From 1773bb9dcb8696dfaceb9edee9ed77b1fc1f57e9 Mon Sep 17 00:00:00 2001 From: Harrison Deng Date: Wed, 22 Jan 2025 21:05:19 +0000 Subject: [PATCH] Updated naming (again). --- .vscode/launch.json | 4 ++-- README.md | 6 +++--- pyproject.toml | 6 +++--- src/{autobigsst => autobigs}/engine/__init__.py | 0 src/{autobigsst => autobigs}/engine/data/__init__.py | 0 .../engine/data/local/__init__.py | 0 src/{autobigsst => autobigs}/engine/data/local/csv.py | 2 +- src/{autobigsst => autobigs}/engine/data/local/fasta.py | 2 +- .../engine/data/remote/__init__.py | 0 .../engine/data/remote/databases/bigsdb.py | 6 +++--- .../engine/data/structures/__init__.py | 0 .../engine/data/structures/genomics.py | 0 .../engine/data/structures/mlst.py | 0 .../engine/exceptions/database.py | 0 .../engine/data/local/test_csv.py | 4 ++-- .../engine/data/local/test_fasta.py | 2 +- .../engine/data/remote/databases/test_bigsdb.py | 8 ++++---- 17 files changed, 20 insertions(+), 20 deletions(-) rename src/{autobigsst => autobigs}/engine/__init__.py (100%) rename src/{autobigsst => autobigs}/engine/data/__init__.py (100%) rename src/{autobigsst => autobigs}/engine/data/local/__init__.py (100%) rename src/{autobigsst => autobigs}/engine/data/local/csv.py (95%) rename src/{autobigsst => autobigs}/engine/data/local/fasta.py (90%) rename src/{autobigsst => autobigs}/engine/data/remote/__init__.py (100%) rename src/{autobigsst => autobigs}/engine/data/remote/databases/bigsdb.py (96%) rename src/{autobigsst => autobigs}/engine/data/structures/__init__.py (100%) rename src/{autobigsst => autobigs}/engine/data/structures/genomics.py (100%) rename src/{autobigsst => autobigs}/engine/data/structures/mlst.py (100%) rename src/{autobigsst => autobigs}/engine/exceptions/database.py (100%) rename tests/{autobigsst => autobigs}/engine/data/local/test_csv.py (82%) rename tests/{autobigsst => autobigs}/engine/data/local/test_fasta.py (78%) rename tests/{autobigsst => autobigs}/engine/data/remote/databases/test_bigsdb.py (97%) diff --git a/.vscode/launch.json b/.vscode/launch.json index fd2e135..448fd4b 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -6,10 +6,10 @@ "configurations": [ { - "name": "autobigsst info -lschema pubmlst_bordetella_seqdef", + "name": "autobigs info -lschema pubmlst_bordetella_seqdef", "type": "debugpy", "request": "launch", - "program": "${workspaceFolder}/src/autobigsst/cli/program.py", + "program": "${workspaceFolder}/src/autobigs/cli/program.py", "console": "integratedTerminal", "args": [ "info", diff --git a/README.md b/README.md index dd8d1e6..f549291 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# autobigsst.Engine +# autoBIGS.Engine A python library implementing common BIGSdb MLST schemes and databases. Implementation follows the RESTful API outlined by the official [BIGSdb documentation](https://bigsdb.readthedocs.io/en/latest/rest.html) up to `V1.50.0`. @@ -18,8 +18,8 @@ Furthermore, this library is highly asynchronous where any potentially blocking This library can be installed through pip. Learn how to [setup and install pip first](https://pip.pypa.io/en/stable/installation/). -Then, it's as easy as running `pip install autobigsst-engine` in any terminal that has pip in it's path (any terminal where `pip --version` returns a valid version and install path). +Then, it's as easy as running `pip install autobigs-engine` in any terminal that has pip in it's path (any terminal where `pip --version` returns a valid version and install path). ### CLI usage -This is a independent python library and thus does not have any form of direct user interface. One way of using it could be to create your own Python script that makes calls to this libraries functions. Alternatively, you may use `autobigsst-cli`, a `Python` package that implements a CLI for calling this library. \ No newline at end of file +This is a independent python library and thus does not have any form of direct user interface. One way of using it could be to create your own Python script that