From eb929c3f38a47daeaaf6c0178b5abc3b83f9ba27 Mon Sep 17 00:00:00 2001
From: gautam8387 <goutamahuja8387@gmail.com>
Date: Tue, 11 Aug 2026 15:48:29 +0200
Subject: [PATCH 1/2] package versioning; wip

---
 .github/workflows/publish.yml | 14 +++++++-------
 .github/workflows/pytest.yml  |  2 ++
 .gitignore                    |  1 +
 cytetype/__init__.py          |  3 +--
 pyproject.toml                | 14 ++++++++++----
 tests/test_cli.py             |  5 +++++
 6 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index b2fbbab..3525a82 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -17,17 +17,17 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
         with:
-          python-version: "3.x" # Use a recent stable version
+          ref: ${{ github.event.release.tag_name }}
+          fetch-depth: 0
 
-      - name: Install build dependencies
-        run: python -m pip install build --user
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.12"
 
       - name: Build package
-        run: python -m build
+        run: uv build --clear
 
       - name: Publish package to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index b3adf8c..b48556e 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -15,6 +15,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
diff --git a/.gitignore b/.gitignore
index af49d6e..eb274c0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@ build/
 dist/
 wheels/
 *.egg-info
+cytetype/_version.py
 
 .venv
 *.env
diff --git a/cytetype/__init__.py b/cytetype/__init__.py
index edd4240..6718fe9 100644
--- a/cytetype/__init__.py
+++ b/cytetype/__init__.py
@@ -1,7 +1,6 @@
-__version__ = "0.19.5"
-
 import requests
 
+from ._version import __version__
 from .config import logger
 from .main import CyteType
 from .plotting import marker_dotplot
diff --git a/pyproject.toml b/pyproject.toml
index b817fa5..fb6bcb0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ dev = [
 ]
 
 [build-system]
-requires = ["setuptools>=80.9.0", "wheel"]
+requires = ["setuptools>=80.9.0", "setuptools-scm>=8", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
@@ -52,8 +52,14 @@ packages = {find = {}}
 [tool.setuptools.package-data]
 cytetype = ["templates/*.html"]
 
-[tool.setuptools.dynamic]
-version = {attr = "cytetype.__version__"}
+[tool.setuptools_scm]
+version_file = "cytetype/_version.py"
+
+[tool.uv]
+cache-keys = [
+    { file = "pyproject.toml" },
+    { git = { commit = true, tags = true } },
+]
 
 [tool.mypy]
 strict = false
@@ -76,4 +82,4 @@ warn_unused_ignores = true
 
 ignore_missing_imports = false
 
-exclude = ["^build/", "^dist/", "^.*\\.egg-info/"]
+exclude = ["^build/", "^dist/", "^.*\\.egg-info/", "^cytetype/_version\\.py$"]
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 5da0f6b..04990d7 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,6 +1,7 @@
 import os
 import stat
 import threading
+from importlib.metadata import version as distribution_version
 from pathlib import Path
 from types import SimpleNamespace
 from urllib.error import HTTPError
@@ -34,6 +35,10 @@ def credentials() -> StoredCredentials:
     )
 
 
+def test_public_version_matches_distribution_metadata() -> None:
+    assert cli.__version__ == distribution_version("cytetype")
+
+
 def test_credentials_round_trip_is_private_and_server_specific(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,

From 09c49b50c9d4c30551835921c69c3420f9d61b4b Mon Sep 17 00:00:00 2001
From: gautam8387 <goutamahuja8387@gmail.com>
Date: Tue, 11 Aug 2026 16:35:59 +0200
Subject: [PATCH 2/2] wip

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index af3a3ae..7781e72 100644
--- a/README.md
+++ b/README.md
@@ -23,6 +23,8 @@
 For Seurat workflows, use [CyteTypeR](https://github.com/NygenAnalytics/CyteTypeR).
 
 > [!IMPORTANT]
+> Already installed CyteType? Open a terminal and run `pip install -U cytetype` to update to the latest version before you start.
+>
 > CyteType requires an API key. Use is free for academic and non-commercial research. Commercial use requires a [license](#license).
 
 ## Quick Start