from importlib.metadata import version
import typer
from . import APP_NAME, console
from .styles import CustomHelpColorsCommand, CustomHelpColorsGroup
app = typer.Typer(
name=APP_NAME,
cls=CustomHelpColorsGroup,
context_settings={"help_option_names": ["-h", "--help"]},
)
def version_callback(value: bool):
if value:
console.print(
f"[bold green]{APP_NAME}[/bold green]: {version(APP_NAME)}")
raise typer.Exit()
@app.callback()
def main(version: bool = typer.Option(
False,
"--version",
callback=version_callback,
is_eager=True,
show_default=False,
help="Display version information",
), ):
pass
# SOURCE https://python.plainenglish.io/how-to-create-a-cli-app-in-python-aea606509332
import typer
import os
from PIL import Image
cli = typer.Typer()
@cli.command()
def stats(filename: str):
'''
Show image info for FILENAME
'''
img = Image.open(filename)
# Print properties
typer.echo(f' Format:\t {img.format}')
typer.echo(f' Mode:\t {img.mode}')
typer.echo(f' Size:\t {img.size[0]} x {img.size[1]}')
typer.echo(f'Palette:\t {img.palette}')
typer.echo(f'Information:\t {img.info}')
@cli.command()
def statsdir(dirname: str):
'''
Show image info for a DIRECTORY
'''
images = os.listdir(dirname)
import typer
from ..pipeline import *
from ..model import *
from .config_cli import config_app
from .train_cli import train
from .export_cli import export
no_args_is_help = False
app = typer.Typer(no_args_is_help=no_args_is_help, add_completion=False)
app.add_typer(config_app, name="config", no_args_is_help=no_args_is_help)
app.command(help="Train the model", no_args_is_help=no_args_is_help)(train)
app.command(help="Export the python file from config", no_args_is_help=no_args_is_help)(export)
def main():
app()
if __name__ == "__main__":
app()
"""
import re
from collections import Counter, OrderedDict
import typer
from Bio import SeqIO
from cupcake import version_callback
from cupcake import cupcake_logger as logger
rex_pbid = re.compile(r"(PB.\d+).(\d+)")
app = typer.Typer(
name="cupcake.sequence.group_ORF_sequences", help="De-duplicate ORF FAA file."
)
def dedup_ORFs(faa_filename, output_prefix, is_pbid):
seq_dict = OrderedDict() # ORF seq --> list of IDs
pbid_counter = Counter() # PB.X --> counter (not used if is_pbid is False)
for r in SeqIO.parse(open(faa_filename), "fasta"):
s = str(r.seq).upper()
if s not in seq_dict:
seq_dict[s] = []
seq_dict[s].append(r.id)
from pathlib import Path
from typing import Optional, Union
import typer
from github_secrets.app import GithubSecretsApp
cli = typer.Typer()
app: GithubSecretsApp
VERBOSE_DOC = 'Show additional output useful for debugging'
@cli.callback(invoke_without_command=True)
def start_app(ctx: typer.Context):
"""
Github Secrets CLI
"""
global app
app = GithubSecretsApp()
if not app.config.settings.config_location.exists():
app.save()
profile_cli = typer.Typer(
help="Manage the profile for working with secrets. Multiple profiles "
"are supported to manage secrets and authentication separately")
@profile_cli.command(name="create")
def create_profile(
import typer as ty
from single import _enums as enums
from single.server import start as start_
app = ty.Typer(help="This is the command line frontend for the single server.")
@app.command()
def start(
port: int = ty.Option(25000, help="The port to broadcast to."),
logging_level: enums.LoggingLevel = ty.Option("INFO",
help="The logging level."),
) -> None:
"""Use this command to start the server."""
