text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
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#!/usr/bin/env python3
# Copyright 2023 Ubuntu
# See LICENSE file for licensing details.
"""Integration tests: Alertmanager TLS web endpoint."""
import logging
import tempfile
from pathlib import Path
import jubilant
import pytest
from helpers import ALERTMANAGER_IMAGE, curl, get_unit_address
logger = logging.getLo... | canonical/alertmanager-k8s-operator | tests/integration/test_tls_web.py | .py | 7a54b43ad739b524 | 7.92 | 6 |
# Copyright 2025 Canonical Ltd.
# See LICENSE file for licensing details.
"""Integration tests: Alertmanager workload tracing over plain HTTP."""
import logging
from pathlib import Path
import jubilant
from helpers import (
ALERTMANAGER_IMAGE,
AM_APP,
TEMPO_APP,
assert_traces_in_tempo,
deploy_tem... | canonical/alertmanager-k8s-operator | tests/integration/test_workload_tracing_http.py | .py | 199e5dc98194655b | 7.92 | 6 |
# Copyright 2025 Canonical Ltd.
# See LICENSE file for licensing details.
"""Integration tests: Alertmanager workload tracing over TLS."""
import logging
from pathlib import Path
import jubilant
from helpers import (
ALERTMANAGER_IMAGE,
AM_APP,
TEMPO_APP,
assert_traces_in_tempo,
deploy_tempo_stac... | canonical/alertmanager-k8s-operator | tests/integration/test_workload_tracing_tls.py | .py | 7bd6b4a598790c80 | 7.92 | 6 |
#!/usr/bin/env python3
# Copyright 2021 Canonical Ltd.
# See LICENSE file for licensing details.
"""Helper functions for writing tests."""
import dataclasses
from unittest.mock import patch
from ops.testing import Container, Context, Exec, PeerRelation, Relation, State
def no_op(*_, **__) -> None:
pass
def t... | canonical/alertmanager-k8s-operator | tests/unit/helpers.py | .py | 5452e0873d138ad5 | 7.92 | 6 |
# Copyright 2023 Canonical Ltd.
# See LICENSE file for licensing details.
from unittest.mock import patch
import pytest
from helpers import add_relation_sequence, begin_with_initial_hooks_isolated
from ops.testing import Context, Relation, State
"""Some brute-force tests, so that other tests can remain focused."""
... | canonical/alertmanager-k8s-operator | tests/unit/test_brute_isolated.py | .py | 90d392e053c2dbc3 | 7.92 | 6 |
#!/usr/bin/env python3
# Copyright 2026 Canonical Ltd.
# See LICENSE file for licensing details.
"""Unit tests for config change detection."""
import dataclasses
import unittest
from unittest.mock import MagicMock, patch
import ops
import pytest
from helpers import begin_with_initial_hooks_isolated
from ops.pebble i... | canonical/alertmanager-k8s-operator | tests/unit/test_config_changes.py | .py | 2dfce475fd331394 | 7.92 | 6 |
#!/usr/bin/env python3
# Copyright 2021 Canonical Ltd.
# See LICENSE file for licensing details.
import textwrap
import unittest
import ops
from charms.alertmanager_k8s.v1.alertmanager_dispatch import AlertmanagerConsumer
from ops.charm import CharmBase
from ops.framework import StoredState
from ops.testing import Ha... | canonical/alertmanager-k8s-operator | tests/unit/test_consumer.py | .py | 9e3851035aeb76d8 | 7.92 | 6 |
#!/usr/bin/env python3
# Copyright 2021 Canonical Ltd.
# See LICENSE file for licensing details.
import logging
import unittest
from typing import Optional
from unittest.mock import patch
import ops
import yaml
from helpers import cli_arg, k8s_resource_multipatch
from ops.testing import Harness
from alertmanager imp... | canonical/alertmanager-k8s-operator | tests/unit/test_external_url.py | .py | 9c98f91f2a6de0c0 | 7.92 | 6 |
#!/usr/bin/env python3
# Copyright 2021 Canonical Ltd.
# See LICENSE file for licensing details.
import logging
import unittest
from unittest.mock import patch
import hypothesis.strategies as st
import ops
import validators
import yaml
from helpers import k8s_resource_multipatch
from hypothesis import given
from ops.... | canonical/alertmanager-k8s-operator | tests/unit/test_push_config_to_workload_on_startup.py | .py | deb85f183123b282 | 7.92 | 6 |
# Copyright 2023 Canonical Ltd.
# See LICENSE file for licensing details.
"""Feature: The workload's scheme is reflected in the pebble command and in relation data.
