Fix typos found by codespell

configs/qap_config_TEMPLATE.yml

@@ -56,5 +56,3 @@ upload_to_s3: False
 
 # bucket output prefix (where to push output files to S3, if applicable)
 bucket_out_prefix: bucket/prefix/output/destination
-
-

docs/index.md

@@ -255,4 +255,3 @@ With the above commands, the outputs will be stored in a directory named `qap_ou
 [^12]: Shehzad, Z., Giavasis, S., Li, Q., Benhajali, Y., Yan, C., Yang, Z., Milham, M., Bellec, P., Craddock, R.C., 2015. The Preprocessed Connectomes Project Quality Assessment Protocol - a Resource for Measuring the Quality of Mri Data. Front. Neurosci. 9. 
 
 [^13]: Yan CG, Cheung B, Kelly C, Colcombe S, Craddock RC, Di Martino A, Li Q, Zuo XN, Castellanos FX, Milham MP (2013). A comprehensive assessment of regional variation in the impact of head micromovements on functional connectomics. Neuroimage. 76:183-201.
-

docs/javascripts/BibTex-0.1.2.js

@@ -74,7 +74,7 @@
  *    2. Output parsed BibTex entries as HTML, RTF, or BibTex.
  *
  *  
- * The following usage instructions have been copyed and adapted from the PHP instructions located
+ * The following usage instructions have been copied and adapted from the PHP instructions located
  * at http://pear.php.net/manual/en/package.structures.structures-bibtex.intro.php
  * Introduction
  * --------------
@@ -143,7 +143,7 @@
  * Author
  * ------
  * As described before the authors are stored in a list. Every entry
- * representing one author as a has table. The hash table consits of four
+ * representing one author as a has table. The hash table consists of four
  * keys: first, von, last and jr. The keys are explained in the following
  * list:
  * 
@@ -934,7 +934,7 @@ BibTex.prototype = {
     }
 	*/
     /**
-     * Parses what is stored in content and clears the content if the parsing is successfull+
+     * Parses what is stored in content and clears the content if the parsing is successful+
      *
      * @access public
      * @return boolean true on success and PEAR_Error if there was a problem
@@ -1045,8 +1045,8 @@ BibTex.prototype = {
      * then you don have to worry about memory+
      * Then the last ',' is searched and the field extracted from that+
      * Again the entry is shortened+
-     * Finally after all field:value pairs the cite and type is extraced and the
-     * authors are splitted+
+     * Finally after all field:value pairs the cite and type is extracted and the
+     * authors are split+
      * If there is a problem false is returned+
      *
      * @access private
@@ -1171,7 +1171,7 @@ BibTex.prototype = {
         if (0 != open) {
             ret = false;
         }
-        //There is still the posibility that the entry is delimited by double quotes+
+        //There is still the possibility that the entry is delimited by double quotes+
         //Then it is possible that the braces are equal even if the '=' is in an equation+
         if (ret) {
             entrycopy = trim(entry);
@@ -1229,7 +1229,7 @@ BibTex.prototype = {
         var ret     = false;
         var opening = array_keys(this._delimiters);
         var closing = array_values(this._delimiters);
-        //Getting the value (at is only allowd in values)
+        //Getting the value (at is only allowed in values)
         if (strrpos(entry,'=') !== false) {
             position = strrpos(entry, '=');
             proceed  = true;
@@ -1626,7 +1626,7 @@ BibTex.prototype = {
     /**
      * Returns the author formatted
      *
-     * The Author is formatted as setted in the authorstring
+     * The Author is formatted as set in the authorstring
      *
      * @access private
      * @param array array Author array
@@ -1864,4 +1864,4 @@ BibTex.prototype = {
         ret += "</p>\n";
         return ret;
     }
-};
+};

