Apply codespell

.github/ISSUE_TEMPLATE/config.yml

@@ -2,7 +2,7 @@ blank_issues_enabled: true
 contact_links:
   - name: DKIST Help Desk
     url: https://nso.atlassian.net/servicedesk/customer/portals
-    about: The offical DKIST support help desk, the best place to ask questions on data access or products etc.
+    about: The official DKIST support help desk, the best place to ask questions on data access or products etc.
   - name: DKIST Community Chat
     url: https://openastronomy.element.io/#/room/#dki-solar-telescope:openastronomy.org
     about: A community support forum to help other community members.

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
     rev: v2.2.6
     hooks:
       - id: codespell
-        # args: [ "--write-changes" ]
+        args: [ "--write-changes" ]
 ci:
   autofix_prs: false
   autoupdate_schedule: "weekly"

CHANGELOG.rst

@@ -52,7 +52,7 @@ Bug Fixes
 ---------
 
 - Bump minimum version of asdf to 2.11.2 to pick up jsonschema bugfix. (`#313 <https://github.com/DKISTDC/dkist/pull/313>`_)
-- Change the ``appdirs`` dependancy for the maintained ``platformdirs`` package. (`#318 <https://github.com/DKISTDC/dkist/pull/318>`_)
+- Change the ``appdirs`` dependency for the maintained ``platformdirs`` package. (`#318 <https://github.com/DKISTDC/dkist/pull/318>`_)
 - Fix an unpinned minimum version of ``asdf-wcs-schemas`` causing potential read errors on newest asdf files with dkist 1.1.0. (`#320 <https://github.com/DKISTDC/dkist/pull/320>`_)
 
 
@@ -222,7 +222,7 @@ Features
 --------
 
 - Add ability to page through the DKIST results and affect the page size. (`#212 <https://github.com/DKISTDC/dkist/pull/212>`_)
-- Fix, and make requried, the unit property on a dataset in ASDF files. (`#221 <https://github.com/DKISTDC/dkist/pull/221>`_)
+- Fix, and make required, the unit property on a dataset in ASDF files. (`#221 <https://github.com/DKISTDC/dkist/pull/221>`_)
 
 
 Bug Fixes
@@ -320,7 +320,7 @@ Features
 --------
 
 - Implement Astropy models to support spatial transforms which change with
-  a thrid pixel axis. (`#148 <https://github.com/DKISTDC/dkist/pull/148>`_)
+  a third pixel axis. (`#148 <https://github.com/DKISTDC/dkist/pull/148>`_)
 - Add ASDF serialization for `VaryingCelestialTransform` and `CoupledCompoundModel`. (`#156 <https://github.com/DKISTDC/dkist/pull/156>`_)
 
 
@@ -334,7 +334,7 @@ Trivial/Internal Changes
 ------------------------
 
 - Migate to the asdf 2.8+ ``Converter`` interface, this bumps various
-  dependancies but should have no effect on reading or writing asdf files. (`#152 <https://github.com/DKISTDC/dkist/pull/152>`_)
+  dependencies but should have no effect on reading or writing asdf files. (`#152 <https://github.com/DKISTDC/dkist/pull/152>`_)
 
 
 v1.0.0b3 (2021-11-30)
@@ -365,7 +365,7 @@ Features
   to the `.FileManager` which generated them, which means that the basepath can
   be dynamically generated by reference. (`#126 <https://github.com/DKISTDC/dkist/pull/126>`_)
 - Modify the `dkist.io.FileManager` class so that most of the functionality
-  exists in the new base class and the dowload method is in the separate child
+  exists in the new base class and the download method is in the separate child
   class. In addition make more of the API private to not confuse end users. (`#130 <https://github.com/DKISTDC/dkist/pull/130>`_)
 
 
@@ -409,7 +409,7 @@ Trivial/Internal Changes
 ------------------------
 
 - Support gwcs 0.14 and ndcube 2.0.0b1 (`#86 <https://github.com/DKISTDC/dkist/pull/86>`_)
-- Update Fido client for changes in sunpy 2.1; bump the sunpy dependancy to at least 2.1rc3. (`#89 <https://github.com/DKISTDC/dkist/pull/89>`_)
+- Update Fido client for changes in sunpy 2.1; bump the sunpy dependency to at least 2.1rc3. (`#89 <https://github.com/DKISTDC/dkist/pull/89>`_)
 
 
 v0.1a2 (2020-04-29)
@@ -481,7 +481,7 @@ Bug Fixes
 - Fix incorrect compound model tree splitting when the split needed to happen at the top layer (`#23 <https://github.com/DKISTDC/dkist/pull/23>`_)
 - Fix a lot of bugs in dataset generation and wcs slicing. (`#24 <https://github.com/DKISTDC/dkist/pull/24>`_)
 - Fix incorrect chunks when creating a dask array from a loader_array. (`#26 <https://github.com/DKISTDC/dkist/pull/26>`_)
-- Add support for dask 2+ and make that the minmum version (`#68 <https://github.com/DKISTDC/dkist/pull/68>`_)
+- Add support for dask 2+ and make that the minimum version (`#68 <https://github.com/DKISTDC/dkist/pull/68>`_)
 
