Replace setup.py with pyproject.toml, update actions to latest ve…

…rsions (#865)

* Replace setup.py with pyproject.toml, update action versions

* Pin hoomd to <5.0

* add command to run mamba list after updating environment

* add latest env, install all mosdef from source, update bleeding edge CI

* add dynamic version to project.toml

* remove dynamic versioning w/setuptools

* fix dynamic version

* use setup tools for dynamic versioning instead of versioningit

* just use environment-dev.yml with new env changes

* fix python versions in env

* add back create-args to bleeding edge test

* update env file

* remove bump2version

.github/workflows/CI.yaml

@@ -30,7 +30,7 @@ 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: >-
@@ -43,7 +43,7 @@ jobs:
         run: python -m pytest -v --cov=gmso --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs gmso
 
       - name: Upload Coverage Report
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           name: GMSO-Coverage
           verbose: true
@@ -67,7 +67,7 @@ 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: >-
@@ -92,30 +92,19 @@ 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 mBuild and Foyer and forcefield-utilities
-        run: |
-          git clone https://github.com/mosdef-hub/mbuild.git
-          git clone https://github.com/mosdef-hub/foyer.git
-          git clone https://github.com/mosdef-hub/forcefield-utilities.git
-
-      - name: Update Environment with mbuild/foyer/ffutils Dependencies
-        run: |
-          micromamba update --name gmso-dev --file mbuild/environment.yml
-          micromamba update --name gmso-dev --file foyer/environment.yml
-          micromamba update --name gmso-dev --file forcefield-utilities/environment-dev.yml
-
       - name: Install Packages from Source
         run: |
-          pip install -e mbuild
-          pip install -e foyer
-          pip install -e forcefield-utilities
           pip install -e .
 
+      - name: Check environment
+        run: |
+          micromamba list
+
       - name: Run Bleeding Edge Tests
         run: |
           python -m pytest -v --color yes --pyargs gmso

environment-dev.yml

@@ -8,25 +8,39 @@ dependencies:
   - sympy
   - unyt>=2.9.5
   - boltons
+  - lark>=1.2
   - lxml
+  - intermol
+  - mdtraj
   - pydantic>=2
   - networkx
+  - nglview>=3
   - pytest
-  - mbuild>=1.1
+  - garnett>=0.7.1
   - openbabel>=3.0.0
-  - foyer>=0.11.3
-  - forcefield-utilities>=0.2.1
+  - openff-toolkit-base >=0.11
+  - openmm
   - gsd>=2.9
   - parmed>=3.4.3
+  - packmol>=20
   - pytest-cov
+  - pycifrw
+  - rdkit>=2021
+  - requests
+  - requests-mock
+  - scipy
+  - treelib
   - codecov
-  - bump2version
   - matplotlib
   - ipywidgets
   - ele>=0.2.0
   - pre-commit
   - pandas
   - symengine
   - python-symengine
-  - hoomd
+  - hoomd>=4.0,<5.0
   - importlib_resources
+  - pip:
+      - git+https://github.com/mosdef-hub/mbuild.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 +1,44 @@
+[build-system]
+requires = ["setuptools>=61.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "gmso"
+description = "A flexible storage of chemical topology for molecular simulation."
+readme = "README.md"
+authors = [
+  {name = "Matthew W Thompson", email = "matt.thompson@vanderbilt.edu"},
+  {name = "Justin Gilmer", email = "justin.b.gilmer@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/gmso"}
+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.dynamic]
+version = {attr = "gmso.__version__"}

setup.cfg

@@ -22,6 +22,4 @@ omit =
 
 [bumpversion:file:gmso/__init__.py]
 
-[bumpversion:file:setup.py]
-
 [bumpversion:file:docs/conf.py]