Merge pull request #48 from OpenCOMPES/spell_check

Spell check

.cspell/custom-dictionary.txt

@@ -0,0 +1,148 @@
+# Custom Dictionary Words
+allclose
+ALLUSERSPROFILE
+amperemeter
+arange
+archiver
+argwhere
+ARPES
+astype
+autoclass
+automodule
+autoreload
+autosummary
+axhline
+AXISNAME
+axvline
+basepath
+bitshift
+bysource
+calib
+checkscan
+clim
+codemirror
+coeff
+COLLECTIONCOLUMN
+colorbar
+COMPES
+configpath
+cropit
+damatrix
+dapolymatrix
+dataconverter
+dataframe
+delaystage
+dtype
+dxda
+dxde
+dyda
+dyde
+Ekin
+electronanalyser
+elems
+endstation
+energydispersion
+eshift
+faddr
+Faradayweg
+fftshift
+filt
+fluence
+fspath
+FWHM
+genindex
+hline
+ifftshift
+IMAGEJ
+imgj
+imread
+imshow
+imutils
+imwrite
+Interp
+ipykernel
+ipympl
+ipython
+ipywidgets
+irfft
+kernelspec
+kwds
+labview
+Laurenz
+lensmodes
+lineh
+linev
+listf
+literalinclude
+loadtxt
+matplotlib
+maxdepth
+mbar
+meshgrid
+modindex
+mpes
+nanos
+nbagg
+nbconvert
+nbformat
+nbsphinx
+ndarray
+ndarrays
+ndim
+ndimage
+ndims
+ndmin
+nesteddict
+nestedentry
+numpy
+nxdl
+Nxpix
+Nxpixels
+Nypixels
+OPCPA
+pcolormesh
+Phoibos
+polyfit
+polyval
+pyenv
+pygments
+pynxtools
+pyplot
+pyproject
+quickstart
+RAWDATA
+Rettig
+rfft
+rrvec
+rtol
+rtype
+scanvector
+specsanalyzer
+Specslab
+specsscan
+stype
+tempa
+tifffile
+tmpdirname
+toctree
+tomlkit
+topfloor
+tqdm
+typehints
+TZCYXS
+undoc
+venv
+vline
+vmax
+vmin
+xarray
+xarrays
+xdata
+xgrid
+Xmpes
+xpos
+Xuser
+ydata
+ygrid
+ypos
+zinner

.github/workflows/linting.yml

@@ -30,15 +30,22 @@ jobs:
           python-version: 3.8
           poetry-version: 1.2.2
 
-      # Linting steps, excute all linters even if one fails
+      # Linting steps, execute all linters even if one fails
       - name: ruff
         run:
           poetry run ruff specsanalyzer specsscan tests
-      - name: ruff formating
+      - name: ruff formatting
         if: ${{ always() }}
         run:
           poetry run ruff format --check specsanalyzer specsscan tests
       - name: mypy
         if: ${{ always() }}
         run:
           poetry run mypy specsanalyzer specsscan tests
+      - name: spellcheck
+        if: ${{ always() }}
+        uses: streetsidesoftware/cspell-action@v6
+        with:
+          check_dot_files: false
+          incremental_files_only: false
+          config: './cspell.json'

.github/workflows/update_dependencies.yml

@@ -1,4 +1,4 @@
-name: Update depencies in poetry lockfile
+name: Update dependencies in poetry lockfile
 
 on:
   schedule:

.gitignore

@@ -138,3 +138,7 @@ dmypy.json
 *.h5
 *.tiff
 *.nxs
+*.pxp
+
+# poetry
+poetry.toml

.pre-commit-config.yaml

@@ -42,3 +42,7 @@ repos:
     rev: 0.6.0
     hooks:
     -   id: nbstripout
+-   repo: https://github.com/streetsidesoftware/cspell-cli
+    rev: v6.31.1
+    hooks:
+      - id: cspell

README.md

@@ -12,7 +12,7 @@ This is the package `specsanalyzer` for conversion and handling of SPECS Phoibos
 
 This package contains two modules:
 `specsanalyzer` is a package to import and convert MCP analyzer images from SPECS Phoibos analyzers into energy and emission angle/physical coordinates.
-`specsscan` is a Python package for loading Specs Phoibos scans accquired with the labview software developed at FHI/EPFL
+`specsscan` is a Python package for loading Specs Phoibos scans acquired with the labview software developed at FHI/EPFL
 
