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max-width: 99%; +} + +/* -- .bd-article-container holds the "text in the middle" (notebook / md) ------ */ +/* -- width is as high as as 100 "ems" (characters) wide, scales with font size -*/ +.bd-main .bd-content .bd-article-container { + max-width: 100em; +} + + +/* Copied from +https://github.com/bokeh/bokeh/blob/branch-2.4/sphinx/source/bokeh/static/custom.css +*/ + +:root { + /* Logo image height + all the paddings/margins make the navbar height. */ + --navbar-height: calc(30px + 0.3125rem * 2 + 0.5rem * 2); +} + +.bd-search { + position: relative; + padding-bottom: 20px; +} + +@media (min-width: 768px) { + .search-front-page { + width: 50%; + } +} + +/* minimal copy paste from bootstrap docs css to get sidebars working */ + +.bd-toc { + -ms-flex-order: 2; + order: 2; + padding-top: 1.5rem; + padding-bottom: 1.5rem; + /* font-size: 0.875rem; */ + /* add scrolling sidebar */ + height: calc(100vh - 2rem); + overflow-y: auto; +} + +@supports ((position: -webkit-sticky) or (position: sticky)) { + .bd-toc { + position: -webkit-sticky; + position: sticky; + top: 4rem; + height: calc(100vh - 4rem); + overflow-y: auto; + } +} + +.section-nav { + padding-left: 0; + border-left: 1px solid #eee; + border-bottom: none; +} + +.section-nav ul { + padding-left: 1rem; +} + +.toc-entry { + display: block; +} + +.toc-entry a { + display: block; + padding: 0.125rem 1.5rem; + color: #77757a; +} + +.toc-entry a:hover { + color: rgba(0, 0, 0, 0.85); + text-decoration: none; +} + +.bd-sidebar { + -ms-flex-order: 0; + order: 0; + border-bottom: 1px solid rgba(0, 0, 0, 0.1); +} + +@media (min-width: 768px) { + .bd-sidebar { + border-right: 1px solid rgba(0, 0, 0, 0.1); + } + @supports ((position: -webkit-sticky) or (position: sticky)) { + .bd-sidebar { + position: -webkit-sticky; + position: sticky; + top: var(--navbar-height); + z-index: 1000; + height: calc(100vh - var(--navbar-height)); + } + } +} + +@media (min-width: 1200px) { + .bd-sidebar { + -ms-flex: 0 1 480px; + flex: 0 1 480px; + } +} + +.bd-links { + padding-top: 1rem; + padding-bottom: 1rem; + margin-right: -15px; + margin-left: -15px; +} + +@media (min-width: 768px) { + @supports ((position: -webkit-sticky) or (position: sticky)) { + .bd-links { + max-height: calc(100vh - 9rem); + overflow-y: auto; + } + } +} + +@media (min-width: 768px) { + .bd-links { + display: block !important; + } +} + +.bd-sidenav { + display: none; +} + +.bd-toc-link { + display: block; + padding: 0.25rem 1.5rem; + font-weight: 400; + color: rgba(0, 0, 0, 0.65); +} + +.bd-toc-link:hover { + color: rgba(0, 0, 0, 0.85); + text-decoration: none; +} + +.bd-toc-item.active { + margin-bottom: 1rem; +} + +.bd-toc-item.active:not(:first-child) { + margin-top: 1rem; +} + +.bd-toc-item.active > .bd-toc-link { + color: rgba(0, 0, 0, 0.85); +} + +.bd-toc-item.active > .bd-toc-link:hover { + background-color: transparent; +} + +.bd-toc-item.active > .bd-sidenav { + display: block; +} + +.bd-sidebar .nav > li > a { + display: block; + padding: 0.25rem 1.5rem; + font-size: 90%; +} + +.bd-sidebar .nav > li > a:hover { + text-decoration: none; + background-color: transparent; +} + +.bd-sidebar .nav > .active > a, +.bd-sidebar .nav > .active:hover > a { + font-weight: 400; + /* adjusted from original + color: rgba(0, 0, 0, 0.85); + background-color: transparent; */ +} + +.bd-sidebar .nav > li > ul { + list-style: none; + padding: 0.25rem 1.5rem; +} + +.bd-sidebar .nav > li > ul > li > a { + display: block; + padding: 0.25rem 1.5rem; + font-size: 90%; +} + +.bd-sidebar .nav > li > ul > .active > a, +.bd-sidebar .nav > li > ul > .active:hover > a { + font-weight: 