diff --git a/.jupytext.toml b/.jupytext.toml index 9e926543f..2d05b3de4 100644 --- a/.jupytext.toml +++ b/.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"] diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 38e80e682..b7ff1c319 100644 --- a/.pre-commit-config.yaml +++ b/.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"] diff --git a/myst_nbs/case_studies/BART_introduction.myst.md b/examples/case_studies/BART_introduction.myst.md similarity index 99% rename from myst_nbs/case_studies/BART_introduction.myst.md rename to examples/case_studies/BART_introduction.myst.md index 8ac2d8eb5..d0eb894a7 100644 --- a/myst_nbs/case_studies/BART_introduction.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/BEST.myst.md b/examples/case_studies/BEST.myst.md similarity index 99% rename from myst_nbs/case_studies/BEST.myst.md rename to examples/case_studies/BEST.myst.md index a2876a5c1..43663062b 100644 --- a/myst_nbs/case_studies/BEST.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/GEV.myst.md b/examples/case_studies/GEV.myst.md similarity index 99% rename from myst_nbs/case_studies/GEV.myst.md rename to examples/case_studies/GEV.myst.md index 3cbef9887..04f6cf135 100644 --- a/myst_nbs/case_studies/GEV.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/LKJ.myst.md b/examples/case_studies/LKJ.myst.md similarity index 99% rename from myst_nbs/case_studies/LKJ.myst.md rename to examples/case_studies/LKJ.myst.md index 6361174ac..a4ee601f5 100644 --- a/myst_nbs/case_studies/LKJ.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/bayesian_ab_testing_introduction.myst.md b/examples/case_studies/bayesian_ab_testing_introduction.myst.md similarity index 99% rename from myst_nbs/case_studies/bayesian_ab_testing_introduction.myst.md rename to examples/case_studies/bayesian_ab_testing_introduction.myst.md index 53c08e528..d76b56cc5 100644 --- a/myst_nbs/case_studies/bayesian_ab_testing_introduction.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/binning.myst.md b/examples/case_studies/binning.myst.md similarity index 99% rename from myst_nbs/case_studies/binning.myst.md rename to examples/case_studies/binning.myst.md index dadb01c7a..6f3b4cbf1 100644 --- a/myst_nbs/case_studies/binning.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/blackbox_external_likelihood.myst.md b/examples/case_studies/blackbox_external_likelihood.myst.md similarity index 99% rename from myst_nbs/case_studies/blackbox_external_likelihood.myst.md rename to examples/case_studies/blackbox_external_likelihood.myst.md index bea2183f7..9d21c84a6 100644 --- a/myst_nbs/case_studies/blackbox_external_likelihood.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/blackbox_external_likelihood_numpy.myst.md b/examples/case_studies/blackbox_external_likelihood_numpy.myst.md similarity index 99% rename from myst_nbs/case_studies/blackbox_external_likelihood_numpy.myst.md rename to examples/case_studies/blackbox_external_likelihood_numpy.myst.md index 2ee5ccb0f..9e100178d 100644 --- a/myst_nbs/case_studies/blackbox_external_likelihood_numpy.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/conditional-autoregressive-model.myst.md b/examples/case_studies/conditional-autoregressive-model.myst.md similarity index 99% rename from myst_nbs/case_studies/conditional-autoregressive-model.myst.md rename to examples/case_studies/conditional-autoregressive-model.myst.md index 07af629e4..fb48add7e 100644 --- a/myst_nbs/case_studies/conditional-autoregressive-model.myst.md +++ b/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) diff --git a/myst_nbs/case_studies/factor_analysis.myst.md b/examples/case_studies/factor_analysis.myst.md similarity index 99% rename from myst_nbs/case_studies/factor_analysis.myst.md rename to examples/case_studies/factor_analysis.myst.md index 33ff60c6e..1b27e3a4e 100644 --- a/myst_nbs/case_studies/factor_analysis.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/hierarchical_partial_pooling.myst.md b/examples/case_studies/hierarchical_partial_pooling.myst.md similarity index 99% rename from myst_nbs/case_studies/hierarchical_partial_pooling.myst.md rename to examples/case_studies/hierarchical_partial_pooling.myst.md index fe9b637b7..91b405387 100644 --- a/myst_nbs/case_studies/hierarchical_partial_pooling.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/item_response_nba.myst.md b/examples/case_studies/item_response_nba.myst.md similarity index 99% rename from myst_nbs/case_studies/item_response_nba.myst.md rename to examples/case_studies/item_response_nba.myst.md index 402b8f25e..73fa3ae0b 100644 --- a/myst_nbs/case_studies/item_response_nba.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/mediation_analysis.myst.md b/examples/case_studies/mediation_analysis.myst.md similarity index 99% rename from myst_nbs/case_studies/mediation_analysis.myst.md rename to examples/case_studies/mediation_analysis.myst.md index e64528a42..26bcd34b6 100644 --- a/myst_nbs/case_studies/mediation_analysis.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/moderation_analysis.myst.md b/examples/case_studies/moderation_analysis.myst.md similarity index 99% rename from myst_nbs/case_studies/moderation_analysis.myst.md rename to examples/case_studies/moderation_analysis.myst.md index a8b78233c..e918436c7 100644 --- a/myst_nbs/case_studies/moderation_analysis.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/multilevel_modeling.myst.md b/examples/case_studies/multilevel_modeling.myst.md similarity index 99% rename from myst_nbs/case_studies/multilevel_modeling.myst.md rename to examples/case_studies/multilevel_modeling.myst.md index 61bb342da..da9bd5c17 100644 --- a/myst_nbs/case_studies/multilevel_modeling.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/probabilistic_matrix_factorization.myst.md b/examples/case_studies/probabilistic_matrix_factorization.myst.md similarity index 99% rename from myst_nbs/case_studies/probabilistic_matrix_factorization.myst.md rename to examples/case_studies/probabilistic_matrix_factorization.myst.md index cd6dde4b2..d46d526ef 100644 --- a/myst_nbs/case_studies/probabilistic_matrix_factorization.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/putting_workflow.myst.md b/examples/case_studies/putting_workflow.myst.md similarity index 99% rename from myst_nbs/case_studies/putting_workflow.myst.md rename to examples/case_studies/putting_workflow.myst.md index ffe45c962..26fc9fdcb 100644 --- a/myst_nbs/case_studies/putting_workflow.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/reinforcement_learning.myst.md b/examples/case_studies/reinforcement_learning.myst.md similarity index 99% rename from myst_nbs/case_studies/reinforcement_learning.myst.md rename to examples/case_studies/reinforcement_learning.myst.md index 9638f4303..88117ce46 100644 --- a/myst_nbs/case_studies/reinforcement_learning.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/rugby_analytics.myst.md b/examples/case_studies/rugby_analytics.myst.md similarity index 99% rename from myst_nbs/case_studies/rugby_analytics.myst.md rename to examples/case_studies/rugby_analytics.myst.md index 211d1212d..cbbd739f3 100644 --- a/myst_nbs/case_studies/rugby_analytics.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/spline.myst.md b/examples/case_studies/spline.myst.md similarity index 99% rename from myst_nbs/case_studies/spline.myst.md rename to examples/case_studies/spline.myst.md index a3259874d..b6bffb2e2 100644 --- a/myst_nbs/case_studies/spline.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/stochastic_volatility.myst.md b/examples/case_studies/stochastic_volatility.myst.md similarity index 99% rename from myst_nbs/case_studies/stochastic_volatility.myst.md rename to examples/case_studies/stochastic_volatility.myst.md index 1409c8f17..141465111 100644 --- a/myst_nbs/case_studies/stochastic_volatility.myst.md +++ b/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 diff --git a/myst_nbs/case_studies/wrapping_jax_function.myst.md b/examples/case_studies/wrapping_jax_function.myst.md similarity index 99% rename from myst_nbs/case_studies/wrapping_jax_function.myst.md rename to examples/case_studies/wrapping_jax_function.myst.md index add11f1c0..49c25fc9b 100644 --- a/myst_nbs/case_studies/wrapping_jax_function.myst.md +++ b/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 diff --git a/myst_nbs/causal_inference/difference_in_differences.myst.md b/examples/causal_inference/difference_in_differences.myst.md similarity index 99% rename from myst_nbs/causal_inference/difference_in_differences.myst.md rename to examples/causal_inference/difference_in_differences.myst.md index 0bceba1a1..b6a18029e 100644 --- a/myst_nbs/causal_inference/difference_in_differences.myst.md +++ b/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 diff --git a/myst_nbs/causal_inference/excess_deaths.myst.md b/examples/causal_inference/excess_deaths.myst.md similarity index 99% rename from myst_nbs/causal_inference/excess_deaths.myst.md rename to examples/causal_inference/excess_deaths.myst.md index 00767c924..e69f0c821 100644 --- a/myst_nbs/causal_inference/excess_deaths.myst.md +++ b/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 diff --git a/myst_nbs/causal_inference/interrupted_time_series.myst.md b/examples/causal_inference/interrupted_time_series.myst.md similarity index 99% rename from myst_nbs/causal_inference/interrupted_time_series.myst.md rename to examples/causal_inference/interrupted_time_series.myst.md index 683ce956a..dcac83139 100644 --- a/myst_nbs/causal_inference/interrupted_time_series.myst.md +++ b/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 diff --git a/myst_nbs/causal_inference/regression_discontinuity.myst.md b/examples/causal_inference/regression_discontinuity.myst.md similarity index 99% rename from myst_nbs/causal_inference/regression_discontinuity.myst.md rename to examples/causal_inference/regression_discontinuity.myst.md index 7aefa892e..e4bf30d96 100644 --- a/myst_nbs/causal_inference/regression_discontinuity.myst.md +++ b/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 diff --git a/examples/conf.py b/examples/conf.py index 976531e9f..b76491ac2 100644 --- a/examples/conf.py +++ b/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 = "" + author = "", 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", @@ -227,7 +228,7 @@ 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), @@ -235,5 +236,5 @@ def setup(app: Sphinx): "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), } diff --git a/myst_nbs/diagnostics_and_criticism/Bayes_factor.myst.md b/examples/diagnostics_and_criticism/Bayes_factor.myst.md similarity index 99% rename from myst_nbs/diagnostics_and_criticism/Bayes_factor.myst.md rename to examples/diagnostics_and_criticism/Bayes_factor.myst.md index 50c9afb0d..8e3b2e3f5 100644 --- a/myst_nbs/diagnostics_and_criticism/Bayes_factor.myst.md +++ b/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 diff --git a/myst_nbs/diagnostics_and_criticism/Diagnosing_biased_Inference_with_Divergences.myst.md b/examples/diagnostics_and_criticism/Diagnosing_biased_Inference_with_Divergences.myst.md similarity index 99% rename from myst_nbs/diagnostics_and_criticism/Diagnosing_biased_Inference_with_Divergences.myst.md rename to examples/diagnostics_and_criticism/Diagnosing_biased_Inference_with_Divergences.myst.md index c28d4c42d..1ff759ff1 100644 --- a/myst_nbs/diagnostics_and_criticism/Diagnosing_biased_Inference_with_Divergences.myst.md +++ b/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 diff --git a/myst_nbs/diagnostics_and_criticism/model_averaging.myst.md b/examples/diagnostics_and_criticism/model_averaging.myst.md similarity index 99% rename from myst_nbs/diagnostics_and_criticism/model_averaging.myst.md rename to examples/diagnostics_and_criticism/model_averaging.myst.md index 54c4ce251..413564b24 100644 --- a/myst_nbs/diagnostics_and_criticism/model_averaging.myst.md +++ b/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 diff --git a/myst_nbs/diagnostics_and_criticism/sampler-stats.myst.md b/examples/diagnostics_and_criticism/sampler-stats.myst.md similarity index 99% rename from myst_nbs/diagnostics_and_criticism/sampler-stats.myst.md rename to examples/diagnostics_and_criticism/sampler-stats.myst.md index 8a3467ad6..07914d0e0 100644 --- a/myst_nbs/diagnostics_and_criticism/sampler-stats.myst.md +++ b/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 diff --git a/myst_nbs/gaussian_processes/GP-Circular.myst.md b/examples/gaussian_processes/GP-Circular.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/GP-Circular.myst.md rename to examples/gaussian_processes/GP-Circular.myst.md index 330da3c84..396bff41a 100644 --- a/myst_nbs/gaussian_processes/GP-Circular.myst.md +++ b/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 diff --git a/myst_nbs/gaussian_processes/GP-Heteroskedastic.myst.md b/examples/gaussian_processes/GP-Heteroskedastic.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/GP-Heteroskedastic.myst.md rename to examples/gaussian_processes/GP-Heteroskedastic.myst.md index d36e73df0..0e05d46ad 100644 --- a/myst_nbs/gaussian_processes/GP-Heteroskedastic.myst.md +++ b/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 diff --git a/myst_nbs/gaussian_processes/GP-Kron.myst.md b/examples/gaussian_processes/GP-Kron.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/GP-Kron.myst.md rename to examples/gaussian_processes/GP-Kron.myst.md index 3b7a30305..b20d44d80 100644 --- a/myst_nbs/gaussian_processes/GP-Kron.myst.md +++ b/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 diff --git a/myst_nbs/gaussian_processes/GP-Latent.myst.md b/examples/gaussian_processes/GP-Latent.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/GP-Latent.myst.md rename to examples/gaussian_processes/GP-Latent.myst.md index 278e0b44f..108954a9f 100644 --- a/myst_nbs/gaussian_processes/GP-Latent.myst.md +++ b/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 diff --git a/myst_nbs/gaussian_processes/GP-Marginal.myst.md b/examples/gaussian_processes/GP-Marginal.