Merge branch 'release/Release-3'

franzbischoff · Jul 21, 2022 · f502dd4 · f502dd4
2 parents a5c0240 + 3b81f6f
commit f502dd4
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Showing 151 changed files with 92,353 additions and 31,000 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -33,8 +33,9 @@
 ^\.radian_history$
 ^\.vscode$
 ^\.whitesource$
-^_classifier$
 ^_regime_change$
+^_classifier$
+^_regimetest$
 ^_targets$
 ^_targets\.R$
 ^_targets\.yaml$

diff --git a/.Rinstignore b/.Rinstignore
@@ -0,0 +1,2 @@
+inst/extdata/.*
+inst/testfiles/.*
diff --git a/.Rprofile b/.Rprofile
@@ -1,37 +1,40 @@
 # nolint start
+options(repos = c(CRAN = "https://cran.rstudio.org"))
+
 if (.Platform$OS.type == "windows") {
   Sys.setenv(LC_CTYPE = "C")
 }
 
 source("renv/activate.R")
 
-if (Sys.getenv("CI") == "") { # not CI
-
-  a <- NULL
-  suppressMessages(if (requireNamespace("languageserver", quietly = TRUE)) {
-    a <- try(suppressWarnings(source(file.path(
-      Sys.getenv(if (.Platform$OS.type == "windows") {
-        "USERPROFILE"
-      } else {
-        "HOME"
-      }),
-      ".vscode-R",
-      "init.R"
-    ))),
-    silent = TRUE
-    ) # if this fails we (probably) are in Binder
-  })
-
-  if (class(a) == "try-error") { # we are in Binder session (hopefully)
-    message("Starting Binder Session")
-    setHook("rstudio.sessionInit", function(newSession) {
-      if (newSession & is.null(rstudioapi::getActiveProject())) {
-        rstudioapi::openProject("false.alarm.Rproj")
-      }
-    }, action = "append")
-  }
+if (Sys.getenv("CI") == "") {
+  # not CI
 
-  rm(a)
+  # a <- NULL
+  # suppressMessages(if (requireNamespace("languageserver", quietly = TRUE)) {
+  #   a <- try(suppressWarnings(source(file.path(
+  #     Sys.getenv(if (.Platform$OS.type == "windows") {
+  #       "USERPROFILE"
+  #     } else {
+  #       "HOME"
+  #     }),
+  #     ".vscode-R",
+  #     "init.R"
+  #   ))),
+  #   silent = TRUE
+  #   ) # if this fails we (probably) are in Binder
+  # })
+
+  # if (class(a) == "try-error") { # we are in Binder session (hopefully)
+  #   message("Starting Binder Session")
+  #   setHook("rstudio.sessionInit", function(newSession) {
+  #     if (newSession & is.null(rstudioapi::getActiveProject())) {
+  #       rstudioapi::openProject("false.alarm.Rproj")
+  #     }
+  #   }, action = "append")
+  # }
+
+  # rm(a)
 
   if (interactive() && Sys.getenv("RSTUDIO") == "") {
     options(
@@ -44,18 +47,25 @@ if (Sys.getenv("CI") == "") { # not CI
     )
     options(
       vsc.rstudioapi = TRUE,
+      max.print = 1000,
+      width = 200,
       # vsc.browser = "Two",
       # vsc.viewer = "Two",
       # vsc.page_viewer = "Two",
       # vsc.view = "Two",
       # vsc.plot = "Two",
       # vsc.helpPanel = "Two",
-      vsc.str.max.level = 2,
+      # vsc.str.max.level = 2,
       vsc.show_object_size = TRUE,
       vsc.globalenv = TRUE,
-      vsc.dev.args = list(width = 1000, height = 1000)
+      vsc.dev.args = list(width = 1000, height = 700)
     )
 
+    options(languageserver.formatting_style = function(options) {
+      style <- styler::tidyverse_style(scope = "tokens", indent_by = 2)
+      style
+    })
+
     # if httpgd is installed, let's use it
     # This breaks rendering video
     # if ("httpgd" %in% .packages(all.available = TRUE)) {
@@ -72,32 +82,38 @@ if (Sys.getenv("CI") == "") { # not CI
         require("devtools", quietly = TRUE)
         require("usethis", quietly = TRUE)
         require("conflicted", quietly = TRUE)
+        # require("tidyverse", quietly = TRUE)
+        # require("tidymodels", quietly = TRUE)
         require("here", quietly = TRUE)
+        require("glue", quietly = TRUE)
         require("workflowr", quietly = TRUE)
         require("targets", quietly = TRUE)
         require("gittargets", quietly = TRUE)
         require("tarchetypes", quietly = TRUE)
       })
     )
 
