scpviz 0.5.0a0__tar.gz

scpviz-0.5.0a0/LICENSE

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+Copyright (c) 2018 The Python Packaging Authority
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

scpviz-0.5.0a0/PKG-INFO

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+Metadata-Version: 2.1
+Name: scpviz
+Version: 0.5.0a0
+Summary: A package to visualize single cell proteomics (and more to come!) data
+Author-email: Marion Pang <sr_pang@hotmail.com>
+Project-URL: Homepage, https://github.com/gnaprs/scpviz
+Project-URL: Issues, https://github.com/gnaprs/scpviz/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Development Status :: 3 - Alpha
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: upsetplot
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: umap-learn
+Requires-Dist: adjustText
+Requires-Dist: anndata
+Requires-Dist: requests
+Requires-Dist: matplotlib_venn
+Requires-Dist: pyarrow
+Requires-Dist: scanpy
+Requires-Dist: IPython
+Requires-Dist: igraph
+Requires-Dist: harmonypy
+Requires-Dist: leidenalg
+Requires-Dist: scikit-misc
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: openpyxl; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+
+# scpviz
+<img src="https://raw.githubusercontent.com/gnaprs/scpviz/refs/heads/main/docs/assets/300ppi/logo_white_label@300x.png"
+ align="right" width="256"/>
+ [![DOI](https://zenodo.org/badge/762480088.svg)](https://doi.org/10.5281/zenodo.17362532)
+
+**Build & Tests:**  
+[![Build Status](https://github.com/gnaprs/scpviz/actions/workflows/python-package.yml/badge.svg)](https://github.com/gnaprs/scpviz/actions/workflows/python-package.yml)
+[![codecov](https://codecov.io/gh/gnaprs/scpviz/branch/main/graph/badge.svg)](https://codecov.io/gh/gnaprs/scpviz)
+
+**Documentation:**  
+[![Docs CI](https://github.com/gnaprs/scpviz/actions/workflows/ci.yml/badge.svg)](https://github.com/gnaprs/scpviz/actions/workflows/ci.yml)
+[![Docs](https://img.shields.io/badge/docs-v0.3.0-brightgreen.svg)](https://gnaprs.github.io/scpviz)
+
+
+**scpviz** is a Python package for single-cell and spatial proteomics data analysis, built around a custom `pAnnData` object.  
+It extends the [AnnData](https://anndata.readthedocs.io/) ecosystem with proteomics-specific functionality, enabling seamless integration of proteins, peptides, and relational data.
+
+* **Documentation**: https://gnaprs.github.io/scpviz/
+* **Conda**: https://anaconda.org/gnaprs/scpviz (FIX)
+* **Python Package Index (PyPI)**: https://pypi.org/project/scpviz/
+
+## Getting started
+### Installation
+
+`scpviz` requires Python 3.8 or later. It is distributed as a Python package and can be installed with `pip`.
+
+    python3 -m pip install scpviz
+
+This will install all required dependencies, including `scanpy`, `anndata`, `pandas`, and common plotting libraries.
+
+Alternatively, scpviz is available on Conda:
+
+    conda install gnaprs::scpviz
+
+For the most up-to-date version of scpviz, clone the repository and
+install the package using pip:
+
+    conda create -n scpviz python=3.8 numpy pandas pip
+    conda activate scpviz
+    pip install git+https://github.com/gnaprs/scpviz.git@development
+
+### Quickstart
+
+Check out the [quickstart](https://gnaprs.github.io/scpviz/tutorials/quickstart/) guide for a run through import, basic preprocessing and quick visualization
+
+### In-depth Tutorials
+For more in-depth guides on importing, filtering, plotting, and running enrichment, see the [tutorials](https://gnaprs.github.io/scpviz/tutorials/).
+
+### API Reference
+
+Full function documentation for the `pAnnData` class and utility modules can be found on our [documentation page](https://gnaprs.github.io/scpviz/reference/).
+
+## Contributing
+
+If you'll like to contribute to `scpviz`, please see the [contributing guidelines](https://gnaprs.github.io/scpviz/dev/contributing/). We welcome contributions from the community to help improve, expand, and document the functionality of scpviz.
+
+## License
+`scpviz` was created by Marion Pang. It is licensed under the terms of the MIT license.