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/GP-Marginal.myst.md rename to examples/gaussian_processes/GP-Marginal.myst.md index 567d39835..e0c39182f 100644 --- a/myst_nbs/gaussian_processes/GP-Marginal.myst.md +++ b/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 diff --git a/myst_nbs/gaussian_processes/GP-MaunaLoa.myst.md b/examples/gaussian_processes/GP-MaunaLoa.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/GP-MaunaLoa.myst.md rename to examples/gaussian_processes/GP-MaunaLoa.myst.md index 0e8f2a827..5a96e4978 100644 --- a/myst_nbs/gaussian_processes/GP-MaunaLoa.myst.md +++ b/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 diff --git a/myst_nbs/gaussian_processes/GP-MaunaLoa2.myst.md b/examples/gaussian_processes/GP-MaunaLoa2.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/GP-MaunaLoa2.myst.md rename to examples/gaussian_processes/GP-MaunaLoa2.myst.md index 6fbd05b34..a10b75640 100644 --- a/myst_nbs/gaussian_processes/GP-MaunaLoa2.myst.md +++ b/examples/gaussian_processes/GP-MaunaLoa2.myst.md @@ -4,7 +4,6 @@ jupytext: extension: .md format_name: myst format_version: 0.13 - jupytext_version: 1.13.7 kernelspec: display_name: dev-pymc language: python @@ -654,7 +653,7 @@ plt.xlabel("year") plt.ylabel("CO2 (ppm)"); ``` -Since the ice core data isn't measured accurately, it won't be possible to backcast the seasonal component *unless we model uncertainty in x*. +Since the ice core data isn't measured accurately, it won't be possible to backcast the seasonal component *unless we model uncertainty in x*. +++ diff --git a/myst_nbs/gaussian_processes/GP-MeansAndCovs.myst.md b/examples/gaussian_processes/GP-MeansAndCovs.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/GP-MeansAndCovs.myst.md rename to examples/gaussian_processes/GP-MeansAndCovs.myst.md index 9ff935c68..460778c4a 100644 --- a/myst_nbs/gaussian_processes/GP-MeansAndCovs.myst.md +++ b/examples/gaussian_processes/GP-MeansAndCovs.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 diff --git a/myst_nbs/gaussian_processes/GP-SparseApprox.myst.md b/examples/gaussian_processes/GP-SparseApprox.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/GP-SparseApprox.myst.md rename to examples/gaussian_processes/GP-SparseApprox.myst.md index 7574bc5ad..3af35fcff 100644 --- a/myst_nbs/gaussian_processes/GP-SparseApprox.myst.md +++ b/examples/gaussian_processes/GP-SparseApprox.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 diff --git a/myst_nbs/gaussian_processes/GP-TProcess.myst.md b/examples/gaussian_processes/GP-TProcess.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/GP-TProcess.myst.md rename to examples/gaussian_processes/GP-TProcess.myst.md index 272695728..bc4d91a8c 100644 --- a/myst_nbs/gaussian_processes/GP-TProcess.myst.md +++ b/examples/gaussian_processes/GP-TProcess.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 diff --git a/myst_nbs/gaussian_processes/GP-smoothing.myst.md b/examples/gaussian_processes/GP-smoothing.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/GP-smoothing.myst.md rename to examples/gaussian_processes/GP-smoothing.myst.md index e277d43f1..ecde091a9 100644 --- a/myst_nbs/gaussian_processes/GP-smoothing.myst.md +++ b/examples/gaussian_processes/GP-smoothing.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 diff --git a/myst_nbs/gaussian_processes/MOGP-Coregion-Hadamard.myst.md b/examples/gaussian_processes/MOGP-Coregion-Hadamard.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/MOGP-Coregion-Hadamard.myst.md rename to examples/gaussian_processes/MOGP-Coregion-Hadamard.myst.md index 7bf7fde2b..28f4ad5cc 100644 --- a/myst_nbs/gaussian_processes/MOGP-Coregion-Hadamard.myst.md +++ b/examples/gaussian_processes/MOGP-Coregion-Hadamard.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 diff --git a/myst_nbs/gaussian_processes/gaussian_process.myst.md b/examples/gaussian_processes/gaussian_process.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/gaussian_process.myst.md rename to examples/gaussian_processes/gaussian_process.myst.md index 9d1a8b69c..f33f17745 100644 --- a/myst_nbs/gaussian_processes/gaussian_process.myst.md +++ b/examples/gaussian_processes/gaussian_process.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 diff --git a/myst_nbs/gaussian_processes/log-gaussian-cox-process.myst.md b/examples/gaussian_processes/log-gaussian-cox-process.myst.md similarity index 99% rename from myst_nbs/gaussian_processes/log-gaussian-cox-process.myst.md rename to examples/gaussian_processes/log-gaussian-cox-process.myst.md index f60586107..b12faf686 100644 --- a/myst_nbs/gaussian_processes/log-gaussian-cox-process.myst.md +++ b/examples/gaussian_processes/log-gaussian-cox-process.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 diff --git a/myst_nbs/generalized_linear_models/GLM-binomial-regression.myst.md b/examples/generalized_linear_models/GLM-binomial-regression.myst.md similarity index 99% rename from myst_nbs/generalized_linear_models/GLM-binomial-regression.myst.md rename to examples/generalized_linear_models/GLM-binomial-regression.myst.md index a8bdf8bd5..c820cec50 100644 --- a/myst_nbs/generalized_linear_models/GLM-binomial-regression.myst.md +++ b/examples/generalized_linear_models/GLM-binomial-regression.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 diff --git a/myst_nbs/generalized_linear_models/GLM-hierarchical-binomial-model.myst.md b/examples/generalized_linear_models/GLM-hierarchical-binomial-model.myst.md similarity index 99% rename from myst_nbs/generalized_linear_models/GLM-hierarchical-binomial-model.myst.md rename to examples/generalized_linear_models/GLM-hierarchical-binomial-model.myst.md index 73c9bdba0..15e9edb7f 100644 --- a/myst_nbs/generalized_linear_models/GLM-hierarchical-binomial-model.myst.md +++ b/examples/generalized_linear_models/GLM-hierarchical-binomial-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 3.9.7 ('base') language: python diff --git a/myst_nbs/generalized_linear_models/GLM-model-selection.myst.md b/examples/generalized_linear_models/GLM-model-selection.myst.md similarity index 99% rename from myst_nbs/generalized_linear_models/GLM-model-selection.myst.md rename to examples/generalized_linear_models/GLM-model-selection.myst.md index 50f2da23a..5ef3b5ea8 100644 --- a/myst_nbs/generalized_linear_models/GLM-model-selection.myst.md +++ b/examples/generalized_linear_models/GLM-model-selection.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 diff --git a/myst_nbs/generalized_linear_models/GLM-negative-binomial-regression.myst.md b/examples/generalized_linear_models/GLM-negative-binomial-regression.myst.md similarity index 99% rename from myst_nbs/generalized_linear_models/GLM-negative-binomial-regression.myst.md rename to examples/generalized_linear_models/GLM-negative-binomial-regression.myst.md index 9bec08432..1ff6a7001 100644 --- a/myst_nbs/generalized_linear_models/GLM-negative-binomial-regression.myst.md +++ b/examples/generalized_linear_models/GLM-negative-binomial-regression.