Use numpy 2 in CI testing. Drop python 3.9, add python 3.13 to testing.

.github/workflows/CI.yaml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     defaults:
       run:
@@ -29,7 +29,7 @@ jobs:
       - uses: actions/checkout@v4
         name: Checkout Branch / Pull Request
 
-      - name: Install Mamba
+      - name: Install Mamba (Linux)
         uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: environment-dev.yml
@@ -47,6 +47,7 @@ jobs:
         with:
           name: GMSO-Coverage
           verbose: true
+          files: ./coverage.xml
 
   arch-test:
     if: github.event.pull_request.draft == false
@@ -56,7 +57,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macOS-latest, macOS-13, ubuntu-latest]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     defaults:
       run:
@@ -66,7 +67,7 @@ jobs:
       - uses: actions/checkout@v4
         name: Checkout Branch / Pull Request
 
-      - name: Install Mamba
+      - name: Install Mamba (Linux)
         uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: environment-dev.yml
@@ -77,36 +78,36 @@ jobs:
         run: python -m pip install -e .
 
       - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
-        run: python -m pytest -v --color yes --pyargs gmso
+        run: python -m pytest -v --cov=gmso --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs gmso
 
-  bleeding-edge-test:
+  wsl-test:
     if: github.event.pull_request.draft == false
-    name: Bleeding Edge mosdef Tests for GMSO
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
+    name: GMSO Tests (WSL)
+    runs-on: windows-latest
 
     steps:
       - uses: actions/checkout@v4
         name: Checkout Branch / Pull Request
 
-      - name: Install Mamba
-        uses: mamba-org/setup-micromamba@v2
+      - uses: Vampire/setup-wsl@v5
         with:
-          environment-file: environment-dev.yml
-          create-args: python=3.12
-
-      - name: Install Packages from Source
-        run: |
-          pip install -e .
-
-      - name: Check environment
-        run: |
-          micromamba list
+          distribution: Ubuntu-24.04
+          wsl-shell-user: runner
+        name: Set up WSL
 
-      - name: Run Bleeding Edge Tests
+      - name: Install GMSO and run pytest
+        shell: wsl-bash {0}
         run: |
+          wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O $HOME/Miniforge3.sh
+          bash $HOME/Miniforge3.sh -b -p $HOME/miniforge
+          echo 'export PATH=$HOME/miniforge/bin:$PATH' >> ~/.bashrc
+          export PATH=$HOME/miniforge/bin:$PATH
+          source ~/.bashrc
+          source $HOME/miniforge/etc/profile.d/conda.sh
+          mamba update -n base --all -y
+          mamba env create -f environment-dev.yml python=3.12 -y
+          conda activate gmso-dev
+          pip install -e . --prefix=$HOME/tmp_egginfo --no-build-isolation
           python -m pytest -v --color yes --pyargs gmso
 
   docker:

environment-dev.yml

@@ -2,9 +2,9 @@ name: gmso-dev
 channels:
   - conda-forge
 dependencies:
-  - python>=3.9,<=3.12
+  - python>=3.10,<=3.13
   - boltons
-  - numpy=1.26.4
+  - numpy>=2.0,<2.3
   - sympy
   - unyt>=2.9.5
   - boltons
@@ -17,12 +17,12 @@ dependencies:
   - nglview>=3
   - pytest
   - garnett>=0.7.1
-  - openbabel>=3.0.0
-  - openff-toolkit-base >=0.11
+  - openff-toolkit-base>0.16.7
   - openmm
   - gsd>=2.9
+  - freud>=3.2
   - parmed>=3.4.3
-  - packmol>=20
+  - packmol>=20.15
   - pytest-cov
   - pycifrw
   - rdkit>=2021
@@ -38,6 +38,7 @@ dependencies:
   - pandas
   - symengine
   - python-symengine
+  - py3Dmol
   - hoomd>=4.0
   - pip:
       - git+https://github.com/mosdef-hub/mbuild.git@main

environment.yml

@@ -2,9 +2,9 @@ name: gmso
 channels:
   - conda-forge
 dependencies:
-  - python>=3.9, <=3.12
+  - python>=3.10, <=3.13
   - boltons
-  - numpy=1.26.4
+  - numpy>=2.0,<2.3
   - sympy
   - unyt>=2.9.5
   - boltons
@@ -13,6 +13,6 @@ dependencies:
   - networkx
   - ele>=0.2.0
   - foyer>=0.11.3
-  - forcefield-utilities>=0.2.1
+  - forcefield-utilities>=0.4.0
   - symengine
   - python-symengine

pyproject.toml

@@ -29,7 +29,7 @@ classifiers=[
     "Operating System :: MacOS",
 ]
 urls = {Homepage = "https://github.com/mosdef-hub/gmso"}
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dynamic = ["version"]
 
 [tool.setuptools]