text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
values | hash stringlengths 16 16 | score float64 7 8.5 | stars int64 0 237k |
|---|---|---|---|---|---|---|
#!/usr/bin/env python
"""
Resolve the nearest available MirMachine node for a species using a local NCBI
Taxonomy dump.
Examples
--------
Download/cache taxonomy once and resolve a species:
python mirmachine_autonode.py --species "Caenorhabditis elegans"
Print a ready-to-run MirMachine command:
python mirmach... | sinanugur/MirMachine | scripts/mirmachine_autonode.py | .py | ad107ff487150d58 | 7.6 | 15 |
#!/usr/bin/env python
'''
Created on 01/02/2024
Seed detector
@author: suu13
'''
import sys
from Bio import SeqIO
#import ast
def check_patterns(patterns, target_sequence):
p=[]
for pattern in patterns:
if pattern.strip().strip("*").replace('U','T') in target_sequence: #star seeds are high confiden... | sinanugur/MirMachine | scripts/seed_detector.py | .py | 665619cb7bc0f342 | 7.6 | 15 |
from setuptools import setup, find_packages, Command
import os
with open("requirements.txt") as req:
requirements=req.readlines()
class CleanCommand(Command):
"""Custom clean command to tidy up the project root."""
user_options = []
def initialize_options(self):
pass
def finalize_options(s... | sinanugur/MirMachine | setup.py | .py | 11da701ba6c2ba51 | 7.6 | 15 |
#!/usr/bin/env python3
import sys
import math
import argparse
import gzip
from scipy.stats import norm, chi2
from scipy.optimize import brentq
# Example usage:
# python3 munge.py biomarkers-30780-both_sexes-irnt.tsv.bgz --chr-col chr --pos-col pos --ref-col ref --alt-col alt --af-col af_EUR --effect-col beta_EUR --se... | FINNGEN/META_ANALYSIS | scripts/munge.py | .py | 5595d89528d2cc3f | 7.63 | 17 |
#!/usr/bin/env python3
import unittest
import sys
import os
import io
import json
import gzip
import tempfile
import shutil
from contextlib import redirect_stderr
from types import SimpleNamespace
from unittest.mock import patch
# Add parent directory to path to import the module under test
sys.path.insert(0, os.path... | FINNGEN/META_ANALYSIS | scripts/tests/test_loo.py | .py | a7e867d0ed008ddf | 8.13 | 17 |
"""
The spherical harmonic classes store the respective definitions and basis
functions, as well as their derivative and inverse. Please refer to the
:doc:`/theory/spherical_harmonic_definition` page for more specific information
on the mathematical definitions of spherical harmonics.
"""
import numpy as np
import pyfa... | pyfar/spharpy | spharpy/classes/sh.py | .py | 70057c66835dd639 | 7.54 | 11 |
"""Interpolation module for spherical data."""
from scipy import interpolate as spinterpolate
import numpy as np
class SmoothSphereBivariateSpline(spinterpolate.SmoothSphereBivariateSpline):
"""Smooth bivariate spline approximation in spherical coordinates.
The implementation uses the method proposed by Dier... | pyfar/spharpy | spharpy/interpolate.py | .py | a6924ed0496ce142 | 7.54 | 11 |
"""
Helper functions for coordinate operations.
"""
import numpy as np
from scipy.spatial import cKDTree, SphericalVoronoi
def coordinates2latlon(coordinates):
r"""Transforms from Cartesian coordinates to Geocentric coordinates.
.. math::
h = \sqrt{x^2 + y^2 + z^2},
\theta = \pi/2 - \arcco... | pyfar/spharpy | spharpy/samplings/helpers.py | .py | 1e14702af737f46d | 7.54 | 11 |
import pytest
import pyfar as pf
import numpy as np
from spharpy import SamplingSphere
from spharpy.samplings import equal_area
@pytest.fixture
def make_coordinates():
"""Fixture factory which can be used to return coordinate storing objects.
Works with every child class of pyfar.Coordinates which supports t... | pyfar/spharpy | tests/conftest.py | .py | 51871fb0296988b8 | 7.04 | 11 |
"""
Tests for the aperture function of a spherical loudspeaker array.
"""
import spharpy.spherical as sh
from scipy.special import legendre
from spharpy.spherical import sph_identity_matrix
import numpy as np
def test_aperture_diag():
n_max = 10
rad_cap = 0.1
rad_sphere = 1
aperture = sh.aperture_vibr... | pyfar/spharpy | tests/test_aperture.py | .py | 10db829846cbc1fc | 7.04 | 11 |
from spharpy import SamplingSphere
from pyfar import Coordinates
import numpy as np
import numpy.testing as npt
import pytest
from spharpy.samplings import gaussian
def test_sampling_sphere_init():
sampling = SamplingSphere()
assert isinstance(sampling, SamplingSphere)
def test_sampling_sphere_init_value():... | pyfar/spharpy | tests/test_coordinates.py | .py | fe8960b1ab328667 | 7.04 | 11 |
"""
Tests for modal strength function.
