Merge pull request #720 from stan-dev/remove-R

Remove any dependency on R
stan-dev · Mar 1, 2024 · 18027a4 · 18027a4
2 parents b57e398 + 4aeb8ba
commit 18027a4
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diff --git a/.gitignore b/.gitignore
@@ -17,6 +17,11 @@ src/_website
 *._pdf
 
 
+src/**/*.html
+src/**/*.tex
+!header.tex
+!json.html
+
 # eBook build output
 *.epub
 *.mobi

diff --git a/README.md b/README.md
@@ -26,9 +26,7 @@ previously, we used [bookdown](https://github.com/rstudio/bookdown).
 [Download quarto](https://quarto.org/docs/download/)
 To build the pdf version of the docs, you will need to [install LaTeX](https://www.latex-project.org/get/) as well.
 
-
-Quarto accepts both [Rmarkdown (`.Rmd`)](https://rmarkdown.rstudio.com)
-and [`.qmd`](https://quarto.org/docs/authoring/markdown-basics.html) source files
+Quarto accepts [`.qmd`](https://quarto.org/docs/authoring/markdown-basics.html) source files
 and uses the [Pandoc](https://pandoc.org) conversion engine.
 
 ## Scripts to build and maintain the docset
@@ -47,7 +45,7 @@ Requires Python 3.7 or higher, due to call to `subprocess.run`, kwarg `capture_o
 * `python build.py 2 35 website` - builds the docs website in `docs/2_42`.
 * `python build.py 2 35 pdf functions-reference` - builds only the pdf version of the Stan functions reference,  resulting document is `docs/2_35/functions-reference-2_35.pdf`
 * `python build.py 2 35 pdf all` - builds all pdfs from the Stan documentation set, resulting pdfs are in `docs/2_35`.
- 
+
 
 **Additional scripts**
 

diff --git a/extract_function_sigs.py b/extract_function_sigs.py
@@ -35,7 +35,7 @@ def main():
     sigs = set()
     ref_dir = os.path.join('src', 'functions-reference')
     with pushd(ref_dir):
-        for file in glob.glob('*.Rmd'):
+        for file in glob.glob('*.qmd'):
             print(file)
             with open(file) as rmd_file:
                 lines = rmd_file.readlines()
@@ -50,7 +50,7 @@ def main():
                             sigs.add('{}; {}; {}'.format(parts[1], parts[2], parts[0]))
                         else:
                             print('not a function sig: {}'.format(line))
-    
+
     with open(outfile_name, 'w') as outfile:
         outfile.write('# This file is semicolon delimited\n')
         outfile.write('StanFunction; Arguments; ReturnType\n')

diff --git a/src/.gitignore b/src/.gitignore
@@ -6,9 +6,4 @@
 *.ind
 *.toc
 
-./**/*.html
-./**/*.tex
-!header.tex
-!json.html
-
 /.quarto/
diff --git a/src/_functions.R b/src/_functions.R
diff --git a/src/_quarto.yml b/src/_quarto.yml
@@ -5,15 +5,15 @@ project:
   render:
     - "index.qmd"
     - "404.qmd"
-    - "cmdstan-guide/overview.qmd"
-    - "functions-reference/overview.qmd"
-    - "reference-manual/overview.qmd"
-    - "stan-users-guide/overview.qmd"
-    - "cmdstan-guide/*.Rmd"
-    - "functions-reference/*.Rmd"
-    - "reference-manual/*.Rmd"
-    - "stan-users-guide/*.Rmd"
-    - "!sdlc.Rmd"
+    - "cmdstan-guide/*.qmd"
+    - "functions-reference/*.qmd"
+    - "reference-manual/*.qmd"
+    - "stan-users-guide/*.qmd"
+    - "!sdlc.qmd"
+    - "!cmdstan-guide/index.qmd"
+    - "!functions-reference/index.qmd"
+    - "!reference-manual/index.qmd"
+    - "!stan-users-guide/index.qmd"
 