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 3.9.12 ('pymc-dev-py39') language: python diff --git a/myst_nbs/generalized_linear_models/GLM-out-of-sample-predictions.myst.md b/examples/generalized_linear_models/GLM-out-of-sample-predictions.myst.md similarity index 99% rename from myst_nbs/generalized_linear_models/GLM-out-of-sample-predictions.myst.md rename to examples/generalized_linear_models/GLM-out-of-sample-predictions.myst.md index 8a9bcce31..2dfd2669d 100644 --- a/myst_nbs/generalized_linear_models/GLM-out-of-sample-predictions.myst.md +++ b/examples/generalized_linear_models/GLM-out-of-sample-predictions.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 3.7.6 64-bit (''website_projects'': conda)' metadata: diff --git a/myst_nbs/generalized_linear_models/GLM-poisson-regression.myst.md b/examples/generalized_linear_models/GLM-poisson-regression.myst.md similarity index 99% rename from myst_nbs/generalized_linear_models/GLM-poisson-regression.myst.md rename to examples/generalized_linear_models/GLM-poisson-regression.myst.md index 864a11722..7ddb4e14d 100644 --- a/myst_nbs/generalized_linear_models/GLM-poisson-regression.myst.md +++ b/examples/generalized_linear_models/GLM-poisson-regression.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-ex language: python diff --git a/myst_nbs/generalized_linear_models/GLM-robust-with-outlier-detection.myst.md b/examples/generalized_linear_models/GLM-robust-with-outlier-detection.myst.md similarity index 99% rename from myst_nbs/generalized_linear_models/GLM-robust-with-outlier-detection.myst.md rename to examples/generalized_linear_models/GLM-robust-with-outlier-detection.myst.md index 8e422c8d5..8d0acd5ae 100644 --- a/myst_nbs/generalized_linear_models/GLM-robust-with-outlier-detection.myst.md +++ b/examples/generalized_linear_models/GLM-robust-with-outlier-detection.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 diff --git a/myst_nbs/generalized_linear_models/GLM-robust.myst.md b/examples/generalized_linear_models/GLM-robust.myst.md similarity index 99% rename from myst_nbs/generalized_linear_models/GLM-robust.myst.md rename to examples/generalized_linear_models/GLM-robust.myst.md index 3f3949b41..ec3983d51 100644 --- a/myst_nbs/generalized_linear_models/GLM-robust.myst.md +++ b/examples/generalized_linear_models/GLM-robust.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 diff --git a/myst_nbs/generalized_linear_models/GLM-rolling-regression.myst.md b/examples/generalized_linear_models/GLM-rolling-regression.myst.md similarity index 99% rename from myst_nbs/generalized_linear_models/GLM-rolling-regression.myst.md rename to examples/generalized_linear_models/GLM-rolling-regression.myst.md index 83545beff..39545c4c5 100644 --- a/myst_nbs/generalized_linear_models/GLM-rolling-regression.myst.md +++ b/examples/generalized_linear_models/GLM-rolling-regression.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 diff --git a/myst_nbs/generalized_linear_models/GLM-simpsons-paradox.myst.md b/examples/generalized_linear_models/GLM-simpsons-paradox.myst.md similarity index 99% rename from myst_nbs/generalized_linear_models/GLM-simpsons-paradox.myst.md rename to examples/generalized_linear_models/GLM-simpsons-paradox.myst.md index 84e14c8cf..e90e2a013 100644 --- a/myst_nbs/generalized_linear_models/GLM-simpsons-paradox.myst.md +++ b/examples/generalized_linear_models/GLM-simpsons-paradox.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 diff --git a/myst_nbs/generalized_linear_models/GLM-truncated-censored-regression.myst.md b/examples/generalized_linear_models/GLM-truncated-censored-regression.myst.md similarity index 99% rename from myst_nbs/generalized_linear_models/GLM-truncated-censored-regression.myst.md rename to examples/generalized_linear_models/GLM-truncated-censored-regression.myst.md index 24c04838b..57000232e 100644 --- a/myst_nbs/generalized_linear_models/GLM-truncated-censored-regression.myst.md +++ b/examples/generalized_linear_models/GLM-truncated-censored-regression.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 diff --git a/myst_nbs/howto/api_quickstart.myst.md b/examples/howto/api_quickstart.myst.md similarity index 99% rename from myst_nbs/howto/api_quickstart.myst.md rename to examples/howto/api_quickstart.myst.md index fc616694e..6b011e3dd 100644 --- a/myst_nbs/howto/api_quickstart.myst.md +++ b/examples/howto/api_quickstart.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 diff --git a/myst_nbs/howto/custom_distribution.myst.md b/examples/howto/custom_distribution.myst.md similarity index 99% rename from myst_nbs/howto/custom_distribution.myst.md rename to examples/howto/custom_distribution.myst.md index 9aec8e1b1..f1834163d 100644 --- a/myst_nbs/howto/custom_distribution.myst.md +++ b/examples/howto/custom_distribution.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 diff --git a/myst_nbs/howto/data_container.myst.md b/examples/howto/data_container.myst.md similarity index 99% rename from myst_nbs/howto/data_container.myst.md rename to examples/howto/data_container.myst.md index 321b00d92..f3167d6fa 100644 --- a/myst_nbs/howto/data_container.myst.md +++ b/examples/howto/data_container.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 diff --git a/myst_nbs/howto/howto_debugging.myst.md b/examples/howto/howto_debugging.myst.md similarity index 99% rename from myst_nbs/howto/howto_debugging.myst.md rename to examples/howto/howto_debugging.myst.md index d4fb0630a..a45512b27 100644 --- a/myst_nbs/howto/howto_debugging.myst.md +++ b/examples/howto/howto_debugging.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 diff --git a/myst_nbs/howto/lasso_block_update.myst.md b/examples/howto/lasso_block_update.myst.md similarity index 99% rename from myst_nbs/howto/lasso_block_update.myst.md rename to examples/howto/lasso_block_update.myst.md index 2bbd83671..9a993f35d 100644 --- a/myst_nbs/howto/lasso_block_update.myst.md +++ b/examples/howto/lasso_block_update.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 diff --git a/myst_nbs/howto/profiling.myst.md b/examples/howto/profiling.myst.md similarity index 98% rename from myst_nbs/howto/profiling.myst.md rename to examples/howto/profiling.myst.md index f7f12b890..b253f3f62 100644 --- a/myst_nbs/howto/profiling.myst.md +++ b/examples/howto/profiling.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 diff --git a/myst_nbs/howto/sampling_callback.myst.md b/examples/howto/sampling_callback.myst.md similarity index 99% rename from myst_nbs/howto/sampling_callback.myst.md rename to examples/howto/sampling_callback.myst.md index 239fee479..adfcbb94e 100644 --- a/myst_nbs/howto/sampling_callback.myst.md +++ b/examples/howto/sampling_callback.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 3.9.7 ('pymc3_stable') language: python diff --git a/myst_nbs/howto/sampling_compound_step.myst.md b/examples/howto/sampling_compound_step.myst.md similarity index 99% rename from myst_nbs/howto/sampling_compound_step.myst.md rename to examples/howto/sampling_compound_step.myst.md index f00445bbc..bbdca1a05 100644 --- a/myst_nbs/howto/sampling_compound_step.myst.md +++ b/examples/howto/sampling_compound_step.