Fix and render the HTML version

danielvartan · Nov 27, 2024 · 5a74c5a · 5a74c5a
1 parent c2dd103
commit 5a74c5a
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diff --git a/.gitignore b/.gitignore
@@ -1,19 +1,20 @@
 # See <https://git-scm.com/docs/gitignore>.
 
-_freeze/
-_print/
-_slides/
-_web/
-_targets/
-_temp/
-_ssh/
-.auth/
-.quarto/
+/_freeze/
+/_print/
+/_slides/
+/_web/
+/_targets/
+/_temp/
+/_ssh/
+/.auth/
+/.quarto/
+/index_cache/
+/site_libs/
+
 .Rapp.history
 .RData
 .Renviron
 .Rhistory
 .Rproj.user
 .Ruserdata
-
-/.quarto/
diff --git a/R/_dev.R b/R/_dev.R
@@ -48,6 +48,9 @@
 # source(here::here("R", "_pre-render-html.R"))
 # source(here::here("R", "_pre-render-revealjs.R"))
 #
+# --cache
+# --no-cache
+# --cache-refresh
 # quarto render
 # quarto render --profile gfm
 # quarto render --profile pdf

diff --git a/R/_post-render-end.R b/R/_post-render-end.R
@@ -45,7 +45,7 @@ output_docs_new_files <-
 output_docs_new_dirs <- list.dirs(
   path = get(paste0("output_dir_", env_vars$format)),
   full.names = FALSE
-)[-1]  %>%
+)[-1] %>%
   here::here(get(paste0("output_docs_", env_vars$format)), .)
 
 for (i in output_docs_old_files) {

diff --git a/R/_setup.R b/R/_setup.R
@@ -6,6 +6,7 @@ library(downlit)
 # library(extrafont)
 # library(here)
 # library(knitr)
+library(lubridate)
 library(magrittr)
 library(ggplot2)
 library(rlang)
@@ -16,7 +17,7 @@ library(xml2)
 
 # Load functions -----
 
-source(here::here("R/utils.R"))
+source(here::here("R", "utils.R"))
 
 # Set general options -----
 
@@ -75,7 +76,7 @@ ggplot2::theme_set(
   ggplot2::theme_bw(
     base_size = base_size,
     base_family = env_vars$sansfont,
-    base_line_size = base_size / 22, # `ggplot2::theme_gray` default
-    base_rect_size = base_size / 22 # `ggplot2::theme_gray` default
+    base_line_size = base_size / 22,
+    base_rect_size = base_size / 22
   )
 )
diff --git a/R/add_solar_data.R b/R/add_solar_data.R
@@ -50,8 +50,7 @@ add_solar_data <- function(
   data |>
     add_ghi(inpe_data) |>
     add_equinox_and_solstice(time_and_date_data) |>
-    add_sun_time() |>
-    nest_solar_vars()
+    add_sun_time()
 }
 
 # library(dplyr)
@@ -243,62 +242,3 @@ add_sun_time <- function(data) {
     ) |>
     dplyr::relocate(dplyr::matches("^december_"), .before = height)
 }
-
-# library(dplyr)
-# library(prettycheck) # github.com/danielvartan/prettycheck
-# library(purrr)
-# library(tidyr)
-
-nest_solar_vars <- function(data) {
-  prettycheck:::assert_tibble(data)
-
-  data |>
-    tidyr::nest(
-      ghi = c(ghi_month, ghi_annual),
-      march_equinox = c(
-        march_equinox, march_equinox_sunrise, march_equinox_sunset,
-        march_equinox_daylight
-      ),
-      june_solstice = c(
-        june_solstice, june_solstice_sunrise, june_solstice_sunset,
-        june_solstice_daylight
-      ),
-      september_equinox = c(
-        september_equinox, september_equinox_sunrise,
-        september_equinox_sunset, september_equinox_daylight
-      ),
-      december_solstice = c(
-        december_solstice, december_solstice_sunrise,
-        december_solstice_sunset, december_solstice_daylight
-      )
-    ) |>
-    dplyr::mutate(
-      ghi = ghi |>
-        purrr::map(
-         .f = ~ .x |>
-           dplyr::rename_with(.fn = ~ c("month", "annual"))
-      )
-    ) |>
-    dplyr::mutate(
-      dplyr::across(
-        .cols = dplyr::all_of(
-          c(
-            "march_equinox", "june_solstice", "september_equinox",
-            "december_solstice"
-          )
-        ),
-        .fns = ~ .x |>
-          purrr::map(
-            .f = ~ .x |>
-              dplyr::rename_with(
-                .fn = ~ c("moment", "sunrise", "sunset", "daylight")
-              )
-          )
-      )
-    ) |>
-    dplyr::relocate(
-      ghi, march_equinox, june_solstice, september_equinox,
-      december_solstice,
-      .after = longitude
-    )
-}
diff --git a/R/categorize_msf_sc.R b/R/categorize_msf_sc.R
@@ -1,10 +1,10 @@
 # library(dplyr)
 # library(here)
-# library(lubridate)
+library(lubridate)
 # library(prettycheck) # github.com/danielvartan/prettycheck
 
-source(here::here("R/get_chronotype_cutoffs.R"))
-source(here::here("R/utils.R"))
+source(here::here("R", "get_chronotype_cutoffs.R"))
+source(here::here("R", "utils.R"))
 
 categorize_msf_sc <- function(x) {
   prettycheck:::assert_hms(x)

diff --git a/R/lock_and_store_data.R b/R/lock_and_store_data.R
@@ -19,36 +19,48 @@ lock_and_store_data <- function(
     upload_to_osf = FALSE,
     name_pattern = deparse(substitute(data))
   ) {
-  prettycheck:::assert_internet()
+  prettycheck:::assert_tibble(data)
   prettycheck:::assert_string(osf_pat, n.chars = 70)
   lockr:::assert_public_key(public_key)
   prettycheck:::assert_flag(upload_to_osf)
   prettycheck:::assert_string(name_pattern)
 
-  osfr::osf_auth(osf_pat) |> rutils::shush()
-  osf_id <- "https://osf.io/cbqsa"
-  test <- try(osfr::osf_retrieve_node(osf_id), silent = TRUE)
+  data |>
+    lock_data(
+      public_key = public_key,
+      name_pattern = name_pattern
+    ) |>
+    store_data(
+      osf_pat = osf_pat,
+      upload_to_osf = upload_to_osf
+    )
+}
 
-  if (inherits(test, "try-error")) {
-    cli::cli_abort(paste0(
-      "The {.strong {cli::col_red('OSF PAT')}} provided is invalid. ",
-      "Please, check the access token and try again."
-    ))
-  }
+# library(cli)
+# library(dplyr)
+# library(hardhat)
+# library(here)
+# library(lockr) # github.com/danielvartan/lockr
+# library(lubridate)
+# library(lubritime)
+# library(prettycheck) # github.com/danielvartan/prettycheck
+# library(tidyr)
+
+source(here::here("R", "save_and_lock.R"))
+
+lock_data <- function(
+    data,
+    public_key = here::here("_ssh", "id_rsa.pub"),
+    name_pattern = deparse(substitute(data))
+  ) {
+  prettycheck:::assert_tibble(data)
+  lockr:::assert_public_key(public_key)
+  prettycheck:::assert_string(name_pattern)
 
   cli::cli_progress_step("Locking and saving data.")
 
   file_name_pattern <- name_pattern
 
-  rds_file <-
-    data |>
-    save_and_lock(
-      file = file.path(tempdir(), paste0(file_name_pattern, ".rds")),
-      type = "rds",
-      public_key = public_key,
-      compress = "bz2"
-    )
-
   csv_file <-
     data |>
     tidyr::unnest(
@@ -80,18 +92,123 @@ lock_and_store_data <- function(
       public_key = public_key
     )
 
+  if (any(c("ghi_month", march_equinox) %in% names(data))) {
+    data <- nest_solar_vars(data)
+  }
+
+  rds_file <-
+    data |>
+    save_and_lock(
+      file = file.path(tempdir(), paste0(file_name_pattern, ".rds")),
+      type = "rds",
+      public_key = public_key,
+      compress = "bz2"
+    )
+
   # file.size(rds_file) / 1e+6
   # file.size(csv_file) / 1e+6
 
