fixing version tracking

Author: sbooeshaghi

Makefile

@@ -1,5 +1,7 @@
 .PHONY : clean build upload release
 
+ 
+
 clean:
 	rm -rf build
 	rm -rf dist
@@ -20,15 +22,15 @@ upload:
 
 # Get current version
 version:
-	@uv run python -c "import setuptools_scm; print(setuptools_scm.get_version())"
+	@uv run python -c "import tomllib, pathlib; print(tomllib.loads(pathlib.Path('pyproject.toml').read_bytes().decode()).get('project',{}).get('version','unknown'))"
 
 # Create a new release
 release:
 	@if [ "$$(git rev-parse --abbrev-ref HEAD)" != "main" ]; then echo "Switch to main before releasing"; exit 1; fi
 	@if [ -n "$$(git status --porcelain)" ]; then echo "Working tree not clean"; git status; exit 1; fi
 	@git pull --ff-only
-	@uv run pytest || { echo "Tests failed"; exit 1; }
-	@read -p "Enter version (e.g., 0.3.2): " version; \
+	@version=$$(uv run python -c "import tomllib, pathlib; print(tomllib.loads(pathlib.Path('pyproject.toml').read_bytes().decode())['project']['version'])"); \
+	uv run pytest || { echo "Tests failed"; exit 1; }; \
 	git tag -a "v$$version" -m "Release v$$version"; \
 	git push origin main && git push origin --tags; \
 	make clean build upload

docs/DEV_GUIDE.md

@@ -35,17 +35,18 @@ authors:
    source .venv/bin/activate
    uv pip install ".[dev]"
 
-   # 4. Sanity-check version resolution
-   make version
+   # 4. Set the release version in pyproject.toml
+   # - Edit [project] version = "X.Y.Z"
+   # - Commit the change on main
+   uv run python -c "import tomllib, pathlib; print(tomllib.loads(pathlib.Path('pyproject.toml').read_bytes().decode())['project']['version'])"  # verify
 
    # 5. Create the release
    make release
    # This will:
    # - Verify you are on main and working tree is clean
    # - Pull with --ff-only
+   # - Read version from pyproject.toml and tag vX.Y.Z
    # - Run tests (uv run pytest)
-   # - Prompt for version number
-   # - Create and push git tag
    # - Build sdist+wheel (uv run python -m build)
    # - Upload to PyPI (uvx twine upload)
 
@@ -75,14 +76,13 @@ Follow semantic versioning:
 2. **Always release from `main` branch**
 
    - Makefile enforces releasing from `main` with a clean tree
-   - Ensures PyPI version matches `main`
+   - Version is stored in `pyproject.toml` and tags are derived from it
    - Git tags point to correct code
    - Tests are run automatically during release
 
-3. **Development versions**
-   - During development: `0.3.1.dev123+gabc123`
-   - After release: `0.3.2`
-   - Handled automatically by setuptools_scm
+3. **Version management**
+   - Bump `[project].version` in `pyproject.toml` before releases
+   - Example: 0.3.1 → 0.4.0 for new features
 
 ## Using uv for Development
 
@@ -238,4 +238,9 @@ All dependencies are managed in `pyproject.toml`:
 - Runtime dependencies under `[project]`
 - Development dependencies under `[project.optional-dependencies]` (includes `twine` for uploads)
 
+Versioning is manual (single source of truth):
+
+- Set `[project].version` in `pyproject.toml` (e.g., `0.4.0`)
+- `seqspec/__init__.py` reads the installed distribution version via `importlib.metadata`
+
 No separate `requirements.txt` or `dev-requirements.txt` files are needed.

pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
-requires = ["setuptools>=61.0", "setuptools_scm>=7.0"]
+requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "seqspec"
-dynamic = ["version"]
+version = "0.4.0"
 description = "A tool for working with sequencing specifications"
 readme = "README.md"
 requires-python = ">=3.12"
@@ -45,7 +45,6 @@ dev = [
     "pytest-mock",
     "pre-commit",
     "build",
-    "setuptools_scm>=7.0",
     "ruff",
     "twine",
 ]
@@ -64,10 +63,7 @@ package-dir = { "" = "." }
 [tool.setuptools.package-data]
 "seqspec" = ["schema/*"]
 
-[tool.setuptools_scm]
-write_to = "seqspec/__init__.py"
-version_scheme = "python-simplified-semver"
-local_scheme = "node-and-date"
+ 
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
@@ -104,7 +100,6 @@ dev = [
     "pytest-mock>=3.14.0",
     "pre-commit>=4.2.0",
     "build>=1.0.0",
-    "setuptools_scm>=7.0",
     "ruff>=0.9.0",
 ]
 

seqspec/__init__.py

@@ -1,33 +1,6 @@
-# file generated by setuptools-scm
-# don't change, don't track in version control
+from importlib.metadata import version as _pkg_version
 
-__all__ = [
-    "__version__",
-    "__version_tuple__",
-    "version",
-    "version_tuple",
-    "__commit_id__",
-    "commit_id",
-]
-
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple, Union
-
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-    COMMIT_ID = Union[str, None]
-else:
-    VERSION_TUPLE = object
-    COMMIT_ID = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-commit_id: COMMIT_ID
-__commit_id__: COMMIT_ID
-
-__version__ = version = "0.3.2.dev43+gf8b27c338.d20250821"
-__version_tuple__ = version_tuple = (0, 3, 2, "dev43", "gf8b27c338.d20250821")
-
-__commit_id__ = commit_id = "gf8b27c338"
+try:
+    __version__ = _pkg_version("seqspec")
+except Exception:
+    __version__ = "@+unknown"