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 |
|---|---|---|---|---|---|---|
"""Generates SLURM submission scripts for HTPolyNet runs.
Author: Cameron F. Abrams <cfa22@drexel.edu>
"""
# #SBATCH directives emitted in this fixed order; any other key in the slurm
# config dict is passed through verbatim with underscores mapped to hyphens.
_KNOWN_DIRECTIVES = [
('job_name', 'job-name')... | cameronabrams/htpolynet | src/htpolynet/external/slurm.py | .py | 16f9cac8da855e00 | 7.77 | 33 |
"""Generate mol2 input files for constituents from SMILES strings.
Two code paths are supported:
* ``obabel`` — uses OpenBabel's ``--gen3d`` to embed coordinates, then renames
atoms by 1-based mol2 index according to ``rename_atoms``. Always available
(the container ships OpenBabel; ``htpolynet`` requires it on ... | cameronabrams/htpolynet | src/htpolynet/external/smiles_input.py | .py | bedf827441d2aa92 | 7.77 | 33 |
"""Handles identification of available software needed by HTPolyNet.
Author: Cameron F. Abrams <cfa22@drexel.edu>
"""
import glob
import json
import logging
import os
import subprocess
from ..utils.stringthings import my_logger
logger = logging.getLogger(__name__)
_ambertools = ['antechamber', 'tleap', 'parmchk2']
... | cameronabrams/htpolynet | src/htpolynet/external/software.py | .py | 533775be43672e6f | 7.77 | 33 |
"""Manages bidirectional interatomic bondlists.
Author: Cameron F. Abrams <cfa22@drexel.edu>
"""
import logging
import networkx as nx
import numpy as np
import pandas as pd
logger=logging.getLogger(__name__)
class Bondlist:
""" The member "B" is a dictionary keyed on atom index whose values of lists
of ato... | cameronabrams/htpolynet | src/htpolynet/geometry/bondlist.py | .py | a6ce80ade2072f3f | 7.77 | 33 |
"""Handles ring-piercing determinations.
Author: Cameron F. Abrams <cfa22@drexel.edu>
"""
# Pierced rings
# Cameron F. Abrams cfa22@drexel.edu
#
# How to use (suggested):
#
# 1. Create a list of rings from a coordinate snapshot:
# Suppose X is an Nx3 numpy array ordered such
# that each consecutive group of six ... | cameronabrams/htpolynet | src/htpolynet/geometry/ring.py | .py | 76931a8e93d14584 | 7.77 | 33 |
"""GROMACS .gro and HTPolyNet .grx file reader/writer.
Author: Cameron F. Abrams <cfa22@drexel.edu>
"""
import logging
import os
import numpy as np
import pandas as pd
logger = logging.getLogger(__name__)
GRO_ATTRIBUTES = [
'resNum', 'resName', 'atomName', 'globalIdx',
'posX', 'posY', 'posZ', 'velX', 'velY'... | cameronabrams/htpolynet | src/htpolynet/io/gro.py | .py | 406b002254c82653 | 7.77 | 33 |
"""Implements a simple checkpointing scheme using a wrapper.
Author: Cameron F. Abrams <cfa22@drexel.edu>
"""
import functools
import logging
import os
import yaml
logger=logging.getLogger(__name__)
class Checkpoint:
default_filename='checkpoint_state.yaml'
def __init__(self,input_dict={}):
self.my_... | cameronabrams/htpolynet | src/htpolynet/utils/checkpoint.py | .py | 41364827c2bbefb4 | 7.77 | 33 |
"""Some convenient tools for handling pandas dataframes in the context of htpolynet coordinates.
Author: Cameron F. Abrams <cfa22@drexel.edu>
"""
import logging
import pandas as pd
logger=logging.getLogger(__name__)
def get_row_as_string(df:pd.DataFrame,attributes):
"""Returns the selected rows as a string, wi... | cameronabrams/htpolynet | src/htpolynet/utils/dataframetools.py | .py | f91b349dbc8fa47a | 7.77 | 33 |
#!/usr/bin/env python3
"""Validate and execute the published tutorial notebooks."""
from __future__ import annotations
import argparse
import copy
import os
from pathlib import Path
import nbformat
from nbclient import NotebookClient
TUTORIAL_NOTEBOOKS = (
"01_working_with_tmol.ipynb",
"02_gpu_batching.ipyn... | uw-ipd/tmol | .github/scripts/smoke_tutorial_notebooks.py | .py | 6b92a9844c17bb7f | 7.97 | 88 |
#!/usr/bin/env python3
import sqlite3
import argparse
import json
import subprocess
import os
import sys
import copy
def main():
parser = argparse.ArgumentParser(
description="Convert nvprof output to Google Event Trace compatible JSON."
