cosmicqc 1.1.2__tar.gz

cosmicqc-1.1.2/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# test data ignores
+*.tif
+*.tiff
+*.sqlite
+*.parquet
+*.zip
+*.csv
+*.csv.gz
+*.npy
+.DS_Store
+
+# jupyter notebook build files from myst-nb
+docs/jupyter_execute
+
+# ignore vscode files
+.vscode/
+settings.json

cosmicqc-1.1.2/.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+default_language_version:
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+# globally exclude manuscript sources from all hooks (see docs/manuscripts)
+exclude: ^docs/manuscripts/
+repos:
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+    rev: 1.0.0
+    hooks:
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+        additional_dependencies:
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+        exclude: ^README\.md$  # README is managed by gh-md-toc
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+        files: ^README\.md$
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cosmicqc-1.1.2/CITATION.cff

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+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+---
+cff-version: 1.2.0
+title: coSMicQC
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Jenna
+    family-names: Tomkinson
+    orcid: 'https://orcid.org/0000-0003-2676-5813'
+  - given-names: David
+    family-names: Bunten
+    orcid: 'https://orcid.org/0000-0001-6041-3665'
+  - given-names: Vincent
+    family-names: Rubinetti
+    orcid: 'https://orcid.org/0000-0002-4655-3773'
+  - given-names: Gregory
+    family-names: Way
+    orcid: 'https://orcid.org/0000-0002-0503-9348'
+repository-code: 'https://github.com/cytomining/coSMicQC'
+identifiers:
+  - description: Software DOI
+    type: doi
+    value: "10.5281/zenodo.14797008"
+  - description: Preprint DOI
+    type: doi
+    value: "10.1101/2025.10.14.682427"
+abstract: >-
+  coSMicQC is a software tool for single-cell quality control of morphology datasets.
+keywords:
+  - python
+  - single-cell-analysis
+  - profiling
+  - quality-control
+  - way-lab
+license: BSD-3-Clause
+references:
+  - authors:
+      - name: "Way Lab CFReT_data Team"
+    date-accessed: "2024-05-13"
+    title: Way Lab CFReT_data CytoTable Data
+    type: data
+    repository-code: "https://github.com/WayScience/CFReT_data"
+    url: "https://github.com/WayScience/CFReT_data/blob/main/3.process_cfret_features/data/converted_profiles/localhost231120090001_converted.parquet"
+    scope: "localhost231120090001_converted.parquet"
+    notes: >-
+      Data from CFReT_data project is used to help validate
+      expected results. Data is generated from CellProfiler
+      and CytoTable.
+    identifiers:
+      - description: "Github Link with Contributors"
+        type: url
+        value: "https://github.com/WayScience/CFReT_data/graphs/contributors"
+  - authors:
+      - name: "Way Lab NF1_cellpainting_data Team"
+    date-accessed: "2024-06-28"
+    title: Way Lab NF1_cellpainting_data CytoTable Data
+    type: data
+    repository-code: "https://github.com/WayScience/nf1_cellpainting_data"
+    notes: >-
+      Data from NF1_cellpainting_data project is used to help validate
+      expected results. Data is generated from CellProfiler
+      and CytoTable. We use the following files from the repository:
+      - "Plate_2_nf1_analysis.sqlite"
+      - "Plate_2.parquet"
+    identifiers:
+      - description: "Github Link with Contributors"
+        type: url
