Add codespell

.codacy.yml

@@ -6,4 +6,3 @@ engines:
  pyflakes:
    disable:
      - F999
-

.codespell-ignores

@@ -0,0 +1,3 @@
+chec
+usera
+nd

.github/ISSUE_TEMPLATE/bug_report.md

@@ -14,7 +14,7 @@ A clear and concise description of what the bug is.
 Steps to reproduce the behavior:
 1.
 2.
-3. 
+3.
 
 **Expected behavior**
 A clear and concise description of what you expected to happen.

.github/workflows/changelog.yml

@@ -19,6 +19,6 @@ jobs:
       - name: Check for news fragment
         if: ${{ ! contains( github.event.pull_request.labels.*.name, 'no-changelog-needed')}}
         uses: andstor/file-existence-action@v3
-        with: 
+        with:
           files: ${{ env.FRAGMENT_NAME }}
           fail: true

.github/workflows/ci.yml

@@ -94,7 +94,7 @@ jobs:
           cache-downloads: true
 
       - name: Python setup
-        if: matrix.install-method == 'pip' && contains(github.event.pull_request.labels.*.name, 'documentation-only') == false 
+        if: matrix.install-method == 'pip' && contains(github.event.pull_request.labels.*.name, 'documentation-only') == false
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}

.github/workflows/release_drafter.yml

@@ -5,7 +5,7 @@ on:
     # branches to consider in the event; optional, defaults to all
     branches:
       - main
-  
+
 
 jobs:
   update_release_draft:

.mailmap

@@ -7,7 +7,7 @@ Alison Mitchell <[email protected]> Alison Mitchell <amitchell@eduro
 Alison Mitchell <[email protected]> Alison Mitchell <[email protected]>
 
 Daniel Nieto <[email protected]> nieto@talos <[email protected]>
-Daniel Parsons <[email protected]> Dan Parsons <[email protected]> 
+Daniel Parsons <[email protected]> Dan Parsons <[email protected]>
 Daniel Parsons <[email protected]> parsonsrd <[email protected]>
 
 Andrés Baquero <[email protected]> Andres-Baquerp <[email protected]>

.pre-commit-config.yaml

@@ -1,4 +1,20 @@
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0  # Use the ref you want to point at
+    hooks:
+    - id: trailing-whitespace
+    - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-merge-conflict
+    - id: end-of-file-fixer
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+    - id: codespell
+      additional_dependencies:
+        - tomli
+
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
     rev: v0.2.1

.pylintrc

@@ -545,7 +545,7 @@ exclude-protected=_asdict,
                   _replace,
                   _source,
                   _make,
-                  _v_attrs, 
+                  _v_attrs,
                   _v_attrnames
 
 # List of valid names for the first argument in a class method.

CHANGES.rst

@@ -6,15 +6,15 @@ API Changes
 -----------
 
 - The ``ctapipe-dump-triggers`` tool was removed, since it wrote a custom data format
-  not compatble with e.g. the output of the ``DataWriter`` and ``ctapipe-process``.
+  not compatible with e.g. the output of the ``DataWriter`` and ``ctapipe-process``.
   If you only want to store trigger and simulation information from simulated / DL0
   input files into the ctapipe format HDF5 files, you can now use
   ``ctapipe-process -i <input> -o <output> --no-write-parameters``. [`#2375 <https://github.com/cta-observatory/ctapipe/pull/2375>`__]
 
 - Change the fill value for invalid telescope ids in ``SubarrayDescription.tel_index_array``
   from ``-1`` to ``np.iinfo(int).minval`` to prevent ``-1`` being used as an index resulting in the last element being used for invalid telescope ids. [`#2376 <https://github.com/cta-observatory/ctapipe/pull/2376>`__]
 
-- Remove ``EventSource.from_config``, simply use ``EventSource(config=config)`` or 
+- Remove ``EventSource.from_config``, simply use ``EventSource(config=config)`` or
   ``EventSource(parent=parent)``. [`#2384 <https://github.com/cta-observatory/ctapipe/pull/2384>`__]
 
 
@@ -145,7 +145,7 @@ Bug Fixes
 New Features
 ------------
 
-- Add ``SubarrayDescription.mulitplicity`` method that can compute
+- Add ``SubarrayDescription.multiplicity`` method that can compute
   telescope multiplicity for a given telescope boolean mask, either for
   all telescope or a given telescope type.
 
