Merge branch 'main' into 189_update_falcon

pharmaverse · Oct 18, 2024 · 42a4134 · 42a4134
2 parents 028bd5c + e3b8418
commit 42a4134
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diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -51,6 +51,7 @@ jobs:
             teal
             riskmetric
             tidyCDISC
+            mirai
 
       - name: Install tinytex
         run: quarto install tool tinytex

diff --git a/.github/workflows/update_post_dates.yml b/.github/workflows/update_post_dates.yml
@@ -14,32 +14,21 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
         with:
-          ref: main  # replace with the branch you want to checkout
+          ref: main
+          token: ${{ secrets.PHARMAVERSE_BOT }}
 
       - name: Run update_post_dates
         run: Rscript R/update_post_dates.R  # running the R script with Rscript
 
       - name: Configure Git safe directory
         run: git config --global --add safe.directory /__w/blog/blog
 
-      - name: Check for changes
-        id: check_changes
-        run: |
-          git config --global user.name 'github-actions[bot]'
-          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
-          if [[ `git status --porcelain` ]]; then
-            echo "changes detected"
-            echo "changes=true" >> $GITHUB_ENV
-          else
-            echo "no changes"
-            echo "changes=false" >> $GITHUB_ENV
-          fi
-
-      - name: Commit results
-        if: env.changes == 'true'
-        run: |
-          git add .
-          git commit -m "Auto-update blog post date"
-          git push origin main
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Commit and push changes
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: "[skip actions] Auto-update blog post date"
+          file_pattern: "."
+          commit_user_name: github-actions
+          commit_user_email: >-
+            41898282+github-actions[bot]@users.noreply.github.com
+        continue-on-error: true
diff --git a/inst/WORDLIST.txt b/inst/WORDLIST.txt
@@ -1120,6 +1120,33 @@ astrazeneca
 laura
 MeetLaura
 needleman
+Alexandros
+clusterSetRNGStream
+CMRG
+doFuture
+elbersb
+filelock
+HPC
+Kouretsis
+L'Ecuyer
+mirai
+nanonext
+opre
+parallelization
+Parallelization
+parallelizes
+parallelMap
+pubsonline
+reprovision
+shikokuchuo
+tensio
+tidylog
+tidyr
+wlandau
+zzz
+axecute
+readRDS
+saveRDS
 WEL
 Parmar
 RMarkdown

