From 343614933d767700d6d76ca093014b513f345fe7 Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Thu, 17 Nov 2022 09:40:47 -0700
Subject: [PATCH 1/2] CI updates

- use CODECOV token
- install alchemlyb<2 via conda-forge
- add version constraints on mdanalysis>=2 and alchemlyb<2
---
 .github/workflows/ci.yaml | 29 ++++++++++++++++-------------
 setup.py                  |  4 ++--
 2 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 55fcd022..77058ede 100644
--- a/.github/workflows/ci.yaml
+++ b/.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:
@@ -60,7 +67,6 @@ jobs:
         show-channel-urls: true
           
     - name: Conda info
-      shell: bash -l {0}
       run: |
          conda info
          conda list
@@ -68,37 +74,34 @@ jobs:
          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
diff --git a/setup.py b/setup.py
index a9b22553..a5d88214 100644
--- a/setup.py
+++ b/setup.py
@@ -54,8 +54,8 @@
                         'GromacsWrapper>=0.5.1',
                         'numkit',
                         'six',
-                        'mdanalysis',
-                        'alchemlyb',
+                        'mdanalysis>=2',
+                        'alchemlyb<2',
                         'pandas',
                         'pymbar',
       ],

From 06eb469994867bbf5373345fd4d0cc0118ced33a Mon Sep 17 00:00:00 2001
From: Oliver Beckstein <orbeckst@gmail.com>
Date: Thu, 17 Nov 2022 09:49:25 -0700
Subject: [PATCH 2/2] test on Python 3.7 - 3.10

- fix #202
- add testing for Python 3.10
- dropped tests for Python 3.6 (should have been removed in 0.8.0)
- update setup.py and CHANGES
---
 .github/workflows/ci.yaml |  8 ++++----
 CHANGES                   | 11 +++++++++--
 setup.py                  |  1 +
 3 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 77058ede..dc8a68e9 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -31,12 +31,9 @@ jobs:
         # macos runners (latest GROMACS, oldest and latest Python)
       
         os: [ubuntu-latest]
-        python-version: ["3.9"]
+        python-version: ["3.10"]
         gromacs-version: ["4.6.5", "2018.6", "2020.6", "2021.1"]
         include:
-          - os: ubuntu-latest
-            python-version: "3.6"
-            gromacs-version: "2021.1"
           - os: ubuntu-latest
             python-version:  "3.7"
             gromacs-version: "2021.1"
@@ -49,6 +46,9 @@ jobs:
           - os: macos-latest
             python-version: "3.9"
             gromacs-version: "2021.1"
+          - os: macos-latest
+            python-version: "3.10"
+            gromacs-version: "2021.1"
 
     env:
       MPLBACKEND: agg
diff --git a/CHANGES b/CHANGES
index 4be47269..16e9555a 100644
--- a/CHANGES
+++ b/CHANGES
@@ -2,11 +2,18 @@
 CHANGES for MDPOW
 =================
 
-Add summary of changes for each release. Use ISO dates. Reference
+Add summary of changes for each release. Use ISO 8061 dates. Reference
 GitHub issues numbers and PR numbers.
 
+
+
 2022-??-??    0.8.1
-cadeduckworth
+cadeduckworth, orbeckst
+
+Changes
+
+* added support for Python 3.10
+* dropped testing on Python 3.6 
 
 Fixes
 
diff --git a/setup.py b/setup.py
index a5d88214..9ade6c7d 100644
--- a/setup.py
+++ b/setup.py
@@ -29,6 +29,7 @@
           "Programming Language :: Python :: 3.7",
           "Programming Language :: Python :: 3.8",
           "Programming Language :: Python :: 3.9",
+          "Programming Language :: Python :: 3.10",
           "Topic :: Scientific/Engineering :: Chemistry",
           "Topic :: Scientific/Engineering :: Physics",
       ],