@@ -219,25 +219,25 @@ ctapipe v0.18.0 (2023-02-09)
 API Changes
 -----------
 
-- ctapipe now uses entry points for plugin discovery. ``EventSource`` implementations 
+- ctapipe now uses entry points for plugin discovery. ``EventSource`` implementations
   now need to advertise a ``ctapipe_io`` entry point, to be discovered by ctapipe.
   Additionally, ctapipe now includes preliminary support for discovering ``Reconstructor``
   implementations via the ``ctapipe_reco`` entry_point. [`#2101 <https://github.com/cta-observatory/ctapipe/pull/2101>`__]
 
 - Migrate muon analysis into the ``ctapipe-process`` tool:
 
-  1. The former ``muon_reconstruction`` tool is dropped and all functionalities are transferred 
+  1. The former ``muon_reconstruction`` tool is dropped and all functionalities are transferred
      into the ``ctapipe-process`` tool.
 
   2. The ``process`` tool now has a ``write_muon_parameters`` flag which defaults to ``false``.
-     Muons are only analyzed and written if the flag is set. Analyzing muons requires DL1 image 
-     parameters, so they are computed in case they are not available from the input even 
+     Muons are only analyzed and written if the flag is set. Analyzing muons requires DL1 image
+     parameters, so they are computed in case they are not available from the input even
      if the user did not explicitly ask for the computation of image parameters.
 
-  3. Two instances of ``QualityQuery``, ``MuonProcessor.ImageParameterQuery`` and ``MuonProcessor.RingQuery`` 
-     are added to the muon analysis to either preselect images according to image parameters and 
-     to select images according to the initial, geometrical ring fit for further processing. 
-     Deselected events or those where the muon analysis fails are being returned and written 
+  3. Two instances of ``QualityQuery``, ``MuonProcessor.ImageParameterQuery`` and ``MuonProcessor.RingQuery``
+     are added to the muon analysis to either preselect images according to image parameters and
+     to select images according to the initial, geometrical ring fit for further processing.
+     Deselected events or those where the muon analysis fails are being returned and written
      filled with invalid value markers instead of being ignored.
      Base configure options for the muon analysis were added to the ``base_config.yaml``.
 
@@ -269,7 +269,7 @@ API Changes
 New Features
 ------------
 
-- Implement Components and Tools to perform training and application of 
+- Implement Components and Tools to perform training and application of
   machine learning models based on scikit-learn.
 
   Four new tools are implemented:
@@ -344,8 +344,8 @@ New Features
   fine-grained control which information should be included in the output file
   and for appending to existing output files. [`#2179 <https://github.com/cta-observatory/ctapipe/pull/2179>`__]
 
-- ``CameraDisplay.overlay_coordinate`` can now be used to 
-  plot coordinates into the camera display, e.g. to show 
+- ``CameraDisplay.overlay_coordinate`` can now be used to
+  plot coordinates into the camera display, e.g. to show
   the source position or the position of stars in the FoV. [`#2203 <https://github.com/cta-observatory/ctapipe/pull/2203>`__]
 
 
@@ -469,15 +469,15 @@ Some Major changes since last release:
 v0.5.3 (unreleased)
 ===================
 
-* Major speed improvements to calibration code, particuarly
+* Major speed improvements to calibration code, particularly
    ``NeighborPeakIntegrator`` (Jason Watson, #490), which now uses some
    compiled c-code for speed.
 
 * ``GeometryConverter`` now works for all cameras (Tino Michael, #)
 
-* Plotting improvements when overlays are used (Max Noe, #489)
+* Plotting improvements when overlays are used (MaxNoe, #489)
 
-* Fixes to coordinate ``PlanarRepresentation`` (Max Noe, #506)
+* Fixes to coordinate ``PlanarRepresentation`` (MaxNoe, #506)
 
 * HDF5 output for charge resolution calculation (Jason Watons, #488)
 
@@ -490,7 +490,7 @@ v0.5.3 (unreleased)
 v0.5.2 (2017-07-31)
 ===================
 
-* improvements to ``core.Container`` (Max Noe)
+* improvements to ``core.Container`` (MaxNoe)
 
 * ``TableWriter`` correctly handles units and metadata
 
@@ -540,7 +540,7 @@ v0.5.1 (2016-07-20)
 * Improvements to ``flow`` framework (Jean Jacquemier)
 
 * Travis CI now builds automatically for multiply python versions and
-  uploads lates documentation
+  uploads latest documentation
 
