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 |
|---|---|---|---|---|---|---|
'''
The range of Pingdom probes from various locations.
The documentation can be found here:
https://documentation.solarwinds.com/en/success_center/pingdom/content/topics/pingdom-probe-servers-ip-addresses.htm?cshid=pd-rd_203682601-pingdom-probe-servers-ip-addresses
This is a parser for the set of IPs / IP ranges in C... | fartbagxp/aas-cidr-ranges | src/dl/download_pingdom.py | .py | ea88ca4b7cc1744a | 7.3 | 3 |
"""
Module for converting GenBank files to GTF format.
Usage:
python gb2gtf.py sequence.gb > sequence.gtf
"""
# download GenBank file from NCBI and then
# Usage:python gb2gtf.py sequence.gb > sequence.gtf
import sys
import Bio
from Bio import SeqIO
def main():
"""Run the CLI."""
if check_args(sys.arg... | CCBR/Tools | src/ccbr_tools/gb2gtf.py | .py | 8a9017e598b54a02 | 7.15 | 1 |
"""
GitHub helper functions
Contributor related functions:
- [](`~ccbr_tools.github.print_contributor_images`) - Print contributor profile images for HTML web pages
- [](`~ccbr_tools.github.get_repo_contributors`) - Get a list of contributors to a GitHub repository
- [](`~ccbr_tools.github.get_user_info`) - Get profi... | CCBR/Tools | src/ccbr_tools/github.py | .py | e115ca494ed5d322 | 7.15 | 1 |
#!/usr/bin/env python3
"""
Finds homologs in human and mouse.
About:
hf or HomologFinder finds homologs in human and mouse.
if the input gene or genelist is human, then it returns mouse homolog(s) and vice versa
Usage:
$ hf -h
Examples:
$ hf -g ZNF365
$ hf -l Wdr53,Zfp365
$ hf -f genelist.... | CCBR/Tools | src/ccbr_tools/homologfinder/hf.py | .py | 8ae9e4222265f58b | 7.15 | 1 |
"""
CLI for pre-commit hooks
"""
import click
from ..pkg_util import (
CustomClickGroup,
get_version,
)
from .detect_absolute_paths import detect_absolute_paths
from .sync_nextflow_version import sync_nextflow_version
@click.group(
cls=CustomClickGroup,
context_settings={"help_option_names": ["-h", ... | CCBR/Tools | src/ccbr_tools/hooks/__main__.py | .py | 110f737eee67162c | 7.15 | 1 |
"""
Detect absolute file paths
Any instances of absolute paths (i.e. paths starting with "/") in the given files will be detected and printed to the console (unless "abs-path:ignore" is included).
An error will be raised at the end if any are found.
## Usage with pre-commit
Add this to your `.pre-commit-config.yaml`... | CCBR/Tools | src/ccbr_tools/hooks/detect_absolute_paths.py | .py | 1c8ed21cbff95f32 | 7.15 | 1 |
"""
Synchronize `manifest.version` in `nextflow.config` with the repo `VERSION` file.
Whenever the `VERSION` file is updated, the `manifest.version` entry in `nextflow.config` will be updated to match it.
## Usage with pre-commit
Add this to your `.pre-commit-config.yaml` file:
```yaml
- repo: https://github.com/CC... | CCBR/Tools | src/ccbr_tools/hooks/sync_nextflow_version.py | .py | 20a6737e4eaa46b6 | 7.15 | 1 |
"""
Find the intersect of two files, returns the inner join
Original author: Skyler Kuhn (@skchronicles)
Usage:
intersect file1 file2
"""
import sys
def indexFile(filename, joinindex, header):
"""Index a tab-delimited file by the join column."""
filedict = {}
with open(filename, "r") as fh:
... | CCBR/Tools | src/ccbr_tools/intersect.py | .py | 9670ae51c5f2c048 | 7.15 | 1 |
"""
Get HPC usage metadata for a list of slurm jobids on biowulf
About:
This wrapper script works only on BIOWULF!
This script usage the "dashboard_cli" utility on biowulf to get HPC usage metadata
for a list of slurm jobids. These slurm jobids can be either provided at command
line or extracted from a... | CCBR/Tools | src/ccbr_tools/jobinfo.py | .py | c708aeab537e7cb5 | 7.15 | 1 |
#!/usr/bin/env python3
"""
module_list
A command-line utility to display information about currently loaded environment modules.
This script interacts with the system's module management system (e.g., Lmod or Environment Modules)
to retrieve and display information about loaded modules. It supports two primary modes ... | CCBR/Tools | src/ccbr_tools/module_list.py | .py | 7e2fac71b6612afe | 7.15 | 1 |
import ast
import glob
import json
import math
import pathlib
import tarfile
import warnings
from .shell import shell_run
def get_tree(pipeline_outdir, args="-aJ --du"):
"""
Generate a directory tree structure using the `tree` command-line utility
Note: when using -J with --du, the output is not valid J... | CCBR/Tools | src/ccbr_tools/paths.py | .py | af7d6518c53500fc | 7.15 | 1 |
"""
Take a peek at tab-delimited files
Usage:
peek <file.tsv> [buffer]
"""
import sys
from pathlib import Path
def usage():
"""Print usage information and exit program"""
bin_stem = Path(sys.argv[0]).stem
print(f"USAGE: {bin_stem} <file.tsv> [buffer]\n")
print("Assumptions:\n\tInput file is tab ... | CCBR/Tools | src/ccbr_tools/peek.py | .py | ffbdf789bc989da1 | 7.15 | 1 |
"""
Helpers for bioinformatics pipelines
Submodules:
- [](`~ccbr_tools.pipeline.cache`)
- [](`~ccbr_tools.pipeline.hpc`)
- [](`~ccbr_tools.pipeline.nextflow`)
- [](`~ccbr_tools.pipeline.util`)
Main classes & functions
- [](`~ccbr_tools.pipeline.count_pipeline_samples`): Count the number of samples in a pipeline run... | CCBR/Tools | src/ccbr_tools/pipeline/__init__.py | .py | fdbfdaacd4b42592 | 7.15 | 1 |
"""
Functions for singularity cache management
"""
import json
import os
import sys
def get_singularity_cachedir(output_dir=None, cache_dir=None):
"""
Returns the singularity cache directory.