docs/javascripts/bib-list.js

@@ -74,7 +74,7 @@
  *    2. Output parsed BibTex entries as HTML, RTF, or BibTex.
  *
  *  
- * The following usage instructions have been copyed and adapted from the PHP instructions located
+ * The following usage instructions have been copied and adapted from the PHP instructions located
  * at http://pear.php.net/manual/en/package.structures.structures-bibtex.intro.php
  * Introduction
  * --------------
@@ -143,7 +143,7 @@
  * Author
  * ------
  * As described before the authors are stored in a list. Every entry
- * representing one author as a has table. The hash table consits of four
+ * representing one author as a has table. The hash table consists of four
  * keys: first, von, last and jr. The keys are explained in the following
  * list:
  * 
@@ -934,7 +934,7 @@ BibTex.prototype = {
     }
 	*/
     /**
-     * Parses what is stored in content and clears the content if the parsing is successfull+
+     * Parses what is stored in content and clears the content if the parsing is successful+
      *
      * @access public
      * @return boolean true on success and PEAR_Error if there was a problem
@@ -1045,8 +1045,8 @@ BibTex.prototype = {
      * then you don have to worry about memory+
      * Then the last ',' is searched and the field extracted from that+
      * Again the entry is shortened+
-     * Finally after all field:value pairs the cite and type is extraced and the
-     * authors are splitted+
+     * Finally after all field:value pairs the cite and type is extracted and the
+     * authors are split+
      * If there is a problem false is returned+
      *
      * @access private
@@ -1171,7 +1171,7 @@ BibTex.prototype = {
         if (0 != open) {
             ret = false;
         }
-        //There is still the posibility that the entry is delimited by double quotes+
+        //There is still the possibility that the entry is delimited by double quotes+
         //Then it is possible that the braces are equal even if the '=' is in an equation+
         if (ret) {
             entrycopy = trim(entry);
@@ -1229,7 +1229,7 @@ BibTex.prototype = {
         var ret     = false;
         var opening = array_keys(this._delimiters);
         var closing = array_values(this._delimiters);
-        //Getting the value (at is only allowd in values)
+        //Getting the value (at is only allowed in values)
         if (strrpos(entry,'=') !== false) {
             position = strrpos(entry, '=');
             proceed  = true;
@@ -1626,7 +1626,7 @@ BibTex.prototype = {
     /**
      * Returns the author formatted
      *
-     * The Author is formatted as setted in the authorstring
+     * The Author is formatted as set in the authorstring
      *
      * @access private
      * @param array array Author array
@@ -2890,4 +2890,4 @@ var bibtexify = (function($) {
             $.get(bibsrc, callbackHandler, "text");
         }
     };
-})(jQuery);
+})(jQuery);

docs/stylesheets/bib-publication-list.css

@@ -15,12 +15,12 @@ span.undefined { color:red; }
 .techreport { background-color: #b77; }
 .legend .pub { width: 10px; height: 10px; display: inline-block; margin: 0 5px 0 15px;}
 .legend { margin-bottom: 20px; text-align: center; width: 100%;}
-table.display thead th { 
-    padding: 3px 18px 3px 10px; 
-    border-bottom: 1px solid black; 
-    border-top: 1px solid black; 
-    font-weight: bold; c
-    cursor: pointer; 
+table.display thead th {
+    padding: 3px 18px 3px 10px;
+    border-bottom: 1px solid black;
+    border-top: 1px solid black;
+    font-weight: bold;
+    cursor: pointer;
     cursor: hand;
     background: #eee; }
 table.display tfoot th { padding: 3px 10px; border-top: 1px solid black; font-weight: bold; }

poster_data/abide/x_combine.R

@@ -40,5 +40,3 @@ qc_func         <- rename(qc_func, c(SITE_ID="site", DX_GROUP="dx", DSM_IV_TR="d
 #+ save
 write.csv(qc_anat, file="../abide_anat.csv")
 write.csv(qc_func, file="../abide_func.csv")
-
-

qap/anatomical_preproc.py

@@ -8,7 +8,7 @@ def anatomical_reorient_workflow(workflow, resource_pool, config, name="_"):
     - This is a seminal workflow that can only take an input directly from
       disk (i.e. no Nipype workflow connections/pointers, and this is where
       the pipeline will actually begin). For the sake of building the
-      pipeine in reverse, if this workflow is called when there is no input
+      pipeline in reverse, if this workflow is called when there is no input
       file available, this function will return the unmodified workflow and
       resource pool directly back.
     - In conjunction with the other workflow-building functions, if this

