galaaz 0.5.0 → 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.
- checksums.yaml +4 -4
- data/CHANGELOG.md +26 -0
- data/LICENSE +0 -0
- data/README.md +1360 -636
- data/Rakefile +61 -41
- data/bin/galaaz-bootstrap +137 -0
- data/bin/galaaz-jruby +14 -0
- data/bin/galaaz_jruby_env.inc.sh +6 -0
- data/bin/gbookdown +64 -0
- data/bin/gknit +84 -13
- data/bin/gknit-draft.rb +0 -0
- data/bin/gstudio +5 -3
- data/bin/gstudio_irb.rb +0 -0
- data/bin/gstudio_pry.rb +0 -0
- data/bin/install-tinytex +6 -0
- data/bin/run_all_rspec +43 -0
- data/bin/run_example +14 -0
- data/bin/run_old_rspec +19 -0
- data/bin/run_rspec +23 -0
- data/bin/run_rspec_subset +38 -0
- data/bin/run_slow_rspec +19 -0
- data/blogs/R-on-Rails-Planning-Document.md +940 -0
- data/blogs/README.md +100 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot.Rmd +38 -66
- data/blogs/galaaz_ggplot/galaaz_ggplot.log +754 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot.md +115 -155
- data/blogs/galaaz_ggplot/galaaz_ggplot.tex +607 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/midwest_rb.png +0 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-html/scatter_plot_rb.png +0 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-markdown_github/midwest_rb.png +0 -0
- data/blogs/galaaz_ggplot/galaaz_ggplot_files/figure-markdown_github/scatter_plot_rb.png +0 -0
- data/blogs/galaaz_ggplot/midwest.Rmd +3 -3
- data/blogs/galaaz_ggplot/midwest_external_png +0 -0
- data/blogs/gknit/gknit.Rmd +47 -52
- data/blogs/gknit/gknit.md +1430 -0
- data/blogs/gknit/gknit_files/figure-html/bubble-1.png +0 -0
- data/blogs/gknit/gknit_files/figure-html/diverging_bar.png +0 -0
- data/blogs/gknit/lst.rds +0 -0
- data/blogs/gknit/model.rb +1 -1
- data/blogs/gknit/stats.bib +0 -0
- data/blogs/manual/include_model_local_repro.Rmd +14 -0
- data/blogs/manual/include_model_local_repro.md +75 -0
- data/blogs/manual/lst.rds +0 -0
- data/blogs/manual/manual.Rmd +852 -239
- data/blogs/manual/manual.log +1786 -0
- data/blogs/manual/manual.md +1360 -636
- data/blogs/manual/manual.tex +1883 -1161
- data/blogs/manual/manual_files/figure-html/bubble-1.png +0 -0
- data/blogs/manual/manual_files/figure-html/diverging_bar.png +0 -0
- data/blogs/manual/manual_files/figure-latex/bubble-1.png +0 -0
- data/blogs/manual/model.rb +1 -1
- data/blogs/nse_dplyr/nse_dplyr.Rmd +84 -111
- data/blogs/nse_dplyr/nse_dplyr.log +928 -0
- data/blogs/nse_dplyr/nse_dplyr.md +198 -229
- data/blogs/oh_my/not_so.rb +0 -0
- data/blogs/oh_my/oh_my.Rmd +1234 -25
- data/blogs/oh_my/oh_my.log +804 -0
- data/blogs/oh_my/oh_my.md +1663 -86
- data/blogs/oh_my/oh_my.tex +821 -0
- data/blogs/oh_my/old.Rmd +15 -14
- data/blogs/ruby_plot/ruby_plot.Rmd +58 -82
- data/blogs/ruby_plot/ruby_plot.log +885 -0
- data/blogs/ruby_plot/ruby_plot.md +71 -102
- data/blogs/ruby_plot/ruby_plot.tex +940 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/dose_len.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_delivery.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facet_by_dose.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_by_delivery_color2.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_decorations.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_jitter.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/facets_with_points.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/final_box_plot.