diff --git a/posts/2024-10-16_the__tensio.../appendix.R b/posts/2024-10-16_the__tensio.../appendix.R
@@ -0,0 +1,73 @@
+suppressMessages(library(dplyr))
+# markdown helpers --------------------------------------------------------
+
+markdown_appendix <- function(name, content) {
+  paste(paste("##", name, "{.appendix}"), " ", content, sep = "\n")
+}
+markdown_link <- function(text, path) {
+  paste0("[", text, "](", path, ")")
+}
+
+
+
+# worker functions --------------------------------------------------------
+
+insert_source <- function(repo_spec, name,
+                          collection = "posts",
+                          branch = "main",
+                          host = "https://github.com",
+                          text = "Source",
+                          file_name) {
+  path <- paste(
+    host,
+    repo_spec,
+    "tree",
+    branch,
+    collection,
+    name,
+    file_name,
+    sep = "/"
+  )
+  return(markdown_link(text, path))
+}
+
+insert_timestamp <- function(tzone = Sys.timezone()) {
+  time <- lubridate::now(tzone = tzone)
+  stamp <- as.character(time, tz = tzone, usetz = TRUE)
+  return(stamp)
+}
+
+insert_lockfile <- function(repo_spec, name,
+                            collection = "posts",
+                            branch = "main",
+                            host = "https://github.com",
+                            text = "Session info") {
+  path <- path <- "https://pharmaverse.github.io/blog/session_info.html"
+
+  return(markdown_link(text, path))
+}
+
+
+
+# top level function ------------------------------------------------------
+
+insert_appendix <- function(repo_spec, name, collection = "posts", file_name) {
+  appendices <- paste(
+    markdown_appendix(
+      name = "Last updated",
+      content = insert_timestamp()
+    ),
+    " ",
+    markdown_appendix(
+      name = "Details",
+      content = paste(
+        insert_source(repo_spec, name, collection, file_name = file_name),
+        # get renv information,
+        insert_lockfile(repo_spec, name, collection),
+        sep = ", "
+      )
+    ),
+    sep = "\n"
+  )
+  knitr::asis_output(appendices)
+}
diff --git a/posts/2024-10-16_the__tensio.../cache_execution.rds b/posts/2024-10-16_the__tensio.../cache_execution.rds
diff --git a/posts/2024-10-16_the__tensio.../mirai_workflow.R b/posts/2024-10-16_the__tensio.../mirai_workflow.R
@@ -0,0 +1,26 @@
+{
+  library("mirai")
+  library("dplyr")
+  log_file <- tempfile()
+  mirai::daemons(4)
+  mirai::everywhere(
+    {
+      library("dplyr")
+      library("tidylog")
+      log_to_file <- function(txt) {
+        cat(txt,
+          file = log_file,
+          sep = "\n", append = TRUE
+        )
+      }
+      options(tidylog.display = list(message, log_to_file))
+    },
+    log_file = log_file
+  )
+  m <- mirai_map(letters[1:5], function(x) {
+    mutate(tibble(.rows = 1), `:=`("{x}", sample(1:100, 1)))
+  })
+  result <- bind_cols(m[])
+  mirai::daemons(0)
+  print(list(logs = readLines(log_file), result = result))
+}
diff --git a/posts/2024-10-16_the__tensio.../mirai_workflow.log b/posts/2024-10-16_the__tensio.../mirai_workflow.log
@@ -0,0 +1,171 @@
+--------------------------------------------------------------------------------
+-                                logrx Metadata                                -
+--------------------------------------------------------------------------------
+This log was generated using logrx 0.3.1
+logrx package version: 0.3.1
+logrx build: RSPM (R 4.3.0)
+logrx link to repository: https://github.com/pharmaverse/logrx
+--------------------------------------------------------------------------------
+-                          User and File Information                           -
+--------------------------------------------------------------------------------
+User: ale
+File Name: mirai_workflow.R
+File Path: /home/ale/blog/posts/zzz_DO_NOT_EDIT_the__tensio...
