fixed FileNotFoundError

`version` file was accidentally left out of `setup.py` file. This has been included now.

MANIFEST.in

@@ -5,3 +5,4 @@ include ./docs/build/*
 include ./CONTRIBUTING*
 include ./CODE_OF_CONDUCT*
 include ./requirements.txt
+include ./version

codemeta.json

@@ -37,8 +37,8 @@
   "description": "BAMnostic is a Pure Python OS, version, and runtime agnostic BAM file parser",
   "keywords": "BAM, pysam, genomics, genetics, htslib, samtools",
   "license": "https://github.com/betteridiot/bamnostic/blob/master/LICENSE",
-  "softwareVersion": "v1.0.8,
-  "version": "v1.0.8",
+  "softwareVersion": "v1.0.10,
+  "version": "v1.0.10",
   "readme": "https://github.com/betteridiot/bamnostic/blob/master/README.md",
   "buildInstructions": "https://github.com/betteridiot/bamnostic/blob/master/README.md",
   "issueTracker": "https://github.com/betteridiot/bamnostic/issues",

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: da346d61a57fbe238b77db2d99796729
+config: 7fa24b6203ce799d5a84455c9dbe3c8e
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_modules/bamnostic/bai.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>bamnostic.bai &mdash; bamnostic 1.0.9 documentation</title>
+  <title>bamnostic.bai &mdash; bamnostic 1.0.10 documentation</title>
 
 
 
@@ -59,7 +59,7 @@
 
 
               <div class="version">
-                1.0.9
+                1.0.10
               </div>
 
 

docs/build/html/_modules/bamnostic/bgzf.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>bamnostic.bgzf &mdash; bamnostic 1.0.9 documentation</title>
+  <title>bamnostic.bgzf &mdash; bamnostic 1.0.10 documentation</title>
 
 
 
@@ -59,7 +59,7 @@
 
 
               <div class="version">
-                1.0.9
+                1.0.10
               </div>
 
 

docs/build/html/_modules/bamnostic/core.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>bamnostic.core &mdash; bamnostic 1.0.9 documentation</title>
+  <title>bamnostic.core &mdash; bamnostic 1.0.10 documentation</title>
 
 
 
@@ -59,7 +59,7 @@
 
 
               <div class="version">
-                1.0.9
+                1.0.10
               </div>
 
 

docs/build/html/_modules/bamnostic/utils.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>bamnostic.utils &mdash; bamnostic 1.0.9 documentation</title>
+  <title>bamnostic.utils &mdash; bamnostic 1.0.10 documentation</title>
 
 
 
@@ -59,7 +59,7 @@
 
 
               <div class="version">
-                1.0.9
+                1.0.10
               </div>
 
 

docs/build/html/_modules/index.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview: module code &mdash; bamnostic 1.0.9 documentation</title>
+  <title>Overview: module code &mdash; bamnostic 1.0.10 documentation</title>
 
 
 
@@ -59,7 +59,7 @@
 
 
               <div class="version">
-                1.0.9
+                1.0.10
               </div>
 
 

docs/build/html/_static/basic.css

@@ -231,6 +231,16 @@ a.headerlink {
     visibility: hidden;
 }
 
+a.brackets:before,
+span.brackets > a:before{
+    content: "[";
+}
+
+a.brackets:after,
+span.brackets > a:after {
+    content: "]";
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -391,6 +401,16 @@ table.citation td {
     border-bottom: none;
 }
 
+th > p:first-child,
+td > p:first-child {
+    margin-top: 0px;
+}
+
+th > p:last-child,
+td > p:last-child {
+    margin-bottom: 0px;
+}
+
 /* -- figures --------------------------------------------------------------- */
 
 div.figure {
@@ -460,11 +480,57 @@ ol.upperroman {
     list-style: upper-roman;
 }
 
+li > p:first-child {
+    margin-top: 0px;
+}
+
+li > p:last-child {
+    margin-bottom: 0px;
+}
+
+dl.footnote > dt,
+dl.citation > dt {
+    float: left;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+    margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+    content: "";
+    clear: both;
+}
+
+dl.field-list {
+    display: flex;
+    flex-wrap: wrap;
+}
+
+dl.field-list > dt {
+    flex-basis: 20%;
+    font-weight: bold;
+    word-break: break-word;
+}
+
+dl.field-list > dt:after {
+    content: ":";
+}
+
+dl.field-list > dd {
+    flex-basis: 70%;
+    padding-left: 1em;
+    margin-left: 0em;
+    margin-bottom: 0em;
+}
+
 dl {
     margin-bottom: 15px;
 }
 