)
parser.add_argument("filename")
args = parser.parse_a... | uw-ipd/tmol | dev/bin/nvprof2json.py | .py | b24b1a6bc6073e28 | 7.97 | 88 |
"""Sphinx configuration for the tmol documentation."""
from __future__ import annotations
import os
import sys
import tomllib
from pathlib import Path
import nbformat
from docutils import nodes
from sphinx.application import Sphinx
DOCS_DIR = Path(__file__).resolve().parent
REPO_ROOT = DOCS_DIR.parent
sys.path.inse... | uw-ipd/tmol | docs/conf.py | .py | 5a8f0eb3044274d4 | 7.97 | 88 |
"""
Runtime loader for tmol's pre-compiled C++/CUDA extensions.
Adapted from xformers/_cpp_lib.py. Loads the ``tmol._C`` shared library
which registers all TORCH_LIBRARY ops into ``torch.ops.tmol_*`` namespaces.
Usage::
from tmol._cpp_lib import _ensure_loaded
_ensure_loaded()
# Now torch.ops.tmol_ljlk.... | uw-ipd/tmol | tmol/_cpp_lib.py | .py | f8420b73ac89b824 | 7.97 | 88 |
"""Helpers to choose between precompiled extensions and JIT dev mode."""
from __future__ import annotations
import logging
import os
from tmol._cpp_lib import (
TmolExtensionIncompatibleError,
TmolExtensionNotBuiltError,
_ensure_loaded,
)
logger = logging.getLogger(__name__)
def _env_flag(name: str) -... | uw-ipd/tmol | tmol/_load_ext.py | .py | 4df24b4f766c451e | 7.97 | 88 |
import numpy
def eye4():
"""Create the identity homogeneous transform
Only necessary because numpy.eye(4, dtype=numpy.float32)
is strangely unsupported in numpy"""
return numpy.eye(4, dtype=numpy.float32)
# m = numpy.zeros((4, 4), dtype=numpy.float32)
# m[0, 0] = 1
# m[1, 1] = 1
# m[... | uw-ipd/tmol | tmol/chemical/_ideal_coords.py | .py | bb6de7ecaca697f1 | 7.97 | 88 |
from typing import Dict, Tuple
from tmol.database._yaml import safe_load
import attr
import cattr
@attr.s(auto_attribs=True, slots=True, frozen=True)
class NaTorsionGlobalParams:
sdev_sugar: float
sdev_chi: float
sdev_backbone: Tuple[float, ...] # alpha beta gamma delta epsilon zeta
weight_bb: float... | uw-ipd/tmol | tmol/database/scoring/_na_torsion.py | .py | 938b5ec519f50cde | 7.97 | 88 |
"""Posit Connect Cloud environment configuration and authentication.
Connect Cloud is a distinct deployment target from Posit Connect and
shinyapps.io. It authenticates with OAuth 2.0 against ``login.posit.cloud``,
using either the device code flow (interactive) or the client credentials
grant (non-interactive, for CI... | posit-dev/rsconnect-python | rsconnect/connect_cloud.py | .py | 9bd5f57a21db1d8c | 7.79 | 37 |
"""Detects the configuration of a Node.js environment.
Given a directory containing a package.json file, this module inspects
the local Node.js/npm installation and returns information needed to
build the deployment manifest.
"""
from __future__ import annotations
import json
import locale
import os
import subproces... | posit-dev/rsconnect-python | rsconnect/environment_node.py | .py | f023259d6771694a | 7.79 | 37 |
"""Detects R dependencies from a project's renv.lock file.
Given a directory that contains an renv.lock lockfile, this module parses it
into the R version and package metadata needed for the deployment manifest.
The parse is pure: it reads only renv.lock and never invokes R or inspects
locally installed R packages. Th... | posit-dev/rsconnect-python | rsconnect/environment_r.py | .py | 6fbc6b33670bfbee | 7.79 | 37 |
"""
Git metadata detection utilities for bundle uploads
"""
from __future__ import annotations
import subprocess
from typing import Optional
from urllib.parse import urlparse
from .log import logger
def _run_git_command(args: list[str], cwd: str) -> Optional[str]:
"""
Run a git command and return its outpu... | posit-dev/rsconnect-python | rsconnect/git_metadata.py | .py | b8bee9ae83cded17 | 7.79 | 37 |
"""
Json Web Token (JWT) utilities
"""
from __future__ import annotations
import base64
import binascii
import os
from datetime import datetime, timedelta, timezone
from typing import Any, Optional
import jwt
from .exception import RSConnectException
from .http_support import HTTPResponse, JsonData
from .models imp... | posit-dev/rsconnect-python | rsconnect/json_web_token.py | .py | 8faf7627f98a0c88 | 7.79 | 37 |
"""
Logging wrapper and shared instance
"""
from __future__ import annotations
import json
import logging
import sys
from functools import partial, wraps
from typing import TYPE_CHECKING, Any, Callable, Literal, Optional, Protocol, TypeVar
if sys.version_info >= (3, 10):
from typing import Concatenate, ParamSpec... | posit-dev/rsconnect-python | rsconnect/log.py | .py | 92c3252b3766fedf | 7.79 | 37 |
"""
Support for detecting various information from python projects metadata.
Metadata can only be loaded from static files (e.g. pyproject.toml, setup.cfg, etc.)
but not from setup.py due to its dynamic nature.
