Duplicate setup method from pipeline in Quarto docs (#93)

* Fixed minicipality name

* debugged changed names

* Started editing actual document

* Got a running document.

* Updated packages

* Removed Packages v2

* Started modifying Dates and text

* Continuing to modify dates

* pre-linting changes

* Modified to improve linting things

* Removed Personal Path and minor changes.

* Switched to Run_Triad

* Added run_triad change

* Added Text

* Fixed City Name

* Fixing panel-tabset

* Pre stash push

* Added noctua

* restored correct packages

* Removed Enters

* Syler

* re-ordered document

* Reordered libraries

* Remove Old Files

* Added libraries

* libraries

* Updated Description and Lock File

* added dependencies for DT

* re-upload changed lock file

* Restore lockfile dependencies

* Add reporting profile file to .dockerignore

* removed ignore_sigpipes()

* don't know alphabet

* re-ordered description

* Add missing dependencies to DESCRIPTION and lockfile

* Add .rmarkdown files to .gitignore

* Re-add sigpipe catch

* Update Quarto deps

* Add relative imports and libraries using here calls

* Revert reporting renv.lock

* Add conditional assignment for Quarto doc context

* Cleanup and comment setup code

---------

Co-authored-by: Damonamajor <[email protected]>
Co-authored-by: Damonamajor <[email protected]>
Co-authored-by: Michael Wagner <[email protected]>

R/setup.R

@@ -3,15 +3,14 @@ options(
   tidymodels.dark = TRUE, # Tidymodels CV output compatible with dark theme
   dplyr.summarise.inform = FALSE, # Disable messages when aggregating
   scipen = 99, # Disable scientific notation
-  knitr.kable.NA = "", # Replace NA with empty string in knitr::kable
-  java.parameters = "-Xmx10g" # Pre-allocate memory for Java JDBC driver
+  knitr.kable.NA = "" # Replace NA with empty string in knitr::kable
 )
 
 # Load R pipeline dependencies from the Depends: key in the DESCRIPTION file.
 # Any new pipeline dependencies should be added there
 suppressPackageStartupMessages({
   purrr::walk(
-    strsplit(yaml::read_yaml("DESCRIPTION")$Depends, ", ")[[1]],
+    strsplit(yaml::read_yaml(here::here("DESCRIPTION"))$Depends, ", ")[[1]],
     library,
     character.only = TRUE
   )
@@ -45,8 +44,15 @@ source(here::here("R", "helpers.R"))
 # Initialize a dictionary of file paths. See misc/file_dict.csv for details
 paths <- model_file_dict()
 
-# Load the parameters file containing the run settings
-params <- read_yaml("params.yaml")
+# Load the parameters file containing the run settings. The conditional here
+# detects rendering in a Quarto/RMarkdown document and assigns to `model_params`
+# instead, since `params` is a reserved variable name in Quarto
+if (knitr::is_html_output() || knitr::is_latex_output()) {
+  params_obj_name <- "model_params"
+} else {
+  params_obj_name <- "params"
+}
+assign(params_obj_name, read_yaml(here("params.yaml")))
 
 # Get the number of available physical cores to use for multi-threading
 # Lightgbm docs recommend using only real cores, not logical
@@ -55,12 +61,15 @@ num_threads <- parallel::detectCores(logical = FALSE)
 
 # Override CV toggle, SHAP toggle, and S3 upload set in params.yaml.
 # Used to disable certain features for CI or limited runs
-cv_enable <- as.logical(
-  Sys.getenv("CV_ENABLE_OVERRIDE", unset = params$toggle$cv_enable)
-)
-shap_enable <- as.logical(
-  Sys.getenv("SHAP_ENABLE_OVERRIDE", unset = params$toggle$shap_enable)
-)
-upload_enable <- as.logical(
-  Sys.getenv("UPLOAD_ENABLE_OVERRIDE", unset = params$toggle$upload_enable)
-)
+cv_enable <- as.logical(Sys.getenv(
+  "CV_ENABLE_OVERRIDE",
+  unset = get(params_obj_name)$toggle$cv_enable
+))
+shap_enable <- as.logical(Sys.getenv(
+  "SHAP_ENABLE_OVERRIDE",
+  unset = get(params_obj_name)$toggle$shap_enable
+))
+upload_enable <- as.logical(Sys.getenv(
+  "UPLOAD_ENABLE_OVERRIDE",
+  unset = get(params_obj_name)$toggle$upload_enable
+))

reports/performance.qmd

@@ -12,44 +12,25 @@ format:
     fontsize: 12pt
 editor: source
 params:
-  run_id: 2023-12-19-recursing-jacob
+  run_id: '2023-12-19-vigilant-jacob'
   year: '2023'
 ---
 
 ```{r setup}
-options(knitr.kable.NA = "", scipen = 99, width = 150)
-
-# Load necessary libraries
-library(arrow)
-library(ccao)
-library(brio)
-library(DBI)
-library(decor)
-library(desc)
-library(dplyr)
-library(DT)
-library(ggplot2)
-library(glue)
-library(grid)
-library(gridExtra)
-library(gtools)
-library(here)
-library(htmltools)
-library(kableExtra)
-library(leaflet)
-library(plotly)
-library(purrr)
-library(recipes)
-library(scales)
-library(sf)
-library(skimr)
-library(stringr)
-library(tableone)
-library(tidyr)
-library(tools)
-source(here("R", "helpers.R"))
-
-# TODO: Catch for weird arrow bug with SIGPIPE. Need to permanently fix later
+# Load list of helper files and main libraries
+purrr::walk(list.files(here::here("R"), "\\.R$", full.names = TRUE), source)
+
+# Load reporting-only libraries
+suppressPackageStartupMessages({
+  reporting_libs <- "Config/renv/profiles/reporting/dependencies"
+  purrr::walk(
+    strsplit(yaml::read_yaml(here::here("DESCRIPTION"))[[reporting_libs]], ", ")[[1]],
+    library,
+    character.only = TRUE
+  )
+})
+
+# TODO: Catch for weird Arrow bug with SIGPIPE. Need to permanently fix later
 # https://github.com/apache/arrow/issues/32026
 cpp11::cpp_source(code = "
 #include <csignal>
@@ -63,7 +44,7 @@ cpp11::cpp_source(code = "
 ignore_sigpipes()
 
 # Initialize a dictionary of file paths. See misc/file_dict.csv for details
-paths <- model_file_dict(params$run_id, params$year)
+paths <- model_file_dict(model_params$run_id, model_params$year)
 
 # Grab metadata to check input alignment
 metadata <- read_parquet(paths$output$metadata$local)
@@ -98,7 +79,6 @@ if (file.exists(paths$output$shap$local)) {
 feat_imp_df <- read_parquet(paths$output$feature_importance$local)
 ```
 
-
 ```{r}
 # This script runs balance tests comparing the universe of residential parcels
 # to the sample of residential parcels with sales in the previous 8 years