Merge pull request #55 from dandi/bf-codespell

codespell: ignore any lines which have data.*base64 - embedded binaries, fix typos introduced in recent PRs

Author: yarikoptic

.codespellrc

@@ -1,6 +1,6 @@
 [codespell]
 skip = .git,*.pdf,*.svg
-# all images embedded in .ipynb jsons
-ignore-regex = "image/png": ".*
+# all images and other binaries embedded in .ipynb jsons
+ignore-regex = "image/png": ".*|^ *".*data:\S+;base64.*
 # nd - people just like it
 ignore-words-list = nd

000005/DataJoint/DJ-NWB-Yu-Gutnisky-2016/notebooks/Yu-Gutnisky-2016-examples.ipynb

@@ -1760,10 +1760,10 @@
        "                                <span class=\"djtooltiptext\">in mm, anterior positive, posterior negative</span>\n",
        "                            </div></th><th><div class=\"djtooltip\">\n",
        "                                <p id=\"primary\">coordinate_ml</p>\n",
-       "                                <span class=\"djtooltiptext\">in mm, always postive, number larger when more lateral</span>\n",
+       "                                <span class=\"djtooltiptext\">in mm, always positive, number larger when more lateral</span>\n",
        "                            </div></th><th><div class=\"djtooltip\">\n",
        "                                <p id=\"primary\">coordinate_dv</p>\n",
-       "                                <span class=\"djtooltiptext\">in mm, always postive, number larger when more ventral (deeper)</span>\n",
+       "                                <span class=\"djtooltiptext\">in mm, always positive, number larger when more ventral (deeper)</span>\n",
        "                            </div></th><th><div class=\"djtooltip\">\n",
        "                                <p id=\"nonprimary\">spike_times</p>\n",
        "                                <span class=\"djtooltiptext\">(s) time of each spike, with respect to the start of session</span>\n",

000005/DataJoint/DJ-NWB-Yu-Gutnisky-2016/pipeline/acquisition.py

@@ -1,5 +1,5 @@
 '''
-Schema of aquisition information.
+Schema of acquisition information.
 '''
 import re
 import os

000005/DataJoint/DJ-NWB-Yu-Gutnisky-2016/pipeline/reference.py

@@ -93,8 +93,8 @@ class ActionLocation(dj.Manual):
     -> BrainLocation
     -> CoordinateReference
     coordinate_ap: decimal(4,2)    # in mm, anterior positive, posterior negative 
-    coordinate_ml: decimal(4,2)    # in mm, always postive, number larger when more lateral
-    coordinate_dv: decimal(4,2)    # in mm, always postive, number larger when more ventral (deeper)
+    coordinate_ml: decimal(4,2)    # in mm, always positive, number larger when more lateral
+    coordinate_dv: decimal(4,2)    # in mm, always positive, number larger when more ventral (deeper)
     """
 
 

000005/DataJoint/DJ-NWB-Yu-Gutnisky-2016/pipeline/virus.py

@@ -29,7 +29,7 @@ class Virus(dj.Manual):
     virus: varchar(64) # name of the virus
     ---
     -> VirusSource
-    virus_lot_number="":  varchar(128)  # lot numnber of the virus
+    virus_lot_number="":  varchar(128)  # lot number of the virus
     virus_titer=null:       float     # x10^12GC/mL
     """
 

000006/DataJoint/DJ-NWB-Economo-2018/README.md

@@ -8,15 +8,15 @@ This notebook presents data and results associated with the following papers:
 >Michael N. Economo, Sarada Viswanathan, Bosiljka Tasic, Erhan Bas, Johan Winnubst, Vilas Menon, Lucas T. Graybuck, Thuc Nghi Nguyen, Kimberly A. Smith, Zizhen Yao, Lihua Wang, Charles R. Gerfen, Jayaram Chandrashekar, Hongkui Zeng, Loren L. Looger & Karel Svoboda. "Distinct descending motor cortex
 pathways and their roles in movement" (2018) Nature (https://doi.org/10.1038/s41586-018-0642-9)
 
-The study identified two types of pyramidal track (PT) neuron in the mouse motor cortex, referred to as PT<sub>upper</sub> and PT<sub>lower</sub>. Further investigation using extracellular recordings in the anterior lateral motor cortex (ALM) during a delay-response task, the study revealed specialized roles for the two neuron types: i) PT<sub>upper</sub> neurons are preferentially involed in motor planning, ii) PT<sub>lower</sub> neurons are more involved in movement execution.  
+The study identified two types of pyramidal track (PT) neuron in the mouse motor cortex, referred to as PT<sub>upper</sub> and PT<sub>lower</sub>. Further investigation using extracellular recordings in the anterior lateral motor cortex (ALM) during a delay-response task, the study revealed specialized roles for the two neuron types: i) PT<sub>upper</sub> neurons are preferentially involved in motor planning, ii) PT<sub>lower</sub> neurons are more involved in movement execution.  
 
 A ***DataJoint*** data pipeline has been constructed for this study, with the presented data ingested into this pipeline. This notebook demonstrates the queries, processing, and reproduction of several figures from the paper. From the pipeline, export capability to ***NWB 2.0*** format is also available.
 
