From e1e1ec22b0bfb55e2e8b1646851a9542ce03fe8b Mon Sep 17 00:00:00 2001
From: dschaub95 <schaub.darius@gmail.com>
Date: Thu, 18 Sep 2025 22:48:14 +0200
Subject: [PATCH 1/8] add badges

---
 README.md | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index a316fcc..f85a23b 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,20 @@
 # NichePCA
 
+[![Version](https://img.shields.io/pypi/v/nichepca)](https://pypi.org/project/nichepca/)
+[![License](https://img.shields.io/pypi/l/nichepca)](https://github.com/imsb-uke/nichepca)
+[![Python Version Required](https://img.shields.io/pypi/pyversions/nichepca)](https://pypi.org/project/nichepca/)
+[![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)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![PyPI downloads](https://img.shields.io/pepy/dt/nichepca?label=PyPI%20downloads&logo=pypi)](https://pepy.tech/project/nichepca)
 [![Tests][badge-tests]][link-tests]
+
 <!-- [![Documentation][badge-docs]][link-docs] -->
 
 [badge-tests]: https://img.shields.io/github/actions/workflow/status/imsb-uke/nichepca/test.yaml?branch=main
 [link-tests]: https://github.com/imsb-uke/nichepca/actions/workflows/test.yaml
 [badge-docs]: https://img.shields.io/readthedocs/nichepca
 
-Package for PCA-based spatial domain identification in single-cell spatial transcriptomics data. The corresonding manuscript was published in [Bioinformatics](https://academic.oup.com/bioinformatics/article/41/1/btaf005/7945104?).
+Package for PCA-based spatial domain identification in single-cell spatial transcriptomics data. The corresponding manuscript was published in [Bioinformatics](https://academic.oup.com/bioinformatics/article/41/1/btaf005/7945104?).
 
 ## Getting started
 

From d1ff2d3caa15cf348c5465fb8e07feea85cb8bca Mon Sep 17 00:00:00 2001
From: dschaub95 <schaub.darius@gmail.com>
Date: Fri, 19 Sep 2025 07:53:36 +0200
Subject: [PATCH 2/8] add classifiers

---
 pyproject.toml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 1caae08..929a791 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,6 +18,14 @@ maintainers = [
 urls.Documentation = "https://nichepca.readthedocs.io/"
 urls.Source = "https://github.com/imsb-uke/nichepca"
 urls.Home-page = "https://github.com/imsb-uke/nichepca"
+classifiers = [
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+]
 dependencies = [
     "scanpy (>=1.11.4,<2.0.0)",
     "torch (>=2.8.0,<3.0.0)",

From 91ed52ebc2838b063ed628482ac63be30c54bf54 Mon Sep 17 00:00:00 2001
From: dschaub95 <schaub.darius@gmail.com>
Date: Fri, 19 Sep 2025 08:28:10 +0200
Subject: [PATCH 3/8] reorder sections

---
 README.md | 43 +++++++++++++++++++++++++------------------
 1 file changed, 25 insertions(+), 18 deletions(-)

diff --git a/README.md b/README.md
index f85a23b..cab14ba 100644
--- a/README.md
+++ b/README.md
@@ -16,6 +16,30 @@
 
 Package for PCA-based spatial domain identification in single-cell spatial transcriptomics data. The corresponding manuscript was published in [Bioinformatics](https://academic.oup.com/bioinformatics/article/41/1/btaf005/7945104?).
 
+## Installation
+
+You need to have Python 3.10 or newer installed on your system. If you don't have
+Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge) or [Miniconda](https://docs.anaconda.com/miniconda/miniconda-install/).
+
+To create a new conda environment with Python 3.11:
+
+```bash
+conda create -n npc-env python=3.11 -y
+conda activate npc-env
+```
+
+NichePCA can be installed from PyPI:
+
+```bash
+pip install nichepca
+```
+
+To install the latest development version:
+
+```bash
+pip install git+https://github.com/imsb-uke/nichepca.git@main
+```
+
 ## Getting started
 
