Merge pull request #716 from PyLops/dev

v2.6.0

Author: mrava87

.github/workflows/build-mkl.yaml

@@ -0,0 +1,41 @@
+name: PyLops Testing with Intel oneAPI Math Kernel Library(oneMKL)
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+
+    runs-on: ${{ matrix.platform }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - 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/*
+    - uses: conda-incubator/setup-miniconda@v3.2.0
+      with:
+        use-mamba: true
+        channels: https://software.repos.intel.com/python/conda, conda-forge
+        conda-remove-defaults: true
+        python-version: ${{ matrix.python-version }}
+        activate-environment: mkl-test-env
+    - name: Install dependencies
+      run: |
+        conda install -y pyfftw
+        pip install -r requirements-intel-mkl.txt
+        pip install -r requirements-dev.txt
+        pip install -r requirements-torch.txt
+    - name: Install pylops
+      run: |
+        python -m setuptools_scm
+        pip install .
+    - name: Tests with pytest
+      run: |
+        pytest

.github/workflows/build.yaml

@@ -6,8 +6,8 @@ jobs:
   build:
     strategy:
       matrix:
-        platform: [ ubuntu-latest, macos-13 ]
-        python-version: ["3.10", ] # "3.11" temporarely removed due to issues with scikit-fmm
+        platform: [ ubuntu-latest, macos-latest ]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     runs-on: ${{ matrix.platform }}
     steps:
@@ -24,7 +24,14 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip install flake8 pytest
-        pip install -r requirements-dev.txt
+
+        if [[ "${{ matrix.platform }}" == ubuntu* ]]; then
+          pip install -r requirements-dev.txt
+          pip install -r requirements-pyfftw.txt
+        else
+          pip install -r requirements-dev-arm.txt
+          pip install -r requirements-pyfftw.txt
+        fi
         pip install -r requirements-torch.txt
     - name: Install pylops
       run: |

.github/workflows/buildcupy.yaml

@@ -8,28 +8,28 @@ jobs:
     steps:
       - name: Check out source repository
         uses: actions/checkout@v4
-      - name: Print checked code and check environments
+      - name: Set up Python environment and Install dependencies and pylops
         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 .
+          python3 -m venv .venv-pylops
+          # write install scripts
+          cat << 'EOF' > pylops_tests.sh
+          #!/bin/bash
+          PYTHON=.venv-pylops/bin/python3
+          PIP=.venv-pylops/bin/pip
+          ls $PYTHON
+          ls $PIP
+          $PIP install 
+          $PIP install --upgrade pip setuptools
+          $PIP install install flake8 pytest setuptools-scm
+          $PIP install -r requirements-dev-gpu.txt
+          $PIP install cupy-cuda12x
+          $PYTHON -m setuptools_scm
+          $PIP install .
+          EOF
+          srun --account=yuxilab -n 1 -N 1 --gres=gpu:L40S:1 bash pylops_tests.sh
       - name: Tests with pytest 
         run: |
-          export CUPY_PYLOPS=1; export TEST_CUPY_PYLOPS=1; 
-          source pylopsvenv/bin/activate 
-          pytest
+          export CUPY_PYLOPS=1; export TEST_CUPY_PYLOPS=1;
+          export PYTEST=.venv-pylops/bin/pytest
+          srun --account=yuxilab -n 1 -N 1 --gres=gpu:L40S:1 $PYTEST
+          echo "done!"

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

@@ -9,7 +9,7 @@ jobs:
     strategy:
       matrix:
         platform: [ ubuntu-latest, ]
-        python-version: ["3.10", ]
+        python-version: ["3.11", ]
 
     runs-on: ${{ matrix.platform }}
     steps:
@@ -27,6 +27,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install flake8 pytest
         pip install -r requirements-dev.txt
+        pip install -r requirements-pyfftw.txt
         pip install -r requirements-torch.txt
     - name: Install pylops
       run: |

.github/workflows/flake8.yaml

@@ -14,7 +14,7 @@ jobs:
       - name: Set up Python environment
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.11"
       - name: flake8 Lint
         uses: py-actions/flake8@v2
         with:

.gitignore

@@ -33,6 +33,7 @@ docs/build
 docs/source/api/generated
 docs/source/gallery
 docs/source/tutorials
+docs/source/sg_execution_times.rst
 
 # Pylint #
 pylint_plot.py

.readthedocs.yaml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.9"
+    python: "3.12"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

CHANGELOG.md

@@ -1,6 +1,40 @@
 Changelog
 =========
 
+# 2.6.0
+* Added `pylops.medical` module and `pylops.medical.CT2D` operator
+* Added `pylops.utils.signalprocessing.pwd_slope_estimate` and
+  `pylops.signalprocessing.PWSprayer2D` and `pylops.signalprocessing.PWSmoother2D`
+  operators
+* Added support for multithreading to `pylops.basicoperators.Block`,
+  `pylops.basicoperators.BlockDiag`, `pylops.basicoperators.HStack`, and
+  `pylops.basicoperators.VStack` (and ``parallel_kind`` parameter)
+* Added `kwargs_fft` to `pylops.waveeqprocessing.BlendingContinuous`,
+  `pylops.waveeqprocessing.BlendingGroup`, and
+  `pylops.waveeqprocessing.BlendingHalf`
+* Added ``nttot`` to `pylops.waveeqprocessing.BlendingContinuous`
+* Added ``fftengine`` to  `pylops.waveeqprocessing.PhaseShift`
+* Added ``mkl_fft`` engine to `pylops.signalprocessing.FFT`,
+  `pylops.signalprocessing.FFT2D`, and `pylops.signalprocessing.FFTND`
+* Added JAX backend to `pylops.signalprocessing.ChirpRadon2D` and
+  `pylops.signalprocessing.ChirpRadon3D` operators.
+* Added `pylops.optimization.callback.CostNanInfCallback`,
+  `pylops.optimization.callback.CostToDataCallback`, and
+  `pylops.optimization.callback.CostToInitialCallback` callbacks, and
+  and ``rtol`` and ``rtol1`` parameters in all solvers
+* Optimized internal handling of `pylops.basicoperators.Zero` operators in
+  `pylops.basicoperators.BlockDiag`, `pylops.basicoperators.HStack`, and
+  `pylops.basicoperators.VStack`
+* Homogenize error/warning/info messages across the library by switching to
+  ``logging/warning``
+* Fixed initialization of ``r`` and ``rw`` in `pylops.optimization.cls_sparsity.IRLS`
+* Fixed `pylops.optimization.cls_sparsity._halfthreshold` for complex valued CuPy arrays
+* Fixed initialization of ``decay`` in sparse solvers to correctly solve complex-valued
+  problems
+* Fixed bug when calling ``__pow__`` of a linear operator with CuPy arrays
+* Fixed dtype handling in `pylops.optimization.cls_sparsity.ISTA` and
+  `pylops.optimization.cls_sparsity.FISTA`
+
 # 2.5.0
 * Added `cuda` engine to `pylops.waveeqprocessing.Kirchhoff`
   operator
@@ -12,19 +46,19 @@ Changelog
 * Added `kwargs_fft` to `pylops.signalprocessing.FFT`,
   `pylops.signalprocessing.FFT2D`, and
   `pylops.signalprocessing.FFTND`
-* Fix bug in `pylops.waveeqprocessing.MDD` when using
+* Fixed 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`
+* Fixed bug in `pylops.signalprocessing.FourierRadon3D`
   in the default choice of `num_threads_per_blocks`
-* Fix bug in `pylops.signalprocessing.Convolve1D`
+* Fixed 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
+* Fixed bug in `pylops.optimization.cls_sparsity.OMP` avoiding
   passing `explicit` in the creation of `_ColumnLinearOperator`
-* Fix bug in `pylops.optimization.cls_sparsity.OMP` callback
+* Fixed 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`
+* Fixed bug in `pylops.waveeqprocessing.SeismicInterpolation`
   in calculation of `sampling` when not passed
 
 # 2.4.0
@@ -33,7 +67,7 @@ Changelog
 * Added `pylops.PyTensorOperator` operator
 * Added `pylops.ToCupy` operator
 * Added `pylops.utils.seismicevents.parabolic3d` method
-* Fix bug in `pylops.Restriction` when passing iava as cupy array
+* Fixed bug in `pylops.Restriction` when passing iava as cupy array
 
