clinipub 0.1.0__tar.gz

clinipub-0.1.0/.github/workflows/pypi-publish.yml

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+name: Publish to `clinipub` on PyPI
+
+on:
+  push:
+    tags:
+      - 'v*' # Triggers the workflow whenever a tag starting with 'v' is pushed (e.g., v0.1.0)
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    
+    # Required permissions for Trusted Publishing (OIDC) authentication
+    permissions:
+      id-token: write
+      contents: read
+
+    steps:
+      - name: Checkout Source Code
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Run Unit Tests
+        run: |
+          uv sync
+          uv run pytest
+
+      - name: Build Distribution Packages 🏗️
+        run: uv build
+
+      - name: Publish Package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

clinipub-0.1.0/.github/workflows/tests-suite.yml

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+name: clinipub Tests Suite
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+          enable-cache: true
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          uv sync
+
+      - name: Run tests
+        run: uv run pytest

clinipub-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+# Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+# poetry.lock
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.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/
+
+# PyCharm
+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#   and can be added to the global gitignore or merged into this file.  For a more nuclear
+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+# .idea/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+# Temporary file for partial code execution
+tempCodeRunnerFile.py
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml

clinipub-0.1.0/CONTRIBUTING.md

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+# Contributing to clinipub
+
+Thank you for contributing to `clinipub`.
+This repository is designed for clinical data scientists and authors who need reproducible, publication-ready tabulation and audit reporting.
+
+## How to contribute
+
+1. Fork the repository and create a feature branch from `main`.
+   - Branch name format: `feature/<short-description>` or `fix/<issue-number>-<short-description>`.
+
+2. Keep changes small and focused.
+   - One issue per branch.
+   - Prefer incremental commits with descriptive messages.
+
+3. Run tests locally before submitting a pull request.
+   - Use the project development workflow with `uv`.
+   - Recommended command:
+     ```bash
+     uv run pytest
+     ```
+
+4. Follow the project style.
+   - Keep code readable and consistent with PEP 8.
+   - Use clear variable names and concise docstrings.
+
+## Reporting issues
+
+- Open a GitHub issue for bugs, enhancement requests, or documentation improvements.
+- Provide a minimal reproduction example and expected behavior.
+- Include the Python version and package versions when relevant.
+
+## Pull request guidelines
+
+- Target the `main` branch.
+- Provide a short summary of the change and the motivation.
+- Mention related issues when applicable.
+- Ensure all tests pass and no new warnings are introduced.
+
+## Development notes
+
+- `clinipub` is a pandas-centric package. New features should preserve compatibility with typical clinical analysis workflows.
+- Use the existing `src/clinipub` package layout and keep public API changes minimal unless necessary.
+- Update `README.md` or add examples if the change affects usage.
+
+## License
+
+By contributing, you agree that your contributions will be licensed under the repository's existing license.

clinipub-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Arsalan Anwar
+
+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.