scpviz-0.5.0a0/README.md

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+# scpviz
+<img src="https://raw.githubusercontent.com/gnaprs/scpviz/refs/heads/main/docs/assets/300ppi/logo_white_label@300x.png"
+ align="right" width="256"/>
+ [![DOI](https://zenodo.org/badge/762480088.svg)](https://doi.org/10.5281/zenodo.17362532)
+
+**Build & Tests:**  
+[![Build Status](https://github.com/gnaprs/scpviz/actions/workflows/python-package.yml/badge.svg)](https://github.com/gnaprs/scpviz/actions/workflows/python-package.yml)
+[![codecov](https://codecov.io/gh/gnaprs/scpviz/branch/main/graph/badge.svg)](https://codecov.io/gh/gnaprs/scpviz)
+
+**Documentation:**  
+[![Docs CI](https://github.com/gnaprs/scpviz/actions/workflows/ci.yml/badge.svg)](https://github.com/gnaprs/scpviz/actions/workflows/ci.yml)
+[![Docs](https://img.shields.io/badge/docs-v0.3.0-brightgreen.svg)](https://gnaprs.github.io/scpviz)
+
+
+**scpviz** is a Python package for single-cell and spatial proteomics data analysis, built around a custom `pAnnData` object.  
+It extends the [AnnData](https://anndata.readthedocs.io/) ecosystem with proteomics-specific functionality, enabling seamless integration of proteins, peptides, and relational data.
+
+* **Documentation**: https://gnaprs.github.io/scpviz/
+* **Conda**: https://anaconda.org/gnaprs/scpviz (FIX)
+* **Python Package Index (PyPI)**: https://pypi.org/project/scpviz/
+
+## Getting started
+### Installation
+
+`scpviz` requires Python 3.8 or later. It is distributed as a Python package and can be installed with `pip`.
+
+    python3 -m pip install scpviz
+
+This will install all required dependencies, including `scanpy`, `anndata`, `pandas`, and common plotting libraries.
+
+Alternatively, scpviz is available on Conda:
+
+    conda install gnaprs::scpviz
+
+For the most up-to-date version of scpviz, clone the repository and
+install the package using pip:
+
+    conda create -n scpviz python=3.8 numpy pandas pip
+    conda activate scpviz
+    pip install git+https://github.com/gnaprs/scpviz.git@development
+
+### Quickstart
+
+Check out the [quickstart](https://gnaprs.github.io/scpviz/tutorials/quickstart/) guide for a run through import, basic preprocessing and quick visualization
+
+### In-depth Tutorials
+For more in-depth guides on importing, filtering, plotting, and running enrichment, see the [tutorials](https://gnaprs.github.io/scpviz/tutorials/).
+
+### API Reference
+
+Full function documentation for the `pAnnData` class and utility modules can be found on our [documentation page](https://gnaprs.github.io/scpviz/reference/).
+
+## Contributing
+
+If you'll like to contribute to `scpviz`, please see the [contributing guidelines](https://gnaprs.github.io/scpviz/dev/contributing/). We welcome contributions from the community to help improve, expand, and document the functionality of scpviz.
+
+## License
+`scpviz` was created by Marion Pang. It is licensed under the terms of the MIT license.

scpviz-0.5.0a0/pyproject.toml

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+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "scpviz"
+version = "0.5.0-alpha"
+authors = [
+  {name="Marion Pang", email="sr_pang@hotmail.com"},
+]
+description = "A package to visualize single cell proteomics (and more to come!) data"
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Development Status :: 3 - Alpha",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+  "numpy",
+  "pandas", 
+  "matplotlib", 
+  "seaborn",
+  "upsetplot", 
+  "scikit-learn", 
+  "scipy",
+  "umap-learn", 
+  "adjustText", 
+  "anndata",
+  "requests",
+  "matplotlib_venn",
+  "pyarrow",
+  "scanpy",
+  "IPython",
+  "igraph",
+  "harmonypy",
+  "leidenalg",
+  "scikit-misc"
+]
+
+[project.urls]
+Homepage = "https://github.com/gnaprs/scpviz"
+Issues = "https://github.com/gnaprs/scpviz/issues"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]
+filterwarnings = [
+    "ignore::DeprecationWarning:jupyter_client.connect",
+    "ignore::DeprecationWarning:upsetplot.plotting"
+]
+
+[project.optional-dependencies]
+dev = ["pytest","coverage","flake8","openpyxl","pytest-cov"]

