galaaz 0.4.10 → 2.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (391) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +26 -0
  3. data/LICENSE +0 -0
  4. data/README.md +3123 -882
  5. data/Rakefile +62 -41
  6. data/bin/galaaz-bootstrap +137 -0
  7. data/bin/galaaz-jruby +14 -0
  8. data/bin/galaaz_jruby_env.inc.sh +6 -0
  9. data/bin/gbookdown +64 -0
  10. data/bin/gknit +223 -6
  11. data/bin/gknit-draft +105 -0
  12. data/bin/gknit-draft.rb +28 -0
  13. data/bin/gknit_Rscript +127 -0
  14. data/bin/grun +27 -1
  15. data/bin/gstudio +49 -4
  16. data/bin/{gstudio.rb → gstudio_irb.rb} +0 -0
  17. data/bin/gstudio_pry.rb +7 -0
  18. data/bin/install-tinytex +6 -0
  19. data/bin/run_all_rspec +43 -0
  20. data/bin/run_example +14 -0
  21. data/bin/run_old_rspec +19 -0
  22. data/bin/run_rspec +23 -0
  23. data/bin/run_rspec_subset +38 -0
  24. data/bin/run_slow_rspec +19 -0
  25. data/blogs/R-on-Rails-Planning-Document.md +940 -0
  26. data/blogs/README.md +100 -0
  27. data/blogs/galaaz_ggplot/galaaz_ggplot.Rmd +38 -66
  28. data/blogs/galaaz_ggplot/galaaz_ggplot.log +754 -0
  29. data/blogs/galaaz_ggplot/galaaz_ggplot.md +364 -0
  30. data/blogs/galaaz_ggplot/galaaz_ggplot.tex +607 -0
  31. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/midwest_rb.png +0 -0
  32. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/scatter_plot_rb.png +0 -0
  33. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-markdown_github/midwest_rb.png +0 -0
  34. data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-markdown_github/scatter_plot_rb.png +0 -0
  35. data/blogs/galaaz_ggplot/midwest.Rmd +3 -3
  36. data/blogs/galaaz_ggplot/midwest_external_png +0 -0
  37. data/blogs/gknit/gknit.Rmd +52 -55
  38. data/blogs/gknit/gknit.md +94 -94
  39. data/blogs/gknit/gknit_files/figure-html/bubble-1.png +0 -0
  40. data/blogs/gknit/gknit_files/figure-html/diverging_bar.png +0 -0
  41. data/blogs/gknit/lst.rds +0 -0
  42. data/blogs/gknit/model.rb +1 -1
  43. data/blogs/gknit/stats.bib +0 -0
  44. data/blogs/manual/include_model_local_repro.Rmd +14 -0
  45. data/blogs/manual/include_model_local_repro.md +75 -0
  46. data/blogs/manual/lst.rds +0 -0
  47. data/blogs/manual/manual.Rmd +1582 -196
  48. data/blogs/manual/manual.log +1786 -0
  49. data/blogs/manual/manual.md +3107 -890
  50. data/blogs/manual/manual.tex +3018 -1086
  51. data/blogs/manual/manual_files/figure-html/bubble-1.png +0 -0
  52. data/blogs/manual/manual_files/figure-html/diverging_bar.png +0 -0
  53. data/blogs/manual/manual_files/figure-latex/bubble-1.png +0 -0
  54. data/blogs/manual/model.rb +41 -0
  55. data/blogs/nse_dplyr/nse_dplyr.Rmd +277 -151
  56. data/blogs/nse_dplyr/nse_dplyr.log +928 -0
  57. data/blogs/nse_dplyr/nse_dplyr.md +457 -293
  58. data/blogs/oh_my/not_so.rb +0 -0
  59. data/blogs/oh_my/oh_my.Rmd +1234 -25
  60. data/blogs/oh_my/oh_my.log +804 -0
  61. data/blogs/oh_my/oh_my.md +1808 -228
  62. data/blogs/oh_my/oh_my.tex +821 -0
  63. data/blogs/oh_my/old.Rmd +15 -14
  64. data/blogs/ruby_plot/ruby_plot.Rmd +58 -82
  65. data/blogs/ruby_plot/ruby_plot.log +885 -0
  66. data/blogs/ruby_plot/ruby_plot.md +71 -103
  67. data/blogs/ruby_plot/ruby_plot.tex +940 -0
  68. data/blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.png +0 -0
  69. data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.png +0 -0
  70. data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_dose.png +0 -0
  71. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color.png +0 -0
  72. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color2.png +0 -0
  73. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_decorations.png +0 -0
