Merge pull request #4048 from ANAMASGARD/GH-4007-segment-dataframe-empty-after-filter

fix(PEcAn.SIPNET): return empty dataframe when date filtering removes all segments (#4007)

Author: infotroph

CHANGELOG.md

@@ -36,6 +36,7 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 - Added note to DEV-INTRO.md documenting Traefik workaround for Apple Silicon (ARM64) Macs: use `traefik:v2.11` with `platform: linux/arm64` to fix 404 errors (#3910)
 - Fixed `web/08-finished.php`: show database info instead of "Still running" when workflow folder doesn't exist locally (#3501).
 - `PEcAn.utils::transformstats()`: corrected the LSD-to-SE conversion. The previous implementation included an extra `sqrt(n)` factor, causing SE estimates derived from LSD to appear `sqrt(n)` times smaller than they should be, non-conservatively over-weighting those observations in meta-analysis. (#3998)
+- `segment_dataframe()` now returns an empty dataframe when date filtering removes all crop-cycle segments, instead of a single row with NA columns that caused downstream segment config errors (#4007).
 
 ### Changed
 - `PEcAn.uncertainty::get.parameter.samples()`: replaced the `save_to_disk` flag (from #3860) with an `outdir` argument (default `settings$outdir`) controlling whether `samples.Rdata` is written; `outdir = NULL` skips the save. Existing callers are unaffected (@omkarrr2533, #4016)

models/sipnet/NEWS.md

@@ -27,6 +27,7 @@
   Sipnet version `sipnet.unk`.
 * Added trait to parameter mappings for 13 nitrogen cycle parameters in `write.config.SIPNET`,
   including tissue C:N ratios, N volatilization/leaching, fixation, and methane rates.
+* `segment_dataframe()` now returns an empty dataframe when date filtering removes all crop-cycle segments, instead of a single row with NA columns that caused downstream segment config errors (#4007).
 
 
 # PEcAn.SIPNET 1.10.0

models/sipnet/R/write_segmented_configs.R

@@ -160,12 +160,12 @@ segment_dataframe <- function(run_settings) {
         # Also clip the end date to avoid edge cases where run_start == end_date
         .data$end_date > .env$run_start
       )
-    if (nrow(segments) < 1) {
-      PEcAn.logger::logger.error(
-        "Filtering resulted in no segments. ",
-        "This is an invalid state; check settings and events.json."
-      )
-    }
+    if (nrow(segments) == 0) {
+    PEcAn.logger::logger.info(
+      "no crop cycle segments fall within the run window; running unsegmented"
+    )
+    return(segments)
+  }
     segments[1, "start_date"] <- run_start
   }
 

models/sipnet/tests/testthat/test-write_segmented_configs.R

@@ -98,3 +98,102 @@ test_that("write_segmented_configs", {
   expect_match(jobsh, "bash .*segment_002/run/1/job.sh", all = FALSE)
   expect_match(jobsh, "bash .*segment_003/run/1/job.sh", all = FALSE)
 })
+
+test_that("segment_dataframe returns empty when run start is after all crop cycles", {
+  pth <- withr::local_tempdir()
+  crp_chg_path <- file.path(pth, "cycles-a.csv")
+  c("date,crop_code", "2025-01-02,D12", "2025-01-05,G6") |>
+    writeLines(crp_chg_path)
+
+  run_settings <- PEcAn.settings::as.Settings(list(
+    run = list(
+      site = list(id = "a", site.pft = list(veg = "pft1")),
+      inputs = list(crop_changes = list(path = crp_chg_path)),
+      start.date = "2025-01-10",
+      end.date = "2025-01-20"
+    )
+  ))
+
+  result <- PEcAn.SIPNET:::segment_dataframe(run_settings)
+
+  expect_equal(nrow(result), 0)
+  expect_named(
+    result, 
+    c("start_date", "crop_code", "end_date")
+  )
+})
+
+test_that("write_segment_configs returns unaltered job.sh when no segments remain", {
+  pth <- withr::local_tempdir()
+
+  event_lines <- "2025 1 irrig 0 1"
+  event_src_path <- file.path(pth, "events-a.in")
+  met_path <- file.path(pth, "a.clim")
+  crp_chg_path <- file.path(pth, "cycles-a.csv")
+  run_path <- file.path(pth, "run", "ENS-00001-a")
+  dir.create(run_path, recursive = TRUE)
+
+  event_lines |>
+    writeLines(con = event_src_path)
+  c("date,crop_code", "2025-01-02,D12", "2025-01-05,G6") |>
+    writeLines(crp_chg_path)
+  c("run_id,site_id", "ENS-00001-a,a") |>
+    writeLines(file.path(pth, "runs_manifest.csv"))
+  data.frame(
+    year = 2025,
+    day = rep(1:31, each = 4),
+    hour = rep(c(0, 6, 12, 18), 31),
+    c4 = NA, c5 = NA, c6 = NA, c7 = NA, c8 = NA, c9 = NA, c10 = NA, c11 = NA,
+    c12 = NA
+  ) |>
+    write.table(
+      file = met_path, quote = FALSE,
+      row.names = FALSE, col.names = FALSE
+    )
+  ens.samples <- list(
+    pft1 = data.frame(Amax = 1, SLA = 2),
+    soil = data.frame(Rd = 0)
+  )
+  save(ens.samples, file = file.path(pth, "ensemble.samples.testid.Rdata"))
+
+  s <- PEcAn.settings::as.Settings(
+    list(
+      outdir = file.path(pth),
+      rundir = file.path(pth, "run"),
+      modeloutdir = file.path(pth, "out"),
+      pfts = list(pft1 = list(), soil = list()),
+      ensemble = list(ensemble.id = "testid"),
+      model = list(binary = "", revision = "2.1.0"),
+      run = list(
+        site = list(id = "a", name = "site1", lat = 40, lon = -88,
+                    site.pft = list(veg = "pft1", soil = "soil")),
+        inputs = list(
+          met = list(path = met_path),
+          events = list(path = event_src_path),
+          crop_changes = list(path = crp_chg_path)
+        ),
+        start.date = "2025-01-10",
+        end.date = "2025-01-20"
+      ),
+      host = list(
+        name = "localhost",
+        outdir = file.path(pth),
+        rundir = file.path(pth, "run")
+      )
+    )
+  )
+
+  write.config.SIPNET(
+    defaults = s$pfts,
+    trait.values = ens.samples["pft1"],
+    IC = list(soil = 3.14),
+    settings = s,
+    run.id = "ENS-00001-a"
+  )
+
+  seg_res <- write_segmented_configs.SIPNET(settings = s)
+
+  expect_equal(seg_res, file.path(run_path, "job.sh"))
+  expect_false(file.exists(file.path(run_path, "job_segmented.sh")))
+  expect_false(dir.exists(file.path(run_path, "segments")))
+})