+    conflicted::conflict_prefer("filter", "dplyr")
+    options(dplyr.summarise.inform = FALSE)
+
     if (.Platform$OS.type != "windows") {
       if (suppressMessages(requireNamespace("prettycode", quietly = TRUE))) {
         suppressMessages(prettycode::prettycode())
       }
     }
 
-    if (suppressMessages(requireNamespace("prompt", quietly = TRUE))) {
-      prompt::set_prompt(function(...) {
-        paste0(
-          "[",
-          prompt::git_branch(),
-          prompt::git_dirty(),
-          prompt::git_arrows(),
-          "] ",
-          prompt::prompt_runtime()
-        )
-      })
-    }
+    # if (suppressMessages(requireNamespace("prompt", quietly = TRUE))) {
+    # prompt::set_prompt(function(...) {
+    #   paste0(
+    #     "[",
+    #     prompt::git_branch(),
+    #     prompt::git_dirty(),
+    #     prompt::git_arrows(),
+    #     "] ",
+    #     prompt::prompt_runtime()
+    #   )
+    # })
+    # }
 
     if (Sys.getenv("RADIAN_VERSION") == "") {
       loadhistory() # if no file, no problem.
@@ -108,7 +124,8 @@ if (Sys.getenv("CI") == "") { # not CI
         cat("bye bye...\n") # print this so we see if any non-interactive session is lost here
       }
     }
-  } else { # is RSTUDIO
+  } else {
+    # is RSTUDIO
     suppressMessages(
       suppressWarnings({
         require("here", quietly = TRUE)
@@ -119,7 +136,8 @@ if (Sys.getenv("CI") == "") { # not CI
       })
     )
   }
-} else { # is CI
+} else {
+  # is CI
   suppressMessages(
     suppressWarnings({
       require("here", quietly = TRUE)

diff --git a/.gitignore b/.gitignore
@@ -4,7 +4,7 @@ cellar/
 lock/
 python/
 staging/
-.Rhistory
+.Rhistory*
 .Renviron
 .Rapp.history
 Pprof.out
@@ -59,6 +59,7 @@ vignettes/*.pdf
 # End of https://www.gitignore.io/api/r
 
 # Personalized
+tmp
 /tmp/
 /tmp_*/
 .future
@@ -73,6 +74,7 @@ debugme.log
 /R/RcppExports.R
 /code/
 /pdfs/
+/docs/reference
 /pkgdown/
 /revdep/*.html
 /revdep/checks
@@ -88,6 +90,7 @@ debugme.log
 LOCAL_APPDATA_FONTCONFIG_CACHE/
 README.html
 Rplots.pdf
+dev
 dev/
 packrat/lib*/
 packrat/src/
@@ -110,3 +113,5 @@ mpxtest.RData
 .devcontainer/mathjax.tgz
 docs/thesis/*.log
 docs/thesis/__*.tex
+analysis/shiny/rsconnect/shinyapps.io/franzbischoff/FLOSS.dcf
+analysis/shiny_land/rsconnect/shinyapps.io/franzbischoff/FLOSS_land.dcf
diff --git a/.lintr b/.lintr
@@ -1,12 +1,46 @@
-linters: with_defaults(open_curly_linter = NULL, T_and_F_symbol_linter, assignment_linter, closed_curly_linter = NULL, commas_linter,
-      commented_code_linter = NULL, cyclocomp_linter(50),
-      object_name_linter(styles = "snake_case"), object_length_linter(30),
-      equals_na_linter, function_left_parentheses_linter, infix_spaces_linter,
-      line_length_linter(500), no_tab_linter, object_usage_linter = NULL, paren_brace_linter,
-      absolute_path_linter(lax = TRUE), nonportable_path_linter = NULL, pipe_continuation_linter,
-      semicolon_terminator_linter(semicolon = "trailing"), seq_linter, single_quotes_linter,
-      spaces_inside_linter, spaces_left_parentheses_linter, trailing_blank_lines_linter,
-      trailing_whitespace_linter, undesirable_function_linter, undesirable_operator_linter,
-      unneeded_concatenation_linter)
+linters: linters_with_defaults(
+  absolute_path_linter(lax = TRUE),
+  any_duplicated_linter(),
+  any_is_na_linter(),
+  backport_linter(),
+  class_equals_linter(),
+  commented_code_linter = NULL,
+  condition_message_linter(),
+  consecutive_stopifnot_linter(),
+  cyclocomp_linter(50),
+  duplicate_argument_linter(),
+  extraction_operator_linter = NULL,
+  fixed_regex_linter(),
+  ifelse_censor_linter(),
+  implicit_integer_linter(),
+  inner_combine_linter(),
+  line_length_linter(150),
+  literal_coercion_linter(),
+  missing_argument_linter(),
+  missing_package_linter(),
+  namespace_linter(),
+  nested_ifelse_linter(),
+  nonportable_path_linter(lax = TRUE),
+  numeric_leading_zero_linter(),
+  object_length_linter(30),
+  object_usage_linter = NULL,
+  outer_negation_linter(),
+  package_hooks_linter(),
+  paste_linter(),
+  pipe_call_linter(),
+  redundant_ifelse_linter(),
+  regex_subset_linter(),
+  semicolon_linter(allow_compound = TRUE),
+  sprintf_linter(),
+  string_boundary_linter(),
+  strings_as_factors_linter(),
+  system_file_linter(),
+  undesirable_function_linter(all_undesirable_functions),
+  undesirable_operator_linter(all_undesirable_operators),
+  unneeded_concatenation_linter(),
+  unreachable_code_linter(),
+  unused_import_linter(),
+  yoda_test_linter()
+  )
 exclusions: list("dev", "renv", "R/RcppExports.R", "README.Rmd")
 
