diff --git a/CHANGELOG.md b/CHANGELOG.md index 68ccab8..616e77e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +# [2.2.25] - 2023-11-15 + +- Fixed multiprocessing + # [2.2.24] - 2023-11-14 - Pass flag CCS feature extract diff --git a/deeplc/deeplc.py b/deeplc/deeplc.py index 5c2c29e..9ca9bc4 100644 --- a/deeplc/deeplc.py +++ b/deeplc/deeplc.py @@ -45,6 +45,8 @@ from copy import deepcopy import random import math +from collections import ChainMap +from itertools import chain # If CLI/GUI/frozen: disable Tensorflow info and warnings before importing IS_CLI_GUI = os.path.basename(sys.argv[0]) in ["deeplc", "deeplc-gui"] @@ -488,7 +490,19 @@ def do_f_extraction_psm_list_parallel(self, psm_list): logger.debug("wait for feature extraction") all_feats_async.wait() logger.debug("get feature extraction results") - all_feats = pd.concat(all_feats_async.get()) + res = all_feats_async.get() + matrix_names = res[0].keys() + all_feats = { + matrix_name: dict( + enumerate( + chain.from_iterable((v[matrix_name].values() for v in res)) + ) + ) + for matrix_name in matrix_names + } + + # all_feats = pd.concat(all_feats_async.get()) + logger.debug("got feature extraction results") pool.close() diff --git a/setup.py b/setup.py index 203bfeb..d7ec175 100644 --- a/setup.py +++ b/setup.py @@ -5,31 +5,35 @@ setup( - name='deeplc', - version='2.2.24', - license='apache-2.0', - description='DeepLC: Retention time prediction for (modified) peptides using Deep Learning.', + name="deeplc", + version="2.2.25", + license="apache-2.0", + description="DeepLC: Retention time prediction for (modified) peptides using Deep Learning.", long_description=LONG_DESCRIPTION, long_description_content_type="text/markdown", - author='Robbin Bouwmeester, Niels Hulstaert, Arthur Declercq, Ralf Gabriels, Prof. Lennart Martens, Prof. Sven Degroeve', - author_email='Robbin.Bouwmeester@UGent.be', - url='http://compomics.github.io/projects/DeepLC', + author="Robbin Bouwmeester, Niels Hulstaert, Arthur Declercq, Ralf Gabriels, Prof. Lennart Martens, Prof. Sven Degroeve", + author_email="Robbin.Bouwmeester@UGent.be", + url="http://compomics.github.io/projects/DeepLC", project_urls={ - 'Documentation': 'http://compomics.github.io/projects/DeepLC', - 'Source': 'https://github.com/compomics/DeepLC', - 'Tracker': 'https://github.com/compomics/DeepLC/issues' + "Documentation": "http://compomics.github.io/projects/DeepLC", + "Source": "https://github.com/compomics/DeepLC", + "Tracker": "https://github.com/compomics/DeepLC/issues", }, packages=find_packages(), include_package_data=True, entry_points={ - 'console_scripts': [ - 'deeplc=deeplc.__main__:main', - 'deeplc-gui=deeplc.gui:start_gui', + "console_scripts": [ + "deeplc=deeplc.__main__:main", + "deeplc-gui=deeplc.gui:start_gui", ] }, keywords=[ - 'DeepLC', 'Proteomics', 'deep learning', 'peptides', 'retention time', - 'prediction' + "DeepLC", + "Proteomics", + "deep learning", + "peptides", + "retention time", + "prediction", ], classifiers=[ "Intended Audience :: Science/Research", @@ -37,25 +41,25 @@ "Operating System :: OS Independent", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics", - "Development Status :: 4 - Beta" + "Development Status :: 4 - Beta", ], install_requires=[ - 'setuptools>=42.0.1', - 'tensorflow>=2.2,<2.13.0', - 'scipy>=1.4.1,<2', - 'numpy>=1.17,<2', - 'pandas>=0.25,<2', - 'matplotlib>=3,<4', - 'h5py>=2.10.0,<4', - 'pygam>=0.8.0,<1', - 'scikit-learn>=0.24.0,<2', - 'deeplcretrainer>=0.1,<1', - 'psm_utils>=0.2.3,<1', - 'hdf5plugin>=4.1.1' + "setuptools>=42.0.1", + "tensorflow>=2.2,<2.13.0", + "scipy>=1.4.1,<2", + "numpy>=1.17,<2", + "pandas>=0.25,<2", + "matplotlib>=3,<4", + "h5py>=2.10.0,<4", + "pygam>=0.8.0,<1", + "scikit-learn>=0.24.0,<2", + "deeplcretrainer>=0.1,<1", + "psm_utils>=0.2.3,<1", + "hdf5plugin>=4.1.1", ], extras_require={ "gui": ["gooey>=1.0"], "plot": ["plotly>=5"], }, - python_requires='>=3.7', + python_requires=">=3.7", )