fix: semantic release as single source of truth for versions

Author: kierandidi

.github/workflows/release_and_docs.yaml

@@ -52,7 +52,7 @@ jobs:
         id: release
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+          PYPI_TOKEN: ${{ secrets.PYPI_TOKEN_PROD }}
           PYPI_REPO_URL: https://test.pypi.org/legacy/
         run: |
           npx semantic-release
@@ -117,7 +117,7 @@ jobs:
               fi
               
               if [[ "$v" == "latest" ]]; then
-                entry="{\"version\": \"latest\", \"url\": \"https://baker-laboratory.github.io/atomworks/latest/\", \"name\": \"dev (latest)\"}"
+                entry="{\"version\": \"latest\", \"url\": \"https://RosettaCommons.github.io/atomworks/latest/\", \"name\": \"dev (latest)\"}"
               else
                 disp="${v#v}"
                 # Mark the newest stable version as preferred
@@ -126,7 +126,7 @@ jobs:
                 else
                   preferred="false"
                 fi
-                entry="{\"version\": \"$disp\", \"url\": \"https://baker-laboratory.github.io/atomworks/$v/\", \"name\": \"v$disp\", \"preferred\": $preferred}"
+                entry="{\"version\": \"$disp\", \"url\": \"https://RosettaCommons.github.io/atomworks/$v/\", \"name\": \"v$disp\", \"preferred\": $preferred}"
               fi
               
               switcher_content="$switcher_content$entry"

.releaserc.js

@@ -10,7 +10,7 @@ module.exports = {
           repoUrl: 'https://test.pypi.org/legacy/',
           distDir: 'dist/',
           setupPy: false,
-          pypiToken: process.env.PYPI_TOKEN,
+          pypiToken: process.env.PYPI_TOKEN_PROD,
         }
       ],
       '@semantic-release/github',

README.md

@@ -1,10 +1,12 @@
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![PyPI version](https://img.shields.io/pypi/v/atomworks.svg)](https://pypi.org/project/atomworks/)
 [![Python versions](https://img.shields.io/pypi/pyversions/atomworks.svg)](https://pypi.org/project/atomworks/)
-[![Documentation Status](https://img.shields.io/badge/docs-latest-brightgreen.svg)](https://baker-laboratory.github.io/atomworks/latest)
+[![Documentation Status](https://img.shields.io/badge/docs-latest-brightgreen.svg)](https://RosettaCommons.github.io/atomworks/latest)
 [![License: BSD 3-Clause](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
-<img src="docs/_static/atomworks_logo_color.svg" width="450" alt="atomworks logo">
+<img src="docs/_static/atomworks_logo_dark.svg" width="350" alt="atomworks logo">
+
+# atomworks
 
 **atomworks** is an open-source platform for next-generation biomolecular data processing, conversion, and machine-learning-ready featurization.  
 It is composed of two symbiotic libraries:
@@ -47,13 +49,20 @@ Built on atomworks.io's structural backbone, atomworks.ml bridges the gap betwee
 
 ```
 pip install atomworks # base installation version without torch (for only atomworks.io)
+pip install "atomworks[openbabel]" # with OpenBabel support (for atomworks.io plus OpenBabel)
 pip install "atomworks[ml]" # with torch and ML dependencies (for atomworks.io plus atomworks.ml)
 pip install "atomworks[dev]" # with development dependencies
-pip install "atomworks[ml,dev]" # with all dependencies
+pip install "atomworks[ml,openbabel,dev]" # with all dependencies
+
+```
 
+If you are using [uv](https://docs.astral.sh/uv/reference/policies/versioning/) for package management, you can install atomworks with:
+
+```
+ uv pip install "atomworks[ml,openbabel,dev]"
 ```
 
-For more advanced setup options (including how to run workflows via apptainers) see the [full documentation](https://baker-laboratory.github.io/atomworks/latest).
+For more advanced setup options (including how to run workflows via apptainers) see the [full documentation](https://RosettaCommons.github.io/atomworks/latest).
 
 ---
 
@@ -77,7 +86,7 @@ Output includes:
 - **assemblies** — Built biological assemblies
 - **metadata** — Experimental and source information
 
-See [usage examples](https://baker-laboratory.github.io/atomworks/latest/auto_examples/).
+See [usage examples](https://RosettaCommons.github.io/atomworks/latest/auto_examples/).
 
