repo stringlengths 7 90 | file_url stringlengths 81 315 | file_path stringlengths 4 228 | content stringlengths 0 32.8k | language stringclasses 1
value | license stringclasses 7
values | commit_sha stringlengths 40 40 | retrieved_at stringdate 2026-01-04 14:38:15 2026-01-05 02:33:18 | truncated bool 2
classes |
|---|---|---|---|---|---|---|---|---|
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/setup.py | setup.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/tests/test_functions.py | tests/test_functions.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/tests/test_conformers.py | tests/test_conformers.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/tests/test_watchers.py | tests/test_watchers.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/tests/test_cli.py | tests/test_cli.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/tests/test_api.py | tests/test_api.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/tests/__init__.py | tests/__init__.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/conformers.py | qtsass/conformers.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/importers.py | qtsass/importers.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/api.py | qtsass/api.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/cli.py | qtsass/cli.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/__main__.py | qtsass/__main__.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/__init__.py | qtsass/__init__.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/functions.py | qtsass/functions.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/watchers/api.py | qtsass/watchers/api.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/watchers/polling.py | qtsass/watchers/polling.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/watchers/qt.py | qtsass/watchers/qt.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/watchers/__init__.py | qtsass/watchers/__init__.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
spyder-ide/qtsass | https://github.com/spyder-ide/qtsass/blob/295e295bf3062c24135458ed300a6b7ced8e2ae7/qtsass/watchers/snapshots.py | qtsass/watchers/snapshots.py | # -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Yann Lanthony
# Copyright (c) 2017-2018 Spyder Project Contributors
#
# Licensed under the terms of the MIT License
# (See LICENSE.txt for details)
# ---------------------------------------------... | python | MIT | 295e295bf3062c24135458ed300a6b7ced8e2ae7 | 2026-01-05T07:11:18.971368Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/get_default_thread.py | get_default_thread.py | import os
def get_default_thread() -> int:
"""_summary_
Automatically get the default number of threads to use for generation
"""
count = os.cpu_count()
if count is not None:
return int(count / 2)
else:
return 8
| python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/get_config.py | get_config.py | from ctransformers import Config
from request_body import ChatCompletionRequestBody, CompletionRequestBody
from get_env import get_env, get_env_or_none
from get_default_thread import get_default_thread
from log import log
from const import DEFAULT_MAX_TOKENS, DEFAULT_CONTEXT_LENGTH
THREADS = int(get_env("THREADS", st... | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/log.py | log.py | import logging
from get_env import get_env
from const import DEFAULT_LOG_LEVEL
LOGGING_LEVEL = get_env("LOGGING_LEVEL", DEFAULT_LOG_LEVEL)
log = logging.getLogger("uvicorn")
try:
log.setLevel(LOGGING_LEVEL)
except ValueError:
log.setLevel(DEFAULT_LOG_LEVEL)
| python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/const.py | const.py | DEFAULT_MAX_TOKENS = "512"
DEFAULT_CONTEXT_LENGTH = "4096"
DEFAULT_LOG_LEVEL = "INFO" | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/main.py | main.py | """_summary_
This module contains the main FastAPI application.
"""
import os
from typing import (
Awaitable,
Callable,
Union,
Annotated,
)
from fastapi import FastAPI, Depends, HTTPException, Body, Request, status
from fastapi.exceptions import RequestValidationError
from fastapi.responses import JSO... | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/get_model_type.py | get_model_type.py | from get_env import get_env
def get_model_type(
filename: str,
) -> str:
ctransformer_model_type = "llama"
filename = filename.lower()
# These are also in "starcoder" format
# https://huggingface.co/TheBloke/WizardCoder-15B-1.0-GGML
# https://huggingface.co/TheBloke/minotaur-15B-GGML
if (
... | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/model_generate.py | model_generate.py | from time import time
from ctransformers import LLM, Config
from log import log
def model_generate(
prompt: str,
model_name: str,
llm: LLM,
config: Config,
):
"""_summary_
returns the response body for /chat/completions
"""
created = time()
top_k = config.top_k
log.debug("top... | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/streamers.py | streamers.py | import json
from os import times
from ctransformers import LLM, Config
from log import log
from get_env import get_env
from const import DEFAULT_CONTEXT_LENGTH, DEFAULT_LOG_LEVEL
def completions_streamer(
prompt: str,
model_name: str,
llm: LLM,
config: Config,
):
"""_summary_
returns a genera... | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/request_body.py | request_body.py | from typing import (
Any,
Literal,
List,
Optional,
)
from pydantic import BaseModel, Field
class CompletionRequestBody(BaseModel):
"""_summary_
from from https://github.com/abetlen/llama-cpp-python/blob/main/llama_cpp/server/app.py
"""
prompt: str = Field(
default="", descript... | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/truncate.py | truncate.py | from get_env import get_env_or_none
def truncate(string, beginning=True):
"""Shorten the given string to the given length.
