Pinned key dependency versions

This reverts commit ade2f3b845.

.vscode/launch.json

@@ -6,10 +6,10 @@
     "configurations": [
         
         {
-            "name": "automlst info -lschema pubmlst_bordetella_seqdef",
+            "name": "autobigs info -lschema pubmlst_bordetella_seqdef",
             "type": "debugpy",
             "request": "launch",
-            "program": "${workspaceFolder}/src/automlst/cli/program.py",
+            "program": "${workspaceFolder}/src/autobigs/cli/program.py",
             "console": "integratedTerminal",
             "args": [
                 "info",

Jenkinsfile

@@ -33,10 +33,10 @@ pipeline {
             parallel {
                 stage ("git.reslate.systems") {
                     environment {
-                        TOKEN = credentials('git.reslate.systems')
+                        CREDS = credentials('username-password-rs-git')
                     }
                     steps {
-                        sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
+                        sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
                     }
                 }
                 stage ("pypi.org") {

README.md

@@ -1,4 +1,4 @@
-# autoMLST.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 automlst-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 `automlst-cli`, a `Python` package that implements a CLI for calling this library.
+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.

pyproject.toml

@@ -3,17 +3,21 @@ requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "automlst.engine"
+name = "autoBIGS.engine"
 dynamic = ["version"]
 readme = "README.md"
 
 dependencies = [
-    "biopython",
-    "aiohttp[speedups]",
+    "biopython==1.85",
+    "aiohttp[speedups]==3.11",
 ]
 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/autoBIGS.engine"
+Issues = "https://github.com/RealYHD/autoBIGS.engine/issues"
+
 [tool.setuptools_scm]
 
 [tool.pyright]

requirements.txt

@@ -1,5 +1,5 @@
-aiohttp[speedups]
-biopython
+aiohttp[speedups]==3.11
+biopython==1.85
 pytest
 pytest-asyncio
 build

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 automlst.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]]):

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 automlst.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")

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 automlst.engine.data.structures.genomics import NamedString
-from automlst.engine.data.structures.mlst import Allele, PartialAllelicMatchProfile, MLSTProfile
-from automlst.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):
 

tests/autobigs/engine/data/local/test_csv.py

@@ -1,5 +1,5 @@
-from automlst.engine.data.local.csv import dict_loci_alleles_variants_from_loci
-from automlst.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():

tests/autobigs/engine/data/local/test_fasta.py

@@ -1,4 +1,4 @@
-from automlst.engine.data.local.fasta import read_fasta
+from autobigs.engine.data.local.fasta import read_fasta
 
 
 async def test_fasta_reader_not_none():

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 automlst.engine.data.structures.genomics import NamedString
-from automlst.engine.data.structures.mlst import Allele, MLSTProfile
-from automlst.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException
-from automlst.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)