"""
import configparser
import dataclasses
import pathlib
import re
import typing
from collections.abc impo... | posit-dev/rsconnect-python | rsconnect/pyproject.py | .py | 73d4f8a237aa02db | 7.79 | 37 |
# The contents of this file are copied from:
# https://github.com/posit-dev/py-shiny/blob/feb4cb7f872922717c39753514ae2d7fa32f10a1/shiny/express/_is_express.py
from __future__ import annotations
import ast
import re
import sys
from pathlib import Path
from typing import Literal, cast
__all__ = ("is_express_app",)
... | posit-dev/rsconnect-python | rsconnect/shiny_express.py | .py | e3e2f5faffa53d99 | 7.79 | 37 |
#!/usr/bin/env python
"""
Environment data class abstraction that is usable as an executable module
```bash
python -m rsconnect.subprocesses.inspect_environment
```
"""
from __future__ import annotations
import argparse
import datetime
import json
import locale
import os
import tempfile
import re
import subprocess
i... | posit-dev/rsconnect-python | rsconnect/subprocesses/inspect_environment.py | .py | f23e6f62ffb80ab3 | 8.29 | 37 |
"""
Utility functions related to packages and versions.
"""
from __future__ import annotations
import re
from typing import NamedTuple, cast
from typing import Literal
import semver
from .environment import Environment
from .log import logger
from .models import AppMode, AppModes
ComparisonOperator = Literal[">="... | posit-dev/rsconnect-python | rsconnect/utils_package.py | .py | feeda72be1afd7c1 | 7.79 | 37 |
from __future__ import annotations
import os
from typing import Any, Optional
import click
from rsconnect.connect_cloud import is_connect_cloud_url
from rsconnect.exception import RSConnectException
def get_parameter_source_name_from_ctx(
var_or_param_name: str,
ctx: Optional[click.Context],
) -> str:
... | posit-dev/rsconnect-python | rsconnect/validation.py | .py | d5e2c11ba3f3d321 | 7.79 | 37 |
"""Background version update check against PyPI.
Checked only on deploy commands. The latest known version is cached on disk and
refreshed at most once per :data:`_CACHE_TTL_SECONDS` in a background thread, so a
warm cache adds no network traffic and no latency and prints on every exit path
(including fast failures). ... | posit-dev/rsconnect-python | rsconnect/version_check.py | .py | 2ca52441c8385ad0 | 7.79 | 37 |
"""Run a scaffolded quickstart project locally and probe whether it boots.
Test-internal helpers used by ``test_quickstart_per_mode_boot_smoke`` to
verify that the local-run command documented for each mode (the one
``rsconnect quickstart`` prints under "To run locally:") actually starts
the project. Owns:
- free-por... | posit-dev/rsconnect-python | tests/_local_run.py | .py | 2d32e39ac01ca282 | 8.29 | 37 |
import sys
from typing import Iterator
import pytest
def _no_system_keyring() -> Iterator[None]:
"""Generator behind the fixture, importable so tests can drive its teardown."""
absent = object()
previous = sys.modules.get("keyring", absent)
sys.modules["keyring"] = None # type: ignore[assignment]
... | posit-dev/rsconnect-python | tests/conftest.py | .py | 62a38185dbf50e80 | 8.29 | 37 |
from pathlib import Path
from tempfile import NamedTemporaryFile
from unittest import TestCase, mock
from rsconnect.certificates import read_certificate_file
from rsconnect.exception import RSConnectException
class ParseCertificateFileTestCase(TestCase):
def test_parse_certificate_file_ca_bundle(self):
r... | posit-dev/rsconnect-python | tests/test_certificates.py | .py | f23d19b264233440 | 7.29 | 37 |
import contextlib
import sys
import types
from typing import Generator, Iterator
import pytest
from tests.conftest import _no_system_keyring
def _drain(gen: Iterator[None]) -> None:
try:
next(gen)
except StopIteration:
pass
@pytest.fixture
def reinstate_marker() -> Iterator[None]:
# Re... | posit-dev/rsconnect-python | tests/test_conftest.py | .py | 7940d40d0ee2da2f | 7.29 | 37 |
"""
Tests for git metadata detection and integration
"""
import subprocess
import tempfile
from pathlib import Path
import pytest
from rsconnect.git_metadata import (
detect_git_metadata,
get_git_branch,
get_git_commit,
get_git_remote_url,
has_uncommitted_changes,
is_git_repo,
normalize_g... | posit-dev/rsconnect-python | tests/test_git_metadata.py | .py | 30472b67df23ad4c | 8.29 | 37 |
import json
import os
from docutils import nodes
from docutils.parsers.rst import directives
from docutils.statemachine import StringList
from sphinx.directives.code import CodeBlock
from . import utils
class HTTPExample(CodeBlock):
required_arguments = 1
option_spec = {
# Unused. Just to skip remov... | ProzorroUKR/openprocurement.api | docs/source/_exts/prozorro/httpexample/directives.py | .py | d49e8a1398d419af | 7.7 | 24 |
import random
from collections import deque
from time import sleep
from data import USERS, bid, tender
from locust import HttpUser, constant, task
TENDERS_URL = "/api/2.5/tenders"
TENDER_URL = None
