From c710d687e8c4d536967e2a10ed7dadc836ff52ce Mon Sep 17 00:00:00 2001
From: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Date: Thu, 15 Aug 2024 16:34:26 -0700
Subject: [PATCH] Fix CI

remove dev openmm

see if this helps anything pass
---
 .github/workflows/CI.yml          | 47 +++++++++----------------------
 devtools/conda-envs/test_env.yaml |  2 +-
 2 files changed, 15 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 280ea828..f21b0d59 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -17,6 +17,10 @@ concurrency:
   group: "${{ github.workflow }}-${{ github.ref }}"
   cancel-in-progress: true
 
+defaults:
+  run:
+    shell: bash -leo pipefail {0}    
+
 jobs:
   test:
     name: ${{ matrix.os }}, py-${{ matrix.python-version }}, OpenMM-${{ matrix.openmm }}, pymbar-${{ matrix.pymbar-version }}
@@ -24,16 +28,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]
-        openmm: ["7.7", "8.0"]
-        os: [macOS-latest, ubuntu-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+        openmm: ["8.0", "8.1.1", "8.1.2"]
+        os: [macOS-latest, ubuntu-latest, macOS-12]
         pymbar-version: ["4"]
         include:
-          # Test openmm dev build on newest python + linux
-          - openmm: "dev"
-            python-version: "3.10"
-            os: ubuntu-latest
-            pymbar-version: "4"
           # Test newest python, openmm, and pymbar we support on windows
           - openmm: "8.0"
             python-version: "3.10"
@@ -44,55 +43,37 @@ jobs:
             python-version: "3.10"
             os: ubuntu-latest
             pymbar-version: "3"
-        exclude:
-          # There are no py 3.10 builds of openmm 7.7
-          - openmm: "7.7"
-            python-version: "3.10"
 
     steps:
       - uses: actions/checkout@v3
       - name: Additional info about the build
-        shell: bash
         run: |
           uname -a
           df -h
           ulimit -a
 
-      - name: Setup micromamba for openmm dev
-        uses: mamba-org/provision-with-micromamba@main
-        if: ${{ matrix.openmm == 'dev' }}
-        with:
-          channels: jaimergp/label/unsupported-cudatoolkit-shim,conda-forge/label/openmm_dev/linux-64,conda-forge
-          environment-file: devtools/conda-envs/test_env.yaml
-          channel-priority: flexible
-          environment-name: openmmtools-test
-          extra-specs: |
-            python==${{ matrix.python-version }}
-            openmm==8.0.0dev3
-            pymbar==${{ matrix.pymbar-version }}.*
-
       - name: Setup micromamba
-        uses: mamba-org/provision-with-micromamba@main
-        if: ${{ matrix.openmm != 'dev' }}
+        uses: mamba-org/setup-micromamba@v1
         with:
-          channels: jaimergp/label/unsupported-cudatoolkit-shim,conda-forge
           environment-file: devtools/conda-envs/test_env.yaml
-          channel-priority: strict
           environment-name: openmmtools-test
-          extra-specs: |
+          create-args: >-
             python==${{ matrix.python-version }}
             openmm==${{ matrix.openmm }}
             pymbar==${{ matrix.pymbar-version }}.*
+          condarc: |
+            channels:
+              - conda-forge
+              - jaimergp/label/unsupported-cudatoolkit-shim
+
             
       - name: Install package
-        shell: bash -l {0}
         run: |
           python -m pip install . --no-deps
           micromamba list
           micromamba info
 
       - name: Run tests
-        shell: bash -l {0}
         run: |
           # pytest -v --cov=openmmtools --cov-report=xml --color=yes openmmtools/tests/
           nosetests openmmtools/tests --nocapture --cover-tests --with-coverage --cover-package=openmmtools --cover-xml --cover-xml-file=coverage.xml --verbosity=2 --with-timer --with-doctest -a '!slow'
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
index ec8a0684..aeaf7a82 100644
--- a/devtools/conda-envs/test_env.yaml
+++ b/devtools/conda-envs/test_env.yaml
@@ -4,7 +4,7 @@ channels:
 dependencies:
     # Base depends
   - cython
-  - hdf5 <=1.14.0  # Macos has problem with newer releases (1.14.x) to date
+    #- hdf5 <=1.14.0  # Macos has problem with newer releases (1.14.x) to date
   - libnetcdf >=4.6.2 # workaround for libssl issues
   - mdtraj
   - mpiplus