CI updates

- use CODECOV token
- install alchemlyb<2 via conda-forge
- add version constraints on mdanalysis>=2 and alchemlyb<2

.github/workflows/ci.yaml

@@ -16,6 +16,10 @@ concurrency:
   group: "${{ github.ref }}-${{ github.head_ref }}"
   cancel-in-progress: true
 
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
   test:
     runs-on: ${{ matrix.os }}
@@ -39,6 +43,9 @@ jobs:
           - os: ubuntu-latest
             python-version: "3.8"
             gromacs-version: "2021.1"
+          - os: ubuntu-latest
+            python-version: "3.9"
+            gromacs-version: "2021.1"
           - os: macos-latest
             python-version: "3.9"
             gromacs-version: "2021.1"
@@ -48,7 +55,7 @@ jobs:
 
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - uses: conda-incubator/setup-miniconda@v2
       with:
@@ -60,45 +67,41 @@ jobs:
         show-channel-urls: true
 
     - name: Conda info
-      shell: bash -l {0}
       run: |
          conda info
          conda list
          conda config --show-sources
          conda config --show
 
     - name: Python version
-      shell: bash -l {0}
       run: |
          python -c "import sys; print(sys.version)"                
 
-    - name: Install non-versioned package dependencies
-      shell: bash -l {0}
+    - name: Install package dependencies
       run: |
-         mamba install six numpy scipy matplotlib-base pandas scikit-learn pyyaml mdanalysis numexpr numkit gromacswrapper
+         mamba install six numpy scipy matplotlib-base pandas scikit-learn pyyaml "mdanalysis>=2" numkit gromacswrapper "alchemlyb<2"
+ 
     - name: Install pytest+plugins and pybol
-      shell: bash -l {0}
       run: |
          mamba install pytest pytest-pep8 pytest-cov codecov
          python -m pip install pybol
 
     - name: Install GROMACS (${{ matrix.gromacs-version }})
-      shell: bash -l {0}
       run: |
          mamba install 'gromacs==${{ matrix.gromacs-version }}' pocl
 
-    - name: Install package (and alchemlyb with dependencies)
-      shell: bash -l {0}
+    - name: Install package (with no dependencies)
       run: |
-        python -m pip install .
+        python -m pip install . --no-deps
 
     - name: Run tests
-      shell: bash -l {0}
       run: |
         pytest -v --durations=20 --cov=mdpow --cov-report=xml --color=yes ./mdpow/tests
 
     - name: Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
         file: ./coverage.xml
         fail_ci_if_error: true

setup.py

@@ -54,8 +54,8 @@
                         'GromacsWrapper>=0.5.1',
                         'numkit',
                         'six',
-                        'mdanalysis',
-                        'alchemlyb',
+                        'mdanalysis>=2',
+                        'alchemlyb<2',
                         'pandas',
                         'pymbar',
       ],