+File HashSum: 93e86d1e6a59ab5475d3c9fbd1948be36228a1fe
+--------------------------------------------------------------------------------
+-                             Session Information                              -
+--------------------------------------------------------------------------------
+─ Session info ───────────────────────────────────────────────────────────────
+ setting  value
+ version  R version 4.3.2 (2023-10-31)
+ os       Ubuntu 22.04.3 LTS
+ system   x86_64, linux-gnu
+ ui       X11
+ language (EN)
+ collate  en_US.UTF-8
+ ctype    en_US.UTF-8
+ tz       Etc/UTC
+ date     2024-10-07
+ pandoc   3.1.1 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown)
+
+─ Packages ───────────────────────────────────────────────────────────────────
+ package     * version date (UTC) lib source
+ backports     1.4.1   2021-12-13 [1] RSPM (R 4.3.0)
+ callr         3.7.3   2022-11-02 [1] RSPM (R 4.3.0)
+ cli           3.6.2   2023-12-11 [1] RSPM (R 4.3.0)
+ crayon        1.5.2   2022-09-29 [1] RSPM (R 4.3.0)
+ cyclocomp     1.1.1   2023-08-30 [1] RSPM (R 4.3.0)
+ data.table    1.15.0  2024-01-30 [1] RSPM (R 4.3.0)
+ desc          1.4.3   2023-12-10 [1] RSPM (R 4.3.0)
+ digest        0.6.34  2024-01-11 [1] RSPM (R 4.3.0)
+ dplyr       * 1.1.4   2023-11-17 [1] RSPM (R 4.3.0)
+ evaluate      0.23    2023-11-01 [1] RSPM (R 4.3.0)
+ fansi         1.0.6   2023-12-08 [1] RSPM (R 4.3.0)
+ fastmap       1.2.0   2024-05-15 [1] RSPM (R 4.3.0)
+ generics      0.1.3   2022-07-05 [1] RSPM (R 4.3.0)
+ glue          1.7.0   2024-01-09 [1] RSPM (R 4.3.0)
+ htmltools     0.5.7   2023-11-03 [1] RSPM (R 4.3.0)
+ htmlwidgets   1.6.4   2023-12-06 [1] RSPM (R 4.3.0)
+ httpuv        1.6.15  2024-03-26 [1] RSPM (R 4.3.0)
+ jsonlite      1.8.8   2023-12-04 [1] RSPM (R 4.3.0)
+ knitr         1.45    2023-10-30 [1] RSPM (R 4.3.0)
+ later         1.3.2   2023-12-06 [1] RSPM (R 4.3.0)
+ lazyeval      0.2.2   2019-03-15 [1] RSPM (R 4.3.0)
+ lifecycle     1.0.4   2023-11-07 [1] RSPM (R 4.3.0)
+ lintr         3.1.2   2024-03-25 [1] RSPM (R 4.3.0)
+ logrx         0.3.1   2024-04-12 [1] RSPM (R 4.3.0)
+ magrittr      2.0.3   2022-03-30 [1] RSPM (R 4.3.0)
+ mime          0.12    2021-09-28 [1] RSPM (R 4.3.0)
+ miniUI        0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0)
+ mirai       * 1.2.0   2024-08-18 [1] RSPM (R 4.3.0)
+ nanonext      1.2.1   2024-08-19 [1] RSPM (R 4.3.0)
+ pillar        1.9.0   2023-03-22 [1] RSPM (R 4.3.0)
+ pkgconfig     2.0.3   2019-09-22 [1] RSPM (R 4.3.0)
+ processx      3.8.3   2023-12-10 [1] RSPM (R 4.3.0)
+ promises      1.3.0   2024-04-05 [1] RSPM (R 4.3.0)
+ ps            1.7.6   2024-01-18 [1] RSPM (R 4.3.0)
+ purrr         1.0.2   2023-08-10 [1] RSPM (R 4.3.0)
+ R6            2.5.1   2021-08-19 [1] RSPM (R 4.3.0)
+ Rcpp          1.0.12  2024-01-09 [1] RSPM (R 4.3.0)
+ remotes       2.5.0   2024-03-17 [1] RSPM (R 4.3.0)
+ rex           1.2.1   2021-11-26 [1] RSPM (R 4.3.0)
+ rlang         1.1.3   2024-01-10 [1] RSPM (R 4.3.0)
+ rmarkdown     2.28    2024-08-17 [1] RSPM (R 4.3.0)
+ rstudioapi    0.15.0  2023-07-07 [1] RSPM (R 4.3.0)
+ sessioninfo   1.2.2   2021-12-06 [1] RSPM (R 4.3.0)
+ shiny         1.9.1   2024-08-01 [1] RSPM (R 4.3.0)
+ stringi       1.8.3   2023-12-11 [1] RSPM (R 4.3.0)
+ stringr       1.5.1   2023-11-14 [1] RSPM (R 4.3.0)
+ tibble        3.2.1   2023-03-20 [1] RSPM (R 4.3.0)
+ tidyr         1.3.1   2024-01-24 [1] RSPM (R 4.3.0)
+ tidyselect    1.2.0   2022-10-10 [1] RSPM (R 4.3.0)
+ utf8          1.2.4   2023-10-22 [1] RSPM (R 4.3.0)
+ vctrs         0.6.5   2023-12-01 [1] RSPM (R 4.3.0)
+ waiter        0.2.5   2022-01-03 [1] RSPM (R 4.3.0)
+ withr         3.0.0   2024-01-16 [1] RSPM (R 4.3.0)
+ xfun          0.42    2024-02-08 [1] RSPM (R 4.3.0)
+ xml2          1.3.6   2023-12-04 [1] RSPM (R 4.3.0)
+ xtable        1.8-4   2019-04-21 [1] RSPM (R 4.3.0)
+ yaml          2.3.8   2023-12-11 [1] RSPM (R 4.3.0)
+
+ [1] /usr/local/lib/R/site-library
