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prune: sweep Science to the shortlist cap

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Per ADR-0001, maintainer-adjudicated at the Data & Science preview
review (2026-08-15, all rows live-verified). Restructure first: Core
narrows to numba, numpy, scipy; mint Symbolic Mathematics (sympy),
Statistics (statsmodels), Graphs and Networks (networkx), and
Computational Geometry (shapely) — five co-obvious tools doing five
different jobs, the decision-13 pattern. Other shrinks to a two-entry
grab-bag; colour renamed to colour-science per the PyPI-name convention
(bare 'colour' on PyPI is an unrelated color-conversion library). Then
cap.

Removed (downloads are PyPI last-30-days via BigQuery, 2026-08-15):

- cclib (29.7K/month): computational-chemistry log parsing, small
  audience
- openbabel (54.9K/month pip; conda-forge adds only 1.8M all-time):
  legacy toolbox next to rdkit
- pydy (1.2K/month): near-zero usage
- PythonRobotics: educational algorithm compilation ("sample codes and
  textbook" per its own description), not a library; not on PyPI
- pathsim (6.3K/month): no adoption

Co-Authored-By: Claude <noreply@anthropic.com>
This commit is contained in:
Vinta Chen
2026-08-15 23:59:05 +08:00
co-authored by Claude
parent 9631207f54
commit 0c1409dea8
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@@ -540,28 +540,27 @@ _Libraries for scientific computing. Also see [Python-for-Scientists](https://gi
- [numba](https://github.com/numba/numba) - Python JIT compiler to LLVM aimed at scientific Python.
- [numpy](https://github.com/numpy/numpy) - A fundamental package for scientific computing with Python.
- [scipy](https://github.com/scipy/scipy) - A Python-based ecosystem of open-source software for mathematics, science, and engineering.
- [statsmodels](https://github.com/statsmodels/statsmodels) - Statistical modeling and econometrics in Python.
- Symbolic Mathematics
- [sympy](https://github.com/sympy/sympy) - A Python library for symbolic mathematics.
- Statistics
- [statsmodels](https://github.com/statsmodels/statsmodels) - Statistical modeling and econometrics in Python.
- Biology and Chemistry
- [biopython](https://github.com/biopython/biopython) - Biopython is a set of freely available tools for biological computation.
- [cclib](https://github.com/cclib/cclib) - A library for parsing and interpreting the results of computational chemistry packages.
- [openbabel](https://github.com/openbabel/openbabel) - A chemical toolbox designed to speak the many languages of chemical data.
- [rdkit](https://github.com/rdkit/rdkit) - Cheminformatics and Machine Learning Software.
- Physics and Engineering
- [astropy](https://github.com/astropy/astropy) - A community Python library for Astronomy.
- [obspy](https://github.com/obspy/obspy) - A Python toolbox for seismology.
- [pydy](https://github.com/pydy/pydy) - Short for Python Dynamics, used to assist with workflow in the modeling of dynamic motion.
- [PythonRobotics](https://github.com/AtsushiSakai/PythonRobotics) - This is a compilation of various robotics algorithms with visualizations.
- Simulation and Modeling
- [mesa](https://github.com/mesa/mesa) - An agent-based modeling framework for building, analyzing, and visualizing complex system simulations.
- [pathsim](https://github.com/pathsim/pathsim) - A block-based system modeling and simulation framework with a browser-based visual editor.
- [pymc](https://github.com/pymc-devs/pymc) - Probabilistic programming and Bayesian modeling in Python.
- [simpy](https://gitlab.com/team-simpy/simpy) - A process-based discrete-event simulation framework.
- Other
- [colour](https://github.com/colour-science/colour) - Implementing a comprehensive number of colour theory transformations and algorithms.
- [manim](https://github.com/ManimCommunity/manim) - An animation engine for explanatory math videos.
- Graphs and Networks
- [networkx](https://github.com/networkx/networkx) - A high-productivity software for complex networks.
- Computational Geometry
- [shapely](https://github.com/shapely/shapely) - Manipulation and analysis of geometric objects in the Cartesian plane.
- Other
- [colour-science](https://github.com/colour-science/colour) - Implementing a comprehensive number of colour theory transformations and algorithms.
- [manim](https://github.com/ManimCommunity/manim) - An animation engine for explanatory math videos.
### Quantum Computing