run web tests before publishing release; updated convert_map, fixes #82…

…; also:

- fixes bugs with Python 3 and url response decoding
- make maps full height in latest iPython notebooks
- update notebooks
- run py.test web tests on Travis to make sure they work across python versions
- website merge instructions
- version 1.1.2

.travis.yml

@@ -10,6 +10,6 @@ before_install:
 install:
   - python setup.py develop
 # # command to run tests
-script: python setup.py test --noweb --pyonly
+script: python setup.py test --pyonly
 notifications:
   email: false

WEBSITE_MERGE

@@ -0,0 +1,7 @@
+git fetch escher
+git merge escher/1.1.2-fix --no-commit --no-ff 
+source env/bin/activate
+python setup.py buildgh
+git add -A :/
+gc -m"version 1.1.2"
+git push

docs/conf.py

@@ -51,9 +51,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.1.1'
+version = '1.1.2'
 # The full version, including alpha/beta/rc tags.
-release = '1.1.1'
+release = '1.1.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

escher/convert_map.py

@@ -82,7 +82,7 @@ def convert(map, model):
 
     # add missing elements
     for k in ['nodes', 'reactions', 'text_labels']:
-        if k not in map_body:
+        if k not in map_body or len(map_body[k]) == 0:
             map_body[k] = {}
     # default canvas
     if 'canvas' not in map_body:
@@ -154,11 +154,21 @@ def convert(map, model):
                            "genes", "metabolites", "segments"]:
                 del reaction[key]
 
+        # cast attributes
+        for k in ['label_x', 'label_y']:
+            reaction[k] = float(reaction[k])
+
         # unsupported attributes in segments
         for s_id, segment in reaction['segments'].items():
             for key in list(segment.keys()):
                 if not key in ["from_node_id", "to_node_id", "b1", "b2"]:
                     del segment[key]
+
+            # cast attributes
+            for k in ['b1', 'b2']:
+                if segment[k] is not None and (segment[k]['x'] is None or segment[k]['y'] is None):
+                    segment[k] = None
+
             # keep track of nodes that have appeared here
             for key in ['from_node_id', 'to_node_id']:
                 try:

escher/css/builder-1.1.1.css → escher/css/builder-1.1.2.css

@@ -23,8 +23,8 @@
     /* position: absolute; */
     /* top: 0px; */
     /* left: 0px; */
-    width: 100%;
-    height: 100%;
+    width: 100% !important;
+    height: 100% !important;
 }
 /* Status */
 #status {

escher/plots.py

@@ -12,9 +12,9 @@
 from warnings import warn
 try:
     from urllib.request import urlopen
-    from urllib.error import HTTPError, URLError
+    from urllib.error import URLError
 except:
-    from urllib2 import urlopen, HTTPError, URLError
+    from urllib2 import urlopen, URLError
 import json
 import shutil
 import re
@@ -81,7 +81,8 @@ def server_index():
         download = urlopen(url)
     except URLError:
         raise URLError('Could not contact Escher server')
-    index = json.loads(download.read())
+    data = _decode_response(download)
+    index = json.loads(data)
     return index
 
 def list_available_maps():
@@ -130,9 +131,9 @@ def match_in_index(name, index, kind):
         warn('%s not in cache. Attempting download from %s' % (kind.title(), url))
         try:
             download = urlopen(url)
-        except HTTPError:
+        except URLError:
             raise ValueError('No %s found in cache or at %s' % (kind, url))
-        data = download.read()
+        data = _decode_response(download)
         # save the file
         org_path = join(cache_dir, kind + 's', org)
         try:
@@ -141,7 +142,7 @@ def match_in_index(name, index, kind):
             pass
         with open(join(org_path, name + '.json'), 'w') as outfile:
             outfile.write(data)
-        return data.decode('utf-8')
+        return data
 
 def model_json_for_name(model_name, cache_dir=get_cache_dir()):
     return _json_for_name(model_name, 'model', cache_dir)
@@ -155,6 +156,19 @@ def _get_an_id():
     return (''.join(random.choice(string.ascii_lowercase)
                     for _ in range(10)))
 