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/final_violin_plot.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-html/violin_with_jitter.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/dose_len.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_delivery.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facet_by_dose.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_by_delivery_color2.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_decorations.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_jitter.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/facets_with_points.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/final_box_plot.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/final_violin_plot.png +0 -0
- data/blogs/ruby_plot/ruby_plot_files/figure-latex/violin_with_jitter.png +0 -0
- data/blogs/test/test.Rmd +14 -0
- data/examples/50Plots_MasterList/Images/midwest-scatterplot.PNG +0 -0
- data/examples/50Plots_MasterList/ScatterPlot.rb +0 -0
- data/examples/50Plots_MasterList/scatter_plot.rb +0 -0
- data/examples/Bibliography/master.bib +0 -0
- data/examples/Bibliography/stats.bib +0 -0
- data/examples/R/calc.R +0 -0
- data/examples/R/java_interop.R +0 -0
- data/examples/bioconductor_deseq2_airway/Documentation/DESeq2-airway-walkthrough.md +56 -0
- data/examples/bioconductor_deseq2_airway/bench_galaaz_three_same_process.rb +53 -0
- data/examples/bioconductor_deseq2_airway/bench_r_three_same_process.R +34 -0
- data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz.rb +33 -0
- data/examples/bioconductor_deseq2_airway/deseq2_airway_galaaz_optimized.rb +34 -0
- data/examples/bioconductor_deseq2_airway/deseq2_airway_minimal.R +30 -0
- data/examples/bioconductor_deseq2_airway/deseq2_airway_pipeline_for_bench.R +36 -0
- data/examples/islr/all.rb +13 -0
- data/examples/islr/ch2.spec.rb +37 -7
- data/examples/islr/ch3.spec.rb +11 -2
- data/examples/islr/ch3_boston.rb +27 -0
- data/examples/islr/ch3_multiple_regression.rb +0 -0
- data/examples/islr/ch6.spec.rb +24 -1
- data/examples/islr/x_y_rnorm.jpg +0 -0
- data/examples/latex_templates/Test-acm_article/acm_proc_article-sp.cls +0 -0
- data/examples/latex_templates/Test-acm_article/sigproc.bib +0 -0
- data/examples/latex_templates/Test-acs_article/acs-Test-acs_article.bib +0 -0
- data/examples/latex_templates/Test-acs_article/acs-my_output.bib +0 -0
- data/examples/latex_templates/Test-aea_article/BibFile.bib +0 -0
- data/examples/latex_templates/Test-aea_article/Test-aea_article.Rmd +0 -0
- data/examples/latex_templates/Test-aea_article/references.bib +0 -0
- data/examples/latex_templates/Test-amq_article/Test-amq_article.Rmd +0 -0
- data/examples/latex_templates/Test-amq_article/Test-amq_article.pdfsync +0 -0
- data/examples/latex_templates/Test-ieee_article/IEEEtran.bst +0 -0
- data/examples/latex_templates/Test-ieee_article/mybibfile.bib +0 -0
- data/examples/latex_templates/Test-rjournal_article/RJournal.sty +0 -0
- data/examples/latex_templates/Test-rjournal_article/RJreferences.bib +0 -0
- data/examples/latex_templates/Test-rjournal_article/Test-rjournal_article.Rmd +0 -0
- data/examples/misc/baseball.csv +0 -0
- data/examples/misc/ggplot.rb +3 -2
- data/examples/misc/moneyball.rb +0 -0
- data/examples/misc/subsetting.rb +0 -0
- data/examples/multithread_shards_to_r/shards_to_r.rb +67 -0