400; +} + +dt:target { + background-color: initial; +} + +/* Offsetting anchored elements within the main content to adjust for fixed header + https://github.com/pandas-dev/pandas-sphinx-theme/issues/6 */ +main *:target::before { + display: block; + content: ''; + height: var(--navbar-height); + margin-top: calc(-1 * var(--navbar-height)); +} + +body { + /* Add padding to body to avoid overlap with navbar. */ + padding-top: var(--navbar-height); + width: 100%; +} + +/* adjust toc font sizes to improve overview */ +.toc-h2 { + font-size: 0.85rem; +} + +.toc-h3 { + font-size: 0.75rem; +} + +.toc-h4 { + font-size: 0.65rem; +} + +.toc-entry > .nav-link.active { + font-weight: 400; + color: #314254; + background-color: transparent; + border-left: 2px solid #A3B9C0; +} + +.nav-link:hover { + border-style: none; +} + +/* Collapsing of the TOC sidebar while scrolling */ + +/* Nav: hide second level (shown on .active) */ +.bd-toc .nav .nav { + display: none; +} + +.bd-toc .nav > .active > ul { + display: block; +} + +/* Main index page overview cards */ + +.sd-card-img-top { + width: 33% !important; + display: block; + margin-left: auto; + margin-right: auto; + margin-top: 10px; +} + +/* Hide ToC on mobile */ +@media (max-width: 1200px) { + .bd-sidebar-secondary { + display: none; + } + + .bd-sidebar-secondary.active .bd-toc.active { + display: block; + } + + + .article-header-buttons .sidebar-toggle { + display: block; + } + + label.sidebar-toggle.primary-toggle { + display: none; + } + label.sidebar-toggle.secondary-toggle { + display: inline-block; /* or 'block', depending on desired layout */ + } + +} \ No newline at end of file diff --git a/docs/_templates/autosummary/accessor.rst b/docs/_templates/autosummary/accessor.rst new file mode 100644 index 000000000..4ba745cd6 --- /dev/null +++ b/docs/_templates/autosummary/accessor.rst @@ -0,0 +1,6 @@ +{{ fullname }} +{{ underline }} + +.. currentmodule:: {{ module.split('.')[0] }} + +.. autoaccessor:: {{ (module.split('.')[1:] + [objname]) | join('.') }} diff --git a/docs/_templates/autosummary/accessor_attribute.rst b/docs/_templates/autosummary/accessor_attribute.rst new file mode 100644 index 000000000..b5ad65d6a --- /dev/null +++ b/docs/_templates/autosummary/accessor_attribute.rst @@ -0,0 +1,6 @@ +{{ fullname }} +{{ underline }} + +.. currentmodule:: {{ module.split('.')[0] }} + +.. autoaccessorattribute:: {{ (module.split('.')[1:] + [objname]) | join('.') }} diff --git a/docs/_templates/autosummary/accessor_callable.rst b/docs/_templates/autosummary/accessor_callable.rst new file mode 100644 index 000000000..7a3301814 --- /dev/null +++ b/docs/_templates/autosummary/accessor_callable.rst @@ -0,0 +1,6 @@ +{{ fullname }} +{{ underline }} + +.. currentmodule:: {{ module.split('.')[0] }} + +.. autoaccessorcallable:: {{ (module.split('.')[1:] + [objname]) | join('.') }}.__call__ diff --git a/docs/_templates/autosummary/accessor_method.rst b/docs/_templates/autosummary/accessor_method.rst new file mode 100644 index 000000000..aefbba6ef --- /dev/null +++ b/docs/_templates/autosummary/accessor_method.rst @@ -0,0 +1,6 @@ +{{ fullname }} +{{ underline }} + +.. currentmodule:: {{ module.split('.')[0] }} + +.. autoaccessormethod:: {{ (module.split('.')