new commit

.gitignore

@@ -1,25 +1,24 @@
 # check which files are ignored: git status --ignored
 
+.venv/
 archive/
-docs/my_notebooks/
-docs/figures/my_figures/
-.vscode/
-
-development/
-environment_long.yml
-.coverage
 .pre-commit-config.yaml
-scripts/info.txt
+HOWTO.md
+info.txt
+main.py
+qDNA/data/raw/geometries/
+requirements/pip_freeze.txt
 
-*.egg-info/
+# created by build
 dist/
 build/
 
-data/raw/geometries
-data/raw/test_params
-data/processed/
-data/figures/
-data/logging.log
-
+# created by pytest
 __pycache__
+.pytest_cache/
+
+# created by coverage
+*.egg-info/
+.coverage
+
 .ipynb_checkpoints

MANIFEST.in

@@ -1,10 +1,19 @@
+# Include the README, LICENSE, and other documentation files
 include README.md
-include installation.md  
+include installation.md
 include LICENSE.txt
 include CITATION.bib
-include qDNA/config.yaml
+
+# Include requirement files
+include requirements/*.txt
+
+# Include the MANIFEST file itself
+include MANIFEST.in
+
+# Include all .py files
+recursive-include qDNA *.py
+
+# Include specific data files
+include qDNA/data/data_paper/*.json
+include qDNA/data/figures_paper/*.pdf *.png
 include qDNA/data/raw/tb_params/*.json
-include qDNA/data/figures/doc_paper/*.png
-include qDNA/data/figures/doc_paper/*.pdf
-include qDNA/data/processed/doc_paper/*.json
-include configs/*

README.md

@@ -103,22 +103,7 @@ The documentation for the [latest release](https://quantumdna.readthedocs.io/en/
 
 ### Tutorials
 
-The code contains some tutorials and demonstrations to better understand and explore the functionalities.
 
-In the [`docs/tutorials`](docs/tutorials) folder you can find the notebook [`0_Paper`](docs/tutorials/0_Paper.ipynb) that contains and reproduces all the figures contained in [D. Herb, M. Rossini and J. Ankerhold, Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence.](https://arxiv.org/abs/2402.16892)
-
-Additionally, the `QuantumDNA/docs/tutorials` folder contains the following tutorials:
-
-| Tutorial Name                                                                                  | Description                                                          |
-|------------------------------------------------------------------------------------------------|----------------------------------------------------------------------|
-| [`1_TB_Models`](docs/tutorials/1_TB_Models.ipynb)                                        | Tutorials on predefined and custom tight-binding models.             |
-| [`2_Data_Visualization`](docs/tutorials/2_Data_Visualization.ipynb)                    | Tutorial on the predefined plotting routines.                        |
-| [`3_DNA_environment`](docs/tutorials/3_DNA_environment.ipynb)                          | Tutorial on different ways to treat DNA relaxation and the DNA environment. |
-| [`4_Parallelized_Calculations`](docs/tutorials/4_Parallelized_Calculations.ipynb)      | Tutorial on how to perform parallelized calculations for several properties. |
-| [`Exploration_Notebook`](docs/tutorials/Exploration_Notebook.ipynb)                    | A place to test the functionality of individual functions isolated from the rest of the code. |
-
-
-These tutorials provide hands-on examples and explanations to help you effectively use the `qDNA` package.
 
 
 ### Graphical user interface

qDNA/data/raw/test_params/Herb2024_relations_between_persons.json → data/raw/test_params/Herb2024_relations_between_persons.json

@@ -1 +1 @@
-[{"relation_AliceBob": 5, "relation_AliceCharlie": 3, "relation_AliceEve": -2, "relation_BobAlice": 5, "relation_CharlieAlice": 3, "relation_EveAlice": -2}, {"author": "Herb2024", "subject": "relations_between_persons", "notes": "The parameters describe relations between persons."}]
+[{"relation_AliceBob": 5, "relation_AliceCharlie": 3, "relation_AliceEve": -2, "relation_BobAlice": 5, "relation_CharlieAlice": 3, "relation_EveAlice": -2}, {"author": "Herb2024", "subject": "relations_between_persons", "notes": "The parameters describe relations between persons."}]

configs/.readthedocs.yaml → docs/.readthedocs.yaml

@@ -17,7 +17,7 @@ build:
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
-  configuration: docs/sphinx_doc/conf.py
+  configuration: docs/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
 # formats:
@@ -29,5 +29,5 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
    install:
-   - requirements: configs/requirements.txt 
-   - requirements: configs/doc-requirements.txt
+   - requirements: requirements/requirements.txt
+   - requirements: requirements/doc-requirements.txt

docs/sphinx_doc/_build/html/_modules/index.html → docs/_build/html/_modules/index.html

@@ -8,11 +8,11 @@
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css" />
       <link rel="stylesheet" type="text/css" href="../_static/plot_directive.css" />
 
-  
+
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
-  
+
         <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/jquery.js"></script>
         <script src="../_static/underscore.js"></script>
@@ -21,17 +21,17 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="copyright" title="Copyright" href="../copyright.html" /> 
+    <link rel="copyright" title="Copyright" href="../copyright.html" />
 </head>
 
-<body class="wy-body-for-nav"> 
+<body class="wy-body-for-nav">
   <div class="wy-grid-for-nav">
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
 
-          
-          
+
+
           <a href="../index.html" class="icon icon-home">
             QuantumDNA
           </a>
@@ -73,7 +73,7 @@
 </div>
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
-             
+
   <h1>All modules for which code is available</h1>
 <ul><li><a href="qDNA/dna_seq.html">qDNA.dna_seq</a></li>
 <li><a href="qDNA/dynamics/reduced_dm.html">qDNA.dynamics.reduced_dm</a></li>
@@ -111,7 +111,7 @@ <h1>All modules for which code is available</h1>
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
     <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
     provided by <a href="https://readthedocs.org">Read the Docs</a>.
-   
+
 
 </footer>
         </div>
@@ -122,7 +122,7 @@ <h1>All modules for which code is available</h1>
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script> 
+  </script>
 
 </body>
-</html>
+</html>

docs/sphinx_doc/_build/html/_modules/qDNA/dna_seq.html → docs/_build/html/_modules/qDNA/dna_seq.html

@@ -8,11 +8,11 @@
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css" />
       <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css" />
 
-  
+
   <!--[if lt IE 9]>
     <script src="../../_static/js/html5shiv.min.js"></script>
   <![endif]-->
-  
+
         <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
         <script src="../../_static/jquery.js"></script>
         <script src="../../_static/underscore.js"></script>
@@ -21,17 +21,17 @@
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
-    <link rel="copyright" title="Copyright" href="../../copyright.html" /> 
+    <link rel="copyright" title="Copyright" href="../../copyright.html" />
 </head>
 
-<body class="wy-body-for-nav"> 
+<body class="wy-body-for-nav">
   <div class="wy-grid-for-nav">
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
 
-          
-          
+
+
           <a href="../../index.html" class="icon icon-home">
             QuantumDNA
           </a>
@@ -74,7 +74,7 @@
 </div>
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
-             
+
   <h1>Source code for qDNA.dna_seq</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">Module for generating DNA sequences. </span>
@@ -299,7 +299,7 @@ <h1>Source code for qDNA.dna_seq</h1><div class="highlight"><pre>
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
     <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
     provided by <a href="https://readthedocs.org">Read the Docs</a>.
-   
+
 
 </footer>
         </div>
@@ -310,7 +310,7 @@ <h1>Source code for qDNA.dna_seq</h1><div class="highlight"><pre>
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script> 
+  </script>
 
 </body>
-</html>
+</html>