 * use Lanscape.io for code quality
 

History.md

@@ -47,7 +47,7 @@
   * Fixed error when taking log of quantity
   * Fixed import problem in hillas intersection test
   * minor cleanup of bug
-  * Inproved documentation for functions guessing the shower maximum given the reconstructed energy
+  * Improved documentation for functions guessing the shower maximum given the reconstructed energy
   * Significantly improved documentation for the ImPACT code
   * solving migrad nan issue and change shower max to return depth (not height)
   * register outputs from ctapipe-dump-instrument with provenance
@@ -69,7 +69,7 @@
   * Updated viewers to allow backgrounds to be added more easily, updated scaling factors on the Hillas parameters
   * Added low gain channel
   * Changed scaling values
-  * Removed unused funtions and added optional fit priors
+  * Removed unused functions and added optional fit priors
   * Added option to use LM minimiser
   * Fixed camera rotation problems and added functions to draw likelihood surfaces
   * Allowed selection of minimiser to be used for ImPACt
@@ -84,13 +84,13 @@
   * Added comments
   * Changed structure such that set parameters function is not need
   * Changed structure such that set parameters function is not need
-  * Added tool for perfomring hillas based reconstruction
-  * Fixed energy reconstruction and added ouput into the correct format
+  * Added tool for performing hillas based reconstruction
+  * Fixed energy reconstruction and added output into the correct format
   * Created tool for reco using Hillas parameters
   * Added MVA based energy reconstruction algorithm
   * Fixed incorrect calculation of impact distance when getting the training parameters
   * Added Tool to output Hillas parameters into FITS files
-  * Code cleanup and addtion of command line options
+  * Code cleanup and addition of command line options
   * Added cut to prevent 0 width events
   * Switched to use of FITS templates and fixed use of depth tables
   * Store system as class member

docs/_templates/autosummary/base.rst

@@ -1,2 +1,2 @@
 {% extends "autosummary_core/base.rst" %}
-{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}
+{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}

docs/_templates/autosummary/class.rst

@@ -1,2 +1,2 @@
 {% extends "autosummary_core/class.rst" %}
-{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}
+{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}

docs/_templates/autosummary/module.rst

@@ -1,2 +1,2 @@
 {% extends "autosummary_core/module.rst" %}
-{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}
+{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #}

docs/api-reference/coordinates/index.rst

@@ -22,7 +22,7 @@ Getting Started
 ===============
 
 The coordinate library defines a set of *frames*,
-which represent different coordinate reprentations.
+which represent different coordinate representations.
 Coordinates should be described using an ``astropy.coordinates.SkyCoord`` in the appropriate frame.
 
 The following special frames are defined for CTA:

docs/api-reference/coordinates/plot_camera_frames.py

@@ -4,7 +4,6 @@
 """
 import astropy.units as u
 import matplotlib.pyplot as plt
-
 from ctapipe.coordinates import EngineeringCameraFrame, TelescopeFrame
 from ctapipe.image.toymodel import Gaussian
 from ctapipe.instrument import SubarrayDescription

docs/api-reference/core/corediagram.dot

@@ -21,4 +21,4 @@ digraph Core {
   Component_1 -> Container_1
   Container_1 -> Component_2
 
-}
+}

docs/api-reference/core/index.rst

@@ -28,7 +28,7 @@ to provide a common interface and to make use of the configuration system.
 For details about creating command-line tools, see :ref:`tools`
 
 The following shows the conceptual difference between `Tools <Tool>`_ and
-`Components <Compenent>`_ with overall pipelines and stages.
+`Components <Component>`_ with overall pipelines and stages.
 Serialization and Deserialization are simply specialized Components that perform data access.
 
 .. image:: tool-component.png

docs/api-reference/image/index.rst

@@ -6,7 +6,7 @@ Imaging (`~ctapipe.image`)
 
 .. currentmodule:: ctapipe.image
 
-`ctapipe.image` contains all algortihms that operate on Cherenkov camera images.
+`ctapipe.image` contains all algorithms that operate on Cherenkov camera images.
 
 A *Cherenkov image* is defined as two pieces of data:
 

docs/api-reference/instrument/camerageometry_example.py

@@ -1,6 +1,5 @@
-from matplotlib import pyplot as plt
-
 from ctapipe.instrument import SubarrayDescription
+from matplotlib import pyplot as plt
 
 subarray = SubarrayDescription.read("dataset://gamma_prod5.simtel.zst")
 geom = subarray.tel[1].camera.geometry

docs/api-reference/instrument/config.dot

@@ -5,19 +5,19 @@ digraph config {
 
 
         ObsConfig [fillcolor=dodgerblue3, fontcolor=white, style=filled]
-        SubarrayConfig [fillcolor=dodgerblue3, fontcolor=white, style=filled] 
+        SubarrayConfig [fillcolor=dodgerblue3, fontcolor=white, style=filled]
         ArrayTriggerConfig [fillcolor=goldenrod4,
                             fontcolor=white, style=filled]
         TelescopeTriggerConfig [fillcolor=goldenrod4,
                                 fontcolor=white, style=filled]
 
