repo stringclasses 454
values | file_path stringlengths 5 201 | extension stringclasses 1
value | content stringlengths 8 509k | num_lines int64 3 16.9k | size_bytes int64 8 511k |
|---|---|---|---|---|---|
deap | examples/ga/onemax_mp.py | .py | #!/usr/bin/env python2.7
# This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
... | 75 | 2,353 |
deap | examples/ga/onemax.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 161 | 5,307 |
deap | examples/ga/tsp.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 77 | 2,494 |
deap | examples/ga/onemax_multidemic.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 100 | 3,148 |
deap | examples/ga/onemax_island.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 155 | 5,253 |
deap | examples/ga/nsga3.py | .py | from math import factorial
import random
import matplotlib.pyplot as plt
import numpy
import pymop.factory
from deap import algorithms
from deap import base
from deap.benchmarks.tools import igd
from deap import creator
from deap import tools
# Problem definition
PROBLEM = "dtlz2"
NOBJ = 3
K = 10
NDIM = NOBJ + K - 1... | 133 | 4,200 |
deap | examples/ga/sortingnetwork.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 123 | 4,361 |
deap | examples/ga/mo_rhv.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 193 | 7,038 |
deap | examples/ga/evoknn.py | .py | #!/usr/bin/env python2.7
# This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
... | 90 | 2,905 |
deap | examples/ga/onemax_numpy.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 95 | 3,166 |
deap | examples/ga/knn.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 104 | 3,438 |
deap | examples/ga/knapsack.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 111 | 3,564 |
deap | examples/ga/evosn.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 145 | 4,982 |
deap | examples/de/dynamic.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 155 | 5,807 |
deap | examples/de/sphere.py | .py | # This file is part of EAP.
#
# EAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# EAP is distributed in ... | 122 | 3,767 |
deap | examples/de/basic.py | .py | # This file is part of EAP.
#
# EAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# EAP is distributed in ... | 86 | 2,816 |
deap | examples/coev/coop_base.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 108 | 3,822 |
deap | examples/coev/coop_evol.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 178 | 6,150 |
deap | examples/coev/symbreg.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 138 | 4,542 |
deap | examples/coev/coop_niche.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 102 | 3,365 |
deap | examples/coev/hillis.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 165 | 5,679 |
deap | examples/coev/coop_adapt.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 139 | 4,952 |
deap | examples/coev/coop_gen.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 131 | 4,762 |
deap | examples/es/cma_mo.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 169 | 5,971 |
deap | examples/es/cma_1+l_minfct.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 56 | 1,996 |
deap | examples/es/cma_bipop.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 200 | 8,278 |
deap | examples/es/onefifth.py | .py |
# This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed... | 81 | 2,770 |
deap | examples/es/fctmin.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 85 | 2,928 |
deap | examples/es/cma_minfct.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 60 | 2,164 |
deap | examples/es/cma_plotting.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 128 | 4,286 |
deap | examples/gp/ant.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 213 | 6,844 |
deap | examples/gp/parity.py | .py | # This file is part of EAP.
#
# EAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# EAP is distributed in ... | 93 | 2,949 |
deap | examples/gp/symbreg.py | .py | # This file is part of EAP.
#
# EAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# EAP is distributed in ... | 95 | 3,374 |
deap | examples/gp/symbreg_epsilon_lexicase.py | .py | # This file is part of EAP.
#
# EAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# EAP is distributed in ... | 93 | 3,343 |
deap | examples/gp/adf_symbreg.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 184 | 6,220 |
deap | examples/gp/multiplexer.py | .py | # This file is part of EAP.
#
# EAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# EAP is distributed in ... | 100 | 3,295 |
deap | examples/gp/symbreg_harm.py | .py | # This file is part of EAP.
#
# EAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# EAP is distributed in ... | 93 | 3,371 |
deap | examples/gp/symbreg_numpy.py | .py | # This file is part of EAP.
#
# EAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# EAP is distributed in ... | 95 | 3,289 |
deap | examples/gp/spambase.py | .py | # This file is part of EAP.
