Merge remote-tracking branch 'upstream/main' into ode_examples_update

Author: gbrunkhorst

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,7 +9,9 @@ if you would like help in addressing a reviewer's comments,
 or if you have been waiting too long to hear back on your PR. -->
 
 + [ ] Notebook follows style guide https://docs.pymc.io/en/latest/contributing/jupyter_style.html
-+ [ ] PR description contains a link to the relevant issue: a tracker one for existing notebooks or a proposal one for new notebooks
++ [ ] PR description contains a link to the relevant issue:
+  * a tracker one for existing notebooks (tracker issues have the "tracker id" label)
+  * or a proposal one for new notebooks
 + [ ] Check the notebook is not excluded from any pre-commit check: https://github.com/pymc-devs/pymc-examples/blob/main/.pre-commit-config.yaml
 
 

.jupytext.toml

@@ -1,5 +1,2 @@
-notebook_metadata_filter = "substitutions"
-
-[formats]
-"examples/" = "ipynb"
-"myst_nbs/" = ".myst.md:myst"
+notebook_metadata_filter = "substitutions,-jupytext.text_representation.jupytext_version"
+formats = ["ipynb", ".myst.md:myst"]

.pre-commit-config.yaml

@@ -1,10 +1,4 @@
 repos:
-- repo: https://github.com/mwouts/jupytext
-  rev: v1.13.7
-  hooks:
-  - id: jupytext
-    files: ^examples/.+\.ipynb$
-    args: ["--sync"]
 - repo: https://github.com/psf/black
   rev: 22.3.0
   hooks:
@@ -63,7 +57,7 @@ repos:
       name: Check no references that should be sphinx cross-references are urls
       description: >-
         'A quick check to prevent urls pointing to pymc docs or other sphinx built docs like arviz, numpy, scipy...'
-      files: ^examples/
+      files: ^examples/.+\.ipynb$
       exclude: >
           (?x)(index.md|
                404.md|
@@ -77,7 +71,6 @@ repos:
                examples/generalized_linear_models/GLM-logistic.ipynb|
                examples/generalized_linear_models/GLM-out-of-sample-predictions.ipynb|
                examples/generalized_linear_models/GLM-poisson-regression.ipynb|
-               examples/generalized_linear_models/GLM-robust.ipynb|
                examples/generalized_linear_models/GLM-rolling-regression.ipynb|
                examples/generalized_linear_models/GLM-simpsons-paradox.ipynb|
                examples/howto/api_quickstart.ipynb|
@@ -90,15 +83,14 @@ repos:
                examples/howto/custom_distribution.ipynb)
       entry: >
           (?x)(arviz-devs.github.io|
-               aesara.readthedocs.io|
-               aeppl.readthedocs.io|
                pymc-experimental.readthedocs.io|
                docs.pymc.io|
                numpy.org/doc|
                pymc-examples.readthedocs.io|
                docs.python.org|
                xarray.pydata.org
                python.arviz.org|
+               pytensor.readthedocs.io|
                docs.xarray.dev|
                www.pymc.io|
                docs.scipy.org/doc)
@@ -109,10 +101,4 @@ repos:
   hooks:
   - id: jupytext
     files: ^examples/.+\.ipynb$
-    args: ["--sync"]
-- repo: https://github.com/codespell-project/codespell
-  rev: v2.1.0
-  hooks:
-  - id: codespell
-    files: myst_nbs/
-    args: ["--write-changes", "--ignore-words-list", "hist,fpr,fro,lik", "--uri-ignore-words-list", "*"]
+    args: [--from, ipynb, --to, ".myst.md:myst"]

README.rst

@@ -8,9 +8,9 @@ PyMC Examples
 
 Supporting examples and tutorials for PyMC, the Python package for Bayesian statistical modeling and Probabilistic Machine Learning!
 
-Check out the `getting started guide <https://docs.pymc.io/en/latest/learning.html#learning>`__,  or
+Check out the `getting started guide <https://www.pymc.io/projects/docs/en/latest/learn.html>`__,  or
 interact with live examples using Binder! Each notebook in `PyMC examples gallery
-<https://pymc-examples.readthedocs.io>`__ has a binder badge.
+<https://www.pymc.io/projects/examples/en/latest/gallery.html>`__ has a binder badge.
 For questions on PyMC, head on over to our `PyMC Discourse <https://discourse.pymc.io/>`__ forum.
 
