From 14a0fe247daed1fb4d9d84e9be2f6e3a303ddf4e Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Thu, 20 Aug 2026 12:08:09 +0200
Subject: [PATCH 01/19] Added regression test for click-modifier, updated
 pixi.toml with tasks and add-features

---
 pixi.toml                              |  5 ++
 tests/test-regression-click-modifier.R | 81 ++++++++++++++++++++++++++
 2 files changed, 86 insertions(+)
 create mode 100644 tests/test-regression-click-modifier.R

diff --git a/pixi.toml b/pixi.toml
index da4de45..c4a149a 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -6,6 +6,7 @@ platforms = ["linux-64"]
 version = "0.1.0"
 
 [tasks]
+test = [{ task = "tests"}]
 
 [dependencies]
 r = "4.*"
@@ -16,6 +17,7 @@ r-stringi = ">=1.8.7,<2"
 
 [feature.agg.tasks]
 aggregate = { cmd = "Rscript aggregate-raw-data.R", cwd = "scripts" }
+add_features = { cmd = "Rscript add-features.R", cwd = "scripts" }
 
 [feature.ci.dependencies]
 r-dplyr = "1.1.1.*"
@@ -26,6 +28,9 @@ r-stringr = ">=1.5.1,<2"
 r-testthat = ">=3.2.1.1,<4"
 r-withr = ">=3.0.0,<4"
 
+[feature.ci.tasks]
+tests = { cmd = "Rscript -e \"testthat::test_dir('.', stop_on_failure=TRUE)\"", cwd = "tests" }
+
 [environments]
 agg = { features = ["agg"] }
 ci = { features = ["ci"] }
diff --git a/tests/test-regression-click-modifier.R b/tests/test-regression-click-modifier.R
new file mode 100644
index 0000000..2286929
--- /dev/null
+++ b/tests/test-regression-click-modifier.R
@@ -0,0 +1,81 @@
+#! /usr/bin/env Rscript
+
+## Regression test for the click/modifier typing in order_ipa() (aggregation-helper-functions.R). 
+## Clicks are deliberately typed "M", the same glyph-type code as real modifier letters
+## so they factor into feature-vector assignment the same way 
+## (see create_glyph_type_variables()/make_typestring()). 
+
+library(stringi, warn.conflicts=FALSE)
+library(testthat, warn.conflicts=FALSE)
+
+source(file.path("..", "scripts", "aggregation-helper-functions.R"))
+
+context("Click/modifier regression")
+
+test_that("a click is not deleted when followed by a modifier letter", {
+    ## dental click U+01C0 + aspirated U+02B0 both typed "M"
+    ## triggering the "MM" canonical-reordering block
+    result <- order_ipa("ǀʰ")
+    expect(stri_detect_fixed(result, "ǀ"),
+           paste("Click character was lost from", shQuote(result)))
+    expect(nchar(result) == 2,
+           paste("Expected a 2-character result, got", shQuote(result),
+                 "(", nchar(result), "characters)"))
+})
+
+test_that("a click is not deleted when preceding a modifier letter", {
+    ## same "MM" span, reversed input order
+    result <- order_ipa("ʰǀ")
+    expect(stri_detect_fixed(result, "ǀ"),
+           paste("Click character was lost from", shQuote(result)))
+    expect(nchar(result) == 2,
+           paste("Expected a 2-character result, got", shQuote(result),
+                 "(", nchar(result), "characters)"))
+})
+
+test_that("a click followed by a diacritic is not swapped the way a modifier would be", {
+    ## dental click + devoiced/ring-below diacritic (U+0325) - Typed "MD"
+    ## Should not be swapped to "DM" because the click is not a real modifier letter.
+    result <- order_ipa("ǀ̥")
+    expect(stri_detect_fixed(result, "ǀ"),
+           paste("Click character was lost from", shQuote(result)))
+    expect(identical(stri_sub(result, 1, 1), "ǀ"),
+           paste("Expected click to remain first, got", shQuote(result)))
+})
+
+test_that("multiple clicks in sequence with a modifier are all preserved", {
+    ## two different clicks + one modifier, all typed "M".
+    result <- order_ipa("ǀǁʰ")
+    expect(stri_detect_fixed(result, "ǀ"),
+           paste("First click character was lost from", shQuote(result)))
+    expect(stri_detect_fixed(result, "ǁ"),
+           paste("Second click character was lost from", shQuote(result)))
+    expect(nchar(result) == 3,
+           paste("Expected a 3-character result, got", shQuote(result),
+                 "(", nchar(result), "characters)"))
+})
+
+test_that("two separate click+diacritic pairs in one string are both skipped", {
+    ## typestring "MDMD" both with clicks, so both should be skipped
+    result <- order_ipa("ǀ̥ǁ̥")
+    expect(stri_detect_fixed(result, "ǀ"),
+           paste("First click character was lost from", shQuote(result)))
+    expect(stri_detect_fixed(result, "ǁ"),
+           paste("Second click character was lost from", shQuote(result)))
+    expect(nchar(result) == 4,
+           paste("Expected a 4-character result, got", shQuote(result),
+                 "(", nchar(result), "characters)"))
+})
+
+test_that("a click preceding a real modifier+diacritic doesn't block their swap", {
+    ## typestring "MMD" with a click first, then a modifier letter, then a diacritic. 
+    ## The modifier+diacritic pair should still be swapped, but the click should remain first.
+    result <- order_ipa("ǀʰ̥")
+    expect(stri_detect_fixed(result, "ǀ"),
+           paste("Click character was lost from", shQuote(result)))
+    expect(identical(stri_sub(result, 1, 1), "ǀ"),
+           paste("Expected click to remain first, got", shQuote(result)))
+    expect(identical(result, "ǀ̥ʰ"),
+           paste("Expected the modifier+diacritic pair to still be swapped",
+                 "(click skip should not suppress it), got", shQuote(result)))
+})