:Parameters:
length (int) = The maximum allowed length before truncating.
beginning (bool) = Trim starting chars, else; ending.
:Return:
(str)
ex. call: ... | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/get_env.py | get_env.py | import os
def get_env(key: str, default_value: str):
"""_summary_
Fallback to default of the env get by key is not set or is empty string
"""
env = os.environ.get(key)
if env is None or len(env) == 0:
return default_value
else:
return env
def get_env_or_none(key: str):
"""... | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/response_body.py | response_body.py | from typing import Literal
from pydantic import BaseModel
class Message(BaseModel):
"""_summary_
Args:
BaseModel (_type_): message in choice
"""
role: Literal["system", "user", "assistant"]
content: str
class Choice(BaseModel):
"""_summary_
Args:
BaseModel (_type_): ch... | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/examples/openai/stream.py | examples/openai/stream.py | import openai
import time
openai.api_key = "placeholder_to_avoid_exception" # needed to avoid an exception
openai.api_base = "http://localhost:8000/v1" # this is the public address of the ialacol server
# Rest are from https://github.com/openai/openai-cookbook/blob/main/examples/How_to_stream_completions.ipynb
#
# Ex... | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
chenhunghan/ialacol | https://github.com/chenhunghan/ialacol/blob/410f6729b6d3a3829fc16b720b0f71af4ec458d2/examples/openai/simple.py | examples/openai/simple.py | import openai
openai.api_key = "placeholder_to_avoid_exception" # needed to avoid an exception
openai.api_base = "http://localhost:8000/v1" # this is the public address of the ialacol server
# create a chat completion
chat_completion = openai.ChatCompletion.create(
model="pythia-70m-q4_0.bin",
messages=[{"role": ... | python | MIT | 410f6729b6d3a3829fc16b720b0f71af4ec458d2 | 2026-01-05T07:11:19.135150Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/test_data.py | test_data.py | import json
import os
import time
from copy import deepcopy
from contextlib import ExitStack, contextmanager
import importlib
from pathlib import Path
from unittest.mock import patch
import pytest
from config import (
EXTERNAL_SPOOL_AMS_ID,
EXTERNAL_SPOOL_ID,
)
from spoolman_service import augmentTrayDataWithS... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/print_history.py | print_history.py | import os
import sqlite3
from datetime import datetime
from pathlib import Path
DEFAULT_DB_NAME = "3d_printer_logs.db"
DB_ENV_VAR = "OPENSPOOLMAN_PRINT_HISTORY_DB"
def _default_db_path() -> Path:
"""Resolve the print history database path, allowing an env override."""
env_path = os.getenv(DB_ENV_VAR)
if... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/filament.py | filament.py | # mapping adapted from https://github.com/spuder/OpenSpool/blob/main/firmware/conf.d/automation.yaml
from logger import log
def generate_filament_brand_code(filament_type, filament_brand, filament_variant):
filament_sub_brand = ""
filament_brand_code = ""
if filament_type == "TPU":
if filament_brand == "Bamb... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/logger.py | logger.py | import os
import time
import re
import builtins
from datetime import datetime
def append_to_rotating_file(file_path: str, text: str, max_size: int = 1_048_576, max_files: int = 5) -> None:
"""
Appends the given text with a timestamp to a rotating log file.
If the file exceeds the maximum size, it is rename... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/spoolman_client.py | spoolman_client.py | import requests
from config import SPOOLMAN_API_URL, SPOOL_SORTING
import json
from logger import append_to_rotating_file, log
SPOOLMAN_LOG_FILE = "/home/app/logs/spoolman.log"
def _log_spoolman_change(action, spool_id=None, payload=None, status=None):
parts = [action]
if spool_id is not None:
parts.append(... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/filament_usage_tracker.py | filament_usage_tracker.py | import json
import math
import os
import tempfile
import xml.etree.ElementTree as ET
import zipfile
from datetime import datetime, timedelta
from pathlib import Path
from urllib.parse import urlparse
from config import EXTERNAL_SPOOL_AMS_ID, EXTERNAL_SPOOL_ID, TRACK_LAYER_USAGE
from spoolman_client import consumeSpool... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/frontend_utils.py | frontend_utils.py | def color_is_dark(bg_color):
# Accept only normalized six-digit hex colors (with or without '#'); everything else is safe to treat as light.
if not isinstance(bg_color, str):
return False
color = bg_color.strip()
color = color[1:] if color.startswith('#') else color
if len(color) != 6:
return False
... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/conftest.py | conftest.py | import pytest
import test_data
import socket
@pytest.fixture
def unused_tcp_port_factory():
"""Return a factory that provides unique, currently unused TCP ports."""
allocated = set()
def factory():
with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
s.bind(("", 0))
... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/mqtt_bambulab.py | mqtt_bambulab.py |
import json
import ssl
import traceback
from threading import Thread
from typing import Any, Iterable
import paho.mqtt.client as mqtt
from config import (
PRINTER_ID,
PRINTER_CODE,
PRINTER_IP,
AUTO_SPEND,
EXTERNAL_SPOOL_ID,
TRACK_LAYER_USAGE,
CLEAR_ASSIGNMENT_WHEN_EMPTY,
)
from messages ... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/config.py | config.py | import builtins
from functools import partial
import os
from pathlib import Path
from dotenv import load_dotenv
# Load environment variables from config.env when present so live runs have access
# to printer and Spoolman credentials without manual exports.
load_dotenv(Path(__file__).resolve().parent / "config.env")
EX... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/spoolman_service.py | spoolman_service.py | import math
import re
from config import (
PRINTER_ID,
EXTERNAL_SPOOL_AMS_ID,
EXTERNAL_SPOOL_ID,
DISABLE_MISMATCH_WARNING,
COLOR_DISTANCE_TOLERANCE,
)
from datetime import datetime
from zoneinfo import ZoneInfo
from pathlib import Path
from print_history import update_filament_spool
import json
imp... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/messages.py | messages.py | GET_VERSION = {"info": {"sequence_id": "0", "command": "get_version"}}
PUSH_ALL = {"pushing": {"sequence_id": "0", "command": "pushall"}}
AMS_FILAMENT_SETTING = {"print":
{
"sequence_id": "0",
"command": "ams_filament_setting",
"ams_id": None,
"tray_id": None,
"tray_color": None,
"nozzle_temp_... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/api_routes.py | api_routes.py | import json
import os
import traceback
from typing import Any, Dict, List, Optional, Tuple
from flask import Blueprint, jsonify, request
import mqtt_bambulab
import spoolman_client
import spoolman_service
import test_data
from config import EXTERNAL_SPOOL_AMS_ID, EXTERNAL_SPOOL_ID, PRINTER_ID, PRINTER_NAME
API_VERSI... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/test.py | test.py | import json
import re
from dotenv import load_dotenv
from mqtt_bambulab import processMessage
from logger import log
load_dotenv()
def run_test():
i = 1
with open("mqtt.log", "r", encoding="utf-8") as file:
for line in file:
cleaned_line = re.sub(r"^\d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2} :: ", "", line.... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/__version__.py | __version__.py | __version__ = '0.2.0'
| python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/tools_3mf.py | tools_3mf.py | import requests
import zipfile
import tempfile
import xml.etree.ElementTree as ET
import pycurl
import urllib.parse
import os
import re
import time
import io
from datetime import datetime
from config import PRINTER_CODE, PRINTER_IP
from urllib.parse import urlparse
from logger import log
def parse_ftp_listing(line):
... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/app.py | app.py | import json
import math
import os
import traceback
import uuid
from collections import Counter
from flask import Flask, request, render_template, redirect, url_for
from config import (
BASE_URL,
AUTO_SPEND,
SPOOLMAN_BASE_URL,
EXTERNAL_SPOOL_AMS_ID,
EXTERNAL_SPOOL_ID,
PRINTER_NAME,
CLEAR_AS... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/wsgi.py | wsgi.py | from app import app
import os
if __name__ == '__main__':
ADHOC_SSL = True
if os.getenv('ADHOC_SSL', "").upper() == "FALSE" :
ADHOC_SSL = False
if ADHOC_SSL:
app.run(debug=os.getenv('DEBUG', False), port=os.getenv('PORT', 8443), host=os.getenv('HOST', '0.0.0.0'), ssl_context='adhoc')
... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/scripts/generate_screenshots.py | scripts/generate_screenshots.py | import argparse
import asyncio
import json
import os
import subprocess
import sys
import time
from dataclasses import dataclass
from pathlib import Path
from typing import Any
import requests
from logger import log
# Ensure repository root is importable when executed from the scripts directory
REPO_ROOT = Path(__file... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/scripts/export_live_snapshot.py | scripts/export_live_snapshot.py | import argparse
import importlib
import json
import os
import sys
import time
from pathlib import Path
from logger import log
# Ensure repository root is importable and the working directory matches the project root
REPO_ROOT = Path(__file__).resolve().parent.parent
if str(REPO_ROOT) not in sys.path:
sys.path.inse... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/scripts/init_bambulab.py | scripts/init_bambulab.py | import requests
import json
from logger import log
# Code from https://github.com/greghesp/ha-bambulab/issues/673#issuecomment-2455955428
# Prompt the user for their Bambu Lab username and password
bambuUsername = input("Enter your Bambu Lab username: ")
bambuPassword = input("Enter your Bambu Lab password: ")
# Def... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/tests/test_filament_mismatch.py | tests/test_filament_mismatch.py | import json
import pytest
import spoolman_service as svc
def _make_tray(tray_type, tray_sub_brands, tray_id="tray-1"):
return {
"tray_type": tray_type,
"tray_sub_brands": tray_sub_brands,
"tray_color": "FFFFFF",
"id": tray_id,
}
def _make_spool(material, extra_type, ams_id=... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/tests/test_mqtt_replay.py | tests/test_mqtt_replay.py | import copy
import json
import logging
import os
import shutil
import tempfile
from pathlib import Path
import pytest
import mqtt_bambulab
from filament_usage_tracker import FilamentUsageTracker
import tools_3mf
import spoolman_client
import spoolman_service
from config import TRACK_LAYER_USAGE
LOG_ROOT = Path(__fi... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/tests/test_screenshots.py | tests/test_screenshots.py | import asyncio
import os
from pathlib import Path
import pytest
from scripts import generate_screenshots as gs
@pytest.mark.screenshots
def test_seeded_screenshots(request, unused_tcp_port_factory):
"""Optionally generate the documentation screenshots via pytest.
Run with ``pytest -m screenshots --generate... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/tests/test_ams_model_detection.py | tests/test_ams_model_detection.py | import mqtt_bambulab
def test_identifies_ams_lite_module():
module = {"name": "ams_f1/0", "product_name": "AMS Lite"}
assert mqtt_bambulab.identify_ams_model_from_module(module) == "AMS Lite"
def test_identifies_ams_2_pro_module():
module = {"name": "n3f/1", "product_name": "AMS 2 Pro (2)"}
assert m... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
drndos/openspoolman | https://github.com/drndos/openspoolman/blob/c45d253a2f102354d43ef16dc316b8b7fe361d73/tests/test_tray_remaining.py | tests/test_tray_remaining.py | from jinja2 import Environment, FileSystemLoader
def _render_tray(*, tray_data, ams_models_by_id):
env = Environment(loader=FileSystemLoader("templates"))
env.globals.update(
AUTO_SPEND=False,
AMS_MODELS_BY_ID=ams_models_by_id,
SPOOLMAN_BASE_URL="http://spoolman",
color_is_dark... | python | MIT | c45d253a2f102354d43ef16dc316b8b7fe361d73 | 2026-01-05T07:11:19.703247Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/make_null.py | bin/make_null.py | from Bio import SeqIO
import numpy as np
import random
import sys
AA_ALPHABET_STANDARD_ORDER = 'ARNDCQEGHILKMFPSTWYV'
def make_n_random_edits(
seq,
nedits,
min_pos=None,
max_pos=None,
):
"""
min_pos is inclusive. max_pos is exclusive
"""
alphabet = AA_ALPHABET_STANDAR... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/plot_fitness_results.py | bin/plot_fitness_results.py | from utils import *
def load_data():
data = []
fname = 'data/fitness_results.txt'
with open(fname) as f:
header = f.readline().rstrip().split('\t')
proteins = [ field.split(', ')[0] for field in header[1:] ]
strains = [ field.split(', ')[1] for field in header[1:] ]
for line... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/hiv.py | bin/hiv.py | from mutation import *
np.random.seed(1)
random.seed(1)
def parse_args():
import argparse
parser = argparse.ArgumentParser(description='HIV sequence analysis')
parser.add_argument('model_name', type=str,
help='Type of language model (e.g., hmm, lstm)')
parser.add_argument('--na... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/locations.py | bin/locations.py | country2continent = {
'Afghanistan': 'Asia (Southern)',
'Algeria': 'Africa (Northern)',
'Anhui': 'Asia (Eastern)',
'Argentina': 'America (Southern)',
'Australia': 'Australia',
'Austria': 'Europe',
'Azerbaijan': 'Asia (Western)',
'Bangladesh': 'Asia (Southern)',
'Beijing': 'Asia (East... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/mutation.py | bin/mutation.py | from utils import *
from copy import deepcopy
def err_model(name):
raise ValueError('Model {} not supported'.format(name))
def get_model(args, seq_len, vocab_size,
inference_batch_size=1500):
if args.model_name == 'hmm':
from hmmlearn.hmm import MultinomialHMM
model = Multinomia... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/cluster_purity.py | bin/cluster_purity.py | from utils import *
def print_purity(metas, entries):
for entry in entries:
tprint('Calculating purity of {}'.format(entry))
cluster2entry = {}
for accession in metas:
meta = metas[accession]
try:
cluster = meta['cluster']
except:
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/cov.py | bin/cov.py | from mutation import *
np.random.seed(1)
random.seed(1)
def parse_args():
import argparse
parser = argparse.ArgumentParser(description='Coronavirus sequence analysis')
parser.add_argument('model_name', type=str,
help='Type of language model (e.g., hmm, lstm)')
parser.add_argume... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/flu.py | bin/flu.py | from mutation import *
np.random.seed(1)
random.seed(1)
def parse_args():
import argparse
parser = argparse.ArgumentParser(description='Flu sequence analysis')
parser.add_argument('model_name', type=str,
help='Type of language model (e.g., hmm, lstm)')
parser.add_argument('--na... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/fitness_energy.py | bin/fitness_energy.py | from utils import *
from sklearn.metrics import auc
def parse_args():
