Added stage for publishing to test.pypi.org when the tag a version number.

Jenkinsfile

@@ -30,6 +30,8 @@ pipeline {
             }
         }
         stage("publish") {
+            parallel {
+                stage ("git.reslate.systems") {
                     environment {
                         CREDS = credentials('4d6f64be-d26d-4f95-8de3-b6a9b0beb311')
                     }
@@ -37,5 +39,18 @@ pipeline {
                         sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/${CREDS_USR}/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
                     }
                 }
+                stage ("test.pypi.org") {
+                    when {
+                        tag '*.*'
+                    }
+                    environment {
+                        TOKEN = credentials('test.pypi.org')
+                    }
+                    steps {
+                        sh returnStatus: true, script: 'python -m twine upload -r testpypi -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
+                    }
+                }
+            }
+        }
     }
 }

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

@@ -1,27 +0,0 @@
-import asyncio
-from Bio import Entrez
-from Bio import SeqIO
-
-# TODO Change this out for a more professional approach
-Entrez.email = "yunyangdeng@outlook.com"
-
-from automlst.engine.data.genomics import AnnotatedString, StringAnnotation
-
-
-async def fetch_ncbi_genbank(genbank_id: str) -> AnnotatedString:
-    with (await asyncio.to_thread(Entrez.efetch, db="nucleotide", id=genbank_id, rettype="gb", retmode="text")) as fetch_stream:
-        record = SeqIO.read(fetch_stream, "genbank")
-        sequence_features = list()
-        for feature in record.features:
-            start = int(feature.location.start)
-            end = int(feature.location.end)
-            qualifiers = feature.qualifiers
-            for qualifier_key in qualifiers:
-                qualifiers[qualifier_key] = set(qualifiers[qualifier_key])
-            sequence_features.append(StringAnnotation(
-                type=feature.type,
-                start=start,
-                end=end+1,  # Position is exclusive
-                feature_properties=qualifiers
-            ))
-        return AnnotatedString(name=genbank_id, sequence=str(record.seq), annotations=sequence_features)