"""
from scipy.io import loadmat
import spharpy.spherical as sh
import numpy as np
def test_modal_strength_open():
n_max = 5
n_bins = 128
k = np.linspace(0.5, 15, n_bins)
fname = './tests/data/modal_strength_open.mat'
reference = loadmat(fname)['matrix']
... | pyfar/spharpy | tests/test_modal_strength.py | .py | e176e2ce75350282 | 8.04 | 11 |
import pytest
import matplotlib.pyplot as plt
from spharpy.plot._utils import _prepare_plot
@pytest.mark.parametrize(
("ax_case", "output_type", "projection"),
[("none", plt.Axes, "3d"), ("single", plt.Axes, None),
("two", list, None)],
)
def test_prepare_plot(ax_case, output_type, projection):
"""
... | pyfar/spharpy | tests/test_plot__utils.py | .py | a0540180f0215434 | 7.04 | 11 |
import numpy as np
import pytest
import spharpy.samplings as samplings
from spharpy import SamplingSphere
from pyfar import Coordinates
import numpy.testing as npt
from spharpy.spherical import (
spherical_harmonic_basis_real, spherical_harmonic_basis)
@pytest.mark.parametrize("flatten_output", [True, False])
de... | pyfar/spharpy | tests/test_samplings.py | .py | c57e28b3dd61352e | 7.04 | 11 |
"""
Tests for spherical harmonic class.
"""
import pytest
import numpy as np
from spharpy import (
SphericalHarmonics, SamplingSphere, SphericalHarmonicDefinition,
)
import pyfar as pf
import deepdiff
def test_spherical_harmonics_definition_init():
"""Test default behavior."""
definition = SphericalHarmon... | pyfar/spharpy | tests/test_sh_class.py | .py | 0a7fc3afebf454d1 | 8.04 | 11 |
"""
Tests for special functions.
"""
import pytest
from spharpy import special
import numpy as np
import numpy.testing as npt
def genfromtxt_complex(filename, delimiter=','):
"""Generate complex numpy array from csv file."""
data_str = np.genfromtxt(filename, delimiter=delimiter, dtype=str)
mapping = np... | pyfar/spharpy | tests/test_special.py | .py | 22b6bb82e9e60540 | 7.04 | 11 |
from spharpy.classes.audio import (
SphericalHarmonicTimeData,
SphericalHarmonicFrequencyData,
_atleast_3d_first_dimension)
from spharpy import SphericalHarmonicDefinition
import numpy as np
import numpy.testing as npt
def test_atleast_3d_data():
"""Test extending the shape of 1D and 2D array likes.""... | pyfar/spharpy | tests/test_spherical_harmonics_audio.py | .py | c3326765f2b6b429 | 8.04 | 11 |
# coding=utf8
# Copyright 2018-2025 JDCLOUD.COM
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http:#www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | jdcloud-api/jdcloud-sdk-python | demo/rds_test.py | .py | a02c309b3ea8c9ae | 7.16 | 20 |
# coding=utf8
# Copyright 2018 JDCLOUD.COM
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | jdcloud-api/jdcloud-sdk-python | jdcloud_sdk/core/signer.py | .py | 165186c1ff080a9d | 7.66 | 20 |
# coding=utf8
# Copyright 2018 JDCLOUD.COM
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | jdcloud-api/jdcloud-sdk-python | jdcloud_sdk/services/ag/apis/CreateAgRequest.py | .py | 1bf51417515304ef | 7.66 | 20 |
# coding=utf8
# Copyright 2018 JDCLOUD.COM
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | jdcloud-api/jdcloud-sdk-python | jdcloud_sdk/services/ag/apis/CreateAsAlarmRequest.py | .py | 43365ee903ba613d | 7.66 | 20 |
# coding=utf8
# Copyright 2018 JDCLOUD.COM
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | jdcloud-api/jdcloud-sdk-python | jdcloud_sdk/services/ag/apis/CreateAsCronRequest.py | .py | 5ea25b956fd3371a | 7.66 | 20 |
# coding=utf8
# Copyright 2018 JDCLOUD.COM
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | jdcloud-api/jdcloud-sdk-python | jdcloud_sdk/services/ag/apis/CreateAsRuleRequest.py | .py | b0513fcd39f0590b | 7.66 | 20 |
# coding=utf8
# Copyright 2018 JDCLOUD.COM
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | jdcloud-api/jdcloud-sdk-python | jdcloud_sdk/services/ag/apis/DescribeAgsRequest.py | .py | bda8a990d143651f | 7.66 | 20 |
# coding=utf8
# Copyright 2018 JDCLOUD.COM
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | jdcloud-api/jdcloud-sdk-python | jdcloud_sdk/services/ag/apis/DescribeAsAlarmsRequest.py | .py | cec437571fde7430 | 7.66 | 20 |
# coding=utf8
# Copyright 2018 JDCLOUD.COM
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | jdcloud-api/jdcloud-sdk-python | jdcloud_sdk/services/ag/apis/DescribeAsCronsRequest.py | .py | 61ed893bb890be89 | 7.66 | 20 |
# coding=utf8
# Copyright 2018 JDCLOUD.COM
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | jdcloud-api/jdcloud-sdk-python | jdcloud_sdk/services/ag/apis/DescribeAsRulesRequest.py | .py | daa5a8ccfe0a7107 | 7.66 | 20 |
# coding=utf8
# Copyright 2018 JDCLOUD.COM
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | jdcloud-api/jdcloud-sdk-python | jdcloud_sdk/services/ag/apis/DescribeScalingActivitiesRequest.py | .py | 6b28b01ca1c7ac64 | 7.66 | 20 |
#!/usr/bin/env python3
# MIT License
#
# Copyright (c) 2020 FABRIC Testbed
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to ... | fabric-testbed/InformationModel | fim/slivers/attached_components.py | .py | 0e2ecd02c9eeefae | 7.42 | 6 |
#!/usr/bin/env python3
# MIT License
#
# Copyright (c) 2020 FABRIC Testbed
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to ... | fabric-testbed/InformationModel | fim/slivers/base_sliver.py | .py | e39d6f4800e15f08 | 7.42 | 6 |
#!/usr/bin/env python3
# MIT License
#
# Copyright (c) 2021 FABRIC Testbed
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to ... | fabric-testbed/InformationModel | fim/slivers/gateway.py | .py | 490f7a21a82f050c | 7.42 | 6 |
#!/usr/bin/env python3
# MIT License
#
# Copyright (c) 2020 FABRIC Testbed
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to ... | fabric-testbed/InformationModel | fim/slivers/maintenance_mode.py | .py | c6957e6d2413e618 | 7.42 | 6 |
"""Entry point for ``python -m microbench`` / ``microbench`` console script."""