DS_URL = "http://ds.k8s.prozorro.gov.ua/upload"
# test process data
BIDS = deque(maxlen=200)
class User(HttpUser):
... | ProzorroUKR/openprocurement.api | loadtesting/bids.py | .py | 89864c95bcd3f66e | 7.2 | 24 |
import random
from collections import deque
from data import USERS
from locust import HttpUser, constant, task
PLANS_URL = "/api/2.5/plans"
# test process data
CREATED_PLANS = deque(maxlen=200)
PLANS = deque(maxlen=10000)
class User(HttpUser):
wait_time = constant(0)
def __init__(self, *args, **kwargs):
... | ProzorroUKR/openprocurement.api | loadtesting/consistency.py | .py | 88b31b3c02d71092 | 7.2 | 24 |
import random
from collections import deque
from data import USERS
from locust import HttpUser, constant, task
PLANS_URL = "/api/2.5/plans"
# test process data
CREATED_PLANS = deque(maxlen=200)
PLANS = deque(maxlen=10000)
class User(HttpUser):
wait_time = constant(0)
def __init__(self, *args, **kwargs):
... | ProzorroUKR/openprocurement.api | loadtesting/plans.py | .py | e5efb1d5e88a56fe | 7.2 | 24 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | src/braket/pennylane_plugin/ahs_translation.py | .py | 28311997c3806a25 | 7.84 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/integ_tests/test_adjoint_gradient.py | .py | d1449d2005148ea5 | 8.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/integ_tests/test_batch.py | .py | d1612fee51c6b8eb | 7.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/integ_tests/test_counts.py | .py | fea69ad2fb5c90e2 | 8.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/integ_tests/test_expval.py | .py | 913c515427868d81 | 7.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/integ_tests/test_integration.py | .py | b7d725266050f7e0 | 8.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/integ_tests/test_sample.py | .py | ef3364f512ec5f8f | 7.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/integ_tests/test_shadow_expval.py | .py | f15c3d0d1548d71e | 8.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/integ_tests/test_state.py | .py | c81902e84895ba7d | 8.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/integ_tests/test_tracking.py | .py | 663672c6a0f8c898 | 8.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/integ_tests/test_var.py | .py | eb9ad81a7a2cc651 | 7.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/unit_tests/test_ahs_device.py | .py | 5cfd939ff6a2ee64 | 7.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/unit_tests/test_ops.py | .py | 78e51d4527b7e1f0 | 8.34 | 47 |
# Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"). You
# may not use this file except in compliance with the License. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file accompany... | amazon-braket/amazon-braket-pennylane-plugin-python | test/unit_tests/test_translation.py | .py | c269ab94b5f9a9e7 | 7.34 | 47 |
"""unittest tests that require a live Drupal at https://islandora.io. In most cases, the host URL,
credentials, etc. are in a configuration file referenced in the test.
This test file contains tests for paged content. Files islandora_tests.py, islandora_tests_paged_check.py,
and islandora_tests_hooks.py also contain t... | mjordan/islandora_workbench | tests/islandora_tests_paged_content.py | .py | 2ae148062c0d50d7 | 7.2 | 24 |
from abc import abstractmethod, ABC
import os
import pytest
from ruamel.yaml import YAML
import sys
import tempfile
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
from workbench_utils import get_nid_from_url_without_config, value_is_numeric
""" The full hostname and scheme of the Drupal... | mjordan/islandora_workbench | tests/workbench_test_class.py | .py | 4752472eeb38e92b | 8.2 | 24 |
"""High-level API for alternative identifiers."""
import logging
from collections.abc import Mapping
from functools import lru_cache
from pydantic import ValidationError
from typing_extensions import Unpack
from .utils import SimpleReferenceHint, _get_pi, get_version_from_kwargs
from ..constants import GetOntologyKw... | biopragmatics/pyobo | src/pyobo/api/alts.py | .py | 344a031644ae2257 | 7.94 | 76 |
"""High-level API for edges."""
import networkx as nx
import pandas as pd
from tqdm import tqdm
from typing_extensions import Unpack
from pyobo.api.names import get_ids
from pyobo.api.utils import get_version_from_kwargs
from pyobo.constants import (
GetOntologyKwargs,
check_should_cache,
check_should_for... | biopragmatics/pyobo | src/pyobo/api/edges.py | .py | 5809571fa0f8ff0f | 7.94 | 76 |
"""High-level API for hierarchies."""
from __future__ import annotations
import logging
import warnings
from collections.abc import Iterable
from functools import lru_cache
from typing import Literal, NotRequired, cast
import networkx as nx
from typing_extensions import Unpack
from .edges import get_edges
from .nam... | biopragmatics/pyobo | src/pyobo/api/hierarchy.py | .py | 52b53cfc2a8296b3 | 7.94 | 76 |
"""High-level API for metadata."""