+ [2] /usr/local/lib/R/library
+
+─ External software ──────────────────────────────────────────────────────────
+ setting        value
+ cairo          1.16.0
+ cairoFT
+ pango          1.50.6
+ png            1.6.37
+ jpeg           8.0
+ tiff           LIBTIFF, Version 4.3.0
+ tcl
+ curl           7.81.0
+ zlib           1.2.11
+ bzlib          1.0.8, 13-Jul-2019
+ xz             5.2.5
+ PCRE           10.39 2021-10-29
+ ICU            70.1
+ TRE            TRE 0.8.0 R_fixes (BSD)
+ iconv          glibc 2.35
+ readline       8.1
+ BLAS           /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
+
+	  lapack         /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
+ lapack_version 3.10.0
+
+─ Python configuration ───────────────────────────────────────────────────────
+ Python is not available
+
+──────────────────────────────────────────────────────────────────────────────
+--------------------------------------------------------------------------------
+-                               Masked Functions                               -
+--------------------------------------------------------------------------------
+function `plot` from {package:base} by package:graphics
+function `body<-` from {package:base} by package:methods
+function `kronecker` from {package:base} by package:methods
+--------------------------------------------------------------------------------
+-                          Used Package and Functions                          -
+--------------------------------------------------------------------------------
+{!!! NOT FOUND !!!} `:=`
+{package:base} library, tempfile, cat, options, list, print, readLines
+{package:dplyr} mutate, bind_cols
+{package:mirai} daemons, everywhere, mirai_map
+{package:tidyr} tibble
+--------------------------------------------------------------------------------
+-                         Program Run Time Information                         -
+--------------------------------------------------------------------------------
+Start time: 2024-10-07 22:16:34 UTC
+End time: 2024-10-07 22:16:36 UTC
+Run time: 2 seconds
+--------------------------------------------------------------------------------
+-                             Errors and Warnings                              -
+--------------------------------------------------------------------------------
+Errors:
+
+
+Warnings:
+
+--------------------------------------------------------------------------------
+-                         Messages, Output, and Result                         -
+--------------------------------------------------------------------------------
+
+Result:
+	$logs
+	[1] "mutate: new variable 'b' (character) with one unique value and 0% NAmutate: new variable 'a' (character) with one unique value and 0% NA"
+	[2] ""                                                                                                                                        
+	[3] "mutate: new variable 'd' (character) with one unique value and 0% NA"                                                                    
+	[4] "mutate: new variable 'e' (character) with one unique value and 0% NA"                                                                    
+	[5] "mutate: new variable 'c' (character) with one unique value and 0% NA"                                                                    
+
+	$result
+	# A tibble: 1 × 5
+	  a     b     c     d     e    
+	  <chr> <chr> <chr> <chr> <chr>
+	1 foo   foo   foo   foo   foo  
+
+--------------------------------------------------------------------------------
+-                               Log Output File                                -
+--------------------------------------------------------------------------------
+Log name: mirai_workflow.log
+Log path: /home/ale/blog/posts/zzz_DO_NOT_EDIT_the__tensio...
diff --git a/posts/2024-10-16_the__tensio.../pharmaverse.PNG b/posts/2024-10-16_the__tensio.../pharmaverse.PNG