From 66016df804722c34bdf87d15013f22e521b781be Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Thu, 20 Aug 2026 12:34:17 +0200
Subject: [PATCH 02/19] Added regression test for special-cases and c-cedilla

---
 tests/test-regression-special-casess.R | 33 ++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 tests/test-regression-special-casess.R

diff --git a/tests/test-regression-special-casess.R b/tests/test-regression-special-casess.R
new file mode 100644
index 0000000..75f5aad
--- /dev/null
+++ b/tests/test-regression-special-casess.R
@@ -0,0 +1,33 @@
+#! /usr/bin/env Rscript
+
+## Regression test for two special-cased exceptions in the R pipeline:
+## c-cedilla staying precomposed in order_ipa() (aggregation-helper-functions.R) and
+## the `special_cases` affricate list in add-features.R having a
+## matching row in special-feature-table.csv for each pair.
+
+library(stringi, warn.conflicts=FALSE)
+library(testthat, warn.conflicts=FALSE)
+
+source(file.path("..", "scripts", "aggregation-helper-functions.R"))
+
+context("Special-case exceptions regression")
+
+test_that("known special-cased exceptions in the pipeline still work", {
+    ## order_ipa() leaves c-cedilla unchanged, rather than decomposing it
+    ordered <- order_ipa("ç")
+    expect(identical(ordered, "ç"),
+           paste("Expected c-cedilla phoneme to be unchanged by order_ipa(), got",
+                 shQuote(ordered)))
+
+    ## every add-features.R `special_cases` pair has a matching row in special-feature-table.csv 
+    special_cases <- c("pɸ", "pf", "tθ", "ts", "tʃ", "ʈʂ", "cç", "kx",
+                       "qχ", "bβ", "bv", "dð", "dz", "dʒ", "ɖʐ", "ɟʝ", "ɡɣ",
+                       "ɢʁ", "kp", "ɡb")
+    special_feats <- read.csv(file.path("..", "raw-data", "FEATURES",
+                              "special-feature-table.csv"),
+                              fileEncoding="UTF-8")
+    missing <- setdiff(special_cases, special_feats$segment)
+    expect(length(missing) == 0,
+           paste("special_cases pair(s) missing from special-feature-table.csv:",
+                 paste(missing, collapse=", ")))
+})

From 776e54843d0ea63d813c5aebdab5c4574a2bb832 Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Thu, 20 Aug 2026 13:30:41 +0200
Subject: [PATCH 03/19] Excluded test-phonemes.R from ci, added output as pr
 comment

---
 .github/workflows/main.yml | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a1729ea..fc714d7 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -6,6 +6,9 @@ on:
   pull_request:
     branches: [ master ]
 