import logging
from functools import lru_cache
from pystow.cache import CachedPydantic
from typing_extensions import Unpack
from ..constants import GetOntologyKwargs, check_should_force
from ..getters import get_ontology
from ..identifier_utils import wrap_norm_prefix
from ..utils.... | biopragmatics/pyobo | src/pyobo/api/metadata.py | .py | 1c16701f88f3bc80 | 7.94 | 76 |
"""High-level API for nomenclature."""
from __future__ import annotations
import logging
import subprocess
from collections.abc import Callable, Mapping
from functools import lru_cache
from typing import TypeVar
import curies
import pandas as pd
import ssslm
from pystow.cache import Cached
from ssslm import LiteralM... | biopragmatics/pyobo | src/pyobo/api/names.py | .py | b9005c69cfff82d1 | 7.94 | 76 |
"""High-level API for properties."""
import logging
from collections.abc import Mapping
import pandas as pd
from tqdm import tqdm
from typing_extensions import Unpack
from .utils import SimpleReferenceHint, _get_pi, get_version_from_kwargs
from ..constants import (
GetOntologyKwargs,
check_should_cache,
... | biopragmatics/pyobo | src/pyobo/api/properties.py | .py | f27678141c4f0127 | 7.94 | 76 |
"""High-level API for relations."""
import logging
from collections.abc import Mapping
from functools import lru_cache
import pandas as pd
from typing_extensions import Unpack
from .utils import get_version_from_kwargs
from ..constants import (
RELATION_COLUMNS,
RELATION_ID,
RELATION_PREFIX,
SOURCE_I... | biopragmatics/pyobo | src/pyobo/api/relations.py | .py | f38d6c2d401ff5ac | 7.94 | 76 |
"""High-level API for typedefs."""
import logging
from functools import lru_cache
import pandas as pd
from typing_extensions import Unpack
from .utils import get_version_from_kwargs
from ..constants import GetOntologyKwargs, check_should_cache, check_should_force
from ..getters import get_ontology
from ..identifier_... | biopragmatics/pyobo | src/pyobo/api/typedefs.py | .py | 1d3ba2d2497f5442 | 7.94 | 76 |
"""High-level API for synonyms."""
import logging
import warnings
from collections.abc import Callable, Mapping
from functools import lru_cache
import bioregistry
import pandas as pd
import sssom_pydantic
from curies import ReferenceTuple
from sssom_pydantic import SemanticMapping
from sssom_pydantic.io import Cached... | biopragmatics/pyobo | src/pyobo/api/xrefs.py | .py | 8719501bb59170d6 | 7.94 | 76 |
"""CLI for PyOBO."""
import logging
import os
from collections.abc import Iterable
from functools import lru_cache
from operator import itemgetter
import click
from .database import main as database_main
from .lookup import lookup
from .obo_lexical_review import obo_lexical_review
from ..constants import GLOBAL_SKIP... | biopragmatics/pyobo | src/pyobo/cli/cli.py | .py | 9ac4443b61267946 | 7.94 | 76 |
"""Pipeline for extracting all xrefs from OBO documents available."""
from __future__ import annotations
import gzip
import logging
from collections.abc import Iterable
from typing import cast
from tqdm.auto import tqdm
from typing_extensions import Unpack
from ..api import (
get_edges_df,
get_id_definition... | biopragmatics/pyobo | src/pyobo/cli/database_utils.py | .py | 23aca0abd5530af6 | 7.94 | 76 |
# /// script
# requires-python = ">=3.11"
# dependencies = [
# "click>=8.3.1",
# "obographs>=0.0.8",
# "pyperclip>=1.11.0",
# "robot-obo-tool>=0.0.1",
# "ssslm[gilda-slim]>=0.1.3",
# "tabulate>=0.9.0",
# "tqdm>=4.67.3",
# ]
# ///
"""Implement lexical review for an ontology."""
from __futur... | biopragmatics/pyobo | src/pyobo/cli/obo_lexical_review.py | .py | 806303a310ee0347 | 7.94 | 76 |
"""Constants for PyOBO."""
from __future__ import annotations
import logging
import re
from collections.abc import Callable
from pathlib import Path
from typing import TYPE_CHECKING, Literal, NamedTuple, NotRequired, TypeAlias
import pystow
from typing_extensions import TypedDict
if TYPE_CHECKING:
import sssom_... | biopragmatics/pyobo | src/pyobo/constants.py | .py | a07120575aaaa04e | 7.94 | 76 |
"""Utilities for handling prefixes."""
from __future__ import annotations
import logging
from collections.abc import Callable
from functools import lru_cache, wraps
from typing import Annotated, Any, ClassVar, Concatenate, ParamSpec, TypeVar
import bioregistry
import click
from bioregistry.constants import FailureRe... | biopragmatics/pyobo | src/pyobo/identifier_utils/api.py | .py | d23d0e9f1bf9bf99 | 7.94 | 76 |
"""Mocks for PyOBO."""
from __future__ import annotations
import unittest.mock
from collections.abc import Mapping
from typing import Any, TypeAlias, TypeVar
from unittest import mock
import pandas as pd
from pyobo.constants import XREF_COLUMNS
__all__ = [
"get_mock_get_xrefs_df",
"get_mock_id_alts_mapping... | biopragmatics/pyobo | src/pyobo/mocks.py | .py | 76ffb3c1735046b0 | 7.94 | 76 |
"""Use synonyms from OBO to normalize names."""