clinipub-0.1.0/PKG-INFO

@@ -0,0 +1,143 @@
+Metadata-Version: 2.4
+Name: clinipub
+Version: 0.1.0
+Summary: Transform clinical dataframes into publication-ready, beautifully styled tables for medical journals and manuscripts.
+Author-email: Arsalan Anwar <arsalan.anwar.7777@gmail.com>
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: jinja2>=3.0.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: scipy>=1.10.0
+Description-Content-Type: text/markdown
+
+# clinipub
+[![PyPI release](https://img.shields.io/pypi/v/clinipub)](https://pypi.org/project/clinipub/)
+[![GitHub release](https://img.shields.io/github/v/release/arsalananwar11/clinipub)](https://github.com/arsalananwar11/clinipub/releases)
+[![Tests](https://github.com/arsalananwar11/clinipub/actions/workflows/tests-suite.yml/badge.svg?branch=main)](https://github.com/arsalananwar11/clinipub/actions/workflows/tests-suite.yml)
+
+A Python package to transform clinical dataframes into publication-ready, beautifully styled tables for medical journals and manuscripts
+
+`clinipub` is a modern Python package designed for data scientists in the life sciences and clinical research fields. It bridges the gap between raw data analysis (`pandas.DataFrame`) and publication-ready medical writing reporting standards (matching *NEJM*, *JAMA*, *The Lancet*, and CDISC/STROBE guidelines).
+
+Unlike existing packages, `clinipub` offers autonomous statistical decision-making, impeccable typography, and native exports to formats that medical writers can use out of the box without manual reformatting.
+
+---
+
+## Key Advantages Over Other Packages
+
+* **Autonomous Statistics:** Automatically detects variable types and evaluates normality (Shapiro-Wilk) to map the correct parametric or non-parametric test.
+* **Regulatory-Grade Precision:** Automatically falls back to Fisher's Exact test if any contingency cross-tab count drops below 5.
+
+---
+
+## 🛠️ Statistical Test Selection Matrix
+
+The framework automatically maps and executes your bivariate comparative analytics using the following clinical logic:
+
+| Variable Type | Distribution | Group Count | Test Executed |
+| :--- | :--- | :--- | :--- |
+| **Continuous** | Normal (Parametric) | 2 Groups | Independent Welch's $t$-test |
+| **Continuous** | Normal (Parametric) | 3+ Groups | One-way ANOVA |
+| **Continuous** | Skewed (Non-Parametric) | 2 Groups | Mann-Whitney U test |
+| **Continuous** | Skewed (Non-Parametric) | 3+ Groups | Kruskal-Wallis test |
+| **Categorical** | Any | 2x2 with Cell Count < 5 | Fisher's Exact test |
+| **Categorical** | Any | Standard Configurations | Chi-Square ($\chi^2$) Contingency |
+
+---
+
+## Developer Setup & Installation
+
+This project is managed efficiently using the **`uv`** package manager.
+
+### Prerequisites
+Ensure you have `uv` installed:
+```bash
+pip install uv
+```
+
+### Installation & Environment Setup
+Clone the repository and sync the isolated project development container:
+
+```bash
+git clone https://github.com/arsalananwar11/clinipub.git
+
+cd clinipub
+uv sync
+```
+
+### Running Unit Tests
+We maintain high test coverage for clinical accuracy using pytest:
+```bash
+uv run pytest
+```
+
+## Pipeline Flow
+1. `MissingDataAuditor` computes raw missingness and validates data completeness.
+2. `ClinicalDataAuditor` classifies variables and checks continuous normality.
+3. `BivariateTestSelector` chooses tests automatically based on group count and distribution.
+4. `TableOneAssembler` builds a stratified Table 1 with descriptive statistics and p-values.
+
+## Quick Usage
+```python
+import pandas as pd
+from clinipub import (
+    MissingDataAuditor,
+    ClinicalDataAuditor,
+    BivariateTestSelector,
+    TableOneAssembler,
+)
+
+# Load your clinical dataset
+df = pd.read_csv("baseline.csv")
+
+# 1. Audit missing data and generate an HTML report
+missing_auditor = MissingDataAuditor(df)
+missing_df = missing_auditor.calculate_missingness()
+html_report = missing_auditor.to_html_report(
+    audit_df=missing_df,
+    thresholds={"low": 1.0, "mid": 20.0},
+)
+
+# 2. Audit variable types and normality
+auditor = ClinicalDataAuditor(df)
+var_types = auditor.detect_variable_types()
+normality = auditor.test_normality(var_types["continuous"])
+
+# 3. Run autonomous bivariate tests
+selector = BivariateTestSelector(df, stratify_by="treatment")
+continuous_result = selector.test_continuous("age", is_normal=normality["age"])
+cat_result = selector.test_categorical("smoker_status")
+
+# 4. Build publication-ready Table 1
+assembler = TableOneAssembler(df, stratify_by="treatment")
+table1 = assembler.build()
+```
+
+## Core API and Arguments
+- `MissingDataAuditor(data: pd.DataFrame)`
+  - `calculate_missingness()`
+    - returns a raw `DataFrame` with `missing_count` and `missing_percentage`
+  - `to_html_report(audit_df: pd.DataFrame = None, thresholds: dict = {'low': 5.0, 'mid': 30.0})`
+    - returns styled HTML for publication-ready missingness reporting
+
+- `ClinicalDataAuditor(data: pd.DataFrame)`
+  - `detect_variable_types(max_categorical_threshold: int = 10)`
+    - returns `{'categorical': [...], 'continuous': [...]}`
+  - `test_normality(continuous_cols: list, alpha: float = 0.05)`
+    - returns `{column_name: bool}`
+
+- `BivariateTestSelector(data: pd.DataFrame, stratify_by: str)`
+  - `test_continuous(col: str, is_normal: bool)`
+    - returns `{'p_value': float, 'test': str}`
+  - `test_categorical(col: str)`
+    - returns `{'p_value': float, 'test': str}`
+
+- `TableOneAssembler(data: pd.DataFrame, stratify_by: str, columns: list = None)`
+  - `build()`
+    - returns a styled `pandas.DataFrame` with stratified descriptive statistics and p-values
+
+## Contributing
+
+Contributions are welcome. Please read [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines on issues, pull requests, testing, and repository workflow.
+

