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 |
|---|---|---|---|---|---|---|
"""Dual data and motif clustering (DDMC).
Contains the `DDMC` model itself — a `sklearn.mixture.GaussianMixture`
subclass that jointly clusters peptides on their phosphorylation signal and
their sequence motif — and `get_pspl_pssm_distances`, the helper it uses to
compare cluster motifs against kinase specificity prof... | meyer-lab/DDMC | ddmc/clustering.py | .py | d9765f3d5339574f | 7.15 | 1 |
"""Loaders for the mass-spec datasets bundled with the package.
Contains:
- `CPTAC`: the CPTAC lung cancer clinical phosphoproteomics cohort, plus
accompanying clinical metadata (mutation calls, tumor/NAT status,
hot/cold immune infiltration labels) used in the DDMC paper.
- `EBDT`: the MCF7 kinase... | meyer-lab/DDMC | ddmc/datasets.py | .py | f55b095ce8e2434f | 7.15 | 1 |
"""Shared plotting and figure-assembly helpers used across `ddmc/figures/figureM*.py`.
Contains:
- `getSetup` / `subplotLabel` / `overlayCartoon`: build a labeled
multi-panel matplotlib figure and overlay static SVG cartoons onto it.
- `genFigure`: the `fbuild` console-script entry point (see
`pypr... | meyer-lab/DDMC | ddmc/figures/common.py | .py | ac999c4c524bebe7 | 7.15 | 1 |
"""
This creates Figure 2: Validations
"""
import numpy as np
import pandas as pd
import seaborn as sns
from ddmc.binomial import AAlist
from ddmc.clustering import DDMC, compute_control_pssm, get_pspl_pssm_distances
from ddmc.datasets import CPTAC, EBDT
from ddmc.figures.common import (
getSetup,
plot_cluste... | meyer-lab/DDMC | ddmc/figures/figureM3.py | .py | c7cb2c90183a3a63 | 7.15 | 1 |
import numpy as np
import pandas as pd
from bioinfokit import visuz
from scipy.stats import mannwhitneyu
from sklearn.linear_model import LogisticRegressionCV
from statsmodels.stats.multitest import multipletests
from ddmc.clustering import DDMC
from ddmc.datasets import CPTAC
from ddmc.figures.common import (
get... | meyer-lab/DDMC | ddmc/figures/figureM6.py | .py | c38a3a82bad946eb | 7.15 | 1 |
"""Logistic Regression Model functions to predict clinical features of CPTAC patients given their clustered phosphoproteomes.
Contains:
- `normalize_cluster_centers`: mean-centers `DDMC` cluster centers along
the patient dimension, for use as classifier features.
- `get_highest_weighted_clusters`: picks ... | meyer-lab/DDMC | ddmc/logistic_regression.py | .py | 5974b2536fba5f93 | 7.15 | 1 |
"""Mapping to Uniprot's Proteome To Generate +/-5AA p-site Motifs.
Contains:
- `get_proteome_name_to_seq`: parses a UniProt FASTA proteome into a
`{protein name: sequence}` dictionary; used by `ddmc.datasets.EBDT`.
- `get_pspls`: loads kinase specificity profiles (position-specific
peptide librarie... | meyer-lab/DDMC | ddmc/motifs.py | .py | c7aaa7b6e7f3c2e2 | 7.15 | 1 |
"""PAM250 sequence-distance model used by `ddmc.clustering.DDMC`.
Contains the `PAM250` class, which scores peptide sequences against each
cluster by their average PAM250 substitution-matrix similarity to the other
sequences currently assigned to that cluster, and `get_pam250_scores`, which
precomputes the full pairwi... | meyer-lab/DDMC | ddmc/pam250.py | .py | 125033d427b080f2 | 7.15 | 1 |
"""
Testing file for the clustering methods by data and sequence.
"""
import numpy as np
import pandas as pd
import pytest
from scipy.spatial.distance import cdist
from sklearn.metrics.pairwise import cosine_similarity
from sklearn.mixture import GaussianMixture
from ddmc.clustering import DDMC, get_pspl_pssm_distanc... | meyer-lab/DDMC | ddmc/tests/test_cluster.py | .py | 86777cd0e7a5c11e | 7.65 | 1 |
# -*- coding: utf-8 -*-
"""
Container and membership like objects (eg, sets)
https://docs.python.org/3/library/collections.abc.html#collections.abc.Container
"""
from ..compat import *
class MembershipSet(set):
"""A set with all the AND, OR, and UNION operations disabled, making it
really only handy for tes... | Jaymon/datatypes | datatypes/collections/container.py | .py | 397c483285ddf375 | 7.39 | 5 |
# -*- coding: utf-8 -*-
import os
import subprocess
from subprocess import (
#CalledProcessError,
SubprocessError,
TimeoutExpired,
)
import sys
import re
import signal
import time
import logging
from collections import deque
import threading
from .compat import *
from .collections import Dict
from .utils i... | Jaymon/datatypes | datatypes/command.py | .py | 483d5a485f68882d | 7.39 | 5 |
# -*- coding: utf-8 -*-
import os
from pathlib import Path
from ...compat import *
class Environ(Mapping):
"""Create an Environ namespace instance
you would usually create this like this:
environ = Environ("PREFIX_")
Then you can access any environment variables with that prefix from the
`... | Jaymon/datatypes | datatypes/config/environ/base.py | .py | f8a657d7b244acb8 | 7.39 | 5 |
# -*- coding: utf-8 -*-
import string
from ...token.base import Tokenizer, Token, Scanner
class EnvironToken(Token):
"""A parsed environ variable name and value
Fields each instance should have:
* `.name` - the variable name
* `.value` - the variable value
* `.start` - the offset th... | Jaymon/datatypes | datatypes/config/environ/token.py | .py | 468ea7fdbdd68c05 | 7.39 | 5 |
from collections import ChainMap
from collections.abc import Generator
from ..collections.mapping import Namespace
from .environ import Environ
from .parser import Config
class Settings(Namespace):
"""A settings object that can source values locally, from the environment,
or from a config file.
