release v2.0.0 with biopython less than v1.85 directive

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 (see issue #99)
 - pandas >= 0.23.1
 - requests >= 2.0
 

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',