chemparseplot 1.2.0__tar.gz → 1.3.0__tar.gz

{chemparseplot-1.2.0 → chemparseplot-1.3.0}/.gitignore

@@ -1,5 +1,10 @@
 .pixi
+CLAUDE.md
+.claude/
 apidocs/*
+doc/source/apidocs/
+doc/jupyter_execute/
+doc/build/
 ### Generated by gibo (https://github.com/simonwhitaker/gibo)
 ### https://raw.github.com/github/gitignore/4488915eec0b3a45b5c63ead28f286819c0917de/Python.gitignore
 

chemparseplot-1.3.0/PKG-INFO

@@ -0,0 +1,199 @@
+Metadata-Version: 2.4
+Name: chemparseplot
+Version: 1.3.0
+Summary: Parsers and plotting tools for computational chemistry
+Project-URL: Documentation, https://chemparseplot.rgoswami.me
+Project-URL: Issues, https://github.com/HaoZeke/chemparseplot/issues
+Project-URL: Source, https://github.com/HaoZeke/chemparseplot
+Project-URL: Changelog, https://github.com/HaoZeke/chemparseplot/blob/main/CHANGELOG.md
+Author-email: Rohit Goswami <rog32@hi.is>
+License: MIT
+License-File: LICENSE
+Keywords: compchem,parser,plot
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python
+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 :: Implementation :: CPython
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.26.2
+Requires-Dist: pint>=0.22
+Requires-Dist: rgpycrumbs>=1.3.0
+Provides-Extra: all
+Requires-Dist: ase>=3.22; extra == 'all'
+Requires-Dist: cmcrameri>=1.7; extra == 'all'
+Requires-Dist: h5py>=3.0; extra == 'all'
+Requires-Dist: matplotlib>=3.8.2; extra == 'all'
+Requires-Dist: polars>=0.20; extra == 'all'
+Requires-Dist: xyzrender>=0.1.2; extra == 'all'
+Provides-Extra: doc
+Requires-Dist: mdit-py-plugins>=0.3.4; extra == 'doc'
+Requires-Dist: myst-nb>=1; extra == 'doc'
+Requires-Dist: myst-parser>=2; extra == 'doc'
+Requires-Dist: sphinx-autodoc2>=0.5; extra == 'doc'
+Requires-Dist: sphinx-copybutton>=0.5.2; extra == 'doc'
+Requires-Dist: sphinx-library>=1.1.2; extra == 'doc'
+Requires-Dist: sphinx-sitemap>=2.5.1; extra == 'doc'
+Requires-Dist: sphinx-togglebutton>=0.3.2; extra == 'doc'
+Requires-Dist: sphinx>=7.2.6; extra == 'doc'
+Requires-Dist: sphinxcontrib-apidoc>=0.4; extra == 'doc'
+Provides-Extra: lint
+Requires-Dist: ruff>=0.1.6; extra == 'lint'
+Provides-Extra: neb
+Requires-Dist: ase>=3.22; extra == 'neb'
+Requires-Dist: h5py>=3.0; extra == 'neb'
+Requires-Dist: polars>=0.20; extra == 'neb'
+Provides-Extra: plot
+Requires-Dist: cmcrameri>=1.7; extra == 'plot'
+Requires-Dist: matplotlib>=3.8.2; extra == 'plot'
+Provides-Extra: test
+Requires-Dist: pytest-cov>=4.1.0; extra == 'test'
+Requires-Dist: pytest>=7.4.3; extra == 'test'
+Provides-Extra: xyzrender
+Requires-Dist: xyzrender>=0.1.2; extra == 'xyzrender'
+Description-Content-Type: text/markdown
+
+
+# Table of Contents
+
+-   [About](#org69d0d18)
+    -   [Installation](#org6425b9a)
+    -   [Ecosystem Overview](#org7717c22)
+    -   [Features](#org7ec2e1c)
+        -   [Supported Engines](#org3c6cfc2)
+    -   [Documentation](#org7d2bbf4)
+    -   [Contributing](#orgc77604d)
+-   [License](#org8180f68)
+-   [Acknowledgments](#org7ebb45c)
+
+
+
+<a id="org69d0d18"></a>
+
+# About
+
+![img](branding/logo/chemparseplot_logo.png)
+
+[![Tests](https://github.com/HaoZeke/chemparseplot/actions/workflows/build_test.yml/badge.svg)](https://github.com/HaoZeke/chemparseplot/actions/workflows/build_test.yml)
+[![Linting](https://github.com/HaoZeke/chemparseplot/actions/workflows/ci_prek.yml/badge.svg)](https://github.com/HaoZeke/chemparseplot/actions/workflows/ci_prek.yml)
+[![Docs](https://github.com/HaoZeke/chemparseplot/actions/workflows/build_docs.yml/badge.svg)](https://github.com/HaoZeke/chemparseplot/actions/workflows/build_docs.yml)
+[![PyPI](https://img.shields.io/pypi/v/chemparseplot)](https://pypi.org/project/chemparseplot/)
+[![Python](https://img.shields.io/pypi/pyversions/chemparseplot)](https://pypi.org/project/chemparseplot/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![One Good Tutorial docs checklist v1: adopted](https://onegoodtutorial.org/badge/adopted-v1.svg)](https://onegoodtutorial.org/about/badge/?v=1)
+[![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch)
+[![DOI](https://zenodo.org/badge/725730118.svg)](https://doi.org/10.5281/zenodo.18529752)
+
+A **pure-python**<sup><a id="fnr.butwhy" class="footref" href="#fn.butwhy" role="doc-backlink">1</a></sup> parsing and plotting library for computational
+chemistry outputs. `chemparseplot` extracts structured data from quantum
+chemistry codes (ORCA, eOn, Sella, ChemGP) and produces publication-quality,
+unit-aware visualizations with [scientific color maps](https://www.fabiocrameri.ch/colourmaps/).
+
+Computational tasks (surface fitting, structure analysis, interpolation) are
+handled by [`rgpycrumbs`](https://github.com/HaoZeke/rgpycrumbs), which is a required dependency. `chemparseplot` parses
+output files, delegates heavy computation to `rgpycrumbs`, and produces
+publication-quality plots.
+
+
+<a id="org6425b9a"></a>
+
+## Installation
+
+    pip install chemparseplot
+    # With plotting support
+    pip install "chemparseplot[plot]"
+    # Everything
+    pip install "chemparseplot[all]"
+
+For development:
+
+    git clone https://github.com/HaoZeke/chemparseplot
+    cd chemparseplot
+    uv sync --all-extras
+
+See the [installation guide](https://chemparseplot.rgoswami.me/installation.html) and [quickstart](https://chemparseplot.rgoswami.me/quickstart.html) for details.
+
+
+<a id="org7717c22"></a>
+
+## Ecosystem Overview
+
+`chemparseplot` is part of the `rgpycrumbs` suite of interlinked libraries.
+
+![img](branding/logo/ecosystem.png)
+
+
+<a id="org7ec2e1c"></a>
+
+## Features
+
+-   **Parsing** computational chemistry output files into structured data
+-   **Plotting** with [scientific color maps](https://www.fabiocrameri.ch/colourmaps/) (camera-ready)
+-   **Unit preserving** throughout via `pint`
+-   **Computation** delegated to [`rgpycrumbs`](https://github.com/HaoZeke/rgpycrumbs) for surface fitting, interpolation,
+    and structure analysis
+
+
+<a id="org3c6cfc2"></a>
+
+### Supported Engines
+
+-   ORCA (**5.x**)
+    -   Geometry scan (`OPT`) energy profiles
+    -   Nudged elastic band (`NEB`) path visualization
+-   eOn
+    -   Saddle search parsing (Dimer, GPRD, LBFGS methods)
+    -   NEB path energy profiles with landscape projections
+-   Sella
+    -   Saddle point optimization result parsing
+-   Trajectory formats
+    -   HDF5 trajectories (ChemGP output with pre-computed forces)
+    -   Generic ASE-readable formats (extxyz, .traj) for NEB analysis
+
+
+<a id="org7d2bbf4"></a>
+
+## Documentation
+
+Full documentation is at <https://chemparseplot.rgoswami.me>. This includes:
+
+-   A [quickstart guide](https://chemparseplot.rgoswami.me/quickstart.html)
+-   [Tutorials](https://chemparseplot.rgoswami.me/tutorials/index.html) for common workflows
+-   [API reference](https://chemparseplot.rgoswami.me/apidocs/index.html)
+
+
+<a id="orgc77604d"></a>
+
+## Contributing
+
+Contributions are welcome. See [CONTRIBUTING.md](https://github.com/HaoZeke/chemparseplot/blob/main/CONTRIBUTING.md) for development setup and
+guidelines, and our [Code of Conduct](https://github.com/HaoZeke/chemparseplot/blob/main/CODE_OF_CONDUCT.md).
+
+For bug reports or questions, open an issue on [GitHub](https://github.com/HaoZeke/chemparseplot/issues).
+
+
+<a id="org8180f68"></a>
+
+# License
+
+MIT. However, this is an academic resource, so **please cite** as much as possible
+via:
+
+-   The [Zenodo DOI](https://doi.org/10.5281/zenodo.18529752) for general use.
+-   The `wailord` paper for ORCA usage
+
+
+<a id="org7ebb45c"></a>
+
+# Acknowledgments
+
+This project builds on work supported by the University of Iceland and the
+Icelandic Research Fund. `chemparseplot` relies on [`rgpycrumbs`](https://github.com/HaoZeke/rgpycrumbs) for computational
+modules.
+
+
+# Footnotes
+
+<sup><a id="fn.1" href="#fnr.1">1</a></sup> To distinguish it from my other thin-python wrapper projects

