From ce74193f8695544aec71208c46b3b9771060005c Mon Sep 17 00:00:00 2001 From: stevenhua0320 Date: Wed, 31 Jul 2024 09:56:33 +0800 Subject: [PATCH 1/3] move untrack doc and requirement files --- .gitattributes | 1 + doc/source/_static/.placeholder | 0 .../api/diffpy.srmise.example_package.rst | 31 ++ doc/source/api/diffpy.srmise.rst | 30 ++ doc/source/conf.py | 289 ++++++++++++++++++ doc/source/index.rst | 44 +++ doc/source/license.rst | 39 +++ doc/source/release.rst | 5 + requirements/README.txt | 11 + requirements/build.txt | 2 + requirements/docs.txt | 4 + requirements/pip.txt | 0 requirements/run.txt | 3 - requirements/test.txt | 1 + 14 files changed, 457 insertions(+), 3 deletions(-) create mode 100644 .gitattributes create mode 100644 doc/source/_static/.placeholder create mode 100644 doc/source/api/diffpy.srmise.example_package.rst create mode 100644 doc/source/api/diffpy.srmise.rst create mode 100644 doc/source/conf.py create mode 100644 doc/source/index.rst create mode 100644 doc/source/license.rst create mode 100644 doc/source/release.rst create mode 100644 requirements/README.txt create mode 100644 requirements/build.txt create mode 100644 requirements/docs.txt create mode 100644 requirements/pip.txt diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..e7c3aea --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +diffpy.srmise/_version.py export-subst diff --git a/doc/source/_static/.placeholder b/doc/source/_static/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/doc/source/api/diffpy.srmise.example_package.rst b/doc/source/api/diffpy.srmise.example_package.rst new file mode 100644 index 0000000..8c7f6ad --- /dev/null +++ b/doc/source/api/diffpy.srmise.example_package.rst @@ -0,0 +1,31 @@ +.. _example_package documentation: + +|title| +======= + +.. |title| replace:: diffpy.srmise.example_package package + +.. automodule:: diffpy.srmise.example_package + :members: + :undoc-members: + :show-inheritance: + +|foo| +----- + +.. |foo| replace:: diffpy.srmise.example_package.foo module + +.. automodule:: diffpy.srmise.example_package.foo + :members: + :undoc-members: + :show-inheritance: + +|bar| +----- + +.. |bar| replace:: diffpy.srmise.example_package.bar module + +.. automodule:: diffpy.srmise.example_package.foo + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/api/diffpy.srmise.rst b/doc/source/api/diffpy.srmise.rst new file mode 100644 index 0000000..958efe0 --- /dev/null +++ b/doc/source/api/diffpy.srmise.rst @@ -0,0 +1,30 @@ +:tocdepth: -1 + +|title| +======= + +.. |title| replace:: diffpy.srmise package + +.. automodule:: diffpy.srmise + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + diffpy.srmise.example_package + +Submodules +---------- + +|module| +-------- + +.. |module| replace:: diffpy.srmise.example_submodule module + +.. automodule:: diffpy.srmise.example_submodule + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/conf.py b/doc/source/conf.py new file mode 100644 index 0000000..65d3685 --- /dev/null +++ b/doc/source/conf.py @@ -0,0 +1,289 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# +# diffpy.srmise documentation build configuration file, created by +# sphinx-quickstart on Thu Jan 30 15:49:41 2014. +# +# 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 +import time +from importlib.metadata import version +from pathlib import Path + +# 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 Path().resolve() to make it absolute, like shown here. +# sys.path.insert(0, str(Path(".").resolve())) +sys.path.insert(0, str(Path("../..").resolve())) +sys.path.insert(0, str(Path("../../src").resolve())) + +# abbreviations +ab_authors = "Billinge Group members and community contributors" + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# 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.todo", + "sphinx.ext.viewcode", + "sphinx.ext.intersphinx", + "sphinx_rtd_theme", + "m2r", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +source_suffix = [".rst", ".md"] + +# The encoding of source files. +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = "index" + +# General information about the project. +project = "diffpy.srmise" +copyright = "%Y, The Trustees of Columbia University in the City of New York" + +# 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. + +fullversion = version(project) +# The short X.Y version. +version = "".join(fullversion.split(".post")[:1]) +# The full version, including alpha/beta/rc tags. +release = fullversion + +# 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 = '' +today = time.strftime("%B %d, %Y", time.localtime()) +year = today.split()[-1] +# Else, today_fmt is used as the format for a strftime call. +# today_fmt = '%B %d, %Y' +# substitute YEAR in the copyright string +copyright = copyright.replace("%Y", year) + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ["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 = ["diffpy.srmise"] + +# Display all warnings for missing links. +nitpicky = True + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = "sphinx_rtd_theme" + +# 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 = { + "navigation_with_keys": "true", +} + +# 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 +# " v documentation". +# html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +# 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 + +# 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'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +# html_extra_path = [] + +# 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 = True + +# Custom sidebar templates, maps document names to template names. +# html_sidebars = {} + +# 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_domain_indices = 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, "Created using Sphinx" is shown in the