Skip to content

PP-3: split run.py into the run package (move only) #109

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
guijacquemet merged 3 commits into from
Nov 1, 2026
Merged

PP-3: split run.py into the run package (move only) #109

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
ef070f7
PP-3: split run.py into the run package, moving code only
claude Nov 1, 2026
6efe206
Merge PP-2 (restacked on the new main) into PP-3
claude Nov 1, 2026
3e60007
Merge main (PP-2 merged, with its review fixes) into PP-3
claude Nov 1, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 8 additions & 2 deletions AGENTS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,11 @@ src/morphobricks_preprocessing/
_io.py write_text_atomic (every file the brick writes) and free_space
manifest.py RunManifest / RunSettings / FileEntry, JSON read/write, SHA-256 of the CSV,
check_sources (images against a run, for other bricks, contract §16)
run.py preflight(), run_experiment() (incremental), sample_planes() for previews
run/ the run (a package since PP-3; `morphobricks_preprocessing.run` re-exports
its public names): preflight.py (Preflight, preflight, sample_planes),
pipeline.py (run_experiment, incremental), result.py (RunResult),
reuse.py (which earlier rows are reused), rows.py (a file's rows and their
pixel checks), publish.py (staged outputs, published together)
report.py plain-language summaries shared by CLI and notebook, group statistics tables
cli.py, __main__ `morphobricks-preprocessing check|run|masks` (also `python -m morphobricks_preprocessing`)
masks.py masks (Q32): find_masks pairs every image with its masks (masks folder with one
Expand Down Expand Up @@ -547,7 +551,9 @@ Technical details go to `logging` (shown in the notebook's "Technical details" p
`write_plate`) writes stores with zarr directly; 0.5 tests
skip with zarr 2.18.
- **Proving "one page at a time":** spy on `planes._read_page`. To prove "only changed
files are read", spy on `run.iter_xyc_planes`. For planes in blocks, spy on
files are read", spy on `run.rows.iter_xyc_planes` (patch the submodule that uses a
name: `run.pipeline.file_sha256`, `run.publish` for `os`/`shutil`). For planes in blocks,
spy on
`planes._read_segment` and make `asarray` of every tifffile class fail.
- **Planes in blocks with small test images:** the memory limit
`plane_layout(path, mapping, memory_limit=1).block_memory_estimate` gives the smallest
Expand Down
6 changes: 6 additions & 0 deletions pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -143,5 +143,11 @@ baseline = "tools/code_rules_baseline.json"
"morphobricks_preprocessing.planes" = "io"
"morphobricks_preprocessing.report" = "pure"
"morphobricks_preprocessing.run" = "orchestration"
"morphobricks_preprocessing.run.pipeline" = "orchestration"
"morphobricks_preprocessing.run.preflight" = "io"
"morphobricks_preprocessing.run.publish" = "io"
"morphobricks_preprocessing.run.result" = "pure"
"morphobricks_preprocessing.run.reuse" = "io"
"morphobricks_preprocessing.run.rows" = "io"
"morphobricks_preprocessing.validation" = "pure"
"morphobricks_preprocessing.zarr_input" = "io"
Loading
Loading