start_(port, logging_level)
if __name__ == "__main__":
app()
from fastapi import FastAPI
from starlette.middleware.cors import CORSMiddleware
from app.routes import views
from app.core import auth
import typer # typerCli
from indexer.indexer import db # db class
app = FastAPI()
appTyper = typer.Typer()
# Set all CORS enabled origins
app.add_middleware(
CORSMiddleware,
allow_origins=["*"],
allow_credentials=True,
allow_methods=["*"],
allow_headers=["*"],
)
app.include_router(auth.router)
app.include_router(views.router)
# si hay error de elasticsearch utilizar
# sudo sysctl -w vm.max_map_count=262144
# updateDB from CLI
@appTyper.command()
def updateDB(namefile: str, index: str):
return None
###############################################################################
# pyrolab Main App
#
# COMMANDS
# --------
# pyrolab up
# pyrolab down
# pyrolab reload
# pyrolab ps
# pyrolab --version
###############################################################################
app = typer.Typer()
print(
f"PyroLab Copyright © 2020-{date.today().year} BYU CamachoLab, PyroLab Project Contributors"
)
print("This program comes with ABSOLUTELY NO WARRANTY.")
print(
"This is free software, and you are welcome to redistribute it under certain conditions."
)
print(
"See the documentation for more information (https://pyrolab.readthedocs.io)."
)
print()
def _version_callback(value: bool = True) -> None:
import typer
from typing import Optional
from .. import config
# Program
program = typer.Typer()
# Helpers
def version(value: bool):
if value:
typer.echo(config.VERSION)
raise typer.Exit()
# Command
@program.callback()
def program_main(
version: Optional[bool] = typer.Option(None, "--version", callback=version)
):
"""Describe, extract, validate and transform tabular data."""
pass
class Listable(str, Enum):
env = "environments"
graph = "graphs"
_type_help = "The type of object to list"
_json_help = "Output the object as JSON Lines"
_organization_help = "The name of the Patterns organization to use"
_environment_help = "The name of the Patterns environment to use"
_organization_option = Option("", "--organization", "-o", help=_organization_help)
_environment_option = Option("", "--environment", "-e", help=_environment_help)
list_command = typer.Typer(name="list", help="List objects of a given type")
@list_command.command()
def graphs(
organization: str = Option("", help=_organization_help),
print_json: bool = Option(False, "--json", help=_json_help),
):
"""List graphs"""
ids = IdLookup(organization_name=organization)
with abort_on_error("Error listing graphs"):
gs = list(paginated_graphs(ids.organization_id))
_print_objects(gs, print_json)
@list_command.command()
import typer
from Bio import SeqIO
from bx.intervals import Interval, IntervalTree
from cupcake import version_callback
from cupcake.sequence import BED, BioReaders
from cupcake.sequence.GFF import collapseGFFReader
class index_base(int, Enum):
zero = (0, )
one = 1
app = typer.Typer(
name="cupcake.targeted.calc_probe_hit_from_sam",
help="Calculate Probe Hit from SAM alignment + probe BED",
)
def get_probe_hit(tree, gene_info, r, is_gtf=False):
"""
Given a dict tree (from read_probe_bed) and a GMAP SAM record
Go through each exon and find probes that hit it
Return: (number of probes hit), (total number of bases overlapping with probes), (genes seen)
"""
probes_seen = set()
genes_seen = set()
base_hit = 0
if is_gtf:
r.sID, r.segments = r.chr, r.ref_exons
from pathlib import Path
from typing import List, Optional
import typer
from eve_esi_jobs import do_workorder
from eve_esi_jobs.models import EsiJob, EsiWorkOrder
from eve_esi_jobs.typer_cli.cli_helpers import (
FormatChoices,
report_finished_task,
validate_input_path,
validate_output_path,
)
from eve_esi_jobs.typer_cli.observer import EsiObserver
app = typer.Typer(help="""Do jobs and workorders.""")
logger = logging.getLogger(__name__)
@app.command()
def job(
ctx: typer.Context,
path_in: str = typer.Argument(..., help="Path to the job file."),
path_out: str = typer.Argument(
"./tmp", help="Path to be prepended to the job output path."),
dry_run: bool = typer.Option(
False,
"-d",
"--dry-run",
help="""
Not implemented yet.
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import os.path
import sys
import typer
from typing import List
paths = lambda: (v.rstrip("/") for v in os.environ["PATH"].split(":"))
app = typer.Typer(help="""PATH editor utility.
Expected usages:
if {cli} exists /usr/local/bin; then TODO; fi
export PATH="$({cli} add /usr/local/bin --unique)"
""".format(cli=os.path.basename(sys.argv[0])))
@app.command(name="list", help="Display all entries in PATH")
def ls():
for p in paths(): print(p)
@app.command(help="Fail any provided value is not in PATH")
def exists(values: List[str]):
raise typer.Exit(len(set(v.rstrip("/") for v in values) - set(paths())))
@app.command(name="add", help="Add to the top of PATH provided values, and remove duplicates if asked")
from rich.console import Console
from xvideos_dl import __version__
from xvideos_dl.xvideos_dl import (
Process,
download,
get_videos_by_playlist_id,
get_videos_from_play_page,
get_videos_from_user_page,
parse_playlist_id,
)
from . import constant as c
app = typer.Typer(
name="xvideos-dl",
help="CLI to download videos from https://xvideos.com",
add_completion=False,
)
console = Console()
def version_callback(value: bool):
"""Prints the version of the package."""
if value:
console.print(f"[yellow]xvideos-dl[/] version: [bold blue]{__version__}[/]")
raise typer.Exit()
@app.command(name="CLI to download videos from https://xvideos.com")
def main(
urls: List[str] = typer.Argument(..., help="URL of the video web page."),
import typer
sub_app = typer.Typer()
variable = "Some text"
@sub_app.command()
def hello(name: str = "World", age: int = typer.Option(0, help="The age of the user")):
"""
Say Hello
"""
typer.echo(f"Hello {name}")
@sub_app.command()
def hi(user: str = typer.Argument("World", help="The name of the user to greet")):
"""
Say Hi
"""
@sub_app.command()
def bye():
"""
Say bye
"""
typer.echo("sub bye")
app = typer.Typer(help="Demo App", epilog="The end")
import http
from collections import defaultdict
from datetime import datetime, timedelta
from typing import Optional
import typer
from pydantic import BaseModel
from pydantic.datetime_parse import parse_datetime
import tinvest as ti
openapi = typer.Typer()
DATETIME_HELP = (
'Use one of [now, day, week, month, 6month, year] or any date-time format'
)
class OpenapiCtx(BaseModel):
token: str = ''
sandbox_token: str = ''
use_sandbox: bool = False
class BaseApi:
client: ti.SyncClient
def do_request(ctx: typer.Context, method, *args, **kwargs):
if ctx.obj.use_sandbox:
client = ti.SyncClient(ctx.obj.sandbox_token, use_sandbox=True)
import random
from enum import Enum
from tqdm import tqdm as tq
from geomloss import SamplesLoss
from torch.nn import Sequential, Linear
from torch.nn import functional as F
from torch_geometric.utils import accuracy, precision, recall, f1_score
from pathlib import Path
from rdkit import Chem
from rdkit.Chem import Draw
from models import GNNExplainer_
from models.encoder import GCNN
from utils import get_split, get_dgn, mol_to_tox21_pyg, mol_to_esol_pyg, mol_from_smiles, morgan_count_fingerprint, x_map_tox21, mol_to_smiles, create_path, rdkit_fingerprint, morgan_bit_fingerprint
app = typer.Typer(add_completion=False)
def read_graphs(dataset_path: Path):
labels = {}
nx_graphs = {}
for name in os.listdir(str(dataset_path)):
if not name.endswith('gexf'):
continue
idx, label = name.split('.')[-3:-1]
idx, label = int(idx), int(label)
nx_graphs[idx] = nx.read_gexf(dataset_path / name)
labels[idx] = label
print('Found %d samples' % len(nx_graphs))
return nx_graphs, labels
import typer
from seq2rel_ds import cdr, dgm, docred, gda
from seq2rel_ds.common.util import set_seeds
set_seeds()
app = typer.Typer(
help="Commands for preprocessing data to conform to the seq2rel format.", )
app.add_typer(cdr.app, name="cdr")
app.add_typer(dgm.app, name="dgm")
app.add_typer(docred.app, name="docred")
app.add_typer(gda.app, name="gda")
if __name__ == "__main__":
app()
"""
import os
import logging
from pathlib import Path
import typer
from rostran.core import exceptions
from rostran.core.format import (
SourceTemplateFormat,
TargetTemplateFormat,
GeneratorFileFormat,
convert_template_to_file_format,
)
app = typer.Typer(help=__doc__)
SOURCE_TEMPLATE_FORMAT_DEFAULT = typer.Option(SourceTemplateFormat.Auto,
help="Source template format")
TARGET_TEMPLATE_FORMAT_DEFAULT = typer.Option(TargetTemplateFormat.Auto,
help="Target template format")
@app.command()
def transform(
source_path: str,
source_format: SourceTemplateFormat = SOURCE_TEMPLATE_FORMAT_DEFAULT,
target_path: str = typer.Option(None),
target_format: TargetTemplateFormat = TARGET_TEMPLATE_FORMAT_DEFAULT,
):
"""
Transform AWS CloudFormation/Terraform/Excel template to ROS template.
from lightning.bot import LightningBot
from lightning.cli import guild, tools
from lightning.cli.utils import asyncd
from lightning.config import CONFIG
from lightning.utils.helpers import create_pool, run_in_shell
try:
import uvloop
except ImportError:
# Lol get f****d windows
pass
else:
uvloop.install()
parser = typer.Typer()
parser.add_typer(tools.parser, name="tools", help="Developer tools")
parser.add_typer(guild.parser, name="guild", help="Guild management commands")
@contextlib.contextmanager
def init_logging():
try:
max_file_size = 1000 * 1000 * 8
file_handler = logging.handlers.RotatingFileHandler(
filename="lightning.log", maxBytes=max_file_size, backupCount=10)
log_format = logging.Formatter(
'[%(asctime)s] %(name)s (%(filename)s:%(lineno)d) %(levelname)s: %(message)s'
)
file_handler.setFormatter(log_format)
import typer
app = typer.Typer()
items_app = typer.Typer()
app.add_typer(items_app, name="items")
users_app = typer.Typer()
app.add_typer(users_app, name="users")
@items_app.command("create")
def items_create(item: str):
typer.echo(f"Creating item: {item}")
@items_app.command("delete")
def items_delete(item: str):
typer.echo(f"Deleting item: {item}")
@items_app.command("sell")
def items_sell(item: str):
typer.echo(f"Selling item: {item}")
@users_app.command("create")
def users_create(user_name: str):
typer.echo(f"Creating user: {user_name}")
@users_app.command("delete")
def users_delete(user_name: str):
import pymongo
import typer
from apps.users.config import users_settings
from fastapi_mongodb.db import db_handler
from fastapi_mongodb.helpers import MakeAsync
__all__ = ["users_commands"]
users_commands = typer.Typer(name="users")
async def setup_app():
await db_handler.create_collection(name=users_settings.USERS_COL)
indexes = [
pymongo.IndexModel(
keys=[("email", pymongo.ASCENDING)],
name="email",
unique=True,
background=True,
)
]
result = await db_handler.create_indexes(col_name=users_settings.USERS_COL, indexes=indexes)
for index_name in result:
typer.secho(
message=f"Index: '{index_name}' for collection '{users_settings.USERS_COL}' created successfully.",
fg=typer.colors.GREEN,
)
from globus_automate_client.cli.callbacks import (
input_validator,
principal_validator,
url_validator_callback,
)
from globus_automate_client.cli.constants import OutputFormat
from globus_automate_client.cli.helpers import (
output_format_option,
process_input,
verbosity_option,
)
from globus_automate_client.cli.rich_helpers import RequestRunner
from globus_automate_client.cli.rich_rendering import live_content
from globus_automate_client.client_helpers import create_action_client
app = typer.Typer(short_help="Manage Globus Automate Actions")
@app.command("introspect")
def action_introspect(
action_url: str = typer.Option(
...,
help="The url at which the target Action Provider is located.",
prompt=True,
callback=url_validator_callback,
),
action_scope: str = typer.Option(
None,
help="The scope this Action Provider uses to authenticate requests.",
callback=url_validator_callback,
),
app = typer.Typer(
cls=NaturalOrderGroup,
help=f"""Run the DIRAC integration tests.
A local DIRAC setup can be created and tested by running:
\b
./integration_tests.py create
This is equivalent to running:
\b
./integration_tests.py prepare-environment
./integration_tests.py install-server
./integration_tests.py install-client
./integration_tests.py test-server
./integration_tests.py test-client
The test setup can be shutdown using:
\b
./integration_tests.py destroy
See below for additional subcommands which are useful during local development.