This feature spans:
- manifest generation (pebble layer)
- schema generation (alertmanager_dispatch provider)
The alertmanager server can serve over HTT... | canonical/alertmanager-k8s-operator | tests/unit/test_server_scheme.py | .py | 9872548e3158e6f5 | 7.92 | 6 |
import json
from common.googleapis import GoogleAPIClient
# Youtube video to look up (look at this graph)
YOUTUBE_VIDEO_ID = 'sIlNIVXpIns'
# Sheet id to look up (DB2019 public sheet)
SHEET_ID = '15t-UsfNlP5xUxLTLH-EUjrOYriOvXuNGAPxi_8EZJhU'
def youtube(client):
client.request('GET', 'https://www.googleapis.com/y... | dbvideostriketeam/wubloader | api_ping/api_ping/main.py | .py | 758f774ead9eca88 | 7.64 | 18 |
import datetime
import math
import os
from io import BytesIO
import argh
from PIL import Image
import common
from common.segments import extract_frame, parse_segment_path
colour_profiles = {
'DBfH_2025':{
'sky_colours': {
'score': (113, 118, 114),
'day': (83, 204, 200),
'dusk': (202, 144, 169),
'nig... | dbvideostriketeam/wubloader | bus_analyzer/bus_analyzer/extract.py | .py | 35a1b9a87c761fc0 | 7.64 | 18 |
import datetime
import logging
import os
import random
import signal
import time
import traceback
import argh
import gevent.event
from gevent.pool import Pool
import prometheus_client as prom
import common
from common import database
from common.segments import parse_segment_path, list_segment_files
from common.stat... | dbvideostriketeam/wubloader | bus_analyzer/bus_analyzer/main.py | .py | 628ee7ceb14fe3cb | 7.64 | 18 |
from vosk import Model, SpkModel, KaldiRecognizer
class BuscribeRecognizer:
segments_start_time = None
def __init__(self, sample_rate=48000, model_path="model_small", spk_model_path="spk_model"):
"""Loads the speech recognition model and initializes the recognizer.
Model paths are file paths... | dbvideostriketeam/wubloader | buscribe/buscribe/recognizer.py | .py | bfdd60ce90255e8b | 7.64 | 18 |
"""A group of greenlets running tasks.
Each task has a key. If a task with that key is already running,
it is not re-run."""
import gevent
class KeyedGroup:
def __init__(self):
self.greenlets = {}
def spawn(self, key, func, *args, **kwargs):
if key not in self.greenlets:
self.greenlets[key] = gevent.spawn... | dbvideostriketeam/wubloader | chat_archiver/chat_archiver/keyed_group.py | .py | 598b48fe179974a2 | 7.64 | 18 |
"""A place for common utilities between wubloader components"""
import datetime
import errno
import logging
import os
import random
from signal import SIGTERM
from uuid import uuid4
import gevent.event
from .segments import get_best_segments, rough_cut_segments, fast_cut_segments, full_cut_segments, parse_segment_pa... | dbvideostriketeam/wubloader | common/common/__init__.py | .py | d16a6b000bdfdd7c | 7.64 | 18 |
import itertools
import gevent.lock
class CachedIterator():
"""Wraps an iterator. When you iterate over this, it pulls items from the wrapped iterator
as needed, but remembers each one. When you iterate over it again, it will re-serve the
yielded items in the same order, until it runs out, in which case it start... | dbvideostriketeam/wubloader | common/common/cached_iterator.py | .py | ca1ae14c4d88eef1 | 7.64 | 18 |
import json
import logging
import os
from datetime import datetime, timedelta
from common import listdir
from common.stats import timed
from common.segments import hour_paths_for_range
# How long each batch is
BATCH_INTERVAL = 60
def format_batch(messages):
# We need to take some care to have a consistent orderi... | dbvideostriketeam/wubloader | common/common/chat.py | .py | 533f7a51fdef83a7 | 7.64 | 18 |
"""
Code shared between components that touch the database.
Note that this code requires psycopg2 and psycogreen, but the common module
as a whole does not to avoid needing to install them for components that don't need it.
"""
from contextlib import contextmanager
import psycopg2
import psycopg2.sql
import psycopg2... | dbvideostriketeam/wubloader | common/common/database.py | .py | f5abb6d1f2b19a96 | 7.64 | 18 |
"""Wrapper code around dateutil to use it more sanely"""
# required so we are able to import dateutil despite this module also being called dateutil
from __future__ import absolute_import
import dateutil.parser
import dateutil.tz
def parse(timestamp):
"""Parse given timestamp, convert to UTC, and return naive U... | dbvideostriketeam/wubloader | common/common/dateutil.py | .py | 6ea8f73e63e3dfa2 | 7.64 | 18 |
import struct
class FixTS():
"""Does stream processing on an MPEG-TS stream, adjusting all timestamps in it.
The stream will be adjusted such that the first packet starts at the given start_time,
with all other packets adjusted to be the same time relative to that packet.
In other words, a video that goes from 0... | dbvideostriketeam/wubloader | common/common/fixts.py | .py | bb65811a143e196f | 7.64 | 18 |
"""
Code shared between components to gather stats from flask methods.
Note that this code requires flask, but the common module as a whole does not
to avoid needing to install them for components that don't need it.
"""
import functools
from flask import request
from flask import g as request_store
from monotonic im... | dbvideostriketeam/wubloader | common/common/flask_stats.py | .py | 19f1bf5cce7f8132 | 7.64 | 18 |
import time
import logging
import gevent
from requests import HTTPError
from .requests import InstrumentedSession
# Wraps all requests in some metric collection and default timeouts
requests = InstrumentedSession()
requests.timeout = 30
class GoogleAPIClient(object):
"""Manages access to google apis and maintain... | dbvideostriketeam/wubloader | common/common/googleapis.py | .py | efba9c30046cac33 | 7.64 | 18 |
import sys
from io import BytesIO
from PIL import Image
from common import database
def get_template(dbmanager, name, crop=None, location=None):
"""Fetch the thumbnail template and any missing parameters from the database"""
with dbmanager.get_conn() as conn:
query = """
SELECT image, crop, location FROM te... | dbvideostriketeam/wubloader | common/common/images.py | .py | 5448a0029ac50cdf | 7.64 | 18 |
import json
import logging
import os
import re
import socket
import time
import urllib.parse
from base64 import b64encode
from hashlib import sha256
from uuid import uuid4
import gevent
import prometheus_client as prom
import requests
import urllib3.connection
from gevent.pool import Pool
from ipaddress import ip_addr... | dbvideostriketeam/wubloader | common/common/media.py | .py | 195af050fab3c438 | 7.64 | 18 |
"""Code for instrumenting requests calls. Requires requests, obviously."""