+permissions:
+  pull-requests: write
+
 jobs:
   test-data:
     runs-on: ubuntu-latest
@@ -18,4 +21,14 @@ jobs:
       - name: run tests
         working-directory: tests
         run: |
-          Rscript -e "testthat::test_dir('.', stop_on_failure=TRUE)"
+            Rscript -e "testthat::test_dir('.', filter = \"^(?test-phoenemes)\", stop_on_failure = TRUE)"
+      - name: run feature test (write to PR comment)
+        working-directory: tests
+        run: |
+          Rscript -e "testthat::test_file('test-phonemes.R', reporter = \"summary\")" > phoneme_feature_test_results.txt 2>&1 || true
+      - name: comment on PR
+        if: github.event_name == 'pull_request'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh pr comment ${{ github.event.pull_request.number }} --body-file phoneme_feature_test_results.txt 

From 21b0eb50462147ebd6bda0d06b098ecf19a2c2b4 Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Thu, 20 Aug 2026 13:46:20 +0200
Subject: [PATCH 04/19] Fixed typo and test commands in workflows

---
 .github/workflows/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index fc714d7..244a7f3 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -21,11 +21,11 @@ jobs:
       - name: run tests
         working-directory: tests
         run: |
-            Rscript -e "testthat::test_dir('.', filter = \"^(?test-phoenemes)\", stop_on_failure = TRUE)"
+            Rscript -e "testthat::test_dir('.', filter = 'phonemes', invert = TRUE, stop_on_failure = TRUE)"
       - name: run feature test (write to PR comment)
         working-directory: tests
         run: |
-          Rscript -e "testthat::test_file('test-phonemes.R', reporter = \"summary\")" > phoneme_feature_test_results.txt 2>&1 || true
+          Rscript -e "testthat::test_file('test-phonemes.R', reporter = 'summary')" > phoneme_feature_test_results.txt 2>&1 || true
       - name: comment on PR
         if: github.event_name == 'pull_request'
         env:

From d8d96b9c54289d4f5838f8da659e723f39beb7eb Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Thu, 20 Aug 2026 13:49:22 +0200
Subject: [PATCH 05/19] changed working directory of pr comment job

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 244a7f3..b9c90ae 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -28,6 +28,7 @@ jobs:
           Rscript -e "testthat::test_file('test-phonemes.R', reporter = 'summary')" > phoneme_feature_test_results.txt 2>&1 || true
       - name: comment on PR
         if: github.event_name == 'pull_request'
+        working-directory: tests
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |

From bb31120c9f1851d0bd3171f411f11e22deb3271c Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Thu, 20 Aug 2026 13:54:31 +0200
Subject: [PATCH 06/19] Added comment about workflow change

---
 .github/workflows/main.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b9c90ae..4148e0f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -22,6 +22,8 @@ jobs:
         working-directory: tests
         run: |
             Rscript -e "testthat::test_dir('.', filter = 'phonemes', invert = TRUE, stop_on_failure = TRUE)"
+      ## The following steps are temporary until we fix the phoneme feature test to pass in CI. 
+      ## Once the phoneme feature test passes, update the above command and remove filter and invert, and delete the following steps.
       - name: run feature test (write to PR comment)
         working-directory: tests
         run: |

From 6add4c27ea5d443aeb98ebc482dd688e278b2fb2 Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Thu, 20 Aug 2026 14:07:21 +0200
Subject: [PATCH 07/19] Added comment to test workflow

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 4148e0f..97eb20f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -28,6 +28,7 @@ jobs:
         working-directory: tests
         run: |
           Rscript -e "testthat::test_file('test-phonemes.R', reporter = 'summary')" > phoneme_feature_test_results.txt 2>&1 || true
+      ## Adds a comment to the PR with the results of the phoneme feature test.
       - name: comment on PR
         if: github.event_name == 'pull_request'
         working-directory: tests

From 9d695d8c6cfb6e0668a68cb4f8a88b42b34d9a96 Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Thu, 20 Aug 2026 14:18:12 +0200
Subject: [PATCH 08/19] Testing edit-last in gh pr comment

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 97eb20f..10c8cd9 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -35,4 +35,4 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          gh pr comment ${{ github.event.pull_request.number }} --body-file phoneme_feature_test_results.txt 
+          gh pr comment ${{ github.event.pull_request.number }} --body-file phoneme_feature_test_results.txt --edit-last --create-if-none

From f45522885ba0154627a16670c7ed190658fc8563 Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Thu, 20 Aug 2026 14:20:03 +0200
Subject: [PATCH 09/19] reverted edit-last in gh pr comment

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 10c8cd9..89bce93 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -35,4 +35,4 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          gh pr comment ${{ github.event.pull_request.number }} --body-file phoneme_feature_test_results.txt --edit-last --create-if-none
+          gh pr comment ${{ github.event.pull_request.number }} --body-file phoneme_feature_test_results.txt

