Merge pull request #146 from PyLops/dev

Merge for v0.7.0

.github/workflows/build.yaml

@@ -4,25 +4,30 @@ on: [push, pull_request]
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        platform: [ ubuntu-latest, macos-latest ]
+        python-version: ["3.8", "3.9", "3.10"]
 
+    runs-on: ${{ matrix.platform }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
+    - name: Get history and tags for SCM versioning to work
+      run: |
+        git fetch --prune --unshallow
+        git fetch --depth=1 origin +refs/tags/*:refs/tags/*
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
+        python -m pip install --upgrade pip setuptools
         pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements-dev.txt; fi
     - name: Install pyproximal
       run: |
+        python -m setuptools_scm
         pip install .
     - name: Test with pytest
       run: |

.readthedocs.yaml

@@ -21,5 +21,5 @@ sphinx:
 python:
   install:
     - requirements: requirements-dev.txt
-    - method: setuptools
+    - method: pip
       path: .

CHANGELOG.md

@@ -1,3 +1,12 @@
+# 0.7.0
+
+* Added ``pyproximal.proximal.RelaxedMumfordShah`` operator
+* Added cuda version to the proximal operator of ``pyproximal.proximal.Simplex`` 
+* Added bilinear update to ``pyproximal.optimization.primal.ProximalGradient``
+* Modified ``pyproximal.optimization.pnp.PlugAndPlay`` function signature to allow using any proximal solver of choice
+* Fixed print in ``pyproximal.optimization.primaldual.PrimalDual`` when using cupy arrays
+* Fixed ``pyproximal.utils.bilinear.LowRankFactorizedMatrix`` when ``n=m``
+
 # 0.6.0
 
 :vertical_traffic_light: :vertical_traffic_light: This is the first release supporting PyLops v2.
@@ -14,7 +23,7 @@
 :vertical_traffic_light: :vertical_traffic_light:
 
 * Added ``pyproximal.proximal.Log1`` operator
-* Allow ``radius`` parameter of ``pyproximal.optimization.primal.L0`` to be a function
+* Allow ``radius`` parameter of ``pyproximal.proximal.L0`` to be a function
 * Allow ``tau`` parameter of ``pyproximal.optimization.primal.HQS`` to be a vector
   and change over iterations
 * Added ``z0`` to ``pyproximal.optimization.primal.HQS``

Makefile

@@ -31,7 +31,7 @@ dev-install_conda:
 
 tests:
 	make pythoncheck
-	$(PYTHON) setup.py test
+	pytest
 
 doc:
 	cd docs  && rm -rf source/api/generated && rm -rf source/gallery &&\

README.md

@@ -1,14 +1,15 @@
-# PyProximal
+![PyProximal](https://github.com/PyLops/pyproximal/blob/dev/docs/source/_static/pyproximal_b.png)
 
 [![PyPI version](https://badge.fury.io/py/pyproximal.svg)](https://badge.fury.io/py/pyproximal)
 [![Build Status](https://travis-ci.com/PyLops/pyproximal.svg?branch=main)](https://travis-ci.com/PyLops/pyproximal)
-[![AzureDevOps Status](https://dev.azure.com/matteoravasi/PyLops/_apis/build/status/PyLops.pyproximal?branchName=main)](https://dev.azure.com/matteoravasi/PyLops/_build/latest?definitionId=10&branchName=main)
+[![AzureDevOps Status](https://dev.azure.com/matteoravasi/PyLops/_apis/build/status%2FPyLops.pyproximal?branchName=refs%2Fpull%2F129%2Fmerge)](https://dev.azure.com/matteoravasi/PyLops/_build/latest?definitionId=10&branchName=refs%2Fpull%2F129%2Fmerge)
 ![GithubAction Status](https://github.com/PyLops/pyproximal/workflows/PyProx/badge.svg)
 [![Documentation Status](https://readthedocs.org/projects/pyproximal/badge/?version=latest)](https://pyproximal.readthedocs.io/en/latest/?badge=latest)
 [![OS-support](https://img.shields.io/badge/OS-linux,osx-850A8B.svg)](https://github.com/PyLops/pyproximal)
 [![Slack Status](https://img.shields.io/badge/chat-slack-green.svg)](https://pylops.slack.com)
 
 
+
 :vertical_traffic_light: :vertical_traffic_light: This library is under early development.
 Expect things to constantly change until version v1.0.0. :vertical_traffic_light: :vertical_traffic_light:
 