import urllib.parse
import requests.sessions
import prometheus_client as prom
from monotonic import monotonic
request_latency = prom.Histogram(
'http_client_request_latency',
'Time taken to make an outgoing HTTP request. '
'Status = "erro... | dbvideostriketeam/wubloader | common/common/requests.py | .py | 6d8bc83f7e949fc5 | 7.64 | 18 |
import logging
from .googleapis import GoogleAPIClient
class Sheets(object):
"""Manages Google Sheets API operations"""
def __init__(self, client_id, client_secret, refresh_token):
self.logger = logging.getLogger(type(self).__name__)
self.client = GoogleAPIClient(client_id, client_secret, refresh_token)
de... | dbvideostriketeam/wubloader | common/common/sheets.py | .py | e60946041db2e36d | 7.64 | 18 |
import datetime
import math
import urllib
import zoneinfo
from common import dateutil
from common.requests import InstrumentedSession
UTC = datetime.timezone.utc
requests = InstrumentedSession()
def parse_shift_time(time_str, timeout=5):
"""
Parse times in the shift definition.
The parser first tries to pars... | dbvideostriketeam/wubloader | common/common/shifts.py | .py | ae44f2972043dfff | 7.64 | 18 |
import atexit
import functools
import logging
import os
import signal
import gevent.lock
from monotonic import monotonic
import prometheus_client as prom
# need to keep global track of what metrics we've registered
# because we're not allowed to re-register
metrics = {}
def timed(name=None,
buckets=[10.**x for x... | dbvideostriketeam/wubloader | common/common/stats.py | .py | e61ca2666923366a | 7.64 | 18 |
# -*- coding: utf-8 -*-
"""
NMChannel module.
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
If you use this software in your research, please cite:
Rothman JS and Silver RA (2018) NeuroMatic: An Integrated Open-Source
Software Toolkit for A... | SilverLabUCL/pyNeuroMatic | pyneuromatic/core/nm_channel.py | .py | 55d2e70c0dca4231 | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
[Module description].
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
If you use this software in your research, please cite:
Rothman JS and Silver RA (2018) NeuroMatic: An Integrated Open-Source
Software Toolkit ... | SilverLabUCL/pyNeuroMatic | pyneuromatic/core/nm_epoch.py | .py | 6c8255616aa1a3a1 | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
Centralized history logging for pyNeuroMatic.
Provides NMHistory, a wrapper around Python's logging module that maintains
an in-memory history buffer and colorama-colored console output, analogous
to Igor Pro's history command window.
Part of pyNeuroMatic, a Python implementation of NeuroM... | SilverLabUCL/pyNeuroMatic | pyneuromatic/core/nm_history.py | .py | b981c5fc7b79078e | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
NMNotes module.
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
If you use this software in your research, please cite:
Rothman JS and Silver RA (2018) NeuroMatic: An Integrated Open-Source
Software Toolkit for Acq... | SilverLabUCL/pyNeuroMatic | pyneuromatic/core/nm_notes.py | .py | 11a572b34c95a6b9 | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
[Module description].
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
If you use this software in your research, please cite:
Rothman JS and Silver RA (2018) NeuroMatic: An Integrated Open-Source
Software Toolkit ... | SilverLabUCL/pyNeuroMatic | pyneuromatic/core/nm_object.py | .py | 4f323c9df24daecb | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
NM Tool Registry - Central registry for lazy tool loading.
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
If you use this software in your research, please cite:
Rothman JS and Silver RA (2018) NeuroMatic: An Inte... | SilverLabUCL/pyNeuroMatic | pyneuromatic/core/nm_tool_registry.py | .py | d78d5a529ee7f52c | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
NM Workspace - User workspace configuration management.
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
If you use this software in your research, please cite:
Rothman JS and Silver RA (2018) NeuroMatic: An Integra... | SilverLabUCL/pyNeuroMatic | pyneuromatic/core/nm_workspace.py | .py | 3defe6d4c6b9eb9f | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
pyNeuroMatic GUI - Optional graphical interface.
This module requires PyQt6. Install with:
pip install pyneuromatic[gui]
"""
# Check if GUI dependencies are available
try:
from PyQt6 import QtWidgets, QtCore
GUI_AVAILABLE = True
_GUI_IMPORT_ERROR = None
except ImportError a... | SilverLabUCL/pyNeuroMatic | pyneuromatic/gui/__init__.py | .py | d1393796368060ac | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
FolderBrowserWidget - read-only tree view over an NMManager's folder hierarchy.
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
If you use this software in your research, please cite:
Rothman JS and Silver RA (2018... | SilverLabUCL/pyNeuroMatic | pyneuromatic/gui/folder_browser.py | .py | 8ed2f52b9eead7af | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
Axograph file format reader.
Supports Axograph X files (.axgx) and classic Axograph files (.axgd).
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
References:
- NeuroMatic Igor import: NM_ImportAxograph.ipf
... | SilverLabUCL/pyNeuroMatic | pyneuromatic/io/axograph.py | .py | 2830ff4c495fc5a4 | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
Base utilities for I/O operations.
