From ee9e77122ee7e8375cea63fdf840d82f06163f56 Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sat, 26 Jun 2021 00:43:27 +0530 Subject: [PATCH 01/12] Add readthedocs yml file --- .readthedocs.yml | 13 +++++++++++++ docs/source/pymc-examples | 2 +- 2 files changed, 14 insertions(+), 1 deletion(-) create mode 100644 .readthedocs.yml diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 0000000000..23370a287f --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,13 @@ +version: 2 + +sphinx: + configuration: docs/source/conf.py + +python: + version: 3.7 + install: + - requirements: requirements-dev.txt + +submodules: + include: all + recursive: true diff --git a/docs/source/pymc-examples b/docs/source/pymc-examples index a093bcc5aa..f99e8797b3 160000 --- a/docs/source/pymc-examples +++ b/docs/source/pymc-examples @@ -1 +1 @@ -Subproject commit a093bcc5aa828e9317bdf9f936f968f76acdb4f7 +Subproject commit f99e8797b3f50210280e461993a9664914f98161 From fa740ab015f4ddfa7ed717cd8169a6b501b44423 Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sat, 26 Jun 2021 01:00:13 +0530 Subject: [PATCH 02/12] Add installation of pymc3 --- .readthedocs.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.readthedocs.yml b/.readthedocs.yml index 23370a287f..70d4c5250a 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -7,6 +7,9 @@ python: version: 3.7 install: - requirements: requirements-dev.txt + - method: pip + path: . + submodules: include: all From 6ab3f48d32acd49bda4139cb33397365db43b094 Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sun, 27 Jun 2021 17:11:36 +0530 Subject: [PATCH 03/12] Manually invoke building gallery instead of using it as an extension --- docs/source/conf.py | 7 ++++++- docs/source/pymc-examples | 2 +- docs/source/sphinxext/gallery_generator.py | 9 --------- 3 files changed, 7 insertions(+), 11 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 9b23a323af..3cbd8b0bea 100755 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -15,6 +15,8 @@ import os import sys +from pathlib import Path + import pymc3 # If extensions (or modules to document with autodoc) are in another directory, @@ -23,6 +25,8 @@ sys.path.insert(0, os.path.abspath(os.path.join("..", ".."))) sys.path.insert(0, os.path.abspath("sphinxext")) +from gallery_generator import build_gallery + # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. @@ -43,7 +47,6 @@ "IPython.sphinxext.ipython_directive", "sphinx.ext.autosectionlabel", "sphinx.ext.napoleon", - "gallery_generator", "recommonmark", ] @@ -330,3 +333,5 @@ def setup(app): app.add_css_file("https://cdn.jsdelivr.net/npm/semantic-ui@2.4.2/dist/semantic.min.css") app.add_css_file("default.css") + for gallery in ("tutorials", "examples"): + build_gallery(Path(__file__).parent, gallery) diff --git a/docs/source/pymc-examples b/docs/source/pymc-examples index f99e8797b3..b51d2e8a80 160000 --- a/docs/source/pymc-examples +++ b/docs/source/pymc-examples @@ -1 +1 @@ -Subproject commit f99e8797b3f50210280e461993a9664914f98161 +Subproject commit b51d2e8a80894800a39ef5017bcc4268366ea6bb diff --git a/docs/source/sphinxext/gallery_generator.py b/docs/source/sphinxext/gallery_generator.py index caf4beb450..696d5eefe3 100644 --- a/docs/source/sphinxext/gallery_generator.py +++ b/docs/source/sphinxext/gallery_generator.py @@ -200,12 +200,3 @@ def build_gallery(srcdir, gallery): ) os.chdir(working_dir) - - -def main(app): - for gallery in ("tutorials", "examples"): - build_gallery(app.builder.srcdir, gallery) - - -def setup(app): - app.connect("builder-inited", main) From 97d837f805ad8bffb9682770d4175da3d9e0eac1 Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sun, 27 Jun 2021 18:45:55 +0530 Subject: [PATCH 04/12] Trying to fix relative paths --- docs/source/sphinxext/gallery_generator.