+  c(rds_file, csv_file)
+}
+
+# library(cli)
+# library(osfr)
+# library(prettycheck) # github.com/danielvartan/prettycheck
+# library(rutils) # github.com/danielvartan/rutils
+
+store_data <- function(
+    file,
+    osf_pat = Sys.getenv("OSF_PAT"),
+    upload_to_osf = TRUE,
+  ) {
+  prettycheck:::assert_flag(upload_to_osf)
+
   if (isTRUE(upload_to_osf)) {
+    prettycheck:::assert_internet()
+    prettycheck:::assert_character(file)
+    for (i in file) prettycheck:::assert_file_exists(i)
+    prettycheck:::assert_string(osf_pat, n.chars = 70)
+
+    osfr::osf_auth(osf_pat) |> rutils::shush()
+    osf_id <- "https://osf.io/cbqsa"
+    test <- try(osfr::osf_retrieve_node(osf_id), silent = TRUE)
+
+    if (inherits(test, "try-error")) {
+      cli::cli_abort(paste0(
+        "The {.strong {cli::col_red('OSF PAT')}} provided is invalid. ",
+        "Please, check the access token and try again."
+      ))
+    }
+
     cli::cli_progress_step("Uploading data to OSF.")
 
     osfr::osf_upload(
       x = osfr::osf_retrieve_node(osf_id),
-      path = c(rds_file, csv_file),
+      path = file,
       conflicts = "overwrite"
     )
   }
 
-  invisible(data)
+  invisible()
+}
+
+# library(dplyr)
+# library(prettycheck) # github.com/danielvartan/prettycheck
+# library(purrr)
+# library(tidyr)
+
+nest_solar_vars <- function(data) {
+  prettycheck:::assert_tibble(data)
+
+  cli::cli_progress_step("Nesting solar variables.")
+
+  data |>
+    tidyr::nest(
+      ghi = c(ghi_month, ghi_annual),
+      march_equinox = c(
+        march_equinox, march_equinox_sunrise, march_equinox_sunset,
+        march_equinox_daylight
+      ),
+      june_solstice = c(
+        june_solstice, june_solstice_sunrise, june_solstice_sunset,
+        june_solstice_daylight
+      ),
+      september_equinox = c(
+        september_equinox, september_equinox_sunrise,
+        september_equinox_sunset, september_equinox_daylight
+      ),
+      december_solstice = c(
+        december_solstice, december_solstice_sunrise,
+        december_solstice_sunset, december_solstice_daylight
+      )
+    ) |>
+    dplyr::mutate(
+      ghi = ghi |>
+        purrr::map(
+          .f = ~ .x |>
+            dplyr::rename_with(.fn = ~ c("month", "annual"))
+        )
+    ) |>
+    dplyr::mutate(
+      dplyr::across(
+        .cols = dplyr::all_of(
+          c(
+            "march_equinox", "june_solstice", "september_equinox",
+            "december_solstice"
+          )
+        ),
+        .fns = ~ .x |>
+          purrr::map(
+            .f = ~ .x |>
+              dplyr::rename_with(
+                .fn = ~ c("moment", "sunrise", "sunset", "daylight")
+              )
+          )
+      )
+    ) |>
+    dplyr::relocate(
+      ghi, march_equinox, june_solstice, september_equinox,
+      december_solstice,
+      .after = longitude
+    )
 }
diff --git a/R/panel_tabset_coef_dfbetas.R b/R/panel_tabset_coef_dfbetas.R
@@ -20,7 +20,8 @@ panel_tabset_coef_dfbetas <- function(
     source = rep("Created by the author.", length(coef)),
     heading = "###",
     fit_engine_name = "fit_engine",
-    suffix = ""
+    suffix = "",
+    root = ".."
   ) {
   prettycheck:::assert_class(fit_engine, "lm")
 
@@ -36,6 +37,7 @@ panel_tabset_coef_dfbetas <- function(
   prettycheck:::assert_string(heading, pattern = "^#*")
   prettycheck:::assert_string(fit_engine_name)
   prettycheck:::assert_string(suffix)
+  prettycheck:::assert_string(root)
 
   if (!file.exists(here::here("qmd"))) dir.create(here::here("qmd"))
 
@@ -117,7 +119,7 @@ panel_tabset_coef_dfbetas <- function(
     readr::write_lines(file)
 
   include_string <- glue::glue(
-    "{{{{< include {to_relative_path(file)} >}}}}"
+    "{{{{< include {to_relative_path(file, root)} >}}}}"
   )
 
   cli::cli_alert_info(glue:::glue(