14 +19,14 @@ jobs:
     strategy:
       matrix:
         os:
-        - macos-13
-        - macos-latest
+        # - macos-13
+        # - macos-latest
         - ubuntu-latest
-        - windows-latest
+        # - windows-latest
         python-version:
-        - "3.8"  # Earliest version supported by ixmp
-        - "3.9"
-        - "3.10"
+        # - "3.8"  # Earliest version supported by ixmp
+        # - "3.9"
+        # - "3.10"
         - "3.11"
         - "3.12"  # Latest supported by ixmp
         gams-version:
@@ -67,39 +67,43 @@ jobs:
       with:
         fetch-depth: ${{ env.depth }}
         fetch-tags: true
+
+    - name: Debug python path
+      run: python -c "import sys; print(sys.executable, sys.path)"
+      shell: bash
 
     - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: pip
         cache-dependency-path: "**/pyproject.toml"
 
-    - uses: ts-graphviz/setup-graphviz@v2
-      # TEMPORARY Work around ts-graphviz/setup-graphviz#630
-      if: ${{ ! startswith(matrix.os, 'macos-') }}
+    # - uses: ts-graphviz/setup-graphviz@v2
+    #   # TEMPORARY Work around ts-graphviz/setup-graphviz#630
+    #   if: ${{ ! startswith(matrix.os, 'macos-') }}
 
     - uses: r-lib/actions/setup-r@v2
       id: setup-r
 
-    - name: Cache GAMS installer and R packages
-      uses: actions/cache@v4
-      with:
-        path: |
-          gams
-          ${{ env.R_LIBS_USER }}
-        key: ${{ matrix.os }}-R${{ steps.setup-r.outputs.installed-r-version }}
-        restore-keys: |
-          ${{ matrix.os }}-
-
-    - uses: iiasa/actions/setup-gams@main
-      with:
-        version: ${{ matrix.gams-version }}
-        license: ${{ secrets.GAMS_LICENSE }}
-
-    - name: Set RETICULATE_PYTHON
-      # Use the environment variable set by the setup-python action, above.
-      run: echo "RETICULATE_PYTHON=$pythonLocation" >> $GITHUB_ENV
-      shell: bash
+    # - name: Cache GAMS installer and R packages
+    #   uses: actions/cache@v4
+    #   with:
+    #     path: |
+    #       gams
+    #       ${{ env.R_LIBS_USER }}
+    #     key: ${{ matrix.os }}-R${{ steps.setup-r.outputs.installed-r-version }}
+    #     restore-keys: |
+    #       ${{ matrix.os }}-
+
+    # - uses: iiasa/actions/setup-gams@main
+    #   with:
+    #     version: ${{ matrix.gams-version }}
+    #     license: ${{ secrets.GAMS_LICENSE }}
+
+    # - name: Set RETICULATE_PYTHON
+    #   # Use the environment variable set by the setup-python action, above.
+    #   run: echo "RETICULATE_PYTHON=$pythonLocation" >> $GITHUB_ENV
+    #   shell: bash
 
     - name: Install Python package and dependencies
       # [docs] contains [tests], which contains [report,tutorial]
@@ -116,21 +120,52 @@ jobs:
         # TEMPORARY Work around pretenders/pretenders#153
         pip install "bottle < 0.13"
 
+    - name: Debug jupyter kernelspec --version
+      run: jupyter kernelspec --version
+      shell: bash
+
+    - name: Debug which Rscript is used below
+      run: which Rscript
+      shell: bash
+
+    - name: Debug PATH
+      run: echo $PATH
+      shell: bash
+
+    - name: Debug python path
+      run: python -c "import sys; print(sys.executable, sys.path)"
+      shell: bash
+
     - name: Install R dependencies and tutorial requirements
       run: |
         install.packages(c("remotes", "Rcpp"))
         remotes::install_cran(
           c("IRkernel", "reticulate"),
           dependencies = TRUE,
-          # force = TRUE,
+          force = TRUE,
         )
 
+        system2('which', 'python', TRUE, TRUE)
+        system2('python', '-c "import sys; print(sys.executable, sys.path)"', TRUE, TRUE)
+
+        system2('which', 'pip', TRUE, TRUE)
+        system2('pip', 'list', TRUE, TRUE)
+
+        system2('which', 'jupyter', TRUE, TRUE)
+        system2('which', 'jupyter-kernelspec', TRUE, TRUE)
+
+        paste(c(shQuote('jupyter'), c('kernelspec', '--version')), collapse = " ")
+
+        system('jupyter-kernelspec --version')
+
+        system2('jupyter-kernelspec', '--version', TRUE, TRUE)
+
         IRkernel::installspec()
 
         # commented: for debugging
         # print(reticulate::py_config())
         # reticulate::py_run_string("import os; print(os.environ)")
-      shell: Rscript {0}
+      shell: Rscript --verbose {0}
 
     - name: Run test suite using pytest
       run: |