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/docs/source/sphinxext/gallery_generator.py b/docs/source/sphinxext/gallery_generator.py index 696d5eefe3..9cf44cb5dd 100644 --- a/docs/source/sphinxext/gallery_generator.py +++ b/docs/source/sphinxext/gallery_generator.py @@ -170,16 +170,20 @@ def build_gallery(srcdir, gallery): if basename.find(".rst") < 1: filename = os.path.join(source_dir, basename + ".ipynb") ex = NotebookGenerator(filename, target_dir) + url = Path(os.path.join(os.sep, gallery, ex.output_html)) + url = "../" + str(Path(*url.parts[3:])) data[basename] = { "title": ex.pagetitle, - "url": os.path.join(os.sep, gallery, ex.output_html), + "url": url, "thumb": os.path.basename(ex.png_path), } else: filename = basename.split(".")[0] + url = Path(os.path.join(os.sep, gallery, "../" + filename + ".html")) + url = "../" + str(Path(*url.parts[3:])) data[basename] = { "title": " ".join(filename.split("_")), - "url": os.path.join(os.sep, gallery, "../" + filename + ".html"), + "url": url, "thumb": os.path.basename(default_png_path), } From f94270db43976717ee1e4b3c5e4e7660bd0ba41a Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sat, 3 Jul 2021 13:20:07 +0530 Subject: [PATCH 05/12] Temporarily disable tests --- .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 +- docs/source/pymc-examples | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/arviz_compat.yml b/.github/workflows/arviz_compat.yml index f4709169ac..5d31808629 100644 --- a/.github/workflows/arviz_compat.yml +++ b/.github/workflows/arviz_compat.yml @@ -1,7 +1,7 @@ name: arviz-compatibility on: - pull_request: + # pull_request: push: branches: [v3] diff --git a/.github/workflows/jaxtests.yml b/.github/workflows/jaxtests.yml index 5bd89e3a27..e9bc29c401 100644 --- a/.github/workflows/jaxtests.yml +++ b/.github/workflows/jaxtests.yml @@ -1,7 +1,7 @@ name: jax-sampling on: - pull_request: + # pull_request: push: branches: [v3] diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 88ea331924..59da304d91 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -1,7 +1,7 @@ name: pre-commit on: - pull_request: + # pull_request: push: branches: [v3] diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 338847271a..38ba9060cc 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -1,7 +1,7 @@ name: pytest on: - pull_request: + # pull_request: push: branches: [v3] diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index be9df7ff4b..b405989d4f 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -1,7 +1,7 @@ name: windows on: - pull_request: + # pull_request: push: branches: [v3] diff --git a/docs/source/pymc-examples b/docs/source/pymc-examples index b51d2e8a80..dafc41c0f8 160000 --- a/docs/source/pymc-examples +++ b/docs/source/pymc-examples @@ -1 +1 @@ -Subproject commit b51d2e8a80894800a39ef5017bcc4268366ea6bb +Subproject commit dafc41c0f8f174190a98630a8a0df2c4c241f4ce From c3001f343e95b5778fb89c0d33737456dba2a4ba Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sat, 3 Jul 2021 14:34:14 +0530 Subject: [PATCH 06/12] Bring back the gallery extension. Just create the required directories for sphinx to build tutorials and examples section --- docs/source/conf.py | 8 ++++---- docs/source/sphinxext/gallery_generator.py | 9 +++++++++ 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 3cbd8b0bea..ea3832a56e 100755 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -25,8 +25,6 @@ sys.path.insert(0, os.path.abspath(os.path.join("..", ".."))) sys.path.insert(0, os.path.abspath("sphinxext")) -from gallery_generator import build_gallery - # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. @@ -47,6 +45,7 @@ "IPython.sphinxext.ipython_directive", "sphinx.ext.autosectionlabel", "sphinx.ext.napoleon", + "gallery_generator", "recommonmark", ] @@ -333,5 +332,6 @@ def setup(app): app.add_css_file("https://cdn.jsdelivr.net/npm/semantic-ui@2.4.2/dist/semantic.min.css") app.add_css_file("default.css") - for gallery in ("tutorials", "examples"): - build_gallery(Path(__file__).parent, gallery) + dir_root = Path(__file__).parent + for directory in ["_static", "nb_tutorials/_images", "nb_examples/_images"]: + os.makedirs(str(dir_root / directory)) diff --git a/docs/source/sphinxext/gallery_generator.py b/docs/source/sphinxext/gallery_generator.py index 9cf44cb5dd..1932e9c90a 