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 python3
"""This entry knows where to download the ImageNet metadata (ground truth, class labels, etc) from, how to unpack it and how to interpret it.
Usage examples :
axs byname base_imagenet_experiment , get ground_truth_path
axs byname base_imagenet_experiment , get cl... | krai/axs | core_collection/workflows_collection/image_classification/base_imagenet_experiment/code_axs.py | .py | c3d2327e81330d9a | 7.42 | 6 |
#!/usr/bin/env python3
import os
import numpy as np
class ImagenetLoader:
def __init__(self, preprocessed_imagenet_dir, input_file_list, height, width, data_layout, normalize_symmetric=None, subtract_mean_bool=None, given_channel_means=None, given_channel_stds=None):
"A trivial constructor"
sel... | krai/axs | core_collection/workflows_collection/image_classification/imagenet_preprocessed_loader/imagenet_loader.py | .py | 9567b9479e7e1b14 | 7.42 | 6 |
#!/usr/bin/env python3
import os
import sys
import numpy as np
from PIL import Image
"""An example Python script that is given its data, necessary Python environment and the output path by wrapping it into an Entry.
Usage examples :
# using all defaults triggers downloading of a 500-sample subset... | krai/axs | core_collection/workflows_collection/image_classification/pillow_process_imagenet/code_axs.py | .py | 8f5b734aeb15f4da | 7.42 | 6 |
#!/usr/bin/env python3
"""A standalone Object Detection program based on ONNX.
Usage examples :
# a short accuracy run:
axs byquery program_output,task=object_detection,framework=onnxrt,num_of_images=20 , mAP
# a short accuracy run with RetinaNet model:
... | krai/axs | core_collection/workflows_collection/object_detection/object_detection_using_onnxrt_py/onnx_detect.py | .py | 8ff31b51bc1c2f49 | 7.42 | 6 |
#!/usr/bin/env python3
import errno
import os
import sys
import json
import numpy as np
import PIL.Image
def generate_file_list(annotation_data, src_images_dir, supported_extensions, first_n=None):
if annotation_data:
sorted_filenames = [ ann_record['file_name'] for ann_record in annotation_data ]
e... | krai/axs | core_collection/workflows_collection/object_detection/pillow_resize_for_object_detection/code_axs.py | .py | 3ebe44ddf318dbde | 7.42 | 6 |
#!/usr/bin/env python3
# Accessing almost any python function or method (collectively called an "action") in CK way
# by feeding it parameters from a list and a dictionary-like object.
#
# Thanks for this SO entry for inspiration:
# https://stackoverflow.com/questions/196960/can-you-list-the-keyword-argume... | krai/axs | function_access.py | .py | ba6a9084ad415ae9 | 7.42 | 6 |
#!/usr/bin/env python3
"""
# Accessing the kernel via API (default and non-default)
if condition:
from kernel import MicroKernel
ak = MicroKernel(name='SpecialKernel')
else:
from kernel import default as ak
"""
__version__ = '0.2.483' # TODO: update with every kernel change
import logging
import os
... | krai/axs | kernel.py | .py | bd446395e56b1e82 | 7.42 | 6 |
"""
Tests for ITMClient initialization and authentication.
"""
import pytest
import responses
from unittest.mock import patch, Mock
from proofpoint_itm.client import ITMClient
class TestClientInitialization:
"""Test client initialization and configuration."""
def test_client_init_with_valid_config(self, ... | drizzo-tech/proofpoint_itm | tests/test_client_init.py | .py | ae895054ca90eadb | 7.92 | 6 |
from __future__ import annotations
from baywatch.bay import Bay
from baywatch.config_control import ConfigUpdateForm, Configuration
from baywatch.version import __version__
import rich
from rich.panel import Panel
from rich.align import Align
from rich.console import RenderableType
from rich.text import Text
from ric... | hdb/baywatch | baywatch/app.py | .py | ab352a861059a8ec | 7.42 | 6 |
#!/usr/bin/env python
from __future__ import annotations
import requests
import urllib.parse
from datetime import datetime
import json
import os
from baywatch.version import __version__
CATEGORIES = os.path.join(os.path.dirname(__file__), 'data/categories.json')
SHORT_CATEGORIES = os.path.join(os.path.dirname(__fil... | hdb/baywatch | baywatch/bay.py | .py | b94dc05f1221f35c | 7.42 | 6 |
from __future__ import annotations
from rich.align import Align
from textual.app import App
from textual.reactive import Reactive
from textual.widgets import Footer, Static
from textual.message import Message
from textual_inputs import TextInput
import os
import json
import asyncio
CONFIG_PATH = os.path.join(os.p... | hdb/baywatch | baywatch/config_control.py | .py | 7e53085852e9e339 | 7.42 | 6 |
"""
Spectral quality evaluation metrics.
Authors: David R. Thompson, david.r.thompson@jpl.nasa.gov
"""
import os
import argparse
import numpy as np
import spectral.io.envi as envi
import matplotlib.pyplot as plt
import logging
def find_header(inputpath:str) -> str:
"""Return the header associated with an image fi... | emit-sds/emit-sds-l2a | spectrum_quality.py | .py | 671c296f4becc851 | 8.02 | 10 |
import hashlib
import json
import os
import sys
from typing import List
from urllib.parse import urlparse, urlunparse
def print_json(data):
"""Pretty print as JSON string"""
print(json.dumps(data, sort_keys=True, indent=2))
def log(*msgs):
"""Print text chunks to stderr"""
print(*msgs, file=sys.stde... | opengisch/qfieldcloud-sdk-python | qfieldcloud_sdk/utils.py | .py | 6b5bbf4f95ba086d | 7.6 | 15 |
"""
Variants of ResidualMLPAutoencoder for TM-negative detection.