The orde... | Jaymon/datatypes | datatypes/config/settings.py | .py | a20475d9fa8451e4 | 7.39 | 5 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, print_function, absolute_import
import copy
from io import IOBase
from .compat import *
class Deepcopy(object):
"""deep copy an object trying to anticipate and handle any errors
The original version of this class comes from endpoints... | Jaymon/datatypes | datatypes/copy.py | .py | 4ebde6cbc226329b | 7.39 | 5 |
# -*- coding: utf-8 -*-
import functools
import inspect
import re
from ..compat import *
from .. import logging
logger = logging.getLogger(__name__)
class Decorator(object):
"""A decorator class that you can be extended that allows you to do normal
decorators with no arguments, or a decorator with argumen... | Jaymon/datatypes | datatypes/decorators/base.py | .py | a7d3628fcaca73bb | 7.39 | 5 |
# -*- coding: utf-8 -*-
"""
https://docs.python.org/3/howto/descriptor.html
"""
import logging
import types
from ..compat import *
from .base import FuncDecorator
logger = logging.getLogger(__name__)
class method(object):
"""method that can be both a classmethod and a regular method so they can
have diffe... | Jaymon/datatypes | datatypes/decorators/descriptor.py | .py | 6347ccb2a9784edd | 7.39 | 5 |
# -*- coding: utf-8 -*-
import warnings
import inspect
from ..compat import *
from .base import FuncDecorator, Decorator
class cache(FuncDecorator):
"""run the decorated function only once for the given arguments
in python 3+ it's better to use functools.cache or functools.lru_cache if
those will work f... | Jaymon/datatypes | datatypes/decorators/misc.py | .py | 0ab7cc2d7bc6219a | 7.39 | 5 |
import re
import os
import mimetypes
import time
from collections.abc import Generator
from email.parser import Parser, BytesParser
from email import message, policy, utils, parser, header
from typing import Self
from functools import cached_property
import io
from .compat import *
from .string import String
from .dat... | Jaymon/datatypes | datatypes/email.py | .py | cd11f8f32667cc63 | 7.39 | 5 |
# -*- coding: utf-8 -*-
import logging
from collections import defaultdict
from contextlib import contextmanager
from .compat import *
logger = logging.getLogger(__name__)
class Event(object):
"""An instance of this class is passed as the first argument to any
callback when an event is broadcast"""
def... | Jaymon/datatypes | datatypes/event.py | .py | caed551dec326a37 | 7.39 | 5 |
# -*- coding: utf-8 -*-
from collections import OrderedDict
import functools
from ..compat import *
from ..path import Filepath, UrlFilepath, Cachepath
from ..token.abnf import ABNFParser
from ..collections.mapping import Namespace
from ..decorators import classproperty
class TOML(object):
"""This is more or les... | Jaymon/datatypes | datatypes/filetypes/toml.py | .py | 8f7619d4180c9ad6 | 7.39 | 5 |
from logging import * # allow this module as a passthrough for builtin logging
from logging import (
config,
root,
_acquireLock,
_releaseLock,
)
import logging # access to stdlib if needed
import sys
from collections.abc import (
Mapping,
Sequence,
Generator,
Callable,
)
from typing impo... | Jaymon/datatypes | datatypes/logging.py | .py | 8420fe88540ea0b8 | 7.39 | 5 |
# -*- coding: utf-8 -*-
import re
from configparser import RawConfigParser
import math
from .compat import *
from .string import String
class Shorten(object):
"""Converts an integer to a base58-like string and vice versa
This code was used in Undrip for its link shortener and was originally
written by C... | Jaymon/datatypes | datatypes/number.py | .py | e68855c6f278afde | 7.39 | 5 |
# -*- coding: utf-8 -*-
import time
from collections import defaultdict
from .compat import *
from .collections import Namespace
class Profile(Namespace):
"""This is the context object that is returned from the Profiler, it's main
purpose is to allow printing of one atomic profiling session"""
@property
... | Jaymon/datatypes | datatypes/profile.py | .py | 04467467a34f3f59 | 7.39 | 5 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, print_function, absolute_import
import subprocess
import os
import inspect
import sys
from .path import Dirpath
# 9-20-2017 -- I'm still testing these with some projects trying to get
# the api right and so they aren't fully integrated yet
... | Jaymon/datatypes | datatypes/service.py | .py | 7b085c2c55cc051d | 7.39 | 5 |
# -*- coding: utf-8 -*-
from ..compat import *
from ..string import String
from .base import Token, Tokenizer