+        value: "https://github.com/WayScience/nf1_cellpainting_data/graphs/contributors"
+  - title: >-
+      Plate 2 (Cell Painting images from Plate 2 for NF1_cellpainting_data project)
+    type: data
+    url: https://figshare.com/articles/dataset/Plate_2/22233700
+    notes: >-
+      Image data for related NF1_cellpainting_data parquet sqlite.
+    authors:
+    - family-names: Tomkinson
+      given-names: Jenna
+    - family-names: Mattson-Hoss
+      given-names: Michelle
+    - family-names: Sarnoff
+      given-names: Herb
+    - family-names: Way
+      given-names: Gregory
+    date-published: "2023-04-12"
+    identifiers:
+    - type: doi
+      value: 10.6084/m9.figshare.22233700.v4
+  - authors:
+      - name: "Way Lab and Alexander Lab Nuclear Speckles Collaboration"
+    date-accessed: "2024-09-04"
+    title: Way Lab and Alexander Lab Nuclear Speckles Collaboration Data
+    type: data
+    repository-code: https://github.com/WayScience/nuclear_speckle_image_profiling
+    notes: >-
+      Data from a collaborative project focusing on nuclear speckles
+      with the Way Lab and Alexander Lab s used to help validate
+      expected results. Parquet data is generated from CellProfiler
+      and CytoTable. Images courtesy of Katherine Alexander
+      and the Alexander Lab.
+    identifiers:
+      - description: "Github Link with Contributors"
+        type: url
+        value: "https://github.com/WayScience/nuclear_speckle_image_profiling/graphs/contributors"
+  - authors:
+      - family-names: Chandrasekaran
+        given-names: Srinivas Niranj
+      - family-names: Cimini
+        given-names: Beth A.
+      - family-names: Goodale
+        given-names: Amy
+      - family-names: Miller
+        given-names: Lisa
+      - family-names: Kost-Alimova
+        given-names: Maria
+      - family-names: Jamali
+        given-names: Nasim
+      - family-names: Doench
+        given-names: John G.
+      - family-names: Fritchman
+        given-names: Briana
+      - family-names: Skepner
+        given-names: Adam
+      - family-names: Melanson
+        given-names: Michelle
+      - family-names: Kalinin
+        given-names: Alexandr A.
+      - family-names: Arevalo
+        given-names: John
+      - family-names: Haghighi
+        given-names: Marzieh
+      - family-names: Caicedo
+        given-names: Juan C.
+      - family-names: Kuhn
+        given-names: Daniel
+      - family-names: Hernandez
+        given-names: Desiree
+      - family-names: Berstler
+        given-names: James
+      - family-names: Shafqat-Abbasi
+        given-names: Hamdah
+      - family-names: Root
+        given-names: David E.
+      - family-names: Swalley
+        given-names: Susanne E.
+      - family-names: Garg
+        given-names: Sakshi
+      - family-names: Singh
+        given-names: Shantanu
+      - family-names: Carpenter
+        given-names: Anne E.
+    date-accessed: "2024-08-21"
+    title: >-
+      Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
+    type: article
+    issn: 1548-7105
+    issue: 6
+    journal: Nature Methods
+    pages: 1114-1121
+    volume: 21
+    url: https://doi.org/10.1038/s41592-024-02241-6
+    date-published: "2024-06-01"
+    identifiers:
+      - type: doi
+        value: 10.1038/s41592-024-02241-6
+    notes: >-
+      JUMP (cpg0000-jump-pilot) was used to help demonstrate coSMicQC performance
+      with large data. See here for more information:
+      https://github.com/broadinstitute/cellpainting-gallery