 bibliography: bibtex/all.bib
 biblio-style: apalike
@@ -93,48 +93,48 @@ website:
         - section: "Version {{< env STAN_DOCS_VERSION >}}"
         - section: "Example Models"
           contents:
-            - stan-users-guide/regression.Rmd
-            - stan-users-guide/time-series.Rmd
-            - stan-users-guide/missing-data.Rmd
-            - stan-users-guide/truncation-censoring.Rmd
-            - stan-users-guide/finite-mixtures.Rmd
-            - stan-users-guide/measurement-error.Rmd
-            - stan-users-guide/latent-discrete.Rmd
-            - stan-users-guide/sparse-ragged.Rmd
-            - stan-users-guide/clustering.Rmd
-            - stan-users-guide/gaussian-processes.Rmd
-            - stan-users-guide/hyperspherical-models.Rmd
-            - stan-users-guide/algebraic-equations.Rmd
-            - stan-users-guide/odes.Rmd
-            - stan-users-guide/one-dimensional-integrals.Rmd
-            - stan-users-guide/complex-numbers.Rmd
-            - stan-users-guide/dae.Rmd
+            - stan-users-guide/regression.qmd
+            - stan-users-guide/time-series.qmd
+            - stan-users-guide/missing-data.qmd
+            - stan-users-guide/truncation-censoring.qmd
+            - stan-users-guide/finite-mixtures.qmd
+            - stan-users-guide/measurement-error.qmd
+            - stan-users-guide/latent-discrete.qmd
+            - stan-users-guide/sparse-ragged.qmd
+            - stan-users-guide/clustering.qmd
+            - stan-users-guide/gaussian-processes.qmd
+            - stan-users-guide/hyperspherical-models.qmd
+            - stan-users-guide/algebraic-equations.qmd
+            - stan-users-guide/odes.qmd
+            - stan-users-guide/one-dimensional-integrals.qmd
+            - stan-users-guide/complex-numbers.qmd
+            - stan-users-guide/dae.qmd
         - section:  "Programming Techniques"
           contents:
-            - stan-users-guide/floating-point.Rmd
-            - stan-users-guide/matrices-arrays.Rmd
-            - stan-users-guide/multi-indexing.Rmd
-            - stan-users-guide/user-functions.Rmd
-            - stan-users-guide/custom-probability.Rmd
-            - stan-users-guide/proportionality-constants.Rmd
-            - stan-users-guide/problematic-posteriors.Rmd
-            - stan-users-guide/reparameterization.Rmd
-            - stan-users-guide/efficiency-tuning.Rmd
-            - stan-users-guide/parallelization.Rmd
+            - stan-users-guide/floating-point.qmd
+            - stan-users-guide/matrices-arrays.qmd
+            - stan-users-guide/multi-indexing.qmd
+            - stan-users-guide/user-functions.qmd
+            - stan-users-guide/custom-probability.qmd
+            - stan-users-guide/proportionality-constants.qmd
+            - stan-users-guide/problematic-posteriors.qmd
+            - stan-users-guide/reparameterization.qmd
+            - stan-users-guide/efficiency-tuning.qmd
+            - stan-users-guide/parallelization.qmd
         - section: "Posterior Inference & Model Checking"
           contents:
-            - stan-users-guide/posterior-prediction.Rmd
-            - stan-users-guide/simulation-based-calibration.Rmd
-            - stan-users-guide/posterior-predictive-checks.Rmd
-            - stan-users-guide/cross-validation.Rmd
-            - stan-users-guide/poststratification.Rmd
-            - stan-users-guide/decision-analysis.Rmd
-            - stan-users-guide/bootstrap.Rmd
+            - stan-users-guide/posterior-prediction.qmd
+            - stan-users-guide/simulation-based-calibration.qmd
+            - stan-users-guide/posterior-predictive-checks.qmd
+            - stan-users-guide/cross-validation.qmd
+            - stan-users-guide/poststratification.qmd
+            - stan-users-guide/decision-analysis.qmd
+            - stan-users-guide/bootstrap.qmd
         - section: "Appendices"
           contents:
-            - stan-users-guide/using-stanc.Rmd
-            - stan-users-guide/style-guide.Rmd
-            - stan-users-guide/for-bugs-users.Rmd
+            - stan-users-guide/using-stanc.qmd
+            - stan-users-guide/style-guide.qmd
+            - stan-users-guide/for-bugs-users.qmd
 
     - id: reference-manual
       title: "Reference Manual"
@@ -143,33 +143,33 @@ website:
         - section: "Version {{< env STAN_DOCS_VERSION >}}"
         - section: "Language"
           contents:
-            - reference-manual/encoding.Rmd
-            - reference-manual/includes.Rmd
-            - reference-manual/comments.Rmd
-            - reference-manual/whitespace.Rmd
-            - reference-manual/types.Rmd
-            - reference-manual/expressions.Rmd
-            - reference-manual/statements.Rmd
-            - reference-manual/blocks.Rmd
-            - reference-manual/user-functions.Rmd
-            - reference-manual/transforms.Rmd
-            - reference-manual/syntax.Rmd
-            - reference-manual/execution.Rmd
-            - reference-manual/deprecations.Rmd
-            - reference-manual/removals.Rmd
+            - reference-manual/encoding.qmd
+            - reference-manual/includes.qmd
+            - reference-manual/comments.qmd
+            - reference-manual/whitespace.qmd
+            - reference-manual/types.qmd
+            - reference-manual/expressions.qmd
+            - reference-manual/statements.qmd
+            - reference-manual/blocks.qmd
+            - reference-manual/user-functions.qmd
+            - reference-manual/transforms.qmd
+            - reference-manual/syntax.qmd
+            - reference-manual/execution.qmd
+            - reference-manual/deprecations.qmd
+            - reference-manual/removals.qmd
         - section: "Algorithms"
           contents:
-            - reference-manual/mcmc.Rmd
-            - reference-manual/analysis.Rmd
-            - reference-manual/optimization.Rmd
-            - reference-manual/pathfinder.Rmd
-            - reference-manual/variational.Rmd
-            - reference-manual/laplace.Rmd
-            - reference-manual/diagnostics.Rmd
+            - reference-manual/mcmc.qmd
+            - reference-manual/analysis.qmd
+            - reference-manual/optimization.qmd
+            - reference-manual/pathfinder.qmd
+            - reference-manual/variational.qmd
+            - reference-manual/laplace.qmd
+            - reference-manual/diagnostics.qmd
         - section: "Usage"
           contents:
-            - reference-manual/reproducibility.Rmd
-            - reference-manual/licenses.Rmd
+            - reference-manual/reproducibility.qmd
+            - reference-manual/licenses.qmd
 
     - id: functions-reference
       title: "Stan Functions"
@@ -178,44 +178,44 @@ website:
         - section: "Version {{< env STAN_DOCS_VERSION >}}"
         - section: "Built-in Functions"
           contents:
-            - functions-reference/void_functions.Rmd
-            - functions-reference/integer-valued_basic_functions.Rmd
-            - functions-reference/real-valued_basic_functions.Rmd
-            - functions-reference/complex-valued_basic_functions.Rmd
-            - functions-reference/array_operations.Rmd
-            - functions-reference/matrix_operations.Rmd
-            - functions-reference/complex_matrix_operations.Rmd
-            - functions-reference/sparse_matrix_operations.Rmd
-            - functions-reference/mixed_operations.Rmd
-            - functions-reference/compound_arithmetic_and_assignment.Rmd
-            - functions-reference/higher-order_functions.Rmd
-            - functions-reference/deprecated_functions.Rmd
-            - functions-reference/removed_functions.Rmd
-            - functions-reference/conventions_for_probability_functions.Rmd
+            - functions-reference/void_functions.qmd
+            - functions-reference/integer-valued_basic_functions.qmd
+            - functions-reference/real-valued_basic_functions.qmd
+            - functions-reference/complex-valued_basic_functions.qmd
+            - functions-reference/array_operations.qmd
+            - functions-reference/matrix_operations.qmd
+            - functions-reference/complex_matrix_operations.qmd
+            - functions-reference/sparse_matrix_operations.qmd
+            - functions-reference/mixed_operations.qmd
+            - functions-reference/compound_arithmetic_and_assignment.qmd
+            - functions-reference/higher-order_functions.qmd
+            - functions-reference/deprecated_functions.qmd
+            - functions-reference/removed_functions.qmd
+            - functions-reference/conventions_for_probability_functions.qmd
         - section: "Discrete Distributions"
           contents:
-            - functions-reference/binary_distributions.Rmd
-            - functions-reference/bounded_discrete_distributions.Rmd
-            - functions-reference/unbounded_discrete_distributions.Rmd
-            - functions-reference/multivariate_discrete_distributions.Rmd
+            - functions-reference/binary_distributions.qmd
+            - functions-reference/bounded_discrete_distributions.qmd
+            - functions-reference/unbounded_discrete_distributions.qmd
+            - functions-reference/multivariate_discrete_distributions.qmd
         - section: "Continuous Distributions"
           contents:
-            - functions-reference/unbounded_continuous_distributions.Rmd
-            - functions-reference/positive_continuous_distributions.Rmd
-            - functions-reference/positive_lower-bounded_distributions.Rmd
-            - functions-reference/continuous_distributions_on_0_1.Rmd
-            - functions-reference/circular_distributions.Rmd
-            - functions-reference/bounded_continuous_distributions.Rmd
-            - functions-reference/distributions_over_unbounded_vectors.Rmd
-            - functions-reference/simplex_distributions.Rmd
-            - functions-reference/correlation_matrix_distributions.Rmd
-            - functions-reference/covariance_matrix_distributions.Rmd
+            - functions-reference/unbounded_continuous_distributions.qmd
+            - functions-reference/positive_continuous_distributions.qmd
+            - functions-reference/positive_lower-bounded_distributions.qmd
+            - functions-reference/continuous_distributions_on_0_1.qmd
+            - functions-reference/circular_distributions.qmd
+            - functions-reference/bounded_continuous_distributions.qmd
+            - functions-reference/distributions_over_unbounded_vectors.qmd
+            - functions-reference/simplex_distributions.qmd
+            - functions-reference/correlation_matrix_distributions.qmd
+            - functions-reference/covariance_matrix_distributions.qmd
         - section: "Additional Distributions"
           contents:
-            - functions-reference/hidden_markov_models.Rmd
+            - functions-reference/hidden_markov_models.qmd
         - section: "Appendix"
           contents:
-            - functions-reference/mathematical_functions.Rmd
+            - functions-reference/mathematical_functions.qmd
 
