From 2cd56ca1ec5f65c6ed364d2c699a1fe6167d3a0e Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Fri, 3 Jan 2025 19:56:55 +0000
Subject: [PATCH] Renaming project to NSBDiagnosisToolkit

---
 .vscode/launch.json                                    |  2 +-
 Jenkinsfile                                            |  2 +-
 pyproject.toml                                         |  4 ++--
 .../cli/aggregator.py                                  | 10 +++++-----
 .../cli/program.py                                     | 10 +++++-----
 .../engine/__init__.py                                 |  0
 .../engine/annotate.py                                 |  4 ++--
 .../engine/data/MLST.py                                |  0
 .../engine/data/__init__.py                            |  0
 .../engine/data/genomics.py                            |  0
 .../engine/local/abif.py                               |  2 +-
 .../engine/local/csv.py                                |  2 +-
 .../engine/local/fasta.py                              |  2 +-
 .../remote/databases/institutpasteur/__init__.py       |  0
 .../remote/databases/institutpasteur/profiling.py      |  4 ++--
 .../engine/remote/databases/ncbi/__init__.py           |  0
 .../engine/remote/databases/ncbi/genbank.py            |  2 +-
 .../http/server.py                                     |  0
 .../engine/local/test_abif.py                          |  2 +-
 .../engine/local/test_fasta.py                         |  2 +-
 .../remote/databases/institutpasteur/test_profiling.py |  4 ++--
 .../engine/remote/databases/ncbi/test_genbank.py       |  2 +-
 .../engine/test_annotate.py                            |  4 ++--
 23 files changed, 29 insertions(+), 29 deletions(-)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/cli/aggregator.py (68%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/cli/program.py (79%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/__init__.py (100%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/annotate.py (92%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/data/MLST.py (100%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/data/__init__.py (100%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/data/genomics.py (100%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/local/abif.py (98%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/local/csv.py (94%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/local/fasta.py (86%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/remote/databases/institutpasteur/__init__.py (100%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/remote/databases/institutpasteur/profiling.py (95%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/remote/databases/ncbi/__init__.py (100%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/engine/remote/databases/ncbi/genbank.py (92%)
 rename src/{mlstmyfasta => nsbdiagnosistoolkit}/http/server.py (100%)
 rename tests/{mlstmyfasta => nsbdiagnosistoolkit}/engine/local/test_abif.py (79%)
 rename tests/{mlstmyfasta => nsbdiagnosistoolkit}/engine/local/test_fasta.py (77%)
 rename tests/{mlstmyfasta => nsbdiagnosistoolkit}/engine/remote/databases/institutpasteur/test_profiling.py (89%)
 rename tests/{mlstmyfasta => nsbdiagnosistoolkit}/engine/remote/databases/ncbi/test_genbank.py (58%)
 rename tests/{mlstmyfasta => nsbdiagnosistoolkit}/engine/test_annotate.py (78%)

diff --git a/.vscode/launch.json b/.vscode/launch.json
index 6ab0726..fdf2e3a 100644
--- a/.vscode/launch.json
+++ b/.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",
diff --git a/Jenkinsfile b/Jenkinsfile
index 4fb6910..bfe76de 100644