 Contributing
@@ -30,11 +30,8 @@ To ask a question regarding modeling or usage of PyMC we encourage posting to ou
 
 To report an issue, please use the following:
 
--  `PyMC Examples - Issue Tracker <https://github.com/pymc-devs/pymc-examples/issues>`__. For
-  issues about the example notebooks, errors in the example codes, outdated information, improvement
-  suggestions...
--  `PyMC - Issue Tracker <https://github.com/pymc-devs/pymc/issues>`__. For issues, bugs or
-  feature requests related to the PyMC library itself.
+-  `PyMC Examples - Issue Tracker <https://github.com/pymc-devs/pymc-examples/issues>`__. For issues about the example notebooks, errors in the example codes, outdated information, improvement suggestions...
+-  `PyMC - Issue Tracker <https://github.com/pymc-devs/pymc/issues>`__. For issues, bugs or feature requests related to the PyMC library itself.
 
 Finally, if you need to get in touch for non-technical information about the project, `send us an e-mail <pymc.devs@gmail.com>`__.
 
@@ -45,9 +42,9 @@ If you already know about Bayesian statistics:
 ----------------------------------------------
 
 
--  `API quickstart guide <http://docs.pymc.io/notebooks/api_quickstart>`__
--  The `PyMC tutorial <http://docs.pymc.io/notebooks/getting_started>`__
--  `PyMC examples <https://docs.pymc.io/nb_examples/index.html>`__ and the `API reference <http://docs.pymc.io/api>`__
+-  `API quickstart guide <https://www.pymc.io/projects/examples/en/latest/howto/api_quickstart.html>`__
+-  The `PyMC tutorial <https://www.pymc.io/projects/docs/en/stable/learn/core_notebooks/pymc_overview.html>`__
+-  `PyMC examples <https://www.pymc.io/projects/examples/en/latest/gallery.html>`__ and the `API reference <https://www.pymc.io/projects/docs/en/stable/api.html>`__
 
 
 
@@ -69,7 +66,7 @@ and as part of `PyMCon 2020 <https://discourse.pymc.io/c/pymcon/2020talks/15>`__
 Installation
 ------------
 
-To install PyMC on your system, see its `installation section here <https://docs.pymc.io/en/stable/>`__
+To install PyMC on your system, see its `installation section here <https://www.pymc.io/projects/docs/en/stable/installation.html>`__
 
 Citing PyMC
 ============
@@ -93,18 +90,6 @@ Support
 
 PyMC is a non-profit project under NumFOCUS umbrella. If you want to support PyMC financially, you can donate `here <https://numfocus.salsalabs.org/donate-to-pymc3/index.html>`__.
 
-PyMC for enterprise
-===================
-`PyMC is now available as part of the Tidelift Subscription!`
-
-Tidelift is working with PyMC and the maintainers of thousands of other open source
-projects to deliver commercial support and maintenance for the open source dependencies
-you use to build your applications. Save time, reduce risk, and improve code health,
-while contributing financially to PyMC -- making it even more robust, reliable and,
-let's face it, amazing!
-
-|tidelift_learn| |tidelift_demo|
-
 Sponsors
 ========
 
@@ -118,7 +103,3 @@ Sponsors
    :target: http://www.numfocus.org/
 .. |PyMCLabs| image:: https://raw.githubusercontent.com/pymc-devs/pymc/main/docs/logos/sponsors/pymc-labs.png
    :target: https://pymc-labs.io
-.. |tidelift_learn| image:: https://img.shields.io/badge/-learn%20more-2dd160.svg?color=orange&labelColor=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
-.. |tidelift_demo| image:: https://img.shields.io/badge/-request%20a%20demo-2dd160.svg?color=orange&labelColor=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/request-a-demo?utm_source=pypi-pymc3&utm_medium=referral&utm_campaign=enterprise

myst_nbs/case_studies/BART_introduction.myst.md renamed to examples/case_studies/BART_introduction.myst.md

@@ -4,7 +4,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.7
 kernelspec:
   display_name: Python 3 (ipykernel)
   language: python

myst_nbs/case_studies/BEST.myst.md renamed to examples/case_studies/BEST.myst.md

@@ -4,7 +4,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.7
 kernelspec:
   display_name: bayes_toolbox
   language: python

