Merge pull request #499 from PyLops/dev

Merge for v2.1.0

.github/workflows/build.yaml

@@ -4,16 +4,16 @@ on: [push, pull_request]
 
 jobs:
   build:
-
-    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        platform: [ ubuntu-latest, macos-latest ]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
 
+    runs-on: ${{ matrix.platform }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - 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

.github/workflows/codacy-coverage-reporter.yaml

@@ -0,0 +1,33 @@
+# This workflow uploads PyLops coverage analysis on Codacy
+# For more information see: https://github.com/codacy/codacy-coverage-reporter-action
+name: PyLops-coverage
+
+on: [push, pull_request_target]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest coverage
+        if [ -f requirements.txt ]; then pip install -r requirements-dev.txt; fi
+    - name: Install pylops
+      run: |
+        pip install .
+    - name: Code coverage with coverage
+      run: |
+        coverage run -m pytest
+        coverage xml
+    - name: Run codacy-coverage-reporter
+      uses: codacy/codacy-coverage-reporter-action@v1
+      with:
+        project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+        coverage-reports: coverage.xml

.github/workflows/flake8.yaml

@@ -10,9 +10,9 @@ jobs:
     name: Lint
     steps:
       - name: Check out source repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up Python environment
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: "3.8"
       - name: flake8 Lint

CHANGELOG.md

@@ -1,3 +1,18 @@
+# 2.1.0
+* Added `pylops.signalprocessing.DCT`, `pylops.signalprocessing.NonStationaryConvolve1D`,
+  `pylops.signalprocessing.NonStationaryConvolve2D`, `pylops.signalprocessing.NonStationaryFilters1D`, and
+  `pylops.signalprocessing.NonStationaryFilters2D` operators
+* Added `pylops.waveeqprocessing.BlendingContinuous`, `pylops.waveeqprocessing.BlendingGroup`, and
+  `pylops.waveeqprocessing.BlendingHalf` operators
+* Added `kind='datamodel'` to `pylops.optimization.cls_sparsity.IRLS`
+* Improved inner working of `pylops.waveeqprocessing.Kirchhoff` operator significantly
+  reducing the memory usage related to storing traveltime, angle, and amplitude tables.
+* Improved handling of `haxes` in `pylops.signalprocessing.Radon2D` and `pylops.signalprocessing.Radon3D` operators
+* Added possibility to feed ND-arrays to `pylops.TorchOperator`
+* Removed `pylops.LinearOperator` inheritance and added `__call__` method to `pylops.TorchOperator`
+* Removed `scipy.sparse.linalg.LinearOperator` and added `abc.ABC` inheritance to `pylops.LinearOperator`
+* All operators are now classes of `pylops.LinearOperator` type
+
 # 2.0.0
 PyLops has undergone significant changes in this release, including new ``LinearOperator``s, more features, new examples and bugfixes.
 To aid users in navigating the breaking changes, we provide the following document [MIGRATION_V1_V2.md](https://github.com/PyLops/pylops/blob/dev/MIGRATION_V1_V2.md).

Makefile

@@ -40,8 +40,14 @@ doc:
 docupdate:
 	cd docs && make html && cd ..
 
+servedoc:
+	$(PYTHON) -m http.server --directory docs/build/html/
+
 lint:
 	flake8 docs/ examples/ pylops/ pytests/ tutorials/
 
 typeannot:
 	mypy pylops/
+
+coverage:
+	coverage run -m pytest && coverage xml && coverage html && $(PYTHON) -m http.server --directory htmlcov/

README.md

@@ -142,3 +142,8 @@ A list of video tutorials to learn more about PyLops:
 * Alan Richardson, ar4
 * BurningKarl, BurningKarl
 * Nick Luiken, NickLuiken
+* BurningKarl, BurningKarl
+* Muhammad Izzatullah, izzatum
+* Juan Daniel Romero, jdromerom
+* Aniket Singh Rawat, dikwickley
+* Rohan Babbar, rohanbabbar04

docs/source/_static/css/custom.css

@@ -0,0 +1,5 @@
+@import 'theme.css'; 
+
+.sphx-glr-multi-img {
+    max-width: 100%;
+}

docs/source/adding.rst

@@ -23,18 +23,19 @@ which will be used as *parent* class for any of our operators:
 
    from pylops import LinearOperator
 
-This class is a child of the
-:py:class:`scipy.sparse.linalg.LinearOperator` class itself which implements the same methods of its parent class
-as well as an additional method for quick inversion: such method can be easily accessed by using ``\`` between the
-operator and the data (e.g., ``A \ y``).
+This class was originally defined as a child of the :py:class:`scipy.sparse.linalg.LinearOperator`, implementing
+the same methods of its parent class as well as additional methods for quick inversion (e.g., ``A \ y``),
+eigenvalues computation, conversion to dense matrices, etc. From version ``v2.1`` onwards, our linear operator
+class has become stand-alone; however, by keeping the same naming structure of the original scipy class, we still
+allow inter-operability with scipy-native linear operators and solvers.
 
