Refactor r tests

.devcontainer/devcontainer.json

@@ -20,7 +20,7 @@
       "updatePackages": true
     },
     "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
-      "packages": "covr,dplyr,devtools,ggplot2,graphics,jsonlite,github::noaa-afsc/SparseNUTS,methods,Rcpp,RcppEigen,scales,snowfall,TMB,tibble,tidyr,usethis",
+      "packages": "covr,dplyr,devtools,furrr,future,ggplot2,graphics,jsonlite,github::noaa-afsc/SparseNUTS,methods,Rcpp,RcppEigen,scales,snowfall,TMB,tibble,tidyr,usethis,yardstick",
       "installSystemRequirements": true
     }
   },

.github/workflows/call-update-data-r.yml

@@ -0,0 +1,22 @@
+# Update data files in /data whenever changes are made to files in /data-raw.
+# This workflow automatically commits changes directly to the working branch.
+name: call-update-data-r
+
+on:
+  push:
+    paths:
+      - 'R/**'
+      - 'inst/**'
+      - 'data/**'
+      - 'data-raw/**'
+      - 'src/**'
+  workflow_dispatch:
+
+jobs:
+  call-workflow:
+    if: github.repository == 'NOAA-FIMS/FIMS'
+    uses: NOAA-FIMS/ecosystemom/.github/workflows/update-data-r.yml@main
+    secrets:
+      PAT: ${{ secrets.PAT }}
+    with:
+      commit-directly: true

.github/workflows/run-slow-tests.yml

@@ -40,7 +40,16 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-    name: ${{ matrix.os }}
+        # Adds the split test categories to the matrix
+        test_type:
+          - slow
+          - integration-caa
+          - integration-fims-bayesian
+          - integration-fims-estimation-random-effects
+          - integration-fleet
+          - integration-proportion
+
+    name: ${{ matrix.os }} (${{ matrix.test_type }})
     runs-on: ${{ matrix.os }}
 
     env:
@@ -85,13 +94,16 @@ jobs:
           needs: check
 
       - name: Run Slow Tests Only
+        env:
+          TEST_FILTER: ${{ matrix.test_type }}
         shell: Rscript {0}
         run: |
           # Windows-specific fix for the "files too big" error
           if (Sys.info()[["sysname"]] == "Windows") {
             withr::local_options(pkg.build_extra_flags = FALSE)
           }
 
-          # The filter looks for files with 'slow' in the name
-          devtools::test(filter = "slow")
+          filter_pattern <- Sys.getenv("TEST_FILTER")
+          message(paste("Running test suite matching filter:", filter_pattern))
 
+          devtools::test(filter = filter_pattern)

.gitignore

@@ -97,8 +97,6 @@
 src/tmp.def
 
 #Testing files
-tests/test_plan/FIMS_Integration_Test_Plan.log
-tests/integration/FIMS-deterministic-inputs/
 tests/testthat/fixtures/fit*.RDS
 tests/testthat/fixtures/data*.RDS
 tests/testthat/fixtures/parameters*.RDS