cosmicqc-1.1.2/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+Please see our full code of conduct at https://cytomining.github.io/coSMicQC/main/code_of_conduct

cosmicqc-1.1.2/CONTRIBUTING.md

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+# Contributing
+
+Please see our [contributing](https://github.com/cytomining/coSMicQC/blob/main/docs/src/contributing.md) documentation for more details on contributions, development, and testing.

cosmicqc-1.1.2/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2024, Way Science
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

cosmicqc-1.1.2/MANIFEST.in

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+# Constrain the sdist to what's needed to build and describe the package.
+# setuptools_scm's file-finder adds every git-tracked file to the sdist by
+# default; docs/, tests/, and media/ carry large notebooks, images, and
+# fixture data that push the tarball past PyPI's 100 MB per-file limit, so
+# prune them here.
+include LICENSE
+include README.md
+include CITATION.cff
+
+prune docs
+prune tests
+prune media
+prune scripts
+prune .github

cosmicqc-1.1.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: cosmicqc
+Version: 1.1.2
+Summary: coSMicQC is a software tool for single-cell quality control of morphology datasets.
+Author: Jenna Tomkinson, Dave Bunten, Gregory P. Way
+License-Expression: BSD-3-Clause
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: <3.14,>=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cytodataframe<0.4,>=0.0.25; python_version < "3.11"
+Requires-Dist: cytodataframe<0.4,>=0.3; python_version >= "3.11"
+Requires-Dist: fire<0.8,>=0.6
+Requires-Dist: llvmlite==0.49
+Requires-Dist: matplotlib<4,>=3.10.3
+Requires-Dist: pandas<3,>=2.2.2
+Requires-Dist: pyarrow<21,>=16; python_version < "3.11"
+Requires-Dist: pyarrow<23,>=22; python_version >= "3.11"
+Requires-Dist: pyyaml<7,>=6.0.1
+Requires-Dist: scipy<2,>=1.13
+Requires-Dist: seaborn<0.14,>=0.13.2
+Requires-Dist: tabulate<1,>=0.9
+Dynamic: license-file
+
+<img height="200" src="https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/with-text-for-light-bg.png?raw=true">
+
+# Single cell Morphology Quality Control
+
+![PyPI - Version](https://img.shields.io/pypi/v/cosmicqc)
+[![Build Status](https://github.com/cytomining/coSMicQC/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/cytomining/coSMicQC/actions/workflows/run-tests.yml?query=branch%3Amain)
+![Coverage Status](https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/coverage-badge.svg)
+[![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)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+[![Preprint DOI badge](https://img.shields.io/badge/Preprint_DOI-10.1101/2025.10.14.682427-blue)](https://doi.org/10.1101/2025.10.14.682427)
+[![Software DOI badge](https://img.shields.io/badge/Software_DOI-10.5281/zenodo.14888111-blue)](https://doi.org/10.5281/zenodo.14797008)
+
+> 🌠 Navigate the cosmos of single-cell morphology with confidence — coSMicQC keeps your data on course!
+
+## Contents
+
+<!--ts-->
+* [Single cell Morphology Quality Control](#single-cell-morphology-quality-control)
+   * [Contents](#contents)
+   * [Overview](#overview)
+   * [Repo Contents](#repo-contents)
+   * [System Requirements](#system-requirements)
+   * [Installation Guide](#installation-guide)
+      * [Stable release (PyPI)](#stable-release-pypi)
+      * [Development version (from source)](#development-version-from-source)
+   * [Demo](#demo)
+   * [Results](#results)
+   * [License](#license)
+   * [Issues](#issues)
+   * [Citation](#citation)
+
+
+<!--te-->
+
+## Overview
+
+coSMicQC is a Python package to evaluate converted single-cell morphology outputs from [CytoTable](https://github.com/cytomining/CytoTable).
+Technical artifacts can arise during segmentation, leading to issues such as under-segmentation, over-segmentation, or the erroneous segmentation of background noise, smudges, or bright artifacts.
+By utilizing specific morphological features extracted with CellProfiler, you can identify technically incorrect segmentations and label or remove them before downstream analysis.
+
+Please confer with our docsite for more comprehensive information about the project: https://cytomining.github.io/coSMicQC/main/
+
+> 🌟 Check out our [blog post](https://waysciencelab.com/2024/12/20/cosmicqc.html) for a deeper background and how coSMicQC can help.
+
+## Repo Contents
+
+- `src/cosmicqc`: coSMicQC source code.
+- `tests`: test suite.
+- `docs`: documentation sources and examples.
+- `media`: project assets (e.g., coverage badge).
+- `reports`: generated artifacts (figures, notebooks, or summaries).
+
+## System Requirements
+
+- Python: `>=3.10` (tested through 3.13).
+- RAM/CPU: standard laptop/desktop is sufficient for typical plate-sized datasets; larger screens benefit from more RAM/cores for faster QC/plotting.
+- OS: Linux, macOS, and Windows are supported via Python; CI tests run on GitHub Actions.
+
+## Installation Guide
+
+### Stable release (PyPI)
+
+```shell
+pip install coSMicQC
+```
+
+### Development version (from source)
+
+```shell
+pip install git+https://github.com/cytomining/coSMicQC.git
+# or with uv for local development
+uv sync
+```
+
+## Demo
+
+- Examples and notebooks live under `docs/src/examples` and the published docs: https://cytomining.github.io/coSMicQC
+- Quickstart blog post: https://waysciencelab.com/2024/12/20/cosmicqc.html
+
+## Results
+
+- Test and lint status: ![Build Status](https://github.com/cytomining/coSMicQC/actions/workflows/run-tests.yml/badge.svg?branch=main)
+- Coverage: ![Coverage Status](https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/coverage-badge.svg)
+
+## License
+
+BSD-3-Clause; see [LICENSE](LICENSE).
+
+## Issues
+
+Please open issues or feature requests at https://github.com/cytomining/coSMicQC/issues.
+
+## Citation
+
+If you use coSMicQC in your work, please cite:
+
+- Software DOI: [10.5281/zenodo.14888111](https://doi.org/10.5281/zenodo.14888111)
+- Preprint: [10.1101/2025.10.14.682427](https://doi.org/10.1101/2025.10.14.682427)
+- Citation metadata: [CITATION.cff](CITATION.cff)