chemparseplot 1.2.0__tar.gz → 1.4.0__tar.gz

{chemparseplot-1.2.0 → chemparseplot-1.4.0}/.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
 
@@ -166,3 +171,11 @@ cython_debug/
 /_version.py
 /.pdm-python
 *.ipynb
+
+# Dolt database files (added by bd init)
+.dolt/
+*.db
+
+# Lychee link checker cache
+.lycheecache
+.beads/

chemparseplot-1.4.0/PKG-INFO

@@ -0,0 +1,199 @@
+Metadata-Version: 2.4
+Name: chemparseplot
+Version: 1.4.0
+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-1.4.0}/_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 = '1.4.0'
+__version_tuple__ = version_tuple = (1, 4, 0)
 
 __commit_id__ = commit_id = None

chemparseplot-1.4.0/chemparseplot/parse/__init__.py

@@ -0,0 +1,9 @@
+# SPDX-FileCopyrightText: 2023-present Rohit Goswami <rog32@hi.is>
+#
+# SPDX-License-Identifier: MIT
+
+from chemparseplot.parse import orca, patterns
+
+# Lazy imports for modules with optional heavy deps (h5py, pandas)
+# Import directly: from chemparseplot.parse.chemgp_hdf5 import read_h5_table
+# Or: from chemparseplot.parse import plumed

chemparseplot-1.4.0/chemparseplot/parse/chemgp_hdf5.py

@@ -0,0 +1,174 @@
+# SPDX-FileCopyrightText: 2023-present Rohit Goswami <rog32@hi.is>
+#
+# SPDX-License-Identifier: MIT
+
+"""HDF5 file I/O utilities for ChemGP data.
+
+This module provides functions for reading structured data from ChemGP HDF5
+output files. The HDF5 layout mirrors the Julia common_plot.jl helpers.
+
+HDF5 Layout
+-----------
+- ``grids/<name>``: 2D arrays with attrs x_range, y_range, x_length, y_length
+- ``table/<name>``: group of same-length 1D arrays
+- ``paths/<name>``: point sequences (x, y or rAB, rBC)
+- ``points/<name>``: point sets (x, y or pc1, pc2)
+- Root attrs: metadata scalars
+
+.. versionadded:: 1.7.0
+    Extracted from chemgp.plt_gp to standalone module.
+"""
+
+from typing import Any
+
+import numpy as np
+
+
+def read_h5_table(f: Any, name: str = "table") -> Any:
+    """Read a group of same-length vectors as a DataFrame.
+
+    Parameters
+    ----------
+    f
+        Open HDF5 file object
+    name
+        Name of the table group (default: "table")
+
+    Returns
+    -------
+    DataFrame
+        DataFrame with columns from the HDF5 group
+    """
+    import pandas as pd
+
+    g = f[name]
+    cols = {}
+    for k in g.keys():
+        arr = g[k][()]
+        if arr.dtype.kind in {"S", "O"}:
+            cols[k] = arr.astype(str).tolist()
+        else:
+            cols[k] = arr.tolist()
+    return pd.DataFrame(cols)
+
+
+def read_h5_grid(
+    f: Any, name: str
+) -> tuple[np.ndarray, np.ndarray | None, np.ndarray | None]:
+    """Read a 2D grid with optional axis ranges.
+
+    Parameters
+    ----------
+    f
+        Open HDF5 file object
+    name
+        Name of the grid dataset
+
+    Returns
+    -------
+    tuple
+        (data, x_coords, y_coords) where x_coords and y_coords may be None
+        if axis range attributes are not present
+    """
+    ds = f[f"grids/{name}"]
+    data = ds[()]
+    x_coords = None
+    y_coords = None
+
+    if "x_range" in ds.attrs and "x_length" in ds.attrs:
+        lo, hi = ds.attrs["x_range"]
+        n = int(ds.attrs["x_length"])
+        x_coords = np.linspace(lo, hi, n)
+
+    if "y_range" in ds.attrs and "y_length" in ds.attrs:
+        lo, hi = ds.attrs["y_range"]
+        n = int(ds.attrs["y_length"])
+        y_coords = np.linspace(lo, hi, n)
+
+    return data, x_coords, y_coords
+
+
+def read_h5_path(f: Any, name: str) -> dict[str, np.ndarray]:
+    """Read a path (ordered point sequence).
+
+    Parameters
+    ----------
+    f
+        Open HDF5 file object
+    name
+        Name of the path dataset
+
+    Returns
+    -------
+    dict
+        Dictionary mapping coordinate names to arrays
+    """
+    g = f[f"paths/{name}"]
+    return {k: g[k][()] for k in g.keys()}
+
+
+def read_h5_points(f: Any, name: str) -> dict[str, np.ndarray]:
+    """Read a point set.
+
+    Parameters
+    ----------
+    f
+        Open HDF5 file object
+    name
+        Name of the points dataset
+
+    Returns
+    -------
+    dict
+        Dictionary mapping coordinate names to arrays
+    """
+    g = f[f"points/{name}"]
+    return {k: g[k][()] for k in g.keys()}
+
+
+def read_h5_metadata(f: Any) -> dict[str, Any]:
+    """Read root-level metadata attributes.
+
+    Parameters
+    ----------
+    f
+        Open HDF5 file object
+
+    Returns
+    -------
+    dict
+        Dictionary of metadata attributes
+    """
+    return {k: f.attrs[k] for k in f.attrs.keys()}
+
+
+def validate_hdf5_structure(
+    f: Any, required_groups: list[str] | None = None
+) -> list[str]:
+    """Validate HDF5 file has expected structure.
+
+    Parameters
+    ----------
+    f
+        Open HDF5 file object
+    required_groups
+        List of required group names (default: ["grids", "table"])
+
+    Returns
+    -------
+    list[str]
+        List of missing groups (empty if all present)
+
+    Raises
+    ------
+    ValueError
+        If required groups are missing
+    """
+    if required_groups is None:
+        required_groups = ["grids", "table"]
+
+    missing = [g for g in required_groups if g not in f]
+    if missing:
+        msg = f"Invalid HDF5 structure. Missing groups: {missing}"
+        raise ValueError(msg)
+    return missing