#
# EAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# EAP is distributed in ... | 113 | 4,043 |
deap | examples/gp/ant/buildAntSimFast.py | .py | from distutils.core import setup, Extension
module1 = Extension('AntC',
sources = ['AntSimulatorFast.cpp'])
setup (name = 'AntC',
version = '1.0',
description = 'Fast version of the Ant Simulator (aims to replace the AntSimulator class)',
ext_modules = [module1])
| 10 | 308 |
deap | examples/pso/speciation.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 182 | 6,580 |
deap | examples/pso/basic_numpy.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 91 | 3,160 |
deap | examples/pso/basic.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 92 | 3,352 |
deap | examples/pso/multiswarm.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 235 | 9,309 |
deap | examples/eda/pbil.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 86 | 2,789 |
deap | examples/eda/emna.py | .py | # This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | 95 | 3,411 |
scikit-bio | setup.py | .py | #!/usr/bin/env python
"""Setup script for scikit-bio installation.
----------------------------------------------------------------------------
Copyright (c) 2013--, scikit-bio development team.
Distributed under the terms of the Modified BSD License.
The full license is in the file LICENSE.txt, distributed with th... | 193 | 5,253 |
scikit-bio | checklist.py | .py | #!/usr/bin/env python
"""Validate the content and structure of a scikit-bio repository.
----------------------------------------------------------------------------
Copyright (c) 2013--, scikit-bio development team.
Distributed under the terms of the Modified BSD License.
The full license is in the file LICENSE.txt... | 510 | 17,451 |
scikit-bio | skbio/workflow.py | .py | r"""Workflow Construction (:mod:`skbio.workflow`)
=============================================
.. currentmodule:: skbio.workflow
Construct arbitrarily complex workflows in which the specific methods run are
determined at runtime. This module supports short circuiting a workflow if an
item fails, supports ordering me... | 568 | 19,012 |
scikit-bio | skbio/_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 58 | 1,709 |
scikit-bio | skbio/_config.py | .py | r"""Configuration Options
=====================
.. currentmodule:: skbio
This module provides a configuration system that controls the global behavior of all
scikit-bio functionalities.
Functions
---------
.. autosummary::
:toctree: generated/
get_config
set_config
Configuration options
----------------... | 148 | 3,931 |
scikit-bio | skbio/__init__.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 101 | 2,592 |
scikit-bio | skbio/test.py | .py | """Run pytest in scikit-bio configuration.
----------------------------------------------------------------------------
Copyright (c) 2013--, scikit-bio development team.
Distributed under the terms of the Modified BSD License.
The full license is in the file LICENSE.txt, distributed with this software.
------------... | 17 | 474 |
scikit-bio | skbio/alignment/_utils.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 479 | 16,010 |
scikit-bio | skbio/alignment/_path.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,360 | 47,617 |
scikit-bio | skbio/alignment/_indexing.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 241 | 8,750 |
scikit-bio | skbio/alignment/_tabular_msa.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 2,586 | 84,640 |
scikit-bio | skbio/alignment/_pair.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,394 | 47,022 |
scikit-bio | skbio/alignment/_pairwise.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 888 | 32,811 |
scikit-bio | skbio/alignment/__init__.py | .py | r"""Sequence Alignments (:mod:`skbio.alignment`)
============================================
.. currentmodule:: skbio.alignment
This module provides functionality for computing and manipulating sequence
alignments. DNA, RNA, and protein sequences can be aligned, as well as
sequences with or without custom alphabets.... | 457 | 15,036 |
scikit-bio | skbio/alignment/_distance.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 264 | 9,815 |
scikit-bio | skbio/alignment/_repr.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 67 | 2,586 |
scikit-bio | skbio/alignment/_score.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 128 | 4,484 |
scikit-bio | skbio/alignment/tests/test_pair.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,422 | 63,640 |
scikit-bio | skbio/alignment/tests/test_path.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 815 | 34,055 |
scikit-bio | skbio/alignment/tests/test_tabular_msa.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 3,941 | 148,166 |
scikit-bio | skbio/alignment/tests/test_distance.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 676 | 28,984 |
scikit-bio | skbio/alignment/tests/test_pairwise.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 774 | 35,402 |
scikit-bio | skbio/alignment/tests/test_score.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 288 | 10,659 |
scikit-bio | skbio/alignment/tests/test_utils.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 410 | 15,911 |
scikit-bio | skbio/binaries/_ordination.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2025--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 202 | 8,317 |
scikit-bio | skbio/binaries/_util.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2025--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 179 | 4,580 |
scikit-bio | skbio/binaries/__init__.py | .py | r"""Optimized libraries from scikit-bio-binaries
============================================
.. currentmodule:: skbio.binaries
This module provides an interface to the optimized functions
that are available in the scikit-bio-binaries package,
via the libskbb shared library.