## Features
The currently known features and their default values are:
\b
HOST_OS: {DEFAULT_HOST_OS!r}
MYSQL_VER: {DEFAULT_MYSQL_VER!r}
ES_VER: {DEFAULT_ES_VER!r}
{(os.linesep + ' ').join(['%s: %r' % x for x in FEATURE_VARIABLES.items()])}
All features can be prefixed with "SERVER_" or "CLIENT_" to limit their scope.
## Extensions
Integration tests can be ran for extensions to DIRAC by specifying the module
name and path such as:
\b
./integration_tests.py create --extra-module MyDIRAC=/path/to/MyDIRAC
This will modify the setup process based on the contents of
`MyDIRAC/tests/.dirac-ci-config.yaml`. See the Vanilla DIRAC file for the
available options.
## Command completion
Command completion of typer based scripts can be enabled by running:
typer --install-completion
After restarting your terminal you command completion is available using:
typer ./integration_tests.py run ...
""",
)
import typer
def callback():
typer.echo("Running a command")
app = typer.Typer(callback=callback)
@app.callback()
def new_callback():
typer.echo("Override callback, running a command")
@app.command()
def create(name: str):
typer.echo(f"Creating user: {name}")
if __name__ == "__main__":
app()
import os
import readline
import signal
from typing import Final
import typer
import twitter
from tweet import settings
from rich.console import Console
APP_NAME: Final[str] = "tweet"
app: Final[typer.Typer] = typer.Typer(help="Tweet Only.")
console: Final[Console] = Console()
api: twitter.Api = twitter.Api(
consumer_key=settings.CONSUMER_TOKEN,
consumer_secret=settings.CONSUMER_SECRET,
access_token_key=settings.ACCESS_TOKEN,
access_token_secret=settings.ACCESS_SECRET,
)
def init_api() -> None:
global api
api = twitter.Api(
consumer_key=settings.CONSUMER_TOKEN,
consumer_secret=settings.CONSUMER_SECRET,
access_token_key=settings.ACCESS_TOKEN,
access_token_secret=settings.ACCESS_SECRET,
)
from pathlib import Path
from typing import Optional
import typer
from .core import RemoteRunner
app = typer.Typer(help='Jupyter Lab Port Forwarding Utility')
def version_callback(value: bool):
from pkg_resources import get_distribution
__version__ = get_distribution('jupyter_forward').version
if value:
typer.echo(f'Jupyter Forward CLI Version: {__version__}')
raise typer.Exit()
@app.command()
def start(
host: str,
port: int = typer.Option(
8888,
help=(
'''The local port the remote notebook server will be forwarded to. If not specified, defaults to 8888.'''
),
show_default=True,
),
conda_env: str = typer.Option(
None,
"""Run evolution."""
ev = Evolution()
date = moex.last_history_date()
port = load_from_yaml(date)
ev.evolve(port)
def dividends(ticker: str):
"""Get dividends status."""
div_status.dividends_validation(ticker)
def optimize(date: str = typer.Argument(..., help="YYYY-MM-DD")):
"""Optimize portfolio."""
port = load_from_yaml(date)
opt = Optimizer(port)
print(opt.portfolio)
print(opt.metrics)
print(opt)
div_status.new_on_smart_lab(tuple(port.index[:-2]))
if __name__ == "__main__":
app = typer.Typer(help="Run poptimizer subcommands.", add_completion=False)
app.command()(evolve)
app.command()(dividends)
app.command()(optimize)
app(prog_name="poptimizer")
import subprocess
import typer
from typer.testing import CliRunner
from docs_src.options.name import tutorial003 as mod
runner = CliRunner()
app = typer.Typer()
app.command()(mod.main)
def test_option_help():
result = runner.invoke(app, ["--help"])
assert result.exit_code == 0
assert "-n" in result.output
assert "TEXT" in result.output
assert "--user-name" not in result.output
assert "--name" not in result.output
def test_call():
result = runner.invoke(app, ["-n", "Camila"])
assert result.exit_code == 0
assert "Hello Camila" in result.output
def test_script():
result = subprocess.run(
["coverage", "run", mod.__file__, "--help"],
import typer
app = typer.Typer()
users_app = typer.Typer()
app.add_typer(users_app, name="users", help="Manage users in the app.")
@users_app.command()
def create(name: str):
print(f"Creating user: {name}")
if __name__ == "__main__":
app()
