From 6dfc9f8fac712f1ead4c2d71b75ef8327a60567e Mon Sep 17 00:00:00 2001 From: mrava87 Date: Thu, 12 Mar 2026 22:58:24 +0000 Subject: [PATCH 1/5] doc: started to update documentation --- Makefile | 26 +- docs/source/_static/style.css | 117 - docs/source/adding.rst | 20 +- docs/source/addingsolver.rst | 7 +- docs/source/api/index.rst | 4 +- docs/source/api/others.rst | 4 +- docs/source/changelog.rst | 4 +- docs/source/citing.rst | 5 +- docs/source/conf.py | 21 +- docs/source/contributing.rst | 10 +- docs/source/credits.rst | 4 +- docs/source/extensions.rst | 4 +- docs/source/faq.rst | 6 +- docs/source/gpu.rst | 19 +- docs/source/index.rst | 33 +- docs/source/installation.rst | 208 +- docs/source/papers.rst | 5 +- docs/source/roadmap.rst | 29 +- environment-dev-arm.yml | 7 +- environment-dev-gpu.yml | 7 +- environment-dev-intel-mkl.yml | 7 +- environment-dev.yml | 7 +- examples/README.txt | 4 +- requirements-dev-arm.txt | 3 +- requirements-dev-gpu.txt | 3 +- requirements-dev.txt | 3 +- requirements-doc.txt | 3 +- tutorials/README.txt | 4 +- uv.lock | 4325 +++++++++++++++++++++++++++++++++ 29 files changed, 4610 insertions(+), 289 deletions(-) delete mode 100644 docs/source/_static/style.css create mode 100644 uv.lock diff --git a/Makefile b/Makefile index 64940b37..096720cb 100644 --- a/Makefile +++ b/Makefile @@ -1,7 +1,10 @@ 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) +UV := $(shell command -v uv 2> /dev/null || command which uv 2> /dev/null) +NOX := $(shell command -v nox 2> /dev/null || command which nox 2> /dev/null) -.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 +.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 +.PHONY: tests tests_cpu_ongpu tests_gpu doc docupdate servedoc lint typeannot coverage pipcheck: ifndef PIP @@ -15,6 +18,18 @@ ifndef PYTHON endif @echo Using python: $(PYTHON) +uvcheck: +ifndef UV + $(error "Ensure uv is in your PATH") +endif + @echo Using uv: $(UV) + +noxcheck: +ifndef NOX + $(error "Ensure nox is in your PATH") +endif + @echo Using nox: $(NOX) + install: make pipcheck $(PIP) install -r requirements.txt && $(PIP) install . @@ -51,11 +66,20 @@ dev-install_conda_arm: dev-install_conda_gpu: conda env create -f environment-dev-gpu.yml && source ${CONDA_PREFIX}/etc/profile.d/conda.sh && conda activate pylops_gpu && pip install -e . +dev-install_uv: + make uvcheck + $(UV) sync --locked --all-extras --all-groups + tests: # Run tests with CPU make pythoncheck pytest +tests_uv: + # Run tests with CPU + make uvcheck + $(UV) run pytest + tests_cpu_ongpu: # Run tests with CPU on a system with GPU (and CuPy installed) make pythoncheck diff --git a/docs/source/_static/style.css b/docs/source/_static/style.css deleted file mode 100644 index 94b9bef8..00000000 --- a/docs/source/_static/style.css +++ /dev/null @@ -1,117 +0,0 @@ -/* To stick the footer to the bottom of the page */ -html { -} - -body { - font-family: 'Open Sans', sans-serif; -} - -h1, h2, h3, h4 { - font-weight: 300; - font-family: "Open Sans",sans-serif; -} - -h1 { - font-size: 200%; -} - -.sidebar-title { - margin-top: 10px; - margin-bottom: 0px; -} - -.banner { - padding-bottom: 60px; - text-align: center; -} - -.banner img { - margin-bottom: 40px; -} - -.api-module { - margin-bottom: 80px; -} - -.youtube-embed { - max-width: 600px; - margin-bottom: 24px; -} - -.video-container { - position:relative; - padding-bottom:56.25%; - padding-top:30px; - height:0; - overflow:hidden; -} - -.video-container iframe, .video-container object, .video-container embed { - position:absolute; - top:0; - left:0; - width:100%; - height:100%; -} - -.wy-nav-content { - max-width: 1000px; -} - -.wy-nav-top { - background-color: #555555; -} - -.wy-side-nav-search { - background-color: #555555; -} - -.wy-side-nav-search > a img.logo { - width: 50%; -} - -.wy-side-nav-search input[type="text"] { - border-color: #555555; -} - -/* Remove the padding from the Parameters table */ -.rst-content table.field-list .field-name { - padding-left: 0px; -} - -/* Lign up the Parameters section with the descriptions */ -.rst-content table.field-list td { - padding-top: 8px; -} - -.rst-content .highlight > pre { - font-size: 14px; -} - -.rst-content img { - max-width: 100%; -} - -.source-link { - float: right; -} - -.strike { - text-decoration: line-through; -} - -/* Don't let the edit and notebook download links disappear on mobile. */ -@media screen and (max-width: 480px) { - .wy-breadcrumbs li.source-link { - float:none; - display: block; - margin-top: 20px; - } -} - -/* Sphinx-Gallery */ -/****************************************************************************/ -/* Don't let captions be italic */ -.rst-content div.figure p.caption { - font-style: normal; -} \ No newline at end of file diff --git a/docs/source/adding.rst b/docs/source/adding.rst index 4420b157..1c9be8e6 100755 --- a/docs/source/adding.rst +++ b/docs/source/adding.rst @@ -1,7 +1,8 @@ .. _addingoperator: -Implementing new operators -========================== +|:paintbrush:| 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 a simplified version of the @@ -10,7 +11,7 @@ to the model in forward mode and to the data in adjoint mode. Creating the operator ---------------------- +********************* The first thing we need to do is to create a new file with the name of the operator we would like to implement. Note that as the operator will be a class, we need to follow the UpperCaseCamelCase convention both for the class itself and for the filename. @@ -42,7 +43,7 @@ input parameters and a ``Notes`` section providing a mathematical explanation of some of the core operators of PyLops to get a feeling of the level of details of the mathematical explanation. 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: @@ -87,7 +88,7 @@ See the docs of :py:class:`pylops.LinearOperator` for more information about wha attributes mean. Forward mode (``_matvec``) -^^^^^^^^^^^^^^^^^^^^^^^^^^ +========================== We can then move onto writing the *forward mode* in the method ``_matvec``. In other words, we will need to write the piece of code that will implement the following operation :math:`\mathbf{y} = \mathbf{A}\mathbf{x}`. Such method is always composed of two inputs (the object itself ``self`` and the input model ``x``). @@ -105,7 +106,7 @@ more details in the decorator documentation, by adding such decorator the input 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 the piece of code that will implement the following operation :math:`\mathbf{x} = \mathbf{A}^H\mathbf{y}`. Such method is also composed of two inputs (the object itself ``self`` and the input data ``y``). @@ -123,8 +124,9 @@ Similar to ``_matvec``, since version ``v2.0.0``, this method can also be decora 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 that the adjoint code is actually the *adjoint* of the forward code. Luckily for us, a simple test can be performed to check the validity of forward and adjoint operators, the so called *dot-test*. @@ -170,7 +172,7 @@ model tested towards the input model. Documenting the operator ------------------------- +************************ Once the operator has been created, we can add it to the documentation of PyLops. To do so, simply add the name of the operator within the ``index.rst`` file in ``docs/source/api`` directory. @@ -180,7 +182,7 @@ can be used as template. Final checklist ---------------- +*************** Before submitting your new operator for review, use the following **checklist** to ensure that your code adheres to the guidelines of PyLops: diff --git a/docs/source/addingsolver.rst b/docs/source/addingsolver.rst index fbd32122..d3866497 100755 --- a/docs/source/addingsolver.rst +++ b/docs/source/addingsolver.rst @@ -1,11 +1,12 @@ .. _addingsolver: -Implementing new solvers -======================== +|:fire:| Implementing new solvers +################################# + Users are welcome to create new solvers and add them to the PyLops library. In this tutorial, we will go through the key steps in the definition of