--- a/Jenkinsfile
+++ b/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") {
diff --git a/pyproject.toml b/pyproject.toml
index 3215489..7f19ad6 100644
--- a/pyproject.toml
+++ b/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"]
diff --git a/src/mlstmyfasta/cli/aggregator.py b/src/nsbdiagnosistoolkit/cli/aggregator.py
similarity index 68%
rename from src/mlstmyfasta/cli/aggregator.py
rename to src/nsbdiagnosistoolkit/cli/aggregator.py
index f708290..fd2b07e 100644
--- a/src/mlstmyfasta/cli/aggregator.py
+++ b/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]:
diff --git a/src/mlstmyfasta/cli/program.py b/src/nsbdiagnosistoolkit/cli/program.py
similarity index 79%
rename from src/mlstmyfasta/cli/program.py
rename to src/nsbdiagnosistoolkit/cli/program.py
index 0564a2c..af10122 100644
--- a/src/mlstmyfasta/cli/program.py
+++ b/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()
diff --git a/src/mlstmyfasta/engine/__init__.py b/src/nsbdiagnosistoolkit/engine/__init__.py
similarity index 100%
rename from src/mlstmyfasta/engine/__init__.py
rename to src/nsbdiagnosistoolkit/engine/__init__.py
diff --git a/src/mlstmyfasta/engine/annotate.py b/src/nsbdiagnosistoolkit/engine/annotate.py
similarity index 92%
rename from src/mlstmyfasta/engine/annotate.py
rename to src/nsbdiagnosistoolkit/engine/annotate.py
index 020031b..5dfbd3f 100644
--- a/src/mlstmyfasta/engine/annotate.py
+++ b/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()):
diff --git a/src/mlstmyfasta/engine/data/MLST.py b/src/nsbdiagnosistoolkit/engine/data/MLST.py
similarity index 100%
rename from src/mlstmyfasta/engine/data/MLST.py
rename to src/nsbdiagnosistoolkit/engine/data/MLST.py
diff --git a/src/mlstmyfasta/engine/data/__init__.py b/src/nsbdiagnosistoolkit/engine/data/__init__.py
similarity index 100%
rename from src/mlstmyfasta/engine/data/__init__.py
rename to src/nsbdiagnosistoolkit/engine/data/__init__.py
diff --git a/src/mlstmyfasta/engine/data/genomics.py b/src/nsbdiagnosistoolkit/engine/data/genomics.py
similarity index 100%
rename from src/mlstmyfasta/engine/data/genomics.py
rename to src/nsbdiagnosistoolkit/engine/data/genomics.py
diff --git a/src/mlstmyfasta/engine/local/abif.py b/src/nsbdiagnosistoolkit/engine/local/abif.py
similarity index 98%
rename from src/mlstmyfasta/engine/local/abif.py
rename to src/nsbdiagnosistoolkit/engine/local/abif.py
index 1296793..dfed5a8 100644
--- a/src/mlstmyfasta/engine/local/abif.py
+++ b/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
 
diff --git a/src/mlstmyfasta/engine/local/csv.py b/src/nsbdiagnosistoolkit/engine/local/csv.py
similarity index 94%
rename from src/mlstmyfasta/engine/local/csv.py
rename to src/nsbdiagnosistoolkit/engine/local/csv.py
index 87beb5c..6165606 100644
--- a/src/mlstmyfasta/engine/local/csv.py
+++ b/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]]):
diff --git a/src/mlstmyfasta/engine/local/fasta.py b/src/nsbdiagnosistoolkit/engine/local/fasta.py
similarity index 86%
rename from src/mlstmyfasta/engine/local/fasta.py
rename to src/nsbdiagnosistoolkit/engine/local/fasta.py
index 82ff798..e75bd6e 100644
--- a/src/mlstmyfasta/engine/local/fasta.py
+++ b/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")
diff --git a/src/mlstmyfasta/engine/remote/databases/institutpasteur/__init__.py b/src/nsbdiagnosistoolkit/engine/remote/databases/institutpasteur/__init__.py
similarity index 100%
rename from src/mlstmyfasta/engine/remote/databases/institutpasteur/__init__.py
rename to src/nsbdiagnosistoolkit/engine/remote/databases/institutpasteur/__init__.py