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
"""
from __future__ import annotations
import re
from typing import NamedTuple
class ParsedUnits(NamedTuple):
"""Result of par... | SilverLabUCL/pyNeuroMatic | pyneuromatic/io/base.py | .py | 811617fb29f8e38e | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
Igor Pro packed experiment (.pxp) file reader.
Reads PXP files created by NeuroMatic in Igor Pro using the igor2 library.
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
References:
- NeuroMatic Igor: https://... | SilverLabUCL/pyNeuroMatic | pyneuromatic/io/pxp.py | .py | 7b43207312c1b265 | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
Matplotlib plotting utilities for NMData and NMFolder.
Provides three public functions:
- :func:`plot_nmdata` — plot a single NMData array.
- :func:`plot_folder` — plot all epochs for a given prefix, one subplot
per channel, with epochs overlaid.
- :func:`plot_channel_data` — shared sub... | SilverLabUCL/pyNeuroMatic | pyneuromatic/tools/nm_plot.py | .py | 595e8d4b009e6e6c | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
NM Tool - Base class for analysis tools.
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
If you use this software in your research, please cite:
Rothman JS and Silver RA (2018) NeuroMatic: An Integrated Open-Source... | SilverLabUCL/pyNeuroMatic | pyneuromatic/tools/nm_tool.py | .py | 56145d6fbef72020 | 7.6 | 15 |
# -*- coding: utf-8 -*-
"""
[Module description].
Part of pyNeuroMatic, a Python implementation of NeuroMatic for analyzing,
acquiring and simulating electrophysiology data.
If you use this software in your research, please cite:
Rothman JS and Silver RA (2018) NeuroMatic: An Integrated Open-Source
Software Toolkit ... | SilverLabUCL/pyNeuroMatic | pyneuromatic/tools/nm_tool_folder.py | .py | b86f17a27f2212dd | 7.6 | 15 |
import os
import numpy as np
import pandas as pd
import nibabel as nb
import pooch
from numba import njit
from time import time
ZENODO_RECORD = "18793343"
ZENODO_URL = f"https://zenodo.org/api/records/{ZENODO_RECORD}/files"
CACHE_DIR = pooch.os_cache("MTB_task_library")
def fetch_task_library(version='V1', atlas='m... | DiedrichsenLab/MultiTaskBattery | MultiTaskBattery/battery.py | .py | e2ce10d43540ed46 | 7.5 | 9 |
# Created 2023: Bassel Arafat, Jorn Diedrichsen, Ince Husain
from psychopy import core, event
class TTLClock:
def __init__(self):
"""
TTLClock class is used for counting the number of TTL pulses and the time of the last TTL pulse
"""
self.clock = core.Clock() #
self.tt... | DiedrichsenLab/MultiTaskBattery | MultiTaskBattery/ttl_clock.py | .py | 063f9c697cd6b515 | 7.5 | 9 |
"""
Sphinx extension to auto-generate task descriptions from task_table.tsv. This way we dont have to manually add tasks.
The only thing that can be added manually (optional) is media for each task. Just go to images/ and add
{task_name}.png, {task_name}_2.png, ... for screenshots, and/or {task_name}.mp4, {task_name}_2... | DiedrichsenLab/MultiTaskBattery | docs/extension/task_docs.py | .py | 794823583c095a65 | 7.5 | 9 |
import os
import json
import numpy as np
import pandas as pd
import nibabel as nb
import pooch
# Same Zenodo source as MultiTaskBattery/battery.py
ZENODO_RECORD = "18793343"
CACHE_DIR = pooch.os_cache("MTB_task_library")
VERSION = "V1"
ATLAS = "multiatlasHCP"
N_DIMS = 8 # MDS dimensions to keep (viewer lets you pick... | DiedrichsenLab/MultiTaskBattery | docs/mds/make_mds_data.py | .py | 693fc53504b5a518 | 7.5 | 9 |
"""One-command dependency install for MultiTaskBattery, on any OS.
python install.py
On Linux this detects your distribution and points pip at the matching
prebuilt wxPython wheels (wxPython has none on PyPI for Linux, so a plain
pip install would try to compile it from source and fail). On Windows and
macOS it i... | DiedrichsenLab/MultiTaskBattery | install.py | .py | 080f5b5e6059f409 | 7.5 | 9 |
import os
from functools import partial
import click
from rich.table import Table
from PyTM import settings
from PyTM.console import console
from PyTM.core import data_handler, hook_handler, project_handler, task_handler
BASH_SNIPPET = """\
# pytm ambient tracking hook (bash)
_pytm_hook_check() {
local _pytm_exit=... | wasi0013/PyTM | PyTM/commands/hook.py | .py | 9859e6b037d5d6ed | 7.63 | 17 |
import os
import shutil
import subprocess
from filelock import FileLock, Timeout
from PyTM import settings
from PyTM.core import data_handler, hook_handler
# Commits made by PyTM itself always use this identity, regardless of
# whatever (if anything) `git config user.name`/`user.email` resolve to on
# the machine — ... | wasi0013/PyTM | PyTM/core/backup_handler.py | .py | 55fee9f36cf66463 | 7.63 | 17 |
import json
import os
import tempfile
from filelock import FileLock
from PyTM import settings
def _default_path(path):
"""
Resolves the effective path for a data-handler call. Falling back to
`settings.data_filepath` here (instead of as a function default) means
the current value of `settings.data_f... | wasi0013/PyTM | PyTM/core/data_handler.py | .py | fbd83393e256b62b | 7.63 | 17 |
import datetime
from PyTM import settings
def _parse(ts):
return datetime.datetime.fromisoformat(ts)
def _session_seconds_in_window(session, window_start, window_end, now):
"""
Seconds of a single session that fall within [window_start, window_end).