 
 Trivial/Internal Changes

dkist/conftest.py

@@ -28,7 +28,7 @@
 @pytest.fixture
 def caplog_dkist(caplog):
     """
-    A `dkist.log` specifc equivalent to caplog.
+    A `dkist.log` specific equivalent to caplog.
     """
     log.addHandler(caplog.handler)
     return caplog
@@ -288,7 +288,7 @@ def small_visp_dataset():
     This fixture is used to test when the array in the FITS file has a length
     one NAXIS 3.
     """
-    # This asdf file wont work with sunpy less than 4
+    # This asdf file won't work with sunpy less than 4
     pytest.importorskip("sunpy", "4.0.0")
 
     # This dataset was generated by the following code:

dkist/dataset/dataset.py

@@ -191,7 +191,7 @@ def files(self):
     @property
     def inventory(self):
         """
-        Convenience attribute to acces the inventory metadata.
+        Convenience attribute to access the inventory metadata.
         """
         return self.meta['inventory']
 

dkist/dataset/utils.py

@@ -125,7 +125,7 @@ def pp_matrix(wcs):
 
 def extract_pc_matrix(headers, naxes=None):
     """
-    Given an astropy table of headers extract one or more PC matricies.
+    Given an astropy table of headers extract one or more PC matrices.
     """
     if naxes is None:
         naxes = headers[0]["NAXIS"]

dkist/io/file_manager.py

@@ -336,7 +336,7 @@ def quality_report(self, path=None, overwrite=None):
         Returns
         -------
         results: `parfive.Results`
-            A `~parfive.Results` obejct containing the filepath of the
+            A `~parfive.Results` object containing the filepath of the
             downloaded file if the download was successful, and any errors if it
             was not.
         """
@@ -364,7 +364,7 @@ def preview_movie(self, path=None, overwrite=None):
         Returns
         -------
         results: `parfive.Results`
-            A `~parfive.Results` obejct containing the filepath of the
+            A `~parfive.Results` object containing the filepath of the
             downloaded file if the download was successful, and any errors if it
             was not.
         """

dkist/logger.py

@@ -1,7 +1,7 @@
 """
 This module contains helpers to use the Python logger to show messages to users.
 
-It is heavily insipired by Astropy's logger, but implemented independantly
+It is heavily insipired by Astropy's logger, but implemented independently
 because Astropy warn you against directly using theirs.
 
 This module sets up the following things:

dkist/net/__init__.py

@@ -30,6 +30,6 @@ class Conf(_config.ConfigNamespace):
 
 conf = Conf()
 
-# Put imports after conf so that conf is initalized before import
+# Put imports after conf so that conf is initialized before import
 from .client import DKISTClient  # noqa
 from .helpers import transfer_complete_datasets  # noqa

dkist/net/attrs_values.py

@@ -108,7 +108,7 @@ def attempt_local_update(*, timeout: int = 1, user_file: Path = None, silence_er
     except Exception as err:
         log.error("Failed to download new attrs values.")
         log.debug(str(err))
-        # If an error has occured then remove the local file so it isn't
+        # If an error has occurred then remove the local file so it isn't
         # corrupted or invalid.
         user_file.unlink(missing_ok=True)
         if not silence_errors:

dkist/net/tests/conftest.py

@@ -25,7 +25,7 @@ def api_param_names():
     """
     A mapping of attrs to param names in the query string.
 
-    Excludes ones with input dependant query params
+    Excludes ones with input dependent query params
     """
     return {
         a.Time: ('endTimeMin', 'startTimeMax'),

dkist/tests/generate_aia_dataset.py

@@ -146,7 +146,7 @@ def main():
     arr = np.array((inds, seconds, waves)).T
     sorter = np.lexsort((arr[:, 1], arr[:, 2]))
 
-    # Using this double-sorted array get the list indicies
+    # Using this double-sorted array get the list indices
     list_sorter = np.array(arr[sorter][:, 0], dtype=int)
 
     # Calculate the desired shape of the output array

dkist/utils/_model_to_graphviz.py

@@ -1,5 +1,5 @@
 """
-This module vizualises compound models by rendering them as a graphviz graph.
+This module visualises compound models by rendering them as a graphviz graph.
 
 It is provided as a helper module which is useful for debugging complex compound models.
 

dkist/wcs/models.py

@@ -101,7 +101,7 @@ class BaseVaryingCelestialTransform(Model, ABC):
     Shared components between the forward and reverse varying celestial transforms.
     """
 
-    # This prevents Model from broadcasting the paramters to the inputs
+    # This prevents Model from broadcasting the parameters to the inputs
     standard_broadcasting = False
     _separable = False
     _input_units_allow_dimensionless = True

docs/topic_guides/loading.rst

@@ -6,7 +6,7 @@ Loading and Working with Level One Data
 As we saw in the :ref:`dkist:topic-guides:downloading-fits` section, once we have an ASDF file representing a DKIST dataset it can be loaded with `dkist.Dataset`.
 The `dkist.Dataset` class provides access to all the components of the dataset, and is a slightly customised `ndcube.NDCube` object, so all functionality provided by ndcube is applicable to the ``Dataset`` class.
 
