chemparseplot 0.1.0__tar.gz → 1.1.0__tar.gz

{chemparseplot-0.1.0 → chemparseplot-1.1.0}/.gitignore

@@ -1,3 +1,4 @@
+.pixi
 apidocs/*
 ### Generated by gibo (https://github.com/simonwhitaker/gibo)
 ### https://raw.github.com/github/gitignore/4488915eec0b3a45b5c63ead28f286819c0917de/Python.gitignore

{chemparseplot-0.1.0 → chemparseplot-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chemparseplot
-Version: 0.1.0
+Version: 1.1.0
 Summary: Parsers and plotting tools for computational chemistry
 Project-URL: Documentation, https://github.com/HaoZeke/chemparseplot#readme
 Project-URL: Issues, https://github.com/HaoZeke/chemparseplot/issues
@@ -12,14 +12,14 @@ Keywords: compchem,parser,plot
 Classifier: Development Status :: 4 - Beta
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.9
 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: >=3.9
+Requires-Python: >=3.10
 Requires-Dist: numpy>=1.26.2
 Requires-Dist: pint>=0.22
+Requires-Dist: rgpycrumbs>=1.1.0
 Provides-Extra: doc
 Requires-Dist: mdit-py-plugins>=0.3.4; extra == 'doc'
 Requires-Dist: myst-nb>=1; extra == 'doc'
@@ -31,22 +31,29 @@ 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: 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'
 Description-Content-Type: text/markdown
 
 
 # Table of Contents
 
-1.  [About](#orgea43256)
-    1.  [Features](#org6a31408)
-        1.  [Supported Engines [WIP]](#orgbfa09d8)
-    2.  [Rationale](#org4c00d67)
-2.  [License](#orge2168a3)
+-   [About](#org1aaacbd)
+    -   [Ecosystem Overview](#org86a8ea7)
+    -   [Features](#org2d23f41)
+        -   [Supported Engines [WIP]](#orgd14b359)
+    -   [Rationale](#orgd89d807)
+-   [License](#orgef56819)
 
 
-<a id="orgea43256"></a>
+
+<a id="org1aaacbd"></a>
 
 # About
 
@@ -57,15 +64,29 @@ Description-Content-Type: text/markdown
 A **pure-python**<sup><a id="fnr.1" class="footref" href="#fn.1" role="doc-backlink">1</a></sup> project to provide unit-aware uniform visualizations
 of common computational chemistry tasks. Essentially this means we provide:
 
+-   Parsers for various computational chemistry software outputs
 -   Plotting scripts for specific workflows
--   Parsers for various software outputs
+
+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.
 
 This is a spin-off from `wailord` ([here](https://wailord.xyz)) which is meant to handle aggregated
 runs in a specific workflow, while here the goal is to do no input handling and
 very pragmatic output parsing, with the goal of generating uniform plots.
 
 
-<a id="org6a31408"></a>
+<a id="org86a8ea7"></a>
+
+## Ecosystem Overview
+
+`chemparseplot` is part of the `rgpycrumbs` suite of interlinked libraries.
+
+![img](branding/logo/ecosystem.png)
+
+
+<a id="org2d23f41"></a>
 
 ## Features
 
@@ -75,7 +96,7 @@ very pragmatic output parsing, with the goal of generating uniform plots.
     -   Via `pint`
 
 
-<a id="orgbfa09d8"></a>
+<a id="orgd14b359"></a>
 
 ### Supported Engines [WIP]
 
@@ -85,7 +106,7 @@ very pragmatic output parsing, with the goal of generating uniform plots.
         coordinate)
 
 
-<a id="org4c00d67"></a>
+<a id="orgd89d807"></a>
 
 ## Rationale
 
@@ -96,7 +117,7 @@ either Bohr/Hartree or Angstron/eV or whatever.
 Also I couldn't find (m)any scripts using the scientific colorschemes.
 