import os
import subprocess
import sys
import threading
from microbench.cli.parser import (
_CAPTURE_CHOICES,
_SIGTERM_GRACE_PERIOD,
_build_parser,
)
from microbench.cli.registry import MIXIN_REGISTRY
from microbench.cli.runne... | alubbock/microbench | microbench/cli/main.py | .py | bdfe2078cbf466d7 | 7.66 | 20 |
"""Subprocess execution and per-iteration capture for the CLI."""
import threading
from datetime import datetime, timezone
class _SubprocessMonitorThread(threading.Thread):
"""Background thread that samples CPU and RSS of a child process."""
def __init__(self, pid, interval):
super().__init__(daemon... | alubbock/microbench | microbench/cli/runner.py | .py | 2979018a7cfd1e40 | 7.66 | 20 |
"""JSON encoding utilities for microbench.
Provides a JSONEncoder that handles datetime, timedelta, timezone,
and numpy scalar/array types, plus a warning class and placeholder
value for unencodable objects.
"""
import json
from datetime import datetime, timedelta, timezone
try:
import numpy
except ImportError:
... | alubbock/microbench | microbench/core/encoding.py | .py | 32affeaee4d4c8cb | 7.66 | 20 |
import json
import logging
import threading
from datetime import datetime
class LiveStream:
"""Tail a benchmark output file and process records as they arrive.
Usage::
stream = MyStream('/path/to/benchmark.jsonl')
# ... runs in background ...
stream.stop()
stream.join()
"... | alubbock/microbench | microbench/livestream.py | .py | b2cdb0b940f55bdb | 7.66 | 20 |
"""Shared mixin utilities: CLIArg descriptor and internal sentinels."""
_UNSET = object()
class CLIArg:
"""Declares a CLI argument that sets a mixin attribute.
Attach a list of ``CLIArg`` instances to a mixin class as ``cli_args``
to expose configurable attributes through ``python -m microbench``.
A... | alubbock/microbench | microbench/mixins/base.py | .py | f823f3c5093a2fa1 | 7.66 | 20 |
"""Call-related mixins: MBFunctionCall, MBReturnValue."""
import warnings
from microbench.core.encoding import _UNENCODABLE_PLACEHOLDER_VALUE, JSONEncodeWarning
class MBFunctionCall:
"""Capture function arguments and keyword arguments"""
def capture_function_args_and_kwargs(self, bm_data):
call = b... | alubbock/microbench | microbench/mixins/call.py | .py | 81980708c4b1257f | 7.66 | 20 |
"""GPU mixins: MBNvidiaSmi."""
import re
import subprocess
from microbench.mixins.base import CLIArg
_NVIDIA_GPU_REGEX = re.compile(r'^[0-9A-Za-z\-:]+$')
def _nvidia_gpu_id(value):
"""argparse type: accept a GPU index, UUID, or PCI bus ID."""
import argparse
if not _NVIDIA_GPU_REGEX.match(value):
... | alubbock/microbench | microbench/mixins/gpu.py | .py | 195d58d8cc20a453 | 7.66 | 20 |
"""Profiling mixins: MBPeakMemory, MBLineProfiler."""
import base64
import pickle
try:
import line_profiler
except ImportError:
line_profiler = None
class MBPeakMemory:
"""Capture peak Python memory allocation during the benchmarked function.
Uses :mod:`tracemalloc` from the Python standard library... | alubbock/microbench | microbench/mixins/profiling.py | .py | 079cc86510de7b29 | 7.66 | 20 |
"""Python environment mixins.
Classes: MBPythonInfo, MBGlobalPackages, MBInstalledPackages, MBCondaPackages.
"""
import inspect
import os
import platform
import shutil
import subprocess
import sys
import types
def _is_microbench_internal(filename):
"""True for source files inside the microbench package, excludi... | alubbock/microbench | microbench/mixins/python.py | .py | 7f28fad072f8e0d5 | 7.66 | 20 |
"""System-info mixins.
Classes: MBHostInfo, MBWorkingDir, MBSlurmInfo, MBCgroupLimits, MBLoadedModules,
MBResourceUsage.