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 diff --git a/myst_nbs/howto/sampling_conjugate_step.myst.md b/examples/howto/sampling_conjugate_step.myst.md similarity index 99% rename from myst_nbs/howto/sampling_conjugate_step.myst.md rename to examples/howto/sampling_conjugate_step.myst.md index e14b9b064..2d09d01a4 100644 --- a/myst_nbs/howto/sampling_conjugate_step.myst.md +++ b/examples/howto/sampling_conjugate_step.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 (PyMC3 Dev) language: python diff --git a/myst_nbs/howto/updating_priors.myst.md b/examples/howto/updating_priors.myst.md similarity index 99% rename from myst_nbs/howto/updating_priors.myst.md rename to examples/howto/updating_priors.myst.md index 510ed5199..d06cc3962 100644 --- a/myst_nbs/howto/updating_priors.myst.md +++ b/examples/howto/updating_priors.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 (PyMC3 Dev) language: python diff --git a/myst_nbs/mixture_models/dependent_density_regression.myst.md b/examples/mixture_models/dependent_density_regression.myst.md similarity index 99% rename from myst_nbs/mixture_models/dependent_density_regression.myst.md rename to examples/mixture_models/dependent_density_regression.myst.md index d387ba8dc..aa2dc78ed 100644 --- a/myst_nbs/mixture_models/dependent_density_regression.myst.md +++ b/examples/mixture_models/dependent_density_regression.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 diff --git a/myst_nbs/mixture_models/dirichlet_mixture_of_multinomials.myst.md b/examples/mixture_models/dirichlet_mixture_of_multinomials.myst.md similarity index 99% rename from myst_nbs/mixture_models/dirichlet_mixture_of_multinomials.myst.md rename to examples/mixture_models/dirichlet_mixture_of_multinomials.myst.md index 51a15e64a..6ad18d1d8 100644 --- a/myst_nbs/mixture_models/dirichlet_mixture_of_multinomials.myst.md +++ b/examples/mixture_models/dirichlet_mixture_of_multinomials.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 diff --git a/myst_nbs/mixture_models/dp_mix.myst.md b/examples/mixture_models/dp_mix.myst.md similarity index 99% rename from myst_nbs/mixture_models/dp_mix.myst.md rename to examples/mixture_models/dp_mix.myst.md index e97d5af6b..e93865cd9 100644 --- a/myst_nbs/mixture_models/dp_mix.myst.md +++ b/examples/mixture_models/dp_mix.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 diff --git a/myst_nbs/mixture_models/gaussian_mixture_model.myst.md b/examples/mixture_models/gaussian_mixture_model.myst.md similarity index 99% rename from myst_nbs/mixture_models/gaussian_mixture_model.myst.md rename to examples/mixture_models/gaussian_mixture_model.myst.md index 1546f2d5b..fc8c668b0 100644 --- a/myst_nbs/mixture_models/gaussian_mixture_model.myst.md +++ b/examples/mixture_models/gaussian_mixture_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: pymc-dev-py39 language: python diff --git a/myst_nbs/mixture_models/marginalized_gaussian_mixture_model.myst.md b/examples/mixture_models/marginalized_gaussian_mixture_model.myst.md similarity index 99% rename from myst_nbs/mixture_models/marginalized_gaussian_mixture_model.myst.md rename to examples/mixture_models/marginalized_gaussian_mixture_model.myst.md index 0ed1504df..fd47287dc 100644 --- a/myst_nbs/mixture_models/marginalized_gaussian_mixture_model.myst.md +++ b/examples/mixture_models/marginalized_gaussian_mixture_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 language: python diff --git a/myst_nbs/ode_models/ODE_API_introduction.myst.md b/examples/ode_models/ODE_API_introduction.myst.md similarity index 99% rename from myst_nbs/ode_models/ODE_API_introduction.myst.md rename to examples/ode_models/ODE_API_introduction.myst.md index 07a3cb10d..dc49f91d9 100644 --- a/myst_nbs/ode_models/ODE_API_introduction.myst.md +++ b/examples/ode_models/ODE_API_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: pymc-dev language: python @@ -61,7 +60,7 @@ An object of mass $m$ is brought to some height and allowed to fall freely until $$ y' = mg - \gamma y $$ -The force the object experiences in the downwards direction is $mg$, while the force the object experiences in the opposite direction (due to air resistance) is proportional to how fast the object is presently moving. Let's assume the object starts from rest (that is, that the object's initial velocity is 0). This may or may not be the case. To showcase how to do inference on initial conditions, I will first assume the object starts from rest, and then relax that assumption later. +The force the object experiences in the downwards direction is $mg$, while the force the object experiences in the opposite direction (due to air resistance) is proportional to how fast the object is presently moving. Let's assume the object starts from rest (that is, that the object's initial velocity is 0). This may or may not be the case. To showcase how to do inference on initial conditions, I will first assume the object starts from rest, and then relax that assumption later. Data on this object's speed as a function of time is shown below. The data may be noisy because of our measurement tools, or because the object is an irregular shape, thus leading to times during freefall when the object is more/less aerodynamic. Let's use this data to estimate the proportionality constant for air resistance. diff --git a/myst_nbs/ode_models/ODE_API_shapes_and_benchmarking.myst.md b/examples/ode_models/ODE_API_shapes_and_benchmarking.myst.md similarity index 99% rename from myst_nbs/ode_models/ODE_API_shapes_and_benchmarking.myst.md rename to examples/ode_models/ODE_API_shapes_and_benchmarking.myst.md index ce2fab06e..57e02ca6d 100644 --- a/myst_nbs/ode_models/ODE_API_shapes_and_benchmarking.myst.md +++ b/examples/ode_models/ODE_API_shapes_and_benchmarking.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 (PyMC3 Dev) language: python diff --git a/myst_nbs/ode_models/ODE_with_manual_gradients.myst.md b/examples/ode_models/ODE_with_manual_gradients.myst.md similarity index 99% rename from myst_nbs/ode_models/ODE_with_manual_gradients.myst.md rename to examples/ode_models/ODE_with_manual_gradients.myst.md index b46326df0..f929a22ad 100644 --- a/myst_nbs/ode_models/ODE_with_manual_gradients.myst.md +++ b/examples/ode_models/ODE_with_manual_gradients.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 PyMC3 (Dev) language: python @@ -318,7 +317,7 @@ plt.xticks(Year, rotation=45) plt.title("Lynx (predator) - Hare (prey): oscillatory dynamics", fontsize=25); ``` -## The probabilistic model +## The probabilistic model I have now got all the ingredients needed in order to define the probabilistic model in PyMC3. As I have mentioned previously I will set up the probabilistic model with the exact same likelihood and priors used in the Stan example. The observed data is defined as follows: diff --git a/examples/references.bib b/examples/references.bib index 4d6591142..258c7359c 100644 --- a/examples/references.bib +++ b/examples/references.bib @@ -250,7 +250,7 @@ @misc{harper2015movielens title = {The MovieLens Datasets: History and Context}, author = {Harper, F. Maxwell and Konstan, Joseph A.