Develop (#188)

* Image augmentation.

* Augment images.

* Augment images.

* Specie update.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Update conf.py

* Update conf.py

* Multi-output graph bacthing.

* Add EDOS dataset.

* Temp.

* Add circuit maker.

* Add circuit maker.

* NELECT update.

* Version update, more DBs added.

* Fix CHGCAR vasp.

* Added volumetric reshape for CHGCAR.

* Tmp

* Tershoff Hamman update, specie update.

* Add crop from center in STM.

* Add Fourier transfor in STM.

* Update STM pytest.

* Add DPI to STM.

* Zeo++ added, Atoms cif update, STM update, random vacancy maker added.

* Atoms tempfile fix, Potcar from atoms module added.

* Test for docs.

* C2DB link update, docs Atoms update.

* C2DB link update, docs Atoms update.

* Version update, COD DB, QM9 JCTC DB added.

* Compostion bug fix, elemental descriptor added.

* Develop (#186)

* Update outputs.py

I added the calculation of the Raman intensities inside parse_raman_dat

* Update outputs.py

* Update outputs.py

* Update outputs.py

* Update cfid.py

* Delete __init__.py

* stylecss added.

* stylecss added.

* Adding extra Makefile/

* Remove examples from docs.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Tutorials update.

* Tutorials docs update.

* Docs update,pdb reader updated.

* Update action_build.yml

* Update action_build.yml

* Remove pytraj strong dependencies.

* Update docs, Added PDBBind and HPOV datasets.

* Docs update.

Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>

.github/workflows/action_build.yml

@@ -24,7 +24,7 @@ jobs:
       run: |
         python setup.py develop
         pip install --upgrade --upgrade-strategy eager -r dev-requirements.txt -e .
-
+        #conda install -c ambermd pytraj
         echo 'CONDA LIST'
         conda list
 

dev-requirements.txt

@@ -4,7 +4,7 @@ ase>=3.21.1
 numpy>=1.18.5
 scipy>=1.4.1
 matplotlib>=3.0.0
-phonopy>=2.8.1
+phonopy==2.10.0
 coverage>=5.5
 lightgbm>=2.1.0
 flask >=1.1.2
@@ -28,3 +28,5 @@ bokeh>=2.3.0
 opencv-python>=4.5.2.52
 scikit-image>=0.16.2
 Pillow>=7.1.2
+sphinx_rtd_theme>=0.5.1
+sphinx>=4.0.3

docs/_static/css/mystyle.css

@@ -0,0 +1,5 @@
+@import "theme.css";
+
+table.docutils div.line-block {
+    margin-left: 0;
+}

docs/requirements.txt

@@ -4,7 +4,7 @@ ase>=3.21.1
 numpy>=1.18.5
 scipy>=1.4.1
 matplotlib>=3.0.0
-phonopy>=2.8.1
+phonopy==2.10.0
 coverage>=5.5
 lightgbm>=2.1.0
 flask >=1.1.2

docs/source/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = jarvis-tools
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Has to be explicit, otherwise we don't get "make" without targets right.
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+# You can add custom targets here.
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%:
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/conf.py

@@ -1,83 +1,94 @@
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))  # Source code dir relative to this file
+
+sys.path.insert(
+    0, os.path.abspath("../..")
+)  # Source code dir relative to this file
 
 extensions = [
-    'sphinx.ext.autodoc','autoapi.extension','sphinx.ext.doctest'  # Core library for html generation from docstrings
+    "sphinx.ext.autodoc",
+    "autoapi.extension",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.doctest",  # Core library for html generation from docstrings
+    #"releases",
 ]
 
-autoapi_type = 'python'
-autoapi_dirs = ['../../jarvis']
-autoapi_ignore = ['*test*']
+autoapi_type = "python"
+autoapi_dirs = ["../../jarvis"]
+autoapi_ignore = ["*test*", "*examples*","*vasp_to_xml*"]
+#exclude_patterns = ["*vasp_to_xml*"]
 
+# 'releases' (changelog) settings
+#releases_issue_uri = "https://github.com/usnistgov/jarvis/issues/%s"
+#releases_release_uri = "https://github.com/usnistgov/jarvis/tree/%s"
 
 # sys.path.append(os.path.dirname(__file__))
 # -- General configuration -----------------------------------------------------
 
 
-
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
-#source_encoding = 'utf-8'
+# source_encoding = 'utf-8'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'JARVIS-Tools'
-copyright = u'2021, Kamal Choudhary'
+project = u"JARVIS-Tools"
+copyright = u"2021, Kamal Choudhary"
 
 # 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 jarvis
+
 version = jarvis.__version__
 # The full version, including alpha/beta/rc tags.
 # release = '0.9'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of documents that shouldn't be included in the build.
-#unused_docs = []
+# unused_docs = []
 
 # List of directories, relative to source directory, that shouldn't be searched
 # for source files.
 exclude_trees = []
 
 # The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# 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
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 
 # -- Options for HTML output ---------------------------------------------------
@@ -94,106 +105,110 @@
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
-   'collapse_navigation': False,
-
+    "collapse_navigation": False,
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# 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 = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+# 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
+# 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']
+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'
+# 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 = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_use_modindex = True
+# html_use_modindex = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# 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 = ''
+# html_use_opensearch = ''
 
 # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = ''
+# html_file_suffix = ''
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'jarvis-tools'
-
+htmlhelp_basename = "jarvis-tools"
+# html_style = "css/mystyle.css"
 
 # -- Options for LaTeX output --------------------------------------------------
 
 # The paper size ('letter' or 'a4').
-#latex_paper_size = 'letter'
+# latex_paper_size = 'letter'
 
 # The font size ('10pt', '11pt' or '12pt').
-#latex_font_size = '10pt'
+# 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', 'jarvis-tools.tex', u'JARVIS-Tools Documentation',
-   u'Kamal Choudhary', 'manual'),
+    (
+        "index",
+        "jarvis-tools.tex",
+        u"JARVIS-Tools Documentation",
+        u"Kamal Choudhary",
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
+# latex_preamble = ''
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_use_modindex = True
+# latex_use_modindex = True
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'http://docs.python.org/': None}
-language = 'en'
+intersphinx_mapping = {"http://docs.python.org/": None}
+language = "en"