     - id: cmdstan-guide
       title: "CmdStan Guide"
@@ -224,38 +224,38 @@ website:
         - section: "Version {{< env STAN_DOCS_VERSION >}}"
         - section: "Quickstart Guide"
           contents:
-            - cmdstan-guide/installation.Rmd
-            - cmdstan-guide/example_model_data.Rmd
-            - cmdstan-guide/compiling_stan_programs.Rmd
-            - cmdstan-guide/mcmc_sampling_intro.Rmd
-            - cmdstan-guide/optimization_intro.Rmd
-            - cmdstan-guide/pathfinder_intro.Rmd
-            - cmdstan-guide/variational_intro.Rmd
-            - cmdstan-guide/generate_quantities_intro.Rmd
+            - cmdstan-guide/installation.qmd
+            - cmdstan-guide/example_model_data.qmd
+            - cmdstan-guide/compiling_stan_programs.qmd
+            - cmdstan-guide/mcmc_sampling_intro.qmd
+            - cmdstan-guide/optimization_intro.qmd
+            - cmdstan-guide/pathfinder_intro.qmd
+            - cmdstan-guide/variational_intro.qmd
+            - cmdstan-guide/generate_quantities_intro.qmd
         - section: "Reference Manual"
           contents:
-            - cmdstan-guide/command_line_options.Rmd
-            - cmdstan-guide/mcmc_config.Rmd
-            - cmdstan-guide/optimize_config.Rmd
-            - cmdstan-guide/pathfinder_config.Rmd
-            - cmdstan-guide/variational_config.Rmd
-            - cmdstan-guide/generate_quantities_config.Rmd
-            - cmdstan-guide/laplace_sample_config.Rmd
-            - cmdstan-guide/log_prob_config.Rmd
-            - cmdstan-guide/diagnose_config.Rmd
-            - cmdstan-guide/parallelization.Rmd
+            - cmdstan-guide/command_line_options.qmd
+            - cmdstan-guide/mcmc_config.qmd
+            - cmdstan-guide/optimize_config.qmd
+            - cmdstan-guide/pathfinder_config.qmd
+            - cmdstan-guide/variational_config.qmd
+            - cmdstan-guide/generate_quantities_config.qmd
+            - cmdstan-guide/laplace_sample_config.qmd
+            - cmdstan-guide/log_prob_config.qmd
+            - cmdstan-guide/diagnose_config.qmd
+            - cmdstan-guide/parallelization.qmd
         - section: "Tools and Utilities"
           contents:
-            - cmdstan-guide/stanc.Rmd
-            - cmdstan-guide/stansummary.Rmd
-            - cmdstan-guide/diagnose_utility.Rmd
-            - cmdstan-guide/print.Rmd
+            - cmdstan-guide/stanc.qmd
+            - cmdstan-guide/stansummary.qmd
+            - cmdstan-guide/diagnose_utility.qmd
+            - cmdstan-guide/print.qmd
         - section: "Appendices"
           contents:
-            - cmdstan-guide/stan_csv_apdx.Rmd
-            - cmdstan-guide/json_apdx.Rmd
-            - cmdstan-guide/rdump_apdx.Rmd
-            - cmdstan-guide/external_code.Rmd
+            - cmdstan-guide/stan_csv_apdx.qmd
+            - cmdstan-guide/json_apdx.qmd
+            - cmdstan-guide/rdump_apdx.qmd
+            - cmdstan-guide/external_code.qmd
 
 format:
   html:

diff --git a/src/before-chapter.R b/src/before-chapter.R