"""
import os
import socket
import sys
try:
import psutil
except ImportError:
psutil = None
try:
import resource as _resource
except ImportError:
_resource = None
class MBHostIn... | alubbock/microbench | microbench/mixins/system.py | .py | 473a5be2cd5a7b01 | 7.66 | 20 |
"""Version-control mixins: MBGitInfo, MBFileHash."""
import os
import subprocess
import sys
from microbench.mixins.base import CLIArg
def _existing_file(value):
"""argparse type: accept an existing file path, reject directories."""
import argparse
if os.path.isdir(value):
raise argparse.Argumen... | alubbock/microbench | microbench/mixins/vcs.py | .py | 533d37c28a0da533 | 7.66 | 20 |
"""Abstract base class for benchmark output sinks."""
class Output:
"""Abstract base class for benchmark output sinks.
Subclass this to implement custom output destinations.
Must implement :meth:`write`. May optionally implement
:meth:`get_results` to allow reading back stored results.
Example::... | alubbock/microbench | microbench/outputs/base.py | .py | 0a88d6c6191d3d0a | 7.66 | 20 |
"""FileOutput — write benchmark results to a file or StringIO buffer."""
import io
import json
try:
import pandas
except ImportError:
pandas = None
from .base import Output
from .utils import _flatten_dict
class FileOutput(Output):
"""Write benchmark results to a file path or file-like object (JSONL fo... | alubbock/microbench | microbench/outputs/file.py | .py | f96c5bcc1cd9ecea | 7.66 | 20 |
"""HttpOutput — POST each benchmark result to an HTTP/HTTPS endpoint."""
import json
import urllib.error
import urllib.request
from .base import Output
class HttpOutput(Output):
"""POST each benchmark result to an HTTP/HTTPS endpoint.
Designed for webhooks and real-time notifications (e.g. Slack, Teams,
... | alubbock/microbench | microbench/outputs/http.py | .py | a2bb5efc3fd13d60 | 7.66 | 20 |
import os
from unittest.mock import patch
from microbench import MBCondaPackages, MicroBench
SAMPLE_CONDA_LIST = """\
# packages in environment at /path/to/env:
#
# Name Version Build Channel
numpy 1.24.3 py311ha0bc626_0 conda-forge
pandas ... | alubbock/microbench | tests/test_conda.py | .py | 90f5a3defd1fa804 | 7.16 | 20 |
from microbench.diff import _align_seqs, _html_diffs, _markup_diff
def test_markup_diff_identical():
"""Identical sequences produce no highlighted spans."""
tokens = ['hello', 'world']
out_a, out_b = _markup_diff(tokens, tokens)
assert out_a == tokens
assert out_b == tokens
def test_markup_diff_... | alubbock/microbench | tests/test_diff.py | .py | 1fa5eb3f8d649be8 | 8.16 | 20 |
import json
import os
import tempfile
import time
from datetime import timedelta
from microbench.livestream import LiveStream
def _write_record(fp, record):
fp.write(json.dumps(record) + '\n')
fp.flush()
def _make_record(**kwargs):
"""Build a v2-schema benchmark record."""
base = {
'call': ... | alubbock/microbench | tests/test_livestream.py | .py | f39cb8d43fd0c0b7 | 7.16 | 20 |
from unittest.mock import patch
import microbench.mixins.system
from microbench import MBHostInfo, MicroBench
def test_mbhostinfo_with_psutil():
"""MBHostInfo captures all five host fields when psutil is available."""
class MyBench(MicroBench, MBHostInfo):
pass
mybench = MyBench()
@mybench... | alubbock/microbench | tests/test_psutil.py | .py | 49703771d855feb4 | 7.16 | 20 |
#!/usr/bin/python3
"""Manage FAUCET config files via RPC (client)."""
import argparse
import inspect
from faucetconfrpc.faucetconfrpc_client_lib import FaucetConfRpcClient
from faucetconfrpc.faucetconfrpc_server import yaml_load, yaml_dump
class ClientError(Exception):
"""Exceptions for client."""
def get_att... | anarkiwi/faucetconfrpc | src/faucetconfrpc/faucetconfrpc_client.py | .py | dbfc7f22b558e2ce | 7.5 | 9 |
"""
MDPSolver
This file defines a `model` class that wraps around the `solvermodule` to create
and solve Markov Decision Processes (MDPs). It provides methods to configure the model,
solve it, and extract the resulting policy and value vectors.
"""
import sys
from mdpsolver import solvermodule
class model:
"""
... | areenberg/MDPSolver | Python/src/mdpsolver/model.py | .py | f9866d55dfab40d2 | 7.5 | 9 |
import configparser
import os
import sys
class FoenixConfig:
"""Configuration data for the FoenixMgr. Exposes the foenix.ini file."""
def __init__(self):
"""Attempt to read and process the config file."""
config = configparser.ConfigParser()
config.read(['foenixmgr.ini', os.path.expand... | pweingar/FoenixMgr | FoenixMgr/foenix_config.py | .py | 7e25f6c570d4f038 | 7.62 | 16 |
import re
class HexFile:
"""Read information from an Intel Hex file."""
file = 0
base_address = 0
handler = 0
def __init__(self):
self.file = 0
self.base_address = 0
self.handler = 0
def open(self, filename):
self.file = open(filename, 'r')
def set_ha... | pweingar/FoenixMgr | FoenixMgr/intelhex.py | .py | d64812771eb3da6f | 7.62 | 16 |
"""Encode host keys as K2 optical-keyboard matrix snapshots."""
