update code with lint and format

clEsperanto · Sep 5, 2023 · f8b4f0e · f8b4f0e
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -10,7 +10,7 @@ updates:
     schedule:
       interval: "weekly"
     version: "~major.minor"
-  
+
   # - package-ecosystem: "gitsubmodule" # See documentation for possible values
   #   directory: "/" # Location of package manifests
   #   schedule:

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9"]
-        platform: [ubuntu-latest, macos-latest, windows-latest] 
+        platform: [ubuntu-latest, macos-latest, windows-latest]
 
     # The setup-miniconda action needs this to activate miniconda
     defaults:
@@ -42,7 +42,7 @@ jobs:
 
       - name: Install OpenCL (pocl)
         if: matrix.platform != 'windows-latest'
-        run: conda install -y pocl 
+        run: conda install -y pocl
 
       - name: Install OpenCL (oclgrind)
         if: matrix.platform == 'windows-latest'
@@ -62,5 +62,3 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
           files: ./coverage.xml
           fail_ci_if_error: true # optional (default = false)
-
-
diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
@@ -26,19 +26,19 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-      
+
       - name: Set up Python environment
         uses: actions/setup-python@v4
         with:
           python-version: 3.8
-          
+
       - name: generat build folder
-        run: | 
+        run: |
           python -m pip install --upgrade pip
-          pip install sphinx nbsphinx sphinx_rtd_theme sphinx-autodoc-typehints sphinx_copybutton 
+          pip install sphinx nbsphinx sphinx_rtd_theme sphinx-autodoc-typehints sphinx_copybutton
           cd docs
           make clean && make html
-      
+
       - name: Setup Pages
         uses: actions/configure-pages@v3
       - name: Upload artifact

diff --git a/.gitignore b/.gitignore
@@ -9,7 +9,7 @@ __pycache__/
 # Mac OS X
 .DS_Store
 
-# IDE 
+# IDE
 .vscode
 
 # Distribution / packaging

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -6,7 +6,7 @@ project(
   ${SKBUILD_PROJECT_NAME}
   VERSION ${SKBUILD_PROJECT_VERSION}
   LANGUAGES CXX)
- 
+
 string(TOLOWER ${PROJECT_NAME} PY_PACKAGE_NAME)
 set(CY_PACKAGE_NAME _${PY_PACKAGE_NAME})
 
@@ -34,7 +34,7 @@ option(BUILD_TESTING  OFF)
 option(BUILD_BENCHMARK  OFF)
 option(BUILD_SHARED_LIBS OFF)
 FetchContent_Declare(
-  CLIc 
+  CLIc
   GIT_REPOSITORY ${CLIC_REPO_URL}
   GIT_TAG ${CLIC_REPO_TAG}
 )

diff --git a/LICENSE b/LICENSE
@@ -1,28 +1,28 @@
 Copyright 2020 Stéphane Rigaud, Robert Haase,
 Institut Pasteur Paris, Max Planck Institute for Molecular Cell Biology and Genetics Dresden
 
-Redistribution and use in source and binary forms, with or without 
+Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
 
-1. Redistributions of source code must retain the above copyright notice, 
+1. Redistributions of source code must retain the above copyright notice,
 this list of conditions and the following disclaimer.
 
-2. Redistributions in binary form must reproduce the above copyright notice, 
-this list of conditions and the following disclaimer in the documentation 
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
 and/or other materials provided with the distribution.
 
