Merge pull request #604 from PyLops/dev

Release v2.3.0

Author: mrava87

.github/workflows/build.yaml

@@ -6,18 +6,18 @@ jobs:
   build:
     strategy:
       matrix:
-        platform: [ ubuntu-latest, macos-latest ]
-        python-version: ["3.8", "3.9", "3.10"]
+        platform: [ ubuntu-latest, macos-13 ]
+        python-version: ["3.9", "3.10", "3.11"]
 
     runs-on: ${{ matrix.platform }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - 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@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

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

@@ -9,13 +9,17 @@ jobs:
     strategy:
       matrix:
         platform: [ ubuntu-latest, ]
-        python-version: ["3.8", ]
+        python-version: ["3.9", ]
 
     runs-on: ${{ matrix.platform }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+    - 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@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/flake8.yaml

@@ -10,9 +10,9 @@ jobs:
     name: Lint
     steps:
       - name: Check out source repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python environment
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.8"
       - name: flake8 Lint

.readthedocs.yaml

@@ -18,6 +18,6 @@ sphinx:
 # Declare the Python requirements required to build your docs
 python:
   install:
-    - requirements: requirements-dev.txt
+    - requirements: requirements-doc.txt
     - method: pip
       path: .

CHANGELOG.md

@@ -1,3 +1,30 @@
+Changelog
+=========
+
+# 2.3.0
+
+* Added `pylops.JaxOperator`, `pylops.signalprocessing.DWTND`, and `pylops.signalprocessing.DTCWT` operators.
+* Added `updatesrc` method to `pylops.waveeqprocessing.AcousticWave2D`.
+* Added `verb` to `pylops.signalprocessing.Sliding1D.sliding1d_design`, `pylops.signalprocessing.Sliding2D.sliding2d_design`, `pylops.signalprocessing.Sliding3D.sliding3d_design`, `pylops.signalprocessing.Patch2D.patch2d_design`, and `pylops.signalprocessing.Patch3D.patch3d_design`.
+* Added `kwargs_fft` to `pylops.signalprocessing.FFTND`.
+* Added `cosinetaper` to `pylops.utils.tapers.cosinetaper`.
+* Added `kind` to `pylops.waveeqprocessing.Deghosting`.
+* Modified all methods in `pylops.utils.backend` to enable jax integration.
+* Modified implementations of `pylops.signalprocessing.Sliding1D`, `pylops.signalprocessing.Sliding2D`,
+`pylops.signalprocessing.Sliding3D`, `pylops.signalprocessing.Patch2D`, and
+`pylops.signalprocessing.Patch3D` to being directly implemented instead of relying on other PyLops operators. Added also `savetaper` parameter and an option to apply the operator `Op` simultaneously to all windows.
+* Modified `pylops.waveeqprocessing.AcousticWave2D._born_oneshot` and
+`pylops.waveeqprocessing.AcousticWave2D._born_allshots` to avoid recreating the devito solver for each shot (and enabling internal caching...)
+* Modified `dtype` of `pylops.signalprocessing.Shift` to be that of the input vector.
+* Modified `pylops.waveeqprocessing.BlendingContinuous` to use `matvec/rmatvec` instead of `@/.H @` for compatibility with pylops solvers.
+* Removed `cusignal` as optional dependency and `cupy`'s equivalent methods (since the library
+is now unmantained and merged into `cupy`).
+* Fixed ImportError of optional dependencies when installed but not correctly functioning (see [Issue #548](https://github.com/PyLops/pylops/issues/548))
+* Fixed bug in :py:func:`pylops.utils.deps.to_cupy_conditional` (see [Issue #579](https://github.com/PyLops/pylops/issues/579))
+* Fixed bug in the definition of `nttot` in :py:class:`pylops.waveeqprocessing.BlendingContinuous`
+* Fixed bug in :py:func:`pylops.utils.signalprocessing.dip_estimate` (see [Issue #572](https://github.com/PyLops/pylops/issues/572))
+
+
 # 2.2.0
 
 * Added `pylops.signalprocessing.NonStationaryConvolve3D` operator
@@ -287,7 +314,7 @@ To aid users in navigating the breaking changes, we provide the following docume
   ``pylops.waveeqprocessing.UpDownComposition3Doperator``, and
   ``pylops.waveeqprocessing.PhaseShift`` operators
 * Fix bug in ``pylops.basicoperators.Kronecker``
-  (see [Issue #125](https://github.com/Statoil/pylops/issues/125))
+  (see [Issue #125](https://github.com/PyLops/pylops/issues/125))
 
 # 1.7.0
 * Added ``pylops.basicoperators.Gradient``,

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 lint typeannot coverage
 
 pipcheck:
 ifndef PIP
@@ -29,6 +29,9 @@ install_conda:
 dev-install_conda:
 	conda env create -f environment-dev.yml && conda activate pylops && pip install -e .
 
+dev-install_conda_arm:
+	conda env create -f environment-dev-arm.yml && conda activate pylops && pip install -e .
+
 tests:
 	make pythoncheck
 	pytest

README.md

@@ -4,7 +4,7 @@
 [![PyPI version](https://badge.fury.io/py/pylops.svg)](https://badge.fury.io/py/pylops)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/pylops/badges/version.svg)](https://anaconda.org/conda-forge/pylops)
 [![AzureDevOps Status](https://dev.azure.com/matteoravasi/PyLops/_apis/build/status/PyLops.pylops?branchName=dev)](https://dev.azure.com/matteoravasi/PyLops/_build/latest?definitionId=9&branchName=dev)
-[![GithubAction Status](https://github.com/mrava87/pylops/actions/workflows/build.yaml/badge.svg)](https://github.com/mrava87/pylops/actions/workflows/build.yaml)
+[![GithubAction Status](https://github.com/PyLops/pylops/actions/workflows/build.yaml/badge.svg?branch=dev)](https://github.com/PyLops/pylops/actions/workflows/build.yaml)
 [![Documentation Status](https://readthedocs.org/projects/pylops/badge/?version=stable)](https://pylops.readthedocs.io/en/stable/?badge=stable)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/17fd60b4266347d8890dd6b64f2c0807)](https://www.codacy.com/gh/PyLops/pylops/dashboard?utm_source=github.com&utm_medium=referral&utm_content=PyLops/pylops&utm_campaign=Badge_Grade)
 [![Codacy Badge](https://app.codacy.com/project/badge/Coverage/17fd60b4266347d8890dd6b64f2c0807)](https://www.codacy.com/gh/PyLops/pylops/dashboard?utm_source=github.com&utm_medium=referral&utm_content=PyLops/pylops&utm_campaign=Badge_Coverage)
@@ -149,3 +149,6 @@ A list of video tutorials to learn more about PyLops:
 * Rohan Babbar, rohanbabbar04
 * Wei Zhang, ZhangWeiGeo
 * Fedor Goncharov, fedor-goncharov
+* Alex Rakowski, alex-rakowski
+* David Sollberger, solldavid
+* Gustavo Coelho, guaacoelho

azure-pipelines.yml

@@ -26,7 +26,7 @@ jobs:
 #   steps:
 #   - task: UsePythonVersion@0
 #     inputs:
-#       versionSpec: '3.7'
+#       versionSpec: '3.9'
 #       architecture: 'x64'
 #
 #   - script: |
@@ -55,7 +55,7 @@ jobs:
   steps:
   - task: UsePythonVersion@0
     inputs:
-      versionSpec: '3.8'
+      versionSpec: '3.9'
       architecture: 'x64'
 
   - script: |
@@ -84,7 +84,7 @@ jobs:
   steps:
   - task: UsePythonVersion@0
     inputs:
-      versionSpec: '3.8'
+      versionSpec: '3.9'
       architecture: 'x64'
 
   - script: |

docs/source/adding.rst

@@ -4,9 +4,9 @@ Implementing new operators
 ==========================
 Users are welcome to create new operators and add them to the PyLops library.
 
-In this tutorial, we will go through the key steps in the definition of an operator, using the
-:py:class:`pylops.Diagonal` as an example. This is a very simple operator that applies a diagonal matrix to the model
-in forward mode and to the data in adjoint mode.
+In this tutorial, we will go through the key steps in the definition of an operator, using a simplified version of the
+:py:class:`pylops.Diagonal` operator as an example. This is a very simple operator that applies a diagonal matrix
+to the model in forward mode and to the data in adjoint mode.
 