 After that we define our new object:
 
 .. code-block:: python
 
    class Diagonal(LinearOperator):
 
-followed by a `numpydoc docstring <https://numpydoc.readthedocs.io/en/latest/format.html/>`_
+followed by a `numpydoc docstring <https://numpydoc.readthedocs.io/en/latest/format.html>`__
 (starting with ``r"""`` and ending with ``"""``) containing the documentation of the operator. Such docstring should
 contain at least a short description of the operator, a ``Parameters`` section with a detailed description of the
 input parameters and a ``Notes`` section providing a mathematical explanation of the operator. Take a look at
@@ -172,7 +173,7 @@ adheres to the guidelines of PyLops:
 
 - the new class contains at least ``__init__``, ``_matvec`` and ``_matvec`` methods.
 
-- the new class (or function) has a `numpydoc docstring <https://numpydoc.readthedocs.io/>`_ documenting
+- the new class (or function) has a `numpydoc docstring <https://numpydoc.readthedocs.io/>`__ documenting
   at least the input ``Parameters`` and with a ``Notes`` section providing a mathematical explanation of the operator
 
 - a new test has been added to an existing ``test_*.py`` file within the ``pytests`` folder. The test should verify

docs/source/addingsolver.rst

@@ -41,7 +41,7 @@ After that we define our new object:
 
     class CG(Solver):
 
-followed by a `numpydoc docstring <https://numpydoc.readthedocs.io/en/latest/format.html/>`_
+followed by a `numpydoc docstring <https://numpydoc.readthedocs.io/en/latest/format.html/>`__
 (starting with ``r"""`` and ending with ``"""``) containing the documentation of the solver. Such docstring should
 contain at least a short description of the solver, a ``Parameters`` section with a description of the
 input parameters of the associated ``_init__`` method and a ``Notes`` section providing a reference to the original
@@ -143,7 +143,7 @@ model and the same hyperparameters of the setup method and runs the entire optim
 
 .. code-block:: python
 
-    def solve(self, y, x0=None, niter=10, tol=1e-4, show=False, itershow=[10, 10, 10]):
+    def solve(self, y, x0=None, niter=10, tol=1e-4, show=False, itershow=(10, 10, 10)):
         x = self.setup(y=y, x0=x0, niter=niter, tol=tol, show=show)
         x = self.run(x, niter, show=show, itershow=itershow)
         self.finalize(show)
@@ -169,7 +169,7 @@ input and returns some of the most valuable properties of the class-based solver
 
 .. code-block:: python
 
-    def cg(Op, y, x0, niter=10, tol=1e-4, show=False, itershow=[10, 10, 10], callback=None):
+    def cg(Op, y, x0, niter=10, tol=1e-4, show=False, itershow=(10, 10, 10), callback=None):
         cgsolve = CG(Op)
         if callback is not None:
             cgsolve.callback = callback
@@ -239,7 +239,7 @@ adheres to the guidelines of PyLops:
 
 - the new class contains at least ``__init__``, ``setup``, ``step``, ``run``, ``finalize``, and ``solve`` methods.
 
-- each of the above methods have a `numpydoc docstring <https://numpydoc.readthedocs.io/>`_ documenting
+- each of the above methods have a `numpydoc docstring <https://numpydoc.readthedocs.io/>`__ documenting
   at least the input ``Parameters`` and the ``__init__`` method contains also a ``Notes`` section providing a
   mathematical explanation of the solver.
 

