Merge pull request #502 from sezelt/black-gh-action

Add a GitHub action that checks for `black` styling

.github/scripts/update_version.py

@@ -8,15 +8,14 @@
 with open(version_file_path, "r") as f:
     lines = f.readlines()
 
-line_split = lines[0].split('.')
-patch_number = line_split[2].split('\'')[0]
+line_split = lines[0].split(".")
+patch_number = line_split[2].split("'")[0]
 
 # Increment patch number
-patch_number = str(int(patch_number) + 1)+'\''
+patch_number = str(int(patch_number) + 1) + "'"
 
 
-new_line = line_split[0]+'.'+line_split[1]+'.'+patch_number
+new_line = line_split[0] + "." + line_split[1] + "." + patch_number
 
-with open(version_file_path,"w") as f:
+with open(version_file_path, "w") as f:
     f.write(new_line)
-

.github/workflows/black.yml

@@ -0,0 +1,14 @@
+name: Check code style
+
+on:
+  push:
+    branches: [ "dev" ]
+  pull_request:
+    branches: [ "dev" ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable

.github/workflows/build-flake.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python application
+name: Check module can be imported
 
 on:
   push:

.github/workflows/linter.yml

@@ -1,4 +1,4 @@
-name: flake8 Lint
+name: Check for errors with flake8
 
 on:
   push:

docs/source/conf.py

@@ -15,15 +15,16 @@
 
 import os
 import sys
-sys.path.insert(0,os.path.dirname(os.getcwd()))
+
+sys.path.insert(0, os.path.dirname(os.getcwd()))
 from py4DSTEM import __version__
 from datetime import datetime
 
 # -- Project information -----------------------------------------------------
 
-project = 'py4dstem'
-copyright = f'{datetime.today().year}, py4DSTEM Development Team'
-author = 'Ben Savitsky & Alex Rakowski'
+project = "py4dstem"
+copyright = f"{datetime.today().year}, py4DSTEM Development Team"
+author = "Ben Savitsky & Alex Rakowski"
 
 # The full version, including alpha/beta/rc tags
 # release = '0.14.0'
@@ -35,9 +36,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc',
-              'sphinx.ext.napoleon',
-              'sphinx.ext.intersphinx']
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon", "sphinx.ext.intersphinx"]
 
 # Other useful extensions
 # sphinx_copybutton
@@ -49,7 +48,7 @@
 
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -58,18 +57,18 @@
 
 # Set autodoc defaults
 autodoc_default_options = {
-    'members': True,
-    'member-order': 'bysource',
-    'special-members': '__init__'
+    "members": True,
+    "member-order": "bysource",
+    "special-members": "__init__",
 }
 
 # Include todo items/lists
 todo_include_todos = True
 
-#autodoc_member_order = 'bysource'
+# autodoc_member_order = 'bysource'
 
 
-# intersphinx options 
+# intersphinx options
 
 # intersphinx_mapping = {
 # 'emdfile': ('https://pypi.org/project/emdfile/0.0.4/', None)
@@ -80,21 +79,19 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['../_static']
+html_static_path = ["../_static"]
 
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = '../_static/py4DSTEM_logo.png'
+html_logo = "../_static/py4DSTEM_logo.png"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-html_favicon = '../_static/py4DSTEM_logo_vsmall.ico'
-
-
+html_favicon = "../_static/py4DSTEM_logo_vsmall.ico"

py4DSTEM/braggvectors/braggvector_methods.py

@@ -458,7 +458,6 @@ def measure_origin_beamstop(
             found_center = np.zeros((R_Nx, R_Ny), dtype=bool)
             for rx in range(R_Nx):
                 for ry in range(R_Ny):
-
                     # Get data
                     pl = braggpeaks_masked[rx, ry]
                     is_paired = np.zeros(len(pl.data), dtype=bool)

py4DSTEM/braggvectors/braggvectors.py

@@ -321,7 +321,6 @@ def _populate_instance(self, group):
     # standard output display
 
     def __repr__(self):
-
         space = " " * len(self.__class__.__name__) + "  "
         string = f"{self.__class__.__name__}( "
         string += f"A {self.shape}-shaped array of lists of bragg vectors )"

