flowgem 0.1.0__tar.gz

flowgem-0.1.0/.github/workflows/ci.yml

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+name: ci
+
+on: [push, pull_request]
+
+jobs:
+  ci:
+    # Set up operating system
+    runs-on: ubuntu-latest
+
+    # Define job steps
+    steps:
+      - name: Check-out repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Upgrade pip
+        run: python -m pip install --upgrade pip
+        
+      - name: Install CPU-only torch
+        run: pip install torch --index-url https://download.pytorch.org/whl/cpu
+
+      - name: Install package
+        run: pip install -e . --group dev --group docs
+
+      - name: Test with pytest
+        run: python -m pytest tests/ --cov=flowgem --cov-report=xml
+
+      - name: Use Codecov to track coverage
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml   # coverage report
+
+      - name: Build documentation
+        run: make html --directory docs/

flowgem-0.1.0/.github/workflows/release.yml

@@ -0,0 +1,106 @@
+name: Publish Python package
+
+on:
+  release:
+    types: [published]
+
+permissions: {}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - name: Check out the release
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
+        with:
+          python-version: "3.12"
+
+      - name: Build and check distributions
+        run: |
+          python -m pip install --upgrade build twine
+          rm -rf dist
+          python -m build
+          python -m twine check --strict dist/*
+
+      - name: Check that the release tag matches the package version
+        env:
+          RELEASE_TAG: ${{ github.event.release.tag_name }}
+        run: |
+          python - <<'PY'
+          import os
+          from pathlib import Path
+          from zipfile import ZipFile
+          from email.parser import BytesParser
+
+          wheel, = Path("dist").glob("*.whl")
+          with ZipFile(wheel) as archive:
+              metadata_path, = (
+                  name for name in archive.namelist()
+                  if name.endswith(".dist-info/METADATA")
+              )
+              metadata = BytesParser().parsebytes(
+                  archive.read(metadata_path)
+              )
+
+          expected_tag = f"v{metadata['Version']}"
+          if os.environ["RELEASE_TAG"] != expected_tag:
+              raise SystemExit(
+                  f"Release tag must be {expected_tag!r}; "
+                  f"got {os.environ['RELEASE_TAG']!r}"
+              )
+          PY
+
+      - name: Store the release files
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        with:
+          name: release-dists
+          path: dist/
+          if-no-files-found: error
+
+  publish-testpypi:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Retrieve the release files
+        uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Upload to TestPyPI
+        uses: pypa/gh-action-pypi-publish@7245906fb61fa33a13554f9d5fb856fe61758086 # v1.14.3
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    needs: [build, publish-testpypi]
+    runs-on: ubuntu-latest
+
+    # Required reviewers MUST be configured for this environment.
+    environment: pypi
+
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Retrieve the same release files
+        uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Upload to PyPI
+        uses: pypa/gh-action-pypi-publish@7245906fb61fa33a13554f9d5fb856fe61758086 # v1.14.3

flowgem-0.1.0/.gitignore

@@ -0,0 +1,142 @@
+# 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/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+**__pycache__
+
+# PyCharm
+.idea/
+
+# RStudio project files
+**.Rproj.user/
+**.Rproj.user*
+**.Rproj
+**.Rhistory
+
+# MacOS
+.DS_Store

flowgem-0.1.0/.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  jobs:
+    post_create_environment:
+      # Update pip to support dependency groups
+      - python -m pip install --upgrade pip
+      # CPU-only torch, so the build doesn't download the CUDA packages
+      - python -m pip install torch --index-url https://download.pytorch.org/whl/cpu
+    post_install:
+      - python -m pip install -e . --group docs
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py

flowgem-0.1.0/CHANGELOG.md

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+# Changelog
+
+<!--next-version-placeholder-->
+
+## v0.1.0 (09/07/2026)
+
+- First release of `flowgem`!

flowgem-0.1.0/CONDUCT.md

@@ -0,0 +1,43 @@
+# Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant homepage](http://contributor-covenant.org/version/1/4), version 1.4.

flowgem-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,81 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+## Types of Contributions
+
+### Report Bugs
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+### Write Documentation
+
+You can never have enough documentation! Please feel free to contribute to any
+part of the documentation, such as the official docs, docstrings, or even
+on the web in blog posts, articles, and such.
+
+### Submit Feedback
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+## Get Started!
+
+Ready to contribute? Here's how to set up `flowgem` for local development.
+
+1. Download a copy of `flowgem` locally.
+
+2. Create and activate a conda environment for `flowgem`:
+
+    ```console
+    $ conda create -n flowgem python=3.12
+    $ conda activate flowgem
+    ```
+
+3. Install `flowgem` using `poetry`:
+
+    ```console
+    $ poetry install
+    ```
+
+4. Use `git` (or similar) to create a branch for local development and make your changes:
+
+    ```console
+    $ git checkout -b name-of-your-bugfix-or-feature
+    ```
+
+5. When you're done making changes, check that your changes conform to any code formatting requirements and pass any tests.
+
+6. Commit your changes and open a pull request.
+
+## Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include additional tests if appropriate.
+2. If the pull request adds functionality, the docs should be updated.
+3. The pull request should work for all currently supported operating systems and versions of Python.
+
+## Code of Conduct
+
+Please note that the `flowgem` project is released with a
+Code of Conduct. By contributing to this project you agree to abide by its terms.