From 7a34af48dac0a62cc2de8c80cebf5769178db2d8 Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Thu, 20 Aug 2026 16:30:29 +0200
Subject: [PATCH 10/19] Added test to verify glottocode-isocode mapping matches
 glottolog

---
 tests/test-inventory-metadata.R | 34 +++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/tests/test-inventory-metadata.R b/tests/test-inventory-metadata.R
index 2aaca1a..754db28 100644
--- a/tests/test-inventory-metadata.R
+++ b/tests/test-inventory-metadata.R
@@ -141,6 +141,7 @@ test_that("glottocodes are valid", {
     glotto_url <- "https://github.com/glottolog/glottolog-cldf/blob/master/cldf/languages.csv?raw=true"
     glotto_table <- readr::read_csv(glotto_url, col_types=default_char_cols)
     glotto_valid <- pull(glotto_table, ID)
+    iso_valid_map <- pull(glotto_table, ISO639P3code)
 
     glotto_phoible <- pull(phoible, Glottocode)
     glotto_invalid <- setdiff(glotto_phoible, glotto_valid)
@@ -166,6 +167,39 @@ test_that("glottocodes are valid", {
                        collapse=" "),
                  sep="\n")
            )
+
+    ## Check that the ISO code in glottolog matches phoible's ISO code, for
+    ## every inventory with a known Glottocode (i.e. excluding Djindewal).
+    has_glottocode <- !is.na(phoible$Glottocode)
+
+    iso_from_glottolog <- iso_valid_map[match(phoible$Glottocode[has_glottocode], glotto_valid)]
+    iso_from_phoible <- phoible$ISO6393[has_glottocode]
+
+    ## Exclude known glottolog-ISO mismatches
+    known_mismatches <- rbind(
+        c(868,  "nepa1253", "kru"), # kxl (deprecated) merged into kru
+        c(1307, "krim1238", "bmf"), # krm (deprecated) merged into bmf
+        c(2750, "dira1238", "dif"), # dit (deprecated) merged into dif
+        c(2875, "band1337", "drl"), # bjd (deprecated) merged into drl
+        c(2256, "dark1243", "khk")  # drh (deprecated) merged into khk
+    )
+
+    overridable <- phoible$Glottocode[has_glottocode] %in% known_mismatches[, 2]
+    override <- setNames(known_mismatches[, 3], known_mismatches[, 2])
+    iso_from_glottolog[overridable] <- override[phoible$Glottocode[has_glottocode][overridable]]
+
+    mismatch_indices <- which(iso_from_glottolog != iso_from_phoible)
+
+    mismatch_ids <- phoible$InventoryID[has_glottocode][mismatch_indices]
+    mismatch_glottocodes <- phoible$Glottocode[has_glottocode][mismatch_indices]
+    mismatches <- unique(paste0(mismatch_ids, " (", mismatch_glottocodes, "): ", iso_from_phoible[mismatch_indices],
+                                " - ", iso_from_glottolog[mismatch_indices]))
+
+    expect(length(mismatches) == 0,
+           paste("MISMATCHED ISO CODES BETWEEN PHOIBLE AND GLOTTOLOG (InventoryID (glottocode)): phoible - glottolog):",
+                 paste0("- ", mismatches, collapse="\n"),
+                 sep="\n")
+           )
     }
 )
 

From 1e6d4513b78ef247e8e79a2ac234c6ec2fe8b24a Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Thu, 20 Aug 2026 16:37:12 +0200
Subject: [PATCH 11/19] Added test to check inventory-bibtex mapping,
 InventoryID duplicates

---
 tests/test-cross-inventory-integrity.R | 100 +++++++++++++++++++++++++
 1 file changed, 100 insertions(+)
 create mode 100644 tests/test-cross-inventory-integrity.R