100644 --- a/docs/source/sphinxext/gallery_generator.py +++ b/docs/source/sphinxext/gallery_generator.py @@ -204,3 +204,12 @@ def build_gallery(srcdir, gallery): ) os.chdir(working_dir) + + +def main(app): + for gallery in ("tutorials", "examples"): + build_gallery(app.builder.srcdir, gallery) + + +def setup(app): + app.connect("builder-inited", main) From dd33464554cb4212c0a9e8d3f58e5fe55a2a97cc Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sat, 3 Jul 2021 14:55:44 +0530 Subject: [PATCH 07/12] Fixup a bug when expected static directories are already present; Simplified to use existing directories path --- docs/source/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index ea3832a56e..6fc8780e8b 100755 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -333,5 +333,5 @@ def setup(app): app.add_css_file("https://cdn.jsdelivr.net/npm/semantic-ui@2.4.2/dist/semantic.min.css") app.add_css_file("default.css") dir_root = Path(__file__).parent - for directory in ["_static", "nb_tutorials/_images", "nb_examples/_images"]: - os.makedirs(str(dir_root / directory)) + for directory in html_static_path: + os.makedirs(str(dir_root / directory), exist_ok=True) From 154823c409a94a9e70b32aa62322a72e6e1cf7e9 Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sat, 3 Jul 2021 19:28:54 +0530 Subject: [PATCH 08/12] Simplified relative urls handling --- docs/source/sphinxext/gallery_generator.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/source/sphinxext/gallery_generator.py b/docs/source/sphinxext/gallery_generator.py index 1932e9c90a..46273e04d6 100644 --- a/docs/source/sphinxext/gallery_generator.py +++ b/docs/source/sphinxext/gallery_generator.py @@ -171,16 +171,19 @@ def build_gallery(srcdir, gallery): filename = os.path.join(source_dir, basename + ".ipynb") ex = NotebookGenerator(filename, target_dir) url = Path(os.path.join(os.sep, gallery, ex.output_html)) - url = "../" + str(Path(*url.parts[3:])) + # Need to chop off "/${gallery}/../" so as redirection works in multi versioned docs. + url = str(Path("..", *url.parts[3:])) data[basename] = { "title": ex.pagetitle, "url": url, "thumb": os.path.basename(ex.png_path), } + else: filename = basename.split(".")[0] url = Path(os.path.join(os.sep, gallery, "../" + filename + ".html")) - url = "../" + str(Path(*url.parts[3:])) + # Need to chop off "/${gallery}/../" so as redirection works in multi versioned docs. + url = str(Path("..", *url.parts[3:])) data[basename] = { "title": " ".join(filename.split("_")), "url": url, From 4b59f6e036ceeede5b5ff646784ce20e3df47d5e Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sat, 3 Jul 2021 19:53:45 +0530 Subject: [PATCH 09/12] Given a mention in release notes --- RELEASE-NOTES.md | 1 + 1 file changed, 1 insertion(+) diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md index aab5e1bb1f..6c47a4751f 100644 --- a/RELEASE-NOTES.md +++ b/RELEASE-NOTES.md @@ -6,6 +6,7 @@ + `theano.printing.pydotprint` is now hotfixed upon import (see [#4594](https://github.com/pymc-devs/pymc3/pull/4594)). + Fix bug in the computation of the log pseudolikelihood values (SMC-ABC). (see [#4672](https://github.com/pymc-devs/pymc3/pull/4672)). + Fix `LKJCorr.random` method to work with `pm.sample_prior_predictive`. (see [#4780](https://github.com/pymc-devs/pymc3/pull/4780)) ++ Enable documentation generation via ReadTheDocs for upcoming v3 releases. (see [#4805](https://github.com/pymc-devs/pymc3/pull/4805)). ### New Features + Generalized BART, bounded distributions like Binomial and Poisson can now be used as likelihoods (see [#4675](https://github.com/pymc-devs/pymc3/pull/4675), [#4709](https://github.com/pymc-devs/pymc3/pull/4709) and From 9aee07cb2ca647aae2021ea551ec5002105dfc13 Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sat, 3 Jul 2021 20:16:36 +0530 Subject: [PATCH 10/12] Add installation links to landing page --- docs/source/index.rst | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index 053e1962f1..e0299667a2 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -44,28 +44,28 @@
-