OPTICAL_SNAPSHOT_SIZE = 16
# These are the first 64 entries of the K2 microkernel key table. Each
# group of eight is a firmware state row. Hardware delivers the rows in reverse
# order and reverses the column bit numbering.
_OPTICAL_ASCII_INDEX = {
... | pweingar/FoenixMgr | FoenixMgr/keyboard.py | .py | 1c5ca217975afa13 | 7.62 | 16 |
#
# Loader for PGX files
#
import sys
import constants
import foenix_config
from pathlib import Path
class PGXBinFile:
"""Reads information from PGX formated file"""
address_size = 0
data = 0
handler = 0
cpu = ""
config = 0
def __init__(self):
self.config = foeni... | pweingar/FoenixMgr | FoenixMgr/pgx.py | .py | 127127fb2aca9afb | 7.62 | 16 |
#
# Loader for PGZ files
#
import foenix_config
from pathlib import Path
class PGZBinFile:
"""Reads information from PGZ formated file"""
address_size = 0
data = 0
handler = 0
cpu = ""
config = 0
def __init__(self):
self.config = foenix_config.FoenixConfig()
... | pweingar/FoenixMgr | FoenixMgr/pgz.py | .py | 3aa5bc439ff6ed90 | 7.62 | 16 |
import re
class SRECFile:
"""Read information from a Motorola SREC file."""
file = 0
handler = 0
def __init__(self):
self.file = 0
self.handler = 0
def open(self, filename):
self.file = open(filename, 'r')
def set_handler(self, proc):
self.handler = proc
... | pweingar/FoenixMgr | FoenixMgr/srec.py | .py | b8331107a8b132df | 7.62 | 16 |
from pathlib import Path
##
# See: http://www.westerndesigncenter.com/wdc/datasheets/Assembler_Linker.pdf
# page 37
#
# Initial byte 'Z' as signature.
#
# Then for each block:
# 3 byte address
# 3 byte length
# length bytes of data
#
# The final block has an address and length of 0.
#
class WdcB... | pweingar/FoenixMgr | FoenixMgr/wdc.py | .py | e93f8886958d3dad | 7.62 | 16 |
import os
from logging.config import fileConfig
from sqlalchemy import engine_from_config
from sqlalchemy import pool
from sqlmodel import SQLModel
from alembic import context
from app.models import bulk_email, food_tracking, forms, judging, meal, user # noqa: F401
# this is the Alembic Config object, which provide... | hackthevalley/hack-the-back | alembic/env.py | .py | f4262db7b547e2fa | 7.42 | 6 |
"""add account security state
Revision ID: 2c1d5e7a9b30
Revises: bf8b33c13520
Create Date: 2026-07-22
"""
from typing import Sequence, Union
import sqlalchemy as sa
from alembic import op
revision: str = "2c1d5e7a9b30"
down_revision: Union[str, Sequence[str], None] = "bf8b33c13520"
branch_labels: Union[str, Seque... | hackthevalley/hack-the-back | alembic/versions/2c1d5e7a9b30_add_account_security_state.py | .py | a077d4361697c215 | 7.42 | 6 |
"""merge renamed race ethnicity question
Revision ID: 94b0f2d61c7a
Revises: 2c1d5e7a9b30
Create Date: 2026-08-05
"""
from typing import Sequence, Union
import sqlalchemy as sa
from alembic import op
revision: str = "94b0f2d61c7a"
down_revision: Union[str, Sequence[str], None] = "2c1d5e7a9b30"
branch_labels: Union[s... | hackthevalley/hack-the-back | alembic/versions/94b0f2d61c7a_merge_race_ethnicity_question.py | .py | fe559e37498b4f96 | 7.42 | 6 |
"""add bulk email jobs
Revision ID: a31f0e8c4d12
Revises: d72b2ec932bf
"""
from collections.abc import Sequence
import sqlalchemy as sa
from alembic import op
revision: str = "a31f0e8c4d12"
down_revision: str | None = "d72b2ec932bf"
branch_labels: str | Sequence[str] | None = None
depends_on: str | Sequence[str] | ... | hackthevalley/hack-the-back | alembic/versions/a31f0e8c4d12_add_bulk_email_jobs.py | .py | 501a3c87ec2754cd | 7.42 | 6 |
"""enforce unique food tracking per user and meal
Revision ID: c61a1db821ae
Revises: 7f3c1a2d9e40
Create Date: 2026-08-06
"""
from typing import Sequence, Union
from alembic import op
revision: str = "c61a1db821ae"
down_revision: Union[str, Sequence[str], None] = "7f3c1a2d9e40"
branch_labels: Union[str, Sequence[st... | hackthevalley/hack-the-back | alembic/versions/c61a1db821ae_unique_food_tracking.py | .py | 73d48a9a56699275 | 7.42 | 6 |
class DomainError(Exception):
"""Base exception for expected domain and application failures."""