All variants share the same IO contract as the baseline so they plug into
_train_deep_binary in run_tm_isoform_model_comparison.py. Configurable
knobs:
* hidden_dim width of residual blocks
* latent_dim bottleneck width (autoencoder)
... | SalomonisLab/altanalyze3 | altanalyze3/components/Daedalus/models/residual_mlp_variants.py | .py | ecd58487c770fc81 | 7.5 | 9 |
"""
baselines.py: Baseline models for Proteus benchmarking.
Three baselines are implemented:
1. SequenceDeltaBaseline
ESM2(alt) − ESM2(ref) → logistic regression per task.
Represents the simplest "what does the sequence difference tell us?" baseline.
2. LengthRatioBaseline
alt_length / ref_length → logistic... | SalomonisLab/altanalyze3 | altanalyze3/components/Proteus/proteus/benchmarking/baselines.py | .py | cf19647e0aa803d1 | 7.5 | 9 |
"""
SyntheticExonSkipDataset: Dataset for self-supervised pretraining.
Loads synthetic exon-skip pairs generated by SyntheticExonSkipGenerator
and their cached embeddings.
"""
from __future__ import annotations
from pathlib import Path
from typing import Any, Dict, List, Optional
import numpy as np
import torch
fro... | SalomonisLab/altanalyze3 | altanalyze3/components/Proteus/proteus/data/pretrain_dataset.py | .py | 1f7f106d0eaf14fb | 7.5 | 9 |
"""
CrossModalFusion: Fuses RNA, protein, disorder, and structural delta
representations into a unified embedding via cross-modal attention and MLP fusion.
"""
from __future__ import annotations
import torch
import torch.nn as nn
from torch import Tensor
class CrossModalFusion(nn.Module):
"""
Fuses four mod... | SalomonisLab/altanalyze3 | altanalyze3/components/Proteus/proteus/delta/cross_modal.py | .py | e9e4f3895b45a346 | 7.5 | 9 |
"""
ReferenceDelta: Asymmetric reference-conditioned delta module.
This is the core novel architectural contribution of Proteus.
"""
from __future__ import annotations
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch import Tensor
class ReferenceDelta(nn.Module):
"""
Asymmetric... | SalomonisLab/altanalyze3 | altanalyze3/components/Proteus/proteus/delta/reference_delta.py | .py | 71d941f5e85272d5 | 7.5 | 9 |
"""
DisorderEncoder: Intrinsic disorder feature extractor.
Attempts to use STARLING first, falls back to metapredict.
Computes a 50-dimensional feature vector summarizing per-residue
disorder scores for downstream use in the Proteus delta model.
"""
from __future__ import annotations
import warnings
from pathlib imp... | SalomonisLab/altanalyze3 | altanalyze3/components/Proteus/proteus/encoders/disorder.py | .py | 18da94e47a65dede | 7.5 | 9 |
"""
ESM2ProteinEncoder: Frozen ESM2 protein language model wrapper.
Encodes protein sequences into 1280-dimensional embeddings using
facebook/esm2_t33_650M_UR50D. Handles absent proteins (NMD isoforms)
via sentinel files and center-crop for long sequences.
"""
from __future__ import annotations
import warnings
from ... | SalomonisLab/altanalyze3 | altanalyze3/components/Proteus/proteus/encoders/protein.py | .py | ef2246fa47321232 | 7.5 | 9 |
"""
OrthrusRNAEncoder: Frozen Orthrus foundation model wrapper for RNA transcript encoding.
Orthrus uses a 6-track Mamba SSM architecture trained on paired RNA transcripts.
This module handles loading, encoding, caching, and graceful fallback.
"""
from __future__ import annotations
import warnings
from pathlib impor... | SalomonisLab/altanalyze3 | altanalyze3/components/Proteus/proteus/encoders/rna.py | .py | 3293e0ad8f231919 | 7.5 | 9 |
"""
topology.py: Sequence-based transmembrane topology and signal peptide prediction.
Uses the same Kyte-Doolittle hydropathy algorithm as Daedalus
build_gencode_protein_sequence_features.py so it can be applied to novel
AltAnalyze3 isoforms not present in the GENCODE FASTA.
CPU-only, no external dependencies beyond ... | SalomonisLab/altanalyze3 | altanalyze3/components/Proteus/proteus/encoders/topology.py | .py | 77985abcd7252203 | 7.5 | 9 |
"""
TaskHeads: Multi-task prediction heads for Proteus.
Ten prediction heads operating on the fused 256-dim representation:
nine binary heads and one 8-class deviation classification head.
New in v1.1:
- localization_preserved : subcellular localization maintained
- tm_insertion_competent : novel TM isoform c... | SalomonisLab/altanalyze3 | altanalyze3/components/Proteus/proteus/heads/task_heads.py | .py | b133a86a8ff271eb | 7.5 | 9 |
"""
ProteusModel: Reference-conditioned isoform function prediction model.
The main trainable model. Uses pre-cached embeddings from frozen foundation
models (Orthrus, ESM2, disorder encoders) as input.
"""
from __future__ import annotations
from pathlib import Path
from typing import Any, Dict, Optional
import tor... | SalomonisLab/altanalyze3 | altanalyze3/components/Proteus/proteus/model.py | .py | ddf244f4f758b127 | 7.5 | 9 |
from abc import ABC, abstractmethod
class CustomSearchAlgorithm(ABC):
"""
Custom search algorithm to be implemented if injecting a custom search class in the properties file
"""
def __init__(self):
"""Initialise the custom search algorithm."""
pass
@abstractmethod
def search(s... | PlanetHunters/tkmatrix | tkmatrix/custom_algorithms/custom_search.py | .py | 5ead1b8674e1d024 | 7.45 | 7 |
"""
Generate sns.regplot for each metric (volume, length, max_axial_damage_ratio) manual vs SCIseg 3D lesion segmentation
BEFORE (phase1) and AFTER (phase3) active learning.
The script:
- fetch subjects from the provided /results folders (each one for a specific seed)
- keep only the unique subjects (to avoid duplic... | ivadomed/model_seg_sci | correlations_with_clinical_scores/02a_generate_regplot_manual_vs_predicted.py | .py | 9c39896ed3cf310b | 7.64 | 18 |
"""
Combine XLSX files (one per subject) with lesion metrics generated by SCT's sct_analyze_lesion into a single CSV file
for easier manipulation and visualization.
Namely, the script:
- reads XLSX files (located under /results) with lesion metrics computed by SCT's sct_analyze_lesion
(one XLSX file per subject)
... | ivadomed/model_seg_sci | midsagittal_measures/02_combine_xlsx_files.py | .py | 43161efff07fe3c7 | 7.64 | 18 |
"""
Figure 3.
Generate scatter plots and Bland-Altman plots between manual and automatic lesion metrics.
The script generates a single figure with 3 scatter plots (first row) and 3 Bland-Altman plots (second row).
The script:
- reads CSV file with lesion metrics with _sct and _manual suffixes.
- for each lesion metri... | ivadomed/model_seg_sci | midsagittal_measures/03_generate_lesion_metric_plots.py | .py | 565f5e3505b179f2 | 7.64 | 18 |
import pandas as pd
CLINICAL_SCORES_MAX = {
'uems': 50, # Maximum UEMS score
'lems': 50, # Maximum LEMS score
'ms': 100, # Maximum Total Motor Score
'pp': 112, # Maximum Pinprick Score
'lt': 112 # Maximum Light-Touch Score
}
METHOD_TO_TITLE = {
'GT': 'Semi-automatic (manual lesion ma... | ivadomed/model_seg_sci | midsagittal_measures/utils.py | .py | edd56f953d759f4c | 7.64 | 18 |
"""
This (cool) script generates a LaTeX table with the lesion-wise metrics for the SCIsegV2 paper.
The input to the script is a CSV file containing the metrics across all the sites and models, which is
output by the 'plot_metrics_per_site.py' script in the 'model_seg_sci/testing' directory.
The table is printed to th... | ivadomed/model_seg_sci | testing/generate_table1.py | .py | 78e6d883e6988b8a | 8.14 | 18 |
"""
This script iterates through all the predictions and keeps only the largest connected object in each lesion mask.
"""
import os
import glob
import subprocess
from concurrent.futures import ThreadPoolExecutor
from tqdm import tqdm
# NOTE: this file has to be moved to dataset-conversion folder to make it run. the fol... | ivadomed/model_seg_sci | testing/keep_largest_object.py | .py | 145852157e842e5a | 8.14 | 18 |
"""
This script generates bar plots for the selected metrics across all sites and models. It automatically
iterates through all the available folds, plots the metrics and also saves them into a CSV file.
The output CSV file is then used to generate the lesion-wise metrics table for the SCIsegV2 paper.
"""
import os
im... | ivadomed/model_seg_sci | testing/plot_metrics_per_site.py | .py | 0f0a778bf153311d | 8.14 | 18 |
import os
import re
def fetch_filename_details(filename_path):
"""
Get dataset name, subject name, session number (if exists), file ID and filename from the input nnUNet-compatible
filename or file path. The function works both on absolute file path as well as filename
:param filename_path: input nif... | ivadomed/model_seg_sci | testing/test_utils.py | .py | 8a97e9cd80c07d75 | 7.14 | 18 |
"""
Combine XLS files (one per subject) with lesion metrics computed using SCT's sct_analyze_lesion into a single CSV file
for easier manipulation and visualization.
The script:
- read XLS files (located under /results) with lesion metrics (computed using sct_analyze_lesion for GT or predicted
using our 3D nnUNet mo... | ivadomed/model_seg_sci | tissue_bridges/02_read_xls_files.py | .py | cf311885bc12e76a | 7.64 | 18 |
"""
Compare tissue bridges obtained using different methods (manual, semi-automatic, automatic)
The script:
- computes normality test
- computes Kruskal-Wallis H-test for the tissue bridges obtained using three methods:
1. manual: manually segmented intramedullary lesions and manually measured tissue bridges
... | ivadomed/model_seg_sci | tissue_bridges/03_compute_stats.py | .py | 41103d5376c4c0d0 | 7.64 | 18 |
#!/usr/bin/env python
import importlib
import inspect
from typing import Any
__all__: list[str] = []
CORE_MODULES: list[str] = [
"gitlab_api.gitlab_input_models",
"gitlab_api.gitlab_response_models",
"gitlab_api.api_client",
]
OPTIONAL_MODULES = {
"gitlab_api.gitlab_gql": "gql",
"gitlab_api.agen... | Knuckles-Team/gitlab-api | gitlab_api/__init__.py | .py | 9007da7afde4610d | 7.52 | 10 |
"""GitLab Authentication Module.
Authentication priority:
1. **OIDC Delegation** — If ``ENABLE_DELEGATION`` is active, exchanges
the IdP-issued user token for a downstream GitLab access token
via RFC 8693 Token Exchange using the shared ``delegated_auth`` helper.
2. **Fixed Credentials** — Falls back to ``GITLAB... | Knuckles-Team/gitlab-api | gitlab_api/auth.py | .py | 6c72053dba7078c3 | 7.52 | 10 |
"""Multi-tenant GitLab instance registry.
The single source of truth for *which* GitLab instances exist is the
agent-utilities XDG config (`~/.config/agent-utilities/config.json`,
`gitlab_instances`) — the same list the KG GitLab indexer reads — so one config
drives both code/metadata indexing AND every `gitlab-api` c... | Knuckles-Team/gitlab-api | gitlab_api/instances.py | .py | f3bfb0c30ee4ccf8 | 7.52 | 10 |
import sys
import os
import pytest
NUMPY_AVAILABLE = False
try:
import numpy as np
NUMPY_AVAILABLE = True
except ImportError:
np = None
sys.path.append(os.path.join(os.path.dirname(__file__), "../src/"))
from mathjson_solver import create_solver
def _create_numpy_test_cases():
"""Create test cas... | LongenesisLtd/mathjson-solver | tests/test_TrapezoidalIntegratel.py | .py | da32dddac5a753d4 | 7.07 | 13 |
import sys
import os
import pytest
import datetime
sys.path.append(os.path.join(os.path.dirname(__file__), "../src/"))
from mathjson_solver import create_solver
class TestDatetimeReturnTypes:
"""Test that datetime functions return strings by default."""
def test_today_returns_string(self):
solver =... | LongenesisLtd/mathjson-solver | tests/test_datetime.py | .py | 1c12613958991b21 | 7.07 | 13 |
import sys
import os
import pytest
sys.path.append(os.path.join(os.path.dirname(__file__), "../src/"))
from mathjson_solver import create_solver
def _create_Interpolate_test_cases():
"""Create test cases for Interpolate function."""
test_cases = [
# Basic linear interpolation
(
{... | LongenesisLtd/mathjson-solver | tests/test_interpolate.py | .py | 6acead7955abdd58 | 8.07 | 13 |
"""
Simple test cases for Reduce functionality
These tests verify that Reduce works with three variables:
- accumulator: carries state between iterations
- current_item: the current element from the array being reduced
- index: the current position in the array (0-based)
"""
import sys
import os
import pytest
sys.pa... | LongenesisLtd/mathjson-solver | tests/test_reduce_simple.py | .py | 73815b1a63af9d2b | 7.07 | 13 |
"""
Test demonstrating state tuples with Reduce for stateful accumulation
This test validates that we can use Reduce with tuple states to maintain
multiple accumulator variables, which is essential for implementing
the NCI discrete approximation method.
"""
import sys
import os
import pytest
sys.path.append(os.path.... | LongenesisLtd/mathjson-solver | tests/test_state_tuples_reduce.py | .py | 476782e169cc91c5 | 7.07 | 13 |
#!/usr/bin/python3
#
# Copyright (c) 2020 Red Hat, Inc.
#
# 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 ... | oVirt/python-ovirt-engine-sdk4 | examples/cancel_transfer.py | .py | c9bfb3a7908611e1 | 7.64 | 18 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
#
# Copyright (c) 2021 Red Hat, Inc.
#
# 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 re... | oVirt/python-ovirt-engine-sdk4 | examples/checkpoints.py | .py | 971645ab8a10b174 | 7.64 | 18 |
"""
pip install uvicorn[standard]
pip install fastapi
"""
from fastapi import APIRouter
from pydantic import BaseModel
from wayfarer import routing, loader, io
import logging
from . import utils
log = logging.getLogger("web")
router = APIRouter()
class ShortestPath(BaseModel):
path: list[int | str]
edits... | compassinformatics/wayfarer | demo/edges.py | .py | a80f372bdb3b6123 | 7.59 | 14 |
r"""
A FastAPI router to handle solving
upstream and downstream paths on a river network
"""
from fastapi import APIRouter
import logging
import osmnx as ox
import networkx as nx
from shapely.geometry import LineString, Point, Polygon
from wayfarer import loader
from pydantic import BaseModel
from functools import lru... | compassinformatics/wayfarer | demo/isochrones.py | .py | 6ed1c5f3bac347e8 | 7.59 | 14 |
"""
pip install uvicorn[standard]
pip install fastapi
"""
from fastapi import APIRouter
from pydantic import BaseModel
from wayfarer import routing, loader, io, functions, splitter
from wayfarer.splitter import SPLIT_KEY_SEPARATOR
import logging
import json
from shapely.geometry import shape
from collections import d... | compassinformatics/wayfarer | demo/routes.py | .py | 267563905fe81c99 | 7.59 | 14 |
import osmnx as ox
from wayfarer import loader
from osmnx import convert, projection
def download_osm():
"""
Download roads from OSM centered around Riga, Latvia
This only needs to be run once.
