From 2adc238f09032b3930e2c655e290154883b1c345 Mon Sep 17 00:00:00 2001 From: Michael Osthege Date: Sat, 5 Jun 2021 21:28:10 +0200 Subject: [PATCH 1/2] Rename references to the PyMC3 master branch to main --- .github/workflows/arviz_compat.yml | 2 +- .github/workflows/jaxtests.yml | 2 +- .github/workflows/pre-commit.yml | 2 +- .github/workflows/pytest.yml | 2 +- .github/workflows/windows.yml | 2 +- CONTRIBUTING.md | 4 ++-- README.rst | 16 ++++++++-------- benchmarks/asv.conf.json | 4 ++-- docs/source/about.rst | 6 +++--- docs/source/api/bounds.rst | 2 +- docs/source/developer_guide.rst | 18 +++++++++--------- docs/source/index.rst | 6 +++--- docs/source/semantic_sphinx/layout.html | 10 +++++----- 13 files changed, 38 insertions(+), 38 deletions(-) diff --git a/.github/workflows/arviz_compat.yml b/.github/workflows/arviz_compat.yml index 55405d0624..ba10a81008 100644 --- a/.github/workflows/arviz_compat.yml +++ b/.github/workflows/arviz_compat.yml @@ -3,7 +3,7 @@ name: arviz-compatibility on: pull_request: push: - branches: [master] + branches: [main] jobs: pytest: diff --git a/.github/workflows/jaxtests.yml b/.github/workflows/jaxtests.yml index 2e2f16b33a..0e57bba3c6 100644 --- a/.github/workflows/jaxtests.yml +++ b/.github/workflows/jaxtests.yml @@ -3,7 +3,7 @@ name: jax-sampling on: pull_request: push: - branches: [master] + branches: [main] jobs: pytest: diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 6131de7400..b92ca1c1ae 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -3,7 +3,7 @@ name: pre-commit on: pull_request: push: - branches: [master] + branches: [main] jobs: pre-commit: diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 57bb97e764..8a1aa3611f 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -3,7 +3,7 @@ name: pytest on: pull_request: push: - branches: [master] + branches: [main] jobs: pytest: diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index 5eb39fedd9..ab9d61d15a 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -3,7 +3,7 @@ name: windows on: pull_request: push: - branches: [master] + branches: [main] jobs: pytest: diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 95d18312fd..af255ecc03 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -43,7 +43,7 @@ The preferred workflow for contributing to PyMC3 is to fork the [GitHub reposito $ git checkout -b my-feature ``` - Always use a ``feature`` branch. It's good practice to never routinely work on the ``master`` branch of any repository. + Always use a ``feature`` branch. It's good practice to never routinely work on the ``main`` branch of any repository. 4. Project requirements are in ``requirements.txt``, and libraries used for development are in ``requirements-dev.txt``. The easiest (and recommended) way to set up a development environment is via [miniconda](https://docs.conda.io/en/latest/miniconda.html): @@ -73,7 +73,7 @@ The preferred workflow for contributing to PyMC3 is to fork the [GitHub reposito After committing, it is a good idea to sync with the base repository in case there have been any changes: ```bash $ git fetch upstream - $ git rebase upstream/master + $ git rebase upstream/main ``` Then push the changes to your GitHub account with: diff --git a/README.rst b/README.rst index 8a4348639a..faa00cbdc9 100644 --- a/README.rst +++ b/README.rst @@ -1,4 +1,4 @@ -.. image:: https://cdn.rawgit.com/pymc-devs/pymc3/master/docs/logos/svg/PyMC3_banner.svg +.. image:: https://cdn.rawgit.com/pymc-devs/pymc3/main/docs/logos/svg/PyMC3_banner.svg :height: 100px :alt: PyMC3 logo :align: center @@ -11,7 +11,7 @@ algorithms. Its flexibility and extensibility make it applicable to a large suite of problems. Check out the `getting started guide `__, or -`interact with live examples `__ +`interact with live examples `__ using Binder! For questions on PyMC3, head on over to our `PyMC Discourse `__ forum. @@ -100,7 +100,7 @@ License ======= `Apache License, Version -2.0 `__ +2.0 `__ Software using PyMC3 @@ -129,7 +129,7 @@ Contributors ============ See the `GitHub contributor -page `__. Also read our `Code of Conduct `__ guidelines for a better contributing experience. +page `__. Also read our `Code of Conduct `__ guidelines for a better contributing experience. Support ======= @@ -158,20 +158,20 @@ Sponsors |ODSC| .. |Binder| image:: https://mybinder.org/badge_logo.svg - :target: https://mybinder.org/v2/gh/pymc-devs/pymc3/master?filepath=%2Fdocs%2Fsource%2Fnotebooks + :target: https://mybinder.org/v2/gh/pymc-devs/pymc3/main?filepath=%2Fdocs%2Fsource%2Fnotebooks .. |Build Status| image:: https://github.com/pymc-devs/pymc3/workflows/pytest/badge.svg :target: https://github.com/pymc-devs/pymc3/actions -.. |Coverage| image:: https://codecov.io/gh/pymc-devs/pymc3/branch/master/graph/badge.svg +.. |Coverage| image:: https://codecov.io/gh/pymc-devs/pymc3/branch/main/graph/badge.svg :target: https://codecov.io/gh/pymc-devs/pymc3 .. |Dockerhub| image:: https://img.shields.io/docker/automated/pymc/pymc3.svg :target: https://hub.docker.com/r/pymc/pymc3 .. |NumFOCUS| image:: https://www.numfocus.org/wp-content/uploads/2017/03/1457562110.png :target: http://www.numfocus.org/ -.. |Quantopian| image:: https://raw.githubusercontent.com/pymc-devs/pymc3/master/docs/quantopianlogo.jpg +.. |Quantopian| image:: https://raw.githubusercontent.com/pymc-devs/pymc3/main/docs/quantopianlogo.jpg :target: https://quantopian.com .. |NumFOCUS_badge| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A :target: http://www.numfocus.org/ -.. |ODSC| image:: https://raw.githubusercontent.com/pymc-devs/pymc3/master/docs/odsc_logo.png +.. |ODSC| image:: https://raw.githubusercontent.com/pymc-devs/pymc3/main/docs/odsc_logo.png :target: https://odsc.com .. |tidelift| image:: https://img.shields.io/badge/-lifted!