ydeng/autoBIGS.cli
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Updated module imports

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Harrison Deng
2025-01-22 21:36:45 +00:00
parent 6305f5dbc9
commit 9498fe7a45
7 changed files with 13 additions and 9 deletions
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8
pyproject.toml
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@@ -7,14 +7,18 @@ name = "autoBIGS.cli"
dynamic = ["version"] dynamic = ["version"]
readme = "README.md" readme = "README.md"
[project.urls]
Repository = "https://github.com/RealYHD/autoBIGS.cli"
Issues = "https://github.com/RealYHD/autoBIGS.cli/issues"
dependencies = [ dependencies = [
"autoBIGS-engine" "autoBIGS.engine"
] ]
requires-python = ">=3.11" requires-python = ">=3.11"
description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases." description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."
[project.scripts] [project.scripts]
autoBIGS = "autoBIGS.cli.program:run" autoBIGS = "autobigs.cli.program:run"
[tool.setuptools_scm] [tool.setuptools_scm]

2
requirements.txt
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@@ -4,4 +4,4 @@ pytest-cov
build build
twine twine
setuptools_scm setuptools_scm
autobigsst.engine autoBIGS.engine

0
src/autoBIGSst/cli/__init__.py → src/autobigs/cli/__init__.py
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2
src/autoBIGSst/cli/info.py → src/autobigs/cli/info.py
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@@ -1,6 +1,6 @@
from argparse import ArgumentParser, Namespace from argparse import ArgumentParser, Namespace
import asyncio import asyncio
from autoBIGS.engine.data.remote.databases.bigsdb import BIGSdbIndex from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex
def setup_parser(parser: ArgumentParser): def setup_parser(parser: ArgumentParser):
parser.description = "Fetches the latest BIGSdb MLST database definitions." parser.description = "Fetches the latest BIGSdb MLST database definitions."

0
src/autoBIGSst/cli/meta.py → src/autobigs/cli/meta.py
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4
src/autoBIGSst/cli/program.py → src/autobigs/cli/program.py
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@@ -3,8 +3,8 @@ from importlib import metadata
from os import path from os import path
import os import os
from autoBIGS.cli import info, st from autobigs.cli import info, st
from autoBIGS.cli.meta import get_module_base_name from autobigs.cli.meta import get_module_base_name
import importlib import importlib
root_parser = argparse.ArgumentParser(epilog='Use "%(prog)s info -h" to learn how to get available MLST databases, and their available schemas.' root_parser = argparse.ArgumentParser(epilog='Use "%(prog)s info -h" to learn how to get available MLST databases, and their available schemas.'

6
src/autoBIGSst/cli/st.py → src/autobigs/cli/st.py
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@@ -2,9 +2,9 @@
from argparse import ArgumentParser, Namespace from argparse import ArgumentParser, Namespace
import asyncio import asyncio
import datetime import datetime
from autoBIGS.engine.data.local.csv import write_mlst_profiles_as_csv from autobigs.engine.data.local.csv import write_mlst_profiles_as_csv
from autoBIGS.engine.data.local.fasta import read_multiple_fastas from autobigs.engine.data.local.fasta import read_multiple_fastas
from autoBIGS.engine.data.remote.databases.bigsdb import BIGSdbIndex from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex
def setup_parser(parser: ArgumentParser): def setup_parser(parser: ArgumentParser):