Merge pull request #120 from computational-psychology/build

Update build-system
computational-psychology · Jan 31, 2024 · d56e528 · d56e528
2 parents 7883ef4 + de8efb4
commit d56e528
Show file tree

Hide file tree

Showing 37 changed files with 225 additions and 214 deletions.
diff --git a/.codespell.ignore b/.codespell.ignore
@@ -0,0 +1,2 @@
+  **F**indable, **A**ccessible, **I**nteroperable, and **R**eusable
+        Pflügers Archiv für die gesamte Physiologie. 3: 13-15.
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -2,6 +2,7 @@ name: Release to PyPI
 
 on:
   release:
+    types: [released]
   workflow_dispatch:
 
 jobs:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -16,4 +16,9 @@ repos:
     hooks:
       - id: flake8
         # Ignore all format-related checks as Black takes care of those.
-        args: ["--ignore", "E203,E501,W503,F403", "--select", "E,W,F", '--per-file-ignores=__init__.py:F401,F405,E402', '--exclude','tests/*']
+        args: ["--ignore", "E203,E501,W503,F403", "--select", "E,W,F", '--per-file-ignores=__init__.py:F401,F405,E402', '--exclude','tests/*']
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+    - id: codespell
diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/README.md b/README.md
@@ -53,7 +53,7 @@ so that they are reproducible, flexible, and easy.
    (e.g. Simultaneous Brightness Contrast, White's illusion, Hermann grid, Ponzo illusion), and many more
 
 - exact replications of stimuli previously published (e.g. ModelFest)
-  as described in their respecive [papers](stimupy/papers/)
+  as described in their respective [papers](stimupy/papers/)
 
 - all stimuli are fully parameterizable
   - with interpretable parameters that are familiar and relevant to vision scientists

diff --git a/docs/contributing/dev_environ.md b/docs/contributing/dev_environ.md
@@ -7,7 +7,7 @@
     - `".[dev,docs]"` to also edit and build the documentation
 
 The `stimupy` project uses a couple of development tools
-to work towards more consisten code quality:
+to work towards more consistent code quality:
 
 - `pytest` for unit and integration tests
 - `pyupgrade` for possible syntax improvements using newer language features

diff --git a/docs/contributing/sets.md b/docs/contributing/sets.md
@@ -3,7 +3,7 @@
 that can generate many parameterizated stimulus images,
 and several complete sets of stimuli
 that all come from the same {py:mod}`source <stimupy.papers>`.
-Development, organization and maintanance of these sets can be arduous,
+Development, organization and maintenance of these sets can be arduous,
 and we are committed to providing a high-quality and well-tested suite of functions.
 Thus, `stimupy` is a curated and maintained _library_ of stimuli
 (stimulus-functions, to be precise),

diff --git a/docs/getting_started/composition.md b/docs/getting_started/composition.md
@@ -238,7 +238,7 @@ This has created the bullseye stimulus that we want,
 and included with this is a `mask` that can separately indicate
 each of the three regions (and background).
 We can easily visualize this mask as well,
-overlayed as colorcoding on top of the stimulus:
+overlaid as colorcoding on top of the stimulus:
 
 ```
 plt.subplot(1,2,1)

diff --git a/docs/getting_started/first_stim.md b/docs/getting_started/first_stim.md
@@ -173,7 +173,7 @@ Thus, this output is self-documenting:
 all the necessary information to produce this stimulus are in the stimulus-`dict`.
 
 A nice feature of these {py:class}`dict`s is that you, the user,
-can add any arbitray (meta)data to them, after creating the stimulus.
+can add any arbitrary (meta)data to them, after creating the stimulus.
 For instance, we can add some label,
 or a creation date:
 ```{code-cell}

diff --git a/docs/howtos/export.md b/docs/howtos/export.md
@@ -59,7 +59,7 @@ or [OpenCV](https://github.com/opencv/opencv-python)
 ## Exporting only parameters
 In some cases, you may wish to save/export only the stimulus parameters
 -- for a given version of `stimupy`,
-these parameters should reproduce the exact same stimulus everytime.
+these parameters should reproduce the exact same stimulus every time.
 For stimuli created using just `stimupy` functions,
 the output stimulus-`dict` contains not just the `img`-array
 but also all parameters for creating that stimulus.

diff --git a/docs/howtos/share.md b/docs/howtos/share.md
@@ -131,7 +131,7 @@ that all come from the same {py:mod}`paper <stimupy.papers>` (/ source).
 The ones currently included span wide range of the stimuli implemented in `stimupy`
 and have formed both the inspiration and a testing benchmark for development.
 
