Merge pull request #44 from TheoChem-VU/main

Merge main into 20

.github/workflows/build_docs.yml

@@ -19,6 +19,8 @@ on:
   pull_request:
     types: [closed]
     branches: [main]
+  release:
+    types: [published]
 
 jobs:
   build_and_deploy:

.github/workflows/build_python_versions.yml

@@ -23,7 +23,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install ruff pytest pytest-cov
+          pip install ruff==0.0.177 pytest pytest-cov
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
           pip install -e .
       - name: Lint with ruff

.github/workflows/pypi_publish.yml

@@ -0,0 +1,42 @@
+name: Publishing to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+
+concurrency:
+  group: "publishing"
+  cancel-in-progress: true
+
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi-publish
+      url: https://pypi.org/project/${{ github.event.repository.name }}/
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11' 
+
+      - name: Build package
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+
+      - name: Publish ${{ github.event.repository.name }} to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true
+

README.md

@@ -1,12 +1,15 @@
-[![Documentation](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_docs.yml/badge.svg)](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_docs.yml) [![Testing](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_python_versions.yml/badge.svg)](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_python_versions.yml)
+[![Documentation](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_docs.yml/badge.svg)](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_docs.yml) [![Testing](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_python_versions.yml/badge.svg)](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_python_versions.yml) [![Publishing to PyPI](https://github.com/TheoChem-VU/TCutility/actions/workflows/pypi_publish.yml/badge.svg?branch=main)](https://github.com/TheoChem-VU/TCutility/actions/workflows/pypi_publish.yml)
+
+
+[![TCutility version](https://badge.fury.io/py/TCutility.svg)](https://pypi.org/project/TCutility/)
 
 # TCutility
 Utility functions/classes for the TheoCheM programs
 
 # Installation
 
-The easiest way is installing this python package via pip (not yet working since it is not published on PyPI):
-``` python -m pip install TCutility ```
+The easiest way is installing this python package via pip:
+``` python -m pip install TCutility```
 
 It is also possible to install in locally by first cloning this repository in your terminal: 
 

TCutility/molecule.py

@@ -0,0 +1,129 @@
+from scm import plams
+from TCutility.results import result
+
+
+def parse_str(s: str):
+    # checks if string should be an int, float, bool or string
+
+    # sanitization first
+    # empty s returns None
+    # if s is not a str return it
+    if s == '':
+        return None
+    if not isinstance(s, str):
+        return s
+
+    # to parse the string we use try/except method
+    try:
+        return int(s)
+    except ValueError:
+        pass
+
+    try:
+        return float(s)
+    except ValueError:
+        pass
+
+    # bool type casting always works, so we have to specifically check for correct strings
+    if s in ['True', 'False']:
+        return bool(s)
+
+    return s
+
+
+def save(mol: plams.Molecule, path: str, comment: str = None):
+    ''' Save a molecule in a custom xyz file format.
+    Molecule and atom flags can be provided as the "flags" parameter of the object (mol.flags and atom.flags).
+    '''
+    comment = comment or mol.comment
+    with open(path, 'w+') as f:
+        f.write(f'{len(mol.atoms)}\n{comment}\n')
+        for atom in mol.atoms:
+            flags_str = ''
+            flags = atom.flags if hasattr(atom, 'flags') else {}
+            for key, value in flags.items():
+                if key == 'tags':
+                    if len(value) > 0:
+                        flags_str += ' '.join([str(x) for x in value]) + ' '
+                    else:
+                        continue
+                else:
+                    flags_str += f'{key}={value} '
+
+            f.write(f'{atom.symbol}\t{atom.coords[0]: .10f}\t{atom.coords[1]: .10f}\t{atom.coords[2]: .10f}\t{flags_str}\n')
+
+        f.write('\n')
+
+        flags = mol.flags if hasattr(mol, 'flags') else {}
+        for key, value in flags.items():
+            if key == 'tags':
+                f.write("\n".join([str(x) for x in value]) + '\n')
+            else:
+                f.write(f'{key} = {value}\n')
+
+
+def load(path) -> plams.Molecule:
+    '''
+    Load a molecule from a given xyz file path.
+    The xyz file is structured as follows:
+        
+        ```
+        [int] number of atoms
+        Comment line
+        Xx X1 Y1 Z1 atom_tag1 atom_tag2 atom_key1=...
+        Xx X2 Y2 Z2 atom_tag1 atom_tag2 atom_key1=...
+        Xx X3 Y3 Z3
+
+        mol_tag1
+        mol_tag2
+        mol_key1=...
+        mol_key2 = ...
+        ```
+
+    The xyz file is parsed and returned as a plams.Molecule object. 
+    Flags and tags are given as mol.flags and mol.flags.tags respectively
+    Similarly for the atoms, the flags and tags are given as mol.atoms[i].flags and mol.atoms[i].flags.tags
+    '''
+    def parse_flags(args):
+        ret = result.Result()
+        ret.tags = []
+        for arg in args:
+            # flags are given as key=value pairs
+            # tags are given as loose keys
+            if '=' in arg:
+                key, value = arg.split('=')
+                ret[key.strip()] = parse_str(value.strip())
+            else:
+                ret.tags.append(parse_str(arg.strip()))
+        return ret
+
+    with open(path) as f:
+        lines = [line.strip() for line in f.readlines()]
+
+    mol = plams.Molecule()
+
+    natoms = int(lines[0])
+    mol.comment = lines[1]
+    # not all lines in the file will define atoms. Lines after line natoms+2 will be used for flags
+    atom_lines = lines[2:natoms+2]
+    for line in atom_lines:
+        # parse every atom first
+        symbol, x, y, z, *args = line.split()
+        atom = plams.Atom(symbol=symbol, coords=(float(x), float(y), float(z)))
+        atom.flags = parse_flags(args)
+        mol.add_atom(atom)
+
+    # after the atoms we parse the flags for the molecule
+    flag_lines = lines[natoms+2:]
+    flag_lines = [line.strip() for line in flag_lines if line.strip()]
+    mol.flags = parse_flags(flag_lines)
+
+    return mol
+
+
+if __name__ == '__main__':
+    mol = load(r"D:\Users\Yuman\Desktop\PhD\ychem\calculations2\5ef3a511141a993d83552515df6bf882a7560dd806f88df4e2c2887b4d2a9595\transitionstate\input_mol.xyz")
+    print(mol)
+    print(mol.flags)
+    print(mol[1].flags)
+