diff --git a/tests/test-cross-inventory-integrity.R b/tests/test-cross-inventory-integrity.R
new file mode 100644
index 0000000..3c4f1d7
--- /dev/null
+++ b/tests/test-cross-inventory-integrity.R
@@ -0,0 +1,100 @@
+#! /usr/bin/env Rscript
+
+## Tests for cross-inventory integrity. Checks that:
+##   1. No source accidentally split one language (Glottocode, LanguageName, SpecificDialect, BibtexKey) across two InventoryIDs
+##   2. Every BibtexKey in the mapping file resolves to a real entry in
+##      phoible-references.bib.
+##   3. Every InventoryID in the mapping files exists in the aggregated
+##      data, and vice versa.
+
+library(dplyr, warn.conflicts=FALSE)
+library(testthat, warn.conflicts=FALSE)
+
+## load PHOIBLE data
+phoible_data_file <- file.path("..", "data", "phoible.csv")
+phoible_col_types <- readr::cols(InventoryID="c", Marginal="l", .default="c")
+phoible <- readr::read_csv(phoible_data_file, col_types=phoible_col_types)
+
+bibtex_mapping_file <- file.path("..", "mappings", "InventoryID-Bibtex.csv")
+bibtex_mapping <- readr::read_csv(bibtex_mapping_file, col_types=readr::cols(.default="c"))
+
+# Join the phoible data with the mapping file to get a combined dataset for testing
+phoible_with_bibtex <- phoible %>%
+    left_join(bibtex_mapping, by="InventoryID", relationship="many-to-many")
+
+references_bib_file <- file.path("..", "mappings", "phoible-references.bib")
+
+context("Cross-inventory integrity")
+
+test_that("no source accidentally split one language across two InventoryIDs", {
+    ## Checks whether the same (Source, Glottocode, LanguageName, SpecificDialect, BibtexKey) tuple
+    ## appears in more than one InventoryID.
+    phoible_with_bibtex %>%
+        filter(!is.na(Glottocode)) %>%
+        distinct(InventoryID, Source, Glottocode, LanguageName, SpecificDialect, BibtexKey) %>%
+        group_by(Source, Glottocode, LanguageName, SpecificDialect, BibtexKey) %>%
+        filter(n_distinct(InventoryID) > 1) %>%
+        ungroup() ->
+        split_duplicates
+
+    expect(nrow(split_duplicates) == 0,
+           paste(c("SAME (Source, Glottocode, LanguageName, SpecificDialect, BibtexKey) APPEARS IN MULTIPLE INVENTORYIDS:",
+                   capture.output(print(split_duplicates, n=Inf))),
+                 sep="\n")
+           )
+    }
+)
+
+test_that("every BibtexKey resolves to a real bib entry", {
+    ## Check that every BibtexKey in the mapping file resolves to a real entry in phoible-references.bib.  
+
+    ## regex to match BibTeX keys in the .bib file  
+    citekey_re <- "(?m)^@\\w+\\s*\\{\\s*([^,]+?)\\s*,"
+
+    bib_keys <- stringr::str_match_all(
+        readr::read_file(references_bib_file), citekey_re
+    )[[1]][, 2]
+
+    mapping_keys <- bibtex_mapping %>% pull(BibtexKey) %>% unique()
+    missing_keys <- setdiff(mapping_keys, bib_keys)
+
+    # Exclude special case of InventoryID 201 (Arrente), which has "NO SOURCE GIVEN" as its BibtexKey
+    missing_keys <- setdiff(missing_keys, bibtex_mapping %>% filter(InventoryID == 201) %>% pull(BibtexKey))
+
+    ## report which InventoryID(s) cite each missing key
+    offending_rows <- bibtex_mapping %>%
+        filter(BibtexKey %in% missing_keys) %>%
+        arrange(BibtexKey, as.integer(InventoryID))
+    offending_summary <- offending_rows %>%
+        group_by(BibtexKey) %>%
+        summarise(InventoryIDs = paste(InventoryID, collapse=", "), .groups="drop")
+
+    expect(length(missing_keys) == 0,
+           paste(c(paste("BIBTEXKEYS WITH NO MATCHING ENTRY IN",
+                         basename(references_bib_file)),
+                   paste0(offending_summary$BibtexKey, " (InventoryID ",
+                          offending_summary$InventoryIDs, ")")),
+                 sep="\n")
+           )
+    }
+)
+
+test_that("mapping-file and aggregated-data InventoryIDs match in both directions", {
+    phoible_ids <- phoible %>% pull(InventoryID) %>% unique()
+    mapping_ids <- bibtex_mapping %>% pull(InventoryID) %>% as.integer() %>% unique()
+
+    only_in_mapping <- setdiff(mapping_ids, phoible_ids)
+    only_in_phoible <- setdiff(phoible_ids, mapping_ids)
+
+    expect(length(only_in_mapping) == 0,
+           paste(c("INVENTORYIDS IN InventoryID-Bibtex.csv BUT MISSING FROM",
+                   "AGGREGATED DATA:", paste(only_in_mapping, collapse=" ")),
+                 sep="\n")
+           )
+    expect(length(only_in_phoible) == 0,
+           paste(c("INVENTORYIDS IN AGGREGATED DATA BUT MISSING FROM",
+                   "InventoryID-Bibtex.csv:", paste(only_in_phoible, collapse=" ")),
+                 sep="\n")
+           )
+    }
+)

