From 4e978cfb05cdd5de19ff7e4cea759786839a9f50 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Wed, 31 May 2023 22:05:19 +0200 Subject: [PATCH 1/7] don't wrap in pd.DataFrame to speed things up --- .../annotation/annotation.py | 5 ++-- spectrum_fundamentals/fragments.py | 24 +++++++++---------- 2 files changed, 15 insertions(+), 14 deletions(-) diff --git a/spectrum_fundamentals/annotation/annotation.py b/spectrum_fundamentals/annotation/annotation.py index 28ba970..024b6bb 100644 --- a/spectrum_fundamentals/annotation/annotation.py +++ b/spectrum_fundamentals/annotation/annotation.py @@ -11,7 +11,7 @@ def match_peaks( - fragments_meta_data: pd.DataFrame, + fragments_meta_data: List[dict], peaks_intensity: np.ndarray, peaks_masses: np.ndarray, tmt_n_term: int, @@ -37,7 +37,8 @@ def match_peaks( next_start_peak = 0 seq_len = len(unmod_sequence) matched_peak = False - for _, fragment in fragments_meta_data.iterrows(): + fragment_no: float + for fragment in fragments_meta_data: min_mass = fragment["min_mass"] max_mass = fragment["max_mass"] fragment_no = fragment["no"] diff --git a/spectrum_fundamentals/fragments.py b/spectrum_fundamentals/fragments.py index 6075ea5..14e0acb 100644 --- a/spectrum_fundamentals/fragments.py +++ b/spectrum_fundamentals/fragments.py @@ -1,4 +1,5 @@ import logging +from operator import itemgetter from typing import Dict, List, Optional, Tuple import numpy as np @@ -106,7 +107,7 @@ def compute_peptide_mass(sequence: str) -> float: return forward_sum + ion_type_offsets[0] + ion_type_offsets[1] -def initialize_peaks(sequence: str, mass_analyzer: str, charge: int) -> Tuple[pd.DataFrame, int, str, float]: +def initialize_peaks(sequence: str, mass_analyzer: str, charge: int) -> Tuple[List[dict], int, str, float]: """ Generate theoretical peaks for a modified peptide sequence. @@ -181,18 +182,17 @@ def initialize_peaks(sequence: str, mass_analyzer: str, charge: int) -> Tuple[pd mass = (ion_type_masses[ion_type] + charge_delta) / charge min_mass, max_mass = get_min_max_mass(mass_analyzer, mass) fragments_meta_data.append( - [ - ion_types[ion_type], # ion type - i + 1, # no - charge, # charge - mass, # mass - min_mass, # min mass - max_mass, # max mass - ] + { + "ion_type": ion_types[ion_type], # ion type + "no": i + 1, # no + "charge": charge, # charge + "mass": mass, # mass + "min_mass": min_mass, # min mass + "max_mass": max_mass, # max mass + } ) - df_out = pd.DataFrame(data=fragments_meta_data, columns=col_dtypes.keys()) - df_out.sort_values(by="mass", inplace=True) - return df_out, tmt_n_term, peptide_sequence, (forward_sum + ion_type_offsets[0] + ion_type_offsets[1]) + fragments_meta_data = sorted(fragments_meta_data, key=itemgetter("mass")) + return fragments_meta_data, tmt_n_term, peptide_sequence, (forward_sum + ion_type_offsets[0] + ion_type_offsets[1]) def get_min_max_mass(mass_analyzer: str, mass: float) -> Tuple[float, float]: From cc3ff768902ebbca40d7c6258d75dcc25886bf18 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Sun, 18 Jun 2023 20:33:23 +0200 Subject: [PATCH 2/7] fixed typeguard --- spectrum_fundamentals/fragments.py | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/spectrum_fundamentals/fragments.py b/spectrum_fundamentals/fragments.py index 14e0acb..c06ff93 100644 --- a/spectrum_fundamentals/fragments.py +++ b/spectrum_fundamentals/fragments.py @@ -3,7 +3,6 @@ from typing import Dict, List, Optional, Tuple import numpy as np -import pandas as pd from . import constants as constants @@ -124,13 +123,9 @@ def initialize_peaks(sequence: str, mass_analyzer: str, charge: int) -> Tuple[Li else: modification_deltas, tmt_n_term, peptide_sequence = modifications - col_dtypes = {"ion_type": str, "no": int, "charge": float, "mass": float, "min_mass": float, "max_mass": float} peptide_length = len(peptide_sequence) - if peptide_length > 30: - df_out = pd.DataFrame(columns=col_dtypes.keys()) - df_out = df_out.astype(col_dtypes) - return df_out, -1, "", 0.0 + return [{}], -1, "", 0.0 # initialize constants if int(round(charge)) <= 3: From f991fffc2746fb85a7f9cc25f2e69901d12e6ac8 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Thu, 22 Jun 2023 18:21:51 +0200 Subject: [PATCH 3/7] Bump version from 0.4.0 to 0.4.1 --- .cookietemple.yml | 2 +- .github/release-drafter.yml | 4 ++-- cookietemple.cfg | 2 +- docs/conf.py | 4 ++-- pyproject.toml | 2 +- spectrum_fundamentals/__init__.py | 2 +- spectrum_fundamentals/__main__.py | 2 +- 7 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.cookietemple.yml b/.cookietemple.yml index ebb8ce2..b81d961 100644 --- a/.cookietemple.yml +++ b/.cookietemple.yml @@ -15,5 +15,5 @@ full_name: Victor Giurcoiu email: victor.giurcoiu@tum.de project_name: spectrum_fundamentals project_short_description: Fundamentals public repo -version: 0.4.0 +version: 0.4.1 license: MIT diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml index df0356f..4f014df 100644 --- a/.github/release-drafter.yml +++ b/.github/release-drafter.yml @@ -1,5 +1,5 @@ -name-template: "0.4.0 🌈" # <> -tag-template: 0.4.0 # <> +name-template: "0.4.1 🌈" # <> +tag-template: 0.4.1 # <> exclude-labels: - "skip-changelog" diff --git a/cookietemple.cfg b/cookietemple.cfg index 741b17b..e2bd9e3 100644 --- a/cookietemple.cfg +++ b/cookietemple.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.4.0 +current_version = 0.4.1 [bumpversion_files_whitelisted] init_file = spectrum_fundamentals/__init__.py diff --git a/docs/conf.py b/docs/conf.py index e3c9833..bdd504b 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -54,9 +54,9 @@ # the built documents. # # The short X.Y version. -version = "0.4.0" +version = "0.4.1" # The full version, including alpha/beta/rc tags. -release = "0.4.0" +release = "0.4.1" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/pyproject.toml b/pyproject.toml index b328970..5d4cc6f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "spectrum_fundamentals" -version = "0.4.0" # <> +version = "0.4.1" # <> description = "Fundamentals public repo" authors = ["WassimG "] license = "MIT" diff --git a/spectrum_fundamentals/__init__.py b/spectrum_fundamentals/__init__.py index f20f3ef..d57fb11 100644 --- a/spectrum_fundamentals/__init__.py +++ b/spectrum_fundamentals/__init__.py @@ -1,7 +1,7 @@ """Initialize fundamentals.""" __author__ = "Victor Giurcoiu" __email__ = "victor.giurcoiu@tum.de" -__version__ = "0.4.0" +__version__ = "0.4.1" import logging import logging.handlers diff --git a/spectrum_fundamentals/__main__.py b/spectrum_fundamentals/__main__.py index 8532b32..db6b3a3 100644 --- a/spectrum_fundamentals/__main__.py +++ b/spectrum_fundamentals/__main__.py @@ -5,7 +5,7 @@ @click.command() -@click.version_option(version="0.4.0", message=click.style("spectrum_fundamentals Version: 0.4.0")) +@click.version_option(version="0.4.1", message=click.style("spectrum_fundamentals Version: 0.4.1")) def main() -> None: """spectrum_fundamentals.""" 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(==4.6.0)", "pytest (==4.6.0)", "pytest (==6.2.5)", "pytest-cov (==3.0.0)", "typing (==3.7.4)"] [[package]] name = "zipp" -version = "3.8.1" +version = "3.15.0" description = "Backport of pathlib-compatible object wrapper for zip files" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "zipp-3.8.1-py3-none-any.whl", hash = "sha256:47c40d7fe183a6f21403a199b3e4192cca5774656965b0a4988ad2f8feb5f009"}, - {file = "zipp-3.8.1.tar.gz", hash = "sha256:05b45f1ee8f807d0cc928485ca40a07cb491cf092ff587c0df9cb1fd154848d2"}, + {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"}, + {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"}, ] [package.extras] -docs = ["jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx"] -testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [metadata] lock-version = "2.0" From 32212d90b20bad7907c59d44ae80e3cf405cdfe6 Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 26 Jun 2023 12:50:00 +0200 Subject: [PATCH 5/7] ignore B905 and fix typeguard --- .flake8 | 2 +- spectrum_fundamentals/metrics/similarity.py | 14 +++++++------- tests/unit_tests/test_charge.py | 2 ++ 3 files changed, 10 insertions(+), 8 deletions(-) diff --git a/.flake8 b/.flake8 index 03584b1..2f89b9d 100644 --- a/.flake8 +++ b/.flake8 @@ -1,6 +1,6 @@ [flake8] select = B,B9,C,D,DAR,E,F,N,RST,S,W -ignore = E203,E501,RST201,RST203,RST301,W503,D100,D212,S101,E731,S404,S603,S607 +ignore = E203,E501,RST201,RST203,RST301,W503,D100,D212,S101,E731,S404,S603,S607,B905 max-line-length = 120 max-complexity = 10 docstring-convention = google diff --git a/spectrum_fundamentals/metrics/similarity.py b/spectrum_fundamentals/metrics/similarity.py index 48647e7..e08a813 100644 --- a/spectrum_fundamentals/metrics/similarity.py +++ b/spectrum_fundamentals/metrics/similarity.py @@ -216,8 +216,8 @@ def correlation( :param method: either pearson or spearman :return: calculated correlations """ - observed_intensities = observed_intensities.toarray() - predicted_intensities = predicted_intensities.toarray() + obs_int_arr = observed_intensities.toarray() + pred_int_arr = predicted_intensities.toarray() if charge != 0: if charge == 1: @@ -232,13 +232,13 @@ def correlation( boolean_array = constants.Y_ION_MASK boolean_array = scipy.sparse.csr_matrix(boolean_array) - observed_intensities = scipy.sparse.csr_matrix(observed_intensities) - predicted_intensities = scipy.sparse.csr_matrix(predicted_intensities) - observed_intensities = observed_intensities.multiply(boolean_array).toarray() - predicted_intensities = predicted_intensities.multiply(boolean_array).toarray() + obs_int_arr = scipy.sparse.csr_matrix(obs_int_arr) + pred_int_arr = scipy.sparse.csr_matrix(pred_int_arr) + obs_int_arr = obs_int_arr.multiply(boolean_array).toarray() + pred_int_arr = pred_int_arr.multiply(boolean_array).toarray() pear_corr = [] - for obs, pred in zip(observed_intensities, predicted_intensities): + for obs, pred in zip(obs_int_arr, pred_int_arr): valid_ion_mask = pred > constants.EPSILON obs = obs[valid_ion_mask] pred = pred[valid_ion_mask] diff --git a/tests/unit_tests/test_charge.py b/tests/unit_tests/test_charge.py index f4d49e9..1f2f708 100644 --- a/tests/unit_tests/test_charge.py +++ b/tests/unit_tests/test_charge.py @@ -1,6 +1,7 @@ import unittest import numpy as np +from typeguard import typeguard_ignore import spectrum_fundamentals.charge as charge @@ -38,6 +39,7 @@ def test_indices_to_one_hot_with_list_and_class(self): expected_output = np.array([[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0]]) np.testing.assert_equal(charge.indices_to_one_hot(labels, classes), expected_output) + @typeguard_ignore def test_indices_to_one_hot_with_wrong_input_type(self): """Test indices_to_one_hot correctly raises TypeError on wrong input type.""" labels = None From 811e5f34af8800701619c37ee80e21a32da0ceed Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 26 Jun 2023 15:04:36 +0200 Subject: [PATCH 6/7] fixed typeguard issues --- tests/unit_tests/test_charge.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/tests/unit_tests/test_charge.py b/tests/unit_tests/test_charge.py index 1f2f708..fc343ad 100644 --- a/tests/unit_tests/test_charge.py +++ b/tests/unit_tests/test_charge.py @@ -1,7 +1,7 @@ +import typing import unittest import numpy as np -from typeguard import typeguard_ignore import spectrum_fundamentals.charge as charge @@ -39,11 +39,12 @@ def test_indices_to_one_hot_with_list_and_class(self): expected_output = np.array([[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0]]) np.testing.assert_equal(charge.indices_to_one_hot(labels, classes), expected_output) - @typeguard_ignore def test_indices_to_one_hot_with_wrong_input_type(self): """Test indices_to_one_hot correctly raises TypeError on wrong input type.""" + typing.TYPE_CHECKING = False labels = None self.assertRaises(TypeError, charge.indices_to_one_hot, labels) + typing.TYPE_CHECKING = True def test_indices_to_one_hot_with_incompatible_classes(self): """Test indices_to_one_hot correctly raises TypeError on wrong input type.""" From 7a42c1c4704dc394807becfaf233ee143b310ece Mon Sep 17 00:00:00 2001 From: Mario Picciani Date: Mon, 26 Jun 2023 16:58:01 +0200 Subject: [PATCH 7/7] fixed typeguard for good --- tests/unit_tests/test_charge.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/tests/unit_tests/test_charge.py b/tests/unit_tests/test_charge.py index fc343ad..fa0e497 100644 --- a/tests/unit_tests/test_charge.py +++ b/tests/unit_tests/test_charge.py @@ -1,4 +1,3 @@ -import typing import unittest import numpy as np @@ -41,10 +40,12 @@ def test_indices_to_one_hot_with_list_and_class(self): def test_indices_to_one_hot_with_wrong_input_type(self): """Test indices_to_one_hot correctly raises TypeError on wrong input type.""" - typing.TYPE_CHECKING = False - labels = None - self.assertRaises(TypeError, charge.indices_to_one_hot, labels) - typing.TYPE_CHECKING = True + try: + labels = None + self.assertRaises(TypeError, charge.indices_to_one_hot, labels) + except Exception as e: # explicitly silence typeguard.TypeCheckError here without importing TypeGuard + if e.__class__.__name__ != "TypeCheckError": + raise def test_indices_to_one_hot_with_incompatible_classes(self): """Test indices_to_one_hot correctly raises TypeError on wrong input type."""