schwartzlab-methods · hoseok-lee · Feb 15, 2026
diff --git a/.gitignore b/.gitignore
@@ -38,4 +38,6 @@ Data/
 Result/
 runPermutation.py
 CLPC/
-altairThemes.py
+altairThemes.py
+ClumPyCells.egg-info/
+build/
diff --git a/ClumPyCells/__init__.py b/ClumPyCells/__init__.py
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
@@ -11,13 +11,12 @@ ClumPyCells is publicly available at [GitHub](https://github.com/schwartzlab-met
 git clone git@github.com:schwartzlab-methods/ClumPyCells.git
 ```
 
+## 3. Installation
 
-## 3. Required Packages
-
-The following dependencies are required to run ClumPyCells. Install them using the `requirements.txt` file:
+ClumPyCells can be installed from the base directory through:
 
 ```bash
-pip install -r requirements.txt
+pip install .
 ```
 
 ## 4. General Workflow
@@ -115,6 +114,3 @@ Analysis Code: [Github](https://github.com/schwartzlab-methods/ClumPyCells_paper
 For more in-depth explanations of functions, please refer to the dedicated markdown files in the [documentation](https://github.com/schwartzlab-methods/ClumPyCells/tree/main/Documentation).
 
 ---
-
-
-
diff --git a/Documentation/Documentation.md → docs/Documentation.md b/Documentation/Documentation.md → docs/Documentation.md
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,144 @@
+[build-system]
+requires = ["setuptools>=63"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ClumPyCells"
+version = "0.1.0"
+requires-python = ">=3.10"
+dependencies = [
+    "altair==5.4.1",
+    "anyio==4.6.0",
+    "appnope==0.1.4",
+    "argon2-cffi==23.1.0",
+    "argon2-cffi-bindings==21.2.0",
+    "arrow==1.3.0",
+    "asttokens==2.4.1",
+    "async-lru==2.0.4",
+    "attrs==24.2.0",
+    "autograd==1.7.0",
+    "autograd-gamma==0.5.0",
+    "babel==2.16.0",
+    "bayesian-optimization==2.0.3",
+    "beautifulsoup4==4.12.3",
+    "bleach==6.1.0",
+    "certifi==2024.8.30",
+    "cffi==1.17.1",
+    "charset-normalizer==3.3.2",
+    "colorama==0.4.6",
+    "colour==0.1.5",
+    "comm==0.2.2",
+    "contourpy==1.3.0",
+    "cryptorandom==0.3",
+    "cycler==0.12.1",
+    "debugpy==1.8.6",
+    "decorator==5.1.1",
+    "defusedxml==0.7.1",
+    "dtreeviz==2.2.2",
+    "ecos==2.0.14",
+    "executing==2.1.0",
+    "fastjsonschema==2.20.0",
+    "fonttools==4.54.1",
+    "formulaic==1.0.2",
+    "fqdn==1.5.1",
+    "graphviz==0.20.3",
+    "h11==0.14.0",
+    "httpcore==1.0.6",
+    "httpx==0.27.2",
+    "idna==3.10",
+    "iniconfig==2.0.0",
+    "interface-meta==1.3.0",
+    "ipykernel==6.29.5",
+    "ipython==8.27.0",
+    "isoduration==20.11.0",
+    "jedi==0.19.1",
+    "jinja2==3.1.4",
+    "joblib==1.4.2",
+    "json5==0.9.25",
+    "jsonpointer==3.0.0",
+    "jsonschema==4.23.0",
+    "jsonschema-specifications==2023.12.1",
+    "jupyter-client==8.6.3",
+    "jupyter-core==5.7.2",
+    "jupyter-events==0.10.0",
+    "jupyter-lsp==2.2.5",
+    "jupyter-server==2.14.2",
+    "jupyter-server-terminals==0.5.3",
+    "jupyterlab==4.2.5",
+    "jupyterlab-pygments==0.3.0",
+    "jupyterlab-server==2.27.3",
+    "kiwisolver==1.4.7",
+    "lifelines==0.30.0",
+    "markupsafe==2.1.5",
+    "matplotlib==3.9.2",
+    "matplotlib-inline==0.1.7",
+    "mistune==3.0.2",
+    "narwhals==1.9.0",
+    "nbclient==0.10.0",
+    "nbconvert==7.16.4",
+    "nbformat==5.10.4",
+    "nest-asyncio==1.6.0",
+    "notebook==7.2.2",
+    "notebook-shim==0.2.4",
+    "numexpr==2.10.1",
+    "numpy==2.1.1",
+    "osqp==0.6.7.post3",
+    "overrides==7.7.0",
+    "packaging==24.1",
+    "pandas==2.2.3",
+    "pandocfilters==1.5.1",
+    "parso==0.8.4",
+    "patsy==0.5.6",
+    "permute==0.2",
+    "pexpect==4.9.0",
+    "pillow==10.4.0",
+    "platformdirs==4.3.6",
+    "pluggy==1.5.0",
+    "prometheus-client==0.21.0",
+    "prompt-toolkit==3.0.48",
+    "psutil==6.0.0",
+    "ptyprocess==0.7.0",
+    "pure-eval==0.2.3",
+    "pycparser==2.22",
+    "pygments==2.18.0",
+    "pyparsing==3.1.4",
+    "pytest==8.3.4",
+    "python-dateutil==2.9.0.post0",
+    "python-json-logger==2.0.7",
+    "pytz==2024.2",
+    "pyyaml==6.0.2",
+    "pyzmq==26.2.0",
+    "qdldl==0.1.7.post4",
+    "referencing==0.35.1",
+    "requests==2.32.3",
+    "rfc3339-validator==0.1.4",
+    "rfc3986-validator==0.1.1",
+    "rpds-py==0.20.0",
+    "scikit-learn==1.5.2",
+    "scikit-survival==0.23.0",
+    "scipy==1.14.1",
+    "send2trash==1.8.3",
+    "setuptools==75.1.0",
+    "six==1.16.0",
+    "sniffio==1.3.1",
+    "soupsieve==2.6",
+    "stack-data==0.6.3",
+    "statsmodels==0.14.3",
+    "terminado==0.18.1",
+    "threadpoolctl==3.5.0",
+    "tinycss2==1.3.0",
+    "tornado==6.4.1",
+    "traitlets==5.14.3",
+    "types-python-dateutil==2.9.0.20240906",
+    "typing-extensions==4.12.2",
+    "tzdata==2024.2",
+    "uri-template==1.3.0",
+    "urllib3==2.2.3",
+    "wcwidth==0.2.13",
+    "webcolors==24.8.0",
+    "webencodings==0.5.1",
+    "websocket-client==1.8.0",
+    "wrapt==1.16.0",
+]
+description = "ClumPyCells is an open-source toolbox for spatial correlation analysis based on point processing methods. By addressing cell-size differences, ClumPyCells helps to avoid biases that arise from tissue heterogeneity. The tool package provides calculations for cell aggregations using mark correlation functions, as well as post-hoc analysis tools that summarize spatial features and provides proper visualizations."
