Move models into package namespace #41

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Merged

atharvashahane28 merged 13 commits into main from feature/37-models-env

Sep 11, 2025

BirdFlowAPI.tar.gz

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NAMESPACE

-Original file line number
+Diff line change
@@ Expand Up / @@ -5,4 +5,3 @@ export(load_models) @@
     export(range_rescale)
     export(save_json_palette)
     export(symbolize_raster_data)
-    import(BirdFlowR)

R/flow.R

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -22,7 +22,6 @@ get_s3_config <- function() {
  
    #' Null coalescing operator for config values

    `%||%` <- function(a, b) if (!is.null(a) && !is.na(a) && nzchar(a)) a else b

    #' @import BirdFlowR

    if(FALSE) {

       # Manually set function arguments for dev and debugging

    @@ -35,12 +34,6 @@ if(FALSE) {
  
       # the other files are correct

       # Load required libraries

       library(BirdFlowR)

       library(jsonlite)

       library(terra)

       library(aws.s3)

       # Load globals and helpers

       original_wd <- getwd()

       if(!grepl("api$", getwd()))

    @@ -99,6 +92,11 @@ save_local_path <- "config/save_local.flag"
  
    #'    `type`

    #' @export

    flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE) {

      # TODO:

      # utils::data("species", package = "BirdFlowAPI", envir = environment())

      # load_models()

      s3_cfg <- get_s3_config()

      s3_enabled <- !is.na(s3_cfg$bucket) && nzchar(s3_cfg$bucket)

    @@ -139,24 +137,24 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
  
      # Snap lat/lon to cell center using the first model (all models use same grid)

      bf <- models[[ifelse(taxa == "total", species$species[1], taxa)]]

      xy <- latlon_to_xy(lat_lon$lat, lat_lon$lon, bf = bf)

      col <- x_to_col(xy$x, bf = bf)

      row <- y_to_row(xy$y, bf = bf)

      x <- col_to_x(col, bf = bf)

      y <- row_to_y(row, bf = bf)

      snapped_latlon <- xy_to_latlon(x, y, bf = bf)

      xy <- BirdFlowR::latlon_to_xy(lat_lon$lat, lat_lon$lon, bf = bf)

      col <- BirdFlowR::x_to_col(xy$x, bf = bf)

      row <- BirdFlowR::y_to_row(xy$y, bf = bf)

      x <- BirdFlowR::col_to_x(col, bf = bf)

      y <- BirdFlowR::row_to_y(row, bf = bf)

      snapped_latlon <- BirdFlowR::xy_to_latlon(x, y, bf = bf)

      snapped_latlon$lat <- round(snapped_latlon$lat, 2)

      snapped_latlon$lon <- round(snapped_latlon$lon, 2)

      lat_lon <- snapped_latlon

      # Re-compute snapped xy for later use

      xy <- latlon_to_xy(lat_lon$lat, lat_lon$lon, bf = bf)

      xy <- BirdFlowR::latlon_to_xy(lat_lon$lat, lat_lon$lon, bf = bf)

      # Form file names and S3 keys using snapped lat/lon

      snapped_lat <- paste(lat_lon$lat, collapse = "_")

      snapped_lon <- paste(lat_lon$lon, collapse = "_")

      cache_prefix <- paste0(direction, "/", taxa, "_", week, "_", snapped_lat, "_", snapped_lon, "/")

      pred_weeks <- lookup_timestep_sequence(bf, start = week, n = n, direction = direction)

      pred_weeks <- BirdFlowR::lookup_timestep_sequence(bf, start = week, n = n, direction = direction)

      png_files <- paste0(flow_type, "_", taxa, "_", pred_weeks, ".png")

      symbology_files <- paste0(flow_type, "_", taxa, "_", pred_weeks, ".json")

      png_bucket_paths <- paste0(s3_flow_path, cache_prefix, png_files)

    @@ -169,14 +167,14 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
  
      cache_hit <- TRUE

      if (!save_local && s3_enabled) {

        for (i in seq_along(pred_weeks)) {

          png_exists <- object_exists(object = png_bucket_paths[i], bucket = s3_cfg$bucket)

          json_exists <- object_exists(object = symbology_bucket_paths[i], bucket = s3_cfg$bucket)

          png_exists <- aws.s3::object_exists(object = png_bucket_paths[i], bucket = s3_cfg$bucket)

          json_exists <- aws.s3::object_exists(object = symbology_bucket_paths[i], bucket = s3_cfg$bucket)

          if (!png_exists || !json_exists) {

            cache_hit <- FALSE

            break

          }

        }

        tiff_exists <- object_exists(object = tiff_bucket_path, bucket = s3_cfg$bucket)

        tiff_exists <- aws.s3::object_exists(object = tiff_bucket_path, bucket = s3_cfg$bucket)

        if (!tiff_exists) cache_hit <- FALSE

      } else {

        # Local cache: check if all files exist in localtmp

    @@ -231,23 +229,23 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
  
      for (i in seq_along(target_species)) {

        sp <- target_species[i]

        bf <- models[[sp]]

        valid <- is_location_valid(bf, timestep = week, x = xy$x, y = xy$y)

        valid <- BirdFlowR::is_location_valid(bf, timestep = week, x = xy$x, y = xy$y)

        if (!all(valid)) {

          next

        }

        any_valid <- TRUE

        start_distr <- as_distr(xy, bf)

        start_distr <- BirdFlowR::as_distr(xy, bf)

        if (nrow(lat_lon) > 1) {

          start_distr <- apply(start_distr, 1, sum)

          start_distr <- start_distr / sum(start_distr)