Adjustment entries written by `task_handler.edit... | wasi0013/PyTM | PyTM/core/digest_handler.py | .py | bed9daa0f4556f8d | 7.63 | 17 |
import os
import subprocess
def normalize(path):
return os.path.realpath(path)
def resolve_project(links, cwd):
"""
Longest-prefix match of `cwd` against linked directories. `links` is
`{normalized_path: project_name}` — `hook link`/`hook unlink` already
normalize keys before storing, so only `c... | wasi0013/PyTM | PyTM/core/hook_handler.py | .py | ff337e1353db8097 | 7.63 | 17 |
import datetime
from PyTM import settings
def calculate_duration(date1, date2):
return abs(
(
datetime.datetime.fromisoformat(date1)
- datetime.datetime.fromisoformat(date2)
).total_seconds()
)
def _close_open_session(task, end):
"""
Closes the most recent op... | wasi0013/PyTM | PyTM/core/task_handler.py | .py | cd47d7562d881557 | 7.63 | 17 |
import json
import os
import threading
import pytest
from PyTM import settings
from PyTM.core import data_handler
def test_init_data(tmpdir):
tmp_path = tmpdir.join("pytm-test.json")
data_handler.init_data(tmp_path)
assert tmp_path.read() == "{}"
def test_load_data_exists(tmpdir):
tmp_path = tmpdi... | wasi0013/PyTM | tests/core/test_data_handler.py | .py | fc610793728508f9 | 7.13 | 17 |
from PyTM.core import hook_handler
def linked(pairs):
"""
Builds a `links` dict the way `hook link` actually stores one: keys
pre-normalized via `hook_handler.normalize`. `resolve_project` relies
on that invariant (it only normalizes `cwd`, not the stored keys, to
avoid redundant syscalls on its h... | wasi0013/PyTM | tests/core/test_hook_handler.py | .py | 4999992492400f0d | 8.13 | 17 |
import datetime
import pytest
from PyTM import settings
from PyTM.core import task_handler
TEST_TIME_NOW = datetime.datetime(
2023,
11,
9,
)
@pytest.fixture
def patch_datetime_now(monkeypatch):
class mydatetime(datetime.datetime):
@classmethod
def now(cls):
return TEST_T... | wasi0013/PyTM | tests/core/test_task_handler.py | .py | 618347b4151c1c49 | 8.13 | 17 |
"""Commands to inspect or modify the contents of pseudo potential families."""
import json
import click
from aiida.cmdline.params import options as options_core
from aiida.cmdline.utils import decorators, echo
from .params import arguments, options, types
from .root import cmd_root
@cmd_root.group('family')
def cmd... | aiidateam/aiida-pseudo | src/aiida_pseudo/cli/family.py | .py | 2336d71be283697b | 7.42 | 6 |
"""Commands to list instances of `PseudoPotentialFamily`."""
import click
from aiida.cmdline.params import options as options_core
from aiida.cmdline.utils import decorators, echo
from .params import options
from .root import cmd_root
PROJECTIONS_VALID = ('pk', 'uuid', 'type_string', 'label', 'description', 'count')
... | aiidateam/aiida-pseudo | src/aiida_pseudo/cli/list.py | .py | 10d5476c254eee75 | 7.42 | 6 |
"""Command line interface `aiida-pseudo`."""
import click
from aiida.cmdline.groups.verdi import VerdiCommandGroup
from .params import options
class CustomVerdiCommandGroup(VerdiCommandGroup):
"""Subclass of :class:`aiida.cmdline.groups.verdi.VerdiCommandGroup` for the CLI.
This subclass overrides the verbo... | aiidateam/aiida-pseudo | src/aiida_pseudo/cli/root.py | .py | 47d1bd4e4defb295 | 7.42 | 6 |
"""Command line interface utilities."""
from contextlib import contextmanager
from pathlib import Path
from aiida.cmdline.utils import echo
__all__ = ('attempt', 'create_family_from_archive')
@contextmanager
def attempt(message, exception_types=Exception, include_traceback=False):
"""Context manager to be used ... | aiidateam/aiida-pseudo | src/aiida_pseudo/cli/utils.py | .py | 139155239d8e87ca | 7.42 | 6 |
"""Module for data plugin to represent a pseudo potential in JTH XML format."""
import pathlib
import re
import typing
from .pseudo import PseudoPotentialData
__all__ = ('JthXmlData',)
REGEX_ELEMENT = re.compile(r"""\s*symbol\s*=\s*['"]\s*(?P<element>[a-zA-Z]{1,2})\s*['"].*""")
def parse_element(stream: typing.Bin... | aiidateam/aiida-pseudo | src/aiida_pseudo/data/pseudo/jthxml.py | .py | 53f738713e02e998 | 7.42 | 6 |
"""Base class for data types representing pseudo potentials."""
from __future__ import annotations
import io
import pathlib
import typing
from aiida import orm, plugins
from aiida.common.constants import elements
from aiida.common.exceptions import StoringNotAllowed
from aiida.common.files import md5_from_filelike
fr... | aiidateam/aiida-pseudo | src/aiida_pseudo/data/pseudo/pseudo.py | .py | e4bd8fd949296f5f | 7.42 | 6 |
"""Module for data plugin to represent a pseudo potential in PSF format."""
