diff --git a/docs/source/api.rst b/docs/source/api.rst index 50b20c8f05..ceb3b3f5d7 100644 --- a/docs/source/api.rst +++ b/docs/source/api.rst @@ -11,22 +11,16 @@ API Reference .. toctree:: :maxdepth: 2 - - api/distributions - api/bounds - api/inference - api/glm - api/gp - api/plots - api/stats + api/backends - api/math - api/data + api/distributions + api/gaussian_process api/model - api/model_graph - api/variables - api/shape_utils api/ode + api/samplers + api/smc + api/step_methods + api/vi Indices and tables =================== diff --git a/docs/source/conf.py b/docs/source/conf.py index 9c9bd828e6..724ea63dca 100755 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -4,7 +4,7 @@ """ #!/usr/bin/env python3 # -# pymc3 documentation build configuration file, created by +# pymc documentation build configuration file, created by # sphinx-quickstart on Sat Dec 26 14:40:23 2015. # # This file is execfile()d with the current directory set to its @@ -78,7 +78,7 @@ master_doc = "index" # General information about the project. -project = "PyMC3" +project = "PyMC" copyright = "2021, The PyMC Development Team" author = "PyMC contributors" @@ -167,7 +167,7 @@ "icon_links": [ { "name": "GitHub", - "url": "https://github.com/pymc-devs/pymc3", + "url": "https://github.com/pymc-devs/pymc", "icon": "fab fa-github-square", }, { @@ -191,7 +191,7 @@ } html_context = { "github_user": "pymc-devs", - "github_repo": "pymc3", + "github_repo": "pymc", "github_version": "main", "doc_path": "docs/source/", } @@ -214,12 +214,12 @@ # The name of an image file (relative to this directory) to place at the top # of the sidebar. -html_logo = "../pymc3_logo.jpg" +html_logo = "../pymc_logo.jpeg" # 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 = "../logos/PyMC3.ico" +html_favicon = "../logos/PyMC.ico" # 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, @@ -287,7 +287,7 @@ # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. -htmlhelp_basename = "pymc3doc" +htmlhelp_basename = "pymcdoc" # -- Options for LaTeX output --------------------------------------------- @@ -305,7 +305,7 @@ # 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 = [(master_doc, "pymc3.tex", "PyMC3 Documentation", "PyMC developers", "manual")] +latex_documents = [(master_doc, "pymc.tex", "PyMC Documentation", "PyMC developers", "manual")] # The name of an image file (relative to this directory) to place at the top of # the title page. @@ -332,7 +332,7 @@ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). -man_pages = [(master_doc, "pymc3", "pymc3 Documentation", [author], 1)] +man_pages = [(master_doc, "pymc", "pymc Documentation", [author], 1)] # If true, show URL addresses after external links. # man_show_urls = False @@ -346,10 +346,10 @@ texinfo_documents = [ ( master_doc, - "pymc3", - "pymc3 Documentation", + "pymc", + "pymc Documentation", author, - "pymc3", + "pymc", "One line description of project.", "Miscellaneous", ) diff --git a/docs/source/contributing/index.md b/docs/source/contributing/index.md index 48ae187929..2141e988db 100644 --- a/docs/source/contributing/index.md +++ b/docs/source/contributing/index.md @@ -1,13 +1,15 @@ # Contributing -Explaining how to contribute to PyMC +PyMC is an open source, collective effort. Find all the ways in which you can help make it better. -## Code related PRs +## Help develop PyMC -## Documentation +reviewing? proofreading... + +## Help improve the documentation ## Others -Issue triaging? reviewing? proofreading... +Issue triaging :::{toctree} :hidden: diff --git a/docs/source/index.md b/docs/source/index.md index cbd61bf044..ebc2302a58 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -1,39 +1,94 @@ -# PyMC3 documentation - -Page in construction. +:::{card} +:img-background: pymc/docs/pymc_logo.jpeg +:margin: 0 2 auto auto +:width: 50% +--- +scale: 80 +--- +::: -For now there are only some examples of https://sphinx-design.readthedocs.io/en/sbt-theme/index.html -usage. +Probabilistic programming in Python :::{button-ref} learning -:ref-type: ref -:color: primary -:expand: +:color: secondary +:shadow: + +Get started! +::: + +:::{dropdown} Announcements: library name change and launching PyMC 4.0! +:color: warning +:icon: rocket +:animate: fade-in +:open: + +We have two major announcements that we're excited to share. First of all, a new name for our library: the PyMC3 library you know and love is now called PyMC. PyMC3 still exists, as a specific major release between PyMC2 and PyMC 4.0. Read more about the renaming and how to solve related issues you might experience from this update [here](). -Getting Started as giant long button +This ties into our second announcement, which is that we are hereby launching the newest version of PyMC: PyMC 4.0! Read more about this new release [here](). ::: -:::::{grid} 1 1 3 3 +# Main Features & Benefits -:::{grid-item} +::::{grid} 1 2 2 2 +:::{grid-item-card} Friendly modelling API +PyMC allows you to write down models using an intuitive syntax to describe a data generating process. ::: +:::{grid-item-card} Cutting edge algorithms and model building blocks +Fit your model using gradient-based MCMC algorithms like NUTS, using ADVI for fast approximate inference — including minibatch-ADVI for scaling to large datasets — or using Gaussian processes to build Bayesian nonparametric models. +::: +:::: + +# Support and Sponsors + +PyMC is a non-profit project under NumFOCUS umbrella. If you value PyMC and want to support its