import argparse
parser = argparse.ArgumentParser(description='Benchmark methods')
parser.add_argument('method', type=str,
help='Benchmarking method to use')
parser.add_argument('virus', type=str,
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/cached_semantics.py | bin/cached_semantics.py | from utils import *
from sklearn.metrics import auc
def compute_p(true_val, n_interest, n_total, n_permutations=10000):
null_distribution = []
norm = n_interest * n_total
for _ in range(n_permutations):
interest = set(np.random.choice(n_total, size=n_interest,
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/reinfection.py | bin/reinfection.py | from utils import *
def load_to2020():
seq = str(SeqIO.read('data/cov/cov2_spike_wt.fasta', 'fasta').seq)
seq = seq[:779] + 'Q' + seq[780:]
muts = [
[ 'L18F', 'A222V', 'D614G', 'Q780E' ],
]
mutants = { 4: [] }
for i in range(len(muts)):
assert(len(muts[i]) == 4)
mutabl... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/TreeCluster.py | bin/TreeCluster.py | #!/usr/bin/env python3
from math import log
import DisjointSet
from queue import PriorityQueue,Queue
from treeswift import read_tree_newick
from sys import stderr
NUM_THRESH = 1000 # number of thresholds for the threshold-free methods to use
VERBOSE = False
# merge two sorted lists into a sorted list
def merge_two_sor... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/hiv_pol.py | bin/hiv_pol.py | from mutation import *
np.random.seed(1)
random.seed(1)
def parse_args():
import argparse
parser = argparse.ArgumentParser(description='HIV sequence analysis')
parser.add_argument('model_name', type=str,
help='Type of language model (e.g., hmm, lstm)')
parser.add_argument('--na... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/fasta2nexus.py | bin/fasta2nexus.py | from Bio import Align, AlignIO, SeqIO, Nexus, Seq
from Bio.Alphabet import IUPAC, Gapped
import sys
seq_set = set()
records = AlignIO.read(sys.argv[1], 'fasta', alphabet=Gapped(IUPAC.protein))
new_records = []
for idx in range(len(records)):
seq = str(records[idx].seq).replace('J', 'L').replace('B', 'N').replace(... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/fb_model.py | bin/fb_model.py | import torch
from esm import Alphabet, FastaBatchedDataset, ProteinBertModel, pretrained
class FBModel(object):
def __init__(self, name, repr_layer=[-1]):
self.name_ = name
self.repr_layer_ = repr_layer
model, alphabet = pretrained.load_model_and_alphabet(name)
model.eval()
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/hmm.py | bin/hmm.py | from hmmlearn.hmm import MultinomialHMM
def fit(seqs, n_components=1):
MultinomialHMM(
n_components=n_components,
startprob_prior=1.0,
transmat_prior=1.0,
algorithm='viterbi',
random_state=1,
n_iter=100,
tol=0.01,
verbose=True,
params='ste',
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/color_protein.py | bin/color_protein.py | from utils import *
import matplotlib
def write_color(chain, resi, acq, of):
cmap = matplotlib.cm.get_cmap('viridis')
of.write('select toColor, resi {} and chain {}\n'
.format(resi, chain))
rgb = cmap(acq)
of.write('color {}, toColor\n'
.format(matplotlib.colors.rgb2hex(rgb)... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/cov_fasta.py | bin/cov_fasta.py | from mutation import *
np.random.seed(1)
random.seed(1)
def parse_args():
import argparse
parser = argparse.ArgumentParser(description='Coronavirus sequence analysis')
parser.add_argument('baseline_fasta', help='Baseline sequence')
parser.add_argument('target_fasta',
help='Sequ... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/plot_cluster_purity.py | bin/plot_cluster_purity.py | from utils import *
def load_phylo(namespace=None):
if namespace is None:
name = 'phylo'
namespace = ''
else:
name = namespace
namespace = '_' + namespace
data = []
with open('target/log/cluster_purity{}.log'.format(namespace)) as f:
for line in f:
l... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/fb_semantics.py | bin/fb_semantics.py | from utils import *
import torch
from esm import Alphabet, FastaBatchedDataset, ProteinBertModel, pretrained
def predict_sequence_prob_fb(