flowgem-0.1.0/LICENSE

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2026, Muhammad Haris Mumtaz, Gitte Kremling
+
+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.
+

flowgem-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: flowgem
+Version: 0.1.0
+Summary: Nonparametric generative sampling for MAR missing data via approximate Wasserstein gradient flows
+Project-URL: Homepage, https://github.com/gkremling/FLOWGEM-package
+Project-URL: Repository, https://github.com/gkremling/FLOWGEM-package
+Project-URL: Documentation, https://flowgem.readthedocs.io
+Author: Muhammad Haris Mumtaz
+Author-email: Gitte Kremling <gitte.kremling@uni-hamburg.de>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.12
+Requires-Dist: hyperimpute>=0.1.17
+Requires-Dist: joblib>=1.5.3
+Requires-Dist: numpy>=2.5.1
+Requires-Dist: scikit-learn>=1.9.0
+Requires-Dist: torch>=2.13.0
+Requires-Dist: tqdm>=4.68.4
+Description-Content-Type: text/markdown
+
+# FLOWGEM
+
+**Generative sampling for missing data under MAR, via approximate Wasserstein gradient flows.**
+
+[![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen)](https://github.com/gkremling/FLOWGEM-package)
+[![Python](https://img.shields.io/badge/python-3.12-blue)](https://www.python.org/)
+[![License](https://img.shields.io/badge/license-MIT-green)](https://github.com/gkremling/FLOWGEM-package/blob/main/LICENSE)
+
+[![Tests](https://github.com/gkremling/FLOWGEM-package/actions/workflows/ci.yml/badge.svg)](https://github.com/gkremling/FLOWGEM-package/actions)
+
+## What is FLOWGEM?
+
+FLOWGEM receives a dataset with missing values and generates a complete dataset sampled from the same distribution. It recovers the complete distribution of the data while preserving variances and correlations which keeps downstream analyses like means, quantiles, and correlations unbiased.
+
+It targets data which is **Missing at Random (MAR)**, including non-monotone MAR. It is nonparametric and makes no assumption about the shape of your data. Under the hood it uses approximate Wasserstein gradient flow which iteratively transports a particle ensemble towards target distribution.
+
+> **Note:** FLOWGEM currently supports **continuous features only**.
+> Support for categorical and mixed type data is future work.
+
+## Installation
+
+Install the released version from PyPI:
+
+```bash
+pip install flowgem
+```
+
+Or install the latest development version from GitHub:
+
+```bash
+pip install git+https://github.com/gkremling/FLOWGEM-package.git
+```
+
+## Quick start
+
+```python
+import numpy as np
+from flowgem import FlowGEM
+
+# Your data, with missing values marked as NaN
+X = np.array([
+    [1.2,    0.8,    3.1],
+    [0.5,    np.nan, 2.7],
+    [np.nan, 1.4,    2.9],
+    [2.1,    0.3,    np.nan],
+])
+
+# Fit and generate a complete sample from the same distribution
+model = FlowGEM(T=1000)
+X_complete = model.fit(X).generate()
+```
+
+`X_complete` is a fully observed array (without missing value) which is drawn from estimated data distribution.
+
+## Features
+
+- **Generative**:- generate entire dataset from the full data distribution while preserving variances and correlations.
+- **Handles non-monotone MAR**:- works with arbitrary, scattered missingness patterns.
+- **Nonparametric** :- No assumption about the shape of your data.
+- **scikit-learn-style API**:- familiar `fit` / `generate` interface.
+- **Tuning-lean**:- sensible defaults; bandwidth is set from a single heuristic
+
+## Key parameters
+
+| Parameter | What it does | Default |
+|-----------|--------------|---------|
+| `T` | number of gradient-flow steps (more = better, slower) | `1000` |
+| `eta` | step size η (smaller = finer, slower) | `0.01` |
+| `sigma` | kernel bandwidth (`None` → chosen by heuristic) | `None` |
+
+## Documentation
+
+Comprehensive and detailed documentation is available at [Read the Docs](https://flowgem.readthedocs.io).
+
+## Citation
+
+The FLOWGEM method is based on:
+
+> Kremling, G., Näf, J., & Lederer, J. (2026). *Generative Modeling under
+> Non-Monotonic MAR Missingness via Approximate Wasserstein Gradient Flows.*
+
+While using the package in course of your research, please cite this paper:
+
+```bibtex
+@article{kremling2026flowgem,
+  title   = {Generative Modeling under Non-Monotonic MAR Missingness
+             via Approximate Wasserstein Gradient Flows},
+  author  = {Kremling, Gitte and N\"af, Jeffrey and Lederer, Johannes},
+  journal = {arXiv preprint arXiv:2604.04567},
+  year    = {2026}
+}
+```
+
+## License
+
+This project is licensed under the MIT License — see the [LICENSE](https://github.com/gkremling/FLOWGEM-package/blob/main/LICENSE) file.