qap/bids_utils.py

@@ -85,7 +85,7 @@ def bids_retrieve_params(bids_config_dict, f_dict, dbg=False):
       using the bids_parse_configs function
     :param f_dict: Dictionary built from the name of a file in the BIDS
       format. This is built using the bids_decode_fname by splitting on
-      "-" and "_" delimeters
+      "-" and "_" delimiters
     :param dbg: boolean flag that indicates whether or not debug statements
       should be printed, defaults to "False"
     :return: returns a dictionary that contains the BIDS parameters

qap/cloud_utils.py

@@ -86,4 +86,3 @@ def upl_qap_output(cfg_file):
                    for ufile in upl_files]
 
     aws_utils.s3_upload(bucket, (upl_files, s3_upl_files))
-

qap/functional_preproc.py

@@ -43,7 +43,7 @@ def func_preproc_workflow(workflow, resource_pool, config, name="_"):
     - This is a seminal workflow that can only take an input directly from
       disk (i.e. no Nipype workflow connections/pointers, and this is where
       the pipeline will actually begin). For the sake of building the
-      pipeine in reverse, if this workflow is called when there is no input
+      pipeline in reverse, if this workflow is called when there is no input
       file available, this function will return the unmodified workflow and
       resource pool directly back.
     - In conjunction with the other workflow-building functions, if this

qap/script_utils.py

@@ -950,10 +950,3 @@ def parse_logs(bundle_log_dir):
 
     print avg_scans
     print avg_mins
-
-
-
-
-
-
-

qap/spatial_qc.py

@@ -25,7 +25,7 @@ def check_datatype(background):
     """Process the image data to only include non-negative integer values.
 
     :type background: NumPy array
-    :param background: The voxel values of teh background (outside of the head
+    :param background: The voxel values of the background (outside of the head
                        ) of the anatomical image.
     :rtype: NumPy array
     :return: The input array with floats converted to integers and
@@ -435,5 +435,3 @@ def ghost_all(epi_data, mask_data):
     gsrs = [ghost_direction(epi_data, mask_data, d) for d in directions]
 
     return tuple(gsrs + [None])
-
-

qap/test_bids_utils.py

@@ -51,4 +51,3 @@ def test_s3_paths(self):
     def test_s3_paths_creds(self):
         # TODO
         pass
-

qap/test_qap_sublist_generator.py

@@ -7,4 +7,3 @@ class TestMain(unittest.TestCase):
 
     def setUp(self):
         pass
-

qap/viz/html/qap_functional_temporal.html

@@ -42,7 +42,7 @@ <h3 id="fd_plot">The framewise displacement plot</h3>
 it easy to determine whether or not the data potentially suffered from significant corruption
 due to motion. For instance, it is possible to detect if the participant's head was slowly sinking into the 
 cushions in the head coil, or whether the participant was possibly restless or agitated, which 
-would result in several postion changes or movement spikes. The framewise displacement is a 
+would result in several position changes or movement spikes. The framewise displacement is a 
 frame-by-frame representation of the differences between the BOLD signal intensity value of 
 the n and n+1 timepoints, the n+1 and n+2 timepoints, and so on. The report page for framewise 
 displacement in the functional scan includes both this frame-by-frame plot, as well as a 
@@ -81,4 +81,4 @@ <h2>For the group reports:</h2>
 stars denoting individual scans. These group reports are intended to provide the user a means of 
 visually inspecting the overall quality of the temporal data for that group of functional scans.</p>
 
-</body>
+</body>

scripts/docker_run.py

@@ -58,7 +58,7 @@ def run(command, env={}):
 c = cpac_utils.Configuration(yaml.load(open(\
     os.path.realpath(args.pipeline_file), 'r')))
 
-# set the parameters using the command line arguements
+# set the parameters using the command line arguments
 
 # we will need to check that the directories exist, and
 # make them if they do not

scripts/qap_cpac_output_sublist_generator.py

@@ -46,6 +46,3 @@ def main():
 
 if __name__ == "__main__":
     main()
-
-
-

scripts/qap_single_anatomical_spatial.py

@@ -44,4 +44,3 @@
     	                                 args.series_id,
     	                                 args.site_name,
     	                                 args.output_directory)
-

scripts/qap_sublist_generator.py

@@ -60,4 +60,3 @@ def main():
 
 if __name__ == "__main__":
     main()
-