seq, alphabet, model, repr_layers,
batch_size=4096, verbose=False
):
seqs = [ seq ]
labels = [ 'seq0' ]
dataset = FastaBatchedDataset(labels, seqs)
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/utils.py | bin/utils.py | from anndata import AnnData
from collections import Counter
import datetime
from dateutil.parser import parse as dparse
import errno
import math
import matplotlib.pyplot as plt
import numpy as np
import os
import pandas as pd
import random
import scanpy as sc
from scipy.sparse import csr_matrix, dok_matrix
import scipy... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/fasta2phylip.py | bin/fasta2phylip.py | from Bio import Align, AlignIO, Seq
import sys
seq_set = set()
records = AlignIO.read(sys.argv[1], 'fasta')
new_records = []
for idx in range(len(records)):
seq = str(records[idx].seq).replace('J', 'L').replace('B', 'N').replace('Z', 'Q')
if seq in seq_set:
continue
seq_set.add(seq)
record = r... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/language_model.py | bin/language_model.py | from utils import *
import tensorflow as tf
from tensorflow.keras import Input
from tensorflow.keras.callbacks import ModelCheckpoint
from tensorflow.keras.layers import (
concatenate, Activation, Dense, Embedding, LSTM, Reshape)
from tensorflow.keras.mixed_precision import experimental as mixed_precision
from ten... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/parse_headline_mods.py | bin/parse_headline_mods.py | from utils import *
from flair.data import Sentence
from flair.models import SequenceTagger
import nltk
from nltk.corpus import wordnet as wn
from pattern3.en import conjugate, singularize
info_prefix = 'Original headline: '
def extract_content(line):
return (': '.join(' | '.join(line.split(' | ')[1:])
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/plot_variants.py | bin/plot_variants.py | import matplotlib.pyplot as plt
import pandas as pd
import sys
if __name__ == '__main__':
fname = sys.argv[1]
df = pd.read_csv(fname, sep='\t')
plt.figure(figsize=(4, 6))
plt.scatter(
df['Grammaticality'],
df['Semantic change']
)
plt.xlabel('Grammaticality')
plt.ylabel('Se... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/combinatorial_fitness.py | bin/combinatorial_fitness.py | from utils import Counter, SeqIO
from Bio.Seq import translate
import numpy as np
def load_doud2016():
strain = 'h1'
fname = 'data/influenza/escape_doud2018/WSN1933_H1_HA.fa'
wt_seq = SeqIO.read(fname, 'fasta').seq
seqs_fitness = {}
fname = ('data/influenza/fitness_doud2016/'
'Suppl... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/headlines.py | bin/headlines.py | from mutation import *
np.random.seed(1)
random.seed(1)
def parse_args():
import argparse
parser = argparse.ArgumentParser(description='Headline analysis')
parser.add_argument('model_name', type=str,
help='Type of language model (e.g., hmm, lstm)')
parser.add_argument('--namesp... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/escape.py | bin/escape.py | from utils import Seq, SeqIO
def load_doud2018(survival_cutoff=0.05):
pos_map = {}
with open('data/influenza/escape_doud2018/pos_map.csv') as f:
f.readline() # Consume header.
for line in f:
fields = line.rstrip().split(',')
pos_map[fields[1]] = int(fields[0]) - 1
fna... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/plot_sweep.py | bin/plot_sweep.py | from utils import *
if __name__ == '__main__':
fname = sys.argv[1]
namespace = fname.split('.')[0].split('_')[-1]
method_dict = {
'Bepler': 'Bepler and Berger',
'epistatic': 'EVcouplings (epi)',
'independent': 'EVcouplings (ind)',
'Mutation frequency': 'MAFFT MSA',
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/clustal2newick.py | bin/clustal2newick.py | import sys
newick = ''
with open(sys.argv[1]) as f:
for line in f:
fields = line.rstrip().split(':')
if len(fields) == 1:
newick += fields[0]
else:
prefix, suffix = fields
newick += prefix[:30]
if suffix != '':
newick += ':'
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/parse_semantic_headlines.py | bin/parse_semantic_headlines.py | from utils import *
def semantic_headlines(dirname):