import pathlib
import re
import typing
from .pseudo import PseudoPotentialData
__all__ = ('PsfData',)
REGEX_ELEMENT = re.compile(r"""\s*(?P<element>[a-zA-Z]{1}[a-z]?)\s+.*""")
def parse_element(stream: typing.BinaryIO):
"""Parse the co... | aiidateam/aiida-pseudo | src/aiida_pseudo/data/pseudo/psf.py | .py | 2426373c4143c380 | 7.42 | 6 |
"""Module for data plugin to represent a pseudo potential in PSML format."""
import pathlib
import re
import typing
from .pseudo import PseudoPotentialData
__all__ = ('PsmlData',)
REGEX_ELEMENT = re.compile(r"""\s*(?P<element>[a-zA-Z]{1}[a-z]?)\s+.*""")
def parse_element(stream: typing.BinaryIO) -> str:
"""Par... | aiidateam/aiida-pseudo | src/aiida_pseudo/data/pseudo/psml.py | .py | 37bebd7366c26e2b | 7.42 | 6 |
"""Module for data plugin to represent a pseudo potential in Psp8 format."""
import pathlib
import typing
from aiida.common.constants import elements
from .pseudo import PseudoPotentialData
__all__ = ('Psp8Data',)
def parse_element(stream: typing.BinaryIO):
"""Parse the content of the Psp8 file to determine th... | aiidateam/aiida-pseudo | src/aiida_pseudo/data/pseudo/psp8.py | .py | 92ff4387c5e6de22 | 7.42 | 6 |
"""Module for data plugin to represent a pseudo potential in UPF format."""
import pathlib
import re
import typing
from .pseudo import PseudoPotentialData
__all__ = ('UpfData',)
REGEX_ELEMENT_V1 = re.compile(r"""(?P<element>[a-zA-Z]{1,2})\s+Element""")
REGEX_ELEMENT_V2 = re.compile(r"""\s*element\s*=\s*['"]\s*(?P<el... | aiidateam/aiida-pseudo | src/aiida_pseudo/data/pseudo/upf.py | .py | 11c9e64d08403f19 | 7.42 | 6 |
"""Module for data plugin to represent a pseudo potential in VPS format."""
import pathlib
import re
import typing
from aiida.common.constants import elements
from .pseudo import PseudoPotentialData
__all__ = ('VpsData',)
PATTERN_FLOAT = r'[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?'
REGEX_ATOMIC_NUMBER = re.compile(r"... | aiidateam/aiida-pseudo | src/aiida_pseudo/data/pseudo/vps.py | .py | 7a9c7027299db628 | 7.42 | 6 |
"""Subclass of ``Group`` that serves as a base class for representing pseudo potential families."""
import re
from typing import List, Mapping, Optional, Tuple, Union
from aiida.common import exceptions
from aiida.common.lang import classproperty, type_check
from aiida.orm import Group, QueryBuilder
from aiida.plugins... | aiidateam/aiida-pseudo | src/aiida_pseudo/groups/family/pseudo.py | .py | 329d0effa161491d | 7.42 | 6 |
"""Subclass of `PseudoPotentialFamily` designed to represent a PseudoDojo configuration."""
from __future__ import annotations
import json
import pathlib
import re
import warnings
from typing import ClassVar, NamedTuple, Sequence
from aiida.common.exceptions import ParsingError
from aiida_pseudo.data.pseudo import J... | aiidateam/aiida-pseudo | src/aiida_pseudo/groups/family/pseudo_dojo.py | .py | 05eb0e8ec3a112cf | 7.42 | 6 |
"""Subclass of ``PseudoPotentialFamily`` designed to represent an SSSP configuration."""
from typing import NamedTuple, Optional, Sequence
from aiida_pseudo.data.pseudo import UpfData
from ..mixins import RecommendedCutoffMixin
from .pseudo import PseudoPotentialFamily
__all__ = ('SsspConfiguration', 'SsspFamily')
... | aiidateam/aiida-pseudo | src/aiida_pseudo/groups/family/sssp.py | .py | 9e19d9fd21813b6d | 7.42 | 6 |
"""Mixin that adds support of recommended cutoffs to a ``Group`` subclass, using its extras."""
import warnings
from typing import Optional
from aiida.common.exceptions import MissingEntryPointError
from aiida.common.lang import type_check
from aiida.plugins import DataFactory
from aiida_pseudo.common.units import U
... | aiidateam/aiida-pseudo | src/aiida_pseudo/groups/mixins/cutoffs.py | .py | 1767423cce88cb7d | 7.42 | 6 |
"""Tests for the :mod:`~aiida_pseudo.cli.params.types` module."""
import click
import pytest
from aiida_pseudo.cli.params import types
from aiida_pseudo.groups.family import PseudoPotentialFamily
def test_pseudo_family_type_param_convert(ctx):
"""Test the `PseudoPotentialFamilyTypeParam.convert` method."""
pa... | aiidateam/aiida-pseudo | tests/cli/params/test_types.py | .py | 9ca6b5e38bceb05c | 7.92 | 6 |
"""Tests for the command `aiida-pseudo family`."""
import json
from copy import deepcopy
import pytest
from aiida.orm import Group
from aiida_pseudo.cli.family import cmd_family_cutoffs_set, cmd_family_show
from aiida_pseudo.data.pseudo.upf import UpfData
from aiida_pseudo.groups.family import CutoffsPseudoPotentialFa... | aiidateam/aiida-pseudo | tests/cli/test_family.py | .py | bababcefdd5aa71b | 7.92 | 6 |
"""Tests for the command `aiida-pseudo list`."""
from aiida_pseudo.cli import cmd_list
from aiida_pseudo.cli.list import PROJECTIONS_VALID
from aiida_pseudo.data.pseudo import UpfData
from aiida_pseudo.groups.family import PseudoPotentialFamily, SsspFamily
def test_list(aiida_profile_clean, run_cli_command, get_pseud... | aiidateam/aiida-pseudo | tests/cli/test_list.py | .py | 9fec3f46acea149b | 7.92 | 6 |
"""Tests for CLI commands."""
from __future__ import annotations
import subprocess
import click
import pytest
from aiida_pseudo.cli import cmd_root
def recurse_commands(command: click.Command, parents: list[str] | None = None):
"""Recursively return all subcommands that are part of ``command``.