[1:] + [objname]) | join('.') }} diff --git a/docs/api.rst b/docs/api.rst new file mode 100644 index 000000000..33b241cbe --- /dev/null +++ b/docs/api.rst @@ -0,0 +1,31 @@ +.. currentmodule:: swiftest + +.. _api: + +######################### +Swiftest API reference +######################### + +This section of the documentation provides a detailed reference for the Production classes in the Swiftest project. + +Simulation +========== + +The Simulation class is the main class for the Swiftest project. + +Creating a Simulation +--------------------- + +.. autosummary:: + :toctree: generated/ + + Simulation + +Running a Simulation +------- + +.. autosummary:: + :toctree: generated/ + + Simulation.run + diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 000000000..466628445 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,182 @@ +import datetime +import os +import sys +import inspect +from contextlib import suppress + +import sphinx_autosummary_accessors +from sphinx.application import Sphinx +from sphinx.util import logging +import os + +import swiftest + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information +project = 'Swiftest' +copyright = f'{datetime.datetime.now().year}, David A. Minton' +author = 'David A. Minton' +with open(os.path.join(os.path.dirname(__file__), os.pardir, "version.txt"), 'r') as file: + version = file.read().strip() +release = version + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.autosummary", + "sphinx.ext.intersphinx", + "sphinx.ext.mathjax", + "sphinx.ext.napoleon", + "sphinx.ext.viewcode", + "IPython.sphinxext.ipython_directive", + "IPython.sphinxext.ipython_console_highlighting", + "nbsphinx", + "sphinx_autosummary_accessors", + "sphinx.ext.linkcode", + "sphinxext.opengraph", + "sphinx_copybutton", + "sphinx_design", + "sphinx_inline_tabs", + "sphinxfortran.fortran_domain", + "sphinxfortran.fortran_autodoc" +] + + +templates_path = ['_templates'] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store','**.ipynb_checkpoints'] + + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = "sphinx" + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + + +# Use Autodoc and Napolean for extracting docstrings +autosummary_generate = True +autodoc_typehints = "none" +napoleon_google_docstring = False +napoleon_numpy_docstring = True +napoleon_use_param = False +napoleon_use_rtype = False + +intersphinx_mapping = { + "python": ("https://docs.python.org/3/", None), + "numpy": ("https://numpy.org/doc/stable", None), + "xarray" : ("https://docs.xarray.dev/en/stable/", None), +} + +templates_path = ["_templates"] + +html_theme = 'sphinx_book_theme' +html_title ="" +html_static_path = ["_static"] + +html_context = { + "github_user": "profminton", + "github_repo": "swiftest", + "github_version": "main", + "doc_path": "docs", +} + +# 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 = dict( + # analytics_id='' this is configured in rtfd.io + # canonical_url="", + repository_url="https://github.com/profminton/swiftest", + repository_branch="main", + navigation_with_keys=False, # pydata/pydata-sphinx-theme#1492 + path_to_docs="docs", + use_edit_page_button=True, + use_repository_button=True, + use_issues_button=True, + home_page_in_toc=False, + extra_footer="""Theme by the Executable Book Project

""", + icon_links=[], # workaround for pydata/pydata-sphinx-theme#1220 + announcement="🍾 Swiftest is currently under development 🎉", +) + + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +html_logo = "_static/logos/swiftest_social_preview.svg" + +# 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 = "_static/logos/swiftest_logo.svg" + +# 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_css_files = ["style.css"] + +# configuration for sphinxext.opengraph +ogp_site_url = "https://swiftest.readthedocs.io/en/latest/" +ogp_image = "https://swiftest.readthedocs.io/en/stable/_static/logos/swiftest_social_preview.png" +ogp_custom_meta_tags = [ + '', +] + + +# based on numpy doc/source/conf.py +def linkcode_resolve(domain, info): + """ + Determine the URL corresponding to Python