"""
location_point = (56.94105, 24.09682)
# get roads within a distance of 500m from this point
... | compassinformatics/wayfarer | docs/examples/create_network.py | .py | 655add34ac4f05b6 | 7.59 | 14 |
r"""
C:\VirtualEnvs\wayfarer\Scripts\activate
pip install numpy
pip install GDAL --extra-index-url https://pypi.compass.ie
pip install fiona --extra-index-url https://pypi.compass.ie
pip install shapely --extra-index-url https://pypi.compass.ie
pip install git+https://github.com/compassinformatics/wayfarer@main
C:\Vi... | compassinformatics/wayfarer | scripts/ptals.py | .py | 3c2e47a230ba0fdd | 7.59 | 14 |
from wayfarer import loader
def simple_features():
"""
Create a list of features representing a network
There are 3 features in a flat line running from 0,0 to 300,0
Each feature is 100 units in length
"""
return [
{
"properties": {"EDGE_ID": 1},
"geometry": {"t... | compassinformatics/wayfarer | tests/helper.py | .py | bdb16e135b536f12 | 7.09 | 14 |
"""
This file contains a collection of various network forms
"""
from networkx import MultiDiGraph, MultiGraph
from wayfarer import (
EDGE_ID_FIELD,
LENGTH_FIELD,
NODEID_FROM_FIELD,
NODEID_TO_FIELD,
loader,
)
def tuples_to_net(tuples, graph_type=MultiGraph):
"""
Takes in a list of tuples ... | compassinformatics/wayfarer | tests/networks.py | .py | a7d58b6e083af7eb | 7.09 | 14 |
"""
pytest -v tests/test_functions.py
"""
import logging
import pytest
import wayfarer
from wayfarer import loader, functions, Edge, WITH_DIRECTION_FIELD
import networkx
@pytest.mark.parametrize("use_reverse_lookup", [(True), (False)])
def test_get_edge_by_key(use_reverse_lookup):
recs = [{"EDGE_ID": 1, "LEN_": ... | compassinformatics/wayfarer | tests/test_functions.py | .py | 9a1f822639617fb0 | 7.09 | 14 |
import pytest
from wayfarer import linearref
from shapely.geometry import LineString, Point, MultiLineString
from shapely.wkt import loads
from decimal import Decimal
def test_invalid_lr():
ls = LineString([(0, 0), (0, 100)])
with pytest.raises(ValueError):
linearref.create_line(ls, -1, 100)
def te... | compassinformatics/wayfarer | tests/test_linearref.py | .py | d9bf2191c179dd67 | 7.09 | 14 |
"""
pytest -v tests/test_splitting.py
"""
import logging
import pytest
from wayfarer import routing, splitter, Edge, WITH_DIRECTION_FIELD
from wayfarer.splitter import SPLIT_KEY_SEPARATOR
from tests import networks
from networkx import NetworkXNoPath, NodeNotFound
def test_solve_all_simple_paths():
net = network... | compassinformatics/wayfarer | tests/test_routing.py | .py | cb7bf65253337b17 | 7.09 | 14 |
"""
pytest -v tests/test_routing_ordered_path.py
"""
import logging
import pytest
from wayfarer import Edge, routing, loops, functions
from tests import networks
import wayfarer
from networkx.exception import NetworkXError
def test_get_path_ends():
edges = [
Edge(0, 1, key="A", attributes={"EDGE_ID": "A... | compassinformatics/wayfarer | tests/test_routing_ordered_path.py | .py | 1f75c5502b8fc54c | 7.09 | 14 |
"""
pytest -v tests/test_splitting.py
"""
import logging
import pytest
from wayfarer import splitter, functions, loader, routing
from tests.helper import simple_features
from shapely import LineString
@pytest.mark.parametrize("use_reverse_lookup", [(True), (False)])
def test_split_network_edge(use_reverse_lookup):
... | compassinformatics/wayfarer | tests/test_splitting.py | .py | 18e838a4546a995d | 7.09 | 14 |
from __future__ import annotations
from typing import NamedTuple
__version__ = "0.13.3"
LENGTH_FIELD = "LEN_"
EDGE_ID_FIELD = "EDGE_ID"
OFFSET_FIELD = "OFFSET"
NODEID_FROM_FIELD = "NODEID_FROM"
NODEID_TO_FIELD = "NODEID_TO"
WITH_DIRECTION_FIELD = "WITH_DIRECTION"
GEOMETRY_FIELD = "geometry"
SPLIT_POINT_ID_FIELD ... | compassinformatics/wayfarer | wayfarer/__init__.py | .py | ce61a155494f275b | 7.59 | 14 |
r"""
This module contains functions relating to linear referencing.
Requires the Shapely module
Reference links:
+ https://pypi.org/project/ligeos/
+ https://www.gaia-gis.it/fossil/libspatialite/wiki?name=VirtualRouting
+ http://plugins.qgis.org/plugins/lrs/
+ http://blazek.github.io/lrs/release/help.1.2.0/index.html... | compassinformatics/wayfarer | wayfarer/linearref.py | .py | ba590e7c62c0e6bf | 7.59 | 14 |
from __future__ import annotations
import logging
import wayfarer
from math import hypot
from wayfarer import (
EDGE_ID_FIELD,
LENGTH_FIELD,
NODEID_FROM_FIELD,
NODEID_TO_FIELD,
GEOMETRY_FIELD,
)
from wayfarer import functions
import pickle
from typing import Iterable
from networkx import MultiGraph,... | compassinformatics/wayfarer | wayfarer/loader.py | .py | b0b3d4d59d3f94a4 | 7.59 | 14 |
"""
Module containing functions relating to loops
"""
from __future__ import annotations
import networkx
from networkx import cycles
from wayfarer import Edge, functions
import logging
from typing import Iterable
log = logging.getLogger("wayfarer")
def is_loop(net: networkx.MultiGraph | networkx.MultiDiGraph) -> b... | compassinformatics/wayfarer | wayfarer/loops.py | .py | 39adfd45eae0e962 | 7.59 | 14 |
from __future__ import annotations
import logging
import itertools
import networkx
from wayfarer import functions, LENGTH_FIELD, Edge
from networkx.algorithms import eulerian_path
from networkx import NetworkXNoPath, NodeNotFound
class MultipleEnds(Exception):
pass
log = logging.getLogger("wayfarer")
def solv... | compassinformatics/wayfarer | wayfarer/routing.py | .py | 0a691a0f83af1372 | 7.59 | 14 |
"""