 # 2.3.1
 * Fixed bug in `pylops.utils.backend` (see [Issue #606](https://github.com/PyLops/pylops/issues/606))
@@ -336,7 +370,7 @@ To aid users in navigating the breaking changes, we provide the following docume
 * Added ``pylops.LinearOperator.asoperator`` method to
   ``pylops.LinearOperator``
 * Added ``pylops.utils.signalprocessing.slope_estimate`` function
-* Fix bug in ``pylops.signalprocessing.Radon2D`` and
+* Fixed bug in ``pylops.signalprocessing.Radon2D`` and
  ``pylops.signalprocessing.Radon3D`` when ``onthefly=True`` returning the
  same result as when ``onthefly=False``
 
@@ -348,7 +382,7 @@ To aid users in navigating the breaking changes, we provide the following docume
 * Added ``pylops.waveeqprocessing.PressureToVelocity``,
   ``pylops.waveeqprocessing.UpDownComposition3Doperator``, and
   ``pylops.waveeqprocessing.PhaseShift`` operators
-* Fix bug in ``pylops.basicoperators.Kronecker``
+* Fixed bug in ``pylops.basicoperators.Kronecker``
   (see [Issue #125](https://github.com/PyLops/pylops/issues/125))
 
 # 1.7.0

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 dev-install_gpu install_conda dev-install_conda dev-install_conda_arm tests tests_cpu_ongpu tests_gpu doc docupdate servedoc lint typeannot coverage
+.PHONY: install dev-install dev-install_intel_mkl dev-install_gpu install_conda dev-install_conda dev-install_conda_intel_mkl dev-install_conda_arm tests tests_cpu_ongpu tests_gpu doc docupdate servedoc lint typeannot coverage
 
 pipcheck:
 ifndef PIP
@@ -22,6 +22,13 @@ install:
 dev-install:
 	make pipcheck
 	$(PIP) install -r requirements-dev.txt &&\
+	$(PIP) install -r requirements-pyfftw.txt &&\
+	$(PIP) install -r requirements-torch.txt && $(PIP) install -e .
+
+dev-install_intel_mkl:
+	make pipcheck
+	$(PIP) install -r requirements-intel-mkl.txt &&\
+	$(PIP) install -r requirements-dev.txt &&\
 	$(PIP) install -r requirements-torch.txt && $(PIP) install -e .
 
 dev-install_gpu:
@@ -30,16 +37,19 @@ dev-install_gpu:
 	$(PIP) install -e .
 
 install_conda:
-	conda env create -f environment.yml && conda activate pylops && pip install .
+	conda env create -f environment.yml && source ${CONDA_PREFIX}/etc/profile.d/conda.sh && conda activate pylops && pip install .
 
 dev-install_conda:
-	conda env create -f environment-dev.yml && conda activate pylops && pip install -e .
+	conda env create -f environment-dev.yml && source ${CONDA_PREFIX}/etc/profile.d/conda.sh && conda activate pylops && pip install -e .
+
+dev-install_conda_intel_mkl:
+	conda env create -f environment-dev-intel-mkl.yml && source ${CONDA_PREFIX}/etc/profile.d/conda.sh && conda activate pylops && pip install -e .
 
 dev-install_conda_arm:
-	conda env create -f environment-dev-arm.yml && conda activate pylops && pip install -e .
+	conda env create -f environment-dev-arm.yml && source ${CONDA_PREFIX}/etc/profile.d/conda.sh && 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 .
+	conda env create -f environment-dev-gpu.yml && source ${CONDA_PREFIX}/etc/profile.d/conda.sh && conda activate pylops_gpu && pip install -e .
 
 tests:
 	# Run tests with CPU

README.md

@@ -152,3 +152,5 @@ A list of video tutorials to learn more about PyLops:
 * Alex Rakowski, alex-rakowski
 * David Sollberger, solldavid
 * Gustavo Coelho, guaacoelho
+* Shaowen Wang, GeophyAI
+* Francesco Brandolin, FB-I