diff --git a/.vscode/c_cpp_properties.json b/.vscode/c_cpp_properties.json
@@ -4,7 +4,7 @@
       "name": "Rtools40-x64",
       "intelliSenseMode": "gcc-x64",
       "includePath": [
-        "C:/Program Files/R/R-4.1.2/include",
+        "C:/Program Files/R/R-4.2.0/include",
         "${workspaceFolder}/src"
       ],
       "defines": [
@@ -24,7 +24,7 @@
       "name": "Rtools40-x86",
       "intelliSenseMode": "gcc-x86",
       "includePath": [ // renv might be on i386-w64-mingw32 if R-32bits
-        "C:/Program Files/R/R-4.1.2/include",
+        "C:/Program Files/R/R-4.2.0/include",
         "${workspaceFolder}/src"
       ],
       "defines": [
@@ -89,10 +89,10 @@
       "includePath": [
         "/usr/share/R/include/**",
         "${workspaceFolder}/src/**",
-        "${workspaceFolder}/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include/**",
-        "${workspaceFolder}/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppParallel/include/**",
-        "${workspaceFolder}/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppThread/include/**",
-        "${workspaceFolder}/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppProgress/include/**"
+        "/usr/lib/R/library/Rcpp/include/**",
+        "/usr/lib/R/library/RcppParallel/include/**",
+        "/usr/lib/R/library/RcppThread/include/**",
+        "/usr/lib/R/library/RcppProgress/include/**"
       ],
       "defines": [
         "RCPP_PARALLEL_USE_TBB",

diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -3,11 +3,9 @@
     "gruntfuggly.todo-tree",
     "spmeesseman.vscode-taskexplorer",
     "meakbiyik.vscode-r-test-adapter",
-    "ikuyadeu.r",
     "hbenl.vscode-test-explorer",
     "cschleiden.vscode-github-actions",
     "editorconfig.editorconfig",
-    "tht13.html-preview-vscode",
     "donjayamanne.git-extension-pack",
     "codezombiech.gitignore",
     "james-yu.latex-workshop",
@@ -29,6 +27,8 @@
     "usernamehw.errorlens",
     "rdebugger.r-debugger",
     "hediet.vscode-drawio",
-    "PsykoSoldi3r.vscode-git-flow"
+    "serhioromano.vscode-gitflow",
+    "reditorsupport.r",
+    "notZaki.pandocciter"
   ]
 }
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -26,7 +26,7 @@
       "debugMode": "function",
       "workingDirectory": "${workspaceFolder}",
       "file": "${file}",
-      "mainFunction": "stompi",
+      "mainFunction": "score_regimes",
       "allowGlobalDebugging": false
     },
     {
@@ -45,6 +45,12 @@
       "request": "attach",
       "name": "Attach to R process",
       "splitOverwrittenOutput": true
+    },
+    {
+      "type": "pwa-chrome",
+      "name": "http://127.0.0.1:3000/docs/regime_optimize.html",
+      "request": "launch",
+      "url": "http://127.0.0.1:3000/docs/regime_optimize.html"
     }
   ]
 }