status_code = 400
def __init__(self, detail: str, *, status_code: int | None = None) -> None:
super().__init__(detail)
self.detail = detail
if status_code is not None:
self.... | hackthevalley/hack-the-back | app/core/errors.py | .py | 2fc0e49675352e91 | 7.42 | 6 |
"""Utilities for compatibility with older versions of Python
"""
import os
import sys
import asyncio
import shutil
import warnings
from typing import TypeVar, Literal
__all__ = [
'StartResponse',
'WSGIEnvironment',
'WSGIApplication',
'rmtree',
'HAVE_EXCEPTION_GROUP',
'warnings_warn',
'asyn... | encukou/freezeyt | freezeyt/compat.py | .py | 2be5c4b0ab9361ed | 7.48 | 8 |
from io import BytesIO
from pathlib import PurePosixPath
from typing import Dict, Union, Iterable, Tuple
from .saver import Saver
# Type for holding simulated directory contents.
DictSaverContents = Dict[
str, # filename; maps to either:
Union[
bytes, # file content, or
'DictSaverContents',... | encukou/freezeyt | freezeyt/dictsaver.py | .py | c0dfce0249c3d05e | 7.48 | 8 |
from urllib.parse import unquote
# See doc/encoding-notes.txt for notes on the string encodings.
def decode_input_path(s: str) -> str:
r"""Decodes a path from URL (text) for internal use
Examples:
/čau/☺フ → /čau/☺フ
/%C4%8Dau → /čau
/%8Dau → '/\udc8dau'
"""
return unquote(s, er... | encukou/freezeyt | freezeyt/encoding.py | .py | 724c4947c1ce179a | 7.48 | 8 |
import base64
from pathlib import Path
import collections.abc
from typing import Mapping, Iterator, Tuple, Union
import sys
from freezeyt.util import get_url_part
from freezeyt.types import ExtraFileConfig
if sys.version_info > (3, 8):
from typing import Literal
literal_content = Literal["content"]
liter... | encukou/freezeyt | freezeyt/extra_files.py | .py | 78510fc53a03b571 | 7.48 | 8 |
import os
import stat
import asyncio
from pathlib import Path, PurePosixPath
from . import compat
from .saver import Saver
from .urls import PrefixURL
from typing import Callable, Iterable, BinaryIO
class DirectoryExistsError(Exception):
"""Attempt to overwrite directory that doesn't contain freezeyt output"""
... | encukou/freezeyt | freezeyt/filesaver.py | .py | 737e93160293bcd2 | 7.48 | 8 |
from typing import Iterable, Callable, Optional, TYPE_CHECKING
from freezeyt.urls import AppURL
if TYPE_CHECKING:
from freezeyt.freezer import Freezer, Task
class TaskInfo:
"""Public information about a task that's being saved"""
def __init__(self, task: 'Task'):
self._task = task
self._... | encukou/freezeyt | freezeyt/hooks.py | .py | 47a80514b151e5f5 | 7.48 | 8 |
from mimetypes import guess_type
import json
from typing import Optional, List, Mapping, Dict
import functools
from pathlib import PurePosixPath
from werkzeug.datastructures import Headers
from werkzeug.http import parse_options_header
from freezeyt.util import WrongMimetypeError
from freezeyt.util import import_vari... | encukou/freezeyt | freezeyt/mimetype_check.py | .py | 83828004241b4f83 | 7.48 | 8 |
import xml.etree.ElementTree
from typing import Iterable, BinaryIO, Optional, Any, TYPE_CHECKING
import asyncio
import html5lib
import tinycss2
import tinycss2.ast
import tinycss2_core_attributes
from werkzeug.datastructures import Headers
from werkzeug.http import parse_options_header
from .util import process_pool... | encukou/freezeyt | freezeyt/url_finders.py | .py | 8036ba03b5697054 | 7.48 | 8 |
import urllib.parse
import functools
from typing import Union
from werkzeug.urls import uri_to_iri
from freezeyt.util import RelativeURLError, UnsupportedSchemeError
from freezeyt.util import BadPrefixError, ExternalURLError
from freezeyt.encoding import decode_input_path
def split_iri(url):
return urllib.parse... | encukou/freezeyt | freezeyt/urls.py | .py | e2dbf5fbfd6979e9 | 7.48 | 8 |
import importlib
import concurrent.futures
from typing import Sequence, TYPE_CHECKING, List, Optional, TypeVar
import enum
from werkzeug.http import HTTP_STATUS_CODES
from freezeyt.compat import _MultiErrorBase, HAVE_EXCEPTION_GROUP
from freezeyt.encoding import decode_input_path
if TYPE_CHECKING:
from freezeyt... | encukou/freezeyt | freezeyt/util.py | .py | 10c319ff2c6e1dd4 | 7.48 | 8 |
import io
import sys
import itertools
from typing import List, Dict, Tuple, Optional
import freezeyt
from freezeyt.types import asgi_types
from freezeyt.encoding import encode_wsgi_path
from freezeyt.urls import PrefixURL
from freezeyt.types import WSGIExceptionInfo, WSGIStartResponseResult
from freezeyt.compat import... | encukou/freezeyt | freezeyt/wsgi_to_asgi.py | .py | 6e6a9f6098166a5f | 7.48 | 8 |
from flask import Flask
app = Flask(__name__)
# For verification that this is the unchanged Flask app
app.is_the_fixture_app_2pages = True
@app.route('/')
def index():
"""Show index page of the web app.
And link to the second page.