  74. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_jitter.png +0 -0
  75. data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_points.png +0 -0
  76. data/blogs/ruby_plot/ruby_plot_files/figure-html/final_box_plot.png +0 -0
  77. data/blogs/ruby_plot/ruby_plot_files/figure-html/final_violin_plot.png +0 -0
  78. data/blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.png +0 -0
  79. data/blogs/ruby_plot/ruby_plot_files/figure-latex/dose_len.png +0 -0
  80. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_delivery.png +0 -0
  81. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_dose.png +0 -0
  82. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color.png +0 -0
  83. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color2.png +0 -0
  84. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_decorations.png +0 -0
  85. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_jitter.png +0 -0
  86. data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_points.png +0 -0
  87. data/blogs/ruby_plot/ruby_plot_files/figure-latex/final_box_plot.png +0 -0
  88. data/blogs/ruby_plot/ruby_plot_files/figure-latex/final_violin_plot.png +0 -0
  89. data/blogs/ruby_plot/ruby_plot_files/figure-latex/violin_with_jitter.png +0 -0
  90. data/blogs/test/test.Rmd +14 -0
  91. data/examples/50Plots_MasterList/Images/midwest-scatterplot.PNG +0 -0
  92. data/examples/50Plots_MasterList/ScatterPlot.rb +0 -0
  93. data/examples/50Plots_MasterList/scatter_plot.rb +0 -0
  94. data/examples/Bibliography/master.bib +50 -0
  95. data/examples/Bibliography/stats.bib +72 -0
  96. data/examples/R/calc.R +0 -0
  97. data/examples/R/java_interop.R +0 -0
  98. data/examples/bioconductor_deseq2_airway/Documentation/DESeq2-airway-walkthrough.md +56 -0
  99. data/examples/bioconductor_deseq2_airway/bench_galaaz_three_same_process.rb +53 -0
  100. data/examples/bioconductor_deseq2_airway/bench_r_three_same_process.R +34 -0
  101. data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz.rb +33 -0
  102. data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz_optimized.rb +34 -0
  103. data/examples/bioconductor_deseq2_airway/deseq2_airway_minimal.R +30 -0
  104. data/examples/bioconductor_deseq2_airway/deseq2_airway_pipeline_for_bench.R +36 -0
  105. data/examples/islr/all.rb +13 -0
  106. data/examples/islr/ch2.spec.rb +37 -7
  107. data/examples/islr/ch3.spec.rb +11 -2
  108. data/examples/islr/ch3_boston.rb +27 -0
  109. data/examples/islr/ch3_multiple_regression.rb +0 -0
  110. data/examples/islr/ch6.spec.rb +24 -1
  111. data/examples/islr/x_y_rnorm.jpg +0 -0
  112. data/examples/latex_templates/Test-acm_article/Makefile +16 -0
  113. data/examples/latex_templates/Test-acm_article/Test-acm_article.Rmd +65 -0
  114. data/examples/latex_templates/Test-acm_article/acm_proc_article-sp.cls +1670 -0
  115. data/examples/latex_templates/Test-acm_article/sensys-abstract.cls +703 -0
  116. data/examples/latex_templates/Test-acm_article/sigproc.bib +59 -0
  117. data/examples/latex_templates/Test-acs_article/Test-acs_article.Rmd +260 -0
  118. data/examples/latex_templates/Test-acs_article/acs-Test-acs_article.bib +11 -0
  119. data/examples/latex_templates/Test-acs_article/acs-my_output.bib +11 -0
  120. data/examples/latex_templates/Test-acs_article/acstest.bib +17 -0
  121. data/examples/latex_templates/Test-aea_article/AEA.cls +1414 -0
  122. data/{blogs/gknit/marshal.dump → examples/latex_templates/Test-aea_article/BibFile.bib} +0 -0
  123. data/examples/latex_templates/Test-aea_article/Test-aea_article.Rmd +108 -0
  124. data/examples/latex_templates/Test-aea_article/aea.bst +1269 -0
  125. data/examples/latex_templates/Test-aea_article/multicol.sty +853 -0