from __future__ import annotations
from collections.abc import Iterable
from typing import Literal, overload
from typing_extensions import Unpack
from .api import get_grounder
from ..constants import GetOntologyKwargs
from ..struct import Reference
__all__ = [
"g... | biopragmatics/pyobo | src/pyobo/ner/normalizer.py | .py | 39349b3f3cdae8b5 | 7.94 | 76 |
"""Tools for loading entry points."""
from __future__ import annotations
from collections.abc import Callable, Iterable, Mapping
from functools import lru_cache
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from .struct import Obo
__all__ = [
"has_nomenclature_plugin",
"iter_nomenclature_plugins",
... | biopragmatics/pyobo | src/pyobo/plugins.py | .py | 0c9149dc4a206f4b | 7.94 | 76 |
"""Resource utilities for PyOBO."""
from __future__ import annotations
from collections.abc import Sequence
from functools import lru_cache
import click
import pandas as pd
from more_click import verbose_option
from zenodo_client import Zenodo
from .constants import (
ALTS_DATA_RECORD,
ALTS_FILE,
DEFINI... | biopragmatics/pyobo | src/pyobo/resource_utils.py | .py | d14797c6b85b42b4 | 7.94 | 76 |
"""Loading of the NCBI Taxonomy names."""
import csv
import gzip
from collections.abc import Mapping
from functools import lru_cache
from pathlib import Path
import requests
__all__ = [
"get_ncbitaxon_id",
"get_ncbitaxon_name",
"load_ncbitaxon",
]
HERE = Path(__file__).parent.resolve()
PATH = HERE.joinp... | biopragmatics/pyobo | src/pyobo/resources/ncbitaxon.py | .py | 92484774b0f45247 | 7.94 | 76 |
"""Loading of the relations ontology names."""
import csv
import os
from collections.abc import Mapping
from functools import lru_cache
import requests
from curies import ReferenceTuple
__all__ = [
"load_ro",
]
HERE = os.path.abspath(os.path.dirname(__file__))
PATH = os.path.join(HERE, "ro.tsv")
URL = "http://p... | biopragmatics/pyobo | src/pyobo/resources/ro.py | .py | f8b1f5c2016b02e7 | 7.94 | 76 |
"""Loading of the relations ontology names."""
from __future__ import annotations
import csv
import os
from functools import lru_cache
import requests
__all__ = [
"get_so_name",
"load_so",
]
HERE = os.path.abspath(os.path.dirname(__file__))
SO_PATH = os.path.join(HERE, "so.tsv")
SO_JSON_URL = "https://gith... | biopragmatics/pyobo | src/pyobo/resources/so.py | .py | 6ec012f622c2fdaf | 7.94 | 76 |
"""Converter for the Antibody Registry.
TODO use API https://www.antibodyregistry.org/api/antibodies?page=1&size=100
"""
import logging
from collections.abc import Iterable, Mapping
import pandas as pd
from bioregistry.utils import removeprefix
from tqdm.auto import tqdm
from pyobo import Obo, Reference, Term
from ... | biopragmatics/pyobo | src/pyobo/sources/antibodyregistry.py | .py | 19b996f6f2754d7b | 7.94 | 76 |
"""Get compartments from BiGG."""
from collections.abc import Iterable
from bioversions.utils import get_soup
from pyobo import Obo, Reference, Term
__all__ = [
"BiGGCompartmentGetter",
"get_compartments",
]
DATA_URL = "http://bigg.ucsd.edu/compartments/"
PREFIX = "bigg.compartment"
GO_MAPPING: dict[str, R... | biopragmatics/pyobo | src/pyobo/sources/bigg/bigg_compartment.py | .py | 3d62e9697c1c9303 | 7.94 | 76 |
"""Converter for models in BiGG."""
import json
import logging
from collections.abc import Iterable
from pyobo.resources.ncbitaxon import get_ncbitaxon_id
from pyobo.struct import Obo, Term
from pyobo.utils.path import ensure_path
__all__ = [
"BiGGModelGetter",
]
logger = logging.getLogger(__name__)
URL = "http... | biopragmatics/pyobo | src/pyobo/sources/bigg/bigg_model.py | .py | 9f8dd98076c2512e | 7.94 | 76 |
"""Converter for BiGG."""
from collections.abc import Iterable
import pandas as pd
from pydantic import ValidationError
from tqdm import tqdm
from pyobo.sources.bigg.bigg_metabolite import _parse_dblinks, _parse_model_links, _split
from pyobo.struct import Obo, Reference, Term
from pyobo.struct.typedef import enable... | biopragmatics/pyobo | src/pyobo/sources/bigg/bigg_reaction.py | .py | e3948821a7b7d86b | 7.94 | 76 |
"""
Event aggregator for computing portfolio state from events.