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 5f993dbd9f9925ccd9eda29ef8d681f1
+config: 9511e45ca111478053fe65e1fb308881
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/TCutility.constants.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TCutility.constants package &#8212; TCutility v0.1.0 documentation</title>
+    <title>TCutility.constants package &#8212; TCutility v0.2.1 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=ac02cc09edc035673794" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=ac02cc09edc035673794"></script>
 
-    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7a6ff16f"></script>
+    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7e7ff5c5"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>

docs/_build/html/TCutility.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TCutility package &#8212; TCutility v0.1.0 documentation</title>
+    <title>TCutility package &#8212; TCutility v0.2.1 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=ac02cc09edc035673794" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=ac02cc09edc035673794"></script>
 
-    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7a6ff16f"></script>
+    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7e7ff5c5"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>

docs/_build/html/TCutility.results.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TCutility.results package &#8212; TCutility v0.1.0 documentation</title>
+    <title>TCutility.results package &#8212; TCutility v0.2.1 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=ac02cc09edc035673794" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=ac02cc09edc035673794"></script>
 
-    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7a6ff16f"></script>
+    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7e7ff5c5"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
@@ -44,7 +44,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="TCutility.constants package" href="TCutility.constants.html" />
-    <link rel="prev" title="TCutility v0.1.0 documentation" href="index.html" />
+    <link rel="prev" title="TCutility v0.2.1 documentation" href="index.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -691,7 +691,7 @@ <h1>TCutility.results package<a class="headerlink" href="#tcutility-results-pack
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">TCutility v0.1.0 documentation</p>
+        <p class="prev-next-title">TCutility v0.2.1 documentation</p>
       </div>
     </a>
     <a class="right-next"

docs/_build/html/_modules/index.html

@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Overview: module code &#8212; TCutility v0.1.0 documentation</title>
+    <title>Overview: module code &#8212; TCutility v0.2.1 documentation</title>
 
 
 
@@ -34,7 +34,7 @@
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=ac02cc09edc035673794" />
   <script src="../_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=ac02cc09edc035673794"></script>
 
-    <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=7a6ff16f"></script>
+    <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=7e7ff5c5"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = '_modules/index';</script>

docs/_build/html/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: 'v0.1.0',
+    VERSION: 'v0.2.1',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/_build/html/genindex.html

@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; TCutility v0.1.0 documentation</title>
+    <title>Index &#8212; TCutility v0.2.1 documentation</title>
 
 
 
@@ -34,7 +34,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=ac02cc09edc035673794" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=ac02cc09edc035673794"></script>
 
-    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7a6ff16f"></script>
+    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7e7ff5c5"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'genindex';</script>

docs/_build/html/index.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TCutility v0.1.0 documentation &#8212; TCutility v0.1.0 documentation</title>
+    <title>TCutility v0.2.1 documentation &#8212; TCutility v0.2.1 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=ac02cc09edc035673794" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=ac02cc09edc035673794"></script>
 
-    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7a6ff16f"></script>
+    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7e7ff5c5"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
@@ -219,7 +219,7 @@
                 <article class="bd-article" role="main">
 
   <section id="tcutility-projectversion-documentation">
-<h1>TCutility v0.1.0 documentation<a class="headerlink" href="#tcutility-projectversion-documentation" title="Permalink to this heading">#</a></h1>
+<h1>TCutility v0.2.1 documentation<a class="headerlink" href="#tcutility-projectversion-documentation" title="Permalink to this heading">#</a></h1>
 <p><strong>TCutility</strong> is a Python library containing many helper functions and classes for use in programs written in the TheoCheM group.</p>
 <div class="toctree-wrapper compound">
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Contents:</span></p>
@@ -284,7 +284,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Pe
   </div>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">TCutility v0.1.0 documentation</a></li>
+<li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#">TCutility v0.2.1 documentation</a></li>
 <li class="toc-h1 nav-item toc-entry"><a class="reference internal nav-link" href="#indices-and-tables">Indices and tables</a></li>
 </ul>
 

docs/_build/html/modules.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TCutility &#8212; TCutility v0.1.0 documentation</title>
+    <title>TCutility &#8212; TCutility v0.2.1 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=ac02cc09edc035673794" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=ac02cc09edc035673794"></script>
 
-    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7a6ff16f"></script>
+    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=7e7ff5c5"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>