- data/examples/rmarkdown/svm-rmarkdown-anon-ms-example/svm-rmarkdown-anon-ms-example.Rmd +0 -0
- data/examples/rmarkdown/svm-rmarkdown-article-example/svm-rmarkdown-article-example.Rmd +0 -0
- data/examples/rmarkdown/svm-rmarkdown-beamer-example/svm-rmarkdown-beamer-example.Rmd +0 -0
- data/examples/rmarkdown/svm-rmarkdown-cv/svm-rmarkdown-cv.Rmd +0 -0
- data/examples/rmarkdown/svm-rmarkdown-syllabus-example/attend-grade-relationships.csv +0 -0
- data/examples/rmarkdown/svm-rmarkdown-syllabus-example/svm-rmarkdown-syllabus-example.Rmd +0 -0
- data/examples/rmarkdown/svm-xaringan-example/svm-xaringan-example.Rmd +0 -0
- data/examples/sthda_ggplot/README.md +0 -0
- data/examples/sthda_ggplot/RUN.md +41 -0
- data/examples/sthda_ggplot/all.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/density_gg.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/geom_area.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/geom_density.rb +2 -0
- data/examples/sthda_ggplot/one_variable_continuous/geom_dotplot.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/geom_freqpoly.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/geom_histogram.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/histogram_density.rb +0 -0
- data/examples/sthda_ggplot/one_variable_continuous/stat.rb +0 -0
- data/examples/sthda_ggplot/one_variable_discrete/bar.rb +0 -0
- data/examples/sthda_ggplot/qplots/box_violin_dot.rb +0 -0
- data/examples/sthda_ggplot/qplots/scatter_plots.rb +0 -0
- data/examples/sthda_ggplot/scatter_gg.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_bin2d.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_density2d.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_bivariate/geom_hex.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_cont/geom_point.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_cont/geom_smooth.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_cont/misc.rb +0 -0
- data/examples/sthda_ggplot/two_variables_cont_function/geom_area.rb +4 -3
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_bar.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_boxplot.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_dotplot.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_jitter.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_line.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_cont/geom_violin.rb +0 -0
- data/examples/sthda_ggplot/two_variables_disc_disc/geom_jitter.rb +0 -0
- data/examples/sthda_ggplot/two_variables_error/geom_crossbar.rb +0 -0
- data/ext/new_bridge/Makefile +46 -0
- data/ext/new_bridge/galaaz_gatekeeper_phase0.cpp +12 -0
- data/ext/new_bridge/galaaz_gatekeeper_phase1.cpp +1639 -0
- data/lib/R_interface/galaaz_device.R +20 -0
- data/lib/R_interface/include_engine.R +109 -0
- data/lib/R_interface/new_bridge_adapter.rb +824 -0
- data/lib/R_interface/r.rb +177 -25
- data/lib/R_interface/r_arrow.rb +113 -0
- data/lib/R_interface/r_libs.R +3 -3
- data/lib/R_interface/r_methods.rb +13 -126
- data/lib/R_interface/r_module_s.rb +0 -0
- data/lib/R_interface/rbinary_operators.rb +20 -2
- data/lib/R_interface/rclosure.rb +5 -1
- data/lib/R_interface/rdata_frame.rb +34 -70
- data/lib/R_interface/rdevice.rb +125 -0
- data/lib/R_interface/rdevices.R +0 -0
- data/lib/R_interface/renvironment.rb +10 -4