"""
import copy
from datetime import date
from typing import Dict, List, Tuple
from .schemas import (
CASH_EVENT_TYPES, DEFAULT_ACCOUNT, Event, EventType, ShareState,
PurchaseState, EstateState, Timeline, InKindFlow, CashFlow, CashState,
)
clas... | pbrissaud/suivi-bourse | app/src/events/aggregator.py | .py | d47bb3b227f71a3d | 7.95 | 80 |
"""
Event loader for CSV and XLSX files.
"""
import csv
from datetime import datetime
from pathlib import Path
from typing import List, Optional
from .schemas import Event, EventType
class EventLoaderError(Exception):
"""Exception raised when loading events fails."""
pass
class EventLoader:
"""Loads p... | pbrissaud/suivi-bourse | app/src/events/loader.py | .py | ad3022d68d5536db | 7.95 | 80 |
"""
Data schemas for the events module.
"""
import bisect
from dataclasses import dataclass, field
from datetime import date, datetime # noqa: F401 — used in dataclass field annotations (eager-evaluated on Python <3.14)
from enum import Enum
from typing import Dict, List, Optional, Set, Tuple, Union
# Canonical acc... | pbrissaud/suivi-bourse | app/src/events/schemas.py | .py | 1959ed38f60f3bf9 | 7.95 | 80 |
"""
File watcher for hot-reload of event files.
"""
import threading
from pathlib import Path
from typing import Callable, Optional
from watchdog.observers import Observer
from watchdog.events import FileSystemEventHandler, FileSystemEvent
class EventFileHandler(FileSystemEventHandler):
"""Handler for event fil... | pbrissaud/suivi-bourse | app/src/events/watcher.py | .py | 48e2b52f927cdf5b | 7.95 | 80 |
"""
Money-weighted performance: XIRR (annualized) and TWR (time-weighted, base 100).
Pure domain module: ``Timeline`` × an injected price callable → performance
results. It knows nothing about InfluxDB or yfinance — the only dependency on the
outside world is the ``price_at(symbol, date) -> Optional[float]`` callable.... | pbrissaud/suivi-bourse | app/src/performance.py | .py | c4e3dd6482964a2e | 7.95 | 80 |
"""
Prometheus Exporter Module for SuiviBourse
Exposes the legacy ``sb_*`` Prometheus gauges on an HTTP ``/metrics`` endpoint,
kept for backward compatibility with pre-InfluxDB deployments. It runs in
parallel with the InfluxDB writer and only reflects the current snapshot of
each share (no historical backfill — Prome... | pbrissaud/suivi-bourse | app/src/prometheus_exporter.py | .py | e2ac56e18ea7de56 | 7.95 | 80 |
"""
Market-aware per-symbol scheduling — pure cadence & context decisions.
Mirror of ``performance.py``: no InfluxDB, no yfinance, ``now`` injected. The
two functions here drive the self-rescheduling per-symbol scrape jobs in
``main.py`` without touching the outside world, so they are exhaustively
testable against dic... | pbrissaud/suivi-bourse | app/src/scheduling.py | .py | e6339a8453728d8d | 7.95 | 80 |
"""
Shared pytest fixtures for the SuiviBourse test suite.
`pytest.ini` sets ``pythonpath = src`` so tests (and this conftest) import the
application modules exactly like ``app/src/main.py`` does::
import main
import influxdb_writer
from events import EventLoader, EventValidator, EventAggregator
from ... | pbrissaud/suivi-bourse | app/tests/conftest.py | .py | 66adfa27ee7ae4c8 | 8.45 | 80 |
""" Function in this file judge triplets, based on ground-truth embedding and possible noise patterns. """
from typing import Dict, Callable, Optional, Union
from sklearn.utils import check_random_state, check_array
from sklearn.metrics import pairwise
import numpy as np
from cblearn import utils
from cblearn.dataset... | cblearn/cblearn | cblearn/datasets/_triplet_response.py | .py | 7fcea087ba87f9eb | 7.67 | 21 |
""" Functions in this file return sampled triplets with answers, based on an artificial embedding and noise.
Usually they combine functions from _triplet_indices and _triplet_answers
and are used as a high-level interface to create artificial datasets.
"""
import numpy as np
from typing import Union
from ._t... | cblearn/cblearn | cblearn/datasets/_triplet_simulation.py | .py | a55b09cedf7b220d | 7.67 | 21 |
import zipfile
import pytest
from cblearn.datasets._material_similarity import _archive_root
def _zip_with_names(path, names):
with zipfile.ZipFile(path, 'w') as zf:
for name in names:
zf.writestr(name, 'x')
return zipfile.ZipFile(path)
def test_archive_root_reads_the_single_top_level_... | cblearn/cblearn | cblearn/datasets/tests/test_material_similarity.py | .py | 8fee4deda8241697 | 8.17 | 21 |
import numpy as np
import pytest
from cblearn import datasets
def test_make_triplets_raises():
with pytest.raises(ValueError):
datasets.make_random_triplet_indices(n_objects=12, size=100000, repeat=False)
def test_make_random_triplets_all():
triplets = datasets.make_random_triplet_indices(n_objects... | cblearn/cblearn | cblearn/datasets/tests/test_triplet_indices.py | .py | 261a03666a3aa2d4 | 7.17 | 21 |
from typing import Optional
import warnings
import numpy as np
from sklearn.base import TransformerMixin
from sklearn.utils.validation import check_is_fitted
from cblearn import datasets
from cblearn import utils
from cblearn import metrics
class TripletEmbeddingMixin(TransformerMixin):
def __sklearn_tags__(sel... | cblearn/cblearn | cblearn/embedding/_base.py | .py | a1928abc461ba4bf | 7.67 | 21 |
import numpy as np
import pytest
from cblearn.datasets import make_random_triplets
from cblearn.embedding import MLDS
def test_mlds_rejects_multiple_components():
""" Test that MLDS rejects n_components != 1, which it cannot estimate.
