diff --git a/docs/.buildinfo b/docs/.buildinfo index 6fef2c1..951a945 100644 --- a/docs/.buildinfo +++ b/docs/.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: 0ffcf54393a856012dadc0b1563f2c43 +config: bf1d0a21c26d9c55c442915740521680 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_modules/bed_reader/_open_bed.html b/docs/_modules/bed_reader/_open_bed.html index 5876fa5..38ccbe2 100644 --- a/docs/_modules/bed_reader/_open_bed.html +++ b/docs/_modules/bed_reader/_open_bed.html @@ -3,16 +3,16 @@ - bed_reader._open_bed — Bed Reader 1.0.1-beta.2 documentation + bed_reader._open_bed — Bed Reader 1.0.1-beta.5 documentation - - - + + + @@ -30,7 +30,7 @@ Bed Reader
- 1.0.1-beta.2 + 1.0.1-beta.5
@@ -183,7 +183,9 @@

Source code for bed_reader._open_bed

     return 8_000_000
 
 
-
[docs]class open_bed:
+

+[docs]
+class open_bed:
     """
     Open a PLINK .bed file, local or cloud, for reading.
 
@@ -433,7 +435,9 @@ 
Source code for bed_reader._open_bed
         else:
             return Path(input)
 
-
[docs]    def read(
+

+[docs]
+    def read(
         self,
         index: Optional[Any] = None,
         dtype: Optional[Union[type, str]] = "float32",
@@ -599,7 +603,6 @@ 
Source code for bed_reader._open_bed
                 reader, location_str, is_cloud = self._pick_reader(dtype)
 
                 if not is_cloud:
-                    # cmk test this
                     reader(
                         location_str,
                         self.cloud_options,
@@ -612,7 +615,6 @@ 
Source code for bed_reader._open_bed
                         num_threads=num_threads,
                     )
                 else:
-                    # cmk test this
                     reader(
                         location_str,
                         self.cloud_options,
@@ -685,6 +687,7 @@ 
Source code for bed_reader._open_bed
 
         return val

 
+
     def _pick_reader(self, dtype):
         if dtype == np.int8:
             file_reader = read_i8
@@ -932,7 +935,9 @@ 
Source code for bed_reader._open_bed
             self.property_item(key)
         return self.properties_dict
 
-
[docs]    def property_item(self, name: str) -> np.ndarray:
+

+[docs]
+    def property_item(self, name: str) -> np.ndarray:
         """
         Retrieve one property by name.
 
@@ -969,6 +974,7 @@ 
Source code for bed_reader._open_bed
             self._read_fam_or_bim(suffix=mm.suffix)
         return self.properties_dict[name]

 
+
     @property
     def chromosome(self) -> np.ndarray:
         """
@@ -1461,7 +1467,9 @@ 
Source code for bed_reader._open_bed
                     output = np.array(output, dtype=mm.dtype)
             self.properties_dict[key] = output
 
-
[docs]    def read_sparse(
+

+[docs]
+    def read_sparse(
         self,
         index: Optional[Any] = None,
         dtype: Optional[Union[type, str]] = "float32",
@@ -1702,7 +1710,6 @@ 
Source code for bed_reader._open_bed
                     batch_index = sid_index[batch_slice]
 
                     if not is_cloud:
-                        # cmk test this
                         reader(
                             location_str,
                             self.cloud_options,
@@ -1715,7 +1722,6 @@ 
Source code for bed_reader._open_bed
                             num_threads=num_threads,
                         )
                     else:
-                        # cmk test this
                         reader(
                             location_str,
                             self.cloud_options,
@@ -1751,7 +1757,6 @@ 
Source code for bed_reader._open_bed
                     batch_index = iid_index[batch_slice]
 
                     if not is_cloud:
-                        # cmk test this
                         reader(
                             location_str,
                             self.cloud_options,
@@ -1764,7 +1769,6 @@ 
Source code for bed_reader._open_bed
                             num_threads=num_threads,
                         )
                     else:
-                        # cmk test this
                         reader(
                             location_str,
                             self.cloud_options,
@@ -1796,6 +1800,7 @@ 
Source code for bed_reader._open_bed
                 (data, indices, indptr), (len(iid_index), len(sid_index))
             )

 
+
     def sparsify(self, val, order, minor_index, batch_slice, data, indices, indptr):
         flatten = np.ravel(val, order=order)
         nz_indices = np.flatnonzero(flatten).astype(np.int32)
@@ -1812,6 +1817,7 @@ 
Source code for bed_reader._open_bed
         indptr[1:][batch_slice] = np.cumsum(counts_with_initial)[1:]

 
 
+
 def _read_csv(filepath, delimiter=None, dtype=None, usecols=None):
     # Prepare the usecols by ensuring it is a list of indices
     usecols_indices = list(usecols)
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index 38df1f6..6fef918 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -3,16 +3,16 @@
 
   
   
-  Overview: module code — Bed Reader 1.0.1-beta.2 documentation
+  Overview: module code — Bed Reader 1.0.1-beta.5 documentation
       
       
   
   
-        
-        
-        
+        
+        
+        
     
     
      
@@ -30,7 +30,7 @@
             Bed Reader
           
               

-                1.0.1-beta.2
+                1.0.1-beta.5
               

 

   
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
index 476cf5e..fe2120b 100644
--- a/docs/_sources/index.rst.txt
+++ b/docs/_sources/index.rst.txt
@@ -11,6 +11,7 @@
 ################################
 
 .. currentmodule:: bed_reader
+
 Read and write the PLINK BED format, simply and efficiently.
 