- data/lib/R_interface/rexpression.rb +5 -1
- data/lib/R_interface/rindexed_object.rb +41 -13
- data/lib/R_interface/rlanguage.rb +20 -62
- data/lib/R_interface/rlist.rb +115 -25
- data/lib/R_interface/rlogical_operators.rb +0 -0
- data/lib/R_interface/rmatrix.rb +2 -11
- data/lib/R_interface/rmd_indexed_object.rb +5 -1
- data/lib/R_interface/robject.rb +348 -290
- data/lib/R_interface/rpkg.rb +0 -0
- data/lib/R_interface/rsupport.rb +609 -328
- data/lib/R_interface/rsupport_scope.rb +2 -1
- data/lib/R_interface/rsymbol.rb +50 -0
- data/lib/R_interface/ruby_callback.rb +2 -3
- data/lib/R_interface/ruby_extensions.rb +225 -175
- data/lib/R_interface/runary_operators.rb +0 -0
- data/lib/R_interface/rvector.rb +147 -31
- data/lib/galaaz.rb +0 -0
- data/lib/galaaz_jruby.rb +22 -0
- data/lib/gknit/diagnostics.rb +50 -0
- data/lib/gknit/draft.rb +23 -17
- data/lib/gknit/include_engine.rb +15 -7
- data/lib/gknit/knitr_engine.rb +223 -74
- data/lib/gknit/rb_engine.rb +3 -3
- data/lib/gknit/ruby_engine.rb +0 -0
- data/lib/gknit.rb +1 -0
- data/lib/new_bridge/bootstrap/windows_bootstrap.rb +285 -0
- data/lib/new_bridge/envelope.rb +51 -0
- data/lib/new_bridge/eval_result.rb +26 -0
- data/lib/new_bridge/framing.rb +39 -0
- data/lib/new_bridge/instance_pool_client.rb +38 -0
- data/lib/new_bridge/r_instance_manager.rb +404 -0
- data/lib/new_bridge/session_client.rb +530 -0
- data/lib/new_bridge/tcp_framed.rb +44 -0
- data/lib/new_bridge.rb +9 -0
- data/lib/util/exec_ruby.rb +95 -20
- data/lib/util/inline_file.rb +35 -30
- data/new_bridge_specs/benchmark_phase5_5_unboxing_spec.rb +96 -0
- data/new_bridge_specs/eval_r_async_spec.rb +113 -0
- data/new_bridge_specs/integration_phase5_1_concurrent_spec.rb +50 -0
- data/new_bridge_specs/integration_phase5_1_eval_spec.rb +16 -0
- data/new_bridge_specs/integration_phase5_1_r_api_spec.rb +25 -0
- data/new_bridge_specs/integration_phase5_1_smoke_spec.rb +31 -0
- data/new_bridge_specs/integration_phase5_2_dataframe_unboxing_spec.rb +19 -0
- data/new_bridge_specs/integration_phase5_2_handle_eval_unboxing_spec.rb +25 -0
- data/new_bridge_specs/integration_phase5_3_callback_args_spec.rb +28 -0
- data/new_bridge_specs/integration_phase5_3_callback_error_spec.rb +22 -0
- data/new_bridge_specs/integration_phase5_3_callback_timeout_spec.rb +28 -0
- data/new_bridge_specs/integration_phase5_3_callbacks_smoke_spec.rb +22 -0
- data/new_bridge_specs/integration_phase5_3_edge_cases_spec.rb +52 -0
- data/new_bridge_specs/integration_phase5_3_nested_spec.rb +30 -0
- data/new_bridge_specs/integration_phase5_4_concurrent_sessions_spec.rb +53 -0
- data/new_bridge_specs/integration_phase5_4_nested_session_callbacks_spec.rb +49 -0
- data/new_bridge_specs/integration_phase5_4_session_routing_spec.rb +38 -0
- data/new_bridge_specs/integration_phase5_5_stress_concurrency_spec.rb +52 -0
- data/new_bridge_specs/integration_phase5_5_unbox_walk_spec.rb +46 -0
- data/new_bridge_specs/phase0_protocol_spec.rb +96 -0
- data/new_bridge_specs/phase1_req_ret_spec.rb +66 -0
- data/new_bridge_specs/phase2_multi_instance_spec.rb +67 -0
- data/new_bridge_specs/phase3_callbacks_spec.rb +71 -0
- data/new_bridge_specs/phase4_2_hardening_spec.rb +252 -0
- data/new_bridge_specs/phase4_3_r_instance_manager_spec.rb +85 -0
- data/new_bridge_specs/phase4_nested_callbacks_spec.rb +123 -0
- data/r_requires/ggplot.rb +0 -0
