From 31da6ec2b79e56f83e2a479cf620479c3f23a6de Mon Sep 17 00:00:00 2001 From: rodvrees Date: Thu, 16 Jul 2026 10:47:53 +0200 Subject: [PATCH 1/3] update docs, remove deepcopy --- CHANGELOG.md | 12 ++++++++++++ README.md | 2 +- docs/source/changelog.rst | 5 +++++ docs/source/index.rst | 1 + im2deep/__init__.py | 4 ++-- im2deep/__main__.py | 2 +- im2deep/_io_helpers.py | 18 ++++++++++++------ im2deep/exceptions.py | 4 ++-- pyproject.toml | 2 +- 9 files changed, 37 insertions(+), 13 deletions(-) create mode 100644 docs/source/changelog.rst diff --git a/CHANGELOG.md b/CHANGELOG.md index 049d537..ab9bf52 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +## [2.0.2] - 2026-07-16 + +### Added +- Sphinx documentation integration with CHANGELOG.md included in docs + +### Changed +- Updated code examples in docstrings and documentation to reflect current API +- Optimized PSM list filtering to use shallow copy instead of full deepcopy for better memory efficiency on large datasets + +### Fixed +- CLI argument passing to `predict` function when calibration data is not provided + ## [2.0.1] - 2026-07-15 ### Fixed diff --git a/README.md b/README.md index 40f9d8e..71803be 100644 --- a/README.md +++ b/README.md @@ -106,7 +106,7 @@ Alternatively, use comma-separated values (CSV) with the following columns: **Example:** -```csv +```text seq,modifications,charge,CCS VVDDFADITTPLK,,2,422.9984309464991 GVEVLSLTPSFMDIPEK,12|Oxidation,2,464.6568644356109 diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst new file mode 100644 index 0000000..868e0d5 --- /dev/null +++ b/docs/source/changelog.rst @@ -0,0 +1,5 @@ +********* +Changelog +********* + +.. mdinclude:: ../../CHANGELOG.md diff --git a/docs/source/index.rst b/docs/source/index.rst index e4a2dd3..2bfbf02 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -8,6 +8,7 @@ :maxdepth: 2 Home + Changelog .. toctree:: diff --git a/im2deep/__init__.py b/im2deep/__init__.py index c0125e1..7b80f43 100644 --- a/im2deep/__init__.py +++ b/im2deep/__init__.py @@ -16,9 +16,9 @@ Example: Basic usage for CCS prediction: - >>> from im2deep.im2deep import predict_ccs + >>> from im2deep import predict >>> from psm_utils.psm_list import PSMList - >>> predictions = predict_ccs(psm_list, calibration_data) + >>> predictions = predict(psm_list) """ diff --git a/im2deep/__main__.py b/im2deep/__main__.py index 9f1a1ca..a2e824e 100644 --- a/im2deep/__main__.py +++ b/im2deep/__main__.py @@ -228,7 +228,7 @@ def _run_predict(*args, **kwargs): LOGGER.info( "No calibration file provided (calibration is HIGHLY recommended), performing prediction only..." ) - predictions = core.predict(*args, **kwargs) + predictions = core.predict(psm_list, multi=kwargs.get("multi", False)) # Output results LOGGER.info("IM2Deep CCS prediction completed successfully!") diff --git a/im2deep/_io_helpers.py b/im2deep/_io_helpers.py index d59cd3b..f2b9288 100644 --- a/im2deep/_io_helpers.py +++ b/im2deep/_io_helpers.py @@ -16,7 +16,6 @@ from __future__ import annotations import logging -from copy import deepcopy from pathlib import Path from typing import Any @@ -253,12 +252,19 @@ 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 - # 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. + # Filtering above shares PSM instances with the input psm_list (no copy). The block below + # mutates psm.metadata in place (writing psm.metadata["CCS"]), so PSMs must be detached from + # the caller's originals before that happens. A full deepcopy also copies the peptidoform and + # other untouched fields, which dominates memory on large PSM lists. Since PSM is a pydantic + # model, a per-PSM shallow copy with a fresh metadata dict is enough: it reuses the (unmutated) + # peptidoform and other fields by reference while giving each PSM its own metadata dict. if needs_target: - psm_list_filtered = deepcopy(psm_list_filtered) + psm_list_filtered = PSMList( + psm_list=[ + psm.model_copy(update={"metadata": dict(psm.metadata) if psm.metadata else {}}) + for psm in psm_list_filtered + ] + ) if len(psm_list_filtered) < original_size: filtered_count = original_size - len(psm_list_filtered) diff --git a/im2deep/exceptions.py b/im2deep/exceptions.py index feaa3e9..01acadd 100644 --- a/im2deep/exceptions.py +++ b/im2deep/exceptions.py @@ -30,7 +30,7 @@ class IM2DeepError(Exception): Examples -------- >>> try: - ... predict_ccs(invalid_data) + ... predict(invalid_psm_list) ... except IM2DeepError as exc: ... print(f"IM2Deep error occurred: {exc}") """ @@ -68,7 +68,7 @@ class CalibrationError(IM2DeepError): Examples -------- >>> try: - ... linear_calibration(pred_df, cal_df, ref_df) + ... predict_and_calibrate(psm_list, psm_list_cal) ... except CalibrationError as exc: ... print(f"Calibration failed: {exc}") """ diff --git a/pyproject.toml b/pyproject.toml index 73419a6..a210b55 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "im2deep" -version = "2.0.1" +version = "2.0.2" description = "Framework for prediction of collisional cross-section of peptides." readme = "README.md" license = "Apache-2.0" From a334a51638753837b196b8618bd573b0ad19a572 Mon Sep 17 00:00:00 2001 From: rodvrees Date: Thu, 16 Jul 2026 11:07:54 +0200 Subject: [PATCH 2/3] fix type errors --- im2deep/_io_helpers.py | 14 ++++++++++---- uv.lock | 16 +++++++++++++++- 2 files changed, 25 insertions(+), 5 deletions(-) diff --git a/im2deep/_io_helpers.py b/im2deep/_io_helpers.py index f2b9288..1b4b17a 100644 --- a/im2deep/_io_helpers.py +++ b/im2deep/_io_helpers.py @@ -280,7 +280,7 @@ def validate_psm_list(psm_list: PSMList, needs_target: bool = False) -> PSMList: if needs_target: # Check if PSMs have either ion_mobility or CCS all_has_targets = all( - psm.ion_mobility is not None or psm.metadata.get("CCS") is not None + psm.ion_mobility is not None or (psm.metadata or {}).get("CCS") is not None for psm in psm_list_filtered ) @@ -290,13 +290,19 @@ def validate_psm_list(psm_list: PSMList, needs_target: bool = False) -> PSMList: if psm.metadata is None: psm.metadata = {} - if psm.ion_mobility is not None: + theoretical_mz = psm.peptidoform.theoretical_mz + precursor_charge = psm.peptidoform.precursor_charge + if ( + psm.ion_mobility is not None + and theoretical_mz is not None + and precursor_charge is not None + ): if "CCS" not in psm.metadata: psm.metadata["CCS"] = _normalize_ccs_metadata_value( im2ccs( psm.ion_mobility, - psm.peptidoform.theoretical_mz, - psm.peptidoform.precursor_charge, + theoretical_mz, + precursor_charge, ) ) elif psm.metadata.get("CCS") is not None: diff --git a/uv.lock b/uv.lock 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Returns @@ -228,6 +228,12 @@ def validate_psm_list(psm_list: PSMList, needs_target: bool = False) -> PSMList: Validate that the PSM list contains necessary fields. And homogenizes the data. Also removes entries with charge state higher than 6. + Notes + ----- + When ``needs_target=True``, this function mutates the PSMs in ``psm_list`` in place + (normalizing/writing ``psm.metadata["CCS"]``) rather than copying them first. Callers + that need to keep their original PSMList untouched should pass a copy. + Parameters ---------- psm_list : PSMList @@ -252,19 +258,10 @@ 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 - # Filtering above shares PSM instances with the input psm_list (no copy). The block below - # mutates psm.metadata in place (writing psm.metadata["CCS"]), so PSMs must be detached from - # the caller's originals before that happens. A full deepcopy also copies the peptidoform and - # other untouched fields, which dominates memory on large PSM lists. Since PSM is a pydantic - # model, a per-PSM shallow copy with a fresh metadata dict is enough: it reuses the (unmutated) - # peptidoform and other fields by reference while giving each PSM its own metadata dict. - if needs_target: - psm_list_filtered = PSMList( - psm_list=[ - psm.model_copy(update={"metadata": dict(psm.metadata) if psm.metadata else {}}) - for psm in psm_list_filtered - ] - ) + # Filtering above shares PSM instances with the input psm_list (no copy), and the + # needs_target block below writes psm.metadata["CCS"] directly onto those shared PSMs. + # This function therefore mutates the caller's psm_list in place when needs_target=True; + # no defensive copy is made, to avoid the memory cost of copying large PSM lists. if len(psm_list_filtered) < original_size: filtered_count = original_size - len(psm_list_filtered) @@ -274,7 +271,7 @@ def validate_psm_list(psm_list: PSMList, needs_target: bool = False) -> PSMList: ) if len(psm_list_filtered) == 0: - raise IM2DeepError("No PSMs present in provided PSMLists.") + raise IM2DeepError("No PSMs present in provided PSMLists after validation.") all_has_targets = True if needs_target: