Merge pull request #183 from clEsperanto/add-pre-commit-check

add pre-commit for auto format, linting

.flake8

@@ -1,9 +1,11 @@
 [flake8]
-# Ignore error codes that may conflict with Black
-ignore = E203, E231, E501, W503, F401, F403
-
-# Enable line length of 88, matching Black's default
+ignore = E203, E266, E501, W503, F401
 max-line-length = 88
-
-# Exclude some directories and files from linting (customize as needed)
 exclude = .git, .venv, __pycache__, .eggs, *.egg, build, dist
+
+# Ignore F401 and F403 only for __init__.py files
+per-file-ignores =
+    */__init__.py: F403
+
+# Warn if the complexity of a function exceeds 10
+max-complexity = 18

.github/ISSUE_TEMPLATE/prototype-related-issue.md

@@ -16,7 +16,7 @@ assignees: ''
 
 **Describe the bug**
 A clear and concise description of what the bug is. What were you trying to do and what happened.
-It can be from a parameter or function name discreptency. to a change of results, or a full crash. 
+It can be from a parameter or function name discreptency. to a change of results, or a full crash.
 
 **To Reproduce**
 Steps to reproduce the behavior, ideally a notebook ready to run, with test data, at minima a code snippet.

.pre-commit-config.yaml

@@ -4,21 +4,30 @@ repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v3.2.0
     hooks:
+    -   id: check-toml
+    -   id: check-yaml
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-added-large-files
-    -   id: check-toml
     -   id: check-case-conflict
+    -   id: check-merge-conflict
+    -   id: check-symlinks
     -   id: mixed-line-ending
 
-    # black - code formatting
+# black - code formatting
 -   repo: https://github.com/psf/black
     rev: 22.8.0
     hooks:
     -   id: black
 
-    # flake8 - linting
+# # isort - import sorting
+# -   repo: https://github.com/pycqa/isort
+#     rev: 5.12.0
+#     hooks:
+#     -   id: isort
+
+# flake8 - linting
 -   repo: https://github.com/pycqa/flake8
     rev: 5.0.4
     hooks:
-      - id: flake8
+    -   id: flake8

docs/source/_static/debug.js

@@ -4,4 +4,4 @@ $(function () {
     $("[data-toggle='rst-debug-badge']").on("click", function () {
         $("[data-toggle='rst-versions']").toggleClass("rst-badge");
     });
-})
+})

docs/source/_templates/layout.html

@@ -52,4 +52,4 @@
     </div>
 </div>
 {%- endif %}
-{%- endblock %}
+{%- endblock %}

docs/source/api.rst

@@ -70,7 +70,7 @@ tier3
     :undoc-members:
 
 tier4
-------  
+------
 
 .. automodule:: pyclesperanto._tier4
     :members:

docs/source/conf.py

@@ -4,29 +4,30 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 import os
-import sys
 import re
+import sys
 
 from sphinx.locale import _
+
 sys.path.insert(0, os.path.abspath("../../"))
 
 # Open the CMakeCache.txt file and search for the project version
-with open('../../pyclesperanto/_version.py', 'r') as f:
+with open("../../pyclesperanto/_version.py", "r") as f:
     for line in f:
-        if 'VERSION_CODE' in line:
-            start = line.find('=') + 1
-            end = line.find('\n', start)
-            release = ".".join(line[start:end].strip().split(', '))
+        if "VERSION_CODE" in line:
+            start = line.find("=") + 1
+            end = line.find("\n", start)
+            release = ".".join(line[start:end].strip().split(", "))
             break
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = u"py-clEsperanto"
-slug = re.sub(r'\W+', '-', project.lower())
-author = u'Stephane Rigaud'
-copyright = f'2024, {author}'
-language = 'en'
+project = "py-clEsperanto"
+slug = re.sub(r"\W+", "-", project.lower())
+author = "Stephane Rigaud"
+copyright = f"2024, {author}"
+language = "en"
 version = release
 