- data/r_requires/knitr.rb +0 -0
- data/specs/all.rb +15 -11
- data/specs/arrow_from_ruby_batches_spec.rb +50 -0
- data/specs/arrow_semantics_spec.rb +64 -0
- data/specs/bridge_concurrent_spec.rb +46 -0
- data/specs/bridge_nested_spec.rb +25 -0
- data/specs/dataframe_semantics_spec.rb +122 -0
- data/specs/dataframe_single_index_logical_filter_spec.rb +21 -0
- data/specs/dispatch_probe_cache_spec.rb +38 -0
- data/specs/dispatch_probe_error_class_fallback_spec.rb +20 -0
- data/specs/dispatch_probe_fallback_spec.rb +18 -0
- data/specs/environment_semantics_spec.rb +89 -0
- data/specs/field_access_spec.rb +31 -0
- data/specs/figures/bg.jpeg +0 -0
- data/specs/figures/bg.png +0 -0
- data/specs/figures/bg.svg +168 -57
- data/specs/figures/dose_len.png +0 -0
- data/specs/figures/no_args.jpeg +0 -0
- data/specs/figures/no_args.png +0 -0
- data/specs/figures/no_args.svg +168 -57
- data/specs/figures/width_height.jpeg +0 -0
- data/specs/figures/width_height.png +0 -0
- data/specs/figures/width_height_units1.jpeg +0 -0
- data/specs/figures/width_height_units1.png +0 -0
- data/specs/figures/width_height_units2.jpeg +0 -0
- data/specs/figures/width_height_units2.png +0 -0
- data/specs/formula_semantics_spec.rb +81 -0
- data/specs/galaaz_util_exec_ruby_spec.rb +85 -0
- data/specs/galaaz_util_inline_file_spec.rb +54 -0
- data/specs/gknit_cli_option_permutation_spec.rb +24 -0
- data/specs/gknit_include_engine_spec.rb +72 -0
- data/specs/gknit_install_timeout_report_spec.rb +69 -0
- data/specs/gknit_internal_error_report_spec.rb +57 -0
- data/specs/gknit_vector_map_output_spec.rb +59 -0
- data/specs/globalenv_guardrail_spec.rb +52 -0
- data/specs/language_expression_semantics_spec.rb +145 -0
- data/specs/list_semantics_spec.rb +111 -0
- data/specs/new_bridge_bulk_dataframe_transfer_spec.rb +44 -0
- data/specs/new_bridge_bulk_vector_transfer_spec.rb +73 -0
- data/specs/new_bridge_callback_timeout_spec.rb +69 -0
- data/specs/new_bridge_eval_r_fallback_spec.rb +55 -0
- data/specs/nil_null_spec.rb +42 -0
- data/specs/object_build_phase2_spec.rb +53 -0
- data/specs/phase1_callback_bridge_spec.rb +84 -0
- data/specs/phase2_gknit_generic_rendering_guardrail_spec.rb +46 -0
- data/specs/phase2_gknit_no_raw_code_leakage_spec.rb +43 -0
- data/specs/phase3_gknit_generic_graphics_capture_spec.rb +71 -0
- data/specs/plot_device_semantics_spec.rb +28 -0
- data/specs/plot_snapshot_semantics_spec.rb +58 -0
- data/specs/protocol_result_spec.rb +236 -0
- data/specs/r_batch_fail_fast_spec.rb +47 -0
- data/specs/r_bridge_bootstrap_spec.rb +11 -0
- data/specs/r_devices.spec.rb +1 -1
- data/specs/r_eval.spec.rb +16 -18
- data/specs/r_function.spec.rb +1 -1
- data/specs/r_instance_manager_spec.rb +285 -0
- data/specs/r_list_apply.spec.rb +15 -15
- data/specs/r_matrix.spec.rb +0 -0
- data/specs/r_nse.spec.rb +5 -5
- data/specs/r_object_send_dispatch_spec.rb +13 -0
- data/specs/r_vector_comparator_spec.rb +8 -0
- data/specs/r_vector_creation.spec.rb +0 -0
- data/specs/r_vector_functions.spec.rb +0 -0
- data/specs/r_vector_object.spec.rb +0 -0
- data/specs/r_vector_operators.spec.rb +0 -0
- data/specs/r_vector_structured_scalar_reads_spec.rb +35 -0
- data/specs/r_vector_subsetting.spec.rb +0 -0
- data/specs/range_helper_spec.rb +21 -0
- data/specs/rsupport_scope_spec.rb +28 -0
- data/specs/rsupport_var_name_thread_safety_spec.rb +24 -0