"""
return """
<html>
<head>
<title>Hello w... | encukou/freezeyt | tests/fixtures/app_2pages/app.py | .py | e350cfdfba1ca5ea | 7.98 | 8 |
from flask import Flask
app = Flask(__name__)
@app.route('/')
def index():
"""Make index page.
Link to the second page.
Link to itself.
"""
return """
<html>
<head>
<title>Hello world</title>
</head>
<body>
Hello world!
<br>
... | encukou/freezeyt | tests/fixtures/app_2pages_cycle/app.py | .py | 810db76bfcf094a6 | 7.98 | 8 |
from flask import Flask, Response, url_for
app = Flask(__name__)
freeze_config = {
'status_handlers': {'3xx': 'follow'},
}
@app.route('/')
def index():
"""Redirect to the second page.
"""
return Response(
"Redirecting to second page...",
status='301 Moved Permanently',
headers=... | encukou/freezeyt | tests/fixtures/app_3pages_redirects/app.py | .py | 8c1a7458166bad12 | 7.98 | 8 |
import falcon
freeze_config = {'cleanup': False}
class Resource(object):
"""Creates Resource object for Falcon App"""
def on_get(self, req, resp):
"""Handles GET requests on index (/)"""
resp.text = """
<html>
<head>
<title>Hello world from Falcon app</title>... | encukou/freezeyt | tests/fixtures/app_cleanup_config/app.py | .py | 6b503ee55346fd3e | 7.98 | 8 |
from flask import Flask, url_for
class TestFailFastError(ValueError):
"""
Error defined for purpose of this test to indetify source of exception easily.
"""
app = Flask(__name__)
freeze_config = {'fail_fast': True}
app.config['PROPAGATE_EXCEPTIONS'] = True
@app.route('/')
def index():
return f"""
... | encukou/freezeyt | tests/fixtures/app_fail_fast/app.py | .py | b3d717c8c05732d3 | 7.98 | 8 |
from flask import Flask, render_template
app = Flask(__name__)
freeze_config = {'extra_pages': ["static/OFL.txt"]}
@app.route("/")
def index():
"""
Demo app for test
HTML template links to CSS which links to a font in a file.
"""
return render_template("index.html")
@app.route("/second_page.ht... | encukou/freezeyt | tests/fixtures/app_links_css/app.py | .py | 24cdeba25cbf2130 | 7.98 | 8 |
from flask import Flask
wsgi_application = Flask(__name__)
@wsgi_application.route('/')
def index():
"""Create the index page of the web app."""
return """
<html>
<head>
<title>Hello world</title>
</head>
<body>
Hello world!
</body>
</html>
... | encukou/freezeyt | tests/fixtures/app_nonstandard_name/application.py | .py | aa434ebd75c1a253 | 7.48 | 8 |
from flask import Flask, url_for
app = Flask(__name__)
@app.route('/')
def index():
"""Show index page of the web app.
And link to the second page.
"""
return f"""
<html>
<head>
<title>Hello world</title>
</head>
<body>
Hello world!
<br... | encukou/freezeyt | tests/fixtures/app_url_for/app.py | .py | 7248380852e87cd9 | 7.98 | 8 |
from flask import Flask, url_for
app = Flask(__name__)
freeze_config = {'prefix': 'http://freezeyt.test:1234/foo/'}
@app.route('/')
def index():
"""Show index page of the web app.
And link to the second page.
"""
return f"""
<html>
<head>
<title>Hello world</title>
</... | encukou/freezeyt | tests/fixtures/app_url_for_port_prefix/app.py | .py | e0491f14dc34cf8d | 7.98 | 8 |
from flask import Flask, url_for
app = Flask(__name__)
freeze_config = {'prefix': 'http://freezeyt.test/foo/'}
@app.route('/')
def index():
"""Show index page of the web app.
And link to the second page.
"""
return f"""
<html>
<head>
<title>Hello world</title>
</head>
... | encukou/freezeyt | tests/fixtures/app_url_for_prefix/app.py | .py | 20cfbb1684325f20 | 7.98 | 8 |
from flask import Flask, url_for
app = Flask(__name__)
freeze_config = {'prefix': 'https://freezeyt.test/foo/'}
@app.route('/')
def index():
"""Show index page of the web app.
And link to the second page.
"""
return f"""
<html>
<head>
<title>Hello world</title>
</head>... | encukou/freezeyt | tests/fixtures/app_url_for_prefix_https/app.py | .py | 674cb078f7e89953 | 7.98 | 8 |
#!/usr/bin/env python3
# vi: ts=4
""" TIC TAC TOE game for WWI
Simple version with one display and light gun
A 3x3 grid of points, crosses and circles is display.
If a point is hit by any light gun,
it is changed to X or O, depending on the player's number.