-Development, organization and maintanance of these sets can be arduous,
+Development, organization and maintenance of these sets can be arduous,
 and we are committed to providing a high-quality and well-tested suite of functions.
 Thus, `stimupy` is a curated and maintained _library_ of stimuli
 (stimulus-functions, to be precise),

diff --git a/docs/reference/demos/stimuli/sbcs.md b/docs/reference/demos/stimuli/sbcs.md
@@ -555,7 +555,7 @@ w_tint_l = iw.FloatSlider(value=0.5, min=0, max=1, description="intensity target
 w_tint_r = iw.FloatSlider(value=0.5, min=0, max=1, description="intensity target right")
 w_int_surround_l = iw.FloatSlider(value=0., min=0, max=1, description="intensity left surround")
 w_int_surround_r = iw.FloatSlider(value=1., min=0, max=1, description="intensity right surround")
-w_int_background = iw.FloatSlider(value=.5, min=0, max=1, description="intenisty background")
+w_int_background = iw.FloatSlider(value=.5, min=0, max=1, description="intensity background")
 
 w_rot_l = iw.FloatSlider(value=0, min=0, max=360, description="rotation left [deg]")
 w_rot_r = iw.FloatSlider(value=0, min=0, max=360, description="rotation right [deg]")
@@ -651,7 +651,7 @@ w_tint_l = iw.FloatSlider(value=0.5, min=0, max=1, description="intensity target
 w_tint_r = iw.FloatSlider(value=0.5, min=0, max=1, description="intensity target right")
 w_int_surround_l = iw.FloatSlider(value=0., min=0, max=1, description="intensity left surround")
 w_int_surround_r = iw.FloatSlider(value=1., min=0, max=1, description="intensity right surround")
-w_int_background = iw.FloatSlider(value=.5, min=0, max=1, description="intenisty background")
+w_int_background = iw.FloatSlider(value=.5, min=0, max=1, description="intensity background")
 
 
 w_mask = iw.ToggleButton(value=False, disabled=False, description="add mask")

diff --git a/docs/topic_guides/organization.md b/docs/topic_guides/organization.md
@@ -20,7 +20,7 @@ Broadly, `stimupy` functions currently fall into the following categories, which
   - a variety of so-called illusions 
    (e.g. Simultaneous Brightness Contrast, White's illusion, Hermann grid, Ponzo illusion), and many more
 - exact replications of stimuli previously published (e.g. ModelFest)
-  as described in their respecive [papers](../reference/_api/stimupy.papers)
+  as described in their respective [papers](../reference/_api/stimupy.papers)
 - [utility functions](https://stimupy.readthedocs.io/en/latest/reference/_api/stimupy.utils.html)
   for stimulus import, export, manipulation (e.g. contrast, size), or plotting
 
@@ -76,7 +76,7 @@ OR as having a [cross-shaped target](todorovics.cross) with adjoining squares.
 For a single stimulus parameterization,
 these two conceptions may produce perfectly identical images ([see fig, top](fig_todorovics)).
 However, when changing parameters,
-you would expect different *behavior* from the stimulus fuction
+you would expect different *behavior* from the stimulus function
 dependent on your conception/interpretation of the stimulus ([see fig, bottom](fig_todorovics)).
 
 ```{code-cell}

diff --git a/docs/topic_guides/waves.md b/docs/topic_guides/waves.md
@@ -14,7 +14,7 @@ kernelspec:
 ```{tip}
 This guide explains the principles behind, behavior of, and relations between
 the parameters of periodic stimuli in `stimupy`.
-For a more hands-on demonstration of how those paramaters affect a specific stimulus,
+For a more hands-on demonstration of how those parameters affect a specific stimulus,
 see, e.g., [](../reference/demos/stimuli/waves.md)
 ```
 
@@ -48,7 +48,7 @@ namely that there are repeated _cycles_ (here of 2 phases/elements per cycle),
 where each cycle is identical to each other cycle.
 This regularity can be expressed in several different ways,
 with several different parameters 
--- and these parameters have some interdependence on eachother.
+-- and these parameters have some interdependence on each other.
 
