Maintenance (#556)

OriolAbril · web-flow · commit 8e84ef6858de · 2023-07-05T21:14:53.000+02:00
* add rtd preview link to PR description

* update myst substitution metadata

* run pre-commit
diff --git a/.github/workflows/rtd-link-preview.yml b/.github/workflows/rtd-link-preview.yml
@@ -0,0 +1,16 @@
+name: Read the Docs Pull Request Preview
+on:
+  pull_request_target:
+    types:
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: "pymc-examples"
diff --git a/.jupytext.toml b/.jupytext.toml
@@ -1,2 +1,2 @@
-notebook_metadata_filter = "substitutions,-jupytext.text_representation.jupytext_version"
+notebook_metadata_filter = "myst,-jupytext.text_representation.jupytext_version"
 formats = ["ipynb", ".myst.md:myst"]
diff --git a/examples/case_studies/conditional_autoregressive_priors.myst.md b/examples/case_studies/conditional_autoregressive_priors.myst.md
@@ -8,6 +8,9 @@ kernelspec:
   display_name: Python [conda env:spatial_pymc_env]
   language: python
   name: conda-env-spatial_pymc_env-py
+myst:
+  substitutions:
+    extra_dependencies: geopandas libpysal
 ---
 
 +++ {"tags": []}
diff --git a/examples/case_studies/factor_analysis.ipynb b/examples/case_studies/factor_analysis.ipynb
@@ -837,8 +837,10 @@
    "pygments_lexer": "ipython3",
    "version": "3.9.10"
   },
-  "substitutions": {
-   "extra_dependencies": "seaborn xarray-einstats"
+  "myst": {
+   "substitutions": {
+    "extra_dependencies": "seaborn"
+   }
   }
  },
  "nbformat": 4,
diff --git a/examples/case_studies/factor_analysis.myst.md b/examples/case_studies/factor_analysis.myst.md
@@ -9,8 +9,9 @@ kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
   name: python3
-substitutions:
-  extra_dependencies: seaborn xarray-einstats
+myst:
+  substitutions:
+    extra_dependencies: seaborn
 ---
 
 (factor_analysis)=
diff --git a/examples/case_studies/putting_workflow.ipynb b/examples/case_studies/putting_workflow.ipynb
@@ -1667,10 +1667,6 @@
    "pygments_lexer": "ipython3",
    "version": "3.10.9"
   },
-  "substitutions": {
-   "conda_dependencies": "!!xarray-einstats not available!!",
-   "pip_dependencies": "xarray-einstats"
-  },
   "vscode": {
    "interpreter": {
     "hash": "087adf61916f8b9a562e3919cc7201fe0599d07c87f54bc57443476208d67f09"
diff --git a/examples/case_studies/putting_workflow.myst.md b/examples/case_studies/putting_workflow.myst.md
@@ -8,9 +8,6 @@ kernelspec:
   display_name: pymc_env
   language: python
   name: python3
-substitutions:
-  conda_dependencies: '!!xarray-einstats not available!!'
-  pip_dependencies: xarray-einstats
 ---
 
 (putting_workflow)=
diff --git a/examples/case_studies/reliability_and_calibrated_prediction.ipynb b/examples/case_studies/reliability_and_calibrated_prediction.ipynb
@@ -8048,8 +8048,10 @@
    "pygments_lexer": "ipython3",
    "version": "3.10.8"
   },
-  "substitutions": {
-   "extra_dependencies": "lifelines"
+  "myst": {
+   "substitutions": {
+    "extra_dependencies": "lifelines"
+   }
   }
  },
  "nbformat": 4,
diff --git a/examples/case_studies/reliability_and_calibrated_prediction.myst.md b/examples/case_studies/reliability_and_calibrated_prediction.myst.md
@@ -8,8 +8,9 @@ kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
   name: python3
-substitutions:
-  extra_dependencies: lifelines
+myst:
+  substitutions:
+    extra_dependencies: lifelines
 ---
 
