Merge pull request #674 from PyLops/dev

Release v2.5.0

Author: mrava87

.github/workflows/build.yaml

@@ -1,4 +1,4 @@
-name: PyLops
+name: PyLops Testing
 
 on: [push, pull_request]
 
@@ -7,7 +7,7 @@ jobs:
     strategy:
       matrix:
         platform: [ ubuntu-latest, macos-13 ]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", ] # "3.11" temporarely removed due to issues with scikit-fmm
 
     runs-on: ${{ matrix.platform }}
     steps:
@@ -30,6 +30,6 @@ jobs:
       run: |
         python -m setuptools_scm
         pip install .
-    - name: Test with pytest
+    - name: Tests with pytest
       run: |
         pytest

.github/workflows/buildcupy.yaml

@@ -0,0 +1,35 @@
+name: PyLops Testing (CuPy)
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: self-hosted
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v4
+      - name: Print checked code and check environments
+        run: |
+          ls -lah
+          echo $(pwd)
+          echo $(which python3)
+          echo $(which pip3)
+      - name: Set up Python environment and Install dependencies
+        run: |
+          python3 -m venv pylopsvenv 
+          source pylopsvenv/bin/activate 
+          echo $(which python3)
+          echo $(which pip3)
+          python3 -m pip install --upgrade pip setuptools
+          pip install flake8 pytest setuptools-scm
+          pip install -r requirements-dev-gpu.txt
+      - name: Install pylops
+        run: |
+          source pylopsvenv/bin/activate 
+          python3 -m setuptools_scm
+          pip install .
+      - name: Tests with pytest 
+        run: |
+          export CUPY_PYLOPS=1; export TEST_CUPY_PYLOPS=1; 
+          source pylopsvenv/bin/activate 
+          pytest

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

@@ -9,7 +9,7 @@ jobs:
     strategy:
       matrix:
         platform: [ ubuntu-latest, ]
-        python-version: ["3.9", ]
+        python-version: ["3.10", ]
 
     runs-on: ${{ matrix.platform }}
     steps:

CHANGELOG.md

@@ -1,6 +1,32 @@
 Changelog
 =========
 
+# 2.5.0
+* Added `cuda` engine to `pylops.waveeqprocessing.Kirchhoff`
+  operator
+* Added `Opbasis` and `optimal_coeff` to
+  `pylops.optimization.cls_sparsity.OMP`
+* Added `solver` to the input parameters of the `_oneshot`
+  internal methods of `pylops.waveeqprocessing.AcousticWave2D`
+  to avoid recreating it for every shot
+* Added `kwargs_fft` to `pylops.signalprocessing.FFT`,
+  `pylops.signalprocessing.FFT2D`, and
+  `pylops.signalprocessing.FFTND`
+* Fix bug in `pylops.waveeqprocessing.MDD` when using
+  CuPy arrays for `G` and `d` with `twosided=True` and `add_negative=True`
+* Fix bug in `pylops.signalprocessing.FourierRadon3D`
+  in the default choice of `num_threads_per_blocks`
+* Fix bug in `pylops.signalprocessing.Convolve1D`
+  in the definition of `pad` and `padd` when applying the
+  operator to a CuPy array
+* Fix bug in `pylops.optimization.cls_sparsity.OMP` avoiding
+  passing `explicit` in the creation of `_ColumnLinearOperator`
+* Fix bug in `pylops.optimization.cls_sparsity.OMP` callback
+  method as `cols` was not passed not allowing ``x`` to be
+  properly reconstructed
+* Fix bug in `pylops.waveeqprocessing.SeismicInterpolation`
+  in calculation of `sampling` when not passed
+
 # 2.4.0
 * Added `pylops.signalprocessing.FourierRadon2d` and
   `pylops.signalprocessing.FourierRadon3d` operators

CONTRIBUTING.md

@@ -63,6 +63,12 @@ that the both old and new tests pass successfully:
     make tests
     ```
 
+If you have access to a GPU, it is advised also that old and new tests run with the CuPy
+backend pass successfully:
+    ```
+    make tests_gpu
+    ```
+
 4. Run flake8 to check the quality of your code:
     ```
     make lint

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 servedoc lint typeannot coverage
+.PHONY: install dev-install dev-install_gpu install_conda dev-install_conda dev-install_conda_arm tests tests_cpu_ongpu tests_gpu doc docupdate servedoc lint typeannot coverage
 
 pipcheck:
 ifndef PIP
@@ -24,6 +24,11 @@ dev-install:
 	$(PIP) install -r requirements-dev.txt &&\
 	$(PIP) install -r requirements-torch.txt && $(PIP) install -e .
 
+dev-install_gpu:
+	make pipcheck
+	$(PIP) install -r requirements-dev-gpu.txt &&\
+	$(PIP) install -e .
+
 install_conda:
 	conda env create -f environment.yml && conda activate pylops && pip install .
 
@@ -33,10 +38,24 @@ dev-install_conda:
 dev-install_conda_arm:
 	conda env create -f environment-dev-arm.yml && conda activate pylops && pip install -e .
 
+dev-install_conda_gpu:
+	conda env create -f environment-dev-gpu.yml && conda activate pylops_gpu && pip install -e .
+
 tests:
+	# Run tests with CPU
 	make pythoncheck
 	pytest
 
+tests_cpu_ongpu:
+	# Run tests with CPU on a system with GPU (and CuPy installed)
+	make pythoncheck
+	export CUPY_PYLOPS=0 && export TEST_CUPY_PYLOPS=0 && pytest
+
+tests_gpu:
+	# Run tests with GPU (requires CuPy to be installed)
+	make pythoncheck
+	export TEST_CUPY_PYLOPS=1 && pytest
+
 doc:
 	cd docs  && rm -rf source/api/generated && rm -rf source/gallery &&\
 	rm -rf source/tutorials && rm -rf build && make html && cd ..

azure-pipelines.yml

@@ -18,25 +18,26 @@ jobs:
 #   displayName: 'Windows'
 #
 #   pool:
-#     vmImage: 'windows-2019'
+#     vmImage: 'windows-2025'
 #
 #   variables:
 #     NUMBA_NUM_THREADS: 1
 #
 #   steps:
 #   - task: UsePythonVersion@0
 #     inputs:
-#       versionSpec: '3.9'
+#       versionSpec: '3.10'
 #       architecture: 'x64'
 #
 #   - script: |
 #       python -m pip install --upgrade pip setuptools wheel django
 #       pip install -r requirements-dev.txt
+#       pip install -r requirements-torch.txt
 #       pip install .
 #     displayName: 'Install prerequisites and library'
 #
 #   - script: |
-#       python setup.py test
+#       pytest
 #     condition: succeededOrFailed()
 #     displayName: 'Run tests'
 
@@ -55,7 +56,7 @@ jobs:
   steps:
   - task: UsePythonVersion@0
     inputs:
-      versionSpec: '3.9'
+      versionSpec: '3.10'
       architecture: 'x64'
 
   - script: |
@@ -85,7 +86,7 @@ jobs:
   steps:
   - task: UsePythonVersion@0
     inputs:
-      versionSpec: '3.9'
+      versionSpec: '3.10'
       architecture: 'x64'
 
   - script: |

docs/source/changelog.rst

@@ -3,6 +3,37 @@
 Changelog
 =========
 
+Version 2.5.0
+-------------
+
+*Released on: 21/06/2025*
+
+* Added `cuda` engine to :py:class:`pylops.waveeqprocessing.Kirchhoff` 
+  operator
+* Added `Opbasis` and `optimal_coeff` to 
+  :py:class:`pylops.optimization.cls_sparsity.OMP`
+* Added `solver` to the input parameters of the `_oneshot`
+  internal methods of :py:class:`pylops.waveeqprocessing.AcousticWave2D`
+  to avoid recreating it for every shot
+* Added `kwargs_fft` to `pylops.signalprocessing.FFT`,
+  :py:class:`pylops.signalprocessing.FFT2D`, and 
+  :py:class:`pylops.signalprocessing.FFTND`
+* Fix bug in :py:func:`pylops.waveeqprocessing.MDD` when using
+  CuPy arrays for `G` and `d` with `twosided=True` and `add_negative=True`
+* Fix bug in :py:class:`pylops.signalprocessing.FourierRadon3D` 
+  in the default choice of `num_threads_per_blocks`
+* Fix bug in :py:class:`pylops.signalprocessing.Convolve1D` 
+  in the definition of `pad` and `padd` when applying the 
+  operator to a CuPy array
+* Fix bug in :py:class:`pylops.optimization.cls_sparsity.OMP` avoiding 
+  passing `explicit` in the creation of `_ColumnLinearOperator`
+* Fix bug in :py:class:`pylops.optimization.cls_sparsity.OMP` callback 
+  method as `cols` was not passed not allowing ``x`` to be 
+  properly reconstructed
+* Fix bug in :py:func:`pylops.waveeqprocessing.SeismicInterpolation` 
+  in calculation of `sampling` when not passed
+
+
 Version 2.4.0
 -------------
 
@@ -189,7 +220,7 @@ 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:class:`pylops.waveeqprocessing.seismicinterpolation.SeismicInterpolation`
+* Added `chirp-sliding` kind to :py:func:`pylops.waveeqprocessing.SeismicInterpolation`
 * Fixed bug due to the new internal structure of `LinearOperator` submodule introduced in `scipy1.8.0`
 
 
@@ -389,7 +420,7 @@ Version 1.9.1
   :py:class:`pylops.signalprocessing.FFT2D` to ensure that the type of the input
   vector is retained when applying forward and adjoint.
 * Added ``dtype`` parameter to the ``FFT`` calls in the definition of the
-  :py:class:`pylops.waveeqprocessing.MDD` operation. This ensure that the type
+  :py:func:`pylops.waveeqprocessing.MDD` operation. This ensure that the type
   of the real part of ``G`` input is enforced to the output vectors of the
   forward and adjoint operations.
 

docs/source/contributing.rst

@@ -75,6 +75,13 @@ that the both old and new tests pass successfully:
 
    >> make tests
 
+If you have access to a GPU, it is advised also that old and new tests run with the CuPy 
+backend pass successfully:
+
+.. code-block:: bash
+
+   >> make tests_gpu
+
 4. Run flake8 to check the quality of your code:
 
 .. code-block:: bash

docs/source/gpu.rst

@@ -32,6 +32,20 @@ be also wrapped into a :class:`pylops.JaxOperator`.
 See below for a comphrensive list of supported operators and additional functionalities for both the
 ``cupy`` and ``jax`` backends.
 
+Install dependencies
+--------------------
+GPU-enabled development environments can created using ``conda`` 
+
+.. code-block:: bash
+
+   >> make dev-install_conda_gpu
+
+or ``pip``
+
+.. code-block:: bash
+
+   >> make dev-install_gpu
+
 
 Examples
 --------