Add package and model versioning

CHANGELOG.md

@@ -0,0 +1,10 @@
+# Changelog
+
+## 1.1.0 (unreleased)
+
+- Rename the distribution from `ms-gen` back to `ms_pred`.
+- Read the package version from `ms_pred.__version__`.
+- Add `ms_pred.model_registry` with the current model versions.
+- Add `python -m ms_pred --version`.
+
+Changes between v1.0.0 and this release, such as `ms_pred.dag_pred` becoming `ms_pred.iceberg`, were not recorded.

pyproject.toml

@@ -3,8 +3,8 @@ requires = ["setuptools>=61", "wheel", "cython>=3", "numpy>=2"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "ms-gen"
-version = "0.1.0"
+name = "ms_pred"
+dynamic = ["version"]
 description = "A package for computational tandem mass spectrometry simulation."
 authors = [
     { name = "Sam Goldman", email = "samlg@mit.edu" },
@@ -132,5 +132,8 @@ url = "https://data.pyg.org/whl/torch-2.6.0+cu118.html"
 format = "flat"
 explicit = true
 
+[tool.setuptools.dynamic]
+version = { attr = "ms_pred.__version__" }
+
 [tool.setuptools.packages.find]
 where = ["src"]

src/ms_pred/__init__.py

@@ -1,3 +1,5 @@
+__version__ = "1.1.0"
+
 # Import all submodules in package
 # from . import common
 # from . import iceberg

src/ms_pred/__main__.py

@@ -0,0 +1,20 @@
+import argparse
+
+from ms_pred import __version__
+from ms_pred.model_registry import MODEL_REGISTRY
+
+
+def main():
+    parser = argparse.ArgumentParser(prog="python -m ms_pred")
+    parser.add_argument("--version", action="store_true", help="show package and model versions")
+    args = parser.parse_args()
+    if not args.version:
+        parser.print_help()
+        return
+    print(f"ms_pred {__version__}")
+    for name, info in MODEL_REGISTRY.items():
+        print(f"{name} {info['version']}")
+
+
+if __name__ == "__main__":
+    main()

src/ms_pred/model_registry.py

@@ -0,0 +1,15 @@
+"""Model versions, kept separate from the ms_pred package version."""
+
+MODEL_REGISTRY = {
+    "iceberg": {
+        "version": "2.1",
+        "reference": "doi:10.1101/2025.05.28.656653",
+        "previous": {
+            "2.0": {"branch": "iceberg_2.0", "reference": "doi:10.1101/2025.05.28.656653"},
+            "1.0": {"branch": "iceberg_1.0", "reference": "doi:10.1021/acs.analchem.3c04654"},
+        },
+    },
+    "scarf": {"version": "1.0", "reference": "arXiv:2303.06470"},
+    "marason": {"version": "1.0", "reference": "arXiv:2502.17874"},
+    "glacier": {"version": "1.0", "reference": "arXiv:2606.29161"},
+}