-2dd160.svg?colorA=58595b&style=flat&logo=data:image/png;base64,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%2FwCjUTnDygkGoVERFQaZFlE9nreO%2BdM5u5wkifvuee892Pu3CyEcA0DeIc%2B9IwftJsR6Cko3uCjguZdjuBZhhwmYDjGrOC96WED41UtsgEdGEAPlmAfpuAbFF%2BFZLfoMfRBGzThDtLgePPwBIpdddGzOArhPHUXowbNptE2www6a%2Fm96Y3pHN7oQ1s%2B13pxt1ENaKzBFWyWzaJ%2BRO0C9Jny6VPSoKjLVbMDC5bn5OPuJF%2BBSe95PVEMuugY5AegS9fCh7BedP45hRnj8TC34QQUe9bTZyh2KgvFk2vc8GIlXyTfsvqr6bPpNgv52ynnlomZJNpB70Xhl%2Bf6Sa02p1bApEfnETwxVa%2Faj%2BW%2FFtHltmxS%2FO3krvpTtTnVgu%2F6gvHRFvG78Ef3kOe5PimJXycY74blT5R%2BAAAAAElFTkSuQmCC :target: https://tidelift.com/subscription/pkg/pypi-pymc3?utm_source=pypi-pymc3&utm_medium=referral&utm_campaign=enterprise diff --git a/benchmarks/asv.conf.json b/benchmarks/asv.conf.json index 59e358cee0..bc1458bdea 100644 --- a/benchmarks/asv.conf.json +++ b/benchmarks/asv.conf.json @@ -13,9 +13,9 @@ // project being benchmarked "repo": "..", - // List of branches to benchmark. If not provided, defaults to "master" + // List of branches to benchmark. If not provided, defaults to "main" // (for git) or "tip" (for mercurial). - "branches": ["master"], + "branches": ["main"], // The DVCS being used. If not set, it will be automatically // determined from "repo" by looking at the protocol in the URL diff --git a/docs/source/about.rst b/docs/source/about.rst index 6dc249ece1..0a06f3c2fd 100644 --- a/docs/source/about.rst +++ b/docs/source/about.rst @@ -189,7 +189,7 @@ Sponsors |NumFOCUS| |Quantopian| |ODSC| -More details about sponsoring PyMC3 can be found `here `_. +More details about sponsoring PyMC3 can be found `here `_. If you are interested in becoming a sponsor, reach out to `pymc.devs@gmail.com `_ ************** @@ -266,9 +266,9 @@ See also .. |NumFOCUS| image:: https://numfocus.org/wp-content/uploads/2017/07/NumFocus_LRG.png :target: http://www.numfocus.org/ :height: 120px -.. |Quantopian| image:: https://raw.githubusercontent.com/pymc-devs/pymc3/master/docs/quantopianlogo.jpg +.. |Quantopian| image:: https://raw.githubusercontent.com/pymc-devs/pymc3/main/docs/quantopianlogo.jpg :target: https://quantopian.com :height: 120px -.. |ODSC| image:: https://raw.githubusercontent.com/pymc-devs/pymc3/master/docs/odsc_logo.png +.. |ODSC| image:: https://raw.githubusercontent.com/pymc-devs/pymc3/main/docs/odsc_logo.png :target: https://odsc.com :height: 120px diff --git a/docs/source/api/bounds.rst b/docs/source/api/bounds.rst index ad90d33cbb..1154af4688 100644 --- a/docs/source/api/bounds.rst +++ b/docs/source/api/bounds.rst @@ -66,7 +66,7 @@ Caveats * Bounds cannot be given to variables that are ``observed``. To model truncated data, use a :func:`~pymc3.model.Potential` in combination with a cumulative - probability function. See `this example notebook `_. + probability function. See `this example notebook `_. * The automatic transformation applied to continuous distributions results in an unnormalized probability distribution. This doesn't effect inference diff --git a/docs/source/developer_guide.rst b/docs/source/developer_guide.rst index 25d4d8db39..512498f461 100644 --- a/docs/source/developer_guide.rst +++ b/docs/source/developer_guide.rst @@ -23,9 +23,9 @@ Distribution A high-level introduction of ``Distribution`` in PyMC3 can be found in the `documentation `__. The source code of the probability distributions is nested under -`pymc3/distributions `__, +`pymc3/distributions `__, with the ``Distribution`` class defined in `distribution.py -`__. +`__. A few important points to highlight in the Distribution Class: .. code:: python @@ -712,7 +712,7 @@ dictionary with the free\_RVs being sampled now has a new value (if accepted, see `here `__ and -`here `__). +`here `__). There are some example in the `CompoundStep doc `__. @@ -720,7 +720,7 @@ Transition kernel ^^^^^^^^^^^^^^^^^ The base class for most MCMC sampler (except SMC) is in -`ArrayStep `__. +`ArrayStep `__. You can see that the ``step.step()`` is mapping the ``point`` into an array, and call ``self.astep()``, which is an array in, array out function. A pymc3 model compile a conditional logp/dlogp function that @@ -764,7 +764,7 @@ The design of the VI module takes a different approach than MCMC - it has a functional design, and everything is done within Aesara (i.e., Optimization and building the variational objective). The base class of variational inference is -`pymc3.variational.Inference `__, +`pymc3.variational.Inference `__, where it builds the objective function by calling: .. code:: python @@ -789,7 +789,7 @@ Approximation, and Test functions to combine them into single objective function. Currently we do not care too much about the test function, it is usually not required (and not implemented). The other primitives are defined as base classes in `this -file `__. +file `__. We use inheritance to easily implement a broad class of VI methods leaving a lot of flexibility for further extensions. @@ -824,7 +824,7 @@ allows you to combine approximation into new approximation, but we will skip this for now and only consider ``SingleGroupApproximation`` like ``MeanField``): The definition of ``datalogp_norm``, ``logq_norm``, ``varlogp_norm`` are in -`variational/opvi `__, +`variational/opvi `__, strip away the normalizing term, ``datalogp`` and ``varlogp`` are expectation of the variational free\_RVs and data logp - we clone the datalogp and varlogp from the model, replace its input with Aesara @@ -859,10 +859,10 @@ Some challenges and insights from implementing VI. on this feature. Internal usages are uncountable: - we use this to `vectorize the - model `__ + model `__ for both MCMC and VI to speed up computations - we use this to `create sampling - graph `__ + graph `__ for VI. This is the case you want posterior predictive as a part of computational graph. diff --git a/docs/source/index.rst b/docs/source/index.rst index c0a5efefea..13cd1d3f05 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -110,7 +110,7 @@

