Merge branch 'master' into jchorl/endswith

README.md

@@ -69,7 +69,7 @@ Install dependencies. On Ubuntu distro run
 
 Install python dependencies via `pip`:
   ```
-  pip3 install pandas biopython
+  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
+- 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

recipe/meta.yaml

@@ -35,7 +35,7 @@ requirements:
         - bowtie2 >=2.3.*
         - mash >=2.0.*
         - bcftools >=1.8.*
-        - biopython >=1.70.*
+        - biopython >=1.70.*,<1.85
         - blast >=2.7.1.*
         - seqtk >=1.2.*
         - requests >=2.*.*

recipe/meta_bioconda.yaml

@@ -1,49 +1,47 @@
-{% set version = data.get('version') %}
-
-about:
-    license: Apache 2
-    summary: ECtyper is a python program for serotyping E. coli genomes
-    author: Chad Laing, Kyrylo Bessonov, Camille La Rose, Sam Sung
-    home: https://github.com/phac-nml/ecoli_serotyping
+{% set name = "ectyper" %}
+{% set version = "2.0.0" %}
 
 package:
     name: ectyper
     version: {{ version }}
 
 source:
-    url: https://github.com/phac-nml/ecoli_serotyping/archive/v{{ version }}.tar.gz
+    url: https://github.com/phac-nml/ecoli_serotyping/archive/{{ version }}.tar.gz
+    sha256: bb363f61ca69d2118e855199d7f9046185bb054509cd0762083b4beec2b8c00e  
 
 build:
     number: 1
-    script: python setup.py install
+    noarch: python
+    run_exports:
+        - {{ pin_subpackage(name, max_pin="x") }}
+    script: python -m pip install --no-deps --ignore-installed .
 
 requirements:
-    build:
+    host:
         - python >=3.5
-
+        - pip
+        - setuptools
     run:
         - python >=3.5
         - pytest >=3.5
-        - pandas 0.23.1.*
-        - samtools 1.8.*
-        - bowtie2 2.3.4.1.*
-        - mash 2.0.*
-        - bcftools 1.8.*
-        - biopython 1.70.*
-        - blast 2.7.1.*
-        - seqtk 1.2.*
-        - requests 2.22.*
+        - pandas >=0.23.1.*,<3
+        - samtools >=1.8.*
+        - bowtie2 >=2.3.*
+        - mash >=2.0.*
+        - bcftools >=1.8.*
+        - biopython >=1.70.*,<1.85
+        - blast >=2.7.1.*
+        - seqtk >=1.2.*
+        - requests >=2.*.*
 test:
     import:
         - ectyper
-    source_files:
-        - test/
-    requires:
-         - pytest
     commands:
         - "ectyper --help"
-        - "pytest -s ectyper/test/test_ectyper_intergration.py"
-        - "pytest -s ectyper/test/test_O_serotyping.py"
-
 
 
+about:
+    license: Apache 2
+    summary: ECtyper is a python program for serotyping E. coli genomes
+    author: Chad Laing, Kyrylo Bessonov, Camille La Rose, Sam Sung
+    home: https://github.com/phac-nml/ecoli_serotyping

setup.py

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