Refactoring project name to autoBIGSst.engine

.vscode/launch.json

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

Jenkinsfile

@@ -26,7 +26,8 @@ pipeline {
             }
             steps {
                 sh "python -m build"
-                sh "conda-build automlst.engine --output-folder conda-bld"
+                sh "grayskull pypi dist/*.tar.gz"
+                sh "conda-build autobigsst.engine --output-folder conda-bld"
             }
         }
         stage("archive") {
@@ -38,10 +39,10 @@ pipeline {
             parallel {
                 stage ("internal") {
                     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 ("external") {
@@ -50,7 +51,6 @@ pipeline {
                     }
                     environment {
                         PYPI_TOKEN = credentials('pypi.org')
-                        CONDA_TOKEN = credentials('anaconda.org')
                     }
                     steps {
                         sh returnStatus: true, script: 'python -m twine upload -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'

README.md

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

automlst.engine/meta.yaml

@@ -1,43 +0,0 @@
-{% set name = "automlst.engine" %}
-{% set version = "0.5.2.dev2+gde36956" %}
-
-package:
-  name: {{ name|lower }}
-  version: {{ version }}
-
-source:
-  url: file:///workspaces/automlst.engine/dist/automlst_engine-0.5.2.dev2%2Bgde36956.tar.gz
-  sha256: 2dee4910744f063b7ec5c923bbf369c23151c82cc59b8b99da19e162414ba61d
-
-build:
-  noarch: python
-  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
-  number: 0
-
-requirements:
-  host:
-    - python >=3.11
-    - setuptools >=64
-    - setuptools-scm >=8
-    - pip
-  run:
-    - python >=3.11
-    - biopython
-    - aiohttp
-
-test:
-  imports:
-    - automlst
-  commands:
-    - pip check
-  requires:
-    - pip
-
-about:
-  summary: A library to rapidly fetch fetch MLST profiles given sequences for various diseases.
-  license: GPL-3.0
-  license_file: LICENSE
-
-extra:
-  recipe-maintainers:
-    - RealYHD

environment.yml

@@ -12,3 +12,6 @@ dependencies:
 - pytest-cov
 - grayskull
 - conda-build
+- anaconda-client
+- conda-utils
+- bioconda-build

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "automlst.engine"
+name = "autobigsst.engine"
 dynamic = ["version"]
 readme = "README.md"
 authors = [
@@ -19,6 +19,10 @@ dependencies = [
 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"
+
 [tool.setuptools_scm]
 
 [tool.pyright]

src/autobigsst/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 autobigsst.engine.data.structures.mlst import Allele, MLSTProfile
 
 
 def dict_loci_alleles_variants_from_loci(alleles_map: Mapping[str, Sequence[Allele]]):

src/autobigsst/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 autobigsst.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/autobigsst/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 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
 
 class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
 

tests/autobigsst/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 autobigsst.engine.data.local.csv import dict_loci_alleles_variants_from_loci
+from autobigsst.engine.data.structures.mlst import Allele
 
 
 def test_dict_loci_alleles_variants_from_loci_single_loci_not_list():

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

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

tests/autobigsst/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 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
 
 def gene_scrambler(gene: str, mutation_site_count: Union[int, float], alphabet: Sequence[str] = ["A", "T", "C", "G"]):
     rand = random.Random(gene)