  126. data/examples/latex_templates/Test-aea_article/references.bib +0 -0
  127. data/examples/latex_templates/Test-aea_article/setspace.sty +546 -0
  128. data/examples/latex_templates/Test-amq_article/Test-amq_article.Rmd +256 -0
  129. data/examples/latex_templates/Test-amq_article/Test-amq_article.pdfsync +3397 -0
  130. data/examples/latex_templates/Test-ams_article/Test-ams_article.Rmd +215 -0
  131. data/examples/latex_templates/Test-ams_article/amstest.bib +436 -0
  132. data/examples/latex_templates/Test-asa_article/Test-asa_article.Rmd +153 -0
  133. data/examples/latex_templates/Test-asa_article/agsm.bst +1353 -0
  134. data/examples/latex_templates/Test-asa_article/bibliography.bib +233 -0
  135. data/examples/latex_templates/Test-ieee_article/IEEEtran.bst +2409 -0
  136. data/examples/latex_templates/Test-ieee_article/IEEEtran.cls +6346 -0
  137. data/examples/latex_templates/Test-ieee_article/Test-ieee_article.Rmd +175 -0
  138. data/examples/latex_templates/Test-ieee_article/mybibfile.bib +20 -0
  139. data/examples/latex_templates/Test-rjournal_article/RJournal.sty +335 -0
  140. data/examples/latex_templates/Test-rjournal_article/RJreferences.bib +18 -0
  141. data/examples/latex_templates/Test-rjournal_article/Test-rjournal_article.Rmd +52 -0
  142. data/examples/latex_templates/Test-springer_article/Test-springer_article.Rmd +65 -0
  143. data/examples/latex_templates/Test-springer_article/bibliography.bib +26 -0
  144. data/examples/latex_templates/Test-springer_article/spbasic.bst +1658 -0
  145. data/examples/latex_templates/Test-springer_article/spmpsci.bst +1512 -0
  146. data/examples/latex_templates/Test-springer_article/spphys.bst +1443 -0
  147. data/examples/latex_templates/Test-springer_article/svglov3.clo +113 -0
  148. data/examples/latex_templates/Test-springer_article/svjour3.cls +1431 -0
  149. data/examples/misc/baseball.csv +0 -0
  150. data/examples/misc/ggplot.rb +3 -2
  151. data/examples/misc/moneyball.rb +0 -0
  152. data/examples/misc/subsetting.rb +0 -0
  153. data/examples/multithread_shards_to_r/shards_to_r.rb +67 -0
  154. data/examples/rmarkdown/svm-rmarkdown-anon-ms-example/svm-rmarkdown-anon-ms-example.Rmd +73 -0
  155. data/examples/rmarkdown/svm-rmarkdown-article-example/svm-rmarkdown-article-example.Rmd +382 -0
  156. data/examples/rmarkdown/svm-rmarkdown-beamer-example/svm-rmarkdown-beamer-example.Rmd +164 -0
  157. data/examples/rmarkdown/svm-rmarkdown-cv/svm-rmarkdown-cv.Rmd +92 -0
  158. data/examples/rmarkdown/svm-rmarkdown-syllabus-example/attend-grade-relationships.csv +482 -0
  159. data/examples/rmarkdown/svm-rmarkdown-syllabus-example/svm-rmarkdown-syllabus-example.Rmd +280 -0
  160. data/examples/rmarkdown/svm-xaringan-example/svm-xaringan-example.Rmd +386 -0
  161. data/examples/sthda_ggplot/README.md +0 -0
  162. data/examples/sthda_ggplot/RUN.md +41 -0
  163. data/examples/sthda_ggplot/all.rb +0 -0
  164. data/examples/sthda_ggplot/one_variable_continuous/density_gg.rb +0 -0
  165. data/examples/sthda_ggplot/one_variable_continuous/geom_area.rb +0 -0
  166. data/examples/sthda_ggplot/one_variable_continuous/geom_density.rb +2 -0
  167. data/examples/sthda_ggplot/one_variable_continuous/geom_dotplot.rb +0 -0
  168. data/examples/sthda_ggplot/one_variable_continuous/geom_freqpoly.rb +0 -0
  169. data/examples/sthda_ggplot/one_variable_continuous/geom_histogram.rb +0 -0
  170. data/examples/sthda_ggplot/one_variable_continuous/histogram_density.rb +0 -0
  171. data/examples/sthda_ggplot/one_variable_continuous/stat.rb +0 -0
  172. data/examples/sthda_ggplot/one_variable_discrete/bar.rb +0 -0
  173. data/examples/sthda_ggplot/qplots/box_violin_dot.rb +0 -0