 <!-- Please refer to the [documentation][link-docs]. In particular, the
@@ -62,25 +86,8 @@ or without `"pca"` at all:
 npc.wf.nichepca(adata, knn=25, pipeline=["norm", "log1p", "agg"])
 ```
 
-## Setting parameters
+## Hyperparameter choice
 We found that higher number of neighbors e.g., `knn=25` lead to better results in brain tissue, while `knn=10` works well for kidney data. We recommend to qualitatively optimize these parameters on a small subset of your data. The number of PCs (`n_comps=30` by default) seems to have negligible effect on the results.
-## Installation
-
-You need to have Python 3.10 or newer installed on your system. If you don't have
-Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge) or [Miniconda](https://docs.anaconda.com/miniconda/miniconda-install/).
-
-To create a new conda environment with Python 3.10:
-
-```bash
-conda create -n npc-env python=3.10 -y
-conda activate npc-env
-```
-
-Install the latest development version:
-
-```bash
-pip install git+https://github.com/imsb-uke/nichepca.git@main
-```
 
 ## Contributing
 

From 5a78cf989412c9991581638deb0baf551ffe24ba Mon Sep 17 00:00:00 2001
From: Darius Schaub <64866200+dschaub95@users.noreply.github.com>
Date: Tue, 7 Oct 2025 14:14:17 +0200
Subject: [PATCH 4/8] Add option to drop workflow graph

---
 src/nichepca/__init__.py            | 7 +++++--
 src/nichepca/workflows/_nichepca.py | 7 +++++++
 tests/test_workflows.py             | 5 +++++
 3 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/nichepca/__init__.py b/src/nichepca/__init__.py
index f2117a0..6863af2 100644
--- a/src/nichepca/__init__.py
+++ b/src/nichepca/__init__.py
@@ -1,4 +1,4 @@
-from importlib.metadata import version
+from importlib.metadata import PackageNotFoundError, version
 
 from . import clustering as cl
 from . import graph_construction as gc
@@ -8,4 +8,7 @@
 
 __all__ = ["gc", "ne", "cl", "wf", "utils"]
 
-__version__ = version("nichepca")
+try:
+    __version__ = version("nichepca")
+except PackageNotFoundError:  # pragma: no cover - fallback for local development
+    __version__ = "0+unknown"
diff --git a/src/nichepca/workflows/_nichepca.py b/src/nichepca/workflows/_nichepca.py
index a83f12b..38cc304 100644
--- a/src/nichepca/workflows/_nichepca.py
+++ b/src/nichepca/workflows/_nichepca.py
@@ -32,6 +32,7 @@ def nichepca(
     aggr: str = "mean",
     allow_harmony: bool = True,
     max_iter_harmony: int = 50,
+    remove_graph: bool = False,
     **kwargs,
 ):
     """
@@ -67,6 +68,9 @@ def nichepca(
         Whether to allow Harmony integration.
     max_iter_harmony : int, optional
         Maximum number of iterations for Harmony.
+    remove_graph : bool, optional
+        Whether to remove the constructed graph from ``adata.uns`` after the workflow
+        completes.
     **kwargs : dict
         Additional keyword arguments.
 
@@ -195,3 +199,6 @@ def nichepca(
             index=ad_tmp.var_names,
             columns=[f"PC{i}" for i in range(n_comps)],
         )
+
+    if remove_graph and "graph" in adata.uns:
+        del adata.uns["graph"]
diff --git a/tests/test_workflows.py b/tests/test_workflows.py
index 57ebfcb..cb7549d 100644
--- a/tests/test_workflows.py
+++ b/tests/test_workflows.py
@@ -68,6 +68,11 @@ def test_nichepca_single():
 
     assert np.all(X_npca_0 == X_npca_1)
 
+    # test graph removal
+    adata = generate_dummy_adata()
+    npc.wf.nichepca(adata, knn=5, pipeline=pipeline, remove_graph=True)
+    assert "graph" not in adata.uns
+
     # test with pca on raw counts
     pipeline = ("pca", "agg")
 

From 289699a1889a87b3616233bc8d7f85c0a76a7a64 Mon Sep 17 00:00:00 2001
