From 60b34c3bf7fe80f579e56a792327f29a29a5c660 Mon Sep 17 00:00:00 2001 From: Martin Larralde Date: Wed, 28 Aug 2024 00:18:28 +0200 Subject: [PATCH] Update documentation to use PyData theme [ci skip] --- docs/_static/css/main.css | 27 ++ docs/_static/js/custom-icon.js | 44 ++ docs/_static/json/switcher.json | 22 + docs/api/alignment.rst | 5 - docs/api/index.rst | 60 +-- docs/api/sequence.rst | 4 + docs/changes.md | 1 - docs/conf.py | 76 ++-- docs/contributing.md | 1 - docs/guide/changes.md | 1 + docs/guide/contributing.md | 1 + docs/guide/copyright.rst | 686 ++++++++++++++++++++++++++++++++ docs/guide/index.rst | 18 + docs/{ => guide}/install.rst | 0 docs/index.rst | 142 ++++++- docs/requirements.txt | 5 +- 16 files changed, 1017 insertions(+), 76 deletions(-) create mode 100644 docs/_static/css/main.css create mode 100644 docs/_static/js/custom-icon.js create mode 100644 docs/_static/json/switcher.json delete mode 120000 docs/changes.md delete mode 120000 docs/contributing.md create mode 120000 docs/guide/changes.md create mode 120000 docs/guide/contributing.md create mode 100644 docs/guide/copyright.rst create mode 100644 docs/guide/index.rst rename docs/{ => guide}/install.rst (100%) diff --git a/docs/_static/css/main.css b/docs/_static/css/main.css new file mode 100644 index 0000000..d9d954b --- /dev/null +++ b/docs/_static/css/main.css @@ -0,0 +1,27 @@ +p { + text-align: justify; +} + +/* a.reference strong { + font-weight: bold; + font-size: 90%; + color: #c7254e; + box-sizing: border-box; + font-family: Menlo,Monaco,Consolas,"Courier New",monospace; +} */ + +.field-list a.reference { + font-weight: bold; + font-size: 90%; + color: #c7254e; + box-sizing: border-box; + font-family: Menlo,Monaco,Consolas,"Courier New",monospace; +} + +.class dd { + margin-left: 2% +} + +.exception dd { + margin-left: 2% +} diff --git a/docs/_static/js/custom-icon.js b/docs/_static/js/custom-icon.js new file mode 100644 index 0000000..035be99 --- /dev/null +++ b/docs/_static/js/custom-icon.js @@ -0,0 +1,44 @@ +/******************************************************************************* + * Set a custom icon for pypi as it's not available in the fa built-in brands + */ +FontAwesome.library.add( + (faListOldStyle = { + prefix: "fa-custom", + iconName: "pypi", + icon: [ + 17.313, // viewBox width + 19.807, // viewBox height + [], // ligature + "e001", // unicode codepoint - private use area + "m10.383 0.2-3.239 1.1769 3.1883 1.1614 3.239-1.1798zm-3.4152 1.2411-3.2362 1.1769 3.1855 1.1614 3.2369-1.1769zm6.7177 0.00281-3.2947 1.2009v3.8254l3.2947-1.1988zm-3.4145 1.2439-3.2926 1.1981v3.8254l0.17548-0.064132 3.1171-1.1347zm-6.6564 0.018325v3.8247l3.244 1.1805v-3.8254zm10.191 0.20931v2.3137l3.1777-1.1558zm3.2947 1.2425-3.2947 1.1988v3.8254l3.2947-1.1988zm-8.7058 0.45739c0.00929-1.931e-4 0.018327-2.977e-4 0.027485 0 0.25633 0.00851 0.4263 0.20713 0.42638 0.49826 1.953e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36226 0.13215-0.65608-0.073306-0.65613-0.4588-6.28e-5 -0.38556 0.2938-0.80504 0.65613-0.93662 0.068422-0.024919 0.13655-0.038114 0.20156-0.039466zm5.2913 0.78369-3.2947 1.1988v3.8247l3.2947-1.1981zm-10.132 1.239-3.2362 1.1769 3.1883 1.1614 3.2362-1.1769zm6.7177 0.00213-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2439-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.016195v3.8275l3.244 1.1805v-3.8254zm16.9 0.21143-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2432-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.019027v3.8247l3.244 1.1805v-3.8254zm13.485 1.4497-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm2.4018 0.38127c0.0093-1.83e-4 0.01833-3.16e-4 0.02749 0 0.25633 0.0085 0.4263 0.20713 0.42638 0.49826 1.97e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36188 