larixite 2024.10.0__tar.gz

larixite-2024.10.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+larixite/version.py
+
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Sphinx documentation
+docs/_build/
+
+# Jupyter Notebook
+.ipynb_checkpoints

larixite-2024.10.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Matthew Newville, The University of Chicago,
+                   Mauro Rovezzi, University Grenoble Alpes, CNRS
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

larixite-2024.10.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: larixite
+Version: 2024.10.0
+Summary: convert CIF data to inputs for XAS calculations Feff, FDMNES, etc
+Author-email: Matthew Newville <newville@cars.uchicago.edu>, Mauro Rovezzi <mauro.rovezzi@esrf.fr>
+License: MIT License
+        
+        Copyright (c) 2024 Matthew Newville, The University of Chicago,
+                           Mauro Rovezzi, University Grenoble Alpes, CNRS
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage,  https://github.com/xraypy/larixite
+Project-URL: Documentation, https://xraypy.github.io/larixite
+Project-URL: Tracker, https://github.com/xraypy/larixite/issues
+Keywords: X-ray spectroscopy,Crystallography
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: xraydb
+Requires-Dist: sqlalchemy>=2
+Requires-Dist: pymatgen
+Requires-Dist: pyshortcuts
+Provides-Extra: web
+Requires-Dist: flask; extra == "web"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Provides-Extra: dev
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Provides-Extra: all
+Requires-Dist: larixite[dev,doc,test,web]; extra == "all"
+
+# Larixite
+
+Crystal structures and clusters of atoms for X-ray absorption spectroscopy.
+
+The main purpose of larixite is to provide a Python package for using
+crystallographic data or calculated clusters of atoms to generate inputs for
+X-ray absorption spectroscopy and other scientific disciplines that use
+non-crystalline clusters of atoms.
+
+This project includes:
+
+1. an sqlite3 database of structures from the [American Mineralogical
+   Crystal Structure Database](https://rruff.geo.arizona.edu/AMS/amcsd.php) (AMCSD)
+2. Python code to convert structures from the AMCSD database, other CIF files,
+   or XYZ coordinates into atomic clusters for XAS calculations with FEFF,
+   FDMNES, and other XAS calculation tools.
+3. A basic web application to guide those conversions. See [Larixite Web App](https://millenia.cars.aps.anl.gov/larixite).
+
+
+## install
+
+Either install from PyPI with
+
+    > pip install larixite
+
+
+Download and unpack this code and install with
+
+
+    > pip install .
+
+
+## Status
+
+Larixite has been in rapid development, but is also a spin-off from code that
+has been in Xraylarch for many years.  That is, while many parts of the code
+are moving rapidly, much of the code is reasonably stable.
+
+
+## Web App
+
+The [Larixite Web App](https://millenia.cars.aps.anl.gov/larixite) can be run
+locally for debugging or for local deployment.  To do this, install the extra
+wed dependencies (essentially only Flask is needed) with
+
+    > pip install ".[web]"
+
+
+and run the script "run_local.py" with
+
+      > python run_local.py
+
+will launch a local web server with the app running at http://127.0.0.1:11564/

larixite-2024.10.0/README.md

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+# Larixite
+
+Crystal structures and clusters of atoms for X-ray absorption spectroscopy.
+
+The main purpose of larixite is to provide a Python package for using
+crystallographic data or calculated clusters of atoms to generate inputs for
+X-ray absorption spectroscopy and other scientific disciplines that use
+non-crystalline clusters of atoms.
+
+This project includes:
+
+1. an sqlite3 database of structures from the [American Mineralogical
+   Crystal Structure Database](https://rruff.geo.arizona.edu/AMS/amcsd.php) (AMCSD)
+2. Python code to convert structures from the AMCSD database, other CIF files,
+   or XYZ coordinates into atomic clusters for XAS calculations with FEFF,
+   FDMNES, and other XAS calculation tools.
+3. A basic web application to guide those conversions. See [Larixite Web App](https://millenia.cars.aps.anl.gov/larixite).
+
+
+## install
+
+Either install from PyPI with
+
+    > pip install larixite
+
+
+Download and unpack this code and install with
+
+
+    > pip install .
+
+
+## Status
+
+Larixite has been in rapid development, but is also a spin-off from code that
+has been in Xraylarch for many years.  That is, while many parts of the code
+are moving rapidly, much of the code is reasonably stable.
+
+
+## Web App
+
+The [Larixite Web App](https://millenia.cars.aps.anl.gov/larixite) can be run
+locally for debugging or for local deployment.  To do this, install the extra
+wed dependencies (essentially only Flask is needed) with
+
+    > pip install ".[web]"
+
+
+and run the script "run_local.py" with
+
+      > python run_local.py
+
+will launch a local web server with the app running at http://127.0.0.1:11564/

