Merge pull request #287 from monarch-initiative/release-0.4.1

Release 0.4.1

docs/conf.py

@@ -62,7 +62,7 @@
 # The short X.Y version.
 version = u'0.4'
 # The full version, including alpha/beta/rc tags.
-release = u'0.4.0'
+release = u'0.4.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -85,6 +85,9 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
+# If `True`, warnings for broken cross-references will be reported
+# during documentation build.
+nitpicky = True
 
 # -- Options for HTML output ----------------------------------------------
 

docs/tutorial.rst

@@ -233,7 +233,7 @@ Testing multiple hypothesis on the same dataset increases the chance of receivin
 However, GPSEA simplifies the application of an appropriate multiple testing correction.
 
 For general use, we recommend using a combination
-of a *Phenotype MTC filter* (:class:`~gpsea.analysis.PhenotypeMtcFilter`) with a *multiple testing correction*.
+of a *Phenotype MTC filter* (:class:`~gpsea.analysis.mtc_filter.PhenotypeMtcFilter`) with a *multiple testing correction*.
 Phenotype MTC filter chooses the HPO terms to test according to several heuristics, which
 reduce the multiple testing burden and focus the analysis
 on the most interesting terms (see :ref:`HPO MTC filter <hpo-mtc-filter-strategy>` for more info).

docs/user-guide/data/Q99593.json

@@ -0,0 +1,93 @@
+{
+    "entryType": "UniProtKB reviewed (Swiss-Prot)",
+    "primaryAccession": "Q99593",
+    "features": [
+        {
+            "type": "Region",
+            "location": {
+                "start": {
+                    "value": 1,
+                    "modifier": "EXACT"
+                },
+                "end": {
+                    "value": 46,
+                    "modifier": "EXACT"
+                }
+            },
+            "description": "Disordered",
+            "evidences": [
+                {
+                    "evidenceCode": "ECO:0000256",
+                    "source": "SAM",
+                    "id": "MobiDB-lite"
+                }
+            ]
+        },
+        {
+            "type": "Region",
+            "location": {
+                "start": {
+                    "value": 250,
+                    "modifier": "EXACT"
+                },
+                "end": {
+                    "value": 356,
+                    "modifier": "EXACT"
+                }
+            },
+            "description": "Disordered",
+            "evidences": [
+                {
+                    "evidenceCode": "ECO:0000256",
+                    "source": "SAM",
+                    "id": "MobiDB-lite"
+                }
+            ]
+        },
+        {
+            "type": "Compositional bias",
+            "location": {
+                "start": {
+                    "value": 263,
+                    "modifier": "EXACT"
+                },
+                "end": {
+                    "value": 299,
+                    "modifier": "EXACT"
+                }
+            },
+            "description": "Polar residues",
+            "evidences": [
+                {
+                    "evidenceCode": "ECO:0000256",
+                    "source": "SAM",
+                    "id": "MobiDB-lite"
+                }
+            ]
+        },
+        {
+            "type": "Compositional bias",
+            "location": {
+                "start": {
+                    "value": 320,
+                    "modifier": "EXACT"
+                },
+                "end": {
+                    "value": 346,
+                    "modifier": "EXACT"
+                }
+            },
+            "description": "Basic and acidic residues",
+            "evidences": [
+                {
+                    "evidenceCode": "ECO:0000256",
+                    "source": "SAM",
+                    "id": "MobiDB-lite"
+                }
+            ]
+        }
+    ],
+    "extraAttributes": {
+        "uniParcId": "UPI0000136AA2"
+    }
+}