+def _decode_response(download):
+    """Decode the urllib.response.addinfourl response."""
+    data = download.read()
+    try:                    # Python 2
+        encoding = download.headers.getparam('charset')
+    except AttributeError:  # Python 3
+        encoding = download.headers.get_param('charset')
+    if encoding:
+        data = data.decode(encoding)
+    else:
+        data = data.decode('utf-8')
+    return data
+
 def _load_resource(resource, name, safe=False):
     """Load a resource that could be a file, URL, or json string."""
     # if it's a url, download it
@@ -164,13 +178,7 @@ def _load_resource(resource, name, safe=False):
         except URLError as err:
             raise err
         else:
-            data = download.read()
-            encoding = download.headers.getparam('charset')
-            if encoding:
-                data = data.decode(encoding)
-            else:
-                data = data.decode('utf-8')
-            return data
+            return _decode_response(download)
     # if it's a filepath, load it
     if os.path.exists(resource):
         if (safe):
@@ -424,16 +432,11 @@ def _embedded_css(self, url_source):
                       local_host=self.local_host, protocol='https')
         try:
             download = urlopen(loc)
-        except ValueError:
+        except URLError:
             raise Exception(('Could not find builder_embed_css. Be sure to pass '
                              'a local_host argument to Builder if js_source is dev or local '
                              'and you are in an iPython notebook or a static html file.'))
-        data = download.read()
-        encoding = download.headers.getparam('charset')
-        if encoding:
-            data = data.decode(encoding)
-        else:
-            data = data.decode('utf-8')
+        data = _decode_response(download)
         return data.replace('\n', ' ')
 
     def _initialize_javascript(self, the_id, url_source):

escher/tests/test_convert_map.py

@@ -14,20 +14,31 @@ def test_convert():
 
     # map
     old_map = {'reactions': {'1': {'bigg_id': 'GAPD',
-                                   'label_x': 0,
+                                   'label_x': '0',
                                    'label_y': 0,
                                    'segments': {'2': {'from_node_id': '0',
                                                       'to_node_id': '1',
-                                                      'b1': None,
+                                                      'b1': {'x': None, 'y': None},
                                                       'b2': None}}},
                              '2': {'bigg_id': 'PDH'}},
-               'nodes': {'3': {'node_type': 'metabolite',
+               'nodes': {'0': {'node_type': 'multimarker',
+                               'x': 1,
+                               'y': 2},
+                         '1': {'node_type': 'metabolite',
+                               'label_x': 10,
+                               'label_y': 12.2,
+                               'x': 1,
+                               'y': 2,
+                               'bigg_id': 'g3p_c',
+                               'name': 'glycerol-3-phosphate'},
+                         '3': {'node_type': 'metabolite',
                                'x': 1,
                                'y': 2,
                                'bigg_id': 'glc__D_c',
                                'name': 'D-Glucose'}}}
 
     new_map = convert(old_map, model)
+    print(new_map)
 
     # no segments: delete reaction
     assert '2' not in new_map[1]['reactions']
@@ -44,5 +55,9 @@ def test_convert():
     # annoying.
     assert '3' not in new_map[1]['nodes']
 
+    # casting
+    assert type(new_map[1]['reactions']['1']['label_x']) is float
+    assert new_map[1]['reactions']['1']['segments']['2']['b1'] is None
+
 def test_genes_for_gene_reaction_rule():
     assert genes_for_gene_reaction_rule('((G1 and G2)or G3and)') == ['G1', 'G2', 'G3and']

escher/version.py

@@ -1,2 +1,2 @@
-__version__ = '1.1.1'
+__version__ = '1.1.2'
 __schema_version__ = '1-0-0'

publish_release

@@ -0,0 +1,25 @@
+#! /usr/bin/env bash
+
+python setup.py test --pyonly
+
+if [ $? = "1" ]; then
+    echo "Did not pass Python tests. Exiting."
+    exit 1
+fi
+
+python setup.py test --jsonly
+
+echo -n "Did the Jasmine tests pass? (y/n): "
+while true; do
+    read character
+    if [ $character = "n" ] ; then
+	echo "Did not pass Jasmine tests. Exiting."
+       exit 1
+    fi
+    if [ $character = "y" ] ; then
+       echo "Publishing."
+       python setup.py sdist bdist upload
+       exit $?
+    fi
+    echo -n "Did the Jasmine tests pass? Must enter 'y' or 'n': "
+done

setup.py

@@ -13,7 +13,10 @@
 
 try:
     from setuptools import setup, Command
-except:
+    from setuptools.command.sdist import sdist as SDistCommand
+    from setuptools.command.bdist import bdist as BDistCommand
+    from setuptools.command.upload import upload as UploadCommand
+except ImportError:
     from distutils.core import setup, Command
 
 directory = dirname(realpath(__file__))

spec/javascripts/support/jasmine.yml

@@ -13,7 +13,7 @@
 #
 src_files:
     - escher/lib/d3.min.js
-    - escher/lib/escher-1.1.1.js
+    - escher/lib/escher-1.1.2.js
     - escher/lib/jquery-2.1.0.min.js
     - escher/lib/bootstrap-3.1.1.min.js