scikit-learn requires that __init__ stores the parameters unaltered and
... | cblearn/cblearn | cblearn/embedding/tests/test_mlds.py | .py | f4840525933609cb | 7.17 | 21 |
import pytest
from cblearn.embedding.wrapper._r_base import RWrapperMixin
def _forget_r_state():
""" Drop the cached rpy2 handles, so the next call re-runs init_r. """
for attribute in ('robjects', 'rpackages'):
if hasattr(RWrapperMixin, attribute):
delattr(RWrapperMixin, attribute)
@py... | cblearn/cblearn | cblearn/embedding/tests/test_r_base.py | .py | f3be10381e75e6d6 | 8.17 | 21 |
import pytest
import numpy as np
from scipy.optimize import check_grad, approx_fprime
from cblearn.datasets import make_random_triplets
from cblearn.embedding import STE, TSTE
from cblearn.embedding._ste import _ste_x_grad
@pytest.mark.parametrize('n,d', [(20, 1), (50, 2), (100, 3)])
@pytest.mark.parametrize('heavy_... | cblearn/cblearn | cblearn/embedding/tests/test_ste.py | .py | 69fe9b96885db54c | 8.17 | 21 |
import pytest
from cblearn.embedding._torch_utils import torch_device, _torch_device_is_available
def test_torch_device_auto():
""" "auto" selects cuda if and only if cuda is available. """
torch = pytest.importorskip('torch', reason='torch is not installed')
expected = "cuda" if torch.cuda.is_available... | cblearn/cblearn | cblearn/embedding/tests/test_torch_utils.py | .py | bad35e7a56819b21 | 8.17 | 21 |
from __future__ import annotations
import xml.etree.ElementTree as et
from typing import Dict, List, Optional
from model.jriver.formats import OutputFormat, OUTPUT_FORMATS
def xpath_to_key_data_value(key_name, data_name):
'''
an ET compatible xpath to get the value from a DSP config via the path /Preset/Key... | 3ll3d00d/beqdesigner | src/main/python/model/jriver/codec.py | .py | 8b45848459dd4e91 | 7.77 | 33 |
import typing
import qtawesome as qta
from qtpy.QtCore import QAbstractTableModel, QModelIndex, QVariant, Qt
from qtpy.QtWidgets import QDialog, QPushButton, QHeaderView
from sortedcontainers import SortedDict, SortedSet
from mpl import NoCaretStyle
from ui.delegates import CheckBoxDelegate
from ui.link import Ui_lin... | 3ll3d00d/beqdesigner | src/main/python/model/link.py | .py | ca03fc69e4e6d2fc | 7.77 | 33 |
import logging
from collections.abc import Sequence
import numpy as np
from qtpy.QtCore import QObject, Signal
from qtpy.QtWidgets import QMainWindow
from model.preferences import LOGGING_LEVEL
from ui.logs import Ui_logsForm
logger = logging.getLogger('log')
class LogViewer(QMainWindow, Ui_logsForm):
change_l... | 3ll3d00d/beqdesigner | src/main/python/model/log.py | .py | 46950652c2880f37 | 7.77 | 33 |
#!/usr/bin/env python3
"""
This script creates an API key that clients can use to access contact
information in Topology pages.
"""
import argparse
import hashlib
import os
import pathlib
import re
import sys
import urllib.request
import uuid
import xml.etree.ElementTree as ET
if __name__ == "__main__" and __package... | opensciencegrid/topology | bin/make_api_key.py | .py | 785345aa30e23c21 | 7.69 | 23 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Download resource and project XML data from Topology;
use the data to create a JSON file (project_resource_allocation.json)
for looking up resource allocations for projects.
In a separate JSON file (resource_info_lookups.json), put dicts for easier
lookups of common q... | opensciencegrid/topology | src/topology_cacher.py | .py | 60ac2ce947358aff | 7.69 | 23 |
import re
import urllib
import urllib.parse
from collections import OrderedDict
from typing import Optional, List, Dict, Tuple, Union, Set
from .common import PELICAN_CACHE, PELICAN_ORIGIN, XROOTD_CACHE_SERVER, XROOTD_ORIGIN_SERVER, ParsedYaml, is_null
try:
from .x509 import generate_dn_hash
except ImportError: #... | opensciencegrid/topology | src/webapp/data_federation.py | .py | 25ab52d556e0e641 | 7.69 | 23 |
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