0.1316-0.65525-0.07375-0.65542-0.4588-1.95e-4 -0.38532 0.29328-0.80469 0.65542-0.93662 0.06842-0.02494 0.13655-0.03819 0.20156-0.03947zm-5.8142 0.86403-3.244 1.1805v1.4201l3.244 1.1805z", // svg path (https://simpleicons.org/icons/pypi.svg) + ], + }), +); + +FontAwesome.library.add( + (faListOldStyle = { + prefix: "fa-custom", + iconName: "sword", + icon: [ + 256, // viewBox width + 256, // viewBox height + [], // ligature + "e002", // unicode codepoint - private use area + "M221.65723,34.34326A8.00246,8.00246,0,0,0,216,32h-.02539l-63.79883.20117A8.00073,8.00073,0,0,0,146.0332,35.106L75.637,120.32275,67.31348,111.999A16.02162,16.02162,0,0,0,44.68555,112L32.001,124.68555A15.99888,15.99888,0,0,0,32,147.31348l20.88672,20.88769L22.94531,198.14258a16.01777,16.01777,0,0,0,.001,22.62695l12.28418,12.28418a16.00007,16.00007,0,0,0,22.62793,0L87.79883,203.1123,108.68652,224.001A16.02251,16.02251,0,0,0,131.31445,224L143.999,211.31445A15.99888,15.99888,0,0,0,144,188.68652l-8.32324-8.32324,85.21679-70.39648a8.00125,8.00125,0,0,0,2.90528-6.14258L224,40.02539A8.001,8.001,0,0,0,221.65723,34.34326Zm-13.84668,65.67822-83.49829,68.97706L111.314,156l54.34327-54.34277a8.00053,8.00053,0,0,0-11.31446-11.31446L100,144.686,87.00195,131.6875,155.97852,48.189l51.99609-.16357Z", // svg path (https://simpleicons.org/icons/pypi.svg) + ], + }), +); + +FontAwesome.library.add( + (faListOldStyle = { + prefix: "fa-custom", + iconName: "knife", + icon: [ + 256, // viewBox width + 256, // viewBox height + [], // ligature + "e003", // unicode codepoint - private use area + "M231.79883,32.2002a28.05536,28.05536,0,0,0-39.667.06933L18.27441,210.41211a8,8,0,0,0,3.92676,13.38281,155.06019,155.06019,0,0,0,34.957,4.00293c33.4209-.001,66.877-10.86914,98.32813-32.1748,31.74512-21.50391,50.14551-45.79981,50.91406-46.82325a8.00114,8.00114,0,0,0-.74316-10.457L186.919,119.60547l44.97753-47.90332A28.03445,28.03445,0,0,0,231.79883,32.2002ZM189.207,144.52148a225.51045,225.51045,0,0,1-43.10351,38.13184c-34.46973,23.23145-69.999,32.665-105.83887,28.13477l106.29492-108.915,23.30176,23.30175q.208.22852.43847.44434l.082.07617Z", // svg path (https://simpleicons.org/icons/pypi.svg) + ], + }), +); diff --git a/docs/_static/json/switcher.json b/docs/_static/json/switcher.json new file mode 100644 index 0000000..0c009d1 --- /dev/null +++ b/docs/_static/json/switcher.json @@ -0,0 +1,22 @@ +[ + { + "name": "v0.4 (latest)", + "version": "0.4.0", + "url": "https://pyfamsa.readthedocs.io/en/v0.3.3/" + }, + { + "name": "v0.3 (latest)", + "version": "0.3.2", + "url": "https://pyfamsa.readthedocs.io/en/v0.3.2/" + }, + { + "name": "v0.2", + "version": "0.2.0", + "url": "https://pyfamsa.readthedocs.io/en/v0.2.0/" + }, + { + "name": "v0.1", + "version": "0.1.1", + "url": "https://pyfamsa.readthedocs.io/en/v0.1.1/" + } +] diff --git a/docs/api/alignment.rst b/docs/api/alignment.rst index 220e03b..916f79e 100644 --- a/docs/api/alignment.rst +++ b/docs/api/alignment.rst @@ -3,11 +3,6 @@ Alignment .. currentmodule:: pyfamsa - .. autoclass:: pyfamsa.Alignment :inherited-members: :members: - -.. autoclass:: pyfamsa.GappedSequence - :inherited-members: - :members: diff --git a/docs/api/index.rst b/docs/api/index.rst index 554fb92..eb3308b 100644 --- a/docs/api/index.rst +++ b/docs/api/index.rst @@ -3,48 +3,62 @@ API Reference .. currentmodule:: pyfamsa +Aligner +------- + +.. autosummary:: + :nosignatures: + + Aligner + .. toctree:: + :caption: Aligner :hidden: aligner - sequence - alignment - guide_tree -.. only:: html +Sequence +-------- - Aligner - ------- +.. autosummary:: + :nosignatures: - .. autosummary:: - :nosignatures: + Sequence + GappedSequence - pyfamsa.Aligner +.. toctree:: + :caption: Sequence + :hidden: - Sequence - -------- + sequence - .. autosummary:: - :nosignatures: - pyfamsa.Sequence +Alignment +--------- +.. autosummary:: + :nosignatures: Alignment - --------- - .. autosummary:: - :nosignatures: +.. toctree:: + :caption: Alignment + :hidden: - pyfamsa.Alignment - pyfamsa.GappedSequence + alignment +GuideTree +--------- + +.. autosummary:: + :nosignatures: + GuideTree - --------- - .. autosummary:: - :nosignatures: +.. toctree:: + :caption: GuideTree + :hidden: - pyfamsa.GuideTree + guide_tree \ No newline at end of file diff --git a/docs/api/sequence.rst b/docs/api/sequence.rst index 5d1738c..0420708 100644 --- a/docs/api/sequence.rst +++ b/docs/api/sequence.rst @@ -6,3 +6,7 @@ Sequence .. autoclass:: pyfamsa.Sequence :inherited-members: :members: + +.. autoclass:: pyfamsa.GappedSequence + :inherited-members: + :members: \ No newline at end of file diff --git a/docs/changes.md b/docs/changes.md deleted file mode 120000 index 04c99a5..0000000 --- a/docs/changes.md +++ /dev/null @@ -1 +0,0 @@ -../CHANGELOG.md \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py index 636bcef..e8f0996 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -12,7 +12,6 @@ import re import semantic_version import shutil -import sphinx_bootstrap_theme import sys # -- Path setup -------------------------------------------------------------- @@ -69,7 +68,7 @@ "sphinx.ext.mathjax", "sphinx.ext.todo", "sphinx.ext.extlinks", - "sphinx_bootstrap_theme", + "sphinx_design", "recommonmark", "nbsphinx", ] @@ -103,54 +102,54 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'bootstrap' +html_theme = 'pydata_sphinx_theme' # 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/js', '_static/css', '_static/json'] +html_js_files = ["custom-icon.js"] +html_css_files = ["custom.css"] # 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 = { - # Bootswatch (http://bootswatch.com/) theme. - "bootswatch_theme": "flatly", - # Choose Bootstrap version. - "bootstrap_version": "3", - # Tab name for entire site. (Default: "Site") - "navbar_site_name": "Documentation", - # HTML navbar class (Default: "navbar") to attach to
element. - # For black navbar, do "navbar navbar-inverse" - "navbar_class": "navbar", - # Render the next and previous page links in navbar. (Default: true) - "navbar_sidebarrel": True, - # Render the current pages TOC in the navbar. (Default: true) - "navbar_pagenav": False, - # A list of tuples containing pages or urls to link to. - "navbar_links": [ - ("GitHub", cfgparser.get("metadata", "url").strip(), True) - ] + [ - (k, v, True) - for k, v in project_urls.items() - if k in {"Zenodo", "PyPI"} + "external_links": [], + "show_toc_level": 2, + "use_edit_page_button": True, + "icon_links": [ + { + "name": "GitHub", + "url": "https://github.com/althonos/pyfamsa", + "icon": "fa-brands fa-github", + }, + { + "name": "PyPI", + "url": "https://pypi.org/project/pyfamsa", + "icon": "fa-custom fa-pypi", + }, ], - "admonition_use_panel": True, + "logo": { + "text": "PyFAMSA", + # "image_light": "_images/logo.png", + # "image_dark": "_images/logo.png", + }, + "navbar_start": ["navbar-logo", "version-switcher"], + "navbar_align": "left", + "footer_start": ["copyright"], + "footer_center": ["sphinx-version"], + "switcher": { + "json_url": "https://pyfamsa.readthedocs.io/en/latest/_static/switcher.json", + "version_match": version, + } } -# Custom sidebar templates, must be a dictionary that maps document names -# to template names. -# -# The default sidebars (for documents that don't match any pattern) are -# defined by theme itself. Builtin themes are using these templates by -# default: ``['localtoc.html', 'relations.html', 'sourcelink.html', -# 'searchbox.html']``. -# -html_sidebars = { - "*": ["localtoc.html"], - "api/*": ["localtoc.html"], - "examples/*": ["localtoc.html"], +html_context = { + "github_user": "althonos", + "github_repo": "pyfamsa", + "github_version": "main", + "doc_path": "docs", } # -- Options for HTMLHelp output --------------------------------------------- @@ -185,7 +184,6 @@ intersphinx_mapping = { "python": ("https://docs.python.org/3/", None), - "biopython": ("https://biopython.org/docs/latest/api/", None), "scoring_matrices": ("https://scoring-matrices.readthedocs.io/en/stable", None), } diff --git a/docs/contributing.md b/docs/contributing.md deleted file mode 120000 index 44fcc63..0000000 --- a/docs/contributing.md +++ /dev/null @@ -1 +0,0 @@ -../CONTRIBUTING.md \ No newline at end of file diff --git a/docs/guide/changes.md b/docs/guide/changes.md new file mode 120000 index 0000000..699cc9e --- /dev/null +++ b/docs/guide/changes.md @@ -0,0 +1 @@ +../../CHANGELOG.md \ No newline at end of file diff --git a/docs/guide/contributing.md b/docs/guide/contributing.md new file mode 120000 index 0000000..f939e75 --- /dev/null +++ b/docs/guide/contributing.md @@ -0,0 +1 @@ +../../CONTRIBUTING.md \ No newline at end of file diff --git a/docs/guide/copyright.rst b/docs/guide/copyright.rst new file mode 100644 index 0000000..b6f7ac0 --- /dev/null +++ b/docs/guide/copyright.rst @@ -0,0 +1,686 @@ +Copyright Notice +================ + +PyFAMSA +------- + +The PyFAMSA library is developed under the GNU General Public License 3.0 +or later:: + + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for + software and other kinds of works. + + The licenses for most software and other practical works are designed + to take away your freedom to share and change the works. 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If your program is a subroutine library, you + may consider it more useful to permit linking proprietary applications with + the library. If this is what you want to do, use the GNU Lesser General + Public License instead of this License. But first, please read + . + + + diff --git a/docs/guide/index.rst b/docs/guide/index.rst new file mode 100644 index 0000000..d623ac2 --- /dev/null +++ b/docs/guide/index.rst @@ -0,0 +1,18 @@ +User Guide +========== + +This section contains guides and documents about PyFAMSA usage. + +.. toctree:: + :maxdepth: 1 + :caption: Getting Started + + Installation + +.. toctree:: + :maxdepth: 1 + :caption: Resources + + Contribution Guide + Changelog + Copyright Notice \ No newline at end of file diff --git a/docs/install.rst b/docs/guide/install.rst similarity index 100% rename from docs/install.rst rename to docs/guide/install.rst diff --git a/docs/index.rst b/docs/index.rst index 3cee780..405ce6b 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -70,6 +70,38 @@ Pythonic interface to align protein sequences using different parameters and access results directly. It interacts with the FAMSA library interface, which has the following advantages: +.. grid:: 1 2 3 3 + :gutter: 1 + + .. grid-item-card:: :fas:`battery-full` Batteries-included + + Just add ``pyfamsa`` as a ``pip`` or ``conda`` dependency, no need + for the FAMSA binary or any external dependency. + + .. grid-item-card:: :fas:`screwdriver-wrench` Flexible + + Create input `~pyfamsa.Sequence` objects programmatically through + the :doc:`Python API `. + + .. grid-item-card:: :fas:`gears` Practical + + Retrieve alignments as dedicated `~pyfamsa.Alignment` objects + using the compressed gap representation from FAMSA. + + .. grid-item-card:: :fas:`server` Parallel + + Run computations in parallel using the FAMSA threading model + built on POSIX threads. + + .. grid-item-card:: :fas:`check` Consistent + + Get the same results as the latest FAMSA version (``2.2.0``). + + .. grid-item-card:: :fas:`toolbox` Feature-complete + + Access all the features of the