- data/specs/scalar_character_spec.rb +44 -0
- data/specs/scoped_symbol_dsl_refinement_spec.rb +40 -0
- data/specs/session_env_bridge_spec.rb +25 -0
- data/specs/simplecov_bootstrap_spec.rb +10 -0
- data/specs/spec_helper.rb +10 -0
- data/specs/tmp.rb +0 -0
- data/specs/unboxing_recursion_regression_spec.rb +30 -0
- data/specs/unboxing_spec.rb +49 -0
- data/specs/verify_callbacks.rb +42 -0
- data/sty/galaaz.sty +0 -0
- data/version.rb +1 -1
- metadata +194 -64
- data/blogs/galaaz_ggplot/galaaz_ggplot.html +0 -520
- data/blogs/galaaz_ggplot/galaaz_ggplot.pdf +0 -0
- data/blogs/galaaz_ggplot/midwest.html +0 -188
- data/blogs/gknit/gknit.html +0 -2266
- data/blogs/gknit/gknit.pdf +0 -0
- data/blogs/manual/manual.html +0 -4638
- data/blogs/manual/manual.pdf +0 -0
- data/blogs/manual/manual_files/figure-latex/diverging_bar.pdf +0 -0
- data/blogs/nse_dplyr/nse_dplyr.html +0 -878
- data/blogs/nse_dplyr/nse_dplyr.pdf +0 -0
- data/blogs/oh_my/oh_my.html +0 -568
- data/blogs/ruby_plot/ruby_plot.html +0 -544
- data/blogs/ruby_plot/ruby_plot.pdf +0 -0
- data/examples/latex_templates/Test-acs_article/Test-acs_article.pdf +0 -0
- data/examples/latex_templates/Test-aea_article/Test-aea_article.pdf +0 -0
- data/examples/latex_templates/Test-amq_article/Test-amq_article.pdf +0 -0
- data/examples/latex_templates/Test-amq_article/pics/Figure2.pdf +0 -0
- data/examples/latex_templates/Test-asa_article/Test-asa_article.pdf +0 -0
- data/examples/latex_templates/Test-ieee_article/Test-ieee_article.pdf +0 -0
- data/examples/latex_templates/Test-rjournal_article/RJwrapper.pdf +0 -0
- data/examples/latex_templates/Test-springer_article/Test-springer_article.pdf +0 -0
- data/examples/rmarkdown/svm-rmarkdown-anon-ms-example/svm-rmarkdown-anon-ms-example.pdf +0 -0
- data/examples/rmarkdown/svm-rmarkdown-article-example/svm-rmarkdown-article-example.pdf +0 -0
- data/examples/rmarkdown/svm-rmarkdown-beamer-example/svm-rmarkdown-beamer-example.pdf +0 -0
- data/examples/rmarkdown/svm-rmarkdown-cv/svm-rmarkdown-cv.pdf +0 -0
- data/examples/rmarkdown/svm-rmarkdown-syllabus-example/svm-rmarkdown-syllabus-example.pdf +0 -0
- data/specs/r_dataframe.spec.rb +0 -379
- data/specs/r_environment.spec.rb +0 -140
- data/specs/r_formula.spec.rb +0 -232
- data/specs/r_language.spec.rb +0 -112
- data/specs/r_list.spec.rb +0 -293
- data/specs/r_plots.spec.rb +0 -72
- data/specs/ruby_expression.spec.rb +0 -316
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data/examples/misc/baseball.csv
CHANGED
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data/examples/misc/ggplot.rb
CHANGED
|
@@ -125,7 +125,7 @@ module LightBlueTheme
|
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125
125
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126
126
|
end
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127
127
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|
128
|
-
R.awt
|
|
128
|
+
# R.awt
|
|
129
129
|
|
|
130
130
|
plot = R.grid__arrange(
|
|
131
131
|
LightBlueTheme.graph_title("Cars: wt x mpg"),
|
|
@@ -137,7 +137,8 @@ plot = R.grid__arrange(
|
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137
137
|
heights: R.c(0.050, 0.025, 0.85, 0.05)
|
|
138
138
|
)
|
|
139
139
|
|
|
140
|
-
plot.print
|
|
140
|
+
# plot.print
|
|
141
|
+
R.ggsave("cars_plot.png", plot)
|
|
141
142
|
|
|
142
143
|
=begin
|
|
143
144
|
sleep(5)
