diff --git a/.gitignore b/.gitignore index 9ae6448e..07ad8713 100644 --- a/.gitignore +++ b/.gitignore @@ -26,6 +26,6 @@ distribute-0.6.34-py2.7.egg distribute-0.6.34.tar.gz -pymatgen_diffusion/\.vscode/ +pymatgen/\.vscode/ .vscode/ diff --git a/docs_rst/change_log.rst b/docs_rst/change_log.rst index a59aa6b4..b6e319d0 100644 --- a/docs_rst/change_log.rst +++ b/docs_rst/change_log.rst @@ -1,5 +1,10 @@ Change Log ----------- +========== + +v2021.3.5 +--------- +* pymatgen-diffusion is now released as a namespace package `pymatgen-analysis-diffusion` on PyPI. It should be + imported via `pymatgen.analysis.diffusion` instead `pymatgen_diffusion`. v2019.2.28 ---------- diff --git a/docs_rst/conf.py b/docs_rst/conf.py index 08add9d5..4ef6d55b 100644 --- a/docs_rst/conf.py +++ b/docs_rst/conf.py @@ -17,40 +17,40 @@ # 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.insert(0, os.path.abspath('.')) -sys.path.insert(0, os.path.dirname('..')) -sys.path.insert(0, os.path.dirname('../pymatgen_diffusion')) -sys.path.insert(0, os.path.dirname('../..')) +sys.path.insert(0, os.path.abspath(".")) +sys.path.insert(0, os.path.dirname("..")) +sys.path.insert(0, os.path.dirname("../pymatgen_diffusion")) +sys.path.insert(0, os.path.dirname("../..")) -from pymatgen_diffusion import __version__, __author__ +from pymatgen.analysis.diffusion import __version__, __author__ # -- General configuration ----------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' +# needs_sphinx = '1.0' # 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.napoleon', 'sphinx.ext.viewcode', "sphinx.ext.mathjax"] -exclude_patterns = ['../**/tests*'] -exclude_dirnames = ['../**/tests*'] -autoclass_content = 'both' +extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon", "sphinx.ext.viewcode", "sphinx.ext.mathjax"] +exclude_patterns = ["../**/tests*"] +exclude_dirnames = ["../**/tests*"] +autoclass_content = "both" # 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-sig' +# source_encoding = 'utf-8-sig' # The master toctree document. -master_doc = 'index' +master_doc = "index" # General information about the project. -project = u'pymatgen-diffusion' -copyright = u'2016, ' + __author__ +project = "pymatgen-diffusion" +copyright = "2016, " + __author__ # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -63,24 +63,24 @@ # 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 patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ['_build'] +exclude_patterns = ["_build"] # 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::). @@ -88,41 +88,41 @@ # 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 ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -sys.path.append(os.path.abspath('_themes')) -html_theme_path = ['_themes'] -html_theme = 'kr' +sys.path.append(os.path.abspath("_themes")) +html_theme_path = ["_themes"] +html_theme = "kr" # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. -#html_theme_options = {} +# html_theme_options = {} # 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 # " v 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 @@ -132,105 +132,99 @@ # 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_domain_indices = True +# html_domain_indices = 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, "Created using Sphinx" is shown in the HTML footer. Default is True. -#html_show_sphinx = True +# html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -#html_show_copyright = True +# html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a 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 = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None +# html_file_suffix = None # Output file base name for HTML help builder. -htmlhelp_basename = 'pymatgen_diffusion_doc' +htmlhelp_basename = "pymatgen_diffusion_doc" # -- Options for LaTeX output ------------------------------------------------ latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', + # The paper size ('letterpaper' or 'a4paper'). + #'papersize': 'letterpaper', + # The font size ('10pt', '11pt' or '12pt'). + #'pointsize': '10pt', + # Additional stuff for the LaTeX preamble. + #'preamble': '', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ('index', 'pymatgen-diffusion.tex', u'pymatgen-diffusion Documentation', - __author__, 'manual'), + ("index", "pymatgen-diffusion.tex", "pymatgen-diffusion Documentation", __author__, "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 # If true, show page references after internal links. -#latex_show_pagerefs = False +# latex_show_pagerefs = False # If true, show URL addresses after external links. -#latex_show_urls = False +# latex_show_urls = False # Documents to append as an appendix to all manuals. -#latex_appendices = [] +# latex_appendices = [] # If false, no module index is generated. -#latex_domain_indices = True +# latex_domain_indices = True # -- Options for manual