  174. data/examples/sthda_ggplot/qplots/scatter_plots.rb +0 -0
  175. data/examples/sthda_ggplot/scatter_gg.rb +0 -0
  176. data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_bin2d.rb +0 -0
  177. data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_density2d.rb +0 -0
  178. data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_hex.rb +0 -0
  179. data/examples/sthda_ggplot/two_variables_cont_cont/geom_point.rb +0 -0
  180. data/examples/sthda_ggplot/two_variables_cont_cont/geom_smooth.rb +0 -0
  181. data/examples/sthda_ggplot/two_variables_cont_cont/misc.rb +0 -0
  182. data/examples/sthda_ggplot/two_variables_cont_function/geom_area.rb +4 -3
  183. data/examples/sthda_ggplot/two_variables_disc_cont/geom_bar.rb +0 -0
  184. data/examples/sthda_ggplot/two_variables_disc_cont/geom_boxplot.rb +0 -0
  185. data/examples/sthda_ggplot/two_variables_disc_cont/geom_dotplot.rb +0 -0
  186. data/examples/sthda_ggplot/two_variables_disc_cont/geom_jitter.rb +0 -0
  187. data/examples/sthda_ggplot/two_variables_disc_cont/geom_line.rb +0 -0
  188. data/examples/sthda_ggplot/two_variables_disc_cont/geom_violin.rb +0 -0
  189. data/examples/sthda_ggplot/two_variables_disc_disc/geom_jitter.rb +0 -0
  190. data/examples/sthda_ggplot/two_variables_error/geom_crossbar.rb +0 -0
  191. data/ext/new_bridge/Makefile +46 -0
  192. data/ext/new_bridge/galaaz_gatekeeper_phase0.cpp +12 -0
  193. data/ext/new_bridge/galaaz_gatekeeper_phase1.cpp +1639 -0
  194. data/lib/R_interface/galaaz_device.R +20 -0
  195. data/lib/R_interface/include_engine.R +109 -0
  196. data/lib/R_interface/new_bridge_adapter.rb +824 -0
  197. data/lib/R_interface/r.rb +177 -25
  198. data/lib/R_interface/r_arrow.rb +113 -0
  199. data/lib/R_interface/r_libs.R +4 -4
  200. data/lib/R_interface/r_methods.rb +13 -116
  201. data/lib/R_interface/r_module_s.rb +0 -0
  202. data/lib/R_interface/rbinary_operators.rb +20 -2
  203. data/lib/R_interface/rclosure.rb +5 -1
  204. data/lib/R_interface/rdata_frame.rb +34 -70
  205. data/lib/R_interface/rdevice.rb +125 -0
  206. data/lib/R_interface/rdevices.R +0 -0
  207. data/lib/R_interface/renvironment.rb +10 -4
  208. data/lib/R_interface/rexpression.rb +5 -1
  209. data/lib/R_interface/rindexed_object.rb +41 -13
  210. data/lib/R_interface/rlanguage.rb +20 -62
  211. data/lib/R_interface/rlist.rb +115 -25
  212. data/lib/R_interface/rlogical_operators.rb +0 -0
  213. data/lib/R_interface/rmatrix.rb +2 -11
  214. data/lib/R_interface/rmd_indexed_object.rb +5 -1
  215. data/lib/R_interface/robject.rb +348 -290
  216. data/lib/R_interface/rpkg.rb +1 -0
  217. data/lib/R_interface/rsupport.rb +610 -331
  218. data/lib/R_interface/rsupport_scope.rb +2 -1
  219. data/lib/R_interface/rsymbol.rb +50 -0
  220. data/lib/R_interface/ruby_callback.rb +2 -3
  221. data/lib/R_interface/ruby_extensions.rb +225 -175
  222. data/lib/R_interface/runary_operators.rb +0 -0
  223. data/lib/R_interface/rvector.rb +147 -31
  224. data/lib/galaaz.rb +0 -0
  225. data/lib/galaaz_jruby.rb +22 -0
  226. data/lib/gknit/diagnostics.rb +50 -0
  227. data/lib/gknit/draft.rb +111 -0
  228. data/lib/gknit/include_engine.rb +15 -7
  229. data/lib/gknit/knitr_engine.rb +223 -107
  230. data/lib/gknit/rb_engine.rb +3 -3
  231. data/lib/gknit/ruby_engine.rb +0 -0
  232. data/lib/gknit.rb +3 -0
  233. data/lib/new_bridge/bootstrap/windows_bootstrap.rb +285 -0
  234. data/lib/new_bridge/envelope.rb +51 -0
  235. data/lib/new_bridge/eval_result.rb +26 -0
  236. data/lib/new_bridge/framing.rb +39 -0
  237. data/lib/new_bridge/instance_pool_client.rb +38 -0
  238. data/lib/new_bridge/r_instance_manager.rb +404 -0
  239. data/lib/new_bridge/session_client.rb +530 -0