 ---
 
@@ -98,4 +107,4 @@ See [usage examples](https://baker-laboratory.github.io/atomworks/latest/auto_ex
 ## Contribution
 
 We welcome improvements!  
-Please see the [contributing guide](CONTRIBUTING.md) or [full documentation](https://baker-laboratory.github.io/atomworks/latest).
+Please see the [full documentation](https://RosettaCommons.github.io/atomworks/latest) for more information on contributing.

docs/conf.py

@@ -71,7 +71,7 @@
     },
     "navbar_start": ["navbar-logo", "version-switcher"],
     "switcher": {
-        "json_url": "https://baker-laboratory.github.io/atomworks/latest/_static/switcher.json",
+        "json_url": "https://RosettaCommons.github.io/atomworks/latest/_static/switcher.json",
         "version_match": switcher_version,
     },
     "favicons": [

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "atomworks"
-dynamic = ["version"]
-description = "A research-oriented data toolkit for training biomolecular deep-learning foundation models."
+version = "1.0.0"
+description = "A research-oriented data toolkit for training biomolecular deep-learning foundation models"
 readme = "README.md"
 requires-python = ">=3.12"
 authors = [
@@ -26,7 +26,8 @@ dependencies = [
     "cython>=3.0.0,<4", # Cython compiler for C extensions
     "cytoolz>=0.12.3,<1", # Cython-optimized tools for itertools and functional programming
     "tqdm>=4.65.0,<5", # Fast, extensible progress bar for loops and more
-    # ... CLI
+    # ... CLI & config management
+    "fire>=0.6.0,<1", # Argument parsing (legacy)
     "typer>=0.12.5,<1", # Modern CLI framework
     # ... linear algebra, maths & ml
     "numpy>=1.25.0,<2",  # TODO: Enable numpy 2.x
@@ -48,8 +49,8 @@ dependencies = [
 [project.optional-dependencies]
 ml = [
     # atomworks-ml dependencies
-    "torch>=2.2.0,<3",
-    "einops>=0.7.0,<1",
+    "torch==2.7.0",
+    "einops==0.7.0",
 ]
 
 openbabel = [
@@ -60,6 +61,7 @@ openbabel = [
 dev = [
     # Linters & formatters
     "ruff==0.8.3",
+    "pre-commit==3.7.1",
     # Debugger/interactive
     "debugpy>=1.8.5,<2",
     "ipykernel>=6.29.4,<7",
@@ -87,9 +89,9 @@ docs = ["atomworks[docs]"]
 openbabel = ["atomworks[openbabel]"]
 
 [project.urls]
-homepage = "https://baker-laboratory.github.io/atomworks/"
-repository = "https://github.com/baker-laboratory/atomworks"
-documentation = "https://baker-laboratory.github.io/atomworks/"
+homepage = "https://RosettaCommons.github.io/atomworks/"
+repository = "https://github.com/RosettaCommons/atomworks"
+documentation = "https://RosettaCommons.github.io/atomworks/"
 
 [project.scripts]
 atomworks = "atomworks.cli.__main__:main"
@@ -99,12 +101,6 @@ atomworks = "atomworks.cli.__main__:main"
 requires = ["hatchling", "hatch-vcs"]
 build-backend = "hatchling.build"
 
-[tool.hatch.version]
-source = "vcs"
-
-[tool.hatch.build.hooks.vcs]
-version-file = "src/atomworks/_version.py"
-
 [tool.hatch.metadata]
 allow-direct-references = true
 dynamic = false  # optional – this disables dynamic metadata guessing
@@ -256,4 +252,4 @@ exclude_lines = [
     "if __name__ == .__main__.:",
     "pass",
     "raise ImportError",
-]
+]

src/atomworks/__init__.py

@@ -5,12 +5,14 @@
 into a unified interface for biological data processing and machine learning.
 """
 
+import importlib
+import importlib.metadata
 import logging
 import os
 import warnings
 
 try:
-    from ._version import __version__
+    __version__ = importlib.metadata.version("atomworks")
 except ImportError:
     __version__ = "unknown"