development, consider donating to the project. -::::{grid-item} :::{button-link} https://numfocus.org/donate-to-pymc3 -:expand: :color: secondary +:shadow: -Donate as button within a grid +Donate +::: + +::::{grid} 1 3 3 3 +:::{grid-item-card} +TODO add sponsor logo +::: +:::{grid-item-card} +TODO add sponsor logo +::: +:::{grid-item-card} +TODO add sponsor logo ::: :::: -:::{grid-item} +# Citing PyMC + +Use this to cite the library: + +Salvatier J., Wiecki T.V., Fonnesbeck C. (2016) Probabilistic programming in Python using PyMC3. PeerJ Computer Science 2:e55 [DOI: 10.7717/peerj-cs.55.](https://doi.org/10.7717/peerj-cs.55) + +See [Google Scholar](https://scholar.google.de/scholar?oi=bibs&hl=en&authuser=1&cites=6936955228135731011) for a continuously updated list of papers citing PyMC3. + +::::{grid} 2 +:gutter: 3 3 4 5 + +:::{grid-item-card} Need help? +[Ask a question!]() + +[Read the User Docs]() + +[Read the Developer Docs]() + ::: -::::: +:::{grid-item-card} Around the web +[Github]() + +[Twitter]() + +[Discourse]() +::: +:::: -Also add a cool icon: in default size {fas}`check-circle`, or extra large -{fas}`check-circle;fa-10x`. See https://fontawesome.com/v5.15/how-to-use/on-the-web/styling/sizing-icons -for options. :::{toctree} :maxdepth: 1 @@ -46,3 +101,4 @@ community contributing/index about ::: + diff --git a/docs/source/index_legagy.rst b/docs/source/index_legacy.rst similarity index 100% rename from docs/source/index_legagy.rst rename to docs/source/index_legacy.rst diff --git a/docs/source/installation.md b/docs/source/installation.md index 387560ba5d..d364f1be1c 100644 --- a/docs/source/installation.md +++ b/docs/source/installation.md @@ -1,33 +1,30 @@ # Installation guide -Move the 3 wiki pages over to here. - -with sphinx_design we can have common content in a single place, -and whenever there is some specific guidance that depends on OS use -tabs, which can be syncronized. That is, if one tab is switched over to -windows, all tabs will be moved to windows. For example: +To install PyMC 4.0, select the operating system where you want to perform the installation. ::::{tab-set} :::{tab-item} Linux :sync: linux -specific linux content +v4.0 linux installation ::: :::{tab-item} MacOS :sync: mac -specific macos content +v4.0 macos installation ::: :::{tab-item} Windows :sync: windows -specific windows content +v4.0 windows installation ::: :::: -more common content +## Uninstalling PyMC3 + +We don't recommend installing pymc3 and pymc 4.0 in the same environment. To uninstall pymc3, do the following: ::::{tab-set} :::{tab-item} Linux @@ -48,3 +45,51 @@ extra specific macosx content, i.e. testing the installation was successful extra specific windows content, i.e. testing the installation was successful ::: :::: + +## Aesara Installation + +PyMC uses Aesara. To install it, do: + + +::::{tab-set} +:::{tab-item} Linux +:sync: linux + +Aesara installation +::: + +:::{tab-item} MacOS +:sync: mac + +Aesara installation +::: + +:::{tab-item} Windows +:sync: windows + +Aesara installation +::: +:::: + +## Arviz Installation +Plots and diagnostics are entirely done by ArviZ - if you follow the installation instructions above, then it will be installed alongside PyMC3. + +::::{grid} 2 +:gutter: 3 3 4 5 + +:::{grid-item-card} Need help? +[Ask a question!]() + +[Read the User Docs]() + +[Read the Developer Docs]() + +::: +:::{grid-item-card} Around the web +[Github]() + +[Twitter]() + +[Discourse]() +::: +:::: \ No newline at end of file diff --git a/docs/source/learning.md b/docs/source/learning.md index 82be5dadb9..38d6859955 100644 --- a/docs/source/learning.md +++ b/docs/source/learning.md @@ -8,8 +8,79 @@ toctree to the pages within that section (if any). This will make the pages appear in the left sidebar for easy navigation while keeping the in page toc on the right sidebar. -## Step 1 overview -Links to books and pymc-devs/resources. +## Getting started + +Start here to get acquainted with the core concepts of Bayesian analysis and PyMC. + +::::::{grid} 1 +:gutter: 1 + +:::::{grid-item} +::::{grid} 2 +:gutter: 1 + +:::{grid-item-card} Bayesian Methods for Hackers +:shadow: none + +By Cameron Davidson-Pilon +::: + +:::{grid-item-card} +:shadow: none + +Hands-on learning of Bayesian statistics and PyMC3 + +[Github repo](https://github.com/CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers) + +[Project homepage](http://camdavidsonpilon.github.io/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers/) +::: +:::: +::::: + +:::::{grid-item} +::::{grid} 2 +:gutter: 1 + +:::{grid-item-card} Bayesian Analysis with Python +:shadow: none + +by Osvaldo Martin +::: + +:::{grid-item-card} +:shadow: none + +A great introductory book written by a maintainer of PyMC. + +[Book website](https://www.packtpub.com/big-data-and-business-intelligence/bayesian-analysis-python-second-edition) + +[Code and errata in PyMC](https://github.com/aloctavodia/BAP) +::: + +:::: +::::: + +:::::{grid-item} +::::{grid} 2 +:gutter: 1 + +:::{grid-item-card} Glossary +:shadow: none + +::: + +:::{grid-item-card} +:shadow: none + +PyMC's glossary, which defines many core terms and provides references. + +:ref: glossary +::: + +:::: +::::: +:::::: + --- ## Step 2 overview @@ -23,10 +94,10 @@ the `examples` folder, or using manual anchors if we decide to create them). Links to intermediate notebooks. {doc}`More about step 3... ` -```{toctree} +:::{toctree} :hidden: learn/step1 learn/step2 learn/step3 -``` +:::