 Tutorials for usage and the API documentation can be found in the [Documentation](https://opencompes.github.io/specsanalyzer/)
 
@@ -47,9 +47,9 @@ python -m ipykernel install --user --name=specs_kernel
 ```
 
 #### Configuration and calib2d file
-The conversion procedures require to set up several configuration parameters in a config file. An example config file is provided as part of the package (see documentation). Configuration files can either be passed to the class constructures, or are read from system-wide or user-defined locations (see documentation).
+The conversion procedures require to set up several configuration parameters in a config file. An example config file is provided as part of the package (see documentation). Configuration files can either be passed to the class constructors, or are read from system-wide or user-defined locations (see documentation).
 
-Most importantly, conversion of analyzer data to energy/angular coordinates requires detector calibration data provided by the manufacturer. The corresponding *.calib2d file (e.g. phoibos150.calbid2d) are provided together with the spectrometer software, and need to be set in the config file.
+Most importantly, conversion of analyzer data to energy/angular coordinates requires detector calibration data provided by the manufacturer. The corresponding *.calib2d file (e.g. phoibos150.calib2d) are provided together with the spectrometer software, and need to be set in the config file.
 
 ### For Contributors
 

cspell.json

@@ -0,0 +1,23 @@
+{
+    "version": "0.2",
+    "ignorePaths": [
+        "./tests/data/*",
+        "*.toml",
+        "Makefile",
+        "*.bat",
+        "*.pxp"
+    ],
+    "dictionaryDefinitions": [
+        {
+            "name": "custom-dictionary",
+            "path": "./.cspell/custom-dictionary.txt",
+            "addWords": true
+        }
+    ],
+    "dictionaries": [
+        "custom-dictionary"
+    ],
+    "words": [],
+    "ignoreWords": [],
+    "import": []
+}

docs/conf.py

@@ -50,8 +50,6 @@ def _get_project_meta():
     "sphinx.ext.autosummary",
     "sphinx.ext.coverage",
     "sphinx_autodoc_typehints",
-    # "bokeh.sphinxext.bokeh_autodoc",
-    # "bokeh.sphinxext.bokeh_plot",
     "nbsphinx",
     "myst_parser",
 ]

docs/specsanalyzer/config.rst

@@ -1,6 +1,6 @@
 Config
 ===================================================
-The config module contains a mechanis to collect configuration parameters from various sources and configuration files, and to combine them in a hierachical manner into a single, consistent configuration dictionary.
+The config module contains a mechanics to collect configuration parameters from various sources and configuration files, and to combine them in a hierarchical manner into a single, consistent configuration dictionary.
 It will load an (optional) provided config file, or alternatively use a passed python dictionary as initial config dictionary, and subsequently look for the following additional config files to load:
 
 * ``folder_config``: A config file of name :file:`specs_config.yaml` in the current working directory. This is mostly intended to pass calibration parameters of the workflow between different notebook instances.

specsanalyzer/config.py

@@ -171,10 +171,10 @@ def load_config(config_path: str) -> dict:
 def save_config(config_dict: dict, config_path: str, overwrite: bool = False):
     """Function to save a given config dictionary to a json or yaml file. Normally, it loads any
     existing file of the given name, and keeps any existing dictionary keys not present in the
-    provided dictionary. The overwrite option creates a fully empty dictionry first.
+    provided dictionary. The overwrite option creates a fully empty dictionary first.
 
     Args:
-        config_dict (dict): The dictionry to save.
+        config_dict (dict): The dictionary to save.
         config_path (str): A string containing the path to the file where to save the dictionary
             to.
         overwrite (bool, optional): Option to overwrite an existing file with the given dictionary.

specsanalyzer/config/default.yaml

@@ -14,5 +14,5 @@ magnification: 4.54
 angle_offset_px: 0
 # offset in pixels along the energy dispersing axis
 energy_offset_px: 0
-# flag controlling the application of a Fourier filter to remove grid artefacts
+# flag controlling the application of a Fourier filter to remove grid artifacts
 apply_fft_filter: false