:param comm... | aiidateam/aiida-pseudo | tests/cli/test_root.py | .py | 55897b568c8cacf4 | 7.92 | 6 |
"""Test the command line interface utilities."""
import shutil
import tarfile
import tempfile
import pytest
from aiida_pseudo.cli.utils import attempt, create_family_from_archive
from aiida_pseudo.groups.family import PseudoPotentialFamily
@pytest.mark.usefixtures('aiida_profile_clean')
@pytest.mark.parametrize(('fm... | aiidateam/aiida-pseudo | tests/cli/test_utils.py | .py | 6c5f2db1f2b07092 | 7.92 | 6 |
"""Configuration and fixtures for unit test suite."""
import io
import os
import pathlib
import re
import shutil
import click
import pytest
from aiida.plugins import DataFactory
from aiida_pseudo.data.pseudo import PseudoPotentialData
from aiida_pseudo.groups.family import CutoffsPseudoPotentialFamily, PseudoPotential... | aiidateam/aiida-pseudo | tests/conftest.py | .py | a62f3fc5c703b594 | 7.92 | 6 |
"""Tests that are common to all data plugins in the :py:mod:`~aiida_pseudo.data.pseudo` module."""
import pytest
from aiida import plugins
def get_entry_point_names():
"""Return the registered entry point names for the given common workflow.
:param workflow: the name of the common workflow.
:param leaf: ... | aiidateam/aiida-pseudo | tests/data/pseudo/test_common.py | .py | 388cc40ed351c334 | 7.92 | 6 |
"""Tests for the :py:`~aiida_pseudo.data.pseudo.jthxml` module."""
import io
import pathlib
import pytest
from aiida.common.exceptions import ModificationNotAllowed
from aiida_pseudo.data.pseudo import JthXmlData
@pytest.fixture
def source(request, filepath_pseudos):
"""Return a pseudopotential, eiter as ``str``... | aiidateam/aiida-pseudo | tests/data/pseudo/test_jthxml.py | .py | 8117d4feb6655e51 | 7.92 | 6 |
"""Tests for the :py:mod:`~aiida_pseudo.data.pseudo.pseudo` module."""
import io
import pathlib
import pytest
from aiida.common.exceptions import ModificationNotAllowed, StoringNotAllowed
from aiida.common.files import md5_from_filelike
from aiida.common.links import LinkType
from aiida.orm import CalcJobNode
from aii... | aiidateam/aiida-pseudo | tests/data/pseudo/test_pseudo.py | .py | ba0c3be61fb2939e | 7.92 | 6 |
"""Tests for the :py:`~aiida_pseudo.data.pseudo.psf` module."""
import io
import pathlib
import pytest
from aiida.common.exceptions import ModificationNotAllowed
from aiida_pseudo.data.pseudo import PsfData
from aiida_pseudo.data.pseudo.psf import parse_element
@pytest.mark.parametrize(
('string', 'element'),
... | aiidateam/aiida-pseudo | tests/data/pseudo/test_psf.py | .py | da972ed1fc84d659 | 7.92 | 6 |
"""Tests for the :py:`~aiida_pseudo.data.pseudo.psml` module."""
import io
import pathlib
import pytest
from aiida.common.exceptions import ModificationNotAllowed
from aiida_pseudo.data.pseudo import PsmlData
@pytest.fixture
def source(request, filepath_pseudos):
"""Return a pseudopotential, eiter as ``str``, ``... | aiidateam/aiida-pseudo | tests/data/pseudo/test_psml.py | .py | 0f74ceb22297f371 | 7.92 | 6 |
"""Utilities for modifying Terraform backend configuration."""
import re
from pathlib import Path
from typing import Union, Optional
import hcl2
import lark
from leverage._utils import ExitError
def set_backend_key(config_file_path: Union[str, Path], key: str) -> None:
"""
Set or update the backend key in ... | binbashar/leverage | leverage/_backend_config.py | .py | 58177f1a3db5ca32 | 7.66 | 20 |
"""
Command line arguments and tasks arguments parsing utilities.
"""
class InvalidArgumentOrderError(RuntimeError):
pass
class DuplicateKeywordArgumentError(RuntimeError):
pass
def parse_task_args(arguments):
"""Parse the arguments for a task and return args and kwargs appropriately
Args:
... | binbashar/leverage | leverage/_parsing.py | .py | 4a8f22d717fae94c | 7.66 | 20 |
"""
General use utilities.
"""
from pathlib import Path
from subprocess import PIPE, run
from typing import List, Optional
import hcl2
import lark
from click.exceptions import ClickException
from configupdater import ConfigUpdater
from leverage import logger
def clean_exception_traceback(exception):
"""Del... | binbashar/leverage | leverage/_utils.py | .py | 013bf86a2870263e | 7.66 | 20 |
"""
Logging utilities.