 ```{tip}
 In the examples in this section,

diff --git a/pyproject.toml b/pyproject.toml
@@ -84,3 +84,8 @@ type = "github"
 
 [tool.semantic_release.publish]
 upload_to_vcs_release = true # upload sdist, wheel to release-tag
+
+
+[tool.codespell]
+skip = "./docs/_build/*"
+exclude-file = ".codespell.ignore"
diff --git a/stimupy/components/frames.py b/stimupy/components/frames.py
@@ -32,7 +32,7 @@ def mask_frames(
         if "mean": set origin to hypothetical image center (default)
         if "center": set origin to real center (closest existing value to mean)
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
 
     Returns
     -------
@@ -77,7 +77,7 @@ def frames(
     radii : Sequence[Number]
         radii of each frame, in degrees visual angle
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     intensity_frames : Sequence[float, ...], optional
         intensity value for each frame, by default (1.0, 0.0).
         Can specify as many intensities as number of frame_widths;

diff --git a/stimupy/components/lines.py b/stimupy/components/lines.py
@@ -158,7 +158,7 @@ def dipole(
     line_gap : Number
         distance between line centers, in degrees visual angle
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     intensity_lines : (Number, Number)
         intensity value of the line (default: (0, 1));
         background intensity is the mean of these two values

diff --git a/stimupy/components/radials.py b/stimupy/components/radials.py
@@ -117,7 +117,7 @@ def rings(
         visual_size = resolution.validate_visual_size(visual_size)
 
     if visual_size is None or visual_size == (None, None):
-        # Two axes are None; make image large enought to fit
+        # Two axes are None; make image large enough to fit
         visual_size = resolution.validate_visual_size(np.max(radii) * 2)
     elif None in visual_size:
         # one axis is None; make square

diff --git a/stimupy/components/shapes.py b/stimupy/components/shapes.py
@@ -49,7 +49,7 @@ def rectangle(
     intensity_background : float, optional
         intensity value of background, by default 0.0
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
 
     Returns
     -------

diff --git a/stimupy/components/waves.py b/stimupy/components/waves.py
@@ -46,7 +46,7 @@ def resolve_grating_params(
     Parameters
     ----------
     length : Number, or None (default)
-        lenght of grating, in pixels
+        length of grating, in pixels
     visual_angle :Number, or None (default)
         visual angle of grating, in degrees
     ppd : Number, or None (default)
@@ -214,7 +214,7 @@ def round_n_phases(n_phases, length, period="either"):
     n_phases : int
         number of phases (e.g., bars), i.e., half the number of full periods
     length : Number
-        lenght of grating, in pixels
+        length of grating, in pixels
     period : "even", "odd", "either" (default)
         whether to ensure the grating has "even" number of phases,
         "odd" number of phases, or "either" even/odd
@@ -281,7 +281,7 @@ def sine(
         number of phases, either or whether not to round the number of
         phases ("ignore")
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     phase_shift : float
         phase shift of grating in degrees, by default 0.0
     intensities : Sequence[float, float]
@@ -512,7 +512,7 @@ def square(
         number of phases, either or whether not to round the number of
         phases ("ignore")
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     phase_shift : float
         phase shift of grating in degrees, by default 0.0
     intensities : Sequence[float, float]
@@ -596,7 +596,7 @@ def staircase(
         number of phases, either or whether not to round the number of
         phases ("ignore")
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     phase_shift : float
         phase shift of grating in degrees, by default 0.o
     origin : "corner", "mean", or "center" (default)

diff --git a/stimupy/papers/domijan2015.py b/stimupy/papers/domijan2015.py
@@ -1224,7 +1224,7 @@ def white_howe(visual_size=VSIZES["white_howe"], ppd=PPD, shape=SHAPES["white_ho
         https://doi.org/10.3389/fnhum.2015.00093
     Howe, P. D. L. (2001).
         A comment on the Anderson (1997), the Todorovic (1997),
-        and the Ross nd Pessoa (2000) explanations of White's eﬀect.
+        and the Ross and Pessoa (2000) explanations of White's eﬀect.
         Perception, 30, 1023-1026
     """
 

diff --git a/stimupy/papers/modelfest.py b/stimupy/papers/modelfest.py
@@ -1654,7 +1654,7 @@ def Line31(ppd=PPD):
 def Dipole32(ppd=PPD):
     """Dipole32: lines x Gaussian, Carney et al (1999)
     Line width: 3 px =
-    Seperation: 1 px =
+    Separation: 1 px =
     Gaussian window: sy=sx=0.5 deg
 
     Parameters
@@ -1708,7 +1708,7 @@ def GaborString33(ppd=PPD):
     """GaborString33 - 5 collinear in-phase Gabors, Carney et al (1999)
     Frequency: 8 cpd
     Gaussian window of individual Gabors: sx=sy=0.07 deg (~1octave)
-    Seperation: 5sx
+    Separation: 5sx
 
