update build process

.codecov.yml

@@ -12,5 +12,3 @@ comment:
   behavior: default
   flags: null
   paths: null
-ignore:
-  - "mdpow-molconfgen/_version.py"

.github/workflows/deploy.yaml

@@ -0,0 +1,53 @@
+name: Build and upload to PyPi
+
+on:
+  push:
+    tags:
+      - "*"
+  release:
+    types:
+      - published
+
+jobs:
+  test_pypi_push:
+    environment:
+      name: deploy
+      url: https://test.pypi.org/p/mdpow-molconfgen
+    permissions:
+      id-token: write
+    if: |
+      github.repository == 'Becksteinlab/mdpow-molconfgen' &&
+      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/'))
+    name: Build, upload and test pure Python wheels to TestPypi
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: testpypi_deploy
+        uses: MDAnalysis/pypi-deployment@main
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+        with:
+          test_submission: true
+          package_name: 'molconfgen'
+
+  pypi_push:
+    environment:
+      name: deploy
+      url: https://pypi.org/p/mdpow-molconfgen
+    permissions:
+      id-token: write
+    if: |
+      github.repository == 'Becksteinlab/mdpow-molconfgen' &&
+      (github.event_name == 'release' && github.event.action == 'published')
+    name: Build, upload and test pure Python wheels to PyPi
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: pypi_deploy
+        uses: MDAnalysis/pypi-deployment@main
+        if: github.event_name == 'release' && github.event.action == 'published'
+        with:
+          package_name: 'molconfgen'

.gitignore

@@ -103,13 +103,16 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# macOS finder
 .DS_Store
 
 # poetry
 poetry.lock
 
 # generated data files when running notebooks
 *.trr
+\#*
 
 # emacs backup files
 *~
@@ -119,5 +122,6 @@ poetry.lock
 SANDBOX/
 tmp/
 
-# versioningit generated files
-molconfgen/_version.py
+
+# cursor config
+settings.json

MANIFEST.in

@@ -3,5 +3,5 @@ include MANIFEST.in
 include AUTHORS.md CHANGELOG.md CODE_OF_CONDUCT.md README.md
 
 graft molconfgen
-recursive-include molconfgen/data *
-global-exclude *.py[cod] __pycache__ *.so *~
+recursive-include molconfgen/data/*
+global-exclude *.py[cod] __pycache__ *.so *~ .DS_Store .ipynb_checkpoints/*

molconfgen/__init__.py

@@ -2,15 +2,23 @@
 mdpow-molconfgen
 ================
 
-Generation of conformers of small molecules.
+Generation of conformers of small molecules via dihedral scanning.
+Evaluate the potential energy of each conformer in vacuo.
+
+The package is meant to work with the input that is used for the
+MDPOW_ package.
+
+.. _MDPOW:: https://mdpow.readthedocs.io
 """
 
 # Version is handled by versioningit
-try:
-    from ._version import __version__
-except ImportError:
-    __version__ = "unknown"
+from importlib.metadata import version
+
+__version__ = version("mdpow-molconfgen")
 
 # Add imports here
 from . import chem
 from . import sampler
+from . import output
+from . import analyze
+from . import workflows

pyproject.toml

@@ -49,18 +49,20 @@ doc = [
 # documentation = "https://mdpow-molconfgen.readthedocs.io"
 
 [tool.setuptools]
-packages = ["molconfgen", "molconfgen.tests"]
+packages = ["molconfgen", "molconfgen.tests", "molconfgen.data"]
 include-package-data = true
 
 [tool.versioningit]
-vcs = "git"
-default-version = "0.0.0"
+default-version = "1+unknown"
 
-[tool.versioningit.tag2version]
-regex = "^(?P<version>[0-9]+\\.[0-9]+\\.[0-9]+)$"
+[tool.versioningit.vcs]
+method = "git"
+match = ["*"]
 
-[tool.versioningit.write]
-file = "molconfgen/_version.py"
+[tool.versioningit.format]
+distance = "{base_version}+{distance}.{vcs}{rev}"
+dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
 
 [tool.pytest.ini_options]
 minversion = "6.0"