 
-<a id="orge2168a3"></a>
+<a id="orgef56819"></a>
 
 # License
 

{chemparseplot-0.1.0 → chemparseplot-1.1.0}/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.1.0'
-__version_tuple__ = version_tuple = (0, 1, 0)
+__version__ = version = '1.1.0'
+__version_tuple__ = version_tuple = (1, 1, 0)
 
 __commit_id__ = commit_id = None

{chemparseplot-0.1.0 → chemparseplot-1.1.0}/chemparseplot/__init__.py

@@ -2,4 +2,4 @@
 #
 # SPDX-License-Identifier: MIT
 
-from chemparseplot import basetypes, parse, units
+from chemparseplot import parse, units

{chemparseplot-0.1.0 → chemparseplot-1.1.0}/chemparseplot/parse/eon/minimization.py

@@ -8,7 +8,7 @@ def min_e_result(eresp: Path) -> dict:
     """Reads and parses the results.dat file.
 
     Args:
-        eresp: Path to the EON results directory.
+        eresp: Path to the eOn results directory.
 
     Returns:
         A dictionary containing the parsed data from results.dat, or None if the file

{chemparseplot-0.1.0 → chemparseplot-1.1.0}/chemparseplot/parse/eon/saddle_search.py

@@ -10,7 +10,7 @@ from rgpycrumbs.parsers.bless import BLESS_LOG
 from rgpycrumbs.parsers.common import _NUM
 from rgpycrumbs.search.helpers import tail
 
-from chemparseplot.basetypes import DimerOpt, MolGeom, SaddleMeasure, SpinID
+from rgpycrumbs.basetypes import DimerOpt, MolGeom, SaddleMeasure, SpinID
 
 
 class EONSaddleStatus(Enum):
@@ -72,7 +72,7 @@ def _read_results_dat(eresp: Path) -> dict:
     """Reads and parses the results.dat file.
 
     Args:
-        eresp: Path to the EON results directory.
+        eresp: Path to the eOn results directory.
 
     Returns:
         A dictionary containing the parsed data from results.dat, or None if the file
@@ -103,10 +103,10 @@ def _read_results_dat(eresp: Path) -> dict:
 
 
 def _find_log_file(eresp: Path) -> Path | None:
-    """Finds the most recent, valid log file within the EON results directory.
+    """Finds the most recent, valid log file within the eOn results directory.
 
     Args:
-        eresp: Path to the EON results directory.
+        eresp: Path to the eOn results directory.
 
     Returns:
         Path to the chosen log file, or None if no suitable log file is found.
@@ -182,7 +182,7 @@ def _extract_saddle_info(
 
     Args:
         log_data: A list of strings representing the lines of the log file.
-        eresp: Path to the EON results directory.
+        eresp: Path to the eOn results directory.
         is_gprd: Boolean flag indicating whether the GPRD method was used.
 
     Returns:
@@ -245,10 +245,10 @@ def _get_methods(eresp: Path) -> DimerOpt:
 
 
 def parse_eon_saddle(eresp: Path, rloc: "SpinID") -> "SaddleMeasure":
-    """Parses EON saddle point search results from a directory.
+    """Parses eOn saddle point search results from a directory.
 
     Args:
-        eresp: Path to the directory containing EON results.
+        eresp: Path to the directory containing eOn results.
         rloc: A SpinID object.
 
     Returns:

{chemparseplot-0.1.0 → chemparseplot-1.1.0}/chemparseplot/parse/orca/neb/interp.py

@@ -14,7 +14,7 @@ import re
 
 import chemparseplot.parse.converter as conv
 import chemparseplot.parse.patterns as pat
-from chemparseplot.basetypes import nebiter, nebpath
+from rgpycrumbs.basetypes import nebiter, nebpath
 from chemparseplot.units import Q_
 
 # fmt: off

{chemparseplot-0.1.0 → chemparseplot-1.1.0}/chemparseplot/parse/sella/saddle_search.py

@@ -5,7 +5,7 @@ from collections import Counter
 from ase.io import read
 from rgpycrumbs.time.helpers import one_day_tdelta
 
-from chemparseplot.basetypes import SaddleMeasure, SpinID
+from rgpycrumbs.basetypes import SaddleMeasure, SpinID
 import ase
 
 import datetime

{chemparseplot-0.1.0 → chemparseplot-1.1.0}/chemparseplot/plot/geomscan.py

@@ -1,6 +1,6 @@
 import matplotlib.pyplot as plt
 
-from chemparseplot.plot._aids import spline_interp
+from rgpycrumbs.interpolation import spline_interp
 from chemparseplot.plot.structs import BasePlotter