release v2.0.0 compatible with biopython version 1.85 now

README.md

@@ -69,7 +69,7 @@ Install dependencies. On Ubuntu distro run
 
 Install python dependencies via `pip`:
   ```
-  pip3 install pandas "biopython<1.85"
+  pip3 install pandas "biopython<=1.85"
   ```
 Clone the repository or checkout a particular release (e.g `v1.0.0`, `v2.0.0` etc.):
   ```
@@ -93,7 +93,7 @@ pip3 install .   # option 2
 - mash >= 2.0
 
 ### Python packages:
-- biopython >= 1.70,<1.85 (see issue #99)
+- biopython >= 1.70,<=1.85
 - pandas >= 0.23.1
 - requests >= 2.0
 
@@ -346,4 +346,4 @@ Licensed under the Apache License, Version 2.0 (the "License"); you may not use
 
 [http://www.apache.org/licenses/LICENSE-2.0](http://www.apache.org/licenses/LICENSE-2.0)
 
-Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
+Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

ectyper/speciesIdentification.py

@@ -242,7 +242,7 @@ def getSampleName(file):
 
 def is_valid_fasta_file(fasta, sampleName):
     # try to read the first sequence of FASTA file and make a format validity decision. No reason to check all reads
-    for contig in SeqIO.parse(fasta, "fasta").records:
+    for contig in SeqIO.parse(fasta, "fasta"):
         if contig.seq != '':
             LOG.debug(f'{sampleName}: input file {fasta} is a valid FASTA')       
             return True

setup.py

@@ -12,7 +12,7 @@
     license='Apache 2',
     scripts=['bin/ectyper'],
     packages=['ectyper'],
-    install_requires=['requests','biopython<1.85','pandas<3'],
+    install_requires=['requests','biopython<=1.85','pandas<3'],
     package_data={'ectyper': ['Data/*.json', 'Data/*.py']},
     zip_safe=False,
     test_suite='py.test',