-3. Neither the name of the copyright holder nor the names of its contributors 
-may be used to endorse or promote products derived from this software without 
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software without
 specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
-ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
-LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -76,4 +76,4 @@ include wrapper/tier3_.cpp
 include wrapper/tier4_.cpp
 include wrapper/tier5_.cpp
 include wrapper/types_.cpp
-exclude MANIFEST.in
+exclude MANIFEST.in
diff --git a/README.md b/README.md
@@ -63,7 +63,7 @@ output_image = cle.pull(labeled)
 imsave("result.tif", output_image)
 ```
 
-## __Example gallery__ 
+## __Example gallery__
 
 <table border="0">
 
@@ -133,8 +133,8 @@ More usage and example can be found as notebooks in the [demos](./user_docs) fol
 
 # __Contributing and Feedback__
 
-clEsperanto is developed in the open because we believe in the [open source community]. 
-Feel free to drop feedback as [github issue] or via [image.sc forum].  
+clEsperanto is developed in the open because we believe in the [open source community].
+Feel free to drop feedback as [github issue] or via [image.sc forum].
 Contribution are also very welcome. Please read our [community guidelines] before you start and get in touch with us so that we can help you get started.
 If you liked our work, star the repository, share it with your friends, and use it to make cool stuff!
 

diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
@@ -6,7 +6,7 @@
 package:
   name: {{ name|lower }}
   version: {{ version }}
-  
+
 source:
   # fn: {{ name }}-{{ version }}.tar.gz
   # url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
@@ -28,14 +28,14 @@ requirements:
     - scikit-build-core
     - pybind11
     - cmake
-    - khronos-opencl-icd-loader      # [win or osx] 
+    - khronos-opencl-icd-loader      # [win or osx]
     - ocl-icd      # [linux]
   run:
     - python
     - numpy
     - toolz
     - matplotlib
-    - khronos-opencl-icd-loader      # [win or osx] 
+    - khronos-opencl-icd-loader      # [win or osx]
     - ocl-icd      # [linux]
 
 test:
@@ -54,9 +54,9 @@ about:
     dev_url: https://github.com/clEsperanto/pyclesperanto/
     license: BSD-3-Clause
     license_file: LICENSE
-    summary: GPU-accelerated Image Processing library using OpenCL 
+    summary: GPU-accelerated Image Processing library using OpenCL
     description: |
-        pyclesperanto is the python package of clEsperanto - a multi-language framework for GPU-accelerated image processing. 
+        pyclesperanto is the python package of clEsperanto - a multi-language framework for GPU-accelerated image processing.
         clEsperanto uses OpenCL kernels from CLIJ. This package relies on the CLIc back-end for processing.
 extra:
     recipe-maintainers:

diff --git a/demos/README.md b/demos/README.md
@@ -22,4 +22,4 @@ conda install scikit-image jupyterlab
 
 # Warning
 
-These demos are not meant to be used for benchmarking. They are meant to be easy to understand and to get you started. Several costly operations are done on purpose to make the code easier to understand. If you want to use pyclesperanto in production, please read the documentation and don't hesitate to get in touch with us to get help with optimizing your code.
+These demos are not meant to be used for benchmarking. They are meant to be easy to understand and to get you started. Several costly operations are done on purpose to make the code easier to understand. If you want to use pyclesperanto in production, please read the documentation and don't hesitate to get in touch with us to get help with optimizing your code.
diff --git a/docs/README.rst b/docs/README.rst
@@ -1,4 +1,4 @@
 pyClesperanto
 =======
 
-**pyClesperanto** is a Python library for image processing with GPU-acceleration.
+**pyClesperanto** is a Python library for image processing with GPU-acceleration.
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -39,7 +39,7 @@ Filters
 .. automodule:: pyclesperanto._tier1
    :members:
    :undoc-members:
-   :imported-members: 
+   :imported-members:
    :exclude-members: Image, Device, _Array, plugin_function
 
 .. automodule:: pyclesperanto._tier2

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -5,37 +5,38 @@
 
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../../'))
+
+sys.path.insert(0, os.path.abspath("../../"))
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'pyclesperanto'
-copyright = '2023, Stephane Rigaud'
-author = 'Stephane Rigaud'
-release = '0.6.5'
+project = "pyclesperanto"
+copyright = "2023, Stephane Rigaud"
+author = "Stephane Rigaud"
+release = "0.6.5"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 
 extensions = [
-  'sphinx.ext.autodoc',  # Parses (sub)modules
-  'sphinx.ext.napoleon',  # Parses Numpy docstrings
-  'sphinx.ext.mathjax',  # Print mathematical expressions
-  'nbsphinx',  # link notebooks
-  'sphinx.ext.autosummary',  # Make module lists in table
+    "sphinx.ext.autodoc",  # Parses (sub)modules
+    "sphinx.ext.napoleon",  # Parses Numpy docstrings
+    "sphinx.ext.mathjax",  # Print mathematical expressions
+    "nbsphinx",  # link notebooks
+    "sphinx.ext.autosummary",  # Make module lists in table
 ]
 
-templates_path = ['_templates']
-exclude_patterns = ['build', '_build', 'Thumbs.db', '.DS_Store']
+templates_path = ["_templates"]
+exclude_patterns = ["build", "_build", "Thumbs.db", ".DS_Store"]
 
 autodoc_mock_imports = ["pyclesperanto._pyclesperanto", "toolz", "matplotlib", "numpy"]
 add_module_names = False
-modindex_common_prefix = ['pyclesperanto.']
+modindex_common_prefix = ["pyclesperanto."]
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'sphinx_rtd_theme' # 'alabaster'
-html_static_path = ['_static']
+html_theme = "sphinx_rtd_theme"  # 'alabaster'
+html_static_path = ["_static"]
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -20,6 +20,3 @@ You will find here a first draft of the API for reference and documentation purp
     usage
     api
     genindex
-
-
-
diff --git a/docs/source/install.rst b/docs/source/install.rst
@@ -25,15 +25,15 @@ or via conda:
     It is advised to install pyClesperanto in a virtual environment. For example, you can create a new environment with conda:
 
     .. code-block:: bash
-            
+
         conda create --name myenv python='3.10' -c conda-forge
         conda activate myenv
 
 
 From source
 ====================
 
-Alternatively, you can also install the latest version from GitHub and build it from source on your system. 
+Alternatively, you can also install the latest version from GitHub and build it from source on your system.
 First start by cloning the repository:
 
 .. code-block:: bash
@@ -55,11 +55,11 @@ and install the package from the source:
     pip install .
 
 .. note::
-    
-    The ``-e`` flag is not supported yet. 
+
+    The ``-e`` flag is not supported yet.
 
 .. note::
 
     You can add the flag ``-vvv`` to enables verbose output of the build process.
 
-pyClesperanto should now be installed in your virtual environment along with all its dependencies.
+pyClesperanto should now be installed in your virtual environment along with all its dependencies.
diff --git a/docs/source/usage.rst b/docs/source/usage.rst
@@ -11,7 +11,7 @@ pyClesperanto is a GPU-accelerated image processing library for Python. The firs
 
 .. warning::
 
-    If an error is thrown at this stage, it is likely that the OpenCL driver is not installed or that you do not have a OpenCL compatible device. 
+    If an error is thrown at this stage, it is likely that the OpenCL driver is not installed or that you do not have a OpenCL compatible device.
     Please, check the installation of your OpenCL and driver.
 
 By default, the first device found will be automatically selected. You can know which device you currently working on, and you can select another one:
@@ -22,7 +22,7 @@ By default, the first device found will be automatically selected. You can know
 
     cle.select_device("GTX")
 
-The device selection is done by name. You can pass a substring of the device name, and the first device that matches will be selected. 
+The device selection is done by name. You can pass a substring of the device name, and the first device that matches will be selected.
 
 Memory transfer
 ================
@@ -61,7 +61,7 @@ The ``push`` will create a memory space on the GPU like ``create`` but will also
     # push arr to the GPU
     gpu_image = cle.push(arr)
 
-The data pushed will keep the same data type as the array. Hence, if you push a ``uint8`` array, the data will be stored as ``uint8`` on the GPU. 
+The data pushed will keep the same data type as the array. Hence, if you push a ``uint8`` array, the data will be stored as ``uint8`` on the GPU.
 The array will then use 24 times less memory than if it was stored as ``float32``. This is a good practice to keep in mind when working with GPUs as their
 memory is limited.
 
@@ -75,9 +75,9 @@ Finally, the ``pull`` function will transfer the data from the GPU back to the h
     # pull gpu_image to the host
     arr = cle.pull(gpu_image)
 
-The data type of the array will be the same as the data type of the image on the GPU. 
+The data type of the array will be the same as the data type of the image on the GPU.
 
-.. note:: 
+.. note::
 
     Some operation done on the GPU image may change the data type if needed. For example, the ``gaussian_blur`` will return a ``float32`` image even if the input image is ``uint8``.
 

diff --git a/pyclesperanto/_operators.py b/pyclesperanto/_operators.py
@@ -370,8 +370,6 @@ def _repr_html_(self):
 
     # In case the image is 2D, 3D and larger than 100 pixels, turn on fancy view
     if len(self.shape) in (2, 3) and size_in_pixels >= 100:
-        import matplotlib.pyplot as plt
-
         imshow(self, labels=labels, continue_drawing=True, colorbar=not labels)
         image = self._png_to_html(self._plt_to_png())
     else:
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,7 +9,7 @@ __pycache__/ @@
     # Mac OS X
     .DS_Store
-    # IDE
+    # IDE
     .vscode
     # Distribution / packaging
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
Expand Up		@@ -22,4 +22,4 @@ conda install scikit-image jupyterlab

		# Warning

		These demos are not meant to be used for benchmarking. They are meant to be easy to understand and to get you started. Several costly operations are done on purpose to make the code easier to understand. If you want to use pyclesperanto in production, please read the documentation and don't hesitate to get in touch with us to get help with optimizing your code.
		These demos are not meant to be used for benchmarking. They are meant to be easy to understand and to get you started. Several costly operations are done on purpose to make the code easier to understand. If you want to use pyclesperanto in production, please read the documentation and don't hesitate to get in touch with us to get help with optimizing your code.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -20,6 +20,3 @@ You will find here a first draft of the API for reference and documentation purp
		usage
		api
		genindex