Merge pull request #28 from yarikoptic/enh-codespell

codespell: add config and action to codespell the code to avoid known typos
dandi · Sep 5, 2023 · 6d9e380 · 6d9e380
2 parents be3a8b3 + 673df9f
commit 6d9e380
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diff --git a/.codespellrc b/.codespellrc
@@ -0,0 +1,6 @@
+[codespell]
+skip = .git,*.pdf,*.svg
+# all images embedded in .ipynb jsons
+ignore-regex = "image/png": ".*
+# nd - people just like it
+ignore-words-list = nd
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/000004/RutishauserLab/000004_demo_analysis.ipynb b/000004/RutishauserLab/000004_demo_analysis.ipynb
@@ -86,7 +86,7 @@
     "## Read Data and Meta-data\n",
     "Here, we read the data and meta-data from the specified NWB file using the NWB read utility. \n",
     "\n",
-    "The NWB file is composed of various Groups, Datasets, and Attributes. The data and cooresponding meta-data are encapsulated within these Groups. The data are thus organized according to these Groups. We can also read the data and meta-data within these Groups, and visualize the components within NWB file via the *nwb2widget* utility -- the following illustrates this process:"
+    "The NWB file is composed of various Groups, Datasets, and Attributes. The data and corresponding meta-data are encapsulated within these Groups. The data are thus organized according to these Groups. We can also read the data and meta-data within these Groups, and visualize the components within NWB file via the *nwb2widget* utility -- the following illustrates this process:"
    ]
   },
   {
@@ -140,7 +140,7 @@
    "source": [
     "## Extracting and Plotting the Mean Waveform(s)\n",
     "\n",
-    "To extract the mean waveform, we simply call waveform_mean_encoding from the \\units table -- *nwb.units['waveform_mean_encoding']*. The brain area of each of the electrodes is located within the \\electrodes table -- *nwb.electrodes['location']*. To see the relationship bewteen the \\units and \\electrodes table, see **Figure 2b** in our data descriptor. "
+    "To extract the mean waveform, we simply call waveform_mean_encoding from the \\units table -- *nwb.units['waveform_mean_encoding']*. The brain area of each of the electrodes is located within the \\electrodes table -- *nwb.electrodes['location']*. To see the relationship between the \\units and \\electrodes table, see **Figure 2b** in our data descriptor. "
    ]
   },
   {

diff --git a/000055/BruntonLab/peterson21/plot_utils.py b/000055/BruntonLab/peterson21/plot_utils.py
@@ -543,7 +543,7 @@ def _plot_electrodes(
             5,
             6,
             5,
-        ]  # different sized subplot to make saggital view similar size to other two slices
+        ]  # different sized subplot to make sagittal view similar size to other two slices
         current_col = 0
         total_colspans = int(np.sum(np.asarray(colspans)))
         for ind, colspan in enumerate(colspans):

diff --git a/000055/BruntonLab/peterson21/spec_utils.py b/000055/BruntonLab/peterson21/spec_utils.py
@@ -11,7 +11,7 @@ def _calc_dens_norm_factor(elec_locs, headGrid, projectionParameter):
     """Calculate the factors (scalar values, each for a electrode) that normalize the elecrode
     projected density inside brain volume (makes its sum to be equal to one)."""
 
-    # create a parameter set but withough normalization
+    # create a parameter set but without normalization
     newProjectionParemeter = projectionParameter.copy()
     newProjectionParemeter["normalizeInBrainDipoleDenisty"] = False
 
@@ -99,7 +99,7 @@ def _getProjectionMatrix(
             -dist_elec_gridlocs[dipoleNumber, :] ** 2 / (2 * sd_est_err_pow2)
         )
 
-        # truncate the dipole denisty Gaussian at ~3 standard deviation
+        # truncate the dipole density Gaussian at ~3 standard deviation
         gaussianWeightMatrix[
             dipoleNumber,
             dist_elec_gridlocs[dipoleNumber, :]
@@ -109,7 +109,7 @@ def _getProjectionMatrix(
             ),
         ] = 0
 
-        # normalize the dipole in-brain denisty (make it sum up to one)
+        # normalize the dipole in-brain density (make it sum up to one)
         if projectionParameter["normalizeInBrainDipoleDenisty"]:
             gaussianWeightMatrix[dipoleNumber, :] = (
                 gaussianWeightMatrix[dipoleNumber, :]