License

-

PyMC3 is licensed under the Apache License, V2.

+

PyMC3 is licensed under the Apache License, V2.

@@ -140,12 +140,12 @@
- +
- +
diff --git a/docs/source/semantic_sphinx/layout.html b/docs/source/semantic_sphinx/layout.html index 25d0c62d69..6151a40491 100644 --- a/docs/source/semantic_sphinx/layout.html +++ b/docs/source/semantic_sphinx/layout.html @@ -54,7 +54,7 @@
- + {% if theme_navbar_links %} {%- for link in theme_navbar_links %} {{ @@ -74,7 +74,7 @@
{% if pagename == 'index' %}
- +

Probabilistic Programming in Python
Quickstart
@@ -89,14 +89,14 @@

Probabilistic Programming in Python

 - - + + - + From 5b3513faf2c77d8d399eb2e1ab65c78f9861f027 Mon Sep 17 00:00:00 2001 From: Michael Osthege Date: Sat, 5 Jun 2021 22:42:37 +0200 Subject: [PATCH 2/2] Apply suggestions from code review Redirect some links in the doc --- docs/source/api/bounds.rst | 2 +- docs/source/developer_guide.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/api/bounds.rst b/docs/source/api/bounds.rst index 1154af4688..250044cfe9 100644 --- a/docs/source/api/bounds.rst +++ b/docs/source/api/bounds.rst @@ -66,7 +66,7 @@ Caveats * Bounds cannot be given to variables that are ``observed``. To model truncated data, use a :func:`~pymc3.model.Potential` in combination with a cumulative - probability function. See `this example notebook `_. + probability function. See `this example notebook `_. * The automatic transformation applied to continuous distributions results in an unnormalized probability distribution. This doesn't effect inference diff --git a/docs/source/developer_guide.rst b/docs/source/developer_guide.rst index 512498f461..c4cd803d5b 100644 --- a/docs/source/developer_guide.rst +++ b/docs/source/developer_guide.rst @@ -712,7 +712,7 @@ dictionary with the free\_RVs being sampled now has a new value (if accepted, see `here `__ and -`here `__). +`here `__). There are some example in the `CompoundStep doc `__.