This module handles splitting existing edges, and creating new nodes
to join the split edges
"""
from __future__ import annotations
import logging
import uuid
from collections import defaultdict, OrderedDict
from wayfarer import functions, linearref
import networkx
from wayfarer import (
LENGTH_FIELD,
OFFS... | compassinformatics/wayfarer | wayfarer/splitter.py | .py | 923cdbd2df99d678 | 7.59 | 14 |
"""
A collection of functions to help validate a network
"""
from __future__ import annotations
from collections import Counter
import networkx
def duplicate_keys(
net: networkx.MultiGraph | networkx.MultiDiGraph,
) -> list[int | str]:
"""
Find any duplicate keys in the network
Keys must be unique fo... | compassinformatics/wayfarer | wayfarer/validator.py | .py | 82f7c3e71ee68f04 | 7.59 | 14 |
"""
Author: Michel Peltriaux
Organization: Spatial data infrastructure Rhineland-Palatinate, Germany
Contact: michel.peltriaux@vermkv.rlp.de
Created on: 25.08.20
"""
import os
import subprocess
import sys
from pathlib import Path
from django.core.management import BaseCommand, call_command
class Command(BaseCommand... | mrmap-community/mrmap | backend/MrMap/management/commands/dev_messages.py | .py | 69896aeb63ee1bcc | 7.54 | 11 |
"""
Author: Michel Peltriaux
Organization: Spatial data infrastructure Rhineland-Palatinate, Germany
Contact: michel.peltriaux@vermkv.rlp.de
Created on: 02.07.20
"""
from django.core.management import BaseCommand
from django.db import transaction
from MrMap.management.commands.setup_settings import LICENCES
class C... | mrmap-community/mrmap | backend/MrMap/management/commands/load_licences.py | .py | 959b33ce3af65beb | 7.54 | 11 |
import warnings
from functools import wraps
from django.conf import settings
from django.db import connection
from django.test.utils import CaptureQueriesContext
def warn_on_queries(fn):
"""
Decorator to warn if the wrapped function executes any database queries.
Usage:
@warn_on_queries
... | mrmap-community/mrmap | backend/extras/decorators.py | .py | 3448c1173a7af485 | 7.54 | 11 |
from django.db.models.enums import ChoicesType, IntegerChoices
class SmartIntegerChoicesMeta(ChoicesType):
"""Erweitert Django’s IntegerChoices-Meta, um Label-Lookup zu erlauben."""
def __call__(cls, value, *args, **kwargs):
# Wenn int → normales Verhalten
if isinstance(value, int):
... | mrmap-community/mrmap | backend/extras/enums.py | .py | 70be682ce757d3b6 | 7.54 | 11 |
import logging
import os.path
import time
from typing import Type, TypeVar, Iterator, Union
import pykube
import pytest
import yaml
from deepdiff import DeepDiff
from deepdiff.helper import NotPresent
from pykube.objects import APIObject
from pytest_helm_charts.clusters import Cluster
from pytest_helm_charts.flux.helm... | giantswarm/gitops-template | tests/ats/test_flux_objects.py | .py | fcff6e1df27da82d | 7.15 | 19 |
import logging
from homeassistant.components.light import (
LightEntity,
ColorMode,
)
from datetime import timedelta
from homeassistant.config_entries import ConfigEntry
from homeassistant.core import HomeAssistant
from homeassistant.helpers.entity_platform import AddEntitiesCallback
from homeassistant... | MrSleeps/Juwel-HeliaLux-Home-Assistant-Custom-Component | custom_components/juwel_helialux/light.py | .py | a7f75a7b7f05b10f | 7.65 | 19 |
import logging
from homeassistant.components.number import NumberEntity
from homeassistant.const import UnitOfTime
from homeassistant.helpers.storage import Store
from homeassistant.util import slugify
from .const import DOMAIN
import asyncio
_LOGGER = logging.getLogger(__name__)
async def async_setup_entry... | MrSleeps/Juwel-HeliaLux-Home-Assistant-Custom-Component | custom_components/juwel_helialux/number.py | .py | 95733da61aad6183 | 7.65 | 19 |
# Original pyHelialux by moretea (https://github.com/moretea/pyHelialux)
# Updated to work with Home Assistant by MrSleeps (https://github.com/MrSleeps/pyHelialuxHomeAssistant)
import aiohttp
import asyncio
import logging
import re
_LOGGER = logging.getLogger(__name__)
# Code added by @gehrausundspiel
REQ... | MrSleeps/Juwel-HeliaLux-Home-Assistant-Custom-Component | custom_components/juwel_helialux/pyhelialux/pyHelialux.py | .py | 82ae7eb8859fc6b8 | 7.65 | 19 |
import logging
from homeassistant.components.select import SelectEntity
from homeassistant.helpers.update_coordinator import CoordinatorEntity
from homeassistant.helpers.entity import EntityCategory
from homeassistant.util import slugify
from .const import DOMAIN, CONF_TANK_NAME
_LOGGER = logging.getLogger(__na... | MrSleeps/Juwel-HeliaLux-Home-Assistant-Custom-Component | custom_components/juwel_helialux/select.py | .py | e0e516ea10b5d0f1 | 7.65 | 19 |
import logging
from homeassistant.components.sensor import (
SensorEntity,
SensorStateClass,
SensorEntityDescription,
)
from homeassistant.helpers.update_coordinator import CoordinatorEntity
from homeassistant.helpers.entity import EntityCategory
from homeassistant.helpers.entity_platform import Add... | MrSleeps/Juwel-HeliaLux-Home-Assistant-Custom-Component | custom_components/juwel_helialux/sensor.py | .py | 50840683807aa865 | 7.65 | 19 |
import logging
from homeassistant.components.switch import SwitchEntity
from homeassistant.util import slugify
from .const import DOMAIN
import asyncio
_LOGGER = logging.getLogger(__name__)
async def async_setup_entry(hass, entry, async_add_entities):
"""Set up switches for Helialux via config entry."""
