Merge branch 'main' into main

choderalab · Sep 27, 2024 · 7efa54e · 7efa54e
2 parents 63f4562 + c2a13c0
commit 7efa54e
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,4 @@
+# See https://github.com/choderalab/openmmtools/pull/741#issuecomment-2341717861
+e7144c193ad307aa9ef2f852feecf0dcdd2ef352
+7ebe1ab6e86582e8ed5e2cc2103d8eaa599ec3f2
+562e0d305b96082cac337ce2320f5f7835385618
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -17,23 +17,22 @@ 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 }}
     runs-on: ${{ matrix.os }}
     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"
@@ -45,61 +44,46 @@ jobs:
             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"
+          # no py312 builds of openmm 8.0
+          - openmm: "8.0"
+            python-version: "3.12"
 
     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
+          python -m pip install -e . --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'
+          pytest -n logical -v --cov=openmmtools --cov-report=xml --cov-report=term --color=yes openmmtools/tests/
 
       - name: CodeCov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           file: ./coverage.xml
           flags: unittests
-          name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}-openmm-${{ matrix.openmm }}
+          name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}-openmm-${{ matrix.openmm }}-pymbar-${{ matrix.pymbar-version }}
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/gpu-runner.yaml b/.github/workflows/gpu-runner.yaml
@@ -0,0 +1,107 @@
+name: Self-Hosted Runner
+on:
+  workflow_dispatch:
+
+jobs:
+  start-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: read
+    outputs:
+      mapping: ${{ steps.aws-start.outputs.mapping }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::009563297724:role/gha-runner-omsf
+          aws-region: us-east-1
+      - name: Create cloud runner
+        id: aws-start
+        uses: omsf-eco-infra/gha-runner@v0.2.0
+        with:
+          provider: "aws"
+          action: "start"
+          aws_image_id: ami-053912f3a44543f8c 
+          aws_instance_type: g4dn.xlarge
+          aws_region_name: us-east-1
+          aws_home_dir: /home/ubuntu
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+
+  self-hosted-test:
+    runs-on: self-hosted
+    timeout-minutes: 720  # 12 hours  
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
+    env:
+      OE_LICENSE: ${{ github.workspace }}/oe_license.txt
+
+    needs:
+      - start-aws-runner
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Print disk usage
+        run: "df -h"
+
+      - name: Print Docker details
+        run: "docker version || true"
+
+      - name: Check for nvidia-smi
+        run: "nvidia-smi"
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: devtools/conda-envs/test_env.yaml
+          environment-name: openfe_env
+
+      - name: "Check if OpenMM can get a GPU"
+        run: python -m openmm.testInstallation
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+          pip list
+
+      - name: Test OE License & Write License to File
+        env:
+          OE_LICENSE_TEXT: ${{ secrets.OE_LICENSE }}
+        run: |
+          echo "${OE_LICENSE_TEXT}" > ${OE_LICENSE}
+          python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'OpenEye license checks failed!'"
+
+      - name: "Run tests"
+        run: |
+          pytest -n 4 -v --durations=10 --cov=openmmtools --cov-report=term
+
+  stop-aws-runner:
+    runs-on: ubuntu-latest
+    permissions:
+        id-token: write
+        contents: read
+    needs:
+      - start-aws-runner
+      - self-hosted-test
+    if: ${{ always() }}
+    steps:
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          role-to-assume: arn:aws:iam::009563297724:role/gha-runner-omsf
+          aws-region: us-east-1
+      - name: Stop instances
+        uses: omsf-eco-infra/gha-runner@v0.2.0
+        with:
+          provider: "aws"
+          action: "stop"
+          instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }}
+          aws_region_name: us-east-1
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
diff --git a/.github/workflows/self-hosted-gpu-test.yml b/.github/workflows/self-hosted-gpu-test.yml
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -2,34 +2,29 @@ name: openmmtools-test
 channels:
   - conda-forge
 dependencies:
-    # Base depends
+  # Base depends
   - cython
-  - 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
-  - netcdf4 >=1.4.2 # after bugfix: "always return masked array by default, even if there are no masked values"
+  - netcdf4
   - numba
   - numpy
   - openmm
-  #- parmed  # Test to see if this fixes the docs
   - pip
   - pymbar
   - python
   - python
   - pyyaml
-  - scipy
+  - scipy < 1.14
   - setuptools
   - sphinxcontrib-bibtex
-    # Testing
+  # Testing
   - codecov
-  - nose
-  - nose-timer
+  - coverage
   - pytest
   - pytest-cov
-  - coverage
-
+  - pytest-xdist
   # docs
   - numpydoc
-  - sphinxcontrib-bibtex
   - sphinx-rtd-theme
+  - sphinxcontrib-bibtex
diff --git a/openmmtools/__init__.py b/openmmtools/__init__.py
@@ -13,3 +13,6 @@
 __version__ = versions['version']
 __git_revision__ = versions['full-revisionid']
 del get_versions, versions
+
+from . import _version
+__version__ = _version.get_versions()['version']