If no user-provided cache directory is provided,
the default singularity cache is in the output directory.
... | CCBR/Tools | src/ccbr_tools/pipeline/cache.py | .py | 45d5a50737c71607 | 7.15 | 1 |
"""
Classes for working with different HPC clusters.
Use [](`~ccbr_tools.pipeline.hpc.get_hpc`) to retrieve an HPC Cluster instance,
which contains default attributes for supported clusters.
"""
import pathlib
import re
import shutil
from ..shell import shell_run
from .cache import get_sif_cache_dir, get_singularity... | CCBR/Tools | src/ccbr_tools/pipeline/hpc.py | .py | 3d625809911623c3 | 7.15 | 1 |
"""
Run Nextflow workflows in local and HPC environments.
Functions:
- init(output, pipeline_name='pipeline', **kwargs)
Initialize the launch directory by copying the system default config files.
- run(nextfile_path=None, nextflow_args=None, mode="local", pipeline_name=None, debug=False, hpc_options={})
Run a ... | CCBR/Tools | src/ccbr_tools/pipeline/nextflow.py | .py | 68579a67accd6840 | 7.15 | 1 |
"""
Utility functions for shell command execution.
"""
import contextlib
import io
import subprocess
def shell_run(
command_str,
capture_output=True,
check=True,
shell=True,
text=True,
concat_output=True,
):
"""
Run a shell command and return stdout/stderr
Args:
command_s... | CCBR/Tools | src/ccbr_tools/shell.py | .py | e7759e5c36ae426d | 7.15 | 1 |
from .pipeline.hpc import Cluster
from .shell import shell_run
from .versions import get_major_minor_version, match_semver
class Software:
@staticmethod
def create_software(tool_name, version, software_type=None):
"""Create a software object for the requested tool."""
tool_lower = tool_name.lo... | CCBR/Tools | src/ccbr_tools/software.py | .py | cdce19422066b989 | 7.15 | 1 |
"""
SPOOKER 👻
This command is designed to be used as part of the OnComplete/OnSuccess/OnError handlers as part of Snakemake and Nextflow pipelines.
It collects metadata about the pipeline run, bundles it into a tarball, and saves it to a common location for later retrieval.
Run `spooker --help` for more information.... | CCBR/Tools | src/ccbr_tools/spooker.py | .py | 4d2e59c298a8e421 | 7.15 | 1 |
"""
Template files for CCBR Tools.
### Templates
- `submit_slurm.sh` -- slurm submission script template
- `mkdocs-fnl` - theme for websites built with mkdocs material.
- `pkgdown-fnl` - theme for R package websites built with pkgdown.
### Quarto extensions
#### fnl
Quarto HTML format with FNL branding guidelines
... | CCBR/Tools | src/ccbr_tools/templates/__init__.py | .py | 69a1802750aa9136 | 7.15 | 1 |
"""
Get information from git tags, commit hashes, and GitHub releases.
"""
import json
import re
import warnings
from .pkg_util import get_url_json
from .shell import shell_run
def get_current_hash():
"""
Get the current commit hash.
Uses git rev-parse HEAD to get the current commit hash.
Returns:... | CCBR/Tools | src/ccbr_tools/versions.py | .py | 4246d9a68087a01d | 7.15 | 1 |
import pathlib
import pytest
@pytest.fixture
def data_dir():
"""Return the absolute path to the test data directory."""
return pathlib.Path(__file__).resolve().parent / "data"
@pytest.fixture
def data_dir_rel():
"""Return the relative path to the test data directory."""
return pathlib.Path("tests")... | CCBR/Tools | tests/conftest.py | .py | 684f281135d4fd3e | 7.15 | 1 |
import os
import pathlib
import pytest
from ccbr_tools.shell import shell_run
is_ci = (
os.environ.get("CI", "false") == "true"
) # Set CI to false if not in a CI environment
def test_version_flag():
"""Test version flag."""
version = shell_run("ccbr_tools --version")
assert version.startswith("cc... | CCBR/Tools | tests/test_cli.py | .py | 96927389f729da9d | 7.65 | 1 |
import pytest
from ccbr_tools import gb2gtf
from ccbr_tools.shell import exec_in_context
def test_check_args():
"""Test check args."""
test_cases = [
(["", "test"], True),
(["test"], False),
(["test", "-h"], False),
(["test", "--help"], False),
]
assert [gb2gtf.check_a... | CCBR/Tools | tests/test_gb2gtf.py | .py | 2585d2133c7d70af | 7.65 | 1 |
import pytest
from ccbr_tools.github import get_user_info, print_contributor_images
def test_print_contributor_images():
"""Test print contributor images."""
assert not print_contributor_images(repo="actions", org="CCBR")
def test_print_contributor_images_skips_apps(mocker):
"""Test that print_contribu... | CCBR/Tools | tests/test_github.py | .py | d647d4b2c5b7e493 | 7.65 | 1 |
import sys
import pytest
from ccbr_tools.GSEA import ncbr_huse
from ccbr_tools.shell import shell_run
def test_help_deg():
"""Test help deg."""