class WordToken(Token):
"""This is what is returned from the Tokenizer and contains pointers to the
left deliminator and the right deliminator, and also the actual token
.ldelim - the delimi... | Jaymon/datatypes | datatypes/token/word.py | .py | 661d90b152442ad3 | 7.39 | 5 |
# -*- coding: utf-8 -*-
import re
import itertools
from .compat import *
def cbany(callback, iterable):
"""Return True if any callback(row) of the iterable is true. If the iterable
is empty, return False
:param callback: callable
:param iterable: Sequence
:returns: bool
"""
for v in iter... | Jaymon/datatypes | datatypes/utils.py | .py | 1f412981d288c52e | 7.39 | 5 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/app.py | .py | 1d8117157a309603 | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/cmd/manage.py | .py | 5e69a47f71412372 | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/common/keystone.py | .py | fa7bc2f6d787a7e1 | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/config.py | .py | 221d39571f6184b7 | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/migrations/env.py | .py | ebcd98716a8ca65b | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/migrations/versions/3840b8c7f97d_rename_organisation.py | .py | fe460920a6850dc4 | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/migrations/versions/52e8555a0886_initial_migration.py | .py | a670213d37c3c049 | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/migrations/versions/53c5ca8ba141_create_external_id_table.py | .py | 82c3a53462fa8795 | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/migrations/versions/b21c9807518a_add_orcid_token.py | .py | 10cf5f69542ff2be | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/migrations/versions/b3a24f35f907_add_domain_idp_mapping_model.py | .py | 83af43682e087cb8 | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/migrations/versions/e9e502fdd76f_change_user_id_to_keystone_user_id.py | .py | b7bbf7441467bfa4 | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/models.py | .py | 7aef8e665c20578a | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/shib_faker.py | .py | 6e0bf3cc65333085 | 7.24 | 2 |
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# ... | NeCTAR-RC/manuka | manuka/tests/functional/test_login.py | .py | c0cb92368f38899a | 7.74 | 2 |
#!/usr/bin/env python3
# MIT License
#
# Copyright (c) 2020 FABRIC Testbed
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to ... | fabric-testbed/CredentialManager | fabric_cm/credmgr/config/config.py | .py | 6da0dd615d1be043 | 7 | 0 |
#!/usr/bin/env python3
# MIT License
#
# Copyright (c) 2020 FABRIC Testbed
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to ... | fabric-testbed/CredentialManager | fabric_cm/credmgr/logging/log_helper.py | .py | 90a021443bae542d | 7 | 0 |
import pprint
import typing
from fabric_cm.credmgr.swagger_server import util
T = typing.TypeVar('T')
class Model(object):
# swaggerTypes: The key is attribute name and the
# value is attribute type.
swagger_types = {}
# attributeMap: The key is attribute name and the
# value is json key in def... | fabric-testbed/CredentialManager | fabric_cm/credmgr/swagger_server/models/base_model_.py | .py | 50575329ddb881fa | 7 | 0 |
#!/usr/bin/env python3
"""
5' end junction rescue figure for the RECTIFY README — v3.
Design intent (per dev/figures/STYLE_GUIDE.md):
- 760px wide, single panel
- 3 rows: genome / read aligned (before) / read after rescue
- No per-base nucleotide grids — use exon/aligned blocks at this scale
- No "Problem / So... | k-roy/RECTIFY | docs/figures/generate_5prime_junction_v3.py | .py | ca863af5ceee5b44 | 7 | 0 |
#!/usr/bin/env python3
"""
DRS poly(A) pre-trim figure for the RECTIFY README — v3.
Design intent (per dev/figures/STYLE_GUIDE.md):
- 760px wide, single panel, two rows (raw vs trimmed)
- No three-pass detection internals; that's an implementation detail
- Show: raw read = body + poly(A) + adapter stub; trimmed ... | k-roy/RECTIFY | docs/figures/generate_polya_pretrim_v3.py | .py | 16f14eb131839434 | 7 | 0 |
"""
5' End Aggregation Module for RECTIFY.
This module clusters reads by their 5' end positions (TSS) and
computes gene attribution based on the 3' ends of reads.
The output is a dataset suitable for:
- Transcription start site (TSS) analysis
- Promoter usage studies
- 5' capping / transcription initiation mapping
F... | k-roy/RECTIFY | rectify/core/aggregate/five_prime.py | .py | 0d40ddd20b50b4b2 | 7 | 0 |
"""
3' End Aggregation Module for RECTIFY.