  240. data/lib/new_bridge/tcp_framed.rb +44 -0
  241. data/lib/new_bridge.rb +9 -0
  242. data/lib/util/exec_ruby.rb +95 -46
  243. data/lib/util/inline_file.rb +35 -30
  244. data/new_bridge_specs/benchmark_phase5_5_unboxing_spec.rb +96 -0
  245. data/new_bridge_specs/eval_r_async_spec.rb +113 -0
  246. data/new_bridge_specs/integration_phase5_1_concurrent_spec.rb +50 -0
  247. data/new_bridge_specs/integration_phase5_1_eval_spec.rb +16 -0
  248. data/new_bridge_specs/integration_phase5_1_r_api_spec.rb +25 -0
  249. data/new_bridge_specs/integration_phase5_1_smoke_spec.rb +31 -0
  250. data/new_bridge_specs/integration_phase5_2_dataframe_unboxing_spec.rb +19 -0
  251. data/new_bridge_specs/integration_phase5_2_handle_eval_unboxing_spec.rb +25 -0
  252. data/new_bridge_specs/integration_phase5_3_callback_args_spec.rb +28 -0
  253. data/new_bridge_specs/integration_phase5_3_callback_error_spec.rb +22 -0
  254. data/new_bridge_specs/integration_phase5_3_callback_timeout_spec.rb +28 -0
  255. data/new_bridge_specs/integration_phase5_3_callbacks_smoke_spec.rb +22 -0
  256. data/new_bridge_specs/integration_phase5_3_edge_cases_spec.rb +52 -0
  257. data/new_bridge_specs/integration_phase5_3_nested_spec.rb +30 -0
  258. data/new_bridge_specs/integration_phase5_4_concurrent_sessions_spec.rb +53 -0
  259. data/new_bridge_specs/integration_phase5_4_nested_session_callbacks_spec.rb +49 -0
  260. data/new_bridge_specs/integration_phase5_4_session_routing_spec.rb +38 -0
  261. data/new_bridge_specs/integration_phase5_5_stress_concurrency_spec.rb +52 -0
  262. data/new_bridge_specs/integration_phase5_5_unbox_walk_spec.rb +46 -0
  263. data/new_bridge_specs/phase0_protocol_spec.rb +96 -0
  264. data/new_bridge_specs/phase1_req_ret_spec.rb +66 -0
  265. data/new_bridge_specs/phase2_multi_instance_spec.rb +67 -0
  266. data/new_bridge_specs/phase3_callbacks_spec.rb +71 -0
  267. data/new_bridge_specs/phase4_2_hardening_spec.rb +252 -0
  268. data/new_bridge_specs/phase4_3_r_instance_manager_spec.rb +85 -0
  269. data/new_bridge_specs/phase4_nested_callbacks_spec.rb +123 -0
  270. data/r_requires/ggplot.rb +0 -0
  271. data/r_requires/knitr.rb +0 -0
  272. data/specs/all.rb +15 -11
  273. data/specs/arrow_from_ruby_batches_spec.rb +50 -0
  274. data/specs/arrow_semantics_spec.rb +64 -0
  275. data/specs/bridge_concurrent_spec.rb +46 -0
  276. data/specs/bridge_nested_spec.rb +25 -0
  277. data/specs/dataframe_semantics_spec.rb +122 -0
  278. data/specs/dataframe_single_index_logical_filter_spec.rb +21 -0
  279. data/specs/dispatch_probe_cache_spec.rb +38 -0
  280. data/specs/dispatch_probe_error_class_fallback_spec.rb +20 -0
  281. data/specs/dispatch_probe_fallback_spec.rb +18 -0
  282. data/specs/environment_semantics_spec.rb +89 -0
  283. data/specs/field_access_spec.rb +31 -0
  284. data/specs/figures/bg.jpeg +0 -0
  285. data/specs/figures/bg.png +0 -0
  286. data/specs/figures/bg.svg +168 -57
  287. data/specs/figures/dose_len.png +0 -0
  288. data/specs/figures/no_args.jpeg +0 -0
  289. data/specs/figures/no_args.png +0 -0
  290. data/specs/figures/no_args.svg +168 -57
  291. data/specs/figures/width_height.jpeg +0 -0
  292. data/specs/figures/width_height.png +0 -0
  293. data/specs/figures/width_height_units1.jpeg +0 -0
  294. data/specs/figures/width_height_units1.png +0 -0
  295. data/specs/figures/width_height_units2.jpeg +0 -0
  296. data/specs/figures/width_height_units2.png +0 -0
  297. data/specs/formula_semantics_spec.rb +81 -0
  298. data/specs/galaaz_util_exec_ruby_spec.rb +85 -0
  299. data/specs/galaaz_util_inline_file_spec.rb +54 -0
  300. data/specs/gknit_cli_option_permutation_spec.rb +24 -0
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