Running Tests¶

emwrap ships integration tests that run a small real processing pipeline end-to-end (import, alignment, CTF, reconstruction, and optionally particle extraction/refinement) against a shared tilt-series dataset, and check that every job in the pipeline finishes successfully and produces the expected output files.

Tests are exposed as subcommands of the ./emh-tomo entry point, through the --test action:

# List the available tests
./emh-tomo --test list

# Show the options for a specific test
./emh-tomo --test apof_warp -h
./emh-tomo --test apof_aretomo3 -h

# Run a test
./emh-tomo --test apof_warp
./emh-tomo --test apof_aretomo3

Test Data¶

Both tests run against the same dataset, WarpApofTutorial (5 apoferritin tilt series from EMPIAR-10491) – see Test Data for how to download it, its expected folder layout, and the acquisition parameters used when importing it.

Both apof_warp and apof_aretomo3 resolve the dataset automatically at $ROOT/testdata/WarpApofTutorial (via TestData.get_dataset_path('WarpApofTutorial')) – no further configuration is needed. If the folder does not exist on disk, the tests fail immediately with a message explaining how to download it.

Common Options¶

Both tests share the same base set of options (defined in the shared TestApoF test case):

Option	Description	Default
`--project`, `-p PATH`	Project folder where the test pipeline is run. When omitted, a temporary folder is created and removed automatically at the end of the test; passing a path keeps the outputs around for inspection.	temporary folder
`--ts NAME`	Restrict the run to a single tilt series (e.g. `TS_11`) instead of all of them.	`*` (all)
`--gpus`, `-g N`	Number of GPUs to request for GPU-enabled jobs.	`1`
`--dry`	Dry run: load and validate the workflow and print which jobs would run, without actually launching them.	off
`-v`, `--verbose`	Increase the verbosity of the underlying `unittest` output. Can be repeated (`-vv`).	off

Available Tests¶

apof_warp¶

Runs the Warp-based ApoF preprocessing pipeline (TestApoFWarp). It adds one extra option on top of the common ones:

Option	Description	Default
`--workflow`, `-w {small,medium,full,otf}`	Selects how much of the pipeline to run (see below).	`small`

The --workflow choices run progressively more of the pipeline:

small – preprocessing only: emw-import-ts, emw-warp-mctf (motion correction and CTF), emw-warp-tsalign (tilt-series alignment), and emw-warp-ctfrec (3D CTF and reconstruction).
medium – the small jobs plus particle picking and an initial 3D refinement: emw-pytom, emw-warp-export_particles, and relion.initialmodel.tomo.
full – intended to also run 3D refinement after the initial model; work in progress, not implemented yet.
otf – runs preprocessing in on-the-fly (OTF) mode instead, using a single combined emw-warp-otf job (import + alignment + reconstruction) rather than the separate small-style steps.

Examples:

# Run the default (small) workflow with a temporary project folder
./emh-tomo --test apof_warp

# Run the medium workflow, keeping outputs, using 2 GPUs
./emh-tomo --test apof_warp --workflow medium --project /tmp/apof_warp_run --gpus 2

# Only check that the workflow and test data are set up correctly
./emh-tomo --test apof_warp --dry

apof_aretomo3¶

Runs the AreTomo3-based ApoF preprocessing pipeline (TestAretomo3ApoF): emw-import-ts followed by emw-aretomo3, which performs tilt-series alignment and reconstruction in a single job. It does not add any options beyond the Common Options.

# Run with a temporary project folder
./emh-tomo --test apof_aretomo3

# Run a single tilt series, keeping outputs, with verbose unittest output
./emh-tomo --test apof_aretomo3 --ts TS_11 --project /tmp/apof_aretomo3_run -v