makes calls to this libraries functions. Alternatively, you may use `autobigs-cli`, a `Python` package that implements a CLI for calling this library. \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index f83d2e3..8d78092 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ requires = ["setuptools>=64", "setuptools_scm>=8"] build-backend = "setuptools.build_meta" [project] -name = "autobigsst.engine" +name = "autoBIGS.engine" dynamic = ["version"] readme = "README.md" @@ -15,8 +15,8 @@ requires-python = ">=3.11" description = "A library to rapidly fetch fetch MLST profiles given sequences for various diseases." [project.urls] -Repository = "https://github.com/RealYHD/autobigsst.engine.git" -Issues = "https://github.com/RealYHD/autobigsst.engine/issues" +Repository = "https://github.com/RealYHD/autobigs.engine.git" +Issues = "https://github.com/RealYHD/autobigs.engine/issues" [tool.setuptools_scm] diff --git a/src/autobigsst/engine/__init__.py b/src/autobigs/engine/__init__.py similarity index 100% rename from src/autobigsst/engine/__init__.py rename to src/autobigs/engine/__init__.py diff --git a/src/autobigsst/engine/data/__init__.py b/src/autobigs/engine/data/__init__.py similarity index 100% rename from src/autobigsst/engine/data/__init__.py rename to src/autobigs/engine/data/__init__.py diff --git a/src/autobigsst/engine/data/local/__init__.py b/src/autobigs/engine/data/local/__init__.py similarity index 100% rename from src/autobigsst/engine/data/local/__init__.py rename to src/autobigs/engine/data/local/__init__.py diff --git a/src/autobigsst/engine/data/local/csv.py b/src/autobigs/engine/data/local/csv.py similarity index 95% rename from src/autobigsst/engine/data/local/csv.py rename to src/autobigs/engine/data/local/csv.py index ed089ae..f5476d3 100644 --- a/src/autobigsst/engine/data/local/csv.py +++ b/src/autobigs/engine/data/local/csv.py @@ -2,7 +2,7 @@ import csv from os import PathLike from typing import AsyncIterable, Mapping, Sequence, Union -from autobigsst.engine.data.structures.mlst import Allele, MLSTProfile +from autobigs.engine.data.structures.mlst import Allele, MLSTProfile def dict_loci_alleles_variants_from_loci(alleles_map: Mapping[str, Sequence[Allele]]): diff --git a/src/autobigsst/engine/data/local/fasta.py b/src/autobigs/engine/data/local/fasta.py similarity index 90% rename from src/autobigsst/engine/data/local/fasta.py rename to src/autobigs/engine/data/local/fasta.py index 5dc3109..0f3a3eb 100644 --- a/src/autobigsst/engine/data/local/fasta.py +++ b/src/autobigs/engine/data/local/fasta.py @@ -3,7 +3,7 @@ from io import TextIOWrapper from typing import Any, AsyncGenerator, Generator, Iterable, Sequence, Union from Bio import SeqIO -from autobigsst.engine.data.structures.genomics import NamedString +from autobigs.engine.data.structures.genomics import NamedString async def read_fasta(handle: Union[str, TextIOWrapper]) -> AsyncGenerator[NamedString, Any]: fasta_sequences = asyncio.to_thread(SeqIO.parse, handle=handle, format="fasta") diff --git a/src/autobigsst/engine/data/remote/__init__.py b/src/autobigs/engine/data/remote/__init__.py similarity index 100% rename from src/autobigsst/engine/data/remote/__init__.py rename to src/autobigs/engine/data/remote/__init__.py diff --git a/src/autobigsst/engine/data/remote/databases/bigsdb.py b/src/autobigs/engine/data/remote/databases/bigsdb.py similarity index 96% rename from src/autobigsst/engine/data/remote/databases/bigsdb.py rename to src/autobigs/engine/data/remote/databases/bigsdb.py index f51cb1d..730a0c2 100644 --- a/src/autobigsst/engine/data/remote/databases/bigsdb.py +++ b/src/autobigs/engine/data/remote/databases/bigsdb.py @@ -5,9 +5,9 @@ from typing import Any, AsyncGenerator, AsyncIterable, Collection, Generator, It from aiohttp import ClientSession, ClientTimeout -from autobigsst.engine.data.structures.genomics import NamedString -from autobigsst.engine.data.structures.mlst import Allele, PartialAllelicMatchProfile, MLSTProfile -from autobigsst.