a solver, using a -sligthly simplified version of :py:class:`pylops.optimization.basic.CG` as an example. +sligthly simplified version of :py:class:`pylops.optimization.cls_basic.CG` as an example. .. note:: In case the solver that you are planning to create falls within the category of proximal solvers, diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst index 374657f5..145c4b96 100755 --- a/docs/source/api/index.rst +++ b/docs/source/api/index.rst @@ -1,7 +1,7 @@ .. _api: -PyLops API -========== +|:wrench:| PyLops API +===================== The Application Programming Interface (API) of PyLops can be loosely seen as composed of a stack of three main layers: diff --git a/docs/source/api/others.rst b/docs/source/api/others.rst index 6eb19031..470740fa 100755 --- a/docs/source/api/others.rst +++ b/docs/source/api/others.rst @@ -1,8 +1,8 @@ .. _others: +|:nut_and_bolt:| PyLops Utilities +================================= -PyLops Utilities -================ Alongside with its *Linear Operators* and *Solvers*, PyLops contains also a number of auxiliary routines performing universal tasks that are used by several operators or simply within one or more :ref:`tutorials` for the preparation of input data and subsequent visualization of results. diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index ce416c22..d09fb90b 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -1,7 +1,7 @@ .. _changlog: -Changelog -========= +|:newspaper_roll:| Changelog +############################ Version 2.6.0 diff --git a/docs/source/citing.rst b/docs/source/citing.rst index b8adfb18..888af854 100755 --- a/docs/source/citing.rst +++ b/docs/source/citing.rst @@ -1,7 +1,8 @@ .. _citing: -How to cite -=========== +|:pencil2:| How to cite +####################### + When using PyLops in scientific publications, please cite the following paper: .. raw:: html diff --git a/docs/source/conf.py b/docs/source/conf.py index 568c7c31..f8f6203d 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -22,9 +22,10 @@ "matplotlib.sphinxext.plot_directive", "numpydoc", "nbsphinx", + "sphinx_design", + "sphinx_iconify", "sphinx_gallery.gen_gallery", "sphinxemoji.sphinxemoji", - # 'sphinx.ext.napoleon', ] # intersphinx configuration @@ -124,15 +125,12 @@ html_show_copyright = True # Theme config -html_theme = "pydata_sphinx_theme" +html_theme = "shibuya" html_theme_options = { + "accent_color": "teal", "github_url": "https://github.com/PyLops/pylops", - # "logo_only": True, - # "display_version": True, - "logo": { - "image_light": "pylops_b.png", - "image_dark": "pylops.png", - } + "light_logo": "_static/pylops_b.png", + "dark_logo": "_static/pylops.png", } html_css_files = [ "css/custom.css", @@ -160,9 +158,4 @@ "github_project": "PyLops", "github_repo": "pylops", "github_version": "master", -} - - -# Load the custom CSS files (needs sphinx >= 1.6 for this to work) -def setup(app): - app.add_css_file("style.css") +} \ No newline at end of file diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 8b8eb9d5..b5140625 100755 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -1,7 +1,7 @@ .. _contributing: -Contributing -############ +|:heart:| Contributing +###################### Contributions are welcome and greatly appreciated! @@ -12,7 +12,6 @@ open new *Issues* directly from the `GitHub repo `_ for operator/feature requests or bugfixes. - Add examples or improve documentation ===================================== @@ -124,8 +121,9 @@ Before you submit a pull request, check that it meets these guidelines: 2. If the pull request adds functionality, the docs should be updated accordingly. 