diff --git a/src/mlstmyfasta/engine/remote/databases/institutpasteur/profiling.py b/src/nsbdiagnosistoolkit/engine/remote/databases/institutpasteur/profiling.py
similarity index 95%
rename from src/mlstmyfasta/engine/remote/databases/institutpasteur/profiling.py
rename to src/nsbdiagnosistoolkit/engine/remote/databases/institutpasteur/profiling.py
index 1b95add..9bd1016 100644
--- a/src/mlstmyfasta/engine/remote/databases/institutpasteur/profiling.py
+++ b/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):
 
diff --git a/src/mlstmyfasta/engine/remote/databases/ncbi/__init__.py b/src/nsbdiagnosistoolkit/engine/remote/databases/ncbi/__init__.py
similarity index 100%
rename from src/mlstmyfasta/engine/remote/databases/ncbi/__init__.py
rename to src/nsbdiagnosistoolkit/engine/remote/databases/ncbi/__init__.py
diff --git a/src/mlstmyfasta/engine/remote/databases/ncbi/genbank.py b/src/nsbdiagnosistoolkit/engine/remote/databases/ncbi/genbank.py
similarity index 92%
rename from src/mlstmyfasta/engine/remote/databases/ncbi/genbank.py
rename to src/nsbdiagnosistoolkit/engine/remote/databases/ncbi/genbank.py
index ae42882..c654385 100644
--- a/src/mlstmyfasta/engine/remote/databases/ncbi/genbank.py
+++ b/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:
diff --git a/src/mlstmyfasta/http/server.py b/src/nsbdiagnosistoolkit/http/server.py
similarity index 100%
rename from src/mlstmyfasta/http/server.py
rename to src/nsbdiagnosistoolkit/http/server.py
diff --git a/tests/mlstmyfasta/engine/local/test_abif.py b/tests/nsbdiagnosistoolkit/engine/local/test_abif.py
similarity index 79%
rename from tests/mlstmyfasta/engine/local/test_abif.py
rename to tests/nsbdiagnosistoolkit/engine/local/test_abif.py
index 7f70024..032194b 100644
--- a/tests/mlstmyfasta/engine/local/test_abif.py
+++ b/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")
diff --git a/tests/mlstmyfasta/engine/local/test_fasta.py b/tests/nsbdiagnosistoolkit/engine/local/test_fasta.py
similarity index 77%
rename from tests/mlstmyfasta/engine/local/test_fasta.py
rename to tests/nsbdiagnosistoolkit/engine/local/test_fasta.py
index 23307fb..83a5864 100644
--- a/tests/mlstmyfasta/engine/local/test_fasta.py
+++ b/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():
diff --git a/tests/mlstmyfasta/engine/remote/databases/institutpasteur/test_profiling.py b/tests/nsbdiagnosistoolkit/engine/remote/databases/institutpasteur/test_profiling.py
similarity index 89%
rename from tests/mlstmyfasta/engine/remote/databases/institutpasteur/test_profiling.py
rename to tests/nsbdiagnosistoolkit/engine/remote/databases/institutpasteur/test_profiling.py
index dde0d74..74aba6c 100644
--- a/tests/mlstmyfasta/engine/remote/databases/institutpasteur/test_profiling.py
+++ b/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():
diff --git a/tests/mlstmyfasta/engine/remote/databases/ncbi/test_genbank.py b/tests/nsbdiagnosistoolkit/engine/remote/databases/ncbi/test_genbank.py
similarity index 58%
rename from tests/mlstmyfasta/engine/remote/databases/ncbi/test_genbank.py
rename to tests/nsbdiagnosistoolkit/engine/remote/databases/ncbi/test_genbank.py
index 95c37a1..21f407e 100644
--- a/tests/mlstmyfasta/engine/remote/databases/ncbi/test_genbank.py
+++ b/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():
diff --git a/tests/mlstmyfasta/engine/test_annotate.py b/tests/nsbdiagnosistoolkit/engine/test_annotate.py
similarity index 78%
rename from tests/mlstmyfasta/engine/test_annotate.py
rename to tests/nsbdiagnosistoolkit/engine/test_annotate.py
index c8ce680..bfb1220 100644
--- a/tests/mlstmyfasta/engine/test_annotate.py
+++ b/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)