Merge pull request #204 from EmmaRenauld/fix_setup

Change the setup setting: copied from scilpy

.github/workflows/test_package.yml

@@ -29,7 +29,6 @@ jobs:
         pip install pytest
         pip install --upgrade pip
         pip install -r requirements_github.txt
-        pip install -r requirements.txt
         pip install .
 
     - name: Tests

.pep8speaks.yml

@@ -1,23 +1,40 @@
-# File : .pep8speaks.yml
-
 scanner:
     diff_only: True  # If False, the entire file touched by the Pull Request is scanned for errors. If True, only the diff is scanned.
-    linter: flake8  # Other option is pycodestyle
+    linter: pycodestyle  # Alternative option - flake8
+
+pycodestyle:  # Valid if scanner.linter is pycodestyle
+    max-line-length: 79
+    ignore: []  # Errors and warnings to ignore
+    exclude: []  # File path patterns to exclude
+    count: False
+    first: False
+    show-pep8: False
+    show-source: False
+    statistics: False
+    hang-closing: False
+    filename: []
+    select: []
 
-flake8:  # Same as scanner.linter value. Other option is pycodestyle
-    max-line-length: 79  # Default is 79 in PEP 8
+flake8:  # Valid if scanner.linter is flake8
+    max-line-length: 79
+    ignore: []
+    exclude: []
+    count: False
+    show-source: False
+    statistics: False
+    hang-closing: False
+    filename: []
+    select: []
 
-descending_issues_order: False  # If True, PEP 8 issues in message will be displayed in descending order of line numbers in the file.
 no_blank_comment: False  # If True, no comment is made on PR without any errors.
-only_mention_files_with_errors: True  # If False, a separate status comment for each file is made.
+descending_issues_order: False  # If True, PEP 8 issues in message will be displayed in descending order of line numbers in the file
+only_mention_files_with_errors: True  # If False, a separate status section for each file is made in the comment.
 
-message:  # Customize the comment made by the bot,
+message:  # Customize the comment made by the bot
     opened:  # Messages when a new PR is submitted
-        header: "Hello @{name}! Thanks for opening this PR. "
-                # The keyword {name} is converted into the author's username
+        header: "Hello @{name}, Thank you for submitting the Pull Request !"
         footer: "Do see the [PEP 8 -- Style Guide for Python Code](https://www.python.org/dev/peps/pep-0008/)"
-                # The messages can be written as they would over GitHub
-    updated:  # Messages when new commits are added to the PR
-        header: "Hello @{name}! Thanks for updating this PR. "
-        footer: ""  # Why to comment the link to the style guide everytime? :)
-    no_errors: "There are currently no PEP 8 issues detected in this Pull Request. Cheers! :rocket: "
+    updated:  # Messages when a PR is updated
+        header: "Hello @{name}, Thank you for updating !"
+        footer: ""
+    no_errors: "There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers: "

.python-version

@@ -0,0 +1 @@
+3.10

Makefile

@@ -1,20 +1,10 @@
-# Minimal makefile for Sphinx documentation
-#
+flake8:
+	@if command -v flake8 > /dev/null; then \
+		echo "Running flake8"; \
+		flake8 flake8 --ignore N802,N806 `find . -name \*.py | grep -v setup.py | grep -v /doc/`; \
+	else \
+		echo "flake8 not found, please install it!"; \
+		exit 1; \
+	fi;
+	@echo "flake8 passed"
 
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = doc
-BUILDDIR      = build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-    @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-    @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

dwi_ml/version.py

@@ -0,0 +1,87 @@
+# -*- coding: utf-8 -*-
+
+import glob
+
+# Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z"
+_version_major = 1
+_version_minor = 0
+_version_micro = 0
+_version_extra = ''
+
+# Construct full version string from these.
+_ver = [_version_major, _version_minor]
+if _version_micro:
+    _ver.append(_version_micro)
+if _version_extra:
+    _ver.append(_version_extra)
+
+__version__ = '.'.join(map(str, _ver))
+
+CLASSIFIERS = ["Development Status :: 3 - Alpha",
+               "Environment :: Console",
+               "Intended Audience :: Science/Research",
+               "License :: OSI Approved :: MIT License",
+               "Operating System :: OS Independent",
+               "Programming Language :: Python :: 3",
+               "Topic :: Scientific/Engineering",
+               'Topic :: Scientific/Engineering ::Neuroimaging']
+
+PYTHON_VERSION = ""
+with open('.python-version') as f:
+    py_version = f.readline().strip("\n").split(".")
+    py_major = py_version[0]
+    py_minor = py_version[1]
+    py_micro = "*"
+    py_extra = None
+    if len(py_version) > 2:
+        py_micro = py_version[2]
+    if len(py_version) > 3:
+        py_extra = py_version[3]
+
+    PYTHON_VERSION = ".".join([py_major, py_minor, py_micro])
+    if py_extra:
+        PYTHON_VERSION = ".".join([PYTHON_VERSION, py_extra])
+
+    PYTHON_VERSION = "".join(["==", PYTHON_VERSION])
+
+# Description should be a one-liner:
+description = 'Diffusion Magnetic Resonance Imaging analysis toolkit ' + \
+              'using machine learning and deep learning methods.'
+
+# Long description will go up on the pypi page
+long_description = """
+DWI_ML
+======
+
+SCIL and VITAL research labs' code for machine learning in medical data.
+
+License
+=======
+``dwi_ml`` is licensed under the terms of the MIT license. See the file
+"LICENSE" for information on the history of this software, terms & conditions
+for usage, and a DISCLAIMER OF ALL WARRANTIES.
+
+All trademarks referenced herein are property of their respective holders.
+
+Copyright (c) 2012--, Sherbrooke Connectivity Imaging Lab [SCIL],
+Université de Sherbrooke.
+"""
+
+NAME = "dwi_ml"
+MAINTAINER = "Emmanuelle Renauld (@EmmaRenauld)"
+MAINTAINER_EMAIL = ""
+DESCRIPTION = description
+LONG_DESCRIPTION = long_description
+URL = "https://github.com/scil-vital/dwi_ml"
+DOWNLOAD_URL = ""
+LICENSE = "MIT"
+AUTHOR = "The SCIL developers"
+AUTHOR_EMAIL = ""
+PLATFORMS = "OS Independent"
+MAJOR = _version_major
+MINOR = _version_minor
+MICRO = _version_micro
+VERSION = __version__
+SCRIPTS = glob.glob("scripts_python/*.py") + glob.glob("bash_utilities/*.sh") + glob.glob("scripts_python/tests/scripts_on_test_model/*.py")
+
+PREVIOUS_MAINTAINERS=[]

scripts_python/tto_visualize_weights.py

@@ -11,7 +11,8 @@
     build_argparser_transformer_visu
 
 
-def main(argv):
+def main():
+    argv = sys.argv
 
     parser = build_argparser_transformer_visu()
     args = parser.parse_args()
@@ -40,4 +41,4 @@ def main(argv):
 
 
 if __name__ == '__main__':
-    main(sys.argv)
+    main()

scripts_python/ttst_visualize_weights.py

@@ -11,7 +11,8 @@
     build_argparser_transformer_visu
 
 
-def main(argv):
+def main():
+    argv = sys.argv
 
     parser = build_argparser_transformer_visu()
     args = parser.parse_args()
@@ -40,4 +41,4 @@ def main(argv):
 
 
 if __name__ == '__main__':
-    main(sys.argv)
+    main()

setup.py

@@ -1,46 +1,47 @@
-#!/usr/bin/env python
-"""Installation script for the DWI_ML package."""
+import os
 
-from setuptools import setup, find_packages
-# To use a consistent encoding
-from codecs import open
-from os import path
-from os.path import join as pjoin
-import glob
+from setuptools import setup, find_packages, Extension
+from setuptools.command.build_ext import build_ext
 
-from setup_helpers import read_vars_from
+with open('requirements.txt') as f:
+    required_dependencies = f.read().splitlines()
+    external_dependencies = []
+    for dependency in required_dependencies:
+        if dependency[0:2] == '-e':
+            repo_name = dependency.split('=')[-1]
+            repo_url = dependency[3:]
+            external_dependencies.append('{} @ {}'.format(repo_name, repo_url))
+        else:
+            external_dependencies.append(dependency)
 
-# Read package information
-info = read_vars_from(pjoin('dwi_ml', 'info.py'))
 
-this_directory = path.abspath(path.dirname(__file__))
+# Get version and release info, which is all stored in version.py
+ver_file = os.path.join('dwi_ml', 'version.py')
+with open(ver_file) as f:
+    exec(f.read())
+opts = dict(name=NAME,
+            maintainer=MAINTAINER,
+            maintainer_email=MAINTAINER_EMAIL,
+            description=DESCRIPTION,
+            long_description=LONG_DESCRIPTION,
+            url=URL,
+            download_url=DOWNLOAD_URL,
+            license=LICENSE,
+            classifiers=CLASSIFIERS,
+            author=AUTHOR,
+            author_email=AUTHOR_EMAIL,
+            platforms=PLATFORMS,
+            version=VERSION,
+            packages=find_packages(),
+            python_requires=PYTHON_VERSION,
+            setup_requires=['numpy'],
+            install_requires=external_dependencies,
+            entry_points={
+                'console_scripts': ["{}=scripts_python.{}:main".format(
+                    os.path.basename(s),
+                    os.path.basename(s).split(".")[0]) for s in SCRIPTS]
+            },
+            data_files=[],
+            include_package_data=True)
 
-dwi_ml_readme_path = pjoin(this_directory, 'README.rst')
-with open(dwi_ml_readme_path, encoding='utf-8') as f:
-    long_description = f.read()
-
-setup(
-    name=info.NAME,
-    version=info.VERSION,
-    description=info.DESCRIPTION,
-    long_description=long_description,
-    long_description_content_type='text/x-rst',
-    url=info.URL,
-    project_urls={'Bug tracker': info.BUG_TRACKER,
-                  'Documentation': info.DOCUMENTATION,
-                  'Source code': info.SOURCE_CODE},
-    license=info.LICENSE,
-    author=info.AUTHOR,
-    author_email=info.AUTHOR_EMAIL,
-    classifiers=info.CLASSIFIERS,
-    keywords=info.KEYWORDS,
-    maintainer=info.MAINTAINER,
-    provides=info.PROVIDES,
-    packages=find_packages(exclude=['contrib', 'doc', 'tests']),
-    install_requires=[],
-    requires=info.REQUIRES,
-    package_data={},
-    data_files=[],
-    entry_points={},
-    scripts=glob.glob("scripts_python/*.py") + glob.glob("bash_utilities/*.sh") + glob.glob("scripts_python/tests/scripts_on_test_model/*.py")
-)
+setup(**opts)