3. Ensure that the updated code passes all tests. + Project structure -################# +***************** This repository is organized as follows: * **pylops**: Python library containing various linear operators and auxiliary routines diff --git a/docs/source/credits.rst b/docs/source/credits.rst index 755b3966..e5163889 100755 --- a/docs/source/credits.rst +++ b/docs/source/credits.rst @@ -1,7 +1,7 @@ .. _credits: -Contributors -============ +|:people_holding_hands:| Contributors +##################################### * `Matteo Ravasi `_, mrava87 * `Carlos da Costa `_, cako diff --git a/docs/source/extensions.rst b/docs/source/extensions.rst index 25220df5..768a3e79 100755 --- a/docs/source/extensions.rst +++ b/docs/source/extensions.rst @@ -1,7 +1,7 @@ .. _extensions: -Extensions -========== +|:link:| Extensions +################### PyLops brings to users the power of linear operators in a simple and easy to use programming interface. diff --git a/docs/source/faq.rst b/docs/source/faq.rst index 61ac7a3c..90d03d5b 100755 --- a/docs/source/faq.rst +++ b/docs/source/faq.rst @@ -1,7 +1,7 @@ .. _faq: -Frequenty Asked Questions -========================= +|:question:| Frequenty Asked Questions +###################################### **1. Can I visualize my operator?** @@ -14,7 +14,7 @@ working with linear operators is indeed that you don't really need to access the of an operator. -**2. Can I have an older version of** ``cupy`` **installed in my system (** ``cupy-cudaXX<10.6.0``**)?** +**2. Can I have an older version of** ``cupy`` **installed in my system (** ``cupy-cudaXX<10.6.0`` **)?** Yes. Nevertheless you need to tell PyLops that you don't want to use its ``cupy`` backend by setting the environment variable ``CUPY_PYLOPS=0``. diff --git a/docs/source/gpu.rst b/docs/source/gpu.rst index 957f5413..0a07ad10 100755 --- a/docs/source/gpu.rst +++ b/docs/source/gpu.rst @@ -1,10 +1,11 @@ .. _gpu: -GPU / TPU Support -================= +|:video_game:| GPU / TPU Support +################################ Overview --------- +******** + From ``v1.12.0``, PyLops supports computations on GPUs powered by `CuPy `_ (``cupy-cudaXX>=13.0.0``). This library must be installed *before* PyLops is installed. @@ -32,8 +33,10 @@ 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 @@ -48,12 +51,12 @@ or ``pip`` Examples --------- +******** Let's now briefly look at some use cases. End-to-end GPU powered inverse problems -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +======================================= First we consider the most common scenario when both the model and data vectors fit onto the GPU memory. We can therefore simply replace all our @@ -122,7 +125,7 @@ Again, the code is almost unchanged apart from the fact that we now use ``jax`` Mixed CPU-GPU powered inverse problems -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +====================================== Let us now consider a more intricate scenario where we have access to a GPU-powered operator, however the model and/or data vectors are too large @@ -208,7 +211,7 @@ These features are currently not available for ``jax`` arrays. Supported Operators -------------------- +******************* In the following, we provide a list of methods in :class:`pylops.LinearOperator` with their current status (available on CPU, GPU with CuPy, and GPU with JAX): diff --git a/docs/source/index.rst b/docs/source/index.rst index 1a8f5a43..0f085cfb 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,5 +1,6 @@ -Overview -======== +PyLops +====== + PyLops is an open-source Python library focused on providing a backend-agnostic, idiomatic, matrix-free library of linear operators and related computations. It is inspired by the iconic MATLAB `Spot – A Linear-Operator Toolbox `_ project. @@ -72,23 +73,23 @@ It is a flexible and scalable python library for large-scale optimization with l that can be tailored to our needs, and as contribution to the free software community. Since June 2021, PyLops is a `NUMFOCUS `_ Affiliated Project. + .. toctree:: :maxdepth: 1 :hidden: - :caption: Getting started + :caption: Getting started: - self installation.rst gpu.rst extensions.rst tutorials/index.rst gallery/index.rst - FAQs + faq.rst .. toctree:: :maxdepth: 2 :hidden: - :caption: Reference documentation + :caption: Reference documentation: api/index.rst api/others.rst @@ -96,13 +97,13 @@ PyLops is a `NUMFOCUS - Implementing new solvers - Contributing - Changelog - Roadmap - Papers using PyLops - How to cite - Credits + :caption: Getting involved: + + adding.rst + addingsolver.rst + contributing.rst + changelog.rst + roadmap.rst + papers.rst + citing.rst + credits.rst diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 669994f6..d0d829a3 100755 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -1,7 +1,7 @@ .. _installation: -Installation -############ +|:desktop_computer:| Installation +################################# Dependencies ************ @@ -13,52 +13,73 @@ Required dependencies are limited to: * `NumPy `_ * `SciPy `_ -We highly encourage using the `Anaconda Python distribution `_ +We encourage using the `Anaconda Python distribution `_ or its standalone package manager `Conda `_. -Especially for Intel processors, this ensures a higher performance with no configuration. +Especially for Intel processors, this ensures a higher performance with no configuration (e.g., +the linking to ``Intel MKL`` library, a highly optimized BLAS library created by Intel). If you are interested in getting the best code performance, read carefully :ref:`Performance`. -For learning, however, the standard installation is often good enough. + +For learning, however, the standard installation is often good enough; in that case, we +recommend using `uv `_, a modern Python package manager that +is easy to use and has a very fast dependency resolver. Some operators have additional, optional "engines" to improve their performance. -These often rely on third-party libraries which are added to the -list of our optional dependencies. -Optional dependencies therefore refer to those dependencies that are not strictly -needed nor installed directly as part of a standard installation. +These often rely on third-party libraries which are added to the list of our optional +dependencies. Optional dependencies therefore refer to those dependencies that are not +strictly needed nor installed directly as part of a standard installation. For details more details, see :ref:`Optional`. Step-by-step installation for users *********************************** -Conda (recommended) -=================== -If using ``conda``, install our ``conda-forge`` distribution via: +From Package Manager +==================== +First install `pylops` with your package manager of choice. -.. code-block:: bash +.. tab-set:: - >> conda install --channel conda-forge pylops + .. tab-item:: :iconify:`devicon:anaconda` conda -Using the ``conda-forge`` distribution is recommended as all the dependencies (both required -and optional) will be automatically installed for you. + .. code-block:: bash -Pip -=== -If you are using ``pip``, and simply type the following command in your terminal -to install the PyPI distribution: + >> conda install --channel conda-forge pylops -.. code-block:: bash + which installs also the *required* dependencies, if not already present + in your environment. + + .. tab-item:: :iconify:`material-icon-theme:uv` uv + + .. code-block:: bash - >> pip install pylops + >> uv add pylops + + which installs also the *required* dependencies, if not already present + in your environment. To also install some of the optional dependencies + (namely ``numba``, ``pyfftw``, ``PyWavelets``, ``scikit-fmm``, ``spgl1``, + ``dtcwt``, ``astra-toolbox``), run: + + .. code-block:: bash -Note that when installing via ``pip``, only *required* dependencies are installed. + >> uv add "pylops[advanced]" From Source =========== -To access the latest source from github: +To access the latest source from GitHub: -.. code-block:: bash +.. tab-set:: + + .. tab-item:: :iconify:`devicon:pypi` pip + + .. code-block:: bash + + >> pip install https://github.com/PyLops/pylops.git@dev - >> pip install https://github.com/PyLops/pylops.git@dev + .. tab-item:: :iconify:`material-icon-theme:uv` uv + + .. code-block:: bash + + >> uv add git+https://github.com/PyLops/pylops.git --branch dev Docker ====== @@ -82,6 +103,7 @@ A