}, journal = {ACM Transactions on Interactive Intelligent Systems}, - volumne = {5}, + volume = {5}, number = {4}, pages = {1--19}, year = {2016}, diff --git a/myst_nbs/samplers/DEMetropolisZ_EfficiencyComparison.myst.md b/examples/samplers/DEMetropolisZ_EfficiencyComparison.myst.md similarity index 99% rename from myst_nbs/samplers/DEMetropolisZ_EfficiencyComparison.myst.md rename to examples/samplers/DEMetropolisZ_EfficiencyComparison.myst.md index 7ff40d5e0..fbebe7f96 100644 --- a/myst_nbs/samplers/DEMetropolisZ_EfficiencyComparison.myst.md +++ b/examples/samplers/DEMetropolisZ_EfficiencyComparison.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 diff --git a/myst_nbs/samplers/DEMetropolisZ_tune_drop_fraction.myst.md b/examples/samplers/DEMetropolisZ_tune_drop_fraction.myst.md similarity index 99% rename from myst_nbs/samplers/DEMetropolisZ_tune_drop_fraction.myst.md rename to examples/samplers/DEMetropolisZ_tune_drop_fraction.myst.md index fc4d227c5..379c0aae3 100644 --- a/myst_nbs/samplers/DEMetropolisZ_tune_drop_fraction.myst.md +++ b/examples/samplers/DEMetropolisZ_tune_drop_fraction.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 diff --git a/myst_nbs/samplers/GLM-hierarchical-jax.myst.md b/examples/samplers/GLM-hierarchical-jax.myst.md similarity index 99% rename from myst_nbs/samplers/GLM-hierarchical-jax.myst.md rename to examples/samplers/GLM-hierarchical-jax.myst.md index edcea30cd..0927c4f7b 100644 --- a/myst_nbs/samplers/GLM-hierarchical-jax.myst.md +++ b/examples/samplers/GLM-hierarchical-jax.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 (PyMC3 Dev) language: python diff --git a/myst_nbs/samplers/MLDA_gravity_surveying.myst.md b/examples/samplers/MLDA_gravity_surveying.myst.md similarity index 99% rename from myst_nbs/samplers/MLDA_gravity_surveying.myst.md rename to examples/samplers/MLDA_gravity_surveying.myst.md index 2d8f6e265..e0f892688 100644 --- a/myst_nbs/samplers/MLDA_gravity_surveying.myst.md +++ b/examples/samplers/MLDA_gravity_surveying.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 PyMC3 (Dev) language: python diff --git a/myst_nbs/samplers/MLDA_introduction.myst.md b/examples/samplers/MLDA_introduction.myst.md similarity index 99% rename from myst_nbs/samplers/MLDA_introduction.myst.md rename to examples/samplers/MLDA_introduction.myst.md index df197e3e9..0824a7c48 100644 --- a/myst_nbs/samplers/MLDA_introduction.myst.md +++ b/examples/samplers/MLDA_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 language: python diff --git a/myst_nbs/samplers/MLDA_simple_linear_regression.myst.md b/examples/samplers/MLDA_simple_linear_regression.myst.md similarity index 99% rename from myst_nbs/samplers/MLDA_simple_linear_regression.myst.md rename to examples/samplers/MLDA_simple_linear_regression.myst.md index 0e59afa29..43c1f7b11 100644 --- a/myst_nbs/samplers/MLDA_simple_linear_regression.myst.md +++ b/examples/samplers/MLDA_simple_linear_regression.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 (PyMC Dev) language: python @@ -194,7 +193,7 @@ print(f"Runtimes: MLDA: {runtime}, Metropolis: {runtime_2}, DEMetropolisZ: {runt **Performance:** -You can see from the summary statistics above that MLDA's ESS is ~13x higher than Metropolis and ~2.5x higher than DEMetropolisZ. The runtime of MLDA is ~3.5x larger than either Metropolis or DEMetropolisZ. Therefore in this toy example MLDA is almost an overkill (especially compared to DEMetropolisZ). For more complex problems, where the difference in computational cost between the coarse and fine models/likelihoods is orders of magnitude, MLDA is expected to outperform the other two samplers, as long as the coarse model is reasonably close to the fine one. This case is often encountered in inverse problems in engineering, ecology, imaging, etc where a forward model can be defined with varying coarseness in space and/or time (e.g. subsurface water flow, predator prey models, etc). For an example of this, please see the `MLDA_gravity_surveying.ipynb notebook` in the same folder. +You can see from the summary statistics above that MLDA's ESS is ~13x higher than Metropolis and ~2.5x higher than DEMetropolisZ. The runtime of MLDA is ~3.5x larger than either Metropolis or DEMetropolisZ. Therefore in this toy example MLDA is almost an overkill (especially compared to DEMetropolisZ). For more complex problems, where the difference in computational cost between the coarse and fine models/likelihoods is orders of magnitude, MLDA is expected to outperform the other two samplers, as long as the coarse model is reasonably close to the fine one. This case is often encountered in inverse problems in engineering, ecology, imaging, etc where a forward model can be defined with varying coarseness in space and/or time (e.g. subsurface water flow, predator prey models, etc). For an example of this, please see the `MLDA_gravity_surveying.ipynb notebook` in the same folder. **Subsampling rate:** diff --git a/myst_nbs/samplers/MLDA_variance_reduction_linear_regression.myst.md b/examples/samplers/MLDA_variance_reduction_linear_regression.myst.md similarity index 99% rename from myst_nbs/samplers/MLDA_variance_reduction_linear_regression.myst.md rename to examples/samplers/MLDA_variance_reduction_linear_regression.myst.md index 99e5cf7f2..4a1acda03 100644 --- a/myst_nbs/samplers/MLDA_variance_reduction_linear_regression.myst.md +++ b/examples/samplers/MLDA_variance_reduction_linear_regression.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 PyMC3 (Dev) language: python @@ -236,7 +235,7 @@ with pm.Model() as model: # convert thetas to a tensor vector theta = tt.as_tensor_variable([intercept, x_coeff]) - # Here we instantiate a Likelihood object using the class defined above + # Here we instantiate a Likelihood object using the class defined above # and we add to the mout list. We pass the fine data x and y # and the fine pymc3 model model. This creates a fine likelihood. mout.append(Likelihood(x, y, model)) diff --git a/myst_nbs/samplers/SMC-ABC_Lotka-Volterra_example.myst.md b/examples/samplers/SMC-ABC_Lotka-Volterra_example.myst.md similarity index 99% rename from myst_nbs/samplers/SMC-ABC_Lotka-Volterra_example.myst.md rename to examples/samplers/SMC-ABC_Lotka-Volterra_example.myst.md index 236ce5e3b..6d850e97e 100644 --- a/myst_nbs/samplers/SMC-ABC_Lotka-Volterra_example.myst.md +++ b/examples/samplers/SMC-ABC_Lotka-Volterra_example.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 3.9.7 ('base') language: python diff --git a/myst_nbs/samplers/SMC2_gaussians.myst.md b/examples/samplers/SMC2_gaussians.myst.md similarity index 99% rename from myst_nbs/samplers/SMC2_gaussians.myst.md rename to examples/samplers/SMC2_gaussians.myst.md index 8d9b02910..dc12d5355 100644 --- a/myst_nbs/samplers/SMC2_gaussians.myst.md +++ b/examples/samplers/SMC2_gaussians.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 3.9.7 ('base') language: python diff --git a/myst_nbs/survival_analysis/bayes_param_survival_pymc3.myst.md b/examples/survival_analysis/bayes_param_survival_pymc3.myst.md similarity index 99% rename from myst_nbs/survival_analysis/bayes_param_survival_pymc3.myst.md rename to examples/survival_analysis/bayes_param_survival_pymc3.myst.md index ac26ca444..bc96b6b4a 100644 --- a/myst_nbs/survival_analysis/bayes_param_survival_pymc3.myst.md +++ b/examples/survival_analysis/bayes_param_survival_pymc3.