py4DSTEM/braggvectors/diskdetection.py

@@ -323,7 +323,6 @@ def _find_Bragg_disks_single(
     _return_cc=False,
     _template_space="real",
 ):
-
     # apply filter function
     er = "filter_function must be callable"
     if filter_function:
@@ -334,7 +333,6 @@ def _find_Bragg_disks_single(
     if template is None:
         cc = DP
     else:
-
         # fourier transform the template
         assert _template_space in ("real", "fourier")
         if _template_space == "real":
@@ -417,11 +415,9 @@ def _find_Bragg_disks_stack(
     maxNumPeaks=100,
     _template_space="real",
 ):
-
     ans = []
 
     for idx in range(dp_stack.shape[0]):
-
         dp = dp_stack[idx, :, :]
         peaks = _find_Bragg_disks_single(
             dp,
@@ -466,7 +462,6 @@ def _find_Bragg_disks_CPU(
     maxNumPeaks=70,
     radial_bksb=False,
 ):
-
     # Make the BraggVectors instance
     braggvectors = BraggVectors(datacube.Rshape, datacube.Qshape)
 
@@ -475,14 +470,13 @@ def _find_Bragg_disks_CPU(
 
     # Loop over all diffraction patterns
     # Compute and populate BraggVectors data
-    for (rx, ry) in tqdmnd(
+    for rx, ry in tqdmnd(
         datacube.R_Nx,
         datacube.R_Ny,
         desc="Finding Bragg Disks",
         unit="DP",
         unit_scale=True,
     ):
-
         # Get a diffraction pattern
 
         # without background subtraction
@@ -538,7 +532,6 @@ def _find_Bragg_disks_CUDA_unbatched(
     edgeBoundary=20,
     maxNumPeaks=70,
 ):
-
     # compute
     from py4DSTEM.braggvectors.diskdetection_cuda import find_Bragg_disks_CUDA
 
@@ -584,7 +577,6 @@ def _find_Bragg_disks_CUDA_batched(
     edgeBoundary=20,
     maxNumPeaks=70,
 ):
-
     # compute
     from py4DSTEM.braggvectors.diskdetection_cuda import find_Bragg_disks_CUDA
 
@@ -633,7 +625,6 @@ def _find_Bragg_disks_ipp(
     edgeBoundary=20,
     maxNumPeaks=70,
 ):
-
     # compute
     from py4DSTEM.braggvectors.diskdetection_parallel import find_Bragg_disks_ipp
 
@@ -684,7 +675,6 @@ def _find_Bragg_disks_dask(
     edgeBoundary=20,
     maxNumPeaks=70,
 ):
-
     # compute
     from py4DSTEM.braggvectors.diskdetection_parallel import find_Bragg_disks_dask
 

py4DSTEM/braggvectors/diskdetection_aiml.py

@@ -494,7 +494,7 @@ def find_Bragg_disks_aiml_serial(
         )
 
     # Loop over all diffraction patterns
-    for (Rx, Ry) in tqdmnd(
+    for Rx, Ry in tqdmnd(
         datacube.R_Nx,
         datacube.R_Ny,
         desc="Finding Bragg Disks using AI/ML",

py4DSTEM/braggvectors/diskdetection_aiml_cuda.py

@@ -198,7 +198,7 @@ def find_Bragg_disks_aiml_CUDA(
         )
 
     # Loop over all diffraction patterns
-    for (Rx, Ry) in tqdmnd(
+    for Rx, Ry in tqdmnd(
         datacube.R_Nx,
         datacube.R_Ny,
         desc="Finding Bragg Disks using AI/ML CUDA",

py4DSTEM/braggvectors/diskdetection_cuda.py

@@ -204,7 +204,7 @@ def find_Bragg_disks_CUDA(
 
     else:
         # Loop over all diffraction patterns
-        for (Rx, Ry) in tqdmnd(
+        for Rx, Ry in tqdmnd(
             datacube.R_Nx,
             datacube.R_Ny,
             desc="Finding Bragg Disks",

py4DSTEM/braggvectors/diskdetection_parallel_new.py

@@ -64,6 +64,7 @@ def register_dill_serializer():
 
 #### DASK WRAPPER FUNCTION ####
 
+
 # Each delayed objected is passed a 4D array, currently implementing only on 2D slices.
 # TODO add batching with fancy indexing  - needs to run a for loop over the batch of arrays
 # TODO add cuda accelerated version
@@ -138,7 +139,6 @@ def beta_parallel_disk_detection(
 
     if dask_client == None:
         if dask_client_params != None:
-
             dask.config.set(
                 {
                     "distributed.worker.memory.spill": False,
@@ -247,7 +247,7 @@ def beta_parallel_disk_detection(
     # temp_peaks[0][0]
 
     # operating over a list so we need the size (0->count) and re-create the probe positions (0->rx,0->ry),
-    for (count, (rx, ry)) in zip(
+    for count, (rx, ry) in zip(
         [i for i in range(dataset.data[..., 0, 0].size)],
         np.ndindex(dataset.data.shape[:-2]),
     ):

py4DSTEM/braggvectors/threshold.py

@@ -28,7 +28,7 @@ def threshold_Braggpeaks(
     assert all(
         [item in pointlistarray.dtype.fields for item in ["qx", "qy", "intensity"]]
     ), "pointlistarray must include the coordinates 'qx', 'qy', and 'intensity'."
-    for (Rx, Ry) in tqdmnd(
+    for Rx, Ry in tqdmnd(
         pointlistarray.shape[0],
         pointlistarray.shape[1],
         desc="Thresholding Bragg disks",
@@ -120,7 +120,7 @@ def universal_threshold(
         _pointlistarray.name = pointlistarray.name + "_unithresh"
 
     HI_array = np.zeros((_pointlistarray.shape[0], _pointlistarray.shape[1]))
-    for (Rx, Ry) in tqdmnd(
+    for Rx, Ry in tqdmnd(
         _pointlistarray.shape[0],
         _pointlistarray.shape[1],
         desc="Thresholding Bragg disks",
@@ -142,7 +142,7 @@ def universal_threshold(
     else:
         _thresh = thresh
 
-    for (Rx, Ry) in tqdmnd(
+    for Rx, Ry in tqdmnd(
         _pointlistarray.shape[0],
         _pointlistarray.shape[1],
         desc="Thresholding Bragg disks",
@@ -205,7 +205,7 @@ def get_pointlistarray_intensities(pointlistarray):
     ), "pointlistarray coords must include 'intensity'"
 
     first_pass = True
-    for (Rx, Ry) in tqdmnd(
+    for Rx, Ry in tqdmnd(
         pointlistarray.shape[0],
         pointlistarray.shape[1],
         desc="Getting disk intensities",

py4DSTEM/datacube/datacube.py

@@ -896,7 +896,6 @@ def find_Bragg_disks(
         )
 
         if isinstance(peaks, Node):
-
             # add metadata
             peaks.name = name
             peaks.metadata = Metadata(

py4DSTEM/datacube/virtualdiffraction.py

@@ -116,7 +116,6 @@ def get_virtual_diffraction(
 
         # ...with no center shifting
         if shift_center == False:
-
             # ...for the whole pattern
             if mask is None:
                 if method == "mean":
@@ -187,7 +186,6 @@ def get_virtual_diffraction(
 
             # ...for integer shifts
             if not subpixel:
-
                 # round shifts -> int
                 qx_shift = qx_shift.round().astype(int)
                 qy_shift = qy_shift.round().astype(int)

py4DSTEM/datacube/virtualimage.py

@@ -201,10 +201,8 @@ def get_virtual_image(
 
         # no center shifting
         if shift_center == False:
-
             # single CPU
             if not dask:
-
                 # allocate space
                 if mask.dtype == "complex":
                     virtual_image = np.zeros(self.Rshape, dtype="complex")
@@ -220,7 +218,6 @@ def get_virtual_image(
 
             # dask
             if dask == True:
-
                 # set up a generalized universal function for dask distribution
                 def _apply_mask_dask(self, mask):
                     virtual_image = np.sum(
@@ -240,7 +237,6 @@ def _apply_mask_dask(self, mask):
 
         # with center shifting
         else:
-
             # get shifts
             assert (
                 self.calibration.get_origin_shift() is not None