From f8d085381c7d49b65901f12e7715c9bb385b0840 Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Fri, 21 Aug 2026 00:44:14 +0200
Subject: [PATCH 12/19] Moved feature test to beginning so we get pr comment
 even if other tests fail

---
 .github/workflows/main.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 89bce93..18a318c 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -18,12 +18,8 @@ jobs:
         with:
           pixi-version: v0.66.0
           activate-environment: "ci"
-      - name: run tests
-        working-directory: tests
-        run: |
-            Rscript -e "testthat::test_dir('.', filter = 'phonemes', invert = TRUE, stop_on_failure = TRUE)"
       ## The following steps are temporary until we fix the phoneme feature test to pass in CI. 
-      ## Once the phoneme feature test passes, update the above command and remove filter and invert, and delete the following steps.
+      ## Once the phoneme feature test passes, update the below run tests command and remove filter and invert, and delete the following steps.
       - name: run feature test (write to PR comment)
         working-directory: tests
         run: |
@@ -36,3 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           gh pr comment ${{ github.event.pull_request.number }} --body-file phoneme_feature_test_results.txt
+            
+      - name: run tests
+        working-directory: tests
+        run: |
+            Rscript -e "testthat::test_dir('.', filter = 'phonemes', invert = TRUE, stop_on_failure = TRUE)"
+     
\ No newline at end of file

From 9e1a2e4a60a1fe363615a182a5e692d4071fff7d Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Fri, 21 Aug 2026 01:04:10 +0200
Subject: [PATCH 13/19] Moved workflow permissions to inside jobs

---
 .github/workflows/main.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 18a318c..3039e5d 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -6,12 +6,12 @@ on:
   pull_request:
     branches: [ master ]
 
-permissions:
-  pull-requests: write
-
 jobs:
   test-data:
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write
     steps:
       - uses: actions/checkout@v7
       - uses: prefix-dev/setup-pixi@v0.10.1
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           gh pr comment ${{ github.event.pull_request.number }} --body-file phoneme_feature_test_results.txt
-            
+
       - name: run tests
         working-directory: tests
         run: |

From 42b863cb318e367166262752211115f1f6483fce Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Fri, 21 Aug 2026 01:22:45 +0200
Subject: [PATCH 14/19] Split PR comment workflow to allow for PR from forked
 repos

---
 .github/workflows/comment-feature-test.yml | 30 ++++++++++++++++++++++
 .github/workflows/main.yml                 | 24 ++++++++++-------
 2 files changed, 45 insertions(+), 9 deletions(-)
 create mode 100644 .github/workflows/comment-feature-test.yml

diff --git a/.github/workflows/comment-feature-test.yml b/.github/workflows/comment-feature-test.yml
new file mode 100644
index 0000000..d4def20
--- /dev/null
+++ b/.github/workflows/comment-feature-test.yml
@@ -0,0 +1,30 @@
+name: comment feature test results
+
+on:
+  workflow_run:
+    workflows: ["test data"]
+    types: [completed]
+
+permissions:
+  actions: read
+  pull-requests: write
+
+jobs:
+  comment:
+    runs-on: ubuntu-latest
+    if: github.event.workflow_run.event == 'pull_request'
+    steps:
+      - name: download feature test results
+        uses: actions/download-artifact@v4
+        with:
+          name: feature-test-results
+          run-id: ${{ github.event.workflow_run.id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: comment on PR
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_REPO: ${{ github.repository }}
+        run: |
+          PR_NUMBER=$(cat pr_number.txt)
+          gh pr comment "$PR_NUMBER" --body-file phoneme_feature_test_results.txt
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 3039e5d..f2962aa 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -5,33 +5,39 @@ on:
     branches: [ master ]
   pull_request:
     branches: [ master ]
-
+ 
 jobs:
   test-data:
     runs-on: ubuntu-latest
     permissions:
       contents: read
-      pull-requests: write
+      actions: write
     steps:
       - uses: actions/checkout@v7
       - uses: prefix-dev/setup-pixi@v0.10.1
         with:
           pixi-version: v0.66.0
           activate-environment: "ci"
-      ## The following steps are temporary until we fix the phoneme feature test to pass in CI. 
+      ## The following steps are temporary until we fix the phoneme feature test to pass in CI.
       ## Once the phoneme feature test passes, update the below run tests command and remove filter and invert, and delete the following steps.
       - name: run feature test (write to PR comment)
         working-directory: tests
         run: |
           Rscript -e "testthat::test_file('test-phonemes.R', reporter = 'summary')" > phoneme_feature_test_results.txt 2>&1 || true
-      ## Adds a comment to the PR with the results of the phoneme feature test.
-      - name: comment on PR
+      ## Fork PRs get a read-only GITHUB_TOKEN here, so this job can't comment
+      ## directly. comment-feature-test.yml (triggered via workflow_run) does it instead.
+      - name: save PR number
         if: github.event_name == 'pull_request'
         working-directory: tests
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          gh pr comment ${{ github.event.pull_request.number }} --body-file phoneme_feature_test_results.txt
+        run: echo "${{ github.event.pull_request.number }}" > pr_number.txt
+      - name: upload feature test results
+        if: github.event_name == 'pull_request'
+        uses: actions/upload-artifact@v4
+        with:
+          name: feature-test-results
+          path: |
+            tests/phoneme_feature_test_results.txt
+            tests/pr_number.txt
 