"""
import logging
from functools import wraps
from rich.console import Console
from rich.logging import RichHandler
from click import get_current_context
_RAW_LOGGING_FORMAT = "%(message)s"
_TASK_LOGGING_FORMAT = (
"[bold light_yellow3][ %(build_script)s -[/bold light_yellow3]"
"... | binbashar/leverage | leverage/logger.py | .py | ddeb7a31ecce4aaa | 7.66 | 20 |
import time
import json
import datetime
import webbrowser
from typing import Any, Dict, Tuple
import boto3
import click
from dateutil.tz import tzutc
from configupdater import ConfigUpdater
from leverage import logger
from leverage.path import PathsHandler
from leverage.modules.runner import Runner
from leverage.modu... | binbashar/leverage | leverage/modules/aws.py | .py | a9470d868487f3d6 | 7.66 | 20 |
import os
from enum import Enum
from pathlib import Path
from dataclasses import dataclass
import click
import ruamel.yaml
import simple_term_menu
from leverage import logger
from leverage.path import PathsHandler
from leverage._utils import ExitError
from leverage.modules.aws import aws
from leverage.modules.runner ... | binbashar/leverage | leverage/modules/kubectl.py | .py | 7aa419d2a5e4a40b | 7.66 | 20 |
"""
Module for managing Leverage projects.
"""
import re
from pathlib import Path
from shutil import copy2
from shutil import copytree
from shutil import ignore_patterns
import click
from click.exceptions import Exit
from ruamel.yaml import YAML
from jinja2 import Environment
from jinja2 import FileSystemLoader
... | binbashar/leverage | leverage/modules/project.py | .py | ffb28ffc5585addf | 7.66 | 20 |
"""
Tasks running module.
"""
import re
import click
from click.exceptions import Exit
from leverage import logger
from leverage.tasks import load_tasks
from leverage.tasks import list_tasks as _list_tasks
from leverage.logger import get_tasks_logger
from leverage._parsing import parse_task_args
from leverage._p... | binbashar/leverage | leverage/modules/run.py | .py | 75c4c5e1851ad7e5 | 7.66 | 20 |
import os
import shutil
import subprocess
from pathlib import Path
from typing import Dict, Optional, Tuple, Union
from leverage import logger
from leverage._utils import ExitError
class Runner:
"""Generic command runner for executing system binaries with environment preservation"""
def __init__(
sel... | binbashar/leverage | leverage/modules/runner.py | .py | 597e6d58c9eaf51a | 7.66 | 20 |
import subprocess
from pathlib import Path
from typing import Dict, Optional
from click.exceptions import Exit
from leverage._utils import ExitError
from leverage.modules.runner import Runner
class TFRunner(Runner):
"""Terraform/OpenTofu runner with appropriate installation guidance"""
TERRAFORM_INSTALL_UR... | binbashar/leverage | leverage/modules/tfrunner.py | .py | 81d7390a0a1972f6 | 7.66 | 20 |
"""
Utilities to obtain relevant files' and directories' locations
"""
from pathlib import Path
from subprocess import CalledProcessError
from subprocess import PIPE
from subprocess import run
import hcl2
from leverage._utils import ExitError
class NotARepositoryError(RuntimeError):
"""When you are not run... | binbashar/leverage | leverage/path.py | .py | 023187f317b277dc | 7.66 | 20 |
"""
Task loading, Task object definition and task creation decorator.
"""
import sys
import importlib
from pathlib import Path
from inspect import getmembers
from inspect import isfunction
from operator import attrgetter
import click
from click.exceptions import Exit
from leverage import __version__
from leverag... | binbashar/leverage | leverage/tasks.py | .py | f2885b91efeb6831 | 7.66 | 20 |
import tempfile
import subprocess
from pathlib import Path
import pytest
import click
from click.testing import CliRunner
from leverage import path as lepath
from leverage import conf
from leverage._internals import State
from leverage._internals import Module
from leverage.logger import _configure_logger, _leverage_... | binbashar/leverage | tests/conftest.py | .py | 1f37fdc565a2aff7 | 8.16 | 20 |
"""Tests for backend configuration utilities."""
import pytest
from leverage._backend_config import set_backend_key, get_backend_key
from leverage._utils import ExitError
@pytest.fixture
def config_without_key(tmp_path):
"""Create a config.tf file without a backend key."""
config_file = tmp_path / "config.tf... | binbashar/leverage | tests/test_backend_config.py | .py | ffc85cb2891428b1 | 7.16 | 20 |
from pathlib import Path, PosixPath
from unittest import mock
from unittest.mock import Mock, patch
from click.testing import CliRunner
from leverage import leverage
from leverage.modules.kubectl import _scan_clusters, ClusterInfo
def test_scan_clusters():
"""
Test that we can find valid metadata.yaml prese... | binbashar/leverage | tests/test_modules/test_kubectl.py | .py | 3be6914e1a09720d | 8.16 | 20 |
from unittest.mock import patch
import pytest
from leverage import leverage
from leverage.modules.tf import has_a_plan_file
@pytest.mark.parametrize(
"args",
[
([]),
(["-migrate-state"]),
(["-r1", "-r2"]),
],
)
def test_init_arguments(leverage_project, leverage_runner, args):
... | binbashar/leverage | tests/test_modules/test_tf.py | .py | 611c5f68f646d1e8 | 8.16 | 20 |
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