Renaming project to NSBDiagnosisToolkit

.vscode/launch.json

@@ -9,7 +9,7 @@
             "name": "Python Debugger: Current File with Arguments",
             "type": "debugpy",
             "request": "launch",
-            "program": "${workspaceFolder}/src/mlstmyfasta/cli/program.py",
+            "program": "${workspaceFolder}/src/nsbdiagnosistoolkit/cli/program.py",
             "console": "integratedTerminal",
             "args": [
                 "-fa",

Jenkinsfile

@@ -27,7 +27,7 @@ pipeline {
         stage("test installation") {
             steps {
                 sh "python3.11 -m pip install dist/*.whl --force-reinstall"
-                sh "mlstmyfasta -h"
+                sh "nsbdiagnosistoolkit -h"
             }
         }
         stage("archive") {

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools >= 61.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "mlstmyfasta"
+name = "nsbdiagnosistoolkit"
 dynamic = ["version"]
 dependencies = [
     "biopython",
@@ -13,7 +13,7 @@ requires-python = ">=3.11"
 description = "A tool to rapidly fetch fetch MLST profiles given sequences for various diseases."
 
 [project.scripts]
-mlstmyfasta = "mlstmyfasta.cli.program:cli"
+nsbdiagnosistoolkit = "nsbdiagnosistoolkit.cli.program:cli"
 
 [tool.pyright]
 extraPaths = ["src"]

src/nsbdiagnosistoolkit/cli/aggregator.py

@@ -1,10 +1,10 @@
 from os import path
 from typing import Any, AsyncGenerator, AsyncIterable, Iterable, Sequence
-from mlstmyfasta.engine.data.MLST import MLSTProfile
-from mlstmyfasta.engine.data.genomics import NamedString
-from mlstmyfasta.engine.local.abif import read_abif
-from mlstmyfasta.engine.local.fasta import read_fasta
-from mlstmyfasta.engine.remote.databases.institutpasteur.profiling import InstitutPasteurProfiler
+from nsbdiagnosistoolkit.engine.data.MLST import MLSTProfile
+from nsbdiagnosistoolkit.engine.data.genomics import NamedString
+from nsbdiagnosistoolkit.engine.local.abif import read_abif
+from nsbdiagnosistoolkit.engine.local.fasta import read_fasta
+from nsbdiagnosistoolkit.engine.remote.databases.institutpasteur.profiling import InstitutPasteurProfiler
 
 
 async def aggregate_sequences(fastas: Iterable[str], abifs: Iterable[str]) -> AsyncGenerator[str, Any]:

src/nsbdiagnosistoolkit/cli/program.py

@@ -2,11 +2,11 @@ import argparse
 import asyncio
 from os import path
 
-from mlstmyfasta.cli import aggregator
-from mlstmyfasta.engine.data.genomics import NamedString
-from mlstmyfasta.engine.local.abif import read_abif
-from mlstmyfasta.engine.local.csv import write_mlst_profiles_as_csv
-from mlstmyfasta.engine.local.fasta import read_fasta
+from nsbdiagnosistoolkit.cli import aggregator
+from nsbdiagnosistoolkit.engine.data.genomics import NamedString
+from nsbdiagnosistoolkit.engine.local.abif import read_abif
+from nsbdiagnosistoolkit.engine.local.csv import write_mlst_profiles_as_csv
+from nsbdiagnosistoolkit.engine.local.fasta import read_fasta
 
 
 parser = argparse.ArgumentParser()

src/nsbdiagnosistoolkit/engine/annotate.py

@@ -6,8 +6,8 @@ from Bio import Entrez
 from Bio import SeqIO
 import numpy as np
 
-from mlstmyfasta.engine.data.genomics import AnnotatedString, StringAnnotation
-from mlstmyfasta.engine.remote.databases.ncbi.genbank import fetch_ncbi_genbank
+from nsbdiagnosistoolkit.engine.data.genomics import AnnotatedString, StringAnnotation
+from nsbdiagnosistoolkit.engine.remote.databases.ncbi.genbank import fetch_ncbi_genbank
 
 
 async def annotate_from_genbank(genbank_id: str, query_name: str, query_string: str, max_annotation_length:int = 512, gene_targets:Set = set()):

src/nsbdiagnosistoolkit/engine/local/abif.py

@@ -2,7 +2,7 @@ import asyncio
 from numbers import Number
 from os import path
 from typing import Sequence, Union
-from mlstmyfasta.engine.data.genomics import SangerTraceData
+from nsbdiagnosistoolkit.engine.data.genomics import SangerTraceData
 from Bio.SeqRecord import SeqRecord
 from Bio import SeqIO
 

src/nsbdiagnosistoolkit/engine/local/csv.py

@@ -3,7 +3,7 @@ from io import TextIOWrapper
 from os import PathLike
 from typing import AsyncIterable, Iterable, Mapping, Sequence, Union
 
