add python 3.12 and macOS-13 to test matrix (#571)

* add python 3.12 and macOS-13 to test matrix * change minimum python version to 3.9 in yml files * change overlap in packmol args * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update py version in windows yml file * bleeding edge tests was not installing hoomd, but needs it for GMSO tests * pin mbuild to >0.17 so python 3.12 tests don't fail * Fix bonding in custom ethane pdb file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove hoomd install from bleeding test workflow, not needed * only test py versions on ubuntu, test arch versions on py3.12 * try to fix formatting --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
mosdef-hub · Jun 26, 2024 · fdd7dcf · fdd7dcf
1 parent 6939db1
commit fdd7dcf
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Showing 7 changed files with 54 additions and 23 deletions.
diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -13,16 +13,13 @@ on:
 jobs:
   test:
     if: github.event.pull_request.draft == false
-    name: Foyer Tests
+    name: Foyer Tests (python)
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11"]
-        exclude:
-          - os: windows-latest
-            python-version: "3.9"
+        os: [ubuntu-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     defaults:
       run:
@@ -37,14 +34,6 @@ jobs:
         with:
           environment-file: environment-dev.yml
           create-args: python=${{ matrix.python-version }}
-        if: runner.os != 'Windows'
-
-      - name: Install Mamba (Windows)
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: environment-dev-win.yml
-          create-args: python=${{ matrix.python-version }}
-        if: runner.os == 'Windows'
 
       - name: Install Package
         run: python -m pip install -e .
@@ -59,6 +48,44 @@ jobs:
           verbose: true
           files: ./coverage.xml
 
+  arch-test:
+    if: github.event.pull_request.draft == false
+    name: Foyer Tests (arch)
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macOS-latest, macOS-13, ubuntu-latest, windows-latest]
+        python-version: ["3.12"]
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v3
+        name: Checkout Branch / Pull Request
+
+      - name: Install Mamba (Linux)
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment-dev.yml
+          create-args: python=${{ matrix.python-version }}
+        if: runner.os != 'Windows'
+
+      - name: Install Mamba (Windows)
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment-dev-win.yml
+          create-args: python=${{ matrix.python-version }}
+        if: runner.os == 'Windows'
+
+      - name: Install Package
+        run: python -m pip install -e .
+
+      - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
+        run: python -m pytest -v -nauto --color yes --pyargs foyer
+
   bleeding-edge-test:
     if: github.event.pull_request.draft == false
     name: Bleeding Edge mosdef Tests for Foyer
@@ -75,7 +102,7 @@ jobs:
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment-dev.yml
-          create-args: python=3.10
+          create-args: python=3.12
       - name: Clone mBuild and GMSO
         run: |
           git clone https://github.com/mosdef-hub/mbuild.git

diff --git a/environment-dev-win.yml b/environment-dev-win.yml
@@ -7,7 +7,7 @@ dependencies:
   - codecov
   - lark-parser
   - lxml
-  - mbuild
+  - mbuild>=0.17
   - treelib
   - gmso
   - networkx>=2.5
@@ -19,6 +19,6 @@ dependencies:
   - pytest-cov
   - pytest-timeout
   - pytest-xdist
-  - python>=3.8
+  - python>=3.9
   - requests
   - requests-mock
diff --git a/environment-dev.yml b/environment-dev.yml
@@ -6,7 +6,7 @@ dependencies:
   - codecov
   - lark-parser
   - lxml
-  - mbuild
+  - mbuild>=0.17
   - treelib
   - gmso
   - networkx>=2.5
@@ -22,6 +22,6 @@ dependencies:
   - pytest-cov
   - pytest-timeout
   - pytest-xdist
-  - python>=3.8
+  - python>=3.9
   - requests
   - requests-mock
diff --git a/environment-win.yml b/environment-win.yml
@@ -6,7 +6,7 @@ dependencies:
   - lark-parser
   - lxml
   - networkx>=2.5
-  - openmm>=7.6
+  - openmm
   - parmed>=3.4.3
   - ele
   - requests
@@ -16,4 +16,4 @@ dependencies:
   - pytest-cov
   - pytest-timeout
   - pytest-xdist
-  - python<=3.8
+  - python>=3.9
diff --git a/environment.yml b/environment.yml
@@ -10,4 +10,4 @@ dependencies:
   - parmed>=3.4.3
   - ele
   - requests
-  - python>=3.8
+  - python>=3.9
diff --git a/foyer/tests/files/ethane_customtype.pdb b/foyer/tests/files/ethane_customtype.pdb
@@ -9,6 +9,8 @@ ATOM    5   _Hb  ETH     1       2.956   1.278  -9.381  0.00  0.00           H
 ATOM    6   _Hb  ETH     1       4.748   0.049  -7.277  0.00  0.00           H
 ATOM    7   _Hb  ETH     1       5.187   0.312  -8.947  0.00  0.00           H
 ATOM    8   _Hb  ETH     1       4.890   1.676  -7.897  0.00  0.00           H
+CONECT 1    2     3     4     5
+CONECT 2    1     6     7     8
 CONECT 1    2
 CONECT 1    3
 CONECT 1    4

diff --git a/foyer/tests/test_forcefield.py b/foyer/tests/test_forcefield.py
@@ -684,7 +684,9 @@ def test_no_overlap_residue_atom_overlap(self):
         mol1.name = "CCC"
         mol2.name = "COC"
 
-        box = mb.fill_box([mol1, mol2], n_compounds=[2, 2], density=700)
+        box = mb.fill_box(
+            [mol1, mol2], n_compounds=[2, 2], overlap=0.01, density=700
+        )
 
         all_substructures = []
         structure = box.to_parmed(residues=["CCC", "COC"])