larger image with ``conda`` a distribution is also available: >> docker run -it -v /path/to/local/folder:/home/jupyter/notebook -p 8888:8888 mrava87/pylops:conda_notebook + .. _DevInstall: Step-by-step installation for developers @@ -101,35 +123,44 @@ Install dependencies We recommend installing dependencies into a separate environment. For that end, we provide a `Makefile` with useful commands for setting up the environment. -Conda (recommended) -------------------- -For a ``conda`` environment, run +.. tab-set:: -.. code-block:: bash - - >> make dev-install_conda # for x86 (Intel or AMD CPUs) - >> make dev-install_conda_arm # for arm (M-series Mac) + .. tab-item:: conda -This will create and activate an environment called ``pylops``, with all required and optional dependencies. + .. code-block:: bash -Pip ---- -If you prefer a ``pip`` installation, we provide the following command + >> make dev-install_conda # for x86 (Intel or AMD CPUs) + >> make dev-install_conda_arm # for arm (M-series Mac) + + This creates and activate an environment called ``pylops``, with + all required and optional dependencies. -.. code-block:: bash + .. tab-item:: :iconify:`material-icon-theme:uv` uv - >> make dev-install + .. code-block:: bash -Note that, differently from the ``conda`` command, the above **will not** create a virtual environment. -Make sure you create and activate your environment previously. + >> make dev-install_uv + + This creates a virtual environment `.venv` that can be activated at + any time with `source .venv/bin/activate` (Linux/macOS). Run tests ========= To ensure that everything has been setup correctly, run tests: -.. code-block:: bash +.. tab-set:: + + .. tab-item:: :iconify:`devicon:anaconda` conda + + .. code-block:: bash - >> make tests + >> make tests + + .. tab-item:: :iconify:`material-icon-theme:uv` uv + + .. code-block:: bash + + >> make tests_uv Make sure no tests fail, this guarantees that the installation has been successful. @@ -149,7 +180,6 @@ From then on, you can pull changes (for example, in the dev branch) with: >> git pull upstream dev - Install pre-commit hooks ======================== To ensure consistency in the coding style of our developers we rely on @@ -159,35 +189,75 @@ that have been configured in the ``.pre-commit-config.yaml`` file. In order to setup such hooks in your local repository, run: -.. code-block:: bash +.. tab-set:: + + .. tab-item:: :iconify:`devicon:anaconda` conda + + .. code-block:: bash - >> pre-commit install + >> pre-commit install + + .. tab-item:: :iconify:`material-icon-theme:uv` uv + + .. code-block:: bash + + >> uv run pre-commit install Once this is set up, when committing changes, ``pre-commit`` will reject and "fix" your code by running the proper hooks. At this point, the user must check the changes and then stage them before trying to commit again. Final steps =========== -PyLops does not enforce the use of a linter as a pre-commit hook, but we do highly encourage using one before submitting a Pull Request. -A properly configured linter (``flake8``) can be run with: +PyLops does enforce the use of a linter (``ruff``), which is run both as a pre-commit hook and as a GitHub Action. +The linter can also be run locally with: -.. code-block:: bash +.. tab-set:: + + .. tab-item:: :iconify:`devicon:anaconda` conda + + .. code-block:: bash + + >> make lint + + .. tab-item:: :iconify:`material-icon-theme:uv` uv + + .. code-block:: bash - >> make lint + >> make lint_uv In addition, it is highly encouraged to build the docs prior to submitting a Pull Request. Apart from ensuring that docstrings are properly formatted, they can aid in catching bugs during development. Build (or update) the docs with: -.. code-block:: bash +.. tab-set:: + + .. tab-item:: :iconify:`devicon:anaconda` conda + + .. code-block:: bash + + >> make doc + + .. tab-item:: :iconify:`material-icon-theme:uv` uv - >> make doc + .. code-block:: bash + + >> make doc_uv or -.. code-block:: bash +.. tab-set:: + + .. tab-item