examples/case_studies/GEV.ipynb

@@ -45,12 +45,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import aesara.tensor as at\n",
     "import arviz as az\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import pymc as pm\n",
     "import pymc_experimental.distributions as pmx\n",
+    "import pytensor.tensor as pt\n",
     "\n",
     "from arviz.plots import plot_utils as azpu"
    ]
@@ -984,7 +984,7 @@
       "Python version       : 3.10.6\n",
       "IPython version      : 8.5.0\n",
       "\n",
-      "aesara: 2.8.6\n",
+      "pytensor: 2.8.6\n",
       "arviz : 0.12.1\n",
       "\n",
       "pymc_experimental: 0.0.1\n",
@@ -993,7 +993,7 @@
       "arviz            : 0.12.1\n",
       "numpy            : 1.23.3\n",
       "json             : 2.0.9\n",
-      "aesara           : 2.8.6\n",
+      "pytensor           : 2.8.6\n",
       "pymc             : 3.9.3+1493.g372d7c24\n",
       "\n",
       "Watermark: 2.3.1\n",
@@ -1003,7 +1003,7 @@
    ],
    "source": [
     "%load_ext watermark\n",
-    "%watermark -n -u -v -iv -w -p aesara,arviz"
+    "%watermark -n -u -v -iv -w -p pytensor,arviz"
    ]
   },
   {

myst_nbs/case_studies/GEV.myst.md renamed to examples/case_studies/GEV.myst.md

@@ -4,7 +4,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.7
 kernelspec:
   display_name: pymc4-dev
   language: python
@@ -41,12 +40,12 @@ Note that this parametrization of the shape parameter $\xi$ is opposite in sign
 We will use the example of the Port Pirie annual maximum sea-level data used in {cite:t}`coles2001gev`, and compare with the frequentist results presented there.
 
 ```{code-cell} ipython3
-import aesara.tensor as at
 import arviz as az
 import matplotlib.pyplot as plt
 import numpy as np
 import pymc as pm
 import pymc_experimental.distributions as pmx
+import pytensor.tensor as pt
 
 from arviz.plots import plot_utils as azpu
 ```
@@ -233,7 +232,7 @@ az.plot_pair(idata, var_names=["μ", "σ", "ξ"], kind="kde", marginals=True, di
 
 ```{code-cell} ipython3
 %load_ext watermark
-%watermark -n -u -v -iv -w -p aesara,arviz
+%watermark -n -u -v -iv -w -p pytensor,arviz
 ```
 
 ```{code-cell} ipython3

examples/case_studies/LKJ.ipynb

@@ -987,7 +987,7 @@
       "Python version       : 3.7.12\n",
       "IPython version      : 5.5.0\n",
       "\n",
-      "aesara: 2.4.0\n",
+      "pytensor: 2.4.0\n",
       "xarray: 0.18.2\n",
       "\n",
       "pymc      : 4.0.0b2\n",
@@ -1004,7 +1004,7 @@
    ],
    "source": [
     "%load_ext watermark\n",
-    "%watermark -n -u -v -iv -w -p aesara,xarray"
+    "%watermark -n -u -v -iv -w -p pytensor,xarray"
    ]
   }
  ],

myst_nbs/case_studies/LKJ.myst.md renamed to examples/case_studies/LKJ.myst.md

@@ -4,7 +4,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.7
 kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
@@ -327,5 +326,5 @@ id: kJCfuzGtr2Pq
 outputId: da547b05-d812-4959-aff6-cf4a12faca15
 ---
 %load_ext watermark
-%watermark -n -u -v -iv -w -p aesara,xarray
+%watermark -n -u -v -iv -w -p pytensor,xarray
 ```

examples/case_studies/bayesian_ab_testing_introduction.ipynb

@@ -2163,7 +2163,7 @@
       "Python version       : 3.8.10\n",
       "IPython version      : 8.4.0\n",
       "\n",
-      "aesara: 2.7.3\n",
+      "pytensor: 2.7.3\n",
       "xarray: 2022.3.0\n",
       "\n",
       "matplotlib: 3.5.2\n",
@@ -2181,7 +2181,7 @@
    ],
    "source": [
     "%load_ext watermark\n",
-    "%watermark -n -u -v -iv -w -p aesara,xarray"
+    "%watermark -n -u -v -iv -w -p pytensor,xarray"
    ]
   },
   {

myst_nbs/case_studies/bayesian_ab_testing_introduction.myst.md renamed to examples/case_studies/bayesian_ab_testing_introduction.myst.md

@@ -4,7 +4,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.7
 kernelspec:
   display_name: Python 3.8.10 ('pymc-examples-ipRlw-UN')
   language: python
@@ -688,7 +687,7 @@ We also plan to create more PyMC tutorials on these topics, so stay tuned!
 
 ```{code-cell} ipython3
 %load_ext watermark
-%watermark -n -u -v -iv -w -p aesara,xarray
+%watermark -n -u -v -iv -w -p pytensor,xarray
 ```
 
 :::{include} ../page_footer.md