 
 Creating the operator
@@ -45,14 +45,17 @@ Initialization (``__init__``)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 We then need to create the ``__init__`` where the input parameters are passed and saved as members of our class.
-While the input parameters change from operator to operator, it is always required to create three members, the first
-called ``shape`` with a tuple containing the dimensions of the operator in the data and model space, the second
-called ``dtype`` with the data type object (:obj:`np.dtype`) of the model and data, and the third
-called ``explicit`` with a boolean (``True`` or ``False``) identifying if the operator can be inverted by a direct
-solver or requires an iterative solver. This member is ``True`` if the operator has also a member ``A`` that contains
-the matrix to be inverted like for example in the :py:class:`pylops.MatrixMult` operator, and it will be ``False`` otherwise.
-In this case we have another member called ``d`` which is equal to the input vector containing the diagonal elements
-of the matrix we want to multiply to the model and data.
+While the input parameters change from operator to operator, it is always required to create three members:
+
+- ``dtype``: data type object (of type :obj:`str` or :obj:`np.dtype`) of the model and data;
+- ``shape``: a tuple containing the dimensions of the operator in the data and model space;
+- ``explicit``: a boolean (``True`` or ``False``) identifying if the operator can be inverted by a direct solver or
+  requires an iterative solver. This member is ``True`` if the operator has also a member ``A`` that contains
+  the matrix to be inverted like for example in the :py:class:`pylops.MatrixMult` operator, and it will be
+  ``False`` otherwise.
+
+In this specific case, we have another member called ``d`` which is equal to the input vector containing the diagonal
+elements of the matrix we want to multiply to the model and data.
 
 .. code-block:: python
 
@@ -62,7 +65,7 @@ of the matrix we want to multiply to the model and data.
         self.dtype = np.dtype(dtype)
         self.explicit = False
 
-Alternatively, since version 2.0.0, the recommended way of initializing operators derived from the base
+Alternatively, since version ``v2.0.0``, the recommended way of initializing operators derived from the base
 :py:class:`pylops.LinearOperator` class is to invoke ``super`` to assign the required attributes:
 
 .. code-block:: python
@@ -72,8 +75,14 @@ Alternatively, since version 2.0.0, the recommended way of initializing operator
         super().__init__(dtype=np.dtype(dtype), shape=(len(self.d), len(self.d)))
 
 In this case, there is no need to declare ``explicit`` as it already defaults to ``False``.
-Since version 2.0.0, every :py:class:`pylops.LinearOperator` class is imbued with ``dims``,
-``dimsd``, ``clinear`` and ``explicit``, in addition to the required ``dtype`` and ``shape``.
+
+Moreover, since version ``v2.0.0``, every :py:class:`pylops.LinearOperator` class is imbued with ``dims``,
+``dimsd``, and ``clinear`` in addition to the required ``dtype``, ``shape``, and ``explicit``. Note that
+``dims`` and ``dimsd`` can be defined in spite of ``shape``, which will be automatically assigned within the
+``super`` method: the main difference between ``dims``/``dimsd`` and ``shape`` is the the former variables can be
+used the define the n-dimensional nature of the input of an operator, whilst the latter variable refers to their overall
+shape when the input is flattened.
+
 See the docs of :py:class:`pylops.LinearOperator` for more information about what these
 attributes mean.
 
@@ -91,6 +100,10 @@ We will finally need to ``return`` the result of this operation:
     def _matvec(self, x):
         return self.d * x
 
+Note that since version ``v2.0.0``, this method can be decorated by the decorator ``@reshaped``. As discussed in
+more details in the decorator documentation, by adding such decorator the input ``x`` is initially reshaped into
+a nd-array of shape ``dims``, fed to the actual code in ``_matvec`` and then flattened.
+
 Adjoint mode (``_rmatvec``)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Finally we need to implement the *adjoint mode* in the method ``_rmatvec``. In other words, we will need to write
@@ -106,6 +119,10 @@ different from operator to operator):
 
 And that's it, we have implemented our first linear operator!
 
+Similar to ``_matvec``, since version ``v2.0.0``, this method can also be decorated by the decorator ``@reshaped``.
+When doing so, the input ``x`` is initially reshaped into
+a nd-array of shape ``dimsd``, fed to the actual code in ``_rmatvec`` and then flattened.
+
 Testing the operator
 --------------------
 Being able to write an operator is not yet a guarantee of the fact that the operator is correct, or in other words

docs/source/api/index.rst

@@ -29,6 +29,7 @@ Templates
     FunctionOperator
     MemoizeOperator
     TorchOperator
+    JaxOperator
 
 Basic operators
 ~~~~~~~~~~~~~~~
@@ -102,7 +103,9 @@ Signal processing
     Shift
     DWT
     DWT2D
+    DWTND
     DCT
+    DTCWT
     Seislet
     Radon2D
     Radon3D