@@ -75,11 +76,10 @@ xladmm, _ = LinearizedADMM(l2, l1, Dop, tau=tau, mu=mu,
 ```
 
 ## Why another library for proximal algorithms?
-
 Several other projects in the Python ecosystem provide implementations of proximal
 operators and/or algorithms, which present some clear overlap with this project.
 
-A (possibly not exahustive) list of other projects is:
+A (possibly not exhaustive) list of other projects is:
 
 * http://proximity-operator.net
 * https://github.com/ganguli-lab/proxalgs/blob/master/proxalgs/operators.py
@@ -110,39 +110,34 @@ This repository is organized as follows:
 * **tutorials**:  set of python script tutorials to be embedded in documentation using sphinx-gallery
 
 ## Getting started
-
 You need **Python 3.8 or greater**.
 
-*Note: Versions prior to v0.3.0 work alsi with Python 3.6 or greater, however they 
+*Note: Versions prior to v0.3.0 work also with Python 3.6 or greater, however they 
 require scipy version to be lower than v1.8.0.*
 
-
 #### From PyPi
-
-If you want to use PyProximal within your codes,
+you want to use PyProximal within your codes,
 install it in your Python environment by typing the following command in your terminal:
 
+To get the most out of PyLops straight out of the box, we recommend `conda` to install PyLops:
+```bash
+conda install -c conda-forge pyproximal
 ```
-pip install pyproximal
-```
-
-Open a python terminal and type:
 
+#### From PyPi
+You can also install pyproximal with `pip`:
+```bash
+pip install pylops
 ```
-import pyproximal
-```
-
 
 #### From Github
-
-You can also directly install from the master node (although this is not reccomended)
+Finally, you can also directly install from the main branch (although this is not recommended)
 
 ```
 pip install git+https://git@github.com/PyLops/pyproximal.git@main
 ```
 
 ## Contributing
-
 *Feel like contributing to the project? Adding new operators or tutorial?*
 
 We advise using the [Anaconda Python distribution](https://www.anaconda.com/download)
@@ -151,7 +146,6 @@ the following instructions and read carefully the [CONTRIBUTING](CONTRIBUTING.md
 file before getting started.
 
 ### 1. Fork and clone the repository
-
 Execute the following command in your terminal:
 
 ```

azure-pipelines.yml

@@ -64,7 +64,7 @@ jobs:
     displayName: 'Install prerequisites and library'
 
   - script: |
-      python setup.py test
+      pytest
     condition: succeededOrFailed()
     displayName: 'Run tests'
 
@@ -93,7 +93,7 @@ jobs:
     displayName: 'Install prerequisites and library'
 
   - script: |
-      python setup.py test
+      pytest
     condition: succeededOrFailed()
     displayName: 'Run tests'
 

docs/source/api/index.rst

@@ -92,6 +92,7 @@ Non-Convex
     Log1
     QuadraticEnvelopeCard
     QuadraticEnvelopeCardIndicator
+    RelaxedMumfordShah
     SCAD
 
 

docs/source/changelog.rst

@@ -3,6 +3,17 @@
 Changelog
 =========
 
+Version 0.7.0
+--------------
+*Released on: 10/11/2023*
+
+* Added :py:class:`pyproximal.proximal.RelaxedMumfordShah`` operator
+* Added cuda version to the proximal operator of :py:class:`pyproximal.proximal.Simplex`
+* Added bilinear update to :py:func:`pyproximal.optimization.primal.ProximalGradient`
+* Modified :py:func:`pyproximal.optimization.pnp.PlugAndPlay` function signature to allow using any proximal solver of choice
+* Fixed print in :py:func:`pyproximal.optimization.primaldual.PrimalDual` when using cupy arrays
+* Fixed :py:class:`pyproximal.utils.bilinear.LowRankFactorizedMatrix` when ``n=m``
+
 Version 0.6.0
 --------------
 *Released on: 18/03/2023*
@@ -23,19 +34,19 @@ Version 0.5.0
 |:vertical_traffic_light:| |:vertical_traffic_light:|
 
 * Added :py:class:`pyproximal.proximal.Log1` operator
-* Allow ``radius`` parameter of :py:class:`pyproximal.optimization.primal.L0` to be a function
-* Allow ``tau`` parameter of :py:class:`pyproximal.optimization.primal.HQS` to be a vector
+* Allow ``radius`` parameter of :py:func:`pyproximal.optimization.primal.L0` to be a function
+* Allow ``tau`` parameter of :py:func:`pyproximal.optimization.primal.HQS` to be a vector
   and change over iterations
-* Added ``z0`` to :py:class:`pyproximal.optimization.primal.HQS`
+* Added ``z0`` to :py:func:`pyproximal.optimization.primal.HQS`
 * Added ``factorize`` option to ``densesolver`` of :py:class:`pyproximal.proximal.L2`
 
 Version 0.4.0
 --------------
 *Released on: 05/06/2022*
 
-* Added :py:class:`pyproximal.optimization.primal.ADMML2`,
-  :py:class:`pyproximal.optimization.primal.HQS`,
-  and :py:class:`pyproximal.optimization.pnp.PlugAndPlay` solvers
+* Added :py:func:`pyproximal.optimization.primal.ADMML2`,
+  :py:func:`pyproximal.optimization.primal.HQS`,
+  and :py:func:`pyproximal.optimization.pnp.PlugAndPlay` solvers
 * Added :py:class:`pyproximal.proximal.ETP`, :py:class:`pyproximal.proximal.Geman`,
   :py:class:`pyproximal.proximal.L0`, :py:class:`pyproximal.proximal.Log`,
   :py:class:`pyproximal.proximal.QuadraticEnvelopeCard`, :py:class:`pyproximal.proximal.SCAD`
@@ -47,8 +58,8 @@ Version 0.3.0
 --------------
 *Released on: 23/03/2022*
 
-* Added :py:class:`pyproximal.optimization.palm.PALM` optimizer
-* Added ``callback`` to :py:class:`pyproximal.optimization.primal.ProximalPoint`
+* Added :py:func:`pyproximal.optimization.palm.PALM` optimizer
+* Added ``callback`` to :py:func:`pyproximal.optimization.primal.ProximalPoint`
   optimizer
 * Added :py:class:`pyproximal.utils.bilinear.BilinearOperator`
   and :py:class:`pyproximal.utils.bilinear.LowRankFactorizedMatrix`
@@ -67,11 +78,11 @@ Version 0.2.0
 * Added
   :py:class:`pyproximal.proximal.Nuclear`, and
   :py:class:`pyproximal.proximal.NuclearBall` operators
-* Added :py:class:`pyproximal.optimization.primal.TwIST` solver
+* Added :py:func:`pyproximal.optimization.primal.TwIST` solver
 * Added `acceleration` in
-  :py:class:`pyproximal.optimization.primal.AcceleratedProximalGradient` solver
+  :py:func:`pyproximal.optimization.primal.AcceleratedProximalGradient` solver
 * Added classes standard deviation in
-  :py:class:`pyproximal.optimization.segmentation.Segment` solver
+  :py:func:`pyproximal.optimization.segmentation.Segment` solver
 * Added `chain` method :py:class:`pyproximal.ProxOperator`
 * Fix :py:class:`pyproximal.proximal.Orthogonal` by introducing `alpha`
   in the proximal evaluation
@@ -81,7 +92,7 @@ Version 0.1.0
 --------------
 *Released on: 24/04/2021*
 
-* Added :py:class:`pyproximal.optimization.sr3.SR3` solver
+* Added :py:func:`pyproximal.optimization.sr3.SR3` solver
 * Added :py:class:`pyproximal.projection.AffineSetProj` and
   :py:class:`pyproximal.AffineSet` operators
 * Fixed :py:class:`pyproximal.Huber` operator

docs/source/conf.py

@@ -2,7 +2,6 @@
 import sys
 import os
 import datetime
-import sphinx_rtd_theme
 import sphinx_gallery
 from sphinx_gallery.sorting import ExampleTitleSortKey
 from pyproximal import __version__
@@ -77,8 +76,9 @@
 
 # Sphinx project configuration
 templates_path = ['_templates']
-exclude_patterns = ['_build', '**.ipynb_checkpoints']
+exclude_patterns = ["_build", "**.ipynb_checkpoints", "**.ipynb", "**.md5"]
 source_suffix = '.rst'
+
 # The encoding of source files.
 source_encoding = 'utf-8-sig'
 master_doc = 'index'
@@ -102,7 +102,7 @@
 html_last_updated_fmt = '%b %d, %Y'
 html_title = 'PyProximal'
 html_short_title = 'PyProximal'
-html_logo = 'pyproximal.png'
+html_logo = '_static/pyproximal.png'
 html_favicon = 'favicon.ico'
 html_extra_path = []
 pygments_style = 'default'
@@ -116,6 +116,10 @@
 html_theme_options = {
     'logo_only': True,
     'display_version': True,
+    "logo": {
+            "image_light": "pyproximal_b.png",
+            "image_dark": "pyproximal.png",
+    }
 }
 html_context = {
     'menu_links_name': 'Repository',

docs/source/installation.rst

@@ -27,21 +27,35 @@ is not just a pure stylistic choice but comes with some *hidden* advantages, suc
 Step-by-step installation for users
 -----------------------------------
 
-Python environment
-~~~~~~~~~~~~~~~~~~
+Conda (recommended)
+===================
+If using ``conda``, install our ``conda-forge`` distribution via:
 
-Activate your Python environment, and simply type the following command in your terminal
-to install the PyPi distribution:
+.. code-block:: bash
+
+   >> conda install --channel conda-forge pyproximal
+
+Using the ``conda-forge`` distribution is recommended as all the dependencies (both required
+and optional) will be automatically installed for you.
+
+Pip
+===
+If you are using ``pip``, and simply type the following command in your terminal
+to install the PyPI distribution:
 
 .. code-block:: bash
 
    >> pip install pyproximal
 
-Alternatively, to access the latest source from github:
+Note that when installing via ``pip``, only *required* dependencies are installed.
+
+From Source
+===========
+To access the latest source from github:
 
 .. code-block:: bash
 
-   >> pip install https://github.com/PyLops/pyproximal/archive/master.zip
+   >> pip install https://github.com/PyLops/pyproximal.git@main
 
 or just clone the repository
 

environment-dev.yml

@@ -20,7 +20,7 @@ dependencies:
     - bm3d
     - pytest-runner
     - setuptools_scm
-    - sphinx-rtd-theme
+    - pydata-sphinx-theme
     - sphinx-gallery
     - nbsphinx
     - image