R/data_big.R

@@ -0,0 +1,119 @@
+#' FIMS input data frame
+#'
+#' A data frame containing the information needed to run an age-structured stock
+#' assessment model in FIMS. This data was generated using
+#' the `ASSAMC` package written for the [model comparison project](
+#' www.github.com/NOAA-FIMS/Age_Structured_Stock_Assessment_Model_Comparison).
+#' The source code to make this dataset is in `data-raw/data_big.R` which is on
+#' GitHub but will not be in your local installation because it is in the
+#' .Rbuildignore file.
+#'
+#' @format
+#' A data frame with `r NROW(data_big)` observations of `r NCOL(data_big)`
+#' variables:
+#' \describe{
+#'   \item{type}{The type of input the row contains. Allowed types include
+#'   `r glue::glue_collapse(fims_input_types, sep = ", ", last = ", and ")`.}
+#'   \item{fleet}{A character string providing the name of the information
+#'     source that the input was collected from, e.g., `"Trawl fishery"` or
+#'     `"age_zero_survey"`. Entries can be `NA` for information that is not
+#'     fleet/vessel specific.}
+#'   \item{age}{An integer age. Entry can be `NA` if information pertains to
+#'     multiple ages, e.g., total landings rather than landings of age-4 fish.
+#'     In this dataset, ages start at one, therefore recruitment happens at age
+#'     one not age zero.}
+#'   \item{length}{A numeric length. Entry can be `NA` if information doesn't
+#'     pertain to length.}
+#'   \item{timing}{The timing, i.e., year the data was collected.}
+#'   \item{value}{The measurement of interest.}
+#'   \item{unit}{A character string specifying the units of `value`. Allowed
+#'     units for each data type are as follows. `mt` is used for `index`,
+#'     `landings`, and `weight_at_age` data. `number` or `proportion` are each
+#'     viable units for the composition data, where the former is the preferred
+#'     unit of measurement.}
+#'   \item{uncertainty}{A real value providing a measurement of uncertainty
+#'     for value. For landings and indices of abundance this should be
+#'     the standard deviation of the logged observations if you are using the
+#'     lognormal distribution to fit your data. For composition data it will
+#'     be your input sample size.
+#' }
+#' }
+#' @source \url{www.github.com/NOAA-FIMS/Age_Structured_Stock_Assessment_Model_Comparison}
+"data_big"
+
+#' FIMS parameters tibble
+#'
+#' A tibble containing the parameters needed to run an age-structured stock
+#' assessment model in FIMS. This data was generated using the `ASSAMC` package
+#' written for the [model comparison project](www.github.com/NOAA-FIMS/Age_Structured_Stock_Assessment_Model_Comparison).
+#' The source code to make this dataset is in `data-raw/parameters_.R` which is
+#' on GitHub but will not be in your local installation because it is in the .Rbuildignore file.
+#'
+#' @format
+#' A tibble with `r NROW(parameters_big)` observations of `r NCOL(parameters_big)` variables:
+#' \describe{
+#'   \item{\code{model_family}:}{The specified model family (e.g.,
+#'     "catch_at_age").}
+#'   \item{\code{module_name}:}{The name of the FIMS module (e.g.,
+#'     "Data", "Selectivity", "Recruitment", "Growth", "Maturity"). These
+#'     entries are always written in PascalCase to match the names used in the
+#'     C++ code.}
+#'   \item{\code{fleet}:}{The name of the fleet the module applies to. This
+#'     will be `NA` for non-fleet-specific modules like "Recruitment".}
+#'   \item{\code{data}:}{A list-column containing a `tibble` with detailed
+#'     parameters. Unnesting this column reveals:
+#'     \describe{
+#'       \item{\code{module_type}:}{The specific type of the module (e.g.,
+#'         "Logistic" for a "Selectivity" module). This column will always be
+#'         written in PascalCase to match the names used in the C++ code.}
+#'       \item{\code{label}:}{The name of the parameter (e.g.,
+#'         "inflection_point").}
+#'       \item{\code{age}:}{The age the parameter applies to.}
+#'       \item{\code{length}:}{The length bin the parameter applies to.}
+#'       \item{\code{time}:}{The time step (i.e., year) the parameter applies
+#'         to.}
+#'       \item{\code{value}:}{The initial value of the parameter.}
+#'       \item{\code{estimation_type}:}{The type of estimation (e.g.,
+#'         "constant", "fixed_effects", "random_effects").}
+#'       \item{\code{distribution_type}:}{The type of distribution (e.g.,
+#'         "Data", "process"), where a process distribution can refer to a
+#'         fixed effect or a random effect but it does not fit to data, e.g.,
+#'         recruitment deviations.}
+#'       \item{\code{distribution}:}{The name of distribution (e.g.,
+#'         "Dlnorm", `Dmultinom`). The column will always be written in
+#'         PascalCase to match the names used in the C++ code.}
+#'     }
+#'   }
+#' }
+#' @source \url{www.github.com/NOAA-FIMS/Age_Structured_Stock_Assessment_Model_Comparison}
+"parameters_big"
+
+#' FIMS fit
+#'
+#' An object of class `FIMSFit`, where the structure is the same
+#' regardless if `optimize = TRUE` or not. Uncertainty information is only
+#' included in the `estimates` slot if `get_sd = TRUE`.
+#'
+#' @format
+#' An object of class `FIMSFit` with the following slots:
+#' `r paste(slotNames(fit_with_optimization_big), collapse = ", ")`
+#' @rdname fit_with_optimization_big
+"fit_with_optimization_big"
+
+#' @rdname fit_with_optimization_big
+"fit_without_optimization_big"
+
+#' FIMS estimates
+#'
+#' A tibble containing the estimates from a fitted FIMS model. The structure is
+#' the same regardless if `optimize = TRUE` or not. Uncertainty information is
+#' only included if `get_sd = TRUE`.
+#' @format
+#' A tibble with `r NROW(estimates_with_optimization_big)`
+#' observations of `r NCOL(estimates_with_optimization_big)` variables:
+#' `r paste(colnames(estimates_with_optimization_big), collapse = ", ")`
+#' @rdname estimates_with_optimization_big
+"estimates_with_optimization_big"
+
+#' @rdname estimates_with_optimization_big
+"estimates_without_optimization_big"

R/fimsframe.R

@@ -686,11 +686,11 @@ methods::setValidity(
     present_types <- unique(object@data[["type"]])
 
     # Issues warning if there are any unrecognized types
-    unknown_types <- sort(setdiff(present_types, fims_input_types))
+    unknown_types <- sort(setdiff(present_types, FIMS::fims_input_types))
     if (length(unknown_types) > 0) {
       cli::cli_warn(c(
         "!" = "Data contains unexpected type{?s}: {.var {unknown_types}}.",
-        "i" = "Allowed types are: {.var {fims_input_types}}.",
+        "i" = "Allowed types are: {.var {FIMS::fims_input_types}}.",
         "i" = "Model will run but check that data types are correct."
       ))
     }