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException, NoSuchBIGSdbDatabaseException +from autobigs.engine.data.structures.genomics import NamedString +from autobigs.engine.data.structures.mlst import Allele, PartialAllelicMatchProfile, MLSTProfile +from autobigs.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException, NoSuchBIGSdbDatabaseException class BIGSdbMLSTProfiler(AbstractAsyncContextManager): diff --git a/src/autobigsst/engine/data/structures/__init__.py b/src/autobigs/engine/data/structures/__init__.py similarity index 100% rename from src/autobigsst/engine/data/structures/__init__.py rename to src/autobigs/engine/data/structures/__init__.py diff --git a/src/autobigsst/engine/data/structures/genomics.py b/src/autobigs/engine/data/structures/genomics.py similarity index 100% rename from src/autobigsst/engine/data/structures/genomics.py rename to src/autobigs/engine/data/structures/genomics.py diff --git a/src/autobigsst/engine/data/structures/mlst.py b/src/autobigs/engine/data/structures/mlst.py similarity index 100% rename from src/autobigsst/engine/data/structures/mlst.py rename to src/autobigs/engine/data/structures/mlst.py diff --git a/src/autobigsst/engine/exceptions/database.py b/src/autobigs/engine/exceptions/database.py similarity index 100% rename from src/autobigsst/engine/exceptions/database.py rename to src/autobigs/engine/exceptions/database.py diff --git a/tests/autobigsst/engine/data/local/test_csv.py b/tests/autobigs/engine/data/local/test_csv.py similarity index 82% rename from tests/autobigsst/engine/data/local/test_csv.py rename to tests/autobigs/engine/data/local/test_csv.py index 4f34924..084df9e 100644 --- a/tests/autobigsst/engine/data/local/test_csv.py +++ b/tests/autobigs/engine/data/local/test_csv.py @@ -1,5 +1,5 @@ -from autobigsst.engine.data.local.csv import dict_loci_alleles_variants_from_loci -from autobigsst.engine.data.structures.mlst import Allele +from autobigs.engine.data.local.csv import dict_loci_alleles_variants_from_loci +from autobigs.engine.data.structures.mlst import Allele def test_dict_loci_alleles_variants_from_loci_single_loci_not_list(): diff --git a/tests/autobigsst/engine/data/local/test_fasta.py b/tests/autobigs/engine/data/local/test_fasta.py similarity index 78% rename from tests/autobigsst/engine/data/local/test_fasta.py rename to tests/autobigs/engine/data/local/test_fasta.py index 14318c8..afbd0e3 100644 --- a/tests/autobigsst/engine/data/local/test_fasta.py +++ b/tests/autobigs/engine/data/local/test_fasta.py @@ -1,4 +1,4 @@ -from autobigsst.engine.data.local.fasta import read_fasta +from autobigs.engine.data.local.fasta import read_fasta async def test_fasta_reader_not_none(): diff --git a/tests/autobigsst/engine/data/remote/databases/test_bigsdb.py b/tests/autobigs/engine/data/remote/databases/test_bigsdb.py similarity index 97% rename from tests/autobigsst/engine/data/remote/databases/test_bigsdb.py rename to tests/autobigs/engine/data/remote/databases/test_bigsdb.py index 73749eb..f7cc7f2 100644 --- a/tests/autobigsst/engine/data/remote/databases/test_bigsdb.py +++ b/tests/autobigs/engine/data/remote/databases/test_bigsdb.py @@ -3,10 +3,10 @@ import re from typing import Collection, Sequence, Union from Bio import SeqIO import pytest -from autobigsst.engine.data.structures.genomics import NamedString -from autobigsst.engine.data.structures.mlst import Allele, MLSTProfile -from autobigsst.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException -from autobigsst.engine.data.remote.databases.bigsdb import BIGSdbIndex, BIGSdbMLSTProfiler +from autobigs.engine.data.structures.genomics import NamedString +from autobigs.engine.data.structures.mlst import Allele, MLSTProfile +from autobigs.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException +from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex, BIGSdbMLSTProfiler def gene_scrambler(gene: str, mutation_site_count: Union[int, float], alphabet: Sequence[str] = ["A", "T", "C", "G"]): rand = random.Random(gene)