This module clusters reads by their 3' end positions (CPA sites) and
computes gene attribution based on the 5' ends of reads (read bodies).
The output is a dataset suitable for:
- Cleavage and polyadenylation site (CPA) analysis
- Alternative polyadenylation (APA) studies
- ... | k-roy/RECTIFY | rectify/core/aggregate/three_prime.py | .py | 65ec42837c984314 | 7 | 0 |
#!/usr/bin/env python3
"""
Preprocessing module for RECTIFY.
Handles input data preparation including:
- Detecting input file format (FASTQ, BAM)
- Running minimap2 alignment for FASTQ files
- Decompressing gzipped reference files
- Index creation
Author: Kevin R. Roy
Date: 2026-03-18
"""
import gzip
import os
impor... | k-roy/RECTIFY | rectify/core/align/preprocess.py | .py | a674352f8959b70c | 7 | 0 |
#!/usr/bin/env python3
"""
A-Tract Refiner Module
This module provides the user-facing API for refining nanopore 3' end positions
within A-tracts using the bundled NET-seq reference data.
Usage:
from rectify.core.analyze.atract_refiner import ATractRefiner
# Initialize (automatically loads bundled reference)... | k-roy/RECTIFY | rectify/core/analyze/atract_refiner.py | .py | d0332af69615b04b | 7 | 0 |
#!/usr/bin/env python3
"""
A-Tract Deconvolution Module
Deconvolves oligo-adenylation spreading artifacts to recover true CPA positions
within A-tracts using the 0A point-spread-function (PSF).
Key Insight:
At 0A sites (no A-tract), ~54% of signal stays at the true CPA position while
~46% spreads downstream due to po... | k-roy/RECTIFY | rectify/core/analyze/deconvolution.py | .py | 5c1bd8ee13b3e1ee | 7 | 0 |
#!/usr/bin/env python3
"""
DESeq2 Differential Expression Analysis Module
Performs differential expression analysis at both gene and cluster level
using pyDESeq2.
Author: Kevin R. Roy
Date: 2026-03-17
"""
import logging
from typing import Dict, List, Optional, Tuple, Union
from pathlib import Path
import re
import n... | k-roy/RECTIFY | rectify/core/analyze/deseq2.py | .py | 3f843eafe7521279 | 7 | 0 |
#!/usr/bin/env python3
"""
Heatmap and Sample Clustering Module
Creates clustered heatmaps for sample QC and visualization.
Author: Kevin R. Roy
Date: 2026-03-17
"""
from typing import Dict, List, Optional, Tuple, Union
from pathlib import Path
import numpy as np
import pandas as pd
# Try to import visualization li... | k-roy/RECTIFY | rectify/core/analyze/heatmap.py | .py | 0ab4789667fef442 | 7 | 0 |
import os
import secrets
import threading
from contextlib import contextmanager
from sqlalchemy import create_engine, inspect as sa_inspect, text
from sqlalchemy.pool import StaticPool
_engine = None
_engine_lock = threading.Lock()
def _build_engine():
url = os.getenv("DATABASE_URL", "sqlite:///./db/surikatajs.d... | nkalexiou/suricatajs | db/database.py | .py | f0d5775859db8bdf | 7.3 | 3 |
"""
Main suricatajs file. Scanner logic lives in scanner/engine.py.
"""
import logging
import os
from logging.handlers import TimedRotatingFileHandler
from db.database import init_db
from scanner.engine import check_target # noqa: F401 — re-exported for scheduler
logger = logging.getLogger("suricatajs")
def config... | nkalexiou/suricatajs | run.py | .py | fff5132997282791 | 7.3 | 3 |
import os
# Set env vars before any app imports so SQLAlchemy and auth pick them up
os.environ["DATABASE_URL"] = "sqlite://"
os.environ["API_KEYS"] = "test-key"
os.environ["JWT_SECRET"] = "test-jwt-secret-32-chars-minimum!!"
import pytest
from fastapi.testclient import TestClient
from sqlalchemy import text
@pytest... | nkalexiou/suricatajs | tests/conftest.py | .py | 36783e8637354477 | 7.8 | 3 |
#!/usr/bin/env python3
"""
Check that all HTTP/HTTPS links in resume.md are reachable.
Connection errors are treated as failures. HTTP 4xx responses are warnings
(not failures) because some sites like LinkedIn block automated requests.
HTTP 5xx responses are treated as failures.
"""
import os
import re
import sys
imp... | tomirish/tom.irish | scripts/build/check_links.py | .py | 8f04d64bfe2015b8 | 7 | 0 |
#!/usr/bin/env python3
"""
Convert resume.md to HTML using Jinja2 templates.