flowgem-0.1.0/README.md

@@ -0,0 +1,96 @@
+# FLOWGEM
+
+**Generative sampling for missing data under MAR, via approximate Wasserstein gradient flows.**
+
+[![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen)](https://github.com/gkremling/FLOWGEM-package)
+[![Python](https://img.shields.io/badge/python-3.12-blue)](https://www.python.org/)
+[![License](https://img.shields.io/badge/license-MIT-green)](https://github.com/gkremling/FLOWGEM-package/blob/main/LICENSE)
+
+[![Tests](https://github.com/gkremling/FLOWGEM-package/actions/workflows/ci.yml/badge.svg)](https://github.com/gkremling/FLOWGEM-package/actions)
+
+## What is FLOWGEM?
+
+FLOWGEM receives a dataset with missing values and generates a complete dataset sampled from the same distribution. It recovers the complete distribution of the data while preserving variances and correlations which keeps downstream analyses like means, quantiles, and correlations unbiased.
+
+It targets data which is **Missing at Random (MAR)**, including non-monotone MAR. It is nonparametric and makes no assumption about the shape of your data. Under the hood it uses approximate Wasserstein gradient flow which iteratively transports a particle ensemble towards target distribution.
+
+> **Note:** FLOWGEM currently supports **continuous features only**.
+> Support for categorical and mixed type data is future work.
+
+## Installation
+
+Install the released version from PyPI:
+
+```bash
+pip install flowgem
+```
+
+Or install the latest development version from GitHub:
+
+```bash
+pip install git+https://github.com/gkremling/FLOWGEM-package.git
+```
+
+## Quick start
+
+```python
+import numpy as np
+from flowgem import FlowGEM
+
+# Your data, with missing values marked as NaN
+X = np.array([
+    [1.2,    0.8,    3.1],
+    [0.5,    np.nan, 2.7],
+    [np.nan, 1.4,    2.9],
+    [2.1,    0.3,    np.nan],
+])
+
+# Fit and generate a complete sample from the same distribution
+model = FlowGEM(T=1000)
+X_complete = model.fit(X).generate()
+```
+
+`X_complete` is a fully observed array (without missing value) which is drawn from estimated data distribution.
+
+## Features
+
+- **Generative**:- generate entire dataset from the full data distribution while preserving variances and correlations.
+- **Handles non-monotone MAR**:- works with arbitrary, scattered missingness patterns.
+- **Nonparametric** :- No assumption about the shape of your data.
+- **scikit-learn-style API**:- familiar `fit` / `generate` interface.
+- **Tuning-lean**:- sensible defaults; bandwidth is set from a single heuristic
+
+## Key parameters
+
+| Parameter | What it does | Default |
+|-----------|--------------|---------|
+| `T` | number of gradient-flow steps (more = better, slower) | `1000` |
+| `eta` | step size η (smaller = finer, slower) | `0.01` |
+| `sigma` | kernel bandwidth (`None` → chosen by heuristic) | `None` |
+
+## Documentation
+
+Comprehensive and detailed documentation is available at [Read the Docs](https://flowgem.readthedocs.io).
+
+## Citation
+
+The FLOWGEM method is based on:
+
+> Kremling, G., Näf, J., & Lederer, J. (2026). *Generative Modeling under
+> Non-Monotonic MAR Missingness via Approximate Wasserstein Gradient Flows.*
+
+While using the package in course of your research, please cite this paper:
+
+```bibtex
+@article{kremling2026flowgem,
+  title   = {Generative Modeling under Non-Monotonic MAR Missingness
+             via Approximate Wasserstein Gradient Flows},
+  author  = {Kremling, Gitte and N\"af, Jeffrey and Lederer, Johannes},
+  journal = {arXiv preprint arXiv:2604.04567},
+  year    = {2026}
+}
+```
+
+## License
+
+This project is licensed under the MIT License — see the [LICENSE](https://github.com/gkremling/FLOWGEM-package/blob/main/LICENSE) file.