-from mlstmyfasta.engine.data.MLST import Allele, MLSTProfile
+from nsbdiagnosistoolkit.engine.data.MLST import Allele, MLSTProfile
 
 
 def loci_alleles_variants_from_loci(alleles_map: Mapping[str, Sequence[Allele]]):

src/nsbdiagnosistoolkit/engine/local/fasta.py

@@ -3,7 +3,7 @@ from io import TextIOWrapper
 from typing import Any, AsyncGenerator, Generator, Sequence, Union
 from Bio import SeqIO
 
-from mlstmyfasta.engine.data.genomics import NamedString
+from nsbdiagnosistoolkit.engine.data.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")

src/nsbdiagnosistoolkit/engine/remote/databases/institutpasteur/profiling.py

@@ -3,8 +3,8 @@ from contextlib import AbstractAsyncContextManager
 import re
 from typing import Any, AsyncGenerator, AsyncIterable, Generator, Iterable, Sequence, Union
 from aiohttp import ClientSession, ClientTimeout
-from mlstmyfasta.engine.data.MLST import Allele, MLSTProfile
-from mlstmyfasta.engine.data.genomics import NamedString
+from nsbdiagnosistoolkit.engine.data.MLST import Allele, MLSTProfile
+from nsbdiagnosistoolkit.engine.data.genomics import NamedString
 
 class InstitutPasteurProfiler(AbstractAsyncContextManager):
 

src/nsbdiagnosistoolkit/engine/remote/databases/ncbi/genbank.py

@@ -5,7 +5,7 @@ from Bio import SeqIO
 # TODO Change this out for a more professional approach
 Entrez.email = "yunyangdeng@outlook.com"
 
-from mlstmyfasta.engine.data.genomics import AnnotatedString, StringAnnotation
+from nsbdiagnosistoolkit.engine.data.genomics import AnnotatedString, StringAnnotation
 
 
 async def fetch_ncbi_genbank(genbank_id: str) -> AnnotatedString:

tests/nsbdiagnosistoolkit/engine/local/test_abif.py

@@ -1,6 +1,6 @@
 import os
 
-from mlstmyfasta.engine.local.abif import read_abif
+from nsbdiagnosistoolkit.engine.local.abif import read_abif
 
 async def test_load_sanger_sequence_has_data():
     assert os.path.exists("tests/resources/1I1_F_P1815443_047.ab1")

tests/nsbdiagnosistoolkit/engine/local/test_fasta.py

@@ -1,4 +1,4 @@
-from mlstmyfasta.engine.local.fasta import read_fasta
+from nsbdiagnosistoolkit.engine.local.fasta import read_fasta
 
 
 async def test_fasta_reader_not_none():

tests/nsbdiagnosistoolkit/engine/remote/databases/institutpasteur/test_profiling.py

@@ -1,6 +1,6 @@
 from Bio import SeqIO
-from mlstmyfasta.engine.data.MLST import Allele, MLSTProfile
-from mlstmyfasta.engine.remote.databases.institutpasteur.profiling import InstitutPasteurProfiler
+from nsbdiagnosistoolkit.engine.data.MLST import Allele, MLSTProfile
+from nsbdiagnosistoolkit.engine.remote.databases.institutpasteur.profiling import InstitutPasteurProfiler
 
 
 async def test_profiling_results_in_exact_matches_when_exact():

tests/nsbdiagnosistoolkit/engine/remote/databases/ncbi/test_genbank.py

@@ -1,4 +1,4 @@
-from mlstmyfasta.engine.remote.databases.ncbi.genbank import fetch_ncbi_genbank
+from nsbdiagnosistoolkit.engine.remote.databases.ncbi.genbank import fetch_ncbi_genbank
 
 
 async def test_fetch_ncbi_genbank_with_id_works():

tests/nsbdiagnosistoolkit/engine/test_annotate.py

@@ -1,7 +1,7 @@
-from mlstmyfasta.engine.annotate import annotate_from_genbank, fetch_ncbi_genbank
+from nsbdiagnosistoolkit.engine.annotate import annotate_from_genbank, fetch_ncbi_genbank
 from Bio import SeqIO
 
-from mlstmyfasta.engine.data.genomics import AnnotatedString
+from nsbdiagnosistoolkit.engine.data.genomics import AnnotatedString
 
 async def test_annotate_from_genbank_for_adk_annotation():
     sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)