     Parameters
     ----------
@@ -1770,7 +1770,7 @@ def GaborString34(ppd=PPD):
     """GaborString33 - 5 collinear out-of-phase Gabors, Carney et al (1999)
     Frequency: 8 cpd
     Gaussian window of individual Gabors: sx=sy= deg (~1octave)
-    Seperation: 5sx
+    Separation: 5sx
 
     Parameters
     ----------

diff --git a/stimupy/stimuli/bullseyes.py b/stimupy/stimuli/bullseyes.py
@@ -137,7 +137,7 @@ def circular_generalized(
     radii : Sequence[Number] or None (default)
         radii of each ring, in degrees visual angle
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     intensity_rings : Sequence[float, float]
         intensities of rings, by default (1.0, 0.0)
     intensity_background : float (optional)
@@ -212,7 +212,7 @@ def rectangular(
     frame_width : Number, or None (default)
         width of a single frame, in degrees visual angle
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     phase_shift : float
         phase shift of grating in degrees
     intensity_frames : Sequence[float, float]
@@ -290,7 +290,7 @@ def rectangular_generalized(
     radii : Sequence[Number] or None (default)
         radii of each frame, in degrees visual angle
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     intensity_frames : Sequence[float, float]
         min and max intensity of square-wave, by default (0.0, 1.0)
     intensity_background : float (optional)

diff --git a/stimupy/stimuli/checkerboards.py b/stimupy/stimuli/checkerboards.py
@@ -25,7 +25,7 @@ def mask_from_idx(checkerboard_stim, check_idc):
     Returns
     -------
     numpy.ndarray
-        mask, as binary 2D numpy.ndarray with 1 for all pixels beloning to
+        mask, as binary 2D numpy.ndarray with 1 for all pixels belonging to
         specified check(s), and 0 everywhere else
 
     Raises
@@ -158,7 +158,7 @@ def checkerboard(
         number of phases, either or whether not to round the number of
         phases ("ignore")
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     intensity_checks : Sequence[float, float]
         intensity values of checks, by default (0.0, 1.0)
     round_phase_width : Bool
@@ -352,7 +352,7 @@ def contrast_contrast(
     tau : Number
         tau of transparency (i.e. value of transparent medium), default 0.5
     alpha : Number or None (default)
-        alpha of transparency (i.e. how transparant the medium is)
+        alpha of transparency (i.e. how transparent the medium is)
     round_phase_width : Bool
         if True, round width of bars given resolution (default: True)
 

diff --git a/stimupy/stimuli/cornsweets.py b/stimupy/stimuli/cornsweets.py
@@ -39,7 +39,7 @@ def cornsweet(
     ramp_width : float
         width of luminance ramp in degrees of visual angle
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     intensity_edges : (float, float)
         intensity of edges
     intensity_plateau : float

diff --git a/stimupy/stimuli/gabors.py b/stimupy/stimuli/gabors.py
@@ -42,7 +42,7 @@ def gabor(
         number of phases, either or whether not to round the number of
         phases ("ignore")
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     phase_shift : float
         phase shift of grating in degrees
     intensities : Sequence[float, ...]

diff --git a/stimupy/stimuli/gratings.py b/stimupy/stimuli/gratings.py
@@ -62,7 +62,7 @@ def on_uniform(
         number of phases, either or whether not to round the number of
         phases ("ignore")
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     phase_shift : float
         phase shift of grating in degrees
     intensity_bars : Sequence[float, ...]
@@ -398,7 +398,7 @@ def grating_induction(
         number of phases, either or whether not to round the number of
         phases ("ignore")
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     phase_shift : float
         phase shift of grating in degrees
     intensity_bars : Sequence[float, ...]
@@ -500,7 +500,7 @@ def grating_induction_blur(
         number of phases, either or whether not to round the number of
         phases ("ignore")
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
     phase_shift : float
         phase shift of grating in degrees
     intensity_bars : Sequence[float, ...]

diff --git a/stimupy/stimuli/rings.py b/stimupy/stimuli/rings.py
@@ -127,7 +127,7 @@ def rectangular_generalized(
         if "mean": set origin to hypothetical image center (default)
         if "center": set origin to real center (closest existing value to mean)
     rotation : float, optional
-        rotation (in degrees), counterclockwise, by default 0.0 (horizonal)
+        rotation (in degrees), counterclockwise, by default 0.0 (horizontal)
 
 
     Returns