object + """ + if domain != "py": + return None + + modname = info["module"] + fullname = info["fullname"] + + submod = sys.modules.get(modname) + if submod is None: + return None + + obj = submod + for part in fullname.split("."): + try: + obj = getattr(obj, part) + except AttributeError: + return None + + try: + fn = inspect.getsourcefile(inspect.unwrap(obj)) + except TypeError: + fn = None + if not fn: + return None + + try: + source, lineno = inspect.getsourcelines(obj) + except OSError: + lineno = None + + if lineno: + linespec = f"#L{lineno}-L{lineno + len(source) - 1}" + else: + linespec = "" + + fn = os.path.relpath(fn, start=os.path.dirname(swiftest.__file__)) + + + +def html_page_context(app, pagename, templatename, context, doctree): + # Disable edit button for docstring generated pages + if "generated" in pagename: + context["theme_use_edit_page_button"] = False + +fortran_src = [os.path.join(os.pardir, "fortran","*/*.f90")] +fortran_ext = ["f90"] +fortran_encoding = "utf-8" \ No newline at end of file diff --git a/docs/contributing.rst b/docs/contributing.rst new file mode 100644 index 000000000..906222d1f --- /dev/null +++ b/docs/contributing.rst @@ -0,0 +1,14 @@ +.. _contributing: + +*************************** +Contributing to Swiftest +*************************** + +.. note:: + + This document is a work in progress. It is not yet complete. + +Overview +======== + +TBD diff --git a/docs/getting-started-guide/index.rst b/docs/getting-started-guide/index.rst new file mode 100644 index 000000000..d6b7e1ebd --- /dev/null +++ b/docs/getting-started-guide/index.rst @@ -0,0 +1,11 @@ +################ +Getting Started +################ + +TBD + +.. toctree:: + :maxdepth: 2 + :hidden: + + diff --git a/docs/index.md b/docs/index.md deleted file mode 100644 index 000ea3455..000000000 --- a/docs/index.md +++ /dev/null @@ -1,17 +0,0 @@ -# Welcome to MkDocs - -For full documentation visit [mkdocs.org](https://www.mkdocs.org). - -## Commands - -* `mkdocs new [dir-name]` - Create a new project. -* `mkdocs serve` - Start the live-reloading docs server. -* `mkdocs build` - Build the documentation site. -* `mkdocs -h` - Print help message and exit. - -## Project layout - - mkdocs.yml # The configuration file. - docs/ - index.md # The documentation homepage. - ... # Other markdown pages, images and other files. diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 000000000..a84d13b53 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,74 @@ +.. module:: swiftest + +Swiftest +==================== +Swiftest is a software packaged designed to model the dynamical evolution of gravitational systems. Swiftest is an upgrade over the `Swifter `_ software package. + +**Useful links**: +`Home `__ | +`Code Repository `__ | +`Issues `__ | +`Discussions `__ | +`Releases `__ | + + +.. grid:: 1 1 2 2 + :gutter: 2 + + .. grid-item-card:: Getting started + :img-top: _static/index_getting_started.svg + :link: getting-started-guide/index + :link-type: doc + + New to *swiftest*? Check out the getting started guides. They contain an + introduction to *Swiftest's* main concepts and links to additional tutorials. + + .. grid-item-card:: User guide + :img-top: _static/index_user_guide.svg + :link: user-guide/index + :link-type: doc + + The user guide provides in-depth information on the + key concepts of Swiftest with useful background information and explanation. + + .. grid-item-card:: API reference + :img-top: _static/index_api_reference.svg + :link: api + :link-type: doc + + The reference guide contains a detailed description of the Swiftest API. + The reference describes how the methods work and which parameters can + be