HTML footer. Default is True. +# html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is 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 = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Output file base name for HTML help builder. +basename = "diffpy.srmise".replace(" ", "").replace(".", "") +htmlhelp_basename = basename + "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': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + ("index", "diffpy.srmise.tex", "diffpy.srmise Documentation", ab_authors, "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 + +# If true, show page references after internal links. +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# latex_appendices = [] + +# If false, no module index is generated. +# 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", "diffpy.srmise", "diffpy.srmise Documentation", ab_authors, 1)] + +# If true, show URL addresses after external links. +# man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ( + "index", + "diffpy.srmise", + "diffpy.srmise Documentation", + ab_authors, + "diffpy.srmise", + "One line description of project.", + "Miscellaneous", + ), +] + +# Documents to append as an appendix to all manuals. +# texinfo_appendices = [] + +# If false, no module index is generated. +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +# texinfo_no_detailmenu = False + + +# Example configuration for intersphinx: refer to the Python standard library. +# intersphinx_mapping = {'http://docs.python.org/': None} diff --git a/doc/source/index.rst b/doc/source/index.rst new file mode 100644 index 0000000..89fa460 --- /dev/null +++ b/doc/source/index.rst @@ -0,0 +1,44 @@ +####### +|title| +####### + +.. |title| replace:: diffpy.srmise documentation + +diffpy.srmise - Peak extraction and peak fitting tool for atomic pair distribution functions.. + +| Software version |release|. +| Last updated |today|. + +======= +Authors +======= + +diffpy.srmise is developed by Billinge Group +and its community contributors. + +For a detailed list of contributors see +https://github.com/diffpy/diffpy.srmise/graphs/contributors. + +============ +Installation +============ + +See the `README `_ +file included with the distribution. + +================= +Table of contents +================= +.. toctree:: + :titlesonly: + + license + release + Package API + +======= +Indices +======= + +* :ref:`genindex` +* :ref:`search` diff --git a/doc/source/license.rst b/doc/source/license.rst new file mode 100644 index 0000000..cfab61c --- /dev/null +++ b/doc/source/license.rst @@ -0,0 +1,39 @@ +:tocdepth: -1 + +.. index:: license + +License +####### + +OPEN SOURCE LICENSE AGREEMENT +============================= +BSD 3-Clause License + +Copyright (c) 2024, The Trustees of Columbia University in +the City of New York. +All Rights Reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/doc/source/release.rst b/doc/source/release.rst new file mode 100644 index 0000000..27cd0cc --- /dev/null +++ b/doc/source/release.rst @@ -0,0 +1,5 @@ +:tocdepth: -1 + +.. index:: release notes + +.. include:: ../../CHANGELOG.rst diff --git a/requirements/README.txt b/requirements/README.txt new file mode 100644 index 0000000..dc34909 --- /dev/null +++ b/requirements/README.txt @@ -0,0 +1,11 @@ +# YOU MAY DELETE THIS FILE AFTER SETTING UP DEPENDENCIES! +# +# This directory is where you should place your project dependencies. +# "pip.txt" should contain all required packages not available on conda. +# All other files should contain only packages available to download from conda. +# build.txt should contain all packages required to build (not run) the project. +# run.txt should contain all packages (including optional packages) required for a user to run the program. +# test.txt should contain all packages required for the testing suite and to ensure all tests pass. +# docs.txt should contain all packages required for building the package documentation page. +# +# YOU MAY DELETE THIS FILE AFTER SETTING UP DEPENDENCIES! diff --git a/requirements/build.txt b/requirements/build.txt new file mode 100644 index 0000000..f72d870 --- /dev/null +++ b/requirements/build.txt @@ -0,0 +1,2 @@ +python +setuptools diff --git a/requirements/docs.txt b/requirements/docs.txt new file mode 100644 index 0000000..ab17b1c --- /dev/null +++ b/requirements/docs.txt @@ -0,0 +1,4 @@ +sphinx +sphinx_rtd_theme +doctr +m2r diff --git a/requirements/pip.txt b/requirements/pip.txt new file mode 100644 index 0000000..e69de29 diff --git a/requirements/run.txt b/requirements/run.txt index 1b57b14..e69de29 100644 --- a/requirements/run.txt +++ b/requirements/run.txt @@ -1,3 +0,0 @@ -numpy -scipy -matplotlib-base diff --git a/requirements/test.txt b/requirements/test.txt index 7666f95..6f9ccf8 100644 --- a/requirements/test.txt +++ b/requirements/test.txt @@ -2,3 +2,4 @@ flake8 pytest codecov coverage +pytest-env From 55420de17074d5d978590ad751bf2d8245274c5c Mon Sep 17 00:00:00 2001 From: stevenhua0320 Date: Wed, 31 Jul 2024 10:02:27 +0800 Subject: [PATCH 2/3] add requirement in run.txt --- requirements/run.txt | 3 +++ 1 file changed, 3 insertions(+) diff --git a/requirements/run.txt b/requirements/run.txt index e69de29..5a34dd1 100644 --- a/requirements/run.txt +++ b/requirements/run.txt @@ -0,0 +1,3 @@ +numpy +scipy +matplotlib-base \ No newline at end of file From 0fa9be2a275933318fe08b242b6820919780d0a3 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 31 Jul 2024 02:02:45 +0000 Subject: [PATCH 3/3] [pre-commit.ci] auto fixes from pre-commit hooks --- requirements/run.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements/run.txt b/requirements/run.txt index 5a34dd1..1b57b14 100644 --- a/requirements/run.txt +++ b/requirements/run.txt @@ -1,3 +1,3 @@ numpy scipy -matplotlib-base \ No newline at end of file +matplotlib-base