PyMisha Dev Cycle

Important context

• •All paths, track names, and benchmark commands below are examples.
• •Replace "/home/aviezerl/mm10" and example track IDs with the DB/tracks relevant to the current task.
• •For routine local tests, the repository test DB (tests/testdb/...) is usually enough.

Use when

• •You changed src/*.cpp or C++-bound behavior.
• •You need quick parity/performance checks.
• •You need to debug multitask hangs in gextract/gscreen/summary paths.

Workflow

1. •Rebuild extension after C++ changes:

• •python -m pip install -e .

1. •Sanity check import + DB (example only; replace DB path):

• •python - <<'PY'
• •import pymisha as pm
• •pm.gdb_init("/home/aviezerl/mm10")
• •print(pm.gtrack_ls()[:5])
• •PY

1. •Run targeted tests:

• •pytest -k <name> -q

1. •Optional benchmark (Python, example DB + track):

• •python - <<'PY'
• •import time, pymisha as pm
• •pm.gdb_init("/home/aviezerl/mm10")
• •track = "seq.IQ.pcg.flashzoi.mm10.rf524k_EB4_cnt"
• •t0 = time.time()
• •res = pm.gextract(track, pm.gintervals_all(), iterator=10000)
• •print("rows", None if res is None else len(res))
• •print("elapsed", time.time() - t0)
• •print(res.head(3))
• •PY

1. •Optional benchmark (R, example DB + track):

• •R -q -e 'library(misha); gsetroot("/home/aviezerl/mm10"); track <- "seq.IQ.pcg.flashzoi.mm10.rf524k_EB4_cnt"; print(system.time(gextract(track, gintervals.all(), iterator = 1e4)))'

Debug checklist for hangs/slowness

1. •Force numeric iterator (iterator=10000).
2. •Disable multitasking to isolate (pm.CONFIG["multitasking"] = False).
3. •Enable progress (pm.CONFIG["progress"] = "text").
4. •If multitask-only issue: inspect FIFO/write serialization behavior.