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