 (Reliability Statistics and Predictive Calibration)=
diff --git a/examples/case_studies/rugby_analytics.ipynb b/examples/case_studies/rugby_analytics.ipynb
@@ -2898,8 +2898,10 @@
    "pygments_lexer": "ipython3",
    "version": "3.9.10"
   },
-  "substitutions": {
-   "extra_dependencies": "seaborn numba xarray-einstats"
+  "myst": {
+   "substitutions": {
+    "extra_dependencies": "seaborn numba"
+   }
   }
  },
  "nbformat": 4,
diff --git a/examples/case_studies/rugby_analytics.myst.md b/examples/case_studies/rugby_analytics.myst.md
@@ -8,8 +8,9 @@ kernelspec:
   display_name: Python 3 (ipykernel)
   language: python
   name: python3
-substitutions:
-  extra_dependencies: seaborn numba xarray-einstats
+myst:
+  substitutions:
+    extra_dependencies: seaborn numba
 ---
 
 # A Hierarchical model for Rugby prediction
diff --git a/examples/case_studies/wrapping_jax_function.ipynb b/examples/case_studies/wrapping_jax_function.ipynb
@@ -1641,8 +1641,10 @@
    "pygments_lexer": "ipython3",
    "version": "3.10.2"
   },
-  "substitutions": {
-   "extra_dependencies": "jax numpyro"
+  "myst": {
+   "substitutions": {
+    "extra_dependencies": "jax numpyro"
+   }
   },
   "toc": {
    "base_numbering": 1,
diff --git a/examples/case_studies/wrapping_jax_function.myst.md b/examples/case_studies/wrapping_jax_function.myst.md
@@ -8,8 +8,9 @@ kernelspec:
   display_name: pymc-examples
   language: python
   name: pymc-examples
-substitutions:
-  extra_dependencies: jax numpyro
+myst:
+  substitutions:
+    extra_dependencies: jax numpyro
 ---
 
 (wrapping_jax_function)=
diff --git a/examples/causal_inference/interventional_distribution.myst.md b/examples/causal_inference/interventional_distribution.myst.md
@@ -9,6 +9,9 @@ kernelspec:
   display_name: pymc_env
   language: python
   name: pymc_env
+myst:
+  substitutions:
+    extra_dependencies: daft pymc_experimental
 ---
 
 +++ {"editable": true, "slideshow": {"slide_type": ""}, "tags": []}
diff --git a/examples/gaussian_processes/GP-MaunaLoa.ipynb b/examples/gaussian_processes/GP-MaunaLoa.ipynb
@@ -1710,8 +1710,10 @@
    "pygments_lexer": "ipython3",
    "version": "3.9.5"
   },
-  "substitutions": {
-   "extra_dependencies": "bokeh"
+  "myst": {
+   "substitutions": {
+    "extra_dependencies": "bokeh"
+   }
   }
  },
  "nbformat": 4,
diff --git a/examples/gaussian_processes/GP-MaunaLoa.myst.md b/examples/gaussian_processes/GP-MaunaLoa.myst.md
@@ -8,8 +8,9 @@ kernelspec:
   display_name: Python 3
   language: python
   name: python3
-substitutions:
-  extra_dependencies: bokeh
+myst:
+  substitutions:
+    extra_dependencies: bokeh
 ---
 
 (GP-MaunaLoa)=
diff --git a/examples/generalized_linear_models/GLM-robust-with-outlier-detection.ipynb b/examples/generalized_linear_models/GLM-robust-with-outlier-detection.ipynb
@@ -1895,8 +1895,10 @@
    "pygments_lexer": "ipython3",
    "version": "3.10.9"
   },
-  "substitutions": {
-   "extra_dependencies": "seaborn"
+  "myst": {
+   "substitutions": {
+    "extra_dependencies": "seaborn"
+   }
   },
   "toc-autonumbering": false,
   "toc-showcode": false,
diff --git a/examples/generalized_linear_models/GLM-robust-with-outlier-detection.myst.md b/examples/generalized_linear_models/GLM-robust-with-outlier-detection.myst.md
@@ -8,8 +8,9 @@ kernelspec:
   display_name: pymc_env
   language: python
   name: python3
-substitutions:
-  extra_dependencies: seaborn
+myst:
+  substitutions:
+    extra_dependencies: seaborn
 ---
 
 (GLM-robust-with-outlier-detection)=

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`		`-notebook_metadata_filter = "substitutions,-jupytext.text_representation.jupytext_version"`
	`1`	`+notebook_metadata_filter = "myst,-jupytext.text_representation.jupytext_version"`
`2`	`2`	`formats = ["ipynb", ".myst.md:myst"]`