update miniconda url (daler#124)

* update miniconda url we we use the latest

* pin requirements to later versions

* use built-in json for now

* force py3.6 for testing

* go back to simplejson for py2 support

Author: daler

.travis.yml

@@ -3,7 +3,7 @@ before_script:
   - export PATH=~/anaconda/bin:$PATH
 env:
   - PY=2
-  - PY=3
+  - PY=3.6
 
 install: "ci/travis-setup.sh"
 script: "ci/travis-run.sh"

ci/travis-setup.sh

@@ -2,7 +2,7 @@
 set -euo pipefail
 set -x
 HERE=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
-curl -O https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
 bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/anaconda
 export PATH=~/anaconda/bin:$PATH
 

gffutils/feature.py

@@ -1,6 +1,6 @@
 from pyfaidx import Fasta
 import six
-import simplejson
+import simplejson as json
 from gffutils import constants
 from gffutils import helpers
 from gffutils import parser
@@ -145,7 +145,7 @@ def __init__(self, seqid=".", source=".", featuretype=".",
                 attributes = helpers._unjsonify(attributes, isattributes=True)
 
             # it's a string but not JSON: assume original attributes string.
-            except simplejson.JSONDecodeError:
+            except json.JSONDecodeError:
 
                 # But Feature.attributes is still a dict
                 attributes, _dialect = parser._split_keyvals(attributes)
@@ -159,7 +159,7 @@ def __init__(self, seqid=".", source=".", featuretype=".",
         if isinstance(extra, six.string_types):
             try:
                 extra = helpers._unjsonify(extra)
-            except simplejson.JSONDecodeError:
+            except json.JSONDecodeError:
                 extra = extra.split('\t')
 
         self.seqid = seqid

gffutils/helpers.py

@@ -1,7 +1,7 @@
 import copy
 import sys
 import os
-import simplejson
+import simplejson as json
 import time
 import tempfile
 import six
@@ -256,16 +256,16 @@ def _bin_from_dict(d):
 def _jsonify(x):
     """Use most compact form of JSON"""
     if isinstance(x, dict_class):
-        return simplejson.dumps(x._d, separators=(',', ':'))
-    return simplejson.dumps(x, separators=(',', ':'))
+        return json.dumps(x._d, separators=(',', ':'))
+    return json.dumps(x, separators=(',', ':'))
 
 
 def _unjsonify(x, isattributes=False):
     """Convert JSON string to an ordered defaultdict."""
     if isattributes:
-        obj = simplejson.loads(x)
+        obj = json.loads(x)
         return dict_class(obj)
-    return simplejson.loads(x)
+    return json.loads(x)
 
 
 def _feature_to_fields(f, jsonify=True):

optional-requirements.txt

@@ -1,5 +1,3 @@
-# use conda install -c bioconda
-biopython
-bedtools
-pybedtools
-bedtools
+biopython>=1.73
+bedtools>=2.27.1
+pybedtools>=0.8.0

requirements.txt

@@ -1,5 +1,5 @@
-pyfaidx
-six
-argh
-argcomplete
+pyfaidx>=0.5.5.2
+six>=1.12.0
+argh>=0.26.2
+argcomplete>=1.9.4
 simplejson