Clean up of codes with pre-commit

.github/workflows/build.yaml

@@ -30,4 +30,4 @@ jobs:
         pip install .
     - name: Test with pytest
       run: |
-        pytest
+        pytest

.gitignore

@@ -25,4 +25,4 @@ spgl1.egg-info/
 # Docs
 docs/build/
 docs/source/api/generated
-docs/source/tutorials
+docs/source/tutorials

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+exclude: "^docs/"
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        args: # arguments to configure black
+          - --line-length=88
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
+        args:
+          [
+            "--profile",
+            "black",
+            "--skip",
+            "__init__.py",
+            "--filter-files",
+            "--line-length=88",
+          ]

Makefile

@@ -1,7 +1,7 @@
 PIP := $(shell command -v pip3 2> /dev/null || command which pip 2> /dev/null)
 PYTHON := $(shell command -v python3 2> /dev/null || command which python 2> /dev/null)
 
-.PHONY: install dev-install install_conda dev-install_conda tests doc docupdate
+.PHONY: install dev-install install_conda dev-install_conda tests doc docupdate servedoc
 
 pipcheck:
 ifndef PIP
@@ -39,3 +39,6 @@ doc:
 
 docupdate:
 	cd docs && make html && cd ..
+
+servedoc:
+	$(PYTHON) -m http.server --directory docs/build/html/

README.md

@@ -16,7 +16,7 @@ It is designed to solve any of the following three problems:
 
 2. Basis pursuit (BP):
    ``minimize   ||x||_1  subject to  Ax = b``
- 
+
 3. Lasso:
    ``minimize  ||Ax - b||_2  subject to  ||x||_1 <= tau``,
 

docs/Makefile

@@ -7,7 +7,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = Pylops
+SPHINXPROJ    = Spgl1
 SOURCEDIR     = source
 BUILDDIR      = build
 

docs/source/conf.py

@@ -3,7 +3,6 @@
 import os
 import datetime
 import sphinx_rtd_theme
-import sphinx_gallery
 from sphinx_gallery.sorting import ExampleTitleSortKey
 from pkg_resources import get_distribution
 
@@ -75,6 +74,7 @@
 templates_path = ['_templates']
 exclude_patterns = ['_build', '**.ipynb_checkpoints']
 source_suffix = '.rst'
+
 # The encoding of source files.
 source_encoding = 'utf-8-sig'
 master_doc = 'index'
@@ -106,7 +106,6 @@
 html_show_copyright = True
 
 # Theme config
-#html_theme = "alabaster"
 html_theme = "sphinx_rtd_theme"
 html_theme_options = {
     'logo_only': True,
@@ -129,4 +128,4 @@
 
 # Load the custom CSS files (needs sphinx >= 1.6 for this to work)
 def setup(app):
-    app.add_stylesheet("style.css")
+    app.add_css_file("style.css")

docs/source/index.rst

@@ -49,6 +49,7 @@ where more appropriate implementation choices were identified for the Python pro
    :hidden:
 
    Installation <installation.rst>
+   Tutorials <tutorials/index.rst>
    Reference documentation <api/index.rst>
    Credits <credits.rst>
 

environment-dev.yml

@@ -4,6 +4,7 @@ channels:
   - conda-forge
 dependencies:
   - python>=3.6.4
+  - pip
   - numpy>=1.15.0
   - scipy
   - matplotlib
@@ -12,10 +13,15 @@ dependencies:
   - pytest
   - Sphinx
   - numpydoc
+  - pre-commit
+  - autopep8
+  - isort
+  - black
   - pip:
     - pytest-runner
     - setuptools_scm
     - sphinx-rtd-theme
     - sphinx-gallery
     - nbsphinx
-    - image
+    - image
+    - flake8

environment.yml

@@ -3,5 +3,6 @@ channels:
   - defaults
 dependencies:
   - python>=3.6.4
+  - pip
   - numpy>=1.15.0
   - scipy