original CLI through the :doc:`Python API `. + + - **single dependency**: ``pyfamsa`` is distributed as a Python package, so you can add it as a dependency to your project, and stop worrying about the FAMSA binary being present on the end-user machine. @@ -86,7 +118,7 @@ Setup Run ``pip install pyfamsa`` in a shell to download the latest release and all its dependencies from PyPi, or have a look at the -:doc:`Installation page ` to find other ways to install ``pyfamsa``. +:doc:`Installation page ` to find other ways to install ``pyfamsa``. Library @@ -95,10 +127,112 @@ Library .. toctree:: :maxdepth: 2 - Installation - Contributing + User Guide API Reference - Changelog + + +Related Projects +---------------- + +The following Python libraries may be of interest for bioinformaticians. + +.. grid:: 1 3 5 5 + :gutter: 1 + + .. grid-item-card:: :fas:`diamond` PyHMMER + :link: https://pyhmmer.readthedocs.io + + Profile Hidden Markov Models (with HMMER). + + .. grid-item-card:: :fas:`fire` Pyrodigal + :link: https://pyrodigal.readthedocs.io + + Prokaryotic Gene Finding (with Prodigal). + + .. grid-item-card:: :fas:`virus-covid` Pyrodigal-gv + :link: https://github.com/althonos/pyrodigal-gv + + Pyrodigal for Giant Viruses. + + .. grid-item-card:: :fas:`align-center` PyFAMSA + :link: https://pyfamsa.readthedocs.io + + Multiple Sequence Alignment (with FAMSA). + + .. grid-item-card:: :fas:`scissors` PytrimAl + :link: https://pytrimal.readthedocs.io + + Alignment Trimming (with trimAl). + + .. grid-item-card:: :fas:`music` LightMotif + :link: https://lightmotif.readthedocs.io + + Platform-accelerated motif scoring. + + .. grid-item-card:: :fas:`knife;fa-custom` Diced + :link: https://diced.readthedocs.io + + CRISPR Detection (with MinCED). + + .. grid-item-card:: :fas:`table-cells` Scoring Matrices + :link: https://scoring-matrices.readthedocs.io + + Scoring matrices for Cython. + + .. grid-item-card:: :fas:`chain` Pyskani + :link: https://pyskani.readthedocs.io + + Average Nucleotide Identity (with skani). + + .. grid-item-card:: :fas:`forward-fast` PyFastANI + :link: https://pyfastani.readthedocs.io + + Average Nucleotide Identity (with FastANI). + + .. grid-item-card:: :fas:`magnifying-glass` PyJess + :link: https://pyjess.readthedocs.io + + Geometric Template Matching (with Jess). + + .. grid-item-card:: :fas:`repeat` PyTantan + :link: https://pytantan.readthedocs.io + + Tandem Repeat Masking (with Tantan). + + .. grid-item-card:: :fas:`gem` PyOpal + :link: https://pyopal.readthedocs.io + + Query/Database Aligner (with Opal). + + .. grid-item-card:: :fas:`sword;fa-custom` PySWRD + :link: https://pyswrd.readthedocs.io + + Database Heuristic Filtering (with SWORD). + + .. grid-item-card:: :fas:`rocket` Mini3di + :link: https://github.com/althonos/mini3di + + Protein structure to 3di in pure Python. + + .. grid-item-card:: :fas:`calculator` ``peptides.py`` + :link: https://peptides.readthedocs.io + + Peptide descriptors for Python. + + .. grid-item-card:: :fas:`diagram-project` Pronto + :link: https://pronto.readthedocs.io + + Open Biomedical Ontologies for Python. + + .. grid-item-card:: :fas:`box` NAFcodec + :link: https://nafcodec.readthedocs.io + + Nucleotide Archival Format for Python. + + .. grid-item-card:: :fas:`bank` ``gb-io.py`` + :link: https://gb-io.readthedocs.io + + Fast GenBank parser for Python (with ``gb-io``). License diff --git a/docs/requirements.txt b/docs/requirements.txt index 48f3003..71c4daf 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -12,6 +12,5 @@ ipython ~=7.19 pygments ~=2.4 nbsphinx ~=0.8 ipykernel ~=6.0 - -# sphinx-bootstrap-theme ~=0.7 with patched admonition -https://github.com/althonos/sphinx-bootstrap-theme/archive/master.zip +sphinx-design +pydata-sphinx-theme