Release fixes (#37)

* @cuttlefishh I think these changes cover your observations

* Sanity checking to protect from testing against an unexpected host

* Set the default host

* Oddly need to specify numpy/scipy in a fresh env

* ah, its because biom imports within its setup...

.travis.yml

@@ -26,5 +26,7 @@ install:
   - alias md5=md5sum
   - pip install -e . --no-deps
 script:
-  - flake8 --ignore=E731 redbiom 
+  - flake8 --ignore=E731 redbiom
+  - redbiom summarize contexts  # will return a nonzero exit status if it cannot communicate with the default host
+  - export REDBIOM_HOST=http://127.0.0.1:7379
   - make test

README.md

@@ -1,5 +1,5 @@
 # ![redbiom](logo.png)
-# ![build-status](https://travis-ci.org/wasade/redbiom.svg?branch=master)
+# ![build-status](https://travis-ci.org/biocore/redbiom.svg?branch=master)
 
 # What is this?
 
@@ -30,9 +30,10 @@ Redbiom depends on [BIOM](http://biom-format.org/) (tested on >= 2.1.5), [Pandas
 
 If you would like to use redbiom as only a client (which is the general case), then the following instructions apply.
 
-    $ git clone https://github.com/wasade/redbiom.git
+    $ git clone https://github.com/biocore/redbiom.git
     $ cd redbiom
-    $ pip install -e .  
+    $ pip install numpy
+    $ pip install -e .
 
 ### Server
 
@@ -59,9 +60,14 @@ Webdis packages its dependencies with the exception of libevent. It is entirely
 
 Last, redbiom itself can be installed as a normal Python package.
 
-    $ git clone https://github.com/wasade/redbiom.git
+    $ git clone https://github.com/biocore/redbiom.git
+    $ pip install numpy
     $ pip install -e .    
 
+### Testing
+
+The test framework is setup to by default only execute tests against `localhost`, specifically, `127.0.0.1:7379`. However, the repository, by default, is setup to communicate with a remote Webdis server. If you wish to execute the test suite, please `export REDBIOM_HOST=http://127.0.0.1:7379`.
+
 # Terminology and notation
 
 In redbiom, the word "context" refers to a way in which the sample data were processed. Data are loaded into contexts and searches for samples by feature happen within contexts.

redbiom/__init__.py

@@ -36,6 +36,6 @@ def _close_sessions():
 def get_config():
     """Deal with all the configy bits"""
     import os
-    hostname = os.environ.get('REDBIOM_HOST', 'http://127.0.0.1:7379')
+    hostname = os.environ.get('REDBIOM_HOST', 'http://qiita.ucsd.edu:7329')
 
     return {'hostname': hostname}

redbiom/tests/__init__.py

@@ -0,0 +1,12 @@
+def assert_test_env():
+    import os
+    import redbiom
+    conf = redbiom.get_config()
+    if not conf['hostname'].startswith('http://127.0.0.1'):
+        if not os.environ.get('REDBIOM_OVERRIDE_HOST_AND_TEST', False):
+            raise ValueError("It appears the REDBIOM_HOST is not 127.0.0.1. "
+                             "By default, the tests will not run on outside "
+                             "of localhost, however if you're sure you want "
+                             "to run the tests against the set host, please "
+                             "set the environment variable "
+                             "REDBIOM_OVERRIDE_HOST_AND_TEST")

redbiom/tests/test_admin.py

@@ -10,7 +10,9 @@
 import redbiom.admin
 import redbiom._requests
 import redbiom.fetch
+from redbiom.tests import assert_test_env
 
+assert_test_env()
 
 table = biom.load_table('test.biom')
 table_with_alt = biom.load_table('test_with_alts.biom')

redbiom/tests/test_fetch.py

@@ -10,6 +10,9 @@
 import redbiom.fetch
 from redbiom.fetch import (_biom_from_samples, sample_metadata,
                            sample_counts_per_category)
+from redbiom.tests import assert_test_env
+
+assert_test_env()
 
 
 table = biom.load_table('test.biom')

redbiom/tests/test_requests.py

@@ -8,6 +8,9 @@
 import redbiom.admin
 from redbiom._requests import (valid, _parse_validate_request, _format_request,
                                make_post, make_get, make_put, buffered)
+from redbiom.tests import assert_test_env
+
+assert_test_env()
 
 
 config = get_config()

redbiom/tests/test_rest.py

@@ -7,6 +7,9 @@
 import json
 import numpy as np
 import pandas as pd
+from redbiom.tests import assert_test_env
+
+assert_test_env()
 
 
 table = biom.load_table('test.biom')

redbiom/tests/test_search.py

@@ -6,6 +6,9 @@
 import redbiom._requests
 import redbiom.admin
 import redbiom.search
+from redbiom.tests import assert_test_env
+
+assert_test_env()
 
 
 metadata = pd.read_csv('test.txt', sep='\t', dtype=str, na_values=[],

redbiom/tests/test_summarize.py

@@ -9,6 +9,9 @@
 import redbiom.admin
 import redbiom._requests
 from redbiom.summarize import contexts
+from redbiom.tests import assert_test_env
+
+assert_test_env()
 
 
 table = biom.load_table('test.biom')

redbiom/tests/test_util.py

@@ -14,7 +14,9 @@
                           partition_samples_by_tags, resolve_ambiguities,
                           _stable_ids_from_ambig, _stable_ids_from_unambig,
                           category_exists, df_to_stems, stems)
+from redbiom.tests import assert_test_env
 
+assert_test_env()
 
 table = biom.load_table('test.biom')
 table_with_alt = biom.load_table('test_with_alts.biom')

test.sh

@@ -8,6 +8,16 @@ else
     md5=md5sum
 fi
 
+# https://stackoverflow.com/a/13864829/19741
+if [ ! -z ${REDBIOM_HOST+x} ]; then 
+    if [[ ${REDBIOM_HOST} != *"http://127.0.0.1"* ]]; then
+        if [ -z ${REDBIOM_OVERRIDE_HOST_AND_TEST+x} ]; then
+            echo "An unexpected host is set for testing, and \$REDBIOM_OVERRIDE_HOST_AND_TEST is not set"
+            exit 1
+        fi
+    fi
+fi
+
 alias md5=md5sum
 function md5test ()
 {