assert shell_run(f"{sys.executable} -m ccbr_tools.GSEA.deg2gs -h").startswith(
"usage: deg2gs.py"
)
def test_help_mt2excel():
"""Test help mt2exce... | CCBR/Tools | tests/test_gsea.py | .py | dd4df80c42fe569b | 7.65 | 1 |
import argparse
from ccbr_tools.homologfinder import hf
from ccbr_tools.shell import shell_run
def test_hf_gene():
"""Test hf gene."""
assert hf.hf(argparse.Namespace(gene="ZNF365", genelist="", genelistfile="")) == [
"Zfp365"
]
def test_hf_list():
"""Test hf list."""
assert hf.hf(
... | CCBR/Tools | tests/test_homologfinder.py | .py | 698b6aa038ab2a8f | 7.65 | 1 |
import pytest
import ccbr_tools.intersect
from ccbr_tools.shell import exec_in_context
def test_intersect(data_dir_rel):
"""Test intersect."""
out = exec_in_context(
ccbr_tools.intersect.run_intersect,
[
"intersect",
str(data_dir_rel / "file.txt"),
str(data... | CCBR/Tools | tests/test_intersect.py | .py | 68a7e4a4e239c630 | 7.65 | 1 |
"""Cross-job build deduplication for concurrent image sourcing."""
from __future__ import annotations
import threading
class BuildCoordinator:
"""Tracks in-flight image builds so concurrent jobs don't duplicate work.
Usage::
event = coordinator.try_acquire(tag)
if event is not None:
... | perftool-incubator/rickshaw | source-images-service/source_images_service/core/build_coordinator.py | .py | de5774afba52d62a | 7.24 | 2 |
"""Custom exception hierarchy for source-images-service."""
from __future__ import annotations
class SourceImagesError(Exception):
"""Base exception for all source-images-service errors."""
class SubprocessError(SourceImagesError):
"""A subprocess exited with a non-zero return code or timed out."""
de... | perftool-incubator/rickshaw | source-images-service/source_images_service/core/exceptions.py | .py | 1f5e0272be5df034 | 7.24 | 2 |
"""Filesystem utilities — port of Perl find_files() (L61-94)."""
from __future__ import annotations
import os
# Directory / file names to skip during recursive walk
_SKIP_NAMES: set[str] = {".", "..", ".git", "docs", ".github", "__pycache__"}
# File extensions to skip
_SKIP_EXTENSIONS: set[str] = {".md"}
def find... | perftool-incubator/rickshaw | source-images-service/source_images_service/core/file_utils.py | .py | 9abcd26ab5ce32ee | 7.24 | 2 |
"""Job lifecycle management with in-memory store and thread pool executor."""
from __future__ import annotations
import logging
import threading
import time
import uuid
from concurrent.futures import ThreadPoolExecutor
from dataclasses import dataclass, field
from typing import Any
from source_images_service.config ... | perftool-incubator/rickshaw | source-images-service/source_images_service/core/job_manager.py | .py | 3b8e25982fe2f641 | 7.24 | 2 |
"""Container registry operations via skopeo/buildah — port of Perl L264-503."""
from __future__ import annotations
import logging
import os
import time
from typing import TYPE_CHECKING
from source_images_service.core.exceptions import RegistryError
from source_images_service.core.subprocess_runner import run_cmd
if... | perftool-incubator/rickshaw | source-images-service/source_images_service/core/registry_ops.py | .py | 9de5fa1b60486614 | 7.24 | 2 |
"""Ordered requirement list builder — port of Perl build_reqs() (L505-583)."""
from __future__ import annotations
import json
import logging
import re
from dataclasses import dataclass, field
from pathlib import Path
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from source_images_service.core.workspace imp... | perftool-incubator/rickshaw | source-images-service/source_images_service/core/requirements_builder.py | .py | e1b509b1f3cc7bd7 | 7.24 | 2 |
"""Thin wrapper around subprocess.run — port of Perl toolbox::run::run_cmd()."""
from __future__ import annotations
import logging
import subprocess
from dataclasses import dataclass
from typing import TYPE_CHECKING
from source_images_service.core.exceptions import SubprocessError
if TYPE_CHECKING:
from source_... | perftool-incubator/rickshaw | source-images-service/source_images_service/core/subprocess_runner.py | .py | b2610431e76e8dbf | 7.24 | 2 |
"""Image building via workshop script — port of Perl workshop_build_image() (L323-378)."""
from __future__ import annotations
import json
import logging
from typing import TYPE_CHECKING
from source_images_service.core.exceptions import SubprocessError, WorkshopBuildError
from source_images_service.core.subprocess_ru... | perftool-incubator/rickshaw | source-images-service/source_images_service/core/workshop_runner.py | .py | 06f14c6a15d21e12 | 7.24 | 2 |
"""Workspace materialization — decode base64 request content to temp directories."""
from __future__ import annotations
import base64
import logging
import os
import shutil
import tempfile
from dataclasses import dataclass, field
from pathlib import Path
from source_images_service.models.requests import (
Base64... | perftool-incubator/rickshaw | source-images-service/source_images_service/core/workspace.py | .py | 02d54dabc9869b77 | 7.24 | 2 |
#!/usr/bin/env python3
# -*- mode: python; indent-tabs-mode: nil; python-indent-level: 4 -*-
# vim: autoindent tabstop=4 shiftwidth=4 expandtab softtabstop=4 filetype=python
"""Unit tests for rickshaw-run.py's RunState.apply_tool_multiplex() -- the
bridge that lets a tool's flat tool-params.json params get validated/
... | perftool-incubator/rickshaw | tests/test_apply_tool_multiplex.py | .py | 161b94b64daa85aa | 7.74 | 2 |
#!/usr/bin/env python3
# -*- mode: python; indent-tabs-mode: nil; python-indent-level: 4 -*-
# vim: autoindent tabstop=4 shiftwidth=4 expandtab softtabstop=4 filetype=python
"""Unit tests for rickshaw-run.py's dropped-follower tracking:
RunState.remove_followers()/remove_dropped_followers()/remove_engine_followers()
a... | perftool-incubator/rickshaw | tests/test_dropped_followers.py | .py | b4c5161425b4f9d0 | 7.74 | 2 |
#!/usr/bin/env python3
# -*- mode: python; indent-tabs-mode: nil; python-indent-level: 4 -*-
# vim: autoindent tabstop=4 shiftwidth=4 expandtab softtabstop=4 filetype=python
"""Unit tests for rickshaw-run.py's dump_params()/render_param().
Covers rickshaw#867: a param value containing a space must be rendered with
en... | perftool-incubator/rickshaw | tests/test_dump_params.py | .py | 0f90b32345e2e109 | 7.74 | 2 |
#!/usr/bin/env python3
# -*- mode: python; indent-tabs-mode: nil; python-indent-level: 4 -*-
# vim: autoindent tabstop=4 shiftwidth=4 expandtab softtabstop=4 filetype=python
"""Unit tests for endpoints.py's do_roadblock() thin wrapper around
toolbox.roadblock.do_roadblock() (PERFNFV-462).
toolbox, roadblock, and the ... | perftool-incubator/rickshaw | tests/test_endpoints_do_roadblock.py | .py | 201729ea0f405457 | 7.74 | 2 |
#!/usr/bin/env python3
# -*- mode: python; indent-tabs-mode: nil; python-indent-level: 4 -*-
# vim: autoindent tabstop=4 shiftwidth=4 expandtab softtabstop=4 filetype=python
"""Unit tests for endpoints.py's process_bench_roadblocks() data-structure
initialization (rickshaw#867's third consumer).
This is a separate, e... | perftool-incubator/rickshaw | tests/test_endpoints_process_bench_roadblocks.py | .py | c72e8b6fe7c78370 | 7.74 | 2 |
#!/usr/bin/env python3
# -*- mode: python; indent-tabs-mode: nil; python-indent-level: 4 -*-
# vim: autoindent tabstop=4 shiftwidth=4 expandtab softtabstop=4 filetype=python
"""Unit tests for rickshaw-run.py's expand_id_ranges() and
RunState.load_bench_params()'s automatic per-instance param id-scoping.
Fixes a bug w... | perftool-incubator/rickshaw | tests/test_load_bench_params_duplicate_names.py | .py | a9a1c728be0735bf | 7.74 | 2 |
#!/usr/bin/env python3
# -*- mode: python; indent-tabs-mode: nil; python-indent-level: 4 -*-
# vim: autoindent tabstop=4 shiftwidth=4 expandtab softtabstop=4 filetype=python
"""Unit tests for rickshaw-post-process-bench.py's dump_params().
This is a second, independently-maintained "port of the Perl
dump_params() fun... | perftool-incubator/rickshaw | tests/test_post_process_bench_dump_params.py | .py | 11a7472ad65da2f6 | 7.74 | 2 |
#!/usr/bin/env python3
"""Summarize Claude Code OTLP telemetry captured during a GitHub Actions run.
Reads the newline-delimited OTLP JSON written by the collector's file exporter
and emits a markdown report of token usage per model, plus Claude Code's own
list-price USD estimate.
When the workflow supplies the diff ... | Lattice-Data/lattice-tools | .github/scripts/summarize_claude_usage.py | .py | 35da6fa8cefdb8a0 | 7.35 | 4 |
"""
Validate and repair CAS Registry Numbers before spending a request on them.
Shared by `chebi_lookup` and `structure_check`. It lives at the `bcp/` top level
rather than inside either package so neither has to import the other for a check
that belongs to both. Without it, `chebi_lookup.cas_to_cid()` and
`structure_... | Lattice-Data/lattice-tools | bcp/cas_registry.py | .py | 6ea8a149e9120c70 | 7.35 | 4 |
"""PubChem PUG REST client: CAS Registry Number → CID → properties + ChEBI xref."""
from __future__ import annotations
import logging
import time
import urllib.parse
from typing import Any
import requests
from cas_registry import CAS_INVALID_FORMAT, CAS_MISSING, classify_cas
# PubChem rate limits: 5 req/s, 400 req... | Lattice-Data/lattice-tools | bcp/chebi_lookup/client.py | .py | 0c098bf4c035849d | 7.35 | 4 |
"""CSV batch I/O and single-CAS output for CAS → ChEBI mapping."""
from __future__ import annotations
import csv
import json
import logging
import sys
from pathlib import Path
from typing import Any, Literal
from .client import OUTPUT_FIELDS_APPENDED, lookup_cas
log = logging.getLogger(__name__)
class CasMappingE... | Lattice-Data/lattice-tools | bcp/chebi_lookup/io.py | .py | bb0efbec58276bb3 | 7.35 | 4 |
"""Record live PubChem JSON responses as committed test fixtures."""
from __future__ import annotations
import argparse
import json
import logging
import sys
import time
import urllib.parse
from pathlib import Path
import requests
from cas_registry import CAS_INVALID_FORMAT, CAS_MISSING, classify_cas
from .client ... | Lattice-Data/lattice-tools | bcp/chebi_lookup/record_fixtures.py | .py | 06d1f896b99d738d | 7.35 | 4 |
"""ChEBI REST client: ChEBI ID → authoritative name, synonyms, and validation verdicts."""
from __future__ import annotations
import html
import logging
import re
import time
from typing import Any, Iterator
import requests
# The ChEBI backend publishes no documented rate limit. Mirror the polite
# spacing chebi_lo... | Lattice-Data/lattice-tools | bcp/chebi_terms/client.py | .py | 574d55d2fb48f76c | 7.35 | 4 |
"""Record live ChEBI JSON responses as committed test fixtures."""
from __future__ import annotations
import argparse
import json
import logging
import sys
from pathlib import Path
from .client import ChebiUnavailableError, fetch_compound, normalize_chebi_id
log = logging.getLogger(__name__)
# bcp/tests/fixtures/c... | Lattice-Data/lattice-tools | bcp/chebi_terms/record_fixtures.py | .py | bea3f4abadb225ca | 7.35 | 4 |
from __future__ import annotations
from dataclasses import dataclass, field
from typing import Any
from .constants import CRAM_COLUMNS, SHEET_HELPER_COLUMNS
from .enrich import fetch_results
from .models import ListedObject, RunSummary
from .s3_utils import s3_uri_for
from .sheets import (
SequenceFileRecord,
... | Lattice-Data/lattice-tools | bcp/file_extract/cram.py | .py | 0367bef1d5cfb117 | 7.35 | 4 |
"""Shared per-file enrichment for deliverables under an S3 order prefix.
FASTQ and CRAM deliverables are enriched identically: fetch the object's
CRC64NVME, then read ``read_count`` from the companion ``<key>-metadata.json``
the CRO writes beside it. Both retry transient S3 errors the same way and both
fan the work ou... | Lattice-Data/lattice-tools | bcp/file_extract/enrich.py | .py | af4d7fe2484ec268 | 7.35 | 4 |
from __future__ import annotations
from dataclasses import dataclass, field
@dataclass(frozen=True)
class S3Location:
"""Parsed S3 URI."""
bucket: str
prefix: str
@dataclass(frozen=True)
class ListedObject:
"""S3 object from a listing."""
key: str
size_bytes: int
@dataclass
class RunSum... | Lattice-Data/lattice-tools | bcp/file_extract/models.py | .py | 2fb56ffda3e13050 | 7.35 | 4 |
from __future__ import annotations
import random
import time
from typing import Callable, TypeVar
from botocore.exceptions import (
ClientError,
ConnectTimeoutError,
ConnectionClosedError,
EndpointConnectionError,
ReadTimeoutError,
)
from .constants import TRANSIENT_ERROR_CODES, TRANSIENT_HTTP_ST... | Lattice-Data/lattice-tools | bcp/file_extract/retry.py | .py | abef4c7d3237b8d9 | 7.35 | 4 |
from __future__ import annotations
from typing import Any, Callable
from urllib.parse import urlparse
from .models import ListedObject, S3Location
from .retry import retry_with_backoff
def parse_s3_uri(uri: str) -> S3Location:
"""Parse s3://bucket/prefix into bucket and normalized prefix (trailing /)."""
pa... | Lattice-Data/lattice-tools | bcp/file_extract/s3_utils.py | .py | 428cb83f9a1357f7 | 7.35 | 4 |
"""Lattice submission-sheet shaping for extracted file metadata.
Turns enriched S3 records into two TSVs whose columns mirror the Lattice
``SequenceFile`` and ``SequenceFileSet`` tabs, so a run's output pastes into the
submission workbook at A2 without reordering. Alias derivation lives here too,
since the sheets refe... | Lattice-Data/lattice-tools | bcp/file_extract/sheets.py | .py | 45c707c5ee2d019f | 7.35 | 4 |
#!/usr/bin/env python3
"""
Annotate CRISPR guides with gene identifiers from GTF file based on coordinate overlap.
Hybrid implementation: one row per overlap, includes gene names, handles edge cases.
"""
import csv
import argparse
from collections import defaultdict
def parse_gtf(gtf_file):
"""
Parse GTF fil... | Lattice-Data/lattice-tools | bcp/guide_to_gene.py | .py | e16b8185f353fb5c | 7.35 | 4 |
#!/usr/bin/env python3
"""
Annotate CRISPR guides with gene identifiers from GTF file using bioframe for overlap detection.
Bioframe implementation: one row per overlap, includes gene names, handles edge cases.
"""
import csv
import argparse
import pandas as pd
import bioframe as bf
def csv_to_bed_dataframe(csv_file... | Lattice-Data/lattice-tools | bcp/guide_to_gene_bioframe.py | .py | b6763266d828e2bf | 7.35 | 4 |
"""Core library for protospacer set signatures."""
from __future__ import annotations
import csv
from hashlib import sha256
from pathlib import Path
_ACGT = frozenset("ACGT")
DEFAULT_COLUMN = "guide_protospacer"
# Single source of truth for the accepted input formats: the parser reads the
# delimiter from here and ... | Lattice-Data/lattice-tools | bcp/guidesig/core.py | .py | 2560578fc2d7a644 | 7.35 | 4 |
from __future__ import annotations
from dataclasses import dataclass
from pathlib import Path
from typing import List, Tuple
@dataclass(frozen=True)
class MappingRow:
"""Single row from a mapping file."""
s3_path: str
local_path: str
line_num: int
def _looks_like_s3(s: str) -> bool:
return s.s... | Lattice-Data/lattice-tools | bcp/mapping_validation/parsing.py | .py | 2bb8ed0bdb4f62da | 7.35 | 4 |
"""Build step: loads Chart.yaml into context."""
import argparse
import logging
import os
from typing import Set
import yaml
from step_exec_lib.errors import ValidationError
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import Context, StepType
from app_build_suite.build_steps.helm_consts import... | giantswarm/app-build-suite | app_build_suite/build_steps/chart_yaml_loader.py | .py | 9598f049bd25f6d3 | 7.39 | 5 |
"""Build step: writes the in-context Chart.yaml dict to disk."""
import argparse
import logging
import os
import shutil
from typing import Set
import yaml
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import Context, StepType
from app_build_suite.build_steps.helm_consts import (
CHART_YAML,
... | giantswarm/app-build-suite | app_build_suite/build_steps/chart_yaml_writer.py | .py | 0ac115a0b9e9c573 | 7.39 | 5 |
"""Build steps implementing helm3 based builds."""
from step_exec_lib.steps import BuildStepsFilteringPipeline
from app_build_suite.build_steps.chart_yaml_loader import ChartYamlLoader
from app_build_suite.build_steps.chart_yaml_writer import ChartYamlWriter
from app_build_suite.build_steps.giantswarm_helm_validator ... | giantswarm/app-build-suite | app_build_suite/build_steps/helm.py | .py | 873056ba2385f692 | 7.39 | 5 |
"""Build step: injects missing Artifact Hub metadata into Chart.yaml at package time."""
import argparse
import logging
import os
import shutil
from typing import Dict, List, Optional, Set
import configargparse
import yaml
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import Context, StepType
fr... | giantswarm/app-build-suite | app_build_suite/build_steps/helm_artifacthub_metadata_setter.py | .py | c161f5e58e9a4120 | 7.39 | 5 |
"""Build step: validates the chart directory contains a valid Helm chart."""
import argparse
import logging
import os
from typing import Set
import configargparse
import yaml
from step_exec_lib.errors import ValidationError
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import Context, StepType
f... | giantswarm/app-build-suite | app_build_suite/build_steps/helm_builder_validator.py | .py | 45085bad0587bcf3 | 7.39 | 5 |
"""Build step: builds a helm chart using helm package."""
import argparse
import logging
import os
from typing import Set
import configargparse
from step_exec_lib.errors import ValidationError
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import Context, StepType
from step_exec_lib.utils.processe... | giantswarm/app-build-suite | app_build_suite/build_steps/helm_chart_builder.py | .py | c36fb0225e4098e8 | 7.39 | 5 |
"""Build step: finalizes metadata generation after chart build."""
import argparse
import copy
import logging
import os
import pathlib
import shutil
from datetime import datetime, timezone
from typing import Any, Set
import yaml
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import Context, StepTy... | giantswarm/app-build-suite | app_build_suite/build_steps/helm_chart_metadata_finalizer.py | .py | 17ddc605bf46488b | 7.39 | 5 |
"""Build step: runs helm ct linter against the chart."""
import argparse
import logging
import os
from typing import Set
import configargparse
from step_exec_lib.errors import ValidationError
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import Context, StepType
from step_exec_lib.utils.processes... | giantswarm/app-build-suite | app_build_suite/build_steps/helm_chart_tool_linter.py | .py | cbe1e8d2278f8e21 | 7.39 | 5 |
"""Build step: sets the 'home' field in Chart.yaml from git remote URL."""
import argparse
import logging
from typing import Optional, Set
import configargparse
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import Context, StepType
from app_build_suite.build_steps.helm_consts import (
CHART_... | giantswarm/app-build-suite | app_build_suite/build_steps/helm_home_url_setter.py | .py | 67002f057def75b5 | 7.39 | 5 |
"""Build step: runs helm dependency update."""
import argparse
import logging
import os
import shutil
from typing import List, Set
from step_exec_lib.errors import ValidationError
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import Context, StepType
from step_exec_lib.utils.processes import run_... | giantswarm/app-build-suite | app_build_suite/build_steps/helm_requirements_updater.py | .py | ce5a7a939ed92e5b | 7.39 | 5 |
"""Build step: renders the chart with 'helm template' and validates the output YAML."""
import argparse
import logging
import os
import re
from typing import Set
import configargparse
import yaml
from step_exec_lib.errors import ValidationError
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import... | giantswarm/app-build-suite | app_build_suite/build_steps/helm_template_validator.py | .py | bf63ff1c1dc84a24 | 7.39 | 5 |
"""Build step: sets chart version/appVersion from command line arguments."""
import argparse
import logging
from typing import Set
import configargparse
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import Context, StepType
from app_build_suite.build_steps.helm_consts import (
CHART_YAML,
... | giantswarm/app-build-suite | app_build_suite/build_steps/helm_version_setter.py | .py | 242a8a0fdbb4bee2 | 7.39 | 5 |
"""Build step: runs kube-linter against the chart."""
import argparse
import logging
import os
from typing import Set
import configargparse
from step_exec_lib.errors import ValidationError
from step_exec_lib.steps import BuildStep
from step_exec_lib.types import Context, StepType
from step_exec_lib.utils.processes im... | giantswarm/app-build-suite | app_build_suite/build_steps/kube_linter.py | .py | 4fc4c117b02fd08a | 7.39 | 5 |
"""Module with git related utilities."""
from typing import Optional
import git
class GitRepoVersionInfo:
"""
Provides application versions information based on the tags and commits in the repo
"""
def __init__(self, path: str):
"""
Create an instance of GitRepoVersionInfo
:... | giantswarm/app-build-suite | app_build_suite/utils/git.py | .py | 7f5b34f14a4ec42a | 7.39 | 5 |
"""Git URL utilities for remote URL manipulation."""
import re
from typing import Optional
class GitUrlConverter:
"""Handles conversion between git URL formats for GitHub repositories."""
# SSH format: git@github.com:org/repo.git or git@github.com:org/repo
_SSH_PATTERN = re.compile(r"^git@github\.com:([... | giantswarm/app-build-suite | app_build_suite/utils/git_url.py | .py | 8a9abfd91fdd31ff | 7.39 | 5 |
"""Strict YAML loading helpers that fail on duplicate mapping keys.