        }

        log_progress(paste("Starting prediction for", sp))

        pred <- predict(bf, start_distr, start = week, n = n, direction = direction)

        location_i <- xy_to_i(xy, bf = bf)

        initial_population_distr <- get_distr(bf, which = week)

        location_i <- BirdFlowR::xy_to_i(xy, bf = bf)

        initial_population_distr <- BirdFlowR::get_distr(bf, which = week)

        start_proportion <- sum(initial_population_distr[location_i]) / 1

        abundance <- pred * species$population[species$species == sp] / prod(res(bf) / 1000) * start_proportion

        this_raster <- rasterize_distr(abundance, bf = bf, format = "terra")

        abundance <- pred * species$population[species$species == sp] / prod(terra::res(bf) / 1000) * start_proportion

        this_raster <- BirdFlowR::rasterize_distr(abundance, bf = bf, format = "terra")

        if (is.null(combined)) {

          combined <- this_raster

        } else {

R/load_models.R

-Original file line number
+Diff line change
@@ Expand Up / @@ -15,6 +15,8 @@ @@
     #'
     #' @export
     load_models <- function() {
+        # utils::data("species", package = "BirdFlowAPI", envir = environment())
         # Load BirdFlow models
         BirdFlowR::birdflow_options(collection_url = "https://birdflow-science.s3.amazonaws.com/sparse_avian_flu/")
         index <- BirdFlowR::load_collection_index()
@@ Expand All / @@ -23,14 +25,16 @@ load_models <- function() { @@
             stop("Expected BirdFlow models:", paste(miss, collapse = ", "), " are missing from the model collection." )
         }
-        # This is slow so skipping if it's already done - useful when developing to
-        # avoid having to wait to reload.
-        if(!exists("models") || !is.environment(models) || !all(species$species %in% names(models))) {
-            models <<- new.env(parent = globalenv())
-            print(paste("Loading", length(species$species), "models from https://birdflow-science.s3.amazonaws.com/avian_flu/"))
+        # This is slow so skipping if it's already done - useful when developing to
+        # avoid having to wait to reload.
+        if(!all(species$species %in% names(models))) {
+            print(paste("Loading", length(species$species), "models from https://birdflow-science.s3.amazonaws.com/sparse_avian_flu/"))
             for (sp in species$species) {
                 print(paste0("Loading model for species: ", sp))
                 models[[sp]] <- BirdFlowR::load_model(model = sp)
             }
         }
-    }
+        else {
+            print("Models already loaded.")
+        }
+    }

R/models.R

Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		models <- new.env()

R/zzz.R

-Original file line number
+Diff line change
@@ -1,9 +1,3 @@
-    .onLoad <- function(libname, pkgname) {
-        utils::data("species", package = "BirdFlowAPI", envir = parent.env(environment()))
-        utils::data("flow_colors", package = "BirdFlowAPI", envir = parent.env(environment()))
-        load_models()
-    }
     .ignore_unused_imports <- function() {
         plumber::plumb
     }

README.md

            
                      Original file line number
                      Diff line number
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    @@ -6,22 +6,21 @@ BirdFlowAPI is an R package containing the API and backend code for the Avian In
  
    You can build and install BirdFlowAPI locally or from GitHub.

    **Build locally:**

    ```sh

    R CMD build .

    ```

    This will create a source tarball (e.g., `BirdFlowAPI_x.y.z.tar.gz`).

    **Install from local tarball:**

    **Install from local cloned repository:**

    ```r

    install.packages("path/to/BirdFlowAPI_x.y.z.tar.gz", repos = NULL, type = "source")

    devtools::install()

    ```

    **Install from GitHub:**

    ```r

    devtools::install_github("UMassCDS/BirdFlowAPI")

    ```

    ## Configure API

    The `load_models.R` file defines a function `load_models` that loads the the models of all species. The `load_models` function must be explicitly called while configuring the API. This is done by running `load_models()`.

    ## Testing

    Run the full test suite:

inst/plumber/flow/endpoints/predict.R

-Original file line number
+Diff line change
@@ -1,4 +1,3 @@
-    library(BirdFlowR)
     birdflow_options(collection_url = "https://birdflow-science.s3.amazonaws.com/avian_flu/")
     #* Test and generate a plot from a BirdFlow model
@@ Expand Down Expand Up / @@ -27,4 +26,4 @@ function(model_name = "ambduc") { @@
         file_exists = file_exists,
         file_size = file_size
       )
-    }
+    }

man/flow.Rd

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man/get_s3_config.Rd

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man/grapes-or-or-grapes.Rd

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man/set_s3_config.Rd

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tests/testthat/setup.R

Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		load_models()

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