-This section of the guide will cover things specifc to the `~dkist.Dataset` class, but will not cover the basics which are in the `ndcube documentation <https://docs.sunpy.org/projects/ndcube>`__.
+This section of the guide will cover things specific to the `~dkist.Dataset` class, but will not cover the basics which are in the `ndcube documentation <https://docs.sunpy.org/projects/ndcube>`__.
 In particular we recommend you read the following sections of the ``ndcube`` documentation:
 
 * :ref:`ndcube:ndcube`

docs/topic_guides/net.rst

@@ -17,7 +17,7 @@ Searching for DKIST Datasets with Fido
    Download of FITS files is not provided through the ``Fido`` interface.
    As is described below, FITS files can be downloaded for some or all of a dataset after reading the ASDF file.
 
-As is descibed in :ref:`sunpy:sunpy-tutorial-acquiring-data-index`, searches through ``Fido`` use "attrs" which specify the search criteria.
+As is described in :ref:`sunpy:sunpy-tutorial-acquiring-data-index`, searches through ``Fido`` use "attrs" which specify the search criteria.
 A single search can match one or more data providers, for example it is possible to search for DKIST data and data provided by the VSO simultaneously.
 In this guide we will focus on searches only for DKIST data through using the client provided in `dkist.net`.
 

docs/tutorial/3_the_dataset.md

@@ -112,11 +112,11 @@ We can get the corresponding **pixel** axis names with:
 ds.wcs.pixel_axis_names
 ```
 
-Note that these are in reverse order compared to the `ds` output ealier.
+Note that these are in reverse order compared to the `ds` output earlier.
 This is because they are in *pixel* order rather than *array* order.
 
 Next we see the description of the world coordinates.
-This information is also accessable through the `wcs` attribute:
+This information is also accessible through the `wcs` attribute:
 
 ```{code-cell} python
 ds.wcs.world_axis_names

docs/tutorial/3_the_dataset_NOTES.md

@@ -162,7 +162,7 @@ ds
 ```
 
 ```{error}
-Due to a known issue with the VBI level 1 FITS headers, the ordering of these tiles in the array are likley incorrect.
+Due to a known issue with the VBI level 1 FITS headers, the ordering of these tiles in the array are likely incorrect.
 ```
 
 The `TiledDataset` stores the FITS headers for all the files of the individual `Dataset`s in the `combined_headers` attribute.

docs/tutorial/4_more_dataset.md

@@ -84,7 +84,7 @@ plt.show()
 
 ## Tracking files
 
-`Dataset` tracks information about the individual files that make up the datset in the `files` attribute.
+`Dataset` tracks information about the individual files that make up the dataset in the `files` attribute.
 
 ```{code-cell} ipython
 ds.files

docs/tutorial/5_downloading_data.md

@@ -63,10 +63,10 @@ Select the preview movie, `BEOGN.mp4`, by clicking the checkbox next to it, then
 You can check the progress of your transfer by going to the "Activity" tab, which shows both active and previous transfers.
 Various useful information is displayed here but for now the most important is whether the transfer task has failed or succeeded.
 In either case Globus will also send an email to your registered email address when the task finishes.
-Of course in this trivial example this is unneccessary, but if you're transfering a whole large dataset it will likely take some time to download and it may be useful to be notified when it's complete.
+Of course in this trivial example this is unnecessary, but if you're transferring a whole large dataset it will likely take some time to download and it may be useful to be notified when it's complete.
 You do not need to leave the web app open for the transfer to continue, but remember that you do need to have GCP running - so if you stop it then your data download will stop as well.
 
-If you try transfering the same file again to the same location, you will find that the task completes successfully but the file is not actually transferred.
+If you try transferring the same file again to the same location, you will find that the task completes successfully but the file is not actually transferred.
 This is to save download time and avoid duplication.
 
 ## Dataset and downloading
@@ -86,7 +86,7 @@ files = Fido.fetch(res)
 ds = dkist.load_dataset(files[0])
 ```
 
-As we saw earlier, we can use the `files` attribute to access information about the number and names of files in the datset even before downloading any.
+As we saw earlier, we can use the `files` attribute to access information about the number and names of files in the dataset even before downloading any.
 
 ```{code-cell} ipython
 print(ds.files)
@@ -118,7 +118,7 @@ But remember that whatever path you specify must be accessible by Globus Connect
 ---
 tags: [skip-execution]
 ---
-ds[0].files.download(path="~/somewhere/globus/cant/reach/")  # will hang for a while and then fail
+ds[0].files.download(path="~/somewhere/globus/can't/reach/")  # will hang for a while and then fail
 ```
 
 The `path` keyword will replace placeholders in the path in the same way as we saw with `Fido.fetch()`.