From 12c14b504d25b203aa80b2b8aa43299762c882a7 Mon Sep 17 00:00:00 2001 From: "Oriol (ZBook)" Date: Wed, 5 Jul 2023 01:45:23 +0200 Subject: [PATCH 1/3] add rtd preview link to PR description --- .github/workflows/rtd-link-preview.yml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 .github/workflows/rtd-link-preview.yml diff --git a/.github/workflows/rtd-link-preview.yml b/.github/workflows/rtd-link-preview.yml new file mode 100644 index 000000000..894fadb4b --- /dev/null +++ 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" From ed5a0b4b52e094dc37e9c4cd6f5eebf6a8e1f5be Mon Sep 17 00:00:00 2001 From: "Oriol (ZBook)" Date: Wed, 5 Jul 2023 01:45:43 +0200 Subject: [PATCH 2/3] update myst substitution metadata --- .jupytext.toml | 2 +- examples/case_studies/factor_analysis.ipynb | 6 ++++-- examples/case_studies/putting_workflow.ipynb | 4 ---- .../reliability_and_calibrated_prediction.ipynb | 6 ++++-- examples/case_studies/rugby_analytics.ipynb | 6 ++++-- examples/case_studies/wrapping_jax_function.ipynb | 6 ++++-- examples/gaussian_processes/GP-MaunaLoa.ipynb | 6 ++++-- .../GLM-robust-with-outlier-detection.ipynb | 6 ++++-- 8 files changed, 25 insertions(+), 17 deletions(-) diff --git a/.jupytext.toml b/.jupytext.toml index 2d05b3de4..84e608ef4 100644 --- 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/factor_analysis.ipynb b/examples/case_studies/factor_analysis.ipynb index d68adb0e7..a8a1fbd0c 100644 --- 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/putting_workflow.ipynb b/examples/case_studies/putting_workflow.ipynb index 2f1ffe986..3c590b485 100644 --- 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/reliability_and_calibrated_prediction.ipynb b/examples/case_studies/reliability_and_calibrated_prediction.ipynb index 7741b5a65..2af46a85f 100644 --- 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/rugby_analytics.ipynb b/examples/case_studies/rugby_analytics.ipynb index daeac5205..9b894b0c8 100644 --- 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/wrapping_jax_function.ipynb b/examples/case_studies/wrapping_jax_function.ipynb index 14c8cfc4f..d48719ae5 100644 --- 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/gaussian_processes/GP-MaunaLoa.ipynb b/examples/gaussian_processes/GP-MaunaLoa.ipynb index 0f77efed7..7db5f214f 100644 --- 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/generalized_linear_models/GLM-robust-with-outlier-detection.ipynb b/examples/generalized_linear_models/GLM-robust-with-outlier-detection.ipynb index ad0509951..593ec0603 100644 --- 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, From a529281bb3f30a02ec0352e4559d28cdbe36aecb Mon Sep 17 00:00:00 2001 From: "Oriol (ZBook)" Date: Wed, 5 Jul 2023 01:47:16 +0200 Subject: [PATCH 3/3] run pre-commit --- .../case_studies/conditional_autoregressive_priors.myst.md | 3 +++ examples/case_studies/factor_analysis.myst.md | 5 +++-- examples/case_studies/putting_workflow.myst.md | 3 --- .../reliability_and_calibrated_prediction.myst.md | 5 +++-- examples/case_studies/rugby_analytics.myst.md | 5 +++-- examples/case_studies/wrapping_jax_function.myst.md | 5 +++-- .../causal_inference/interventional_distribution.myst.md | 3 +++ examples/gaussian_processes/GP-MaunaLoa.myst.md | 5 +++-- .../GLM-robust-with-outlier-detection.myst.md | 5 +++-- 9 files changed, 24 insertions(+), 15 deletions(-) diff --git a/examples/case_studies/conditional_autoregressive_priors.myst.md b/examples/case_studies/conditional_autoregressive_priors.myst.md index e0ad3e450..502b2f459 100644 --- 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.myst.md b/examples/case_studies/factor_analysis.myst.md index 66f23a692..164d939ea 100644 --- 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.myst.md b/examples/case_studies/putting_workflow.myst.md index 65004a4ed..a896273e7 100644 --- 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.myst.md b/examples/case_studies/reliability_and_calibrated_prediction.myst.md index f7d0adea0..0d893d9db 100644 --- 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.myst.md b/examples/case_studies/rugby_analytics.myst.md index 03454b1df..73d3993d3 100644 --- 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.myst.md b/examples/case_studies/wrapping_jax_function.myst.md index 45c6a9ed3..72b50d1d5 100644 --- 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 index 1d5c9de47..f7411f86c 100644 --- 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.myst.md b/examples/gaussian_processes/GP-MaunaLoa.myst.md index 5a96e4978..313a73aea 100644 --- 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.myst.md b/examples/generalized_linear_models/GLM-robust-with-outlier-detection.myst.md index a8fe05a56..cbae9debf 100644 --- 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)=