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Fix unnecessary deepcopy in validate_psm_list causing OOM on large PSM lists #24

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Merged
ArthurDeclercq merged 1 commit into from
Jul 15, 2026
Merged

Fix unnecessary deepcopy in validate_psm_list causing OOM on large PSM lists #24

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8 changes: 6 additions & 2 deletions im2deep/_io_helpers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -253,8 +253,12 @@ def validate_psm_list(psm_list: PSMList, needs_target: bool = False) -> PSMList:
charges = np.array([psm.peptidoform.precursor_charge for psm in psm_list])
psm_list_filtered = psm_list[(charges != None) & (charges <= 6)] # noqa: E711

# TODO: Is deepcopy really necessary or can it be avoided?
psm_list_filtered = deepcopy(psm_list_filtered)
# Filtering above shares PSM instances with the input psm_list (no copy). A deep copy is only
# needed when the block below will mutate PSMs in place (writing psm.metadata["CCS"]); for the
# plain prediction path (needs_target=False) nothing downstream mutates PSMs, so skip it there
# to avoid an O(n) full-object-graph copy on large PSM lists.
if needs_target:
psm_list_filtered = deepcopy(psm_list_filtered)

if len(psm_list_filtered) < original_size:
filtered_count = original_size - len(psm_list_filtered)
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