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 (PyMC3 Dev) language: python diff --git a/myst_nbs/survival_analysis/censored_data.myst.md b/examples/survival_analysis/censored_data.myst.md similarity index 99% rename from myst_nbs/survival_analysis/censored_data.myst.md rename to examples/survival_analysis/censored_data.myst.md index 677b112dd..930f52895 100644 --- a/myst_nbs/survival_analysis/censored_data.myst.md +++ b/examples/survival_analysis/censored_data.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 diff --git a/myst_nbs/survival_analysis/survival_analysis.myst.md b/examples/survival_analysis/survival_analysis.myst.md similarity index 99% rename from myst_nbs/survival_analysis/survival_analysis.myst.md rename to examples/survival_analysis/survival_analysis.myst.md index 90fbf09a9..42d75d2ce 100644 --- a/myst_nbs/survival_analysis/survival_analysis.myst.md +++ b/examples/survival_analysis/survival_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 language: python @@ -333,7 +332,7 @@ These plots also show the pointwise 95% high posterior density interval for each ##### Time varying effects -Another of the advantages of the model we have built is its flexibility. From the plots above, we may reasonable believe that the additional hazard due to metastization varies over time; it seems plausible that cancer that has metastasized increases the hazard rate immediately after the mastectomy, but that the risk due to metastization decreases over time. We can accommodate this mechanism in our model by allowing the regression coefficients to vary over time. In the time-varying coefficient model, if $s_j \leq t < s_{j + 1}$, we let $\lambda(t) = \lambda_j \exp(\mathbf{x} \beta_j).$ The sequence of regression coefficients $\beta_1, \beta_2, \ldots, \beta_{N - 1}$ form a normal random walk with $\beta_1 \sim N(0, 1)$, $\beta_j\ |\ \beta_{j - 1} \sim N(\beta_{j - 1}, 1)$. +Another of the advantages of the model we have built is its flexibility. From the plots above, we may reasonable believe that the additional hazard due to metastization varies over time; it seems plausible that cancer that has metastasized increases the hazard rate immediately after the mastectomy, but that the risk due to metastization decreases over time. We can accommodate this mechanism in our model by allowing the regression coefficients to vary over time. In the time-varying coefficient model, if $s_j \leq t < s_{j + 1}$, we let $\lambda(t) = \lambda_j \exp(\mathbf{x} \beta_j).$ The sequence of regression coefficients $\beta_1, \beta_2, \ldots, \beta_{N - 1}$ form a normal random walk with $\beta_1 \sim N(0, 1)$, $\beta_j\ |\ \beta_{j - 1} \sim N(\beta_{j - 1}, 1)$. We implement this model in `pymc3` as follows. diff --git a/myst_nbs/survival_analysis/weibull_aft.myst.md b/examples/survival_analysis/weibull_aft.myst.md similarity index 99% rename from myst_nbs/survival_analysis/weibull_aft.myst.md rename to examples/survival_analysis/weibull_aft.myst.md index 18e082acd..0c0971c45 100644 --- a/myst_nbs/survival_analysis/weibull_aft.myst.md +++ b/examples/survival_analysis/weibull_aft.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 diff --git a/myst_nbs/time_series/AR.myst.md b/examples/time_series/AR.myst.md similarity index 99% rename from myst_nbs/time_series/AR.myst.md rename to examples/time_series/AR.myst.md index 5b061850c..8a88feb58 100644 --- a/myst_nbs/time_series/AR.myst.md +++ b/examples/time_series/AR.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 3.8.2 64-bit (''pymc3'': conda)' language: python diff --git a/myst_nbs/time_series/Air_passengers-Prophet_with_Bayesian_workflow.myst.md b/examples/time_series/Air_passengers-Prophet_with_Bayesian_workflow.myst.md similarity index 99% rename from myst_nbs/time_series/Air_passengers-Prophet_with_Bayesian_workflow.myst.md rename to examples/time_series/Air_passengers-Prophet_with_Bayesian_workflow.myst.md index 1a7ec7fc4..b0ff85919 100644 --- a/myst_nbs/time_series/Air_passengers-Prophet_with_Bayesian_workflow.myst.md +++ b/examples/time_series/Air_passengers-Prophet_with_Bayesian_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 (ipykernel) language: python diff --git a/myst_nbs/time_series/Euler-Maruyama_and_SDEs.myst.md b/examples/time_series/Euler-Maruyama_and_SDEs.myst.md similarity index 99% rename from myst_nbs/time_series/Euler-Maruyama_and_SDEs.myst.md rename to examples/time_series/Euler-Maruyama_and_SDEs.myst.md index 677fbc539..699ab8dc1 100644 --- a/myst_nbs/time_series/Euler-Maruyama_and_SDEs.myst.md +++ b/examples/time_series/Euler-Maruyama_and_SDEs.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 diff --git a/myst_nbs/time_series/Forecasting_with_structural_timeseries.myst.md b/examples/time_series/Forecasting_with_structural_timeseries.myst.md similarity index 99% rename from myst_nbs/time_series/Forecasting_with_structural_timeseries.myst.md rename to examples/time_series/Forecasting_with_structural_timeseries.myst.md index 0984b40e6..b2e9e42b0 100644 --- a/myst_nbs/time_series/Forecasting_with_structural_timeseries.myst.md +++ b/examples/time_series/Forecasting_with_structural_timeseries.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 3.9.6 ('prod_streamlit') language: python diff --git a/myst_nbs/time_series/MvGaussianRandomWalk_demo.myst.md b/examples/time_series/MvGaussianRandomWalk_demo.myst.md similarity index 99% rename from myst_nbs/time_series/MvGaussianRandomWalk_demo.myst.md rename to examples/time_series/MvGaussianRandomWalk_demo.myst.md index 77b375a46..cec5b4179 100644 --- a/myst_nbs/time_series/MvGaussianRandomWalk_demo.myst.md +++ b/examples/time_series/MvGaussianRandomWalk_demo.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 diff --git a/myst_nbs/time_series/bayesian_var_model.myst.md b/examples/time_series/bayesian_var_model.myst.md similarity index 99% rename from myst_nbs/time_series/bayesian_var_model.myst.md rename to examples/time_series/bayesian_var_model.myst.md index 732953cf3..5db56d28f 100644 --- a/myst_nbs/time_series/bayesian_var_model.myst.md +++ b/examples/time_series/bayesian_var_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 3.9.0 ('pymc_ar_ex') language: python diff --git a/myst_nbs/variational_inference/GLM-hierarchical-advi-minibatch.myst.md b/examples/variational_inference/GLM-hierarchical-advi-minibatch.myst.md similarity index 99% rename from myst_nbs/variational_inference/GLM-hierarchical-advi-minibatch.myst.md rename to examples/variational_inference/GLM-hierarchical-advi-minibatch.myst.md index 387e7d506..02c0ca0a9 100644 --- a/myst_nbs/variational_inference/GLM-hierarchical-advi-minibatch.myst.md +++ b/examples/variational_inference/GLM-hierarchical-advi-minibatch.