Release StraWBerryPy 0.3.0

.gitignore

@@ -2,5 +2,8 @@ __pycache__/
 strawberrypy/__pycache__/
 strawberrypy/_pythtb/__pycache__/
 strawberrypy/_tbmodels/__pycache__/
+tests/__pycache__
 .devcontainer/
-.pytest_cache
+.pytest_cache
+.DS_Store
+docs/_build/

.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+  # Fail on all warnings to avoid broken references
+  fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+  - pdf
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt

README.rst

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+============
+StraWBerryPy
+============
+
+**StraWBerryPy** (Single-poinT and local invaRiAnts for Wannier Berriologies in Python) is a Python package to calculate topological invariants and quantum-geometrical quantities in non-crystalline topological insulators.
+
+The code reads tight-binding models from `PythTB <http://www.physics.rutgers.edu/pythtb/>`_, `TBmodels <https://tbmodels.greschd.ch/en/latest/>`_ and `Wannier90 <https://wannier.org/>`_ (through `WannierBerri <https://wannier-berri.org/index.html>`_). 
+
+StraWBerryPy can work both with periodic (PBCs) and open (OBCs) boundary conditions. The code allows to create and manipulate supercells and finite models, for example adding disorder. Single-point and local topological markers can be computed, in addition to other quantum-geometrical quantities (e.g., the localization marker).
+
+* `Github page <https://github.com/strawberrypy-developers/strawberrypy>`_
+* `Documentation <http://strawberrypy.readthedocs.io/>`_
+
+
+How to cite
++++++++++++
+Please cite the following papers in any publication arising from the use of 
+this code. 
+
+In particular, if you use the implementation of the single-point (Chern or Z2) invariants
+
+  R. Favata and A. Marrazzo
+  Single-point spin Chern number in a supercell framework
+  `Electronic Structure 5, 014005 (2023)`_
+
+.. _Electronic Structure 5, 014005 (2023): https://doi.org/10.1088/2516-1075/acba6f
+
+If you use the implementation of the local Chern marker in periodic boundary conditions:
+
+  N. Baù and A. Marrazzo
+  Local Chern marker for periodic systems
+  `accepted in PRB, arxiv (2023)`_
+
+.. _accepted in PRB, arxiv (2023): https://doi.org/10.48550/arXiv.2310.15783
+
+If you use the implementation of the localization marker:
+
+  A. Marrazzo and R. Resta
+  A local theory of the insulating state
+  `Phys. Rev. Lett. 122, 166602 (2019)`_
+
+.. _Phys. Rev. Lett. 122, 166602 (2019): https://doi.org/10.1103/PhysRevLett.122.166602
+

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/custom.css

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+/* From: https://framagit.org/coslo/template-docs */
+
+body {
+  font-family: Noto Serif, Georgia, serif;
+}
+div.sphinxsidebar {
+    height: 100vh;
+    overflow: auto;
+}
+div.sphinxsidebar hr {
+    width: 100%;
+}
+/* div.sphinxsidebar ul { */
+/*     margin: 0 0 !important; */
+/* } */
+div.sphinxsidebar a.current.reference.internal {
+    font-weight: bold;
+    /* display: none; */
+}
+div.sphinxsidebar li.toctree-l1 {
+    padding-top: 2px !important;
+    padding-bottom: 2px !important;
+}
+div.sphinxsidebar li.toctree-l1 ul {
+    font-weight: normal;
+    /* list-style-type: none; /\* Remove bullets *\/ */
+    padding: 0; /* Remove padding */
+    margin: 0; /* Remove margins */
+    margin-bottom: 10px;
+    margin-left: 18px;
+}
+pre {
+    padding: 7px 15px;
+}
+pre, tt, code {
+  font-size: 0.9em;
+}
+code {
+    background-color: rgba(0, 0, 0, 0)
+}
+div.admonition code {
+    background: #c9dbe8;
+    /* color: #60a0b0; */
+}
+div.body h4, div.body h5, div.body h6 {
+    margin: 10px 0px 10px 0px;
+}
+div.body h3 {
+    margin: 20px 0px 10px 0px;
+}
+div.admonition {
+    padding: 10px 15px;
+}
+div.note {
+    background-color: #0e84b51c;
+}
+img {
+    display: block;
+    margin-left: auto;
+    margin-right: auto;
+    max-width: 70%
+}
+div.highlight-none pre {
+    background-color: rgb(255, 255, 255);
+    color: #7B8591;
+    padding: 0px 15px;
+}
+@media screen and (max-width: 870px) {
+div.sphinxsidebar {
+    height: auto;
+}
+}
+div.body h2 {
+  padding-bottom: 4px;
+  border-bottom: 1px solid rgb(151, 157, 164);
+}
+div.sphinxsidebarwrapper p.blurb {
+  margin-bottom: 20px;
+}
+.highlight .si, .highlight .c1  {
+  font-style: normal !important;
+}
+div.sphinxsidebar {
+    max-height: 100%;
+    overflow-y: auto;
+}
+.highlight{
+    background-color: #F5F5F5
+}

docs/_templates/navigation.html

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+<!-- From: https://framagit.org/coslo/template-docs -->
+
+{{ toctree(includehidden=theme_sidebar_includehidden, collapse=theme_sidebar_collapse) }}
+{% if theme_extra_nav_links %}
+<hr />
+<ul>
+    {% for text, uri in theme_extra_nav_links.items() %}
+    <li class="toctree-l1"><a href="{{ uri }}">{{ text }}</a></li>
+    {% endfor %}
+</ul>
+{% endif %}