From c916cf8b2d7fb546a17a5d747bec0e99c157f0cb Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 21 Jun 2026 16:46:56 +0200
Subject: [PATCH] tests: drop the serial [large] test (serial dataset not
 shipped)

Only the ~1800-image rotation dataset is kept in LFS; a separate ~5000-image serial set is too
large to ship, and the serial path can be exercised by running the rotation series in serial
mode if needed. Removes JFJochProcess_LysoSerial and the serial entry from the start-up listener
and README. The rotation [large] test now runs against the committed data and passes.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 tests/JFJochProcessLargeTest.cpp | 40 +-------------------------------
 tests/data/README.md             | 25 ++++++++------------
 2 files changed, 11 insertions(+), 54 deletions(-)

diff --git a/tests/JFJochProcessLargeTest.cpp b/tests/JFJochProcessLargeTest.cpp
index e20fe7de..064d06ef 100644
--- a/tests/JFJochProcessLargeTest.cpp
+++ b/tests/JFJochProcessLargeTest.cpp
@@ -26,10 +26,8 @@ namespace {
         using Catch::EventListenerBase::EventListenerBase;
         void testRunStarting(Catch::TestRunInfo const &) override {
             const bool rot = jfjoch_test::LargeDataFile("lyso_rotation_master.h5").has_value();
-            const bool ser = jfjoch_test::LargeDataFile("lyso_serial_master.h5").has_value();
-            std::cout << "[jfjoch_test] large datasets in " << jfjoch_test::LargeDataDir()
+            std::cout << "[jfjoch_test] large dataset in " << jfjoch_test::LargeDataDir()
                       << ": rotation=" << (rot ? "yes" : "no")
-                      << " serial=" << (ser ? "yes" : "no")
                       << " ([large] tests skip when absent)" << std::endl;
         }
     };
@@ -82,39 +80,3 @@ TEST_CASE("JFJochProcess_LysoRotation", "[large]") {
     reader.Close();
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
-
-TEST_CASE("JFJochProcess_LysoSerial", "[large]") {
-    const auto master = jfjoch_test::LargeDataFile("lyso_serial_master.h5");
-    if (!master)
-        SKIP("lyso_serial_master.h5 not available (git-lfs data not pulled)");
-
-    RegisterHDF5Filter();
-    JFJochHDF5Reader reader;
-    REQUIRE_NOTHROW(reader.ReadFile(*master));
-    auto dataset = reader.GetDataset();
-    REQUIRE(dataset);
-
-    DiffractionExperiment experiment(dataset->experiment);
-    IndexingSettings indexing;
-    indexing.Algorithm(IndexingAlgorithmEnum::Auto);
-    indexing.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
-    experiment.ImportIndexingSettings(indexing);
-
-    ProcessConfig config;
-    config.mode = ProcessMode::FullAnalysis;
-    config.nthreads = default_threads();
-    config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
-    config.spot_finding.indexing = true;
-
-    JFJochProcess process(reader, experiment, dataset->pixel_mask, config);
-    ProcessResult result;
-    REQUIRE_NOTHROW(result = process.Run());
-
-    CHECK_FALSE(result.cancelled);
-    CHECK(result.images_processed == reader.GetNumberOfImages());
-    REQUIRE(result.indexing_rate.has_value());
-    CHECK(result.indexing_rate.value() > 0.0f);          // serial stills: at least some hits index
-
-    reader.Close();
-    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
-}
diff --git a/tests/data/README.md b/tests/data/README.md
index 9a711c5d..ccf842d5 100644
--- a/tests/data/README.md
+++ b/tests/data/README.md
@@ -16,20 +16,15 @@ git lfs install
 git lfs pull            # or: git lfs pull --include "tests/data/*.h5"
 ```
 
-## Expected files
+## Datasets
 
-Place each dataset's master **and its `_data_NNNNNN.h5` files** in this directory:
+| File                       | Dataset                                 | Shipped   |
+|----------------------------|-----------------------------------------|-----------|
+| `lyso_rotation_master.h5`  | lysozyme rotation series (~1800 images) | yes (LFS) |
 
-| File                          | Dataset                                  |
-|-------------------------------|------------------------------------------|
-| `lyso_rotation_master.h5`     | lysozyme rotation series (~1800 images)  |
-| `lyso_serial_master.h5`       | lysozyme serial / jet stills (~5000 images) |
-
-To point the tests at an existing local dataset without copying, symlink it:
-
-```
-ln -s /path/to/your_master.h5            tests/data/lyso_rotation_master.h5
-ln -s /path/to/your_data_000001.h5       tests/data/...
-```
-
-(The master references its data files by relative name, so keep them side by side.)
+`lyso_rotation_master.h5` (plus its `_data_NNNNNN.h5` files) is fetched by `git lfs pull` and
+drives `JFJochProcess_LysoRotation`. A separate serial dataset is intentionally **not** shipped
+to keep the repository small — the rotation series can be run in serial mode (full analysis
+without rotation indexing) to exercise that path. To add your own dataset, drop the master + its
+data files here as real files (not symlinks, if you intend to commit them via LFS); the master
+references its data files by relative name, so keep them side by side.