scpviz-0.5.0a0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

scpviz-0.5.0a0/src/scpviz/TrackedDataFrame.py

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+import pandas as pd
+
+class TrackedDataFrame(pd.DataFrame):
+    """
+    A subclass of :class:`pandas.DataFrame` that integrates with a parent 
+    :class:`pAnnData` object to track when derived tables (e.g., `.summary`) 
+    have been modified outside the canonical workflow.
+
+    Any in-place modifications automatically mark the parent object as "stale"
+    using the provided callback (`mark_stale_fn`). This ensures downstream
+    code can detect unsynchronized changes and prompt recomputation if needed.
+
+    Attributes:
+        _parent (pAnnData): The parent object associated with this DataFrame.
+        _mark_stale_fn (callable): Function called when the DataFrame is modified.
+        _raw_loc, _raw_iloc: Direct accessors for untracked indexing (safe use).
+
+    !!! warning "Internal Utility"
+        `TrackedDataFrame` is primarily intended for internal use within `pAnnData`.  
+        Direct use in analysis code is not recommended, as stale-tracking may
+        interfere with expected pandas behaviors.
+
+    !!! tip
+        Use `.raw_loc` and `.raw_iloc` to bypass stale-marking when read-only
+        access is explicitly desired.
+
+    """
+    _metadata = ["_parent", "_mark_stale_fn"]
+
+    @property
+    def _constructor(self):
+        return TrackedDataFrame
+
+    def __new__(cls, *args, **kwargs):
+        return super().__new__(cls)
+
+    def __init__(self, *args, parent=None, mark_stale_fn=None, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._parent = parent
+        self._mark_stale_fn = mark_stale_fn
+        # Bind raw .loc/.iloc for safe use
+        self._raw_loc = super().loc
+        self._raw_iloc = super().iloc
+
+    def __repr__(self):
+        base = super().__repr__()
+        stale_msg = ""
+        if getattr(self, "_mark_stale_fn", None) and getattr(self._parent, "_summary_is_stale", False):
+            stale_msg = "\n⚠️  [TrackedDataFrame] This summary has been modified and is not synced back to .obs."
+        return base + stale_msg
+
+    def _mark_stale(self):
+        """
+        Mark the parent pAnnData object as stale.
+
+        Called internally before any modifying operations (e.g. `__setitem__`,
+        `drop`, `assign`). Triggers the parent’s `_mark_stale_fn` if provided.
+        """
+        if self._mark_stale_fn is not None:
+            self._mark_stale_fn()
+
+    def __setitem__(self, key, value):
+        self._mark_stale()
+        return super().__setitem__(key, value)
+
+    def drop(self, *args, **kwargs):
+        self._mark_stale()
+        return super().drop(*args, **kwargs)
+
+    def assign(self, *args, **kwargs):
+        self._mark_stale()
+        return super().assign(*args, **kwargs)
+
+    def pop(self, *args, **kwargs):
+        self._mark_stale()
+        return super().pop(*args, **kwargs)
+
+    @property
+    def loc(self):
+        self._mark_stale()
+        return super().loc
+
+    @property
+    def iloc(self):
+        self._mark_stale()
+        return super().iloc

scpviz-0.5.0a0/src/scpviz/__init__.py

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+import pandas as pd
+import numpy as np
+import re
+
+import matplotlib.pyplot as plt
+import matplotlib.patches as mpatches
+import matplotlib.colors as mcolors
+from matplotlib.colors import TwoSlopeNorm
+from matplotlib.ticker import MaxNLocator
+import matplotlib.collections as clt
+from upsetplot import plot, generate_counts, from_contents, query, UpSet
+import seaborn as sns
+sns.set_theme(context='paper', style='ticks')
+
+from sklearn.decomposition import PCA
+from scipy.stats import ttest_ind
+from decimal import Decimal
+
+from .pAnnData import pAnnData  # imports the class
+__all__ = ["pAnnData"]
+
+import warnings
+warnings.filterwarnings('ignore')

scpviz-0.5.0a0/src/scpviz/enrichment.py

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+# scpviz/enrichment.py
+
+"""
+Shim module to expose enrichment functions at top-level `scpviz.enrichment`.
+Delegates to `scpviz.pAnnData.enrichment`.
+"""
+
+from scpviz.pAnnData.enrichment import (
+    enrichment_functional,
+    enrichment_ppi,
+    _resolve_de_key,
+    _pretty_vs_key,
+    EnrichmentMixin,
+)
+
+import requests  # so patch("scpviz.enrichment.requests.post") still works

scpviz-0.5.0a0/src/scpviz/pAnnData/__init__.py

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+from .pAnnData import pAnnData  # expose the main class
+
+__all__ = ["pAnnData"]