|
data/examples/misc/moneyball.rb
CHANGED
|
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|
data/examples/misc/subsetting.rb
CHANGED
|
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|
|
@@ -0,0 +1,67 @@
|
|
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1
|
+
# frozen_string_literal: true
|
|
2
|
+
|
|
3
|
+
# Multithreaded Ruby → single R workflow
|
|
4
|
+
#
|
|
5
|
+
# Pattern: JRuby runs several threads (e.g. one connection per shard). Each thread
|
|
6
|
+
# performs I/O-bound work (here simulated; replace with Sequel/SQLite/pg per shard).
|
|
7
|
+
# Results are merged in Ruby, then passed to R in one or a few bridge calls for
|
|
8
|
+
# analytics (dplyr on an Arrow table, or a plain data.frame).
|
|
9
|
+
#
|
|
10
|
+
# Run from repo root (JRuby + R as for other examples):
|
|
11
|
+
# jruby examples/multithread_shards_to_r/shards_to_r.rb
|
|
12
|
+
#
|
|
13
|
+
# See also:
|
|
14
|
+
# specs/bridge_concurrent_spec.rb — many threads calling R; bridge serializes.
|
|
15
|
+
# specs/arrow_from_ruby_batches_spec.rb — same merge → R pattern with Arrow.
|
|
16
|
+
|
|
17
|
+
require 'galaaz'
|
|
18
|
+
|
|
19
|
+
SHARD_COUNT = 3
|
|
20
|
+
ROWS_PER_SHARD = 200
|
|
21
|
+
|
|
22
|
+
# Replace this with a real query, e.g.:
|
|
23
|
+
# Sequel.connect(ENV.fetch("DATABASE_URL_SHARD_#{shard_id}"))
|
|
24
|
+
# .fetch("SELECT id, region, amount FROM events WHERE shard_id = ?", shard_id)
|
|
25
|
+
# .map { |r| r.symbolize_keys }
|
|
26
|
+
def fetch_rows_from_shard(shard_id)
|
|
27
|
+
base = shard_id * ROWS_PER_SHARD
|
|
28
|
+
(0...ROWS_PER_SHARD).map do |j|
|
|
29
|
+
n = base + j
|
|
30
|
+
{
|
|
31
|
+
shard: shard_id,
|
|
32
|
+
id: n,
|
|
33
|
+
region: "r#{n % 4}",
|
|
34
|
+
amount: (n % 17) + 1.0
|
|
35
|
+
}
|
|
36
|
+
end
|
|
37
|
+
end
|
|
38
|
+
|
|
39
|
+
batches = []
|
|
40
|
+
batch_mx = Mutex.new
|
|
41
|
+
|
|
42
|
+
threads = SHARD_COUNT.times.map do |sid|
|
|
43
|
+
Thread.new do
|
|
44
|
+
rows = fetch_rows_from_shard(sid)
|
|
45
|
+
batch_mx.synchronize { batches << rows }
|
|
46
|
+
end
|
|
47
|
+
end
|
|
48
|
+
threads.each(&:join)
|
|
49
|
+
|
|
50
|
+
merged = batches.flatten
|
|
51
|
+
puts "Collected #{merged.size} rows from #{SHARD_COUNT} threads in Ruby"
|
|
52
|
+
|
|
53
|
+
unless R::Support.eval("requireNamespace('arrow', quietly=TRUE) && requireNamespace('dplyr', quietly=TRUE)") == true
|
|
54
|
+
warn 'Skipping R aggregation: install R packages arrow and dplyr, or use R.data__frame from merged hashes.'
|
|
55
|
+
exit 0
|
|
56
|
+
end
|
|
57
|
+
|
|
58
|
+
tbl = R::Arrow.from_ruby_batches(merged)
|
|
59
|
+
grouped = R.dplyr___group_by(tbl, :region)
|
|
60
|
+
summarised = R.dplyr___summarise(
|
|
61
|
+
grouped,
|
|
62
|
+
n: E.n,
|
|
63
|
+
total: E.sum(:amount),
|
|
64
|
+
mean_amt: E.mean(:amount)
|
|
65
|
+
)
|
|
66
|
+
out = R.dplyr___collect(summarised)
|
|
67
|
+
puts R.as__data__frame(out)
|
|
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|
|
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|
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|
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|
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|
|
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|
|
@@ -0,0 +1,41 @@
|
|
|
1
|
+
# Running sthda_ggplot examples
|
|
2
|
+
|
|
3
|
+
Use the same JRuby and JVM options as the specs (required for Apache Arrow).
|
|
4
|
+
|
|
5
|
+
## Run all sthda_ggplot examples
|
|
6
|
+
|
|
7
|
+
From the project root:
|
|
8
|
+
|
|
9
|
+
```bash
|
|
10
|
+
jruby -I lib -J--add-opens=java.base/java.nio=org.apache.arrow.memory.core,ALL-UNNAMED examples/sthda_ggplot/all.rb
|
|
11
|
+
```
|
|
12
|
+
|
|
13
|
+
Or with the helper script (if present):
|
|
14
|
+
|
|
15
|
+
```bash
|
|
16
|
+
bin/run_example examples/sthda_ggplot/all.rb
|
|
17
|
+
```
|
|
18
|
+
|
|
19
|
+
## Run a single example
|
|
20
|
+
|
|
21
|
+
```bash
|
|
22
|
+
jruby -I lib -J--add-opens=java.base/java.nio=org.apache.arrow.memory.core,ALL-UNNAMED examples/sthda_ggplot/one_variable_continuous/geom_density.rb
|
|
23
|
+
```
|
|
24
|
+
|
|
25
|
+
Examples that open a display (e.g. `R.awt` / X11) will show a window; some examples use `sleep(2)` between plots.
|
|
26
|
+
|
|
27
|
+
## Via Rake (default Ruby)
|
|
28
|
+
|
|
29
|
+
The default task runs all sthda examples:
|
|
30
|
+
|
|
31
|
+
```bash
|
|
32
|
+
rake sthda:all
|
|
33
|
+
```
|
|
34
|
+
|
|
35
|
+
A single example (replace with the file path under `examples/sthda_ggplot/`):
|
|
36
|
+
|
|
37
|
+
```bash
|
|
38
|
+
rake "sthda:one_variable_continuous/geom_density"
|
|
39
|
+
```
|
|
40
|
+
|
|
41
|
+
Note: Rake uses `ruby --polyglot --jvm -Ilib/` (TruffleRuby-style). For JRuby + Shadow Bridge, use the `jruby` command above.