... | MrSleeps/Juwel-HeliaLux-Home-Assistant-Custom-Component | custom_components/juwel_helialux/switch.py | .py | 6294dc91bc4fc77c | 7.65 | 19 |
# -*- coding: utf-8 -*-
"""Helper code for file system (directory/file) manipulation
The routines in this package provides helpers for creating files from templates, for example,
and creating directories and files while printing log messages.
"""
import datetime
import difflib
import os
import shutil
from .logging i... | bihealth/snappy-pipeline | snappy_pipeline/apps/impl/fsmanip.py | .py | 74a678a2b1afa7a9 | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Utilities for processing YAML configuration"""
import re
from collections.abc import MutableMapping, MutableSequence
from ruamel.yaml.comments import CommentedMap, CommentedSeq
def remove_yaml_comment_lines(yaml_str):
"""
:param yaml_str: YAML configuration as string. Expected use... | bihealth/snappy-pipeline | snappy_pipeline/apps/impl/yaml_utils.py | .py | 3e28c971d0c4b8ad | 7.52 | 10 |
#!/usr/bin/env python
"""Pull biomedsheet sample sheet from SODAR API."""
import argparse
import re
import sys
import requests
#: The URL template to use.
URL_TPL = "https://%(sodar_host)s/samplesheets/api/remote/get/%(project_uuid)s/%(api_key)s"
#: Template for the to-be-generated file.
HEADER_TPL = (
"[Metada... | bihealth/snappy-pipeline | snappy_pipeline/apps/snappy_pull_sheet.py | .py | fe1ea769c381e0bf | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Tool for refreshing pipeline_job.sh file for a step.
Global configuration will not be touched.
"""
import argparse
import os
import sys
import ruamel.yaml as ruamel_yaml
from .. import __version__
from .impl.fsmanip import assume_path_existing, create_directory, create_from_tpl
from .impl... | bihealth/snappy-pipeline | snappy_pipeline/apps/snappy_refresh_step.py | .py | 3213e9ae042d13ec | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Tool for starting a pipeline step instance
The tool will update the existing global configuration with sensible default
settings for the given step.
"""
import argparse
import io
import os
import sys
import ruamel.yaml as ruamel_yaml
from ruamel.yaml.comments import CommentedMap
from .. i... | bihealth/snappy-pipeline | snappy_pipeline/apps/snappy_start_step.py | .py | 8137b3db11ec957d | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Basic utility code for snappy_pipeline"""
import os
import sys
import warnings
from collections import OrderedDict
from collections.abc import MutableMapping
from copy import deepcopy
from typing import TYPE_CHECKING, Any, AnyStr, Dict
import ruamel.yaml as ruamel_yaml
from .models import ... | bihealth/snappy-pipeline | snappy_pipeline/base.py | .py | 8653d1488b2150ac | 7.52 | 10 |
import enum
import json
import re
import types
import typing
from enum import Enum
from inspect import isclass
from io import StringIO
from typing import Annotated
import ruamel
import typing_extensions
from annotated_types import Predicate
from pydantic import BaseModel, ConfigDict, Field
from pydantic_core import Py... | bihealth/snappy-pipeline | snappy_pipeline/models/__init__.py | .py | 55faee877d76abe6 | 7.52 | 10 |
from typing import Annotated
from pydantic import ConfigDict, Field
from snappy_pipeline.models import SnappyModel
class TargetIntervalEntry(SnappyModel):
"""
The following will match both the stock IDT library kit and the ones
with spike-ins seen fromr Yale genomics. The path above would be
mapped... | bihealth/snappy-pipeline | snappy_pipeline/models/gcnv.py | .py | ac34b6466e32a059 | 7.52 | 10 |
import pydantic
from pydantic import BaseModel
def validate_tools():
def ensure_tools_are_configured(instance):
for tool in instance.tools:
if not getattr(instance, str(tool)):
raise ValueError(f"Tool {tool} not configured")
return instance
return pydantic.model_va... | bihealth/snappy-pipeline | snappy_pipeline/models/validators.py | .py | 45da7cfea841dd86 | 7.52 | 10 |
"""Commonly used code and types"""
import re
import typing
from itertools import chain
from snakemake.io import Wildcards
from snappy_wrappers.resource_usage import ResourceUsage
#: Type for a Snaekmake key/path dict.
SnakemakeDict = typing.Dict[str, typing.Union[typing.List[str], str]]
#: Type for a Snakemake inp... | bihealth/snappy-pipeline | snappy_pipeline/workflows/abstract/common.py | .py | d133a06adb424182 | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Generic variant annotation step
The assumption is that variant annotation is similar for all kind of variants,
germline or somatic.