         ObsConfig -> SubarrayConfig [label="obs_id"];
         ObsConfig -> ArrayTriggerConfig [label="run_type"];
-        ArrayTriggerConfig -> TelescopeTriggerConfig [label="run_type,\ntel_id"];       
-        SubarrayConfig -> ArrayConfig [label="site_id,\nversion"]      
+        ArrayTriggerConfig -> TelescopeTriggerConfig [label="run_type,\ntel_id"];
+        SubarrayConfig -> ArrayConfig [label="site_id,\nversion"]
         ArrayConfig -> TelescopeConfig [label="tel_id"];
         TelescopeConfig -> CameraConfig [label="tel_id"];
         TelescopeConfig -> OpticsConfig [label="tel_id"];
 
 
-}
+}

docs/api-reference/io/index.rst

@@ -71,7 +71,7 @@ Container Classes
 =================
 
 Event data that is intended to be read or written from files is stored
-in subclasses of `~ctapipe.core.Container`, the structre of which is
+in subclasses of `~ctapipe.core.Container`, the structure of which is
 defined in the `~ctapipe.containers` module (See reference API below). Each
 element in the container is a `~ctapipe.core.Field`, containing the
 default value, a description, and default unit if necessary. The
@@ -156,7 +156,7 @@ In addition to using an `EventSource` to read R0-DL1 data files, one can also ac
 `~ctapipe.io.TableLoader` is a a convenient way to load and join together the
 tables in a ctapipe output file into one or more high-level tables useful for analysis.
 Which information is read and joined is controlled by the TableLoader's configuration
-options. 
+options.
 
 By default, TableLoader will read the dl1 parameters for each telescope
 into one big table, joining the simulation information if available:
@@ -187,7 +187,7 @@ You can also load telescope events for specific selections of telescopes:
 
 
 Loading the DL1 image data for telescopes with different numbers of pixels
-does not work as astropy tables do not support heterogenous data in columns.
+does not work as astropy tables do not support heterogeneous data in columns.
 In this case, use:
 
 .. code-block:: python

docs/api-reference/reco/ImPACT.rst

@@ -83,7 +83,7 @@ of the brightest 3 camera pixels). The minimisation can then be performed over a
 modification factor to the estimated Xmax, greatly reducing the time taken for the fit
 procedure.
 
-Fitting is performed using the `iminuit <https://iminuit.readthedocs.io/en/stable/>`_ 
+Fitting is performed using the `iminuit <https://iminuit.readthedocs.io/en/stable/>`_
 package (a wrapper around the MINUIT minimiser), providing a fast and reliable minimisation.
 The algorithm finds a function minimum in the majority of cases, typically taking
 around 500 function calls to reach the minimum.

docs/bibliography.rst

@@ -32,7 +32,7 @@ References
 .. [lts_regression] P. J. Rousseeuw, K. van Driessen, "Computing LTS Regression for Large Data Sets",
     Data Mining and Knowledge Discovery, 12, 29-45, DOI: 10.1007/s10618-005-0024-4
 
-.. [hillas_uncertainties] W. Wittek, "Image Parameters", MAGIC-TDAS internal note 02-03, (2002). 
+.. [hillas_uncertainties] W. Wittek, "Image Parameters", MAGIC-TDAS internal note 02-03, (2002).
 
 .. [cta_sb_ob] Oya et al, Scheduling Block Data Model Specification, CTA-SPE-COM-000000-0003, Issue 1, Rev. c
 

docs/changes/2411.features.rst

@@ -1,3 +1,3 @@
 Add option ``override_obs_id`` to ``SimTelEventSource`` which allows
-assigning new, unique ``obs_ids`` in case productions re-use CORSIKA run
+assigning new, unique ``obs_ids`` in case productions reuse CORSIKA run
 numbers.

docs/changes/2414.bugfix.rst

@@ -1,2 +1,2 @@
-Add the example config for ctapipe-train-disp-reconstructor 
+Add the example config for ctapipe-train-disp-reconstructor
 to the list of configs generated by ctapipe-quickstart.

docs/changes/2421.bugfix.rst

@@ -1,5 +1,5 @@
 Remove warnings about missing R1 or DL0 data when using the CameraCalibrator.
-These were previously emitted directly as python warnings and did not use the 
+These were previously emitted directly as python warnings and did not use the
 component logging system, which they now do.
 As we do not actually expect R1 to be present it was also moved down to
 debug level.

docs/changes/2438.api.rst

@@ -9,7 +9,7 @@ resolution of the monitoring is much lower.
 For simulated events, the event time is the timestamp of the simulation
 and pointing is fixed in ``AltAz``.
 ``ctapipe`` was using the closest point in time for simulated events when
-reading data back in, however, this is problematic in case of many 
+reading data back in, however, this is problematic in case of many
 simulation runs processed in parallel.
 
 We now store the first received pointing information