-dd p {
+dd > p:first-child {
     margin-top: 0px;
 }
 
@@ -537,6 +603,12 @@ dl.glossary dt {
     font-style: oblique;
 }
 
+.classifier:before {
+    font-style: normal;
+    margin: 0.5em;
+    content: ":";
+}
+
 abbr, acronym {
     border-bottom: dotted 1px;
     cursor: help;

docs/build/html/_static/doctools.js

@@ -87,14 +87,13 @@ jQuery.fn.highlightText = function(text, className) {
           node.nextSibling));
         node.nodeValue = val.substr(0, pos);
         if (isInSVG) {
-          var bbox = span.getBBox();
           var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
-       	  rect.x.baseVal.value = bbox.x;
+          var bbox = node.parentElement.getBBox();
+          rect.x.baseVal.value = bbox.x;
           rect.y.baseVal.value = bbox.y;
           rect.width.baseVal.value = bbox.width;
           rect.height.baseVal.value = bbox.height;
           rect.setAttribute('class', className);
-          var parentOfText = node.parentNode.parentNode;
           addItems.push({
               "parent": node.parentNode,
               "target": rect});

docs/build/html/_static/documentation_options.js

@@ -1,10 +1,10 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.0.9',
+    VERSION: '1.0.10',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',
     HAS_SOURCE: true,
     SOURCELINK_SUFFIX: '.txt',
-    NAVIGATION_WITH_KEYS: false,
+    NAVIGATION_WITH_KEYS: false
 };

docs/build/html/_static/searchtools.js

@@ -36,8 +36,10 @@ if (!Scorer) {
 
     // query found in title
     title: 15,
+    partialTitle: 7,
     // query found in terms
-    term: 5
+    term: 5,
+    partialTerm: 2
   };
 }
 
@@ -56,6 +58,14 @@ var Search = {
   _queued_query : null,
   _pulse_status : -1,
 
+  htmlToText : function(htmlString) {
+      var htmlElement = document.createElement('span');
+      htmlElement.innerHTML = htmlString;
+      $(htmlElement).find('.headerlink').remove();
+      docContent = $(htmlElement).find('[role=main]')[0];
+      return docContent.textContent || docContent.innerText;
+  },
+
   init : function() {
       var params = $.getQueryParameters();
       if (params.q) {
@@ -65,16 +75,6 @@ var Search = {
       }
   },
 
-  loadIndex : function(url) {
-    $.ajax({type: "GET", url: url, data: null,
-            dataType: "script", cache: true,
-            complete: function(jqxhr, textstatus) {
-              if (textstatus != "success") {
-                document.getElementById("searchindexloader").src = url;
-              }
-            }});
-  },
-
   setIndex : function(index) {
     var q;
     this._index = index;
@@ -120,7 +120,7 @@ var Search = {
     this.out = $('#search-results');
     this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
     this.dots = $('<span></span>').appendTo(this.title);
-    this.status = $('<p style="display: none"></p>').appendTo(this.out);
+    this.status = $('<p class="search-summary">&nbsp;</p>').appendTo(this.out);
     this.output = $('<ul class="search"/>').appendTo(this.out);
 
     $('#search-progress').text(_('Preparing search...'));
@@ -259,11 +259,7 @@ var Search = {
             displayNextItem();
           });
         } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
-          var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
-          if (suffix === undefined) {
-            suffix = '.txt';
-          }
-          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
+          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX,
                   dataType: "text",
                   complete: function(jqxhr, textstatus) {
                     var data = jqxhr.responseText;
@@ -385,6 +381,19 @@ var Search = {
         {files: terms[word], score: Scorer.term},
         {files: titleterms[word], score: Scorer.title}
       ];
+      // add support for partial matches
+      if (word.length > 2) {
+        for (var w in terms) {
+          if (w.match(word) && !terms[word]) {
+            _o.push({files: terms[w], score: Scorer.partialTerm})
+          }
+        }
+        for (var w in titleterms) {
+          if (w.match(word) && !titleterms[word]) {
+              _o.push({files: titleterms[w], score: Scorer.partialTitle})
+          }
+        }
+      }
 
       // no match but word was a required one
       if ($u.every(_o, function(o){return o.files === undefined;})) {
@@ -424,8 +433,12 @@ var Search = {
       var valid = true;
 
       // check if all requirements are matched
-      if (fileMap[file].length != searchterms.length)
-          continue;
+      var filteredTermCount = // as search terms with length < 3 are discarded: ignore
+        searchterms.filter(function(term){return term.length > 2}).length
+      if (
+        fileMap[file].length != searchterms.length &&
+        fileMap[file].length != filteredTermCount
+      ) continue;
 
       // ensure that none of the excluded terms is in the search result
       for (i = 0; i < excluded.length; i++) {
@@ -456,7 +469,8 @@ var Search = {
    * words. the first one is used to find the occurrence, the
    * latter for highlighting it.
    */
-  makeSearchSummary : function(text, keywords, hlwords) {
+  makeSearchSummary : function(htmlText, keywords, hlwords) {
+    var text = Search.htmlToText(htmlText);
     var textLower = text.toLowerCase();
     var start = 0;
     $.each(keywords, function() {