       - name: run tests
         working-directory: tests

From 520b59211adbbda89351c2ae076a91adedc4ea28 Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Sun, 23 Aug 2026 14:15:00 +0200
Subject: [PATCH 15/19] Removed write permissions from main.yml actions,
 removed stray whitespaces

---
 .github/workflows/main.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index f2962aa..9fec851 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -5,13 +5,11 @@ on:
     branches: [ master ]
   pull_request:
     branches: [ master ]
- 
 jobs:
   test-data:
     runs-on: ubuntu-latest
     permissions:
       contents: read
-      actions: write
     steps:
       - uses: actions/checkout@v7
       - uses: prefix-dev/setup-pixi@v0.10.1
@@ -38,9 +36,8 @@ jobs:
           path: |
             tests/phoneme_feature_test_results.txt
             tests/pr_number.txt
-
+      ## Run the rest of the tests, excluding the phoneme feature test (which is run above).
       - name: run tests
         working-directory: tests
         run: |
-            Rscript -e "testthat::test_dir('.', filter = 'phonemes', invert = TRUE, stop_on_failure = TRUE)"
-     
\ No newline at end of file
+            Rscript -e "testthat::test_dir('.', filter = 'phonemes', invert = TRUE, stop_on_failure = TRUE)"
\ No newline at end of file

From 9af55311dba594647b11e4ed98436bd2b0a5b7bc Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Sun, 23 Aug 2026 14:18:58 +0200
Subject: [PATCH 16/19] Removed two unnecessary tests from click-modifier
 regression test

---
 tests/test-regression-click-modifier.R | 24 ------------------------
 1 file changed, 24 deletions(-)

diff --git a/tests/test-regression-click-modifier.R b/tests/test-regression-click-modifier.R
index 2286929..1615ec2 100644
--- a/tests/test-regression-click-modifier.R
+++ b/tests/test-regression-click-modifier.R
@@ -43,30 +43,6 @@ test_that("a click followed by a diacritic is not swapped the way a modifier wou
            paste("Expected click to remain first, got", shQuote(result)))
 })
 
-test_that("multiple clicks in sequence with a modifier are all preserved", {
-    ## two different clicks + one modifier, all typed "M".
-    result <- order_ipa("ǀǁʰ")
-    expect(stri_detect_fixed(result, "ǀ"),
-           paste("First click character was lost from", shQuote(result)))
-    expect(stri_detect_fixed(result, "ǁ"),
-           paste("Second click character was lost from", shQuote(result)))
-    expect(nchar(result) == 3,
-           paste("Expected a 3-character result, got", shQuote(result),
-                 "(", nchar(result), "characters)"))
-})
-
-test_that("two separate click+diacritic pairs in one string are both skipped", {
-    ## typestring "MDMD" both with clicks, so both should be skipped
-    result <- order_ipa("ǀ̥ǁ̥")
-    expect(stri_detect_fixed(result, "ǀ"),
-           paste("First click character was lost from", shQuote(result)))
-    expect(stri_detect_fixed(result, "ǁ"),
-           paste("Second click character was lost from", shQuote(result)))
-    expect(nchar(result) == 4,
-           paste("Expected a 4-character result, got", shQuote(result),
-                 "(", nchar(result), "characters)"))
-})
-
 test_that("a click preceding a real modifier+diacritic doesn't block their swap", {
     ## typestring "MMD" with a click first, then a modifier letter, then a diacritic. 
     ## The modifier+diacritic pair should still be swapped, but the click should remain first.

From f1c78ca125a6ea5cc9556e9d15b6745051391213 Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Sun, 23 Aug 2026 14:34:46 +0200
Subject: [PATCH 17/19] Changed special-case regression test to only c-cedilla

---
 tests/test-regression-special-casess.R | 21 +++------------------
 1 file changed, 3 insertions(+), 18 deletions(-)

diff --git a/tests/test-regression-special-casess.R b/tests/test-regression-special-casess.R
index 75f5aad..785e9f4 100644
--- a/tests/test-regression-special-casess.R
+++ b/tests/test-regression-special-casess.R
@@ -1,9 +1,7 @@
 #! /usr/bin/env Rscript
 
-## Regression test for two special-cased exceptions in the R pipeline:
-## c-cedilla staying precomposed in order_ipa() (aggregation-helper-functions.R) and
-## the `special_cases` affricate list in add-features.R having a
-## matching row in special-feature-table.csv for each pair.
+## Regression test for c-cedilla staying precomposed in order_ipa()
+## (aggregation-helper-functions.R), rather than decomposing it.
 
 library(stringi, warn.conflicts=FALSE)
 library(testthat, warn.conflicts=FALSE)
@@ -12,22 +10,9 @@ source(file.path("..", "scripts", "aggregation-helper-functions.R"))
 
 context("Special-case exceptions regression")
 
-test_that("known special-cased exceptions in the pipeline still work", {
-    ## order_ipa() leaves c-cedilla unchanged, rather than decomposing it
+test_that("c-cedilla is unchanged by order_ipa()", {
     ordered <- order_ipa("ç")
     expect(identical(ordered, "ç"),
            paste("Expected c-cedilla phoneme to be unchanged by order_ipa(), got",
                  shQuote(ordered)))
-
-    ## every add-features.R `special_cases` pair has a matching row in special-feature-table.csv 
-    special_cases <- c("pɸ", "pf", "tθ", "ts", "tʃ", "ʈʂ", "cç", "kx",
-                       "qχ", "bβ", "bv", "dð", "dz", "dʒ", "ɖʐ", "ɟʝ", "ɡɣ",
-                       "ɢʁ", "kp", "ɡb")
-    special_feats <- read.csv(file.path("..", "raw-data", "FEATURES",
-                              "special-feature-table.csv"),
-                              fileEncoding="UTF-8")
-    missing <- setdiff(special_cases, special_feats$segment)
-    expect(length(missing) == 0,
-           paste("special_cases pair(s) missing from special-feature-table.csv:",
-                 paste(missing, collapse=", ")))
 })

From 792ea5a5508e5ed0bdc163a1d06610d9ec60a2ec Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Sun, 23 Aug 2026 14:36:20 +0200
Subject: [PATCH 18/19] Renamed test file suffix from special-casess to
 c-cedilla

---
 ...st-regression-special-casess.R => test-regression-c-cedilla.R} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename tests/{test-regression-special-casess.R => test-regression-c-cedilla.R} (100%)

diff --git a/tests/test-regression-special-casess.R b/tests/test-regression-c-cedilla.R
similarity index 100%
rename from tests/test-regression-special-casess.R
rename to tests/test-regression-c-cedilla.R

From 9f8864d53d48ae839561c0366ab6020921e16d42 Mon Sep 17 00:00:00 2001
From: varunghat <varungr2540@gmail.com>
Date: Sun, 23 Aug 2026 15:04:35 +0200
Subject: [PATCH 19/19] Added check special_cases lookup returns exactly one
 row in add-features.R

---
 scripts/add-features.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/add-features.R b/scripts/add-features.R
index f5530b2..da5d865 100644
--- a/scripts/add-features.R
+++ b/scripts/add-features.R
@@ -144,6 +144,7 @@ make_feat_vec_from_mat <- function(feat_mat) {
                                             zero=TRUE)
             ## look up the combined base glyphs in the special_feats table
             base_vec <- special_feats[special_feats$segment == base_pair, ]
+            stopifnot(nrow(base_vec) == 1)
             ## populate the feature vector from the special_feats table
             feat_vec[feature_cols] <- base_vec[feature_cols]
             # delete two bases