Reads resume.md (single source of truth) and renders two Jinja2 templates:
- index.template.html → index.html (web site)
- resume.template.html → resume.html (PDF input for generate_pdf_browser.py)
Usage:
python3 scripts/convert_re... | tomirish/tom.irish | scripts/build/convert_resume.py | .py | 26f794642ef4dbd8 | 7 | 0 |
#!/usr/bin/env python3
"""
Validate resume.md format before the build pipeline runs.
Checks for:
- Required sections (Professional Summary, Work Experience, Skills, Education)
- Job entries with properly formatted date ranges
- Common markdown issues (tabs, unusual trailing whitespace, consecutive blank lines)
Exits ... | tomirish/tom.irish | scripts/build/validate_resume.py | .py | e82a5752df10740b | 7 | 0 |
#!/usr/bin/env python3
"""
Generates all site icons:
- assets/images/favicon.png — 256×256, crimson bg
- assets/images/favicon-dark.png — 256×256, dark bg
- assets/images/apple-touch-icon.png — 1024×1024, crimson bg with atomic number
Deletes any existing files and rebuilds all three on every run.
Twe... | tomirish/tom.irish | scripts/tools/generate_icons.py | .py | 816146a16a289705 | 7 | 0 |
"""
Unit tests for scripts/check_links.py
"""
import os
import sys
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'scripts', 'build'))
from check_links import extract_urls
def test_extracts_https_urls():
content = "See [my site](https://example.com) for details."
assert extract_urls(conte... | tomirish/tom.irish | tests/test_check_links.py | .py | 449968dd4e60a05b | 7.5 | 0 |
import socks
class SocksManager:
"""Socks manager class."""
def __init__(self, socks_host: str | None, socks_port: int | None) -> None:
"""Constructor.
:Parameters:
- `socks_host`: str, SOCKS5 proxy host.
- `socks_port`: str, SOCKS5 proxy port.
"""
sel... | tropicoo/ssh-key-transmitter | src/ssh_key_transmitter/core/socks_manager.py | .py | 7c1466330c5669f0 | 7.15 | 1 |
import logging
import posixpath
from collections.abc import Iterable
from pathlib import Path
from typing import cast
import socks
from paramiko import AuthenticationException
from paramiko.sftp_client import SFTPClient
from ssh_key_transmitter.constants import (
DEFAULT_SSH_AUTH_KEYS,
DEFAULT_SSH_DIR,
DE... | tropicoo/ssh-key-transmitter | src/ssh_key_transmitter/core/transmitter.py | .py | 1072c6502082004a | 7.15 | 1 |
#!/usr/bin/env python3
"""
shasrv - Content-addressed file storage using SHA-256 deduplication.
This utility creates a deduplicated storage structure where:
1. Each file is stored under its SHA256 hash in <target>/data/<sha[:2]>/<sha>
2. Symlinks are created in <target>/files/<path> pointing to the actual file
3. Mult... | jovlinger/utils | dedup/dedup.py | .py | ccba5d62f17bb78a | 7.15 | 1 |
#!/usr/bin/env python3
"""
Run the target script under this interpreter (the venv Python).
Invoked only by ``venv-run.py`` as ``python venv-run-launch.py SCRIPT [ARGS...]``.
Catches ``ModuleNotFoundError`` so we can point at ``setup-venv.sh`` instead of
only a traceback (same remedy as when no venv exists: sync the en... | jovlinger/utils | extdeps/venv-run-launch.py | .py | 85f279fa4e780e74 | 7.15 | 1 |
#!/usr/bin/env python3
"""
Exec a Python script under the nearest ancestor virtualenv.
Designed to be used as a shebang interpreter:
#!/usr/bin/env venv-run
When the kernel runs a script with that shebang, it invokes
``venv-run SCRIPT [ARGS...]``. ``venv-run`` then:
1. Resolves SCRIPT through any symlinks (so P... | jovlinger/utils | extdeps/venv-run.py | .py | c68ab10c67cb813d | 7.15 | 1 |
"""Compositor ABC."""
from __future__ import annotations
from abc import ABC, abstractmethod
from dataclasses import dataclass
from pathlib import Path
from typing import Literal, Optional
from imgcomp.object import Object
from imgcomp.scene import Scene, as_z_list
from imgcomp.surface import Surface
EventKind = Li... | jovlinger/utils | imgcomp/imgcomp/compositor.py | .py | 928e8ed4a5117c6e | 7.15 | 1 |
"""Backward-compatible re-exports; prefer Compositor.render_png and Surface.write_png."""
from __future__ import annotations
from pathlib import Path
from imgcomp.compositor import Compositor
from imgcomp.scene import Scene
from imgcomp.surface import Surface
def surface_to_png(surface: Surface, path: Path | str) ... | jovlinger/utils | imgcomp/imgcomp/export.py | .py | b01ea5efc1af877b | 7.15 | 1 |
"""Pure-Python per-pixel compositor."""
from __future__ import annotations
from typing import Optional
from imgcomp.compositor import Compositor, PickResult
from imgcomp.probe import hit_color, pick_target
from imgcomp.rgba import RGBA, TRANSPARENT, src_over
from imgcomp.scene import Scene, as_z_list
from imgcomp.su... | jovlinger/utils | imgcomp/imgcomp/naive.py | .py | 37cb9c1df2c8c9f4 | 7.15 | 1 |
"""Scene object ABC."""
from __future__ import annotations
from abc import ABC, abstractmethod
from imgcomp.rgba import RGBA
class Object(ABC):
"""Maps center-based local pixel coordinates to color and hit tests."""
@abstractmethod
def sample(self, x: float, y: float) -> RGBA:
"""Return straig... | jovlinger/utils | imgcomp/imgcomp/object.py | .py | a2956dc7aa5ef83c | 7.15 | 1 |
"""Loaded leaf objects (non-SDF)."""
from __future__ import annotations
import math
from pathlib import Path
from typing import Sequence
from imgcomp.object import Object
from imgcomp.rgba import RGBA, TRANSPARENT
from imgcomp.surface import ArraySurface
class ImageObject(Object):
"""Bitmap sampled in center-b... | jovlinger/utils | imgcomp/imgcomp/primitives.py | .py | 4717ae72adf0a653 | 7.15 | 1 |
"""Hit and color probing for naive per-pixel compositing."""
from __future__ import annotations
from typing import Optional
from imgcomp.object import Object
from imgcomp.rgba import RGBA, modulate
from imgcomp.wrappers import Color, ColorMod, Rotate, Stretch, Translate
def hit_at(obj: Object, x: float, y: float) ... | jovlinger/utils | imgcomp/imgcomp/probe.py | .py | d86660b391142527 | 7.15 | 1 |
"""Straight RGBA helpers (non-premultiplied)."""
from __future__ import annotations
from typing import Tuple
RGBA = Tuple[int, int, int, int]
TRANSPARENT: RGBA = (0, 0, 0, 0)
WHITE: RGBA = (255, 255, 255, 255)
def clamp_channel(value: float) -> int:
"""Clamp a color channel to [0, 255]."""
if value <= 0.0... | jovlinger/utils | imgcomp/imgcomp/rgba.py | .py | a629f4d000d03976 | 7.15 | 1 |
"""Normalize a scene root to a z-ordered object list (back to front)."""
from __future__ import annotations
from collections.abc import Sequence
from imgcomp.object import Object
Scene = Object | Sequence[Object]
def as_z_list(root: Scene) -> tuple[Object, ...]:
"""Return scene layers ordered furthest (index ... | jovlinger/utils | imgcomp/imgcomp/scene.py | .py | 72a846dd2d76e996 | 7.15 | 1 |
"""SDF-backed geometry objects (white fill until wrapped in Color)."""
from __future__ import annotations
from imgcomp.object import Object
from imgcomp.rgba import TRANSPARENT, WHITE
from imgcomp.sdf import (
CircleSDF,
OvalSDF,
RectangleSDF,
SDF,
)
class SDFShape(Object):
"""White-filled geome... | jovlinger/utils | imgcomp/imgcomp/shapes.py | .py | a3cc573f2078b309 | 7.15 | 1 |
"""Surface ABC and a CPU byte-buffer implementation (no numpy)."""
from __future__ import annotations
from abc import ABC, abstractmethod
from array import array
from pathlib import Path
from typing import Iterable, Iterator, List, Sequence
from imgcomp.rgba import RGBA, TRANSPARENT
class Surface(ABC):
"""Muta... | jovlinger/utils | imgcomp/imgcomp/surface.py | .py | 69e3e56479b0cf82 | 7.15 | 1 |
"""Tests for straight-alpha helpers."""
from __future__ import annotations
from imgcomp.rgba import src_over
def test_src_over_opaque_source_replaces_destination() -> None:
assert src_over((10, 20, 30, 255), (200, 100, 50, 255)) == (200, 100, 50, 255)
def test_src_over_transparent_source_keeps_destination() -... | jovlinger/utils | imgcomp/tests/test_rgba.py | .py | f2a5cbcf2fed9f1c | 7.15 | 1 |
"""Tests for ArraySurface."""
from __future__ import annotations
from imgcomp.rgba import TRANSPARENT
from imgcomp.surface import ArraySurface
def test_array_surface_round_trip_pixel() -> None:
surface = ArraySurface(2, 2)
surface.set_pixel(1, 0, (1, 2, 3, 4))
assert surface.get_pixel(1, 0) == (1, 2, 3,... | jovlinger/utils | imgcomp/tests/test_surface.py | .py | 1bc0f131684c175d | 7.65 | 1 |
#!/usr/bin/env python3
"""Build utils/README.md from nested .www/blurb.md files."""
from __future__ import annotations
import sys
from pathlib import Path
from typing import Iterator, List, Optional, Sequence
UTILS_ROOT: Path = Path(__file__).resolve().parent.parent
README_PATH: Path = UTILS_ROOT / "README.md"
BLURB... | jovlinger/utils | lib/build-index.py | .py | 56d80e7cd63a6d5d | 7.15 | 1 |
#!/usr/bin/env python3
"""
Command-line interface for Merkle FUSE filesystem.
"""
import argparse
import logging
import os
import sys
from pathlib import Path
from mfusepy import FUSE
from .config import load_config
from .filesystem import MerkleFuseFS
def setup_logging(log_level: str = "INFO") -> None:
"""Set... | jovlinger/utils | merklefuse/merklefuse/cli.py | .py | 53ff8667ab9e2ef5 | 7.15 | 1 |
"""
Configuration management for Merkle FUSE filesystem.
"""
import json
import os
from pathlib import Path
from typing import Dict, Any
DEFAULT_CONFIG = {
"debug": False,
"log_level": "INFO",
"critical_debug_duration": 300,
"data_directory": "./data",
"root_file_prefix": "root_",
"max_file_s... | jovlinger/utils | merklefuse/merklefuse/config.py | .py | 040832aa9e16cf06 | 7.15 | 1 |
"""
Merkle FUSE filesystem implementation.
This module contains the main filesystem class that implements the FUSE interface
using a merkle tree for storage.
"""
import os
import errno
import hashlib
import json
import time
from pathlib import Path
from typing import Dict, Any, Optional, List
from mfusepy import Ope... | jovlinger/utils | merklefuse/merklefuse/filesystem.py | .py | 67a78289d80ea508 | 7.15 | 1 |
"""
Integration tests for filesystem operations.
These tests run sequences of operations and verify the state in the test area.
"""
import os
import tempfile
import pytest
from pathlib import Path
from merklefuse.filesystem import MerkleFuseFS
from merklefuse.config import DEFAULT_CONFIG
class TestFilesystemIntegr... | jovlinger/utils | merklefuse/tests/integration/test_filesystem_operations.py | .py | 83806b9c42371b91 | 7.65 | 1 |
"""
The task is to write a Java program which reads the file, calculates the min, mean, and max temperature value per weather station, and emits the results on stdout like this (i.e. sorted alphabetically by station name, and the result values per station in the format <min>/<mean>/<max>, rounded to one fractional digi... | jovlinger/utils | misc/1brc/jovlinger.py | .py | 152e412a0d2e6927 | 7.15 | 1 |
# This file contains legacy functions for compatibility with older downstream
# tools. Internally the functions use the newer GrouperClient.
import json
import logging
import requests
from .utils import (
read_json_data,
read_grouper_credentials,
read_credentials,
)
from .client import (
GrouperClient,... | ryanlovett/grouper-cli | grouper/grouper.py | .py | 5898c73041f25b91 | 7 | 0 |
# vim: set et sw=4 ts=4:
import os
import json
from dotenv import load_dotenv
def has_all_keys(d, keys):
return all(k in d for k in keys)
def read_json_data(filename, required_keys):
"""Read and validate data from a json file."""
if not os.path.exists(filename):
raise Exception(f"No such file: {... | ryanlovett/grouper-cli | grouper/utils.py | .py | 4e80b525992570e9 | 7 | 0 |
#!/usr/bin/env python3
"""
Tests for the subject functionality in grouper-cli.
Uses pytest for testing framework.
"""
import pytest
from unittest.mock import Mock, patch
import sys
import os
# Add the grouper module to the path
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
from grouper import gro... | ryanlovett/grouper-cli | tests/test_subject.py | .py | f62fb4343d14cc69 | 7.5 | 0 |
import math
from decimal import Decimal
from typing import Final
def _validate_numeric(op, other):
# TODO: alternatively `return NotImplemented`
if not isinstance(other, (int, float, Decimal)):
raise TypeError(f"'{op}' not supported between instances of 'int' and '{type(other)}'")
class IntInf(int):... | anentropic/python-faker-jsonschema | faker_jsonschema/utils.py | .py | ab5793e335d72fcf | 7 | 0 |
"""The implementation of the js-regex library."""
import re
try:
import re._compiler as sre_compile
import re._constants as sre_constants
import re._parser as sre_parse
except ImportError:
import sre_compile # type: ignore[no-redef]
import sre_constants # type: ignore[no-redef]
import sre_pa... | anentropic/python-faker-jsonschema | js_regex/_impl.py | .py | 07d5d74f86e27581 | 7 | 0 |
import os
import random
import pytest
from faker import Faker
from faker_jsonschema.provider import JSONSchemaProvider
_DEFAULT_REPEATS_SLOW = 10
_DEFAULT_REPEATS_FAST = 50
@pytest.fixture(scope="session")
def faker(record_testsuite_property):
seed = int(os.getenv("SEED", random.randint(0, 9999999)))
# TOD... | anentropic/python-faker-jsonschema | tests/conftest.py | .py | a30586f2f03c2629 | 7.5 | 0 |
from jsonschema import validate
def test_jsonschema_boolean_direct(faker, repeats_for_fast):
"""Direct call returns a bool."""
for _ in range(repeats_for_fast):
result = faker.jsonschema_boolean()
assert isinstance(result, bool)
def test_jsonschema_boolean_from_schema(faker, repeats_for_fast... | anentropic/python-faker-jsonschema | tests/unit/test_boolean.py | .py | a476972623bf2c3d | 7.5 | 0 |
#
# Copyright (c) 2016-2026 Wind River Systems, Inc.
#
# SPDX-License-Identifier: Apache-2.0
#
import json
import os
import requests
from nfv_client.auth_types import AUTH_TYPES
from nfv_client import sw_update
CAFILE = os.environ.get("REQUESTS_CA_BUNDLE")
STRATEGY_EXISTS = "strategy already exists."