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 diff --git a/myst_nbs/variational_inference/bayesian_neural_network_advi.myst.md b/examples/variational_inference/bayesian_neural_network_advi.myst.md similarity index 99% rename from myst_nbs/variational_inference/bayesian_neural_network_advi.myst.md rename to examples/variational_inference/bayesian_neural_network_advi.myst.md index 17cdb6387..678586c8a 100644 --- a/myst_nbs/variational_inference/bayesian_neural_network_advi.myst.md +++ b/examples/variational_inference/bayesian_neural_network_advi.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 diff --git a/myst_nbs/variational_inference/convolutional_vae_keras_advi.myst.md b/examples/variational_inference/convolutional_vae_keras_advi.myst.md similarity index 99% rename from myst_nbs/variational_inference/convolutional_vae_keras_advi.myst.md rename to examples/variational_inference/convolutional_vae_keras_advi.myst.md index 54d7a4b2e..8c1297c87 100644 --- a/myst_nbs/variational_inference/convolutional_vae_keras_advi.myst.md +++ b/examples/variational_inference/convolutional_vae_keras_advi.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 diff --git a/myst_nbs/variational_inference/empirical-approx-overview.myst.md b/examples/variational_inference/empirical-approx-overview.myst.md similarity index 99% rename from myst_nbs/variational_inference/empirical-approx-overview.myst.md rename to examples/variational_inference/empirical-approx-overview.myst.md index 999b5495c..ea18932ae 100644 --- a/myst_nbs/variational_inference/empirical-approx-overview.myst.md +++ b/examples/variational_inference/empirical-approx-overview.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 PyMC3 (Dev) language: python diff --git a/myst_nbs/variational_inference/gaussian-mixture-model-advi.myst.md b/examples/variational_inference/gaussian-mixture-model-advi.myst.md similarity index 99% rename from myst_nbs/variational_inference/gaussian-mixture-model-advi.myst.md rename to examples/variational_inference/gaussian-mixture-model-advi.myst.md index 5945001bf..1c41a258c 100644 --- a/myst_nbs/variational_inference/gaussian-mixture-model-advi.myst.md +++ b/examples/variational_inference/gaussian-mixture-model-advi.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 @@ -152,7 +151,7 @@ cov = approx.cov.eval() sds = approx.bij.rmap(np.diag(cov) ** 0.5) ``` -The function returns three variables. 'means' and 'sds' are the mean and standard deviations of the variational posterior. Note that these values are in the transformed space, not in the original space. For random variables in the real line, e.g., means of the Gaussian components, no transformation is applied. Then we can see the variational posterior in the original space. +The function returns three variables. 'means' and 'sds' are the mean and standard deviations of the variational posterior. Note that these values are in the transformed space, not in the original space. For random variables in the real line, e.g., means of the Gaussian components, no transformation is applied. Then we can see the variational posterior in the original space. ```{code-cell} ipython3 from copy import deepcopy diff --git a/myst_nbs/variational_inference/lda-advi-aevb.myst.md b/examples/variational_inference/lda-advi-aevb.myst.md similarity index 99% rename from myst_nbs/variational_inference/lda-advi-aevb.myst.md rename to examples/variational_inference/lda-advi-aevb.myst.md index 1a1a40bc4..2cfc860de 100644 --- a/myst_nbs/variational_inference/lda-advi-aevb.myst.md +++ b/examples/variational_inference/lda-advi-aevb.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 @@ -145,7 +144,7 @@ In the last line of the below cell, `DensityDist` class is used to define the lo ```{code-cell} ipython3 n_topics = 10 -# we have sparse dataset. It's better to have dense batch so that all words accrue there +# we have sparse dataset. It's better to have dense batch so that all words accrue there minibatch_size = 128 # defining minibatch diff --git a/myst_nbs/variational_inference/normalizing_flows_overview.myst.md b/examples/variational_inference/normalizing_flows_overview.myst.md similarity index 99% rename from myst_nbs/variational_inference/normalizing_flows_overview.myst.md rename to examples/variational_inference/normalizing_flows_overview.myst.md index a8de69e9b..b6e66c107 100644 --- a/myst_nbs/variational_inference/normalizing_flows_overview.myst.md +++ b/examples/variational_inference/normalizing_flows_overview.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 @@ -284,7 +283,7 @@ We also require an objective: inference.objective(nmc=None) ``` -Theano can be used to calculate the gradient of the objective with respect to the parameters: +Theano can be used to calculate the gradient of the objective with respect to the parameters: ```{code-cell} ipython3 with theano.configparser.change_flags(compute_test_value="off"): diff --git a/myst_nbs/variational_inference/pathfinder.myst.md b/examples/variational_inference/pathfinder.myst.md similarity index 98% rename from myst_nbs/variational_inference/pathfinder.myst.md rename to examples/variational_inference/pathfinder.myst.md index 743a79026..fe7195fac 100644 --- a/myst_nbs/variational_inference/pathfinder.myst.md +++ b/examples/variational_inference/pathfinder.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 language: python diff --git a/myst_nbs/variational_inference/variational_api_quickstart.myst.md b/examples/variational_inference/variational_api_quickstart.myst.md similarity index 99% rename from myst_nbs/variational_inference/variational_api_quickstart.myst.md rename to examples/variational_inference/variational_api_quickstart.myst.md index 0cc900a00..9cbc0d31e 100644 --- a/myst_nbs/variational_inference/variational_api_quickstart.myst.md +++ b/examples/variational_inference/variational_api_quickstart.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 (PyMC3 Dev) language: python @@ -459,7 +458,7 @@ So, `Tracker` allows us to monitor our approximation and choose good training sc ## Minibatches When dealing with large datasets, using minibatch training can drastically speed up and improve approximation performance. Large datasets impose a hefty cost on the computation of gradients. -There is a nice API in pymc3 to handle these cases, which is available through the `pm.Minibatch` class. The minibatch is just a highly specialized Theano tensor: +There is a nice API in pymc3 to handle these cases, which is available through the `pm.Minibatch` class. The minibatch is just a highly specialized Theano tensor: ```{code-cell} ipython3 issubclass(pm.Minibatch, theano.tensor.TensorVariable) diff --git a/scripts/rerun.py b/scripts/rerun.py index a3474732b..2c817f2e3 100644 --- a/scripts/rerun.py +++ b/scripts/rerun.py @@ -111,7 +111,7 @@ def commit(fp: pathlib.Path, branch: str) -> bool: _log.info("⏳ Committing changes in %s to %s", fp, branch) subprocess.check_call(["git", "stage", str(fp)]) subprocess.check_call(["git", "commit", "-m", f"Re-run {fp.name} notebook"]) - _log.info("✔ Changes in %s were commited to branch %s.", fp, branch) + _log.info("✔ Changes in %s were committed to branch %s.", fp, branch) return True except subprocess.CalledProcessError as ex: _log.exception("❌ Failed to commit.", exc_info=ex)