page output ------------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'pymatgen-diffusion', u'pymatgen-diffusion Documentation', - [__author__], 1) -] +man_pages = [("index", "pymatgen-diffusion", "pymatgen-diffusion Documentation", [__author__], 1)] # If true, show URL addresses after external links. -#man_show_urls = False +# man_show_urls = False # -- Options for Texinfo output ---------------------------------------------- @@ -239,59 +233,65 @@ # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - ('index', 'pymatgen-diffusion', u'pymatgen-diffusion Documentation', - __author__, 'pymatgen-diffusion', 'One line description of project.', - 'Miscellaneous'), + ( + "index", + "pymatgen-diffusion", + "pymatgen-diffusion Documentation", + __author__, + "pymatgen-diffusion", + "One line description of project.", + "Miscellaneous", + ), ] # Documents to append as an appendix to all manuals. -#texinfo_appendices = [] +# texinfo_appendices = [] # If false, no module index is generated. -#texinfo_domain_indices = True +# texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' +# texinfo_show_urls = 'footnote' # -- Options for Epub output --------------------------------------------------- # Bibliographic Dublin Core info. -epub_title = u'pymatgen-diffusion' +epub_title = "pymatgen-diffusion" epub_author = __author__ -epub_publisher = u'Materials Virtual Lab' +epub_publisher = "Materials Virtual Lab" epub_copyright = copyright # The language of the text. It defaults to the language option # or en if the language is not set. -#epub_language = '' +# epub_language = '' # The scheme of the identifier. Typical schemes are ISBN or URL. -#epub_scheme = '' +# epub_scheme = '' # The unique identifier of the text. This can be a ISBN number # or the project homepage. -#epub_identifier = '' +# epub_identifier = '' # A unique identification for the text. -#epub_uid = '' +# epub_uid = '' # A tuple containing the cover image and cover page html template filenames. -#epub_cover = () +# epub_cover = () # HTML files that should be inserted before the pages created by sphinx. # The format is a list of tuples containing the path and title. -#epub_pre_files = [] +# epub_pre_files = [] # HTML files shat should be inserted after the pages created by sphinx. # The format is a list of tuples containing the path and title. -#epub_post_files = [] +# epub_post_files = [] # A list of files that should not be packed into the epub file. -#epub_exclude_files = [] +# epub_exclude_files = [] # The depth of the table of contents in toc.ncx. -#epub_tocdepth = 3 +# epub_tocdepth = 3 # Allow duplicate toc entries. -#epub_tocdup = True +# epub_tocdup = True diff --git a/docs_rst/modules.rst b/docs_rst/modules.rst index ea256aa5..a0ff599a 100644 --- a/docs_rst/modules.rst +++ b/docs_rst/modules.rst @@ -1,7 +1,7 @@ -pymatgen_diffusion -================== +pymatgen +======== .. toctree:: - :maxdepth: 6 + :maxdepth: 7 - pymatgen_diffusion + pymatgen diff --git a/pymatgen/analysis/diffusion/__init__.py b/pymatgen/analysis/diffusion/__init__.py index def30f3c..445a4f7f 100644 --- a/pymatgen/analysis/diffusion/__init__.py +++ b/pymatgen/analysis/diffusion/__init__.py @@ -2,4 +2,6 @@ Package for diffusion analysis. """ +__author__ = "Materials Virtual Lab" +__email__ = "ongsp@eng.ucsd.edu" __version__ = "2021.3.5" diff --git a/setup.py b/setup.py index 9250294c..5b3bfeb7 100644 --- a/setup.py +++ b/setup.py @@ -14,8 +14,8 @@ setup( name="pymatgen-analysis-diffusion", - packages=find_namespace_packages(include=['pymatgen.analysis.*']), - version="2020.10.8", + packages=find_namespace_packages(include=["pymatgen.analysis.*"]), + version="2021.3.5", install_requires=["pymatgen>=2022.0.3", "joblib"], extras_require={}, package_data={}, @@ -38,6 +38,6 @@ "Topic :: Scientific/Engineering :: Information Analysis", "Topic :: Scientific/Engineering :: Physics", "Topic :: Scientific/Engineering :: Chemistry", - "Topic :: Software Development :: Libraries :: Python Modules" - ] + "Topic :: Software Development :: Libraries :: Python Modules", + ], ) diff --git a/tasks.py b/tasks.py index 26ec3e80..9bb7f880 100644 --- a/tasks.py +++ b/tasks.py @@ -1,7 +1,7 @@ #!/usr/bin/env python """ -Deployment file to facilitate releases of pymatgen_diffusion. +Deployment file to facilitate releases of pymatgen.analysis.diffusion. """ from __future__ import division @@ -28,7 +28,7 @@ def make_doc(ctx): with cd("docs_rst"): ctx.run("cp ../CHANGES.rst change_log.rst") ctx.run("sphinx-apidoc --implicit-namespaces --separate -d 7 -o . -f ../pymatgen") - ctx.run("rm pymatgen_diffusion*.tests.rst") + ctx.run("rm pymatgen*.tests.rst") for f in glob.glob("*.rst"): if f.startswith("pymatgen") and f.endswith("rst"): newoutput = [] @@ -116,7 +116,7 @@ def release_github(ctx): @task def test(ctx): - ctx.run("pytest pymatgen_diffusion") + ctx.run("pytest pymatgen") @task