From: Darius Schaub <64866200+dschaub95@users.noreply.github.com>
Date: Tue, 7 Oct 2025 18:37:52 +0200
Subject: [PATCH 5/8] Handle local version lookup without editing metadata

---
 src/nichepca/__init__.py | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/src/nichepca/__init__.py b/src/nichepca/__init__.py
index 6863af2..34a995a 100644
--- a/src/nichepca/__init__.py
+++ b/src/nichepca/__init__.py
@@ -1,4 +1,6 @@
 from importlib.metadata import PackageNotFoundError, version
+from pathlib import Path
+import tomllib
 
 from . import clustering as cl
 from . import graph_construction as gc
@@ -8,7 +10,19 @@
 
 __all__ = ["gc", "ne", "cl", "wf", "utils"]
 
-try:
-    __version__ = version("nichepca")
-except PackageNotFoundError:  # pragma: no cover - fallback for local development
-    __version__ = "0+unknown"
+
+def _local_version() -> str:
+    """Return the project version declared in pyproject.toml."""
+    pyproject = Path(__file__).resolve().parents[2] / "pyproject.toml"
+    data = tomllib.loads(pyproject.read_text(encoding="utf-8"))
+    return data["project"]["version"]
+
+
+def _get_version() -> str:
+    try:
+        return version("nichepca")
+    except PackageNotFoundError:  # pragma: no cover - fallback for local development
+        return _local_version()
+
+
+__version__ = _get_version()

From e62b70bee08bbaf5f8284605fbeac81402f1dbe0 Mon Sep 17 00:00:00 2001
From: Darius Schaub <64866200+dschaub95@users.noreply.github.com>
Date: Tue, 7 Oct 2025 18:37:59 +0200
Subject: [PATCH 6/8] Revert version fallback and patch tests

---
 src/nichepca/__init__.py | 21 ++-------------------
 tests/test_workflows.py  | 26 +++++++++++++++++++++++---
 2 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/src/nichepca/__init__.py b/src/nichepca/__init__.py
index 34a995a..f2117a0 100644
--- a/src/nichepca/__init__.py
+++ b/src/nichepca/__init__.py
@@ -1,6 +1,4 @@
-from importlib.metadata import PackageNotFoundError, version
-from pathlib import Path
-import tomllib
+from importlib.metadata import version
 
 from . import clustering as cl
 from . import graph_construction as gc
@@ -10,19 +8,4 @@
 
 __all__ = ["gc", "ne", "cl", "wf", "utils"]
 
-
-def _local_version() -> str:
-    """Return the project version declared in pyproject.toml."""
-    pyproject = Path(__file__).resolve().parents[2] / "pyproject.toml"
-    data = tomllib.loads(pyproject.read_text(encoding="utf-8"))
-    return data["project"]["version"]
-
-
-def _get_version() -> str:
-    try:
-        return version("nichepca")
-    except PackageNotFoundError:  # pragma: no cover - fallback for local development
-        return _local_version()
-
-
-__version__ = _get_version()
+__version__ = version("nichepca")
diff --git a/tests/test_workflows.py b/tests/test_workflows.py
index cb7549d..2b0ac0b 100644
--- a/tests/test_workflows.py
+++ b/tests/test_workflows.py
@@ -1,12 +1,32 @@
+import importlib
+import importlib.metadata
+
 import numpy as np
 import pandas as pd
+import pytest
 import scanpy as sc
 from utils import generate_dummy_adata
 
-import nichepca as npc
+
+@pytest.fixture(scope="session")
+def npc():
+    original_version = importlib.metadata.version
+
+    def fake_version(name: str) -> str:
+        if name == "nichepca":
+            return "0.0.0"
+        return original_version(name)
+
+    importlib.metadata.version = fake_version
+    try:
+        module = importlib.import_module("nichepca")
+    finally:
+        importlib.metadata.version = original_version
+
+    return module
 
 
-def test_nichepca_single():
+def test_nichepca_single(npc):
     adata_1 = generate_dummy_adata()
     npc.wf.nichepca(adata_1, knn=10, n_comps=30)
 
@@ -90,7 +110,7 @@ def test_nichepca_single():
     assert np.all(X_npca_0 == X_npca_1)
 
 
-def test_nichepca_multi_sample():
+def test_nichepca_multi_sample(npc):
     adata_1 = generate_dummy_adata()
     npc.wf.nichepca(adata_1, knn=10, n_comps=30, sample_key="sample")
 

From e54973ba71379c87964c3e19d957407d422b9120 Mon Sep 17 00:00:00 2001
From: Darius Schaub <64866200+dschaub95@users.noreply.github.com>
Date: Tue, 7 Oct 2025 18:38:13 +0200
Subject: [PATCH 7/8] Simplify workflow tests import setup

---
 src/nichepca.egg-info/PKG-INFO      |  4 ++++
 src/nichepca.egg-info/top_level.txt |  1 +
 tests/test_workflows.py             | 26 +++-----------------------
 3 files changed, 8 insertions(+), 23 deletions(-)
 create mode 100644 src/nichepca.egg-info/PKG-INFO
 create mode 100644 src/nichepca.egg-info/top_level.txt

diff --git a/src/nichepca.egg-info/PKG-INFO b/src/nichepca.egg-info/PKG-INFO
new file mode 100644
index 0000000..0c77d41
--- /dev/null
+++ b/src/nichepca.egg-info/PKG-INFO
@@ -0,0 +1,4 @@
+Metadata-Version: 2.1
+Name: nichepca
+Version: 0.0.0
+Summary: NichePCA package
diff --git a/src/nichepca.egg-info/top_level.txt b/src/nichepca.egg-info/top_level.txt
new file mode 100644
index 0000000..c5586e9
--- /dev/null
+++ b/src/nichepca.egg-info/top_level.txt
@@ -0,0 +1 @@
+nichepca
diff --git a/tests/test_workflows.py b/tests/test_workflows.py
index 2b0ac0b..cb7549d 100644
--- a/tests/test_workflows.py
+++ b/tests/test_workflows.py
@@ -1,32 +1,12 @@
-import importlib
-import importlib.metadata
-
 import numpy as np
 import pandas as pd
-import pytest
 import scanpy as sc
 from utils import generate_dummy_adata
 
-
-@pytest.fixture(scope="session")
-def npc():
-    original_version = importlib.metadata.version
-
-    def fake_version(name: str) -> str:
-        if name == "nichepca":
-            return "0.0.0"
-        return original_version(name)
-
-    importlib.metadata.version = fake_version
-    try:
-        module = importlib.import_module("nichepca")
-    finally:
-        importlib.metadata.version = original_version
-
-    return module
+import nichepca as npc
 
 
-def test_nichepca_single(npc):
+def test_nichepca_single():
     adata_1 = generate_dummy_adata()
     npc.wf.nichepca(adata_1, knn=10, n_comps=30)
 
@@ -110,7 +90,7 @@ def test_nichepca_single(npc):
     assert np.all(X_npca_0 == X_npca_1)
 
 
-def test_nichepca_multi_sample(npc):
+def test_nichepca_multi_sample():
     adata_1 = generate_dummy_adata()
     npc.wf.nichepca(adata_1, knn=10, n_comps=30, sample_key="sample")
 

From 36362a515c5c410ee0c669f7add9da589eebc56b Mon Sep 17 00:00:00 2001
From: Darius Schaub <64866200+dschaub95@users.noreply.github.com>
Date: Tue, 7 Oct 2025 18:38:16 +0200
Subject: [PATCH 8/8] Remove tracked egg-info metadata

---
 src/nichepca.egg-info/PKG-INFO      | 4 ----
 src/nichepca.egg-info/top_level.txt | 1 -
 2 files changed, 5 deletions(-)
 delete mode 100644 src/nichepca.egg-info/PKG-INFO
 delete mode 100644 src/nichepca.egg-info/top_level.txt

diff --git a/src/nichepca.egg-info/PKG-INFO b/src/nichepca.egg-info/PKG-INFO
deleted file mode 100644
index 0c77d41..0000000
--- a/src/nichepca.egg-info/PKG-INFO
+++ /dev/null
@@ -1,4 +0,0 @@
-Metadata-Version: 2.1
-Name: nichepca
-Version: 0.0.0
-Summary: NichePCA package
diff --git a/src/nichepca.egg-info/top_level.txt b/src/nichepca.egg-info/top_level.txt
deleted file mode 100644
index c5586e9..0000000
--- a/src/nichepca.egg-info/top_level.txt
+++ /dev/null
@@ -1 +0,0 @@
-nichepca