+readme = "README.md"
diff --git a/ClumPyCells/Analysis/__init__.py → src/ClumPyCells/Analysis/__init__.py b/ClumPyCells/Analysis/__init__.py → src/ClumPyCells/Analysis/__init__.py
diff --git a/ClumPyCells/Analysis/decisionTree.py → src/ClumPyCells/Analysis/decisionTree.py b/ClumPyCells/Analysis/decisionTree.py → src/ClumPyCells/Analysis/decisionTree.py
diff --git a/ClumPyCells/Analysis/interactivePlot.py → src/ClumPyCells/Analysis/interactivePlot.py b/ClumPyCells/Analysis/interactivePlot.py → src/ClumPyCells/Analysis/interactivePlot.py
diff --git a/ClumPyCells/Analysis/markcorrResult.py → src/ClumPyCells/Analysis/markcorrResult.py b/ClumPyCells/Analysis/markcorrResult.py → src/ClumPyCells/Analysis/markcorrResult.py
diff --git a/ClumPyCells/Analysis/metadata.py → src/ClumPyCells/Analysis/metadata.py b/ClumPyCells/Analysis/metadata.py → src/ClumPyCells/Analysis/metadata.py
@@ -10,6 +10,9 @@
 import pandas as pd
 from matplotlib.lines import Line2D
 
+# TODO: This does not allow the package to be imported without having this file
+# in the correct location (which will not be possible for users)
+# Make sure to resolve this issue before publishing!
 with open("config.json", "r") as file:
     config = json.load(file)
 HOMEDIR = config["HOMEDIR"]

diff --git a/ClumPyCells/Analysis/survivalAnalysis.py → src/ClumPyCells/Analysis/survivalAnalysis.py b/ClumPyCells/Analysis/survivalAnalysis.py → src/ClumPyCells/Analysis/survivalAnalysis.py
diff --git a/ClumPyCells/ClumPyCells.py → src/ClumPyCells/ClumPyCells.py b/ClumPyCells/ClumPyCells.py → src/ClumPyCells/ClumPyCells.py
diff --git a/ClumPyCells/Markcorr/__init__.py → src/ClumPyCells/Markcorr/__init__.py b/ClumPyCells/Markcorr/__init__.py → src/ClumPyCells/Markcorr/__init__.py
diff --git a/ClumPyCells/Markcorr/breakpts.py → src/ClumPyCells/Markcorr/breakpts.py b/ClumPyCells/Markcorr/breakpts.py → src/ClumPyCells/Markcorr/breakpts.py
diff --git a/ClumPyCells/Markcorr/closepairs.py → src/ClumPyCells/Markcorr/closepairs.py b/ClumPyCells/Markcorr/closepairs.py → src/ClumPyCells/Markcorr/closepairs.py
diff --git a/ClumPyCells/Markcorr/markcorr.py → src/ClumPyCells/Markcorr/markcorr.py b/ClumPyCells/Markcorr/markcorr.py → src/ClumPyCells/Markcorr/markcorr.py
diff --git a/ClumPyCells/Markcorr/pointPattern.py → src/ClumPyCells/Markcorr/pointPattern.py b/ClumPyCells/Markcorr/pointPattern.py → src/ClumPyCells/Markcorr/pointPattern.py
diff --git a/ClumPyCells/Markcorr/sm_density.py → src/ClumPyCells/Markcorr/sm_density.py b/ClumPyCells/Markcorr/sm_density.py → src/ClumPyCells/Markcorr/sm_density.py
diff --git a/ClumPyCells/Markcorr/unnormdensity.py → src/ClumPyCells/Markcorr/unnormdensity.py b/ClumPyCells/Markcorr/unnormdensity.py → src/ClumPyCells/Markcorr/unnormdensity.py
diff --git a/ClumPyCells/Markcorr/window.py → src/ClumPyCells/Markcorr/window.py b/ClumPyCells/Markcorr/window.py → src/ClumPyCells/Markcorr/window.py
diff --git a/src/ClumPyCells/__init__.py b/src/ClumPyCells/__init__.py
@@ -0,0 +1 @@
+from .ClumPyCells import *