diff --git a/000402/MICrONS/demo/000402_microns_demo.ipynb b/000402/MICrONS/demo/000402_microns_demo.ipynb
@@ -923,7 +923,7 @@
     "\n",
     "The movie data is stored in an `ImageSeries` object.\n",
     "\n",
-    "The frames are stored in a 4D array where the first dimension is time (frame), the second and third dimenion represents the size of the image and the last dimension are the RGB channels."
+    "The frames are stored in a 4D array where the first dimension is time (frame), the second and third dimension represents the size of the image and the last dimension are the RGB channels."
    ]
   },
   {
@@ -1207,7 +1207,7 @@
     }
    },
    "source": [
-    "The traces are stored in a 2D array where the first dimension is time, the second dimenion is the number of ROIs for this field."
+    "The traces are stored in a 2D array where the first dimension is time, the second dimension is the number of ROIs for this field."
    ]
   },
   {
@@ -2097,7 +2097,7 @@
    "source": [
     "# Access the treadmill velocity\n",
     "treadmill_velocity = nwbfile.acquisition[\"treadmill_velocity\"]\n",
-    "# Acess the timestamps for the treadmill velocity\n",
+    "# Access the timestamps for the treadmill velocity\n",
     "treadmill_timestamps = treadmill_velocity.timestamps[:]\n",
     "            \n",
     "treadmill_velocity"

diff --git a/dandi/DANDI User Guide, Part I.ipynb b/dandi/DANDI User Guide, Part I.ipynb
@@ -173,7 +173,7 @@
    "source": [
     "# Uploading to DANDI\n",
     "\n",
-    "When you register a dandiset, it creates a permenant ID. For instructional purposes, we will be using a staging version of DANDI, so that we do not create real IDs for pretend datasets.\n",
+    "When you register a dandiset, it creates a permanent ID. For instructional purposes, we will be using a staging version of DANDI, so that we do not create real IDs for pretend datasets.\n",
     "\n",
     "We are going to use a staging version of DANDI. \n",
     "\n",

diff --git a/dandi/DANDI User Guide, Part II.ipynb b/dandi/DANDI User Guide, Part II.ipynb
@@ -313,7 +313,7 @@
     "\n",
     "3. (\"optional\"- bonus point) What is different between draft and published (0.210831.2033) version of the dandiset?\n",
     "\n",
-    "   *Hint:* `diff -Naur folder1/ folder2/` could be used in the Terminal to find an anwser.\n",
+    "   *Hint:* `diff -Naur folder1/ folder2/` could be used in the Terminal to find an answer.\n",
     "\n",
     "\n",
     "4. Download the `sub-anm369962/` folder from `000006` dandiset. "
@@ -386,7 +386,7 @@
    "source": [
     "## dandi Python library\n",
     "\n",
-    "The `dandi` command line interface we have practiced with above is a part ofthe `dandi` Python package, which also provides Python interfaces to interact with any instance of the DANDI archive (*hint*: the `dandi instances` command will list known instances of the archive).\n",
+    "The `dandi` command line interface we have practiced with above is a part of the `dandi` Python package, which also provides Python interfaces to interact with any instance of the DANDI archive (*hint*: the `dandi instances` command will list known instances of the archive).\n",
     "\n",
     "In the previous section you already used the library in the following Python code snippet:\n",
     "\n",

diff --git a/tutorials/cosyne_2020/NWB_tutorial_2019.ipynb b/tutorials/cosyne_2020/NWB_tutorial_2019.ipynb
@@ -141,7 +141,7 @@
    "metadata": {},
    "source": [
     "## Electrodes table\n",
-    "Extracellular electrodes are stored in a `electrodes`, which is a `DynamicTable`. `electrodes` has several required fields: x, y, z, impedence, location, filtering, and electrode_group. Here, we also demonstate how to add optional columns to a table by adding the `'label'` column.<img src=\"images/electrodes_table.png\" width=\"300\">"
+    "Extracellular electrodes are stored in a `electrodes`, which is a `DynamicTable`. `electrodes` has several required fields: x, y, z, impedance, location, filtering, and electrode_group. Here, we also demonstate how to add optional columns to a table by adding the `'label'` column.<img src=\"images/electrodes_table.png\" width=\"300\">"
    ]
   },
   {

diff --git a/tutorials/cosyne_2020/NWB_tutorial_2019.m b/tutorials/cosyne_2020/NWB_tutorial_2019.m
@@ -68,7 +68,7 @@
 %% Electrode table
 % Extracellular |electrodes| are stored in a electrodes, which is a 
 % |DynamicTable|. |electrodes| has several required fields: x, y, z, 
-% impedence, location, filtering, and electrode_group. Here, we also 
+% impedance, location, filtering, and electrode_group. Here, we also 
 % demonstate how to add optional columns to a table by adding the |'label'|
 % column.
 

diff --git a/tutorials/cosyne_2023/advanced_asset_search.ipynb b/tutorials/cosyne_2023/advanced_asset_search.ipynb
@@ -209,7 +209,7 @@
    "outputs": [],
    "source": [
     "from warnings import simplefilter\n",
-    "simplefilter(\"ignore\")  # Supress namespace warnings from reading older NWB files\n",
+    "simplefilter(\"ignore\")  # Suppress namespace warnings from reading older NWB files\n",
     "\n",
     "from nwbinspector.tools import get_s3_urls_and_dandi_paths\n",
     "from pynwb import NWBHDF5IO"