 Features:
diff --git a/docs/_static/basic.css b/docs/_static/basic.css
index 7577acb..30fee9d 100644
--- a/docs/_static/basic.css
+++ b/docs/_static/basic.css
@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -738,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 28c7d6b..fa1bd15 100644
--- a/docs/_static/documentation_options.js
+++ b/docs/_static/documentation_options.js
@@ -1,6 +1,5 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.0.1-beta.2',
+const DOCUMENTATION_OPTIONS = {
+    VERSION: '1.0.1-beta.5',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
index 97d56a7..7918c3f 100644
--- a/docs/_static/searchtools.js
+++ b/docs/_static/searchtools.js
@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**
diff --git a/docs/_static/sphinx_highlight.js b/docs/_static/sphinx_highlight.js
index aae669d..8a96c69 100644
--- a/docs/_static/sphinx_highlight.js
+++ b/docs/_static/sphinx_highlight.js
@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});
diff --git a/docs/cloud_urls.html b/docs/cloud_urls.html
index 0523cc2..b8f3bc3 100644
--- a/docs/cloud_urls.html
+++ b/docs/cloud_urls.html
@@ -4,16 +4,16 @@
   
 
   
-  Cloud URL Examples — Bed Reader 1.0.1-beta.2 documentation
+  Cloud URL Examples — Bed Reader 1.0.1-beta.5 documentation
       
       
   
   
-        
-        
-        
+        
+        
+        
     
     
     
@@ -32,7 +32,7 @@
             Bed Reader
           
               

-                1.0.1-beta.2
+                1.0.1-beta.5
               

 

   
@@ -79,7 +79,7 @@
            

              
   

-
Cloud URL Examples

+
Cloud URL Examples

 
Table of Contents:

 
    
 
  • Http
    • 
@@ -93,7 +93,7 @@ 
    Cloud URL Examples
-
    Http
    
+
    Http
    
 
    You can read *.bed files from web sites directly. For small files, access will be fast. For medium-sized files,
 you may need to extend the default timeout.
    
 
    Reading from large files can also be practical and even fast under these conditions:
    
@@ -199,11 +199,11 @@ 
    Cloud URL Examples
-
    Local File
    
+
    Local File
    
 
    We can specify a local file as if it is in the cloud. This is a great way to test cloud functions. For real work and better efficiency, however,
 use the file’s path rather than its URL.
    
 
    
-
    Local File URL
    
+
    Local File URL
    
 
    The URL for a local file takes the form file:///{encoded_file_name}. No cloud options are needed.
    
 
    Example:
    
 
    >>> import numpy as np
@@ -227,7 +227,7 @@ 
    Local File URL
-
    AWS S3
    
+
    AWS S3
    
 
    Let’s look next at reading a file (or part of a file) from AWS S3.
    
 
    The URL for an AWS S3 file takes the form s3://{bucket_name}/{s3_path}.
    
 
    AWS forbids putting some needed information in the URL. Instead, that information must go into a string-to-string
diff --git a/docs/genindex.html b/docs/genindex.html
index 59e7536..d89bf0e 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -3,16 +3,16 @@
 
   
   
-  Index — Bed Reader 1.0.1-beta.2 documentation
+  Index — Bed Reader 1.0.1-beta.5 documentation
       
       
   
   
-        
-        
-        
+        
+        
+        
     
     
      
@@ -30,7 +30,7 @@
             Bed Reader
           
               
    
-                1.0.1-beta.2
+                1.0.1-beta.5
               
    
 
    
   
diff --git a/docs/index.html b/docs/index.html
index 6b37149..573e350 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -4,16 +4,16 @@
   
 
   
-  bed_reader Documentation — Bed Reader 1.0.1-beta.2 documentation
+  bed_reader Documentation — Bed Reader 1.0.1-beta.5 documentation
       
       
   
   
-        
-        
-        
+        
+        
+        
     
     
     
@@ -32,7 +32,7 @@
             Bed Reader
           
               
    
-                1.0.1-beta.2
+                1.0.1-beta.5
               
    
 
    
   
@@ -82,7 +82,7 @@
 https://github.com/fastlmm/bed-reader/actions/workflows/ci.yml/badge.svg?branch=master
 https://img.shields.io/pypi/pyversions/bed-reader
 
    
-
    bed_reader Documentation
    
+
    bed_reader Documentation
    
 
    Read and write the PLINK BED format, simply and efficiently.
    
 
    Features:
    
 
      
@@ -93,7 +93,7 @@ 
      
 
    • Read data locally or from the cloud, efficiently and directly.
      • 
 
    
 
    
-
    Install
    
+
    Install
    
 
    Full version: With all optional dependencies:
    
 
    pip install bed-reader[samples,sparse]
 
    
@@ -104,7 +104,7 @@ 
    Install
-
    Usage
    
+
    Usage
    
 
    Read genotype data from a .bed file.
    
 
    >>> import numpy as np
 >>> from bed_reader import open_bed, sample_file
@@ -156,7 +156,7 @@ 
    Usage