 ## About the data
 
 The dataset comprises of extracellular recordings and spike sorted results of the mouse's ALM during a delay-response task. The behavior data includes detailed description of the trial structure (e.g. trial timing, trial instruction, trial response, etc.) and the timing of the lick events (e.g. lick left, lick right onset). 
 
-Original data is publically available at: doi: 10.25378/janelia.7007846
+Original data is publicly available at: doi: 10.25378/janelia.7007846
 
 The data in original MATLAB format (.mat) have been ingested into a DataJoint data pipeline presented below. 
 

000006/DataJoint/DJ-NWB-Economo-2018/notebooks/Economo-2018-examples.ipynb

@@ -10,7 +10,7 @@
     ">Michael N. Economo, Sarada Viswanathan, Bosiljka Tasic, Erhan Bas, Johan Winnubst, Vilas Menon, Lucas T. Graybuck,Thuc Nghi Nguyen, Kimberly A. Smith, Zizhen Yao, Lihua Wang, Charles R. Gerfen, Jayaram Chandrashekar, Hongkui Zeng, Loren L. Looger & Karel Svoboda. \"Distinct descending motor cortex\n",
     "pathways and their roles in movement\" (2018) Nature (https://doi.org/10.1038/s41586-018-0642-9)\n",
     "\n",
-    "The study identified two types of pyramidal track (PT) neuron in the mouse motor cortex, referred to as PT<sub>upper</sub> and PT<sub>lower</sub>. Further investigation using extracellular recordings in the anterior lateral motor cortex (ALM) during a delay-response task, the study revealed specialized roles for the two neuron types: i) PT<sub>upper</sub> neurons are preferentially involed in motor planning, ii) PT<sub>lower</sub> neurons are more involved in movement execution.  \n",
+    "The study identified two types of pyramidal track (PT) neuron in the mouse motor cortex, referred to as PT<sub>upper</sub> and PT<sub>lower</sub>. Further investigation using extracellular recordings in the anterior lateral motor cortex (ALM) during a delay-response task, the study revealed specialized roles for the two neuron types: i) PT<sub>upper</sub> neurons are preferentially involved in motor planning, ii) PT<sub>lower</sub> neurons are more involved in movement execution.  \n",
     "\n",
     "A ***DataJoint*** data pipeline has been constructed for this study, with the presented data ingested into this pipeline. This notebook demonstrates the queries, processing, and reproduction of several figures from the paper. From the pipeline, export capability to ***NWB 2.0*** format is also available."
    ]
@@ -23,7 +23,7 @@
     "\n",
     "The dataset comprises of extracellular recordings and spike sorted results of the mouse's ALM during a delay-response task. The behavior data includes detailed description of the trial structure (e.g. trial timing, trial instruction, trial response, etc.) and the timing of the lick events (e.g. lick left, lick right onset). \n",
     "\n",
-    "Original data is publically available at: doi: 10.25378/janelia.7007846\n",
+    "Original data is publicly available at: doi: 10.25378/janelia.7007846\n",
     "\n",
     "The data in original MATLAB format (.mat) have been ingested into a DataJoint data pipeline presented below. \n",
     "\n",

000006/DataJoint/DJ-NWB-Economo-2018/pipeline/reference.py

@@ -73,8 +73,8 @@ class ActionLocation(dj.Manual):
     -> BrainLocation
     -> CoordinateReference
     coordinate_ap: decimal(4,2)    # in mm, anterior positive, posterior negative 
-    coordinate_ml: decimal(4,2)    # in mm, always postive, number larger when more lateral
-    coordinate_dv: decimal(4,2)    # in mm, always postive, number larger when more ventral (deeper)
+    coordinate_ml: decimal(4,2)    # in mm, always positive, number larger when more lateral
+    coordinate_dv: decimal(4,2)    # in mm, always positive, number larger when more ventral (deeper)
     """
 
 

000007/DataJoint/DJ-NWB-Gao-2018/pipeline/acquisition.py

@@ -1,5 +1,5 @@
 '''
-Schema of aquisition information.
+Schema of acquisition information.
 '''
 import datajoint as dj
 from pipeline import reference, subject
@@ -49,6 +49,6 @@ class PhotoStim(dj.Manual):
     -> reference.Hemisphere
     -> reference.CoordinateReference
     photo_stim_coordinate_ap: float    # in mm, anterior positive, posterior negative
-    photo_stim_coordinate_ml: float    # in mm, always postive, number larger when more lateral
-    photo_stim_coordinate_dv: float    # in mm, always postive, number larger when more ventral (deeper)
+    photo_stim_coordinate_ml: float    # in mm, always positive, number larger when more lateral
+    photo_stim_coordinate_dv: float    # in mm, always positive, number larger when more ventral (deeper)
     """

000007/DataJoint/DJ-NWB-Gao-2018/pipeline/reference.py

@@ -95,7 +95,7 @@ class Virus(dj.Lookup):
     virus: varchar(32) # name of the virus
     ---
     -> VirusSource
-    virus_lot_number="":  varchar(128)  # lot numnber of the virus
+    virus_lot_number="":  varchar(128)  # lot number of the virus
     """
     contents = [{
         'virus': 'AAV2-hSyn-hChR2(H134R)-EYFP',