PyYAML's SafeLoader silently keeps the last value when a mapping key is duplicated,
which for rendered Helm manifests means silently dropped configuration.
"""
from typing import Any, Dict, Optional
import yaml
class DuplicateKeyError(yaml.YAMLErr... | giantswarm/app-build-suite | app_build_suite/utils/yaml_strict.py | .py | a1b03aaf8c827a45 | 7.39 | 5 |
import pytest
from app_build_suite.utils.git_url import GitUrlConverter
class TestGitUrlConverter:
"""Tests for GitUrlConverter utility class."""
@pytest.mark.parametrize(
"url,expected",
[
# SSH format URLs
("git@github.com:org/repo.git", True),
("git@git... | giantswarm/app-build-suite | tests/utils/test_git_url.py | .py | fa1ffa646abb7d2f | 7.89 | 5 |
from typing import List, Optional
import pytest
import yaml
from app_build_suite.utils.yaml_strict import DuplicateKeyError, UniqueKeyLoader, find_nearest_source
VALID_MULTI_DOC = """---
# Source: my-app/templates/deployment.yaml
apiVersion: apps/v1
kind: Deployment
metadata:
name: my-app
---
# Source: my-app/temp... | giantswarm/app-build-suite | tests/utils/test_yaml_strict.py | .py | e813e09c0d206eb9 | 7.89 | 5 |
"""Provide CLI helpers."""
import asyncio
from collections.abc import Awaitable, Callable
import logging
from aiomysensors.exceptions import (
AIOMySensorsError,
InvalidMessageError,
MissingChildError,
MissingNodeError,
)
from aiomysensors.gateway import Gateway
LOGGER = logging.getLogger("aiomysenso... | MartinHjelmare/aiomysensors | src/aiomysensors/cli/helper.py | .py | 4e8d7e272426f123 | 7.24 | 2 |
"""Provide a gateway."""
from __future__ import annotations
from collections.abc import AsyncGenerator
from dataclasses import dataclass, field
import logging
from types import TracebackType
from typing import Self
from .model.message import Message, MessageSchema
from .model.node import Node
from .model.protocol im... | MartinHjelmare/aiomysensors | src/aiomysensors/gateway.py | .py | 49ce0b3792e00146 | 7.24 | 2 |
"""Provide a MySensors message abstraction.
Validation should be done on a protocol level, i.e. not with gateway state.
"""
from __future__ import annotations
from dataclasses import dataclass
from typing import TYPE_CHECKING, Literal, Self
from mashumaro import DataClassDictMixin
from aiomysensors.exceptions impo... | MartinHjelmare/aiomysensors | src/aiomysensors/model/message.py | .py | f1bb9da4dd6a78c9 | 7.24 | 2 |
"""Provide a MySensors node and child abstraction."""
from __future__ import annotations
from dataclasses import dataclass, field
from mashumaro import DataClassDictMixin, field_options
from mashumaro.config import BaseConfig
from aiomysensors.exceptions import MissingChildError
@dataclass(kw_only=True)
class Nod... | MartinHjelmare/aiomysensors | src/aiomysensors/model/node.py | .py | 335652e9898b2c32 | 7.24 | 2 |
"""Provide MySensors protocols."""
from __future__ import annotations
from enum import IntEnum
from functools import cache
from typing import (
Protocol,
cast,
)
from awesomeversion import AwesomeVersion
from aiomysensors.model.const import DEFAULT_PROTOCOL_VERSION
from . import protocol_14, protocol_15, p... | MartinHjelmare/aiomysensors | src/aiomysensors/model/protocol/__init__.py | .py | ad300d598a7cef14 | 7.24 | 2 |
"""Provide the protocol for MySensors version 1.4."""
from __future__ import annotations
import calendar
from collections.abc import Awaitable, Callable, Coroutine
from enum import IntEnum
import time
from typing import Any
from aiomysensors.exceptions import (
InvalidMessageError,
MissingChildError,
Mis... | MartinHjelmare/aiomysensors | src/aiomysensors/model/protocol/protocol_14.py | .py | 2c1a707224df72a1 | 7.24 | 2 |
"""Provide the protocol for MySensors version 1.5."""
from enum import IntEnum
from .protocol_14 import ( # noqa: F401
INTERNAL_COMMAND_TYPE,
STRICT_SYSTEM_COMMAND_TYPES,
VALID_SYSTEM_COMMAND_TYPES,
Command,
Stream,
)
from .protocol_14 import (
IncomingMessageHandler as IncomingMessageHandler... | MartinHjelmare/aiomysensors | src/aiomysensors/model/protocol/protocol_15.py | .py | c236f8962c3a57a2 | 7.24 | 2 |
"""Provide the protocol for MySensors version 2.0."""
from __future__ import annotations
from collections.abc import Awaitable, Callable, Coroutine
from enum import IntEnum
from functools import wraps
from typing import Any
from aiomysensors.exceptions import MissingChildError, MissingNodeError
from aiomysensors.mod... | MartinHjelmare/aiomysensors | src/aiomysensors/model/protocol/protocol_20.py | .py | b7f6acdd5b7e18c0 | 7.24 | 2 |
"""Provide the protocol for MySensors version 2.1."""
from enum import IntEnum
from .protocol_20 import ( # noqa: F401
INTERNAL_COMMAND_TYPE,
STRICT_SYSTEM_COMMAND_TYPES,
VALID_MESSAGE_TYPES,
VALID_SYSTEM_COMMAND_TYPES,
Command,
Presentation,
SetReq,
Stream,
)
from .protocol_20 import... | MartinHjelmare/aiomysensors | src/aiomysensors/model/protocol/protocol_21.py | .py | ccf296c2de1049d2 | 7.24 | 2 |
"""Provide the protocol for MySensors version 2.2."""