docs/source/api/index.rst

@@ -89,6 +89,10 @@ Signal processing
     Convolve1D
     Convolve2D
     ConvolveND
+    NonStationaryConvolve1D
+    NonStationaryConvolve2D
+    NonStationaryFilters1D
+    NonStationaryFilters2D
     Interp
     Bilinear
     FFT
@@ -97,6 +101,7 @@ Signal processing
     Shift
     DWT
     DWT2D
+    DCT
     Seislet
     Radon2D
     Radon3D
@@ -121,6 +126,9 @@ Wave-Equation processing
     PressureToVelocity
     UpDownComposition2D
     UpDownComposition3D
+    BlendingContinuous
+    BlendingGroup
+    BlendingHalf
     MDC
     PhaseShift
     Kirchhoff

docs/source/changelog.rst

@@ -3,6 +3,26 @@
 Changelog
 =========
 
+Version 2.1.0
+-------------
+
+*Released on: 17/03/2023*
+
+* Added :class:`pylops.signalprocessing.DCT`, :class:`pylops.signalprocessing.NonStationaryConvolve1D`,
+  :class:`pylops.signalprocessing.NonStationaryConvolve2D`, :class:`pylops.signalprocessing.NonStationaryFilters1D`, and
+  :class:`pylops.signalprocessing.NonStationaryFilters2D` operators
+* Added :class:`pylops.waveeqprocessing.BlendingContinuous`, :class:`pylops.waveeqprocessing.BlendingGroup`, and
+  :class:`pylops.waveeqprocessing.BlendingHalf` operators
+* Added `kind='datamodel'` to :class:`pylops.optimization.cls_sparsity.IRLS`
+* Improved inner working of :class:`pylops.waveeqprocessing.Kirchhoff` operator significantly
+  reducing the memory usage related to storing traveltime, angle, and amplitude tables.
+* Improved handling of `haxes` in :class:`pylops.signalprocessing.Radon2D` and :class:`pylops.signalprocessing.Radon3D` operators
+* Added possibility to feed ND-arrays to :class:`pylops.TorchOperator`
+* Removed :class:`pylops.LinearOperator` inheritance and added `__call__` method to :class:`pylops.TorchOperator`
+* Removed `scipy.sparse.linalg.LinearOperator` and added :class:`abc.ABC` inheritance to :class:`pylops.LinearOperator`
+* All operators are now classes of `:class:`pylops.LinearOperator` type
+
+
 Version 2.0.0
 -------------
 
@@ -98,7 +118,7 @@ Version 1.18.0
 * Extended :py:func:`pylops.Laplacian` to N-dimensional arrays
 * Added `forward` kind to :py:class:`pylops.SecondDerivative` and
   :py:func:`pylops.Laplacian`
-* Added `chirp-sliding` kind to :py:func:`pylops.waveeqprocessing.seismicinterpolation.SeismicInterpolation`
+* Added `chirp-sliding` kind to :py:class:`pylops.waveeqprocessing.seismicinterpolation.SeismicInterpolation`
 * Fixed bug due to the new internal structure of `LinearOperator` submodule introduced in `scipy1.8.0`
 
 
@@ -245,7 +265,7 @@ Version 1.11.1
 *Released on: 24/10/2020*
 
 * Fixed import of ``pyfttw`` when not available in
-  :py:class:``pylops.signalprocessing.ChirpRadon3D`
+  :py:class:`pylops.signalprocessing.ChirpRadon3D`
 
 
 Version 1.11.0

docs/source/conf.py

@@ -79,8 +79,10 @@
 
 # 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"
@@ -101,13 +103,12 @@
 """.format(
     year=year
 )
-
+html_static_path = ["_static"]
 html_last_updated_fmt = "%b %d, %Y"
 html_title = "PyLops"
 html_short_title = "PyLops"
 html_logo = "_static/pylops.png"
 html_favicon = "_static/favicon.ico"
-html_static_path = ["_static"]
 html_extra_path = []
 pygments_style = "default"
 add_function_parentheses = False
@@ -116,11 +117,19 @@
 html_show_copyright = True
 
 # Theme config
-html_theme = "sphinx_rtd_theme"
+html_theme = "pydata_sphinx_theme"
 html_theme_options = {
     "logo_only": True,
     "display_version": True,
+    "logo": {
+        "image_light": "pylops_b.png",
+        "image_dark": "pylops.png",
+    }
 }
+html_css_files = [
+    'css/custom.css',
+]
+
 html_context = {
     "menu_links_name": "Repository",
     "menu_links": [

docs/source/credits.rst

@@ -15,3 +15,7 @@ Contributors
 *  `Alan Richardson <https://github.com/ar4>`_, ar4
 *  `BurningKarl <https://github.com/BurningKarl>`_, BurningKarl
 *  `Nick Luiken <https://github.com/NickLuiken>`_, NickLuiken
+*  `Muhammad Izzatullah <https://github.com/izzatum>`_, izzatum
+*  `Juan Daniel Romero <https://github.com/jdromerom>`_, jdromerom
+*  `Aniket Singh Rawat <https://github.com/dikwickley>`_, dikwickley
+*  `Rohan Babbar <https://github.com/rohanbabbar04>`_, rohanbabbar04