{chemparseplot-1.2.0 → chemparseplot-1.3.0}/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '1.2.0'
-__version_tuple__ = version_tuple = (1, 2, 0)
+__version__ = version = '1.3.0'
+__version_tuple__ = version_tuple = (1, 3, 0)
 
 __commit_id__ = commit_id = None

chemparseplot-1.3.0/chemparseplot/plot/__init__.py

@@ -0,0 +1,36 @@
+# SPDX-FileCopyrightText: 2023-present Rohit Goswami <rog32@hi.is>
+#
+# SPDX-License-Identifier: MIT
+
+from chemparseplot.plot.theme import (
+    RUHI_COLORS,
+    RUHI_THEME,
+    PlotTheme,
+    get_theme,
+    setup_global_theme,
+    setup_publication_theme,
+)
+
+
+# Lazy imports for submodules with heavy deps (cmcrameri, pint, etc.)
+def __getattr__(name):
+    if name == "geomscan":
+        from chemparseplot.plot import geomscan as _mod
+
+        return _mod
+    if name == "structs":
+        from chemparseplot.plot import structs as _mod
+
+        return _mod
+    if name == "chemgp":
+        from chemparseplot.plot import chemgp as _mod
+
+        return _mod
+    if name == "ureg":
+        from chemparseplot.units import ureg as _ureg
+
+        _ureg.setup_matplotlib(True)
+        _ureg.mpl_formatter = "{:~P}"
+        return _ureg
+    msg = f"module {__name__!r} has no attribute {name!r}"
+    raise AttributeError(msg)