simplify pre-commit and jupytext settings (#483)

* modify pre-commit and jupytext

* ignore myst files when building docs

Author: OriolAbril

.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|
@@ -108,10 +102,4 @@ 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"]

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

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

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

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

myst_nbs/case_studies/binning.myst.md renamed to examples/case_studies/binning.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 [conda env:pymc_env]
   language: python

myst_nbs/case_studies/blackbox_external_likelihood.myst.md renamed to examples/case_studies/blackbox_external_likelihood.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
@@ -573,7 +572,7 @@ import warnings
 
 warnings.simplefilter(
     action="ignore", category=FutureWarning
-)  # suppress emcee autocorr FutureWarning
+)  # suppress emcee autocorr FutureWarning
 
 matplotlib.rcParams["font.size"] = 18
 

myst_nbs/case_studies/blackbox_external_likelihood_numpy.myst.md renamed to examples/case_studies/blackbox_external_likelihood_numpy.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/conditional-autoregressive-model.myst.md renamed to examples/case_studies/conditional-autoregressive-model.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
@@ -644,7 +643,7 @@ class Sparse_CAR(distribution.Continuous):
         self.W = theano.sparse.as_sparse_variable(w_sparse)
         self.D = tt.as_tensor_variable(D)
 
-        # Precision Matrix (inverse of Covariance matrix)
+        # Precision Matrix (inverse of Covariance matrix)
         # d_sparse = scipy.sparse.csr_matrix(np.diag(D))
         # self.D = theano.sparse.as_sparse_variable(d_sparse)
         # self.Phi = self.tau * (self.D - self.alpha*self.W)

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

@@ -5,7 +5,6 @@ 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/hierarchical_partial_pooling.myst.md renamed to examples/case_studies/hierarchical_partial_pooling.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 3.10.5 ('pymc-dev')
   language: python

myst_nbs/case_studies/item_response_nba.myst.md renamed to examples/case_studies/item_response_nba.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/mediation_analysis.myst.md renamed to examples/case_studies/mediation_analysis.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/moderation_analysis.myst.md renamed to examples/case_studies/moderation_analysis.myst.md

@@ -4,7 +4,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.7
 kernelspec:
   display_name: pymc-dev-py39
   language: python

myst_nbs/case_studies/multilevel_modeling.myst.md renamed to examples/case_studies/multilevel_modeling.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/probabilistic_matrix_factorization.myst.md renamed to examples/case_studies/probabilistic_matrix_factorization.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/putting_workflow.myst.md renamed to examples/case_studies/putting_workflow.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 3.10.6 ('pymc_env')
   language: python

myst_nbs/case_studies/reinforcement_learning.myst.md renamed to examples/case_studies/reinforcement_learning.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/rugby_analytics.myst.md renamed to examples/case_studies/rugby_analytics.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/spline.myst.md renamed to examples/case_studies/spline.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/stochastic_volatility.myst.md renamed to examples/case_studies/stochastic_volatility.myst.md

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

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

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

myst_nbs/causal_inference/difference_in_differences.myst.md renamed to examples/causal_inference/difference_in_differences.myst.md

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

myst_nbs/causal_inference/excess_deaths.myst.md renamed to examples/causal_inference/excess_deaths.myst.md

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

myst_nbs/causal_inference/interrupted_time_series.myst.md renamed to examples/causal_inference/interrupted_time_series.myst.md

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

myst_nbs/causal_inference/regression_discontinuity.myst.md renamed to examples/causal_inference/regression_discontinuity.myst.md

@@ -5,7 +5,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.7
 kernelspec:
   display_name: pymc-dev-py39
   language: python

examples/conf.py

@@ -42,6 +42,7 @@
     "**/.ipynb_checkpoints/*",
     "extra_installs.md",
     "page_footer.md",
+    "**/*.myst.md",
 ]
 
 
@@ -174,7 +175,7 @@ def setup(app: Sphinx):
 citation_code = f"""
 ```bibtex
 @incollection{{citekey,
-  author    = "<notebook authors, see above>"
+  author    = "<notebook authors, see above>",
   title     = "<notebook title>",
   editor    = "PyMC Team",
   booktitle = "PyMC examples",
@@ -190,7 +191,7 @@ def setup(app: Sphinx):
     "extra_install_notes": "",
     "citation_code": citation_code,
 }
-jupyter_execute_notebooks = "off"
+nb_execution_mode = "off"
 
 rediraffe_redirects = {
     "index.md": "gallery.md",
@@ -227,13 +228,13 @@ def setup(app: Sphinx):
 intersphinx_mapping = {
     "aesara": ("https://aesara.readthedocs.io/en/latest/", None),
     "arviz": ("https://python.arviz.org/en/latest/", None),
-    "bambi": ("https://bambinos.github.io/bambi/main", None),
+    "bambi": ("https://bambinos.github.io/bambi", None),
     "einstats": ("https://einstats.python.arviz.org/en/latest/", None),
     "mpl": ("https://matplotlib.org/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
     "pymc": ("https://www.pymc.io/projects/docs/en/stable/", None),
     "pmx": ("https://www.pymc.io/projects/experimental/en/latest/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
-    "xarray": ("http://docs.xarray.dev/en/stable/", None),
+    "xarray": ("https://docs.xarray.dev/en/stable/", None),
 }

myst_nbs/diagnostics_and_criticism/Bayes_factor.myst.md renamed to examples/diagnostics_and_criticism/Bayes_factor.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
   language: python

myst_nbs/diagnostics_and_criticism/Diagnosing_biased_Inference_with_Divergences.myst.md renamed to examples/diagnostics_and_criticism/Diagnosing_biased_Inference_with_Divergences.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/diagnostics_and_criticism/model_averaging.myst.md renamed to examples/diagnostics_and_criticism/model_averaging.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/diagnostics_and_criticism/sampler-stats.myst.md renamed to examples/diagnostics_and_criticism/sampler-stats.myst.md

@@ -5,7 +5,6 @@ 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/gaussian_processes/GP-Circular.myst.md renamed to examples/gaussian_processes/GP-Circular.myst.md

@@ -4,7 +4,6 @@ jupytext:
     extension: .md
     format_name: myst
     format_version: 0.13
-    jupytext_version: 1.13.7
 kernelspec:
   display_name: pymc3
   language: python

myst_nbs/gaussian_processes/GP-Heteroskedastic.myst.md renamed to examples/gaussian_processes/GP-Heteroskedastic.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 [conda env:pymc3]
   language: python

myst_nbs/gaussian_processes/GP-Kron.myst.md renamed to examples/gaussian_processes/GP-Kron.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/gaussian_processes/GP-Latent.myst.md renamed to examples/gaussian_processes/GP-Latent.myst.md

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

myst_nbs/gaussian_processes/GP-Marginal.myst.md renamed to examples/gaussian_processes/GP-Marginal.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
   language: python

myst_nbs/gaussian_processes/GP-MaunaLoa.myst.md renamed to examples/gaussian_processes/GP-MaunaLoa.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
   language: python