datasets = [ '1', 'A', '2', 'B' ]
responses = [ '1', '2' ]
data = []
for dataset in datasets:
fname = ('{}/semantic_headlines_labeled_{}.csv'
.format(dirname, dataset))
headline_type = {}
with open(fname) as ... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/escape_energy.py | bin/escape_energy.py | from utils import *
from sklearn.metrics import auc
def parse_args():
import argparse
parser = argparse.ArgumentParser(description='Benchmark methods')
parser.add_argument('method', type=str,
help='Benchmarking method to use')
parser.add_argument('virus', type=str,
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/plot_reinfection.py | bin/plot_reinfection.py | from utils import *
def plot_reinfection(namespace='reinfection'):
with open('target/cov/reinfection/cache/cov_mut_{}.txt'
.format(namespace)) as f:
fields = f.readline().rstrip().split()
base_prob, base_change = float(fields[2]), float(fields[3])
n_hprob_hchange = 0
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/newick_reformat.py | bin/newick_reformat.py | import sys
newick = ''
with open(sys.argv[1]) as f:
orig = f.read().rstrip()
orig = orig.replace('(', '(\n').replace(',', '\n,\n').replace(')', ')\n')
for line in orig.split('\n'):
fields = line.rstrip().split(':')
if len(fields) == 0:
continue
elif len(fields) == 1:
newick += fields... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/transformer_layers.py | bin/transformer_layers.py | import numpy as np
import tensorflow as tf
def get_angles(pos, i, d_model):
angle_rates = 1 / np.power(10000, (2 * (i//2)) / np.float32(d_model))
return pos * angle_rates
def positional_encoding(position, d_model):
angle_rads = get_angles(np.arange(position)[:, np.newaxis],
np.... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/mammals.py | bin/mammals.py | species2group = {
'Alpaca': 'camelid',
'Anteater': 'anteater',
'Antelope': 'bovid',
'Bat': 'bat',
'Beluga_Whale': 'cetacean',
'Bovine': 'bovid',
'Buffalo': 'bovid',
'Bulbul': 'avian',
'Bustard': 'avian',
'Camel': 'camelid',
'Cat': 'felid',
'Cattle': 'bovid',
'Chicken'... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/DisjointSet.py | bin/DisjointSet.py | #! /usr/bin/env python
try:
from Queue import Queue
except ImportError:
from queue import Queue
class DisjointSet:
'''``DisjointSet`` class, implemented using the Up-Tree data structure for amortized O(1) find and union operations'''
def __init__(self, initial=None):
'''``DisjointSet`` construct... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/benchmark_subset.py | bin/benchmark_subset.py | from Bio import AlignIO
from Bio.Align import MultipleSeqAlignment
import sys
def msa_subset(ifname, ofname, anchor_id, cutoff=0):
align = AlignIO.read(ifname, 'fasta')
anchor_idx = [ align[i].id
for i in range(len(align)) ].index(anchor_id)
anchor = align[anchor_idx]
subset = []
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/plot_escape_results.py | bin/plot_escape_results.py | from utils import *
def load_data():
data = []
fname = 'data/escape_results.txt'
with open(fname) as f:
header = f.readline().rstrip().split('\t')
strains = [ field.split()[-1].rstrip(')') for field in header[1:] ]
for line in f:
fields = line.rstrip().split('\t')
... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
brianhie/viral-mutation | https://github.com/brianhie/viral-mutation/blob/81c80d41671670eb58cc46e957a1b0c4bf14856a/bin/regional_escape.py | bin/regional_escape.py | from utils import *
from intervaltree import IntervalTree
def load(virus):
if virus == 'h1':
escape_fname = ('results/flu/semantics/'
'analyze_semantics_flu_h1_bilstm_512.txt')
region_fname = 'data/influenza/h1_regions.txt'
elif virus == 'h3':
escape_fname = ('r... | python | MIT | 81c80d41671670eb58cc46e957a1b0c4bf14856a | 2026-01-05T07:10:30.718940Z | false |
harrisonvanderbyl/rwkvstic | https://github.com/harrisonvanderbyl/rwkvstic/blob/55826c8d0bdf89ba36bc4eb6518fa736aa479913/src/__init__.py | src/__init__.py | python | MIT | 55826c8d0bdf89ba36bc4eb6518fa736aa479913 | 2026-01-05T07:11:22.708425Z | false |
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