used. It assumes that you have an understanding of the key concepts. + + .. grid-item-card:: Developer guide + :img-top: _static/index_contribute.svg + :link: contributing + :link-type: doc + + Saw a typo in the documentation? Want to improve existing functionalities? + The contributing guidelines will guide you through the process of improving + Swiftest. + +.. toctree:: + :maxdepth: 2 + :hidden: + :caption: For users + + Getting Started + User Guide + API Reference + +.. toctree:: + :maxdepth: 2 + :hidden: + :caption: For developers/contributors + + Contributing Guide + GitHub repository + +.. toctree:: + :maxdepth: 1 + :hidden: + :caption: Community + + GitHub discussions diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 000000000..ef0ad58ab --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,12 @@ +sphinx +sphinx-autosummary-accessors +sphinx-book-theme >= 0.3.0 +sphinx-copybutton +sphinx-design +sphinx-inline-tabs +sphinxext-rediraffe +sphinxext-opengraph +sphinx-fortran +nbsphinx +ipython +swiftest \ No newline at end of file diff --git a/docs/user-guide/index.rst b/docs/user-guide/index.rst new file mode 100644 index 000000000..b63a21e90 --- /dev/null +++ b/docs/user-guide/index.rst @@ -0,0 +1,10 @@ +########### +User Guide +########### + +TBD + + +.. toctree:: + :maxdepth: 2 + :hidden: diff --git a/mkdocs.yml b/mkdocs.yml deleted file mode 100644 index d15a0315d..000000000 --- a/mkdocs.yml +++ /dev/null @@ -1,6 +0,0 @@ -site_name: MkLorum -site_url: https://example.com/ -nav: - - Home: index.md - - About: about.md -theme: readthedocs \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index db94e4c3e..4460d80d3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "swiftest" -version = "2023.11.0" +version = "2023.12.0" authors=[ {name = 'David A. Minton', email='daminton@purdue.edu'}, {name = 'Carlisle Wishard'}, @@ -37,8 +37,7 @@ dependencies = [ 'astropy>=5.2', 'astroquery>=0.4.6', 'tqdm>=4.66', - 'cython>=3.0.0', - 'mkdocs>=1.5.3' + 'cython>=3.0.0' ] [project.urls] @@ -48,8 +47,18 @@ Repository = 'https://github.itap.purdue.edu/MintonGroup/swiftest' requires = [ "scikit-build-core", "cython>=3.0.0", + "cmake", "pyproject_metadata", "pytest", + "sphinx", + "sphinx-autosummary-accessors", + "sphinx-book-theme >= 0.3.0", + "sphinx-copybutton", + "sphinx-design", + "sphinx-inline-tabs", + "sphinxext-rediraffe", + "sphinxext-opengraph", + "nbsphinx" ] build-backend = "scikit_build_core.build" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 79d85b58b..000000000 --- a/requirements.txt +++ /dev/null @@ -1,14 +0,0 @@ -python>=3.8 -numpy>=1.24.3 -scipy>=1.10.1 -xarray>=2022.11.0 -dask>=2022.1 -bottleneck>=1.3.5 -distributed>=2022.1 -h5netcdf>=1.0.2 -netcdf4>=1.6.2 -matplotlib>=3.7.1 -astropy>=5.1 -astroquery>=0.4.6 -tqdm>=4.65.0 -cython>=3.0.0 \ No newline at end of file diff --git a/src/globals/globals_module.f90 b/src/globals/globals_module.f90 index 7485c19ec..8bf98c6cd 100644 --- a/src/globals/globals_module.f90 +++ b/src/globals/globals_module.f90 @@ -48,7 +48,7 @@ module globals integer(I4B), parameter :: UPPERCASE_OFFSET = iachar('A') - iachar('a') !! ASCII character set parameter for lower to upper !! conversion - offset between upper and lower - character(*), parameter :: VERSION = "2023.11.0" !! Swiftest version + character(*), parameter :: VERSION = "2023.12.0" !! Swiftest version !> Symbolic name for integrator types character(*), parameter :: UNKNOWN_INTEGRATOR = "UKNOWN INTEGRATOR" diff --git a/version.txt b/version.txt index 82ba9e59f..aa240b72d 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -2023.11.0 \ No newline at end of file +2023.12.0 \ No newline at end of file