This implementation attepmts to provide annotation for a set of variants stored in vcf
format, using a generic sample sheet (_i.e._ without restriction on tumo... | bihealth/snappy-pipeline | snappy_pipeline/workflows/any_variant_annotation/__init__.py | .py | 0aa2baf72718265e | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Abstract class for somatic & germline variant callers"""
import os
from snakemake.io import expand
from biomedsheets.shortcuts import GenericSampleSheet
from snappy_pipeline.utils import listify
from snappy_pipeline.workflows.abstract import BaseStep
from snappy_pipeline.workflows.ngs_mapp... | bihealth/snappy-pipeline | snappy_pipeline/workflows/any_variant_calling/__init__.py | .py | ffbe1ffa4062deea | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Implementation of the gCNV COHORT mode methods - used to build models."""
from snakemake.io import expand, touch
from snappy_pipeline.utils import dictify, listify
from snappy_pipeline.workflows.common.gcnv.gcnv_common import GcnvCommonStepPart
class AnnotateGcMixin:
"""Mixin providin... | bihealth/snappy-pipeline | snappy_pipeline/workflows/common/gcnv/gcnv_build_model.py | .py | b4c8e999b6b34462 | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Implementation of the gCNV common methods."""
from collections import OrderedDict
from snappy_pipeline.utils import dictify
from snappy_pipeline.workflows.abstract import BaseStepPart, ResourceUsage
class GcnvWarning(UserWarning):
"""Base class for custom warning of the gCNV integrati... | bihealth/snappy-pipeline | snappy_pipeline/workflows/common/gcnv/gcnv_common.py | .py | d2dadc6759ce616b | 7.52 | 10 |
from importlib.resources import files
import numpy as np
import pandas as pd
from smart_data_hub.property2dataframe import load_rock_property
def load_default_df(lithologies):
"""Load default rock property DataFrame for the given lithologies.
Args:
lithologies (list): list of lithologies.
Return... | mbd-rwth/smart_data_hub | src/smart_data_hub/add_default.py | .py | e2a6389eb8a77bc6 | 7.54 | 11 |
import pandas as pd
def string_in_strings(target, strings) -> bool:
"""Check if 'target' exists in 'strings'.
Args:
target (str): string to search for.
strings (list, str, None): list or string containing multiple entries
Returns:
bool: True if target is found in the strings, Fal... | mbd-rwth/smart_data_hub | src/smart_data_hub/data_tagging.py | .py | d519cad639570958 | 7.54 | 11 |
import yaml
# keep the flow sequence style when writing as a YAML sequence
class List_flow_sequence(list):
pass
def flow_sequence_representer(dumper, data):
return dumper.represent_sequence("tag:yaml.org,2002:seq", data, flow_style=True)
def convert_to_flow_sequence(unit_base):
"""Convert unit_base to... | mbd-rwth/smart_data_hub | src/smart_data_hub/dataframe2yaml.py | .py | 8bb52ed6ecb98fb2 | 7.54 | 11 |
import os
from importlib.resources import files
import gempy as gp
import numpy as np
import pyvista as pv
from gempy_engine.core.data.stack_relation_type import StackRelationType
def generate_geomodel(
site_orientation_path,
site_points_path,
extent_geometry,
refinement,
resolution,
structura... | mbd-rwth/smart_data_hub | src/smart_data_hub/generate_geomodel.py | .py | 56172ad0e83b1796 | 7.54 | 11 |
import uuid
from importlib.resources import files
from ruamel.yaml import YAML
from smart_data_hub.load_path import get_path_in_dir
# Preserve quotes and save None to null in YAML
yaml = YAML()
yaml.preserve_quotes = True
yaml.representer.add_representer(
type(None),
lambda dumper, _: dumper.represent_scalar("... | mbd-rwth/smart_data_hub | src/smart_data_hub/generate_id.py | .py | 77268ae3bfa27f2a | 7.54 | 11 |
import numpy as np
import scipy.constants as sc
def convert_value(type, convert_ratio, value):
"""Convert a value based on its type and a conversion ratio.
Args:
type (scalar): The type of the value.
convert_ratio (float): The conversion ratio to apply.
value (float, str, dict, None):... | mbd-rwth/smart_data_hub | src/smart_data_hub/hydraulic2intrinic.py | .py | 91847bbae58eed19 | 7.54 | 11 |
import numpy as np
import pandas as pd
from scipy import stats
from smart_data_hub.hydraulic2intrinic import hydraulic2intrinic
from smart_data_hub.property2dataframe import combine_rock_site_property
def value_best_mask(input_pd_df):
"""Filter data in the input DataFrame that contains the best estimate value.
... | mbd-rwth/smart_data_hub | src/smart_data_hub/recommended_CV.py | .py | 9d75b6e4b3d04e4f | 7.54 | 11 |
import os
from importlib.resources import files
from pathlib import Path
import pytest
import pyvista as pv
from smart_data_hub.load_path import get_path_in_dir
from smart_data_hub.merge_method import value_empty_mask
from smart_data_hub.merge_method import value_invalid_mask
from smart_data_hub.property2dataframe impo... | mbd-rwth/smart_data_hub | tests/test_property_data_validation.py | .py | 54a8e017e05bea7c | 7.04 | 11 |
# Copyright 2022-2026 Fictionlab sp. z o.o.
#
# 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 use, copy, modify, merge, publi... | LeoRover/leo_robot-ros2 | leo_fw/leo_fw/board.py | .py | 910554781a9fc731 | 7.52 | 10 |
# Copyright 2026 Fictionlab sp. z o.o.
#
# 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 use, copy, modify, merge, publish, d... | LeoRover/leo_robot-ros2 | leo_fw/leo_fw/console.py | .py | d3031a841813c548 | 7.52 | 10 |
# Copyright 2022-2026 Fictionlab sp. z o.o.
#
# 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 use, copy, modify, merge, publi... | LeoRover/leo_robot-ros2 | leo_fw/leo_fw/utils.py | .py | a1681752768f730f | 7.52 | 10 |
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