A point is shown in the b... | gfedorkow/Whirlwind-Instruction-Simulator | Py/Shell/tictactoe.py | .py | 34a4769107531f72 | 7.65 | 19 |
#!/usr/bin/env python3
# vi: ts=4
""" Stand-alone test for the WWI vector interface
Shows some tests, switches to next by key
Last one uses light pen
uses floating point numbers for convenience,
not (yet) fixed point fractions as in WWI
"""
#
import math
import random
import time
import vecI... | gfedorkow/Whirlwind-Instruction-Simulator | Py/Shell/vecIF.py | .py | 042ed0a9cf6dfee8 | 7.65 | 19 |
#!/usr/bin/env python3
# vi: ts=4
""" Basic functions for vector interface
"""
#
import RPi.GPIO as gpio
import spidev
import time
import math
import random
#
version = "0.2c"
# pin definitions in BCM numbering
pin_doMove = 17
pin_doDraw = 22
pin_enZ1 = 18
pin_enZ2 = 23
pin_isKey = 27
pin_isGun1 = 25
pin_isGun2 = 2... | gfedorkow/Whirlwind-Instruction-Simulator | Py/Shell/vecIFbase.py | .py | 5a5a863a9137cb61 | 7.65 | 19 |
from vpython import *
# Bruce Sherwood
N = 4 # N by N by N array of atoms
# Surrounding the N**3 atoms is another layer of invisible fixed-position atoms
# that provide stability to the lattice.
k = 1
m = 1
spacing = 1
atom_radius = 0.3*spacing
L0 = spacing-1.8*atom_radius
V0 = pi*(0.5*atom_radius)**2*L0 # initial vo... | gfedorkow/Whirlwind-Instruction-Simulator | Py/Tester/VPythonDemos_no_notebook/AtomicSolid.py | .py | 09bcef291009fb28 | 7.15 | 19 |
import uuid
import datetime
import traceback
import logging
import aio_pika
from PikaBus.tools import PikaConstants
from PikaBus.abstractions.AbstractPikaProperties import AbstractPikaProperties
ISO_TIME_FORMAT = None
LEGACY_TIME_FORMAT = '%m/%d/%Y %H:%M:%S'
def UtcNow() -> datetime.datetime:
"""
Timezone... | hansehe/PikaBus | PikaBus/PikaProperties.py | .py | 82ba9e7c7d8986dd | 7.5 | 9 |
import json
import logging
from PikaBus.abstractions.AbstractPikaSerializer import AbstractPikaSerializer
class PikaSerializer(AbstractPikaSerializer):
def __init__(self,
contentEncoding: str = 'utf-8',
logger=logging.getLogger(__name__)):
"""
:param str contentEn... | hansehe/PikaBus | PikaBus/PikaSerializer.py | .py | 81f98d8efb3a1b8b | 7.5 | 9 |
import abc
from PikaBus.abstractions.AbstractPikaBus import AbstractPikaBus
class AbstractPikaMessageHandler(abc.ABC):
@abc.abstractmethod
def HandleMessage(self, data: dict, bus: AbstractPikaBus, payload: dict):
"""
Handle an incoming message.
May be implemented as either `def Handl... | hansehe/PikaBus | PikaBus/abstractions/AbstractPikaMessageHandler.py | .py | 42477f87dcbfbebd | 7.5 | 9 |
import abc
class AbstractPikaSerializer(abc.ABC):
@abc.abstractmethod
def Serialize(self, data: dict, payload: dict):
"""
:param dict data: General data holder dictionary
:param payload: payload to serialize
:return: (bytes, str, str) body, contentType, contentEncoding
... | hansehe/PikaBus | PikaBus/abstractions/AbstractPikaSerializer.py | .py | 8c38c525ae3c96c6 | 7.5 | 9 |
import json
from PikaBus.tools import PikaConstants
from PikaBus.abstractions.AbstractPikaBus import AbstractPikaBus
from PikaBus.abstractions.AbstractPikaMessageHandler import AbstractPikaMessageHandler
class PikaMessageHandler(AbstractPikaMessageHandler):
"""An asynchronous AbstractPikaMessageHandler subclass.... | hansehe/PikaBus | tests/PikaMessageHandler.py | .py | 9983921a63f78dbe | 8 | 9 |
r"""
The module :mod:`espm.datasets.base` implements the functions that combines a spatial distribution and associated spectra into a 3D dataset. It also implements the functions to convert the dataset into hyperspy compatible objects.
"""
from pathlib import Path
import hyperspy.api as hs
import numpy as np
from tqd... | adriente/espm | espm/datasets/base.py | .py | 37f64f8beff2a74a | 7.64 | 18 |
import numpy as np
from espm.conf import dicotomy_tol, log_shift, maxit_dichotomy
def dichotomy_simplex(
num, denum, log_shift=log_shift, tol=dicotomy_tol, maxit=maxit_dichotomy
):
"""
Function to solve the num/(x+denum) -1 = 0 equation. Here, x is the Lagragian multiplier which is used to apply the simp... | adriente/espm | espm/estimators/dicotomy.py | .py | 7f6a1683701fdeda | 7.64 | 18 |
"""
Test suite for the docstrings of the espm package.
"""
import doctest
import os
def gen_recursive_file(root, ext):
for root, _, filenames in os.walk(root):
for name in filenames:
if name.lower().endswith(ext):
yield os.path.join(root, name)
def func_test_docstrings(root,... | adriente/espm | tests/test_docstring.py | .py | 20015cf3ead90d95 | 8.14 | 18 |
import numpy as np
from espm.conf import log_shift
from espm.measures import (
Frobenius_loss,
KL_loss_surrogate,
KLdiv,
KLdiv_loss,
find_min_angle,
find_min_MSE,
log_reg,
log_surrogate,
mse,
ordered_angles,
ordered_mse,
spectral_angle,
trace_xtLx,
)
from espm.utils ... | adriente/espm | tests/test_measures.py | .py | 6f2667724ec627cc | 7.14 | 18 |
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