clinipub-0.1.0/README.md

@@ -0,0 +1,130 @@
+# clinipub
+[![PyPI release](https://img.shields.io/pypi/v/clinipub)](https://pypi.org/project/clinipub/)
+[![GitHub release](https://img.shields.io/github/v/release/arsalananwar11/clinipub)](https://github.com/arsalananwar11/clinipub/releases)
+[![Tests](https://github.com/arsalananwar11/clinipub/actions/workflows/tests-suite.yml/badge.svg?branch=main)](https://github.com/arsalananwar11/clinipub/actions/workflows/tests-suite.yml)
+
+A Python package to transform clinical dataframes into publication-ready, beautifully styled tables for medical journals and manuscripts
+
+`clinipub` is a modern Python package designed for data scientists in the life sciences and clinical research fields. It bridges the gap between raw data analysis (`pandas.DataFrame`) and publication-ready medical writing reporting standards (matching *NEJM*, *JAMA*, *The Lancet*, and CDISC/STROBE guidelines).
+
+Unlike existing packages, `clinipub` offers autonomous statistical decision-making, impeccable typography, and native exports to formats that medical writers can use out of the box without manual reformatting.
+
+---
+
+## Key Advantages Over Other Packages
+
+* **Autonomous Statistics:** Automatically detects variable types and evaluates normality (Shapiro-Wilk) to map the correct parametric or non-parametric test.
+* **Regulatory-Grade Precision:** Automatically falls back to Fisher's Exact test if any contingency cross-tab count drops below 5.
+
+---
+
+## 🛠️ Statistical Test Selection Matrix
+
+The framework automatically maps and executes your bivariate comparative analytics using the following clinical logic:
+
+| Variable Type | Distribution | Group Count | Test Executed |
+| :--- | :--- | :--- | :--- |
+| **Continuous** | Normal (Parametric) | 2 Groups | Independent Welch's $t$-test |
+| **Continuous** | Normal (Parametric) | 3+ Groups | One-way ANOVA |
+| **Continuous** | Skewed (Non-Parametric) | 2 Groups | Mann-Whitney U test |
+| **Continuous** | Skewed (Non-Parametric) | 3+ Groups | Kruskal-Wallis test |
+| **Categorical** | Any | 2x2 with Cell Count < 5 | Fisher's Exact test |
+| **Categorical** | Any | Standard Configurations | Chi-Square ($\chi^2$) Contingency |
+
+---
+
+## Developer Setup & Installation
+
+This project is managed efficiently using the **`uv`** package manager.
+
+### Prerequisites
+Ensure you have `uv` installed:
+```bash
+pip install uv
+```
+
+### Installation & Environment Setup
+Clone the repository and sync the isolated project development container:
+
+```bash
+git clone https://github.com/arsalananwar11/clinipub.git
+
+cd clinipub
+uv sync
+```
+
+### Running Unit Tests
+We maintain high test coverage for clinical accuracy using pytest:
+```bash
+uv run pytest
+```
+
+## Pipeline Flow
+1. `MissingDataAuditor` computes raw missingness and validates data completeness.
+2. `ClinicalDataAuditor` classifies variables and checks continuous normality.
+3. `BivariateTestSelector` chooses tests automatically based on group count and distribution.
+4. `TableOneAssembler` builds a stratified Table 1 with descriptive statistics and p-values.
+
+## Quick Usage
+```python
+import pandas as pd
+from clinipub import (
+    MissingDataAuditor,
+    ClinicalDataAuditor,
+    BivariateTestSelector,
+    TableOneAssembler,
+)
+
+# Load your clinical dataset
+df = pd.read_csv("baseline.csv")
+
+# 1. Audit missing data and generate an HTML report
+missing_auditor = MissingDataAuditor(df)
+missing_df = missing_auditor.calculate_missingness()
+html_report = missing_auditor.to_html_report(
+    audit_df=missing_df,
+    thresholds={"low": 1.0, "mid": 20.0},
+)
+
+# 2. Audit variable types and normality
+auditor = ClinicalDataAuditor(df)
+var_types = auditor.detect_variable_types()
+normality = auditor.test_normality(var_types["continuous"])
+
+# 3. Run autonomous bivariate tests
+selector = BivariateTestSelector(df, stratify_by="treatment")
+continuous_result = selector.test_continuous("age", is_normal=normality["age"])
+cat_result = selector.test_categorical("smoker_status")
+
+# 4. Build publication-ready Table 1
+assembler = TableOneAssembler(df, stratify_by="treatment")
+table1 = assembler.build()
+```
+
+## Core API and Arguments
+- `MissingDataAuditor(data: pd.DataFrame)`
+  - `calculate_missingness()`
+    - returns a raw `DataFrame` with `missing_count` and `missing_percentage`
+  - `to_html_report(audit_df: pd.DataFrame = None, thresholds: dict = {'low': 5.0, 'mid': 30.0})`
+    - returns styled HTML for publication-ready missingness reporting
+
+- `ClinicalDataAuditor(data: pd.DataFrame)`
+  - `detect_variable_types(max_categorical_threshold: int = 10)`
+    - returns `{'categorical': [...], 'continuous': [...]}`
+  - `test_normality(continuous_cols: list, alpha: float = 0.05)`
+    - returns `{column_name: bool}`
+
+- `BivariateTestSelector(data: pd.DataFrame, stratify_by: str)`
+  - `test_continuous(col: str, is_normal: bool)`
+    - returns `{'p_value': float, 'test': str}`
+  - `test_categorical(col: str)`
+    - returns `{'p_value': float, 'test': str}`
+
+- `TableOneAssembler(data: pd.DataFrame, stratify_by: str, columns: list = None)`
+  - `build()`
+    - returns a styled `pandas.DataFrame` with stratified descriptive statistics and p-values
+
+## Contributing
+
+Contributions are welcome. Please read [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines on issues, pull requests, testing, and repository workflow.
+