UNKNOWN_FAILURE ... | starlingx/nfv | nfv/nfv-client/nfv_client/openstack/rest_api.py | .py | 7637da18706c7f26 | 7.3 | 3 |
#
# Copyright (c) 2015-2016, 2026 Wind River Systems, Inc.
#
# SPDX-License-Identifier: Apache-2.0
#
import stevedore
from nfv_common import debug
from nfv_common.helpers import Singleton
DLOG = debug.debug_get_logger("nfv_common.alarm.alarm_handlers")
class AlarmHandlers(stevedore.enabled.EnabledExtensionManager, ... | starlingx/nfv | nfv/nfv-common/nfv_common/alarm/_alarm_handlers.py | .py | c606ea15dc7b6021 | 7.3 | 3 |
#
# Copyright (c) 2015-2016, 2026 Wind River Systems, Inc.
#
# SPDX-License-Identifier: Apache-2.0
#
import datetime
from nfv_common.alarm._alarm_handlers import AlarmHandlers
from nfv_common import debug
from nfv_common.helpers import coroutine
from nfv_common.helpers import Singleton
from nfv_common import thread
fr... | starlingx/nfv | nfv/nfv-common/nfv_common/alarm/_alarm_thread.py | .py | 3b2f7a525dcadab9 | 7.3 | 3 |
#
# Copyright (c) 2015-2016, 2026 Wind River Systems, Inc.
#
# SPDX-License-Identifier: Apache-2.0
#
from datetime import datetime
class AlarmStateData:
"""Alarm State Data."""
def __init__(self, state):
self.state = state
def as_dict(self):
return dict.copy(self.__dict__)
class AlarmT... | starlingx/nfv | nfv/nfv-common/nfv_common/alarm/objects/v1/_alarm_data.py | .py | ac0d529b080a683c | 7.3 | 3 |
#
# Copyright (c) 2015-2023, 2026 Wind River Systems, Inc.
#
# SPDX-License-Identifier: Apache-2.0
#
from nfv_common.helpers import Constant
from nfv_common.helpers import Constants
from nfv_common.helpers import Singleton
class _AlarmType(Constants, metaclass=Singleton):
"""Alarm Type Constants."""
UNKNOWN... | starlingx/nfv | nfv/nfv-common/nfv_common/alarm/objects/v1/_alarm_defs.py | .py | f4d96d00c3b61990 | 7.3 | 3 |
#
# Copyright (c) 2015-2016, 2026 Wind River Systems, Inc.
#
# SPDX-License-Identifier: Apache-2.0
#
import stevedore
from nfv_common import debug
from nfv_common.helpers import Singleton
DLOG = debug.debug_get_logger("nfv_common.catalog.catalog_backend")
class CatalogBackend(stevedore.named.NamedExtensionManager, ... | starlingx/nfv | nfv/nfv-common/nfv_common/catalog/_catalog_backend.py | .py | 62ffc561123f566a | 7.3 | 3 |
#
# Copyright (c) 2015-2016, 2026 Wind River Systems, Inc.
#
# SPDX-License-Identifier: Apache-2.0
#
from nfv_common.helpers import Constant
from nfv_common.helpers import Singleton
class ConnectionType(metaclass=Singleton):
"""Connection Type Constants."""
UNKNOWN = Constant("unknown")
VIRTUAL_PORT = C... | starlingx/nfv | nfv/nfv-common/nfv_common/catalog/model/_defs.py | .py | cde0ad0905fca171 | 7.3 | 3 |
#
# Copyright (c) 2015-2016, 2026 Wind River Systems, Inc.
#
# SPDX-License-Identifier: Apache-2.0
#
import configparser
from nfv_common import debug
DLOG = debug.debug_get_logger("nfv_common.config")
# Configuration Global used by other modules to get access to the configuration
# specified in the ini file.
CONF = ... | starlingx/nfv | nfv/nfv-common/nfv_common/config.py | .py | 35a5065e94dba46c | 7.3 | 3 |
import re
import unicodedata
import xml.etree.ElementTree as etree
from xml.sax.saxutils import escape as _xml_escape
from xml.sax.saxutils import unescape as _xml_unescape
from spans_and_trees import spans_to_passages, spans_to_tree, tree_to_spans
# Remove empty brackets (that could happen if the contents have been... | jakelever/bioconverters | bioconverters/utils.py | .py | e2f43229170e79c3 | 7 | 0 |
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