larixite-2024.10.0/doc/Makefile

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+# Makefile for Sphinx documentation
+#
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+INSTALLDIR = /home/newville/public_html/larixite/
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: html pdf all help clean dirhtml latex
+
+
+all: html
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) _build/html
+	@echo "Build finished. The HTML pages are in _build/html."
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+pdf: latex
+	cd $(BUILDDIR)/latex && make all-pdf
+	cp -pr $(BUILDDIR)/latex/larixite.pdf ./larixite.pdf
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html      to make standalone HTML files"
+	@echo "  pdf       pdf from latex version"
+	@echo "  all       html, pdf, and doc.zip"
+	@echo "  clean     to remove all output"
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) _build/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in _build/latex."
+	@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
+	      "run these through (pdf)latex."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) _build/latex
+	@echo "Running LaTeX files through pdflatex..."
+	make -C _build/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in _build/latex."
+
+clean:
+	-rm -rf _build/*

larixite-2024.10.0/doc/_static/empty

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+empty

larixite-2024.10.0/doc/_templates/indexsidebar.html

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+<h3>Get Larixite</h3>
+<p>Current version: <b>{{ release }}</b></p>
+<p>Install:   <tt>pip install larixite</tt></p>
+<p>Develop:
+  &nbsp; <a href="https://github.com/xraypy/larixite/">github.com</a>
+  <p>
+
+<hr>

larixite-2024.10.0/doc/conf.py

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+# -*- coding: utf-8 -*-
+#
+# documentation build configuration file
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+from datetime import date
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.append(os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc',
+              'sphinx.ext.todo',
+              'sphinx.ext.coverage',
+              'sphinx.ext.mathjax', 'sphinx.ext.intersphinx']
+
+intersphinx_mapping = {'py': ('https://docs.python.org/3/', None)}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'larixite'
+copyright = f"""{date.today().year}, Matthew Newville, The University of Chicago,
+                   Mauro Rovezzi, University Grenoble Alpes, CNRS"""
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+import larixite
+release = larixite.__version__.split('+', 1)[0]
+
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  Major themes that come with
+# Sphinx are currently 'default' and 'sphinxdoc'.
+html_theme = 'bizstyle'
+
+# html_theme = 'nature'
+# html_theme = 'agogo'
+# html_theme_options = {'pagewidth':'85em', 'documentwidth':'60em', 'sidebarwidth': '25em',
+#                       # 'headercolor1': '#000080',
+#                       # 'headercolor2': '#0000A0',
+#                       }
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+html_title = 'Larixite: Crystallographic Structures for X-ray Absorption Spectroscopy'
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+html_short_title = 'Larixite: Crystals for XAS'
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+# html_use_smartypants = False # True
+
+# Custom sidebar templates, maps document names to template names.
+html_sidebars = {'index': ['indexsidebar.html','searchbox.html']}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_use_modindex = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+html_show_sourcelink = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'larixitedoc'
+
+# -- Options for LaTeX output --------------------------------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'larixite.tex', u'larixite documentation',
+   u'Matthew Newville, Mauro Rovezzi', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True

larixite-2024.10.0/doc/index.rst

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+.. larixite  documentation master file
+
+Larixite: Crystal structures for X-ray absorption spectroscopy
+===============================================================
+
+.. _xraylarch: https://xraypy.github.io/xraylarch/
+.. _Larixite Webapp: https://millenia.cars.aps.anl.gov/larixite
+.. _American Mineralogical Crystal Structure Database: https://rruff.geo.arizona.edu/AMS/amcsd.php
+
+Larixite is a Python package to help use crystallographic data to build
+clusters of atoms to generate inputs for X-ray absorption spectroscopy and
+other scientific disciplines that use non-crystalline clusters of atoms.
+
+This project includes:
+
+1. an sqlite3 database of structures from the `American Mineralogical Crystal Structure Database`_ (AMCSD).
+2. Python code to convert structures from the AMCSD database, other CIF files,
+   or XYZ coordinates into atomic clusters for XAS calculations with FEFF,
+   FDMNES, and other XAS calculation tools.
+3. A basic web application to guide those conversions. See `Larixite WebApp`_.
+
+
+Installation
+------------------
+
+Either install from PyPI with::
+
+    > pip install larixite
+
+
+or download and unpack this code and install with::
+
+
+    > pip install .
+
+
+Status
+--------
+
+Larixite has been in rapid development, but is also a spin-off from code that
+has been in `xraylarch`_ for many years.  That is, while many parts of the code
+are moving rapidly, much of the code is reasonably stable.
+
+
+Web App
+----------
+
+
+The `Larixite WebApp`_ can be run locally for debugging or for local
+deployment.  To do this, install the extra wed dependencies (essentially only
+Flask is needed) with::
+
+    > pip install ".[web]"
+
+
+and run the script "run_local.py" with::
+
+      > python run_local.py
+
+will launch a local web server with the app running at http://127.0.0.1:11564/

larixite-2024.10.0/larixite/__init__.py

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+from .version import __version__
+from .amcsd import get_amcsd
+from .cif_cluster import cif_cluster, cif2feffinp, read_cif_structure