Fix pythonapp

.github/workflows/pythonapp.yml

@@ -3,42 +3,40 @@ name: Python application
 on: [push, pull_request]
 
 jobs:
-  lint:
+  pretest:
+    name: AMS Pretest
+
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.11]  # Only run flake8 on Python 3.11
+
+    if: ${{ github.ref != 'refs/heads/misc' }}
+
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+    - uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+        python-version: 3.11
+        mamba-version: "*"
+        miniforge-version: "latest"
+        channels: conda-forge,defaults
+        channel-priority: true
+        activate-environment: anaconda-client-env
+    - shell: bash -el {0}
+      name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install flake8
-    - name: Lint with flake8
+        mamba install -y nbmake pytest-xdist line_profiler  # add'l packages for notebook tests.
+        mamba install --file requirements.txt --file requirements-extra.txt
+        python -m pip install pyscipopt
+        python -m pip install -e .
+    - shell: bash -el {0}
+      name: Run pip check
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 .
-
-  test-notebooks:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.11]  # Only test notebooks on Python 3.11
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+        pip check || true  # Allow pip check to fail without failing the job
+    - shell: bash -el {0}
+      name: Test with pytest
       run: |
-        python -m pip install --upgrade pip
-        pip install nbmake
-    - name: Test notebooks
+        pytest
+    - shell: bash -el {0}
+      name: Test notebooks.
       run: |
         pytest --nbmake examples --ignore=examples/verification
 
@@ -78,6 +76,10 @@ jobs:
       name: Test with pytest
       run: |
         pytest
+    - shell: bash -el {0}
+      name: Test notebooks.
+      run: |
+        pytest --nbmake examples --ignore=examples/verification
     - name: Build a distribution if tagged
       if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') && matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'
       run: |