 # -- General configuration ---------------------------------------------------
@@ -39,9 +40,9 @@
     "sphinx.ext.mathjax",  # Print mathematical expressions
     "nbsphinx",  # link notebooks
     "sphinx.ext.autosummary",  # Make module lists in table
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.viewcode',
-    'sphinx_rtd_theme',
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx_rtd_theme",
 ]
 
 templates_path = ["_templates"]
@@ -51,74 +52,70 @@
 add_module_names = False
 modindex_common_prefix = ["pyclesperanto."]
 gettext_compact = False
-master_doc = 'index'
-suppress_warnings = ['image.nonlocal_uri']
-pygments_style = 'default'
+master_doc = "index"
+suppress_warnings = ["image.nonlocal_uri"]
+pygments_style = "default"
 
 # -- 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_theme_options = {
-    'logo_only': False,
-    'navigation_depth': 5,
-    'display_version': True,
-    'collapse_navigation': False,
+    "logo_only": False,
+    "navigation_depth": 5,
+    "display_version": True,
+    "collapse_navigation": False,
 }
 html_context = {}
 
-if not 'READTHEDOCS' in os.environ:
-    html_static_path = ['_static/']
-    html_js_files = ['debug.js']
+if "READTHEDOCS" not in os.environ:
+    html_static_path = ["_static/"]
+    html_js_files = ["debug.js"]
 
     # Add fake versions for local QA of the menu
-    html_context['test_versions'] = list(map(
-        lambda x: str(x / 10),
-        range(1, 100)
-    ))
+    html_context["test_versions"] = list(map(lambda x: str(x / 10), range(1, 100)))
 
 # html_logo = "demo/static/logo-wordmark-light.svg"
 html_show_sourcelink = True
 # html_favicon = "demo/static/favicon.ico"
 htmlhelp_basename = slug
 
 latex_documents = [
-  ('index', '{0}.tex'.format(slug), project, author, 'manual'),
+    ("index", "{0}.tex".format(slug), project, author, "manual"),
 ]
 
-man_pages = [
-    ('index', slug, project, [author], 1)
-]
+man_pages = [("index", slug, project, [author], 1)]
 
 texinfo_documents = [
-  ('index', slug, project, author, slug, project, 'Miscellaneous'),
+    ("index", slug, project, author, slug, project, "Miscellaneous"),
 ]
 
-html_static_path = ['_static']
+html_static_path = ["_static"]
+
 
 # Extensions to theme docs
 def setup(app):
     from sphinx.domains.python import PyField
     from sphinx.util.docfields import Field
 
     app.add_object_type(
-        'confval',
-        'confval',
-        objname='configuration value',
-        indextemplate='pair: %s; configuration value',
+        "confval",
+        "confval",
+        objname="configuration value",
+        indextemplate="pair: %s; configuration value",
         doc_field_types=[
             PyField(
-                'type',
-                label=_('Type'),
+                "type",
+                label=_("Type"),
                 has_arg=False,
-                names=('type',),
-                bodyrolename='class'
+                names=("type",),
+                bodyrolename="class",
             ),
             Field(
-                'default',
-                label=_('Default'),
+                "default",
+                label=_("Default"),
                 has_arg=False,
-                names=('default',),
+                names=("default",),
             ),
-        ]
-    )
+        ],
+    )

docs/source/index.rst

@@ -18,7 +18,7 @@ You will find here a first draft of the API for reference and documentation purp
 .. toctree::
    :caption: User Guide
    :maxdepth: 1
-   
+
    install
    usage
    api
@@ -28,4 +28,4 @@ You will find here a first draft of the API for reference and documentation purp
    :caption: Developper Guide
    :maxdepth: 1
 
-   contribute
+   contribute

docs/source/install.rst

@@ -25,7 +25,7 @@ or via conda:
         mamba create --name myenv
         mamba activate myenv
 
-.. note:: 
+.. note::
 
     It is often require to also install an additional package to use pyClesperanto, especially on MacOS or Linux:
 