Installation

- -
-
-

Via conda-forge:

- -.. code-block:: bash - - conda install -c conda-forge pymc3 - - -.. raw:: html - -

Latest (unstable):

+
+

Installation

+
-.. code-block:: bash + +
+
Instructions for Linux
+
+ - pip install git+https://github.com/pymc-devs/pymc3 + +
+
Instructions for MacOS
+
+ -.. raw:: html + +
+
Instructions for Windows
+
+ -
From a4e3be4745fad4e5389181c25b86c8b525e519e4 Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sat, 3 Jul 2021 21:34:06 +0530 Subject: [PATCH 11/12] Re-enable tests and update pymc-examples submodule --- .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 +- docs/source/pymc-examples | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/arviz_compat.yml b/.github/workflows/arviz_compat.yml index 5d31808629..f4709169ac 100644 --- a/.github/workflows/arviz_compat.yml +++ b/.github/workflows/arviz_compat.yml @@ -1,7 +1,7 @@ name: arviz-compatibility on: - # pull_request: + pull_request: push: branches: [v3] diff --git a/.github/workflows/jaxtests.yml b/.github/workflows/jaxtests.yml index e9bc29c401..5bd89e3a27 100644 --- a/.github/workflows/jaxtests.yml +++ b/.github/workflows/jaxtests.yml @@ -1,7 +1,7 @@ name: jax-sampling on: - # pull_request: + pull_request: push: branches: [v3] diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 59da304d91..88ea331924 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -1,7 +1,7 @@ name: pre-commit on: - # pull_request: + pull_request: push: branches: [v3] diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 38ba9060cc..338847271a 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -1,7 +1,7 @@ name: pytest on: - # pull_request: + pull_request: push: branches: [v3] diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index b405989d4f..be9df7ff4b 100644 --- a/.github/workflows/windows.yml +++ b/.github/workflows/windows.yml @@ -1,7 +1,7 @@ name: windows on: - # pull_request: + pull_request: push: branches: [v3] diff --git a/docs/source/pymc-examples b/docs/source/pymc-examples index dafc41c0f8..0bbf199c46 160000 --- a/docs/source/pymc-examples +++ b/docs/source/pymc-examples @@ -1 +1 @@ -Subproject commit dafc41c0f8f174190a98630a8a0df2c4c241f4ce +Subproject commit 0bbf199c462a65e3c9a7b5155f7b47c69eae2581 From 7569d8c59c08df824690f8cff74cb4dd0034e830 Mon Sep 17 00:00:00 2001 From: Sayam753 Date: Sat, 3 Jul 2021 22:13:00 +0530 Subject: [PATCH 12/12] Fix relative links for in-depth guides --- docs/source/index.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index e0299667a2..205f8ee902 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -73,7 +73,7 @@

In-Depth Guides

- +
Probability Distributions
PyMC3 includes a comprehensive set of pre-defined statistical distributions that can be used as model building blocks. @@ -81,7 +81,7 @@
- +
Gaussian Processes
Sometimes an unknown parameter or variable in a model is not a scalar value or a fixed-length vector, but a function. A Gaussian process (GP) can be used as a prior probability distribution whose support is over the space of continuous functions. PyMC3 provides rich support for defining and using GPs. @@ -89,7 +89,7 @@
- +
Variational Inference
Variational inference saves computational cost by turning a problem of integration into one of optimization. PyMC3's variational API supports a number of cutting edge algorithms, as well as minibatch for scaling to large datasets. @@ -97,7 +97,7 @@
- +
PyMC3 and Theano
Theano is the deep-learning library PyMC3 uses to construct probability distributions and then access the gradient in order to implement cutting edge inference algorithms. More advanced models may be built by understanding this layer.