Since scikit-bio-binaries is not guarante... | 50 | 1,239 |
scikit-bio | skbio/binaries/_distance.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2025--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 198 | 7,344 |
scikit-bio | skbio/binaries/tests/test_util.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 67 | 2,430 |
scikit-bio | skbio/metadata/_testing.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,374 | 52,348 |
scikit-bio | skbio/metadata/io.py | .py | """Contains io functionality for the Metadata module."""
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this sof... | 541 | 22,250 |
scikit-bio | skbio/metadata/_interval.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,056 | 35,687 |
scikit-bio | skbio/metadata/__init__.py | .py | r"""Metadata (:mod:`skbio.metadata`)
================================
.. currentmodule:: skbio.metadata
This module provides functionality for storing and working with metadata -- the data
that describes other data. While a typical data table (see :mod:`skbio.table`) stores
the measurements of features in samples, me... | 88 | 1,947 |
scikit-bio | skbio/metadata/_mixin.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 563 | 18,268 |
scikit-bio | skbio/metadata/missing.py | .py | """Defines Handling of different Missing classes for Metadata module."""
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distribut... | 116 | 3,361 |
scikit-bio | skbio/metadata/_repr.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 189 | 6,664 |
scikit-bio | skbio/metadata/_metadata.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | 1,365 | 45,678 |
scikit-bio | skbio/metadata/base.py | .py | """Base for the metadata module."""
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------... | 66 | 2,125 |
scikit-bio | skbio/metadata/_enan.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | 88 | 3,667 |
scikit-bio | skbio/metadata/tests/test_enan.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | 43 | 1,372 |
scikit-bio | skbio/metadata/tests/test_mixin.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 119 | 4,518 |
scikit-bio | skbio/metadata/tests/test_metadata.py | .py | import collections
import unittest
import warnings
from packaging.version import Version
import pandas as pd
import numpy as np
from skbio.metadata._metadata import (SampleMetadata, CategoricalMetadataColumn,
NumericMetadataColumn)
PANDAS_3 = Version(pd.__version__) >= Version(... | 987 | 41,415 |
scikit-bio | skbio/metadata/tests/test_metadata_column.py | .py | import os.path
import tempfile
import unittest
from packaging.version import Version
import pandas as pd
import numpy as np
from skbio.metadata._metadata import (MetadataColumn, CategoricalMetadataColumn,
NumericMetadataColumn)
PANDAS_3 = Version(pd.__version__) >= Version("3.0.... | 900 | 34,099 |
scikit-bio | skbio/metadata/tests/test_missing.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | 102 | 3,613 |
scikit-bio | skbio/metadata/tests/test_io.py | .py | import collections
import os.path
import tempfile
import unittest
from packaging.version import Version
import numpy as np
import pandas as pd
from skbio.util import get_data_path
from skbio.metadata._metadata import (SampleMetadata, CategoricalMetadataColumn,
NumericMetadataColum... | 1,614 | 57,044 |
scikit-bio | skbio/metadata/tests/test_intersection.py | .py | # checklist.py:CopyrightHeadersValidator IGNORE
# ----------------------------------------------------------------------------
# This code is taken from bx-python project and added with a test for a new
# function `update` from line 195 to 211. The license for this code is
# included in licenses/bx_python.txt.
# ------... | 242 | 8,188 |
scikit-bio | skbio/metadata/tests/test_interval.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 796 | 32,405 |
scikit-bio | skbio/table/_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 39 | 1,196 |
scikit-bio | skbio/table/_tabular.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 301 | 10,607 |
scikit-bio | skbio/table/__init__.py | .py | r"""Data Table (:mod:`skbio.table`)
==================================
.. currentmodule:: skbio.table
Tabular data are among the most common data structures in bioinformatics and many other
fields. scikit-bio provides a powerful table class for biological data (:class:`Table`),
a flexible system that accepts multiple... | 256 | 9,524 |
scikit-bio | skbio/table/_augment.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 991 | 34,229 |
scikit-bio | skbio/table/tests/test_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 62 | 2,535 |
scikit-bio | skbio/table/tests/test_tabular.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 528 | 20,364 |
scikit-bio | skbio/table/tests/test_augment.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 873 | 37,200 |
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