Replace setup.py with pyproject.toml, update CI

.github/workflows/pytest.yml

@@ -39,13 +39,11 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Build environment
-      uses: conda-incubator/setup-miniconda@v3
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: environment-dev.yml
-        python-version: ${{ matrix.python-version }}
-        miniforge-variant: Miniforge3
-        miniforge-version: 24.11.0-0
-        use-mamba: true
+        create-args: >-
+          python=${{ matrix.python-version }}
 
     - name: Install package
       shell: bash -l {0}
@@ -56,7 +54,7 @@ jobs:
       run: python -m pytest -rs -v --cov=./ --cov-report=xml
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -99,12 +97,11 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Build environment
-      uses: conda-incubator/setup-miniconda@v3
+      uses: mamba-org/setup-micromamba@v2
       with:
         environment-file: environment-dev.yml
-        miniforge-variant: Miniforge3
-        miniforge-version: 24.11.0-0
-        use-mamba: true
+        create-args: >-
+          python=3.12
 
     - name: Install package
       shell: bash -l {0}

flowermd/__init__.py

@@ -10,3 +10,5 @@
     Simulation,
     System,
 )
+
+__version__ = "1.3.1"

pyproject.toml

@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools>=61.2", "versioningit"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "flowermd"
+description = "Framework for building and running coplex simulaiton workflows with MosDeF and HOOMD-Blue."
+readme = "README.md"
+authors = [
+  {name = "Chris Jones", email = "[email protected]"},
+  {name = "Marjan Albooyeh", email = "[email protected]"},
+  {name = "Eric Jankowski", email = "[email protected]"}
+]
+license= {text = "GPLv3"}
+classifiers=[
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+]
+urls = {Homepage = "https://github.com/cmelab/flowermd"}
+requires-python = ">=3.10"
+dynamic = ["version"]
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+license-files = ["LICENSE"]
+
+[tool.setuptools.packages]
+find = {namespaces = false}
+
+[tool.setuptools.package-data]
+flowermd = [
+  '"modules/**"',
+  '"library/**"',
+  '"assets/forcefields/**"',
+  '"assets/molecule_files/**"',
+  '"utils/**"',
+  '"internal/**"',
+]
+
+[tool.setuptools.dynamic]
+version = {attr = "flowermd.__version__"}