Merge pull request #28 from reactome/develop

teslajoy · web-flow · commit f17e78bdb3b3 · 2021-01-06T09:27:17.000-08:00
renaming module to fiviz
diff --git a/docs/analysis.html b/docs/analysis.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Analysis Service &#8212; reactome2py 2.0.0 documentation</title>
+    <title>Analysis Service &#8212; reactome2py 3.0.0 documentation</title>
     <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="static/pygments.css" type="text/css" />
     <script id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
@@ -743,7 +743,7 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2020, Nasim Sanati.
+      &copy;2021, Nasim Sanati.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 3.2.1</a>
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 5c6efcecf511e240c4af31449d730e44
+config: d974c7ced08491c5c667aead3bac5bd1
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '2.0.0',
+    VERSION: '3.0.0',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/content.html b/docs/content.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Content Service &#8212; reactome2py 2.0.0 documentation</title>
+    <title>Content Service &#8212; reactome2py 3.0.0 documentation</title>
     <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="static/pygments.css" type="text/css" />
     <script id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
@@ -1238,7 +1238,7 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2020, Nasim Sanati.
+      &copy;2021, Nasim Sanati.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 3.2.1</a>
diff --git a/docs/genindex.html b/docs/genindex.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; reactome2py 2.0.0 documentation</title>
+    <title>Index &#8212; reactome2py 3.0.0 documentation</title>
     <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="static/pygments.css" type="text/css" />
     <script id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
@@ -428,7 +428,7 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2020, Nasim Sanati.
+      &copy;2021, Nasim Sanati.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 3.2.1</a>
diff --git a/docs/index.html b/docs/index.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>reactome2py Docs &#8212; reactome2py 2.0.0 documentation</title>
+    <title>reactome2py Docs &#8212; reactome2py 3.0.0 documentation</title>
     <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="static/pygments.css" type="text/css" />
     <script id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
@@ -115,7 +115,7 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2020, Nasim Sanati.
+      &copy;2021, Nasim Sanati.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 3.2.1</a>
diff --git a/docs/py-modindex.html b/docs/py-modindex.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Python Module Index &#8212; reactome2py 2.0.0 documentation</title>
+    <title>Python Module Index &#8212; reactome2py 3.0.0 documentation</title>
     <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="static/pygments.css" type="text/css" />
     <script id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
@@ -46,7 +46,7 @@ <h1>Python Module Index</h1>
      <tr class="cap" id="cap-r"><td></td><td>
        <strong>r</strong></td><td></td></tr>
      <tr>
-       <td><img src="static/minus.png" class="toggler"
+       <td><img src="_static/minus.png" class="toggler"
               id="toggle-1" style="display: none" alt="-" /></td>
        <td>
        <code class="xref">reactome2py</code></td><td>
@@ -122,7 +122,7 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2020, Nasim Sanati.
+      &copy;2021, Nasim Sanati.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 3.2.1</a>
diff --git a/docs/search.html b/docs/search.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Search &#8212; reactome2py 2.0.0 documentation</title>
+    <title>Search &#8212; reactome2py 3.0.0 documentation</title>
     <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="static/pygments.css" type="text/css" />
     
@@ -101,7 +101,7 @@ <h3>Related Topics</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2020, Nasim Sanati.
+      &copy;2021, Nasim Sanati.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 3.2.1</a>
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -18,11 +18,11 @@
 # -- Project information -----------------------------------------------------
 
 project = 'reactome2py'
-copyright = '2020, Nasim Sanati'
+copyright = '2021, Nasim Sanati'
 author = 'Nasim Sanati'
 
 # The full version, including alpha/beta/rc tags
-release = '2.0.0'
+release = '3.0.0'
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/docs/utils.html b/docs/utils.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Utils &#8212; reactome2py 2.0.0 documentation</title>
+    <title>Utils &#8212; reactome2py 3.0.0 documentation</title>
     <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
     <link rel="stylesheet" href="static/pygments.css" type="text/css" />
     <script id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
@@ -286,7 +286,7 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2020, Nasim Sanati.
+      &copy;2021, Nasim Sanati.
       
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 3.2.1</a>
diff --git a/reactome2py/fiviz.py b/reactome2py/fiviz.py
@@ -1,5 +1,6 @@
 """
-Utility functions for Reactome data-fetch, mappings, and overlay networks in human.
+ Human functional protein interactions (FI) services api calls
+ and utility functions for Reactome data-fetch, mappings, and overlay networks in human.
 """
 from requests.exceptions import ConnectionError
 import requests
diff --git a/setup.py b/setup.py
@@ -1,6 +1,6 @@
 from setuptools import setup, find_packages
 
-__version__ = '2.0.0'
+__version__ = '3.0.0'
 
 with open("README.md", "r") as f:
     long_description = f.read()
diff --git a/tests/unit/test_fiviz.py b/tests/unit/test_fiviz.py
@@ -0,0 +1,56 @@
+from reactome2py import fiviz
+
+
+def test_ehld_stids():
+    assert isinstance(fiviz.ehld_stids(), list)
+
+
+def test_sbgn_stids():
+    assert isinstance(fiviz.sbgn_stids(), list)
+
+
+def test_sbgn_notin_ehld():
+    sbgn_stIds = fiviz.sbgn_stids()
+    ehld_stIds = fiviz.ehld_stids()
+    is_subset = set(sbgn_stIds).intersection(ehld_stIds)
+    assert bool(is_subset) is False
+
+
+def test_gene_mappings():
+    assert isinstance(fiviz.gene_mappings()[0], dict)
+
+
+def test_pathway_fi():
+    assert isinstance(fiviz.pathway_fi(), dict)
+
+
+def test_genelist_fi():
+    assert isinstance(fiviz.genelist_fi(), dict)
+
+
+def test_pathway_boolean_network():
+    assert isinstance(fiviz.pathway_boolean_network(), dict)
+
+
+def test_pathway_factor_graph():
+    assert isinstance(fiviz.pathway_factor_graph(), dict)
+
+
+def test_drug_data_source():
+    assert isinstance(fiviz.drug_data_source(), dict)
+
+
+def test_genelist_drug_target():
+    assert isinstance(fiviz.genelist_drug_target(), dict)
+
+
+def test_pathway_pe_drug_target():
+    assert isinstance(fiviz.pathway_pe_drug_target(), dict)
+
+
+def test_pathway_drug_target():
+    assert isinstance(fiviz.pathway_drug_target(), dict)
+
+
+def test_drug_targets():
+    assert isinstance(fiviz.drug_targets(), dict)
diff --git a/tests/unit/test_utils.py b/tests/unit/test_utils.py