@@ -81,4 +81,4 @@ However, any modification of the source code will require you to re-install the
 
 .. warning::
 
-    If using an install from source, do not import the package from the source directory as it will not work properly.    
+    If using an install from source, do not import the package from the source directory as it will not work properly.

docs/source/usage.rst

@@ -33,8 +33,8 @@ Memory transfer
 ===============
 
 It is a good practice to consider the GPU as another computer. Its memory is separated from your computer (host) memory, hence you need to transfer your data to the device memory in order to process it.
-Going both ways, you will need to transfer it back to your computer (host) memory when you are done running GPU operations so that you can read the results. In pyclesperanto this is managed by the 
-functions ``push``, ``pull``, and ``create``. ``push`` and ``pull`` are used to transfer data from the host to the GPU and vice versa. ``create`` is used to allocate an empty space on the GPU which will be 
+Going both ways, you will need to transfer it back to your computer (host) memory when you are done running GPU operations so that you can read the results. In pyclesperanto this is managed by the
+functions ``push``, ``pull``, and ``create``. ``push`` and ``pull`` are used to transfer data from the host to the GPU and vice versa. ``create`` is used to allocate an empty space on the GPU which will be
 then use, for example to store a result.
 
 
@@ -77,7 +77,7 @@ The ``push`` will create a memory space on the GPU like ``create`` but will also
 
 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 4 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. 
+memory is limited.
 
 .. warning::
     Python natively manage only 2 type of scalar, ``float`` and ``int``, correspondint to ``float64``, also known as ``double`` and ``int64``. However, ``double`` type

pyclesperanto/__init__.py

@@ -1,17 +1,17 @@
+from ._array import Array, Image, is_image
 from ._core import (
+    Device,
+    default_initialisation,
+    get_device,
     gpu_info,
+    list_available_backends,
+    list_available_devices,
     select_backend,
     select_device,
-    get_device,
     wait_for_kernel_to_finish,
-    list_available_devices,
-    list_available_backends,
-    default_initialisation,
-    Device,
 )
-from ._array import Array, Image, is_image
-from ._memory import create, create_like, push, pull
-from ._functionalities import imshow, list_operations, execute, native_execute
+from ._functionalities import execute, imshow, list_operations, native_execute
+from ._memory import create, create_like, pull, push
 
 from ._tier1 import *
 from ._tier2 import *
@@ -21,11 +21,11 @@
 from ._tier6 import *
 from ._tier7 import *
 from ._tier8 import *
+
 from ._interroperability import *
 
-from ._version import VERSION as __version__
 from ._version import CLIC_VERSION as __clic_version__
 from ._version import COMMON_ALIAS as __common_alias__
-
+from ._version import VERSION as __version__
 
 default_initialisation()

pyclesperanto/_array.py

@@ -1,10 +1,12 @@
-from ._pyclesperanto import _Array as Array
+from typing import Union
+
+import numpy as np
+
 from ._core import Device, get_device
+from ._pyclesperanto import _Array as Array
 from ._utils import _assert_supported_dtype
-from . import _operators
 
-from typing import Union
-import numpy as np
+from . import _operators
 
 
 def _prepare_array(arr) -> np.ndarray:

pyclesperanto/_core.py

@@ -1,9 +1,10 @@
+import warnings
 from typing import Optional, Union
+
 import numpy as np
-import warnings
 
-from ._pyclesperanto import _Device as Device
 from ._pyclesperanto import _BackendManager as BackendManager
+from ._pyclesperanto import _Device as Device
 
 
 class _current_device:

pyclesperanto/_decorators.py

@@ -1,11 +1,12 @@
-from typing import Callable, Optional
+import inspect
 from functools import wraps
+from typing import Callable, Optional
+
 from toolz import curry
-import inspect
 
-from ._memory import push
-from ._array import is_image, Image
+from ._array import Image, is_image
 from ._core import Device
+from ._memory import push
 
 
 @curry