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
@@ -38,6 +38,8 @@ a = wdata.ggplot(E.aes(x: :weight))
|
|
|
38
38
|
# Aggregate the data by sex
|
|
39
39
|
mu = R.aggregate(wdata.weight, by: R.list(wdata.sex), FUN: :mean)
|
|
40
40
|
mu.names = R.c("sex", "grp_mean")
|
|
41
|
+
puts "MU CLASS: #{R.bridge.eval_r("paste(class(#{mu.r_interop}), collapse=' ')")}"
|
|
42
|
+
puts "MU NAMES: #{R.bridge.eval_r("names(#{mu.r_interop})")}"
|
|
41
43
|
puts mu
|
|
42
44
|
|
|
43
45
|
R.awt
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
@@ -46,9 +46,10 @@ R.grid__newpage
|
|
|
46
46
|
# a subset of economics data set is used
|
|
47
47
|
R.set__seed(1234)
|
|
48
48
|
|
|
49
|
-
#
|
|
50
|
-
|
|
51
|
-
|
|
49
|
+
# nrow returns a numeric (or R vector); use it in a Ruby range for sampling row indices
|
|
50
|
+
n = economics.nrow
|
|
51
|
+
n = n.respond_to?(:pop) ? n.pop : n
|
|
52
|
+
ss = economics[R.sample((1..n), 20), :all]
|
|
52
53
|
|
|
53
54
|
print ss.ggplot(E.aes(x: :date, y: :unemploy)) +
|
|
54
55
|
R.geom_step
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
@@ -0,0 +1,46 @@
|
|
|
1
|
+
# Makefile for Galaaz Gatekeeper shared library
|
|
2
|
+
# Usage: make clean all
|
|
3
|
+
|
|
4
|
+
# R configuration
|
|
5
|
+
R_HOME := $(shell R RHOME)
|
|
6
|
+
R_CPPFLAGS := $(shell $(R_HOME)/bin/R CMD config --cppflags)
|
|
7
|
+
R_LIBS := $(shell $(R_HOME)/bin/R CMD config --ldflags)
|
|
8
|
+
|
|
9
|
+
# Rcpp configuration
|
|
10
|
+
RCPP_INCLUDE := $(shell $(R_HOME)/bin/Rscript -e "cat(system.file('include', package='Rcpp'))")
|
|
11
|
+
RCPP_CPPFLAGS := -I$(RCPP_INCLUDE)
|
|
12
|
+
|
|
13
|
+
# Compiler settings
|
|
14
|
+
CXX := $(shell $(R_HOME)/bin/R CMD config CXX)
|
|
15
|
+
CXXFLAGS := $(shell $(R_HOME)/bin/R CMD config CXXFLAGS)
|
|
16
|
+
CPPFLAGS := $(R_CPPFLAGS) $(RCPP_CPPFLAGS) -I.
|
|
17
|
+
# Core R library only (avoid system libs that may not be present)
|
|
18
|
+
LDFLAGS := -L$(R_HOME)/lib -lR -Wl,-rpath,$(R_HOME)/lib
|
|
19
|
+
|
|
20
|
+
# Target library
|
|
21
|
+
TARGET := galaaz_gatekeeper.so
|
|
22
|
+
SRC := galaaz_gatekeeper_phase1.cpp
|
|
23
|
+
OBJ := $(SRC:.cpp=.o)
|
|
24
|
+
|
|
25
|
+
.PHONY: all clean check
|
|
26
|
+
|
|
27
|
+
all: $(TARGET)
|
|
28
|
+
|
|
29
|
+
$(TARGET): $(OBJ)
|
|
30
|
+
$(CXX) -shared -o $@ $^ $(LDFLAGS)
|
|
31
|
+
|
|
32
|
+
%.o: %.cpp
|
|
33
|
+
$(CXX) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c $< -o $@
|
|
34
|
+
|
|
35
|
+
check: $(TARGET)
|
|
36
|
+
@echo "Checking library..."
|
|
37
|
+
@$(R_HOME)/bin/Rscript -e "dyn.load('$(TARGET)'); cat('Library loads successfully\n')"
|
|
38
|
+
|
|
39
|
+
clean:
|
|
40
|
+
rm -f $(OBJ) $(TARGET)
|
|
41
|
+
|
|
42
|
+
# Development helpers
|
|
43
|
+
install: $(TARGET)
|
|
44
|
+
@echo "Copying to galaaz lib directory..."
|
|
45
|
+
mkdir -p ../../lib/new_bridge
|
|
46
|
+
cp $(TARGET) ../../lib/new_bridge/
|