Merge pull request #1217 from chrisjonesBSU/update-ci

Replace `setup.py` with `pyproject.toml`, update actions to latest versions

.github/workflows/CI.yaml

@@ -30,15 +30,15 @@ jobs:
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba (Linux)
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         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
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: environment-dev-win.yml
           create-args: >-
@@ -52,7 +52,7 @@ jobs:
         run: python -m pytest -v --cov=mbuild --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs mbuild
 
       - name: Upload Coverage Report
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           name: mBuild-Coverage
           verbose: true
@@ -76,15 +76,15 @@ jobs:
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba (Linux)
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         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
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: environment-dev-win.yml
           create-args: >-
@@ -110,25 +110,13 @@ jobs:
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: environment-dev.yml
           create-args: python=3.12
 
-      - name: Clone Foyer and GMSO
-        run: |
-          git clone https://github.com/mosdef-hub/foyer.git
-          git clone https://github.com/mosdef-hub/gmso.git
-
-      - name: Update Environment with foyer/gmso Dependencies
-        run: |
-          micromamba update --name mbuild-dev --file foyer/environment.yml
-          micromamba update --name mbuild-dev --file gmso/environment.yml
-
       - name: Install Packages from Source
         run: |
-          pip install -e foyer
-          pip install -e gmso
           pip install -e .
 
       - name: Run Bleeding Edge Tests

environment-dev.yml

@@ -2,32 +2,45 @@ name: mbuild-dev
 channels:
   - conda-forge
 dependencies:
-  - bump2version
-  - codecov
-  - ele
-  - gmso>=0.9.0
-  - foyer>=0.11.0
-  - freud>=2.0.0
-  - garnett>=0.7.1
-  - gsd>=2.9
-  - hoomd>=3
+  - python>=3.9,<=3.12
+  - boltons
+  - numpy=1.26.4
+  - sympy
+  - unyt>=2.9.5
+  - boltons
+  - lark>=1.2
+  - lxml
   - intermol
   - mdtraj
+  - pydantic>=2
   - networkx
   - nglview>=3
-  - numpy=1.26.4
-  - openbabel>=3
-  - packmol>=20
-  - parmed>=3.4.3
-  - pip
-  - pre-commit
-  - py3Dmol
-  - pycifrw
   - pytest
-  - pytest-azurepipelines
+  - garnett>=0.7.1
+  - openbabel>=3.0.0
+  - openff-toolkit-base >=0.11
+  - openmm
+  - gsd>=2.9
+  - parmed>=3.4.3
+  - packmol>=20
   - pytest-cov
-  - python>=3.8
+  - pycifrw
   - rdkit>=2021
+  - requests
+  - requests-mock
   - scipy
   - treelib
+  - codecov
+  - matplotlib
+  - ipywidgets
+  - ele>=0.2.0
+  - pre-commit
+  - pandas
+  - symengine
+  - python-symengine
+  - hoomd>=4.0,<5.0
   - importlib_resources
+  - pip:
+      - git+https://github.com/mosdef-hub/gmso.git@main
+      - git+https://github.com/mosdef-hub/foyer.git@main
+      - git+https://github.com/mosdef-hub/forcefield-utilities.git@main

pyproject.toml

@@ -0,0 +1,54 @@
+[build-system]
+requires = ["setuptools>=61.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "mbuild"
+description = "A hierarchical, component based molecule builder."
+readme = "README.md"
+authors = [
+  {name = "Janos Sallai", email = "janos.sallai@vanderbilt.edu"},
+  {name = "Christopher Klein", email = "christoph.klein@vanderbilt.edu"},
+]
+maintainers = [
+  {name = "Nicholas Craven", email = "nicholas.c.craven@vanderbilt.edu"},
+  {name = "Chris Jones", email = "chrisjones4@u.boisestate.edu"},
+]
+license= {text = "MIT"}
+classifiers=[
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: MIT License",
+    "Natural Language :: English",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS",
+]
+urls = {Homepage = "https://github.com/mosdef-hub/mbuild"}
+requires-python = ">=3.9"
+dynamic = ["version"]
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+license-files = ["LICENSE"]
+
+[tool.setuptools.packages]
+find = {namespaces = false}
+
+[tool.setuptools.package-data]
+mbuild = ['"utils/**"', '"lib/**"']
+
+[tool.setuptools.dynamic]
+version = {attr = "mbuild.__version__"}
+
+[project.entry-points."mbuild.plugins"]
+Alkane = "mbuild.lib.recipes.alkane:Alkane"
+Monolayer = "mbuild.lib.recipes.monolayer:Monolayer"
+Polymer = "mbuild.lib.recipes.polymer:Polymer"
+SilicaInterface = "mbuild.lib.recipes.silica_interface:SilicaInterface"
+TiledCompound = "mbuild.lib.recipes.tiled_compound:TiledCompound"

setup.cfg

@@ -24,6 +24,4 @@ omit =
 
 [bumpversion:file:mbuild/__init__.py]
 
-[bumpversion:file:setup.py]
-
 [bumpversion:file:docs/conf.py]