from __future__ import annotations
from enum import IntEnum
from aiomysensors.exceptions import MissingNodeError
from aiomysensors.model.message import Message
from .protocol_20 import handle_missing_node_child
from .protocol_21 import ( # noqa: F401
INTERN... | MartinHjelmare/aiomysensors | src/aiomysensors/model/protocol/protocol_22.py | .py | 5daee74241df0b22 | 7.24 | 2 |
"""Provide persistence."""
import asyncio
from collections.abc import Callable, Coroutine
from dataclasses import dataclass, field
import json
import logging
from pathlib import Path
from typing import Any
from .exceptions import PersistenceReadError, PersistenceWriteError
from .model.node import Node
LOGGER = loggi... | MartinHjelmare/aiomysensors | src/aiomysensors/persistence.py | .py | b658a65ee6a9b52a | 7.24 | 2 |
"""Provide an MQTT transport."""
from abc import abstractmethod
import asyncio
import contextlib
from dataclasses import dataclass
from enum import Enum
import logging
import uuid
from aiomqtt import Client as AsyncioClient
from aiomqtt import MqttError
from aiomysensors.exceptions import TransportError, TransportFa... | MartinHjelmare/aiomysensors | src/aiomysensors/transport/mqtt.py | .py | fc6fbb5e842c2bf2 | 7.24 | 2 |
"""Provide a serial transport."""
import asyncio
from serialx import open_serial_connection
from . import StreamTransport
class SerialTransport(StreamTransport):
"""Represent a serial transport."""
def __init__(self, port: str, baud: int = 115200) -> None:
"""Set up serial transport."""
su... | MartinHjelmare/aiomysensors | src/aiomysensors/transport/serial.py | .py | 067cc435d7eab526 | 7.24 | 2 |
"""Provide a TCP transport."""
import asyncio
from . import StreamTransport
class TCPTransport(StreamTransport):
"""Represent a TCP transport."""
def __init__(self, host: str, port: int = 5003) -> None:
"""Set up TCP transport."""
super().__init__()
self.host = host
self.por... | MartinHjelmare/aiomysensors | src/aiomysensors/transport/tcp.py | .py | 7a512bdeed41885f | 7.24 | 2 |
"""Provide common fixtures for the CLI."""
from collections.abc import Generator
from unittest.mock import AsyncMock, patch
import pytest
from aiomysensors.gateway import Gateway
@pytest.fixture(name="gateway_cli", autouse=True)
def gateway_cli_fixture() -> Generator[Gateway]:
"""Mock the CLI gateway handler."... | MartinHjelmare/aiomysensors | tests/cli/conftest.py | .py | 9a08c98bcb42d568 | 7.74 | 2 |
"""Provide test tools."""
from copy import deepcopy
from typing import Any
from aiomysensors.transport import Transport
NODE_SERIALIZED = {
"children": {},
"protocol_version": "2.0",
"sketch_version": "",
"node_type": 17,
"sketch_name": "",
"node_id": 0,
"battery_level": None,
"sleepi... | MartinHjelmare/aiomysensors | tests/common.py | .py | 5fa8b6a1134e33dc | 7.74 | 2 |
"""Provide common fixtures."""
from collections.abc import Generator
from pathlib import Path
from unittest.mock import MagicMock, patch
import pytest
from aiomysensors.gateway import Gateway
from aiomysensors.model.const import DEFAULT_PROTOCOL_VERSION
from aiomysensors.model.message import Message, MessageSchema
f... | MartinHjelmare/aiomysensors | tests/conftest.py | .py | 68eff70fc8d2b6db | 7.74 | 2 |
"""Provide common protocol fixtures."""
import pytest
from aiomysensors.gateway import Gateway
from aiomysensors.model.message import Message, MessageSchema
from aiomysensors.model.node import Node
from tests.common import MockTransport
@pytest.fixture(name="command")
def command_fixture(
message_schema: Messag... | MartinHjelmare/aiomysensors | tests/model/protocol/conftest.py | .py | a47f55ae5883bb95 | 7.74 | 2 |
"""Test the node and child model."""
from mashumaro.exceptions import MissingField
import pytest
from aiomysensors.exceptions import MissingChildError
from aiomysensors.model.node import Child, Node
from tests.common import NODE_CHILD_SERIALIZED, NODE_SERIALIZED
def test_dump(child: Child) -> None:
"""Test dump... | MartinHjelmare/aiomysensors | tests/model/test_node.py | .py | 1f37a43d4ff82931 | 7.74 | 2 |
"""Compatibility shim for implementation-specific ``greenlet._greenlet`` APIs.
Most functions in this module exist to satisfy greenlet compatibility tests and
downstream callers that probe internal greenlet APIs. They do not implement core
tealet switching semantics.
In upstream greenlet, the optional-cleanup APIs (a... | kristjanvalur/pytealet | packages/tealet-greenlet/src/tealet_greenlet/_greenlet.py | .py | 6b981c91737f2ce5 | 7 | 0 |
# -*- coding: utf-8 -*-
"""
If we have a run callable passed to the constructor or set as an
attribute, but we don't actually use that (because ``__getattribute__``
or the like interferes), then when we clear callable before beginning
to run, there's an opportunity for Python code to run.
"""
import greenlet
g = None... | kristjanvalur/pytealet | packages/tealet-greenlet/tests/compat_greenlet/fail_clearing_run_switches.py | .py | a38df7a00fe7502b | 7.5 | 0 |
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