Fix test-coverage CI failure: pin leiden deps in scverse env, surface covr test output

.github/workflows/test-coverage.yaml

@@ -72,10 +72,32 @@ jobs:
           extra-packages: any::covr any::reticulate
           cache-version: 1
 
+      # install_path must live outside the R session tempdir: R deletes its
+      # own Rtmp* directory when the process exits (clean = FALSE does not
+      # prevent that), which used to take testthat.Rout.fail with it.
       - name: Run test coverage
         shell: Rscript {0}
         run: |
           covr::codecov(
             quiet = FALSE,
-            clean = FALSE
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "covr-install")
           )
+
+      # covr runs the test suite via tools::testInstalledPackage, which writes
+      # test output only to testthat.Rout(.fail) inside its install library --
+      # the job log otherwise shows nothing but "running the tests failed",
+      # making CI failures undiagnosable. Surface the file on failure.
+      - name: Show testthat output on failure
+        if: failure()
+        shell: bash
+        run: |
+          found=0
+          while IFS= read -r f; do
+            found=1
+            echo "=== $f ==="
+            tail -n 500 "$f"
+          done < <(find "$RUNNER_TEMP/covr-install" /tmp -name 'testthat.Rout*' 2>/dev/null)
+          if [ "$found" -eq 0 ]; then
+            echo "No testthat.Rout* files found"
+          fi

.gitignore

@@ -85,3 +85,9 @@ inst/bin/scconvert
 inst/bin/scconvert.exe
 inst/bin/*.dll
 vignettes/cosmx_lung9
+
+# gcov coverage artifacts (covr / --coverage builds)
+src/*.gcda
+src/*.gcno
+src/cli_obj/*.gcda
+src/cli_obj/*.gcno

tests/scverse-env.yml

@@ -8,6 +8,11 @@ dependencies:
   - squidpy>=1.3
   - mudata>=0.2
   - loompy>=3.0
+  # sc.tl.leiden dependencies: conda-forge scanpy does not depend on these,
+  # so they must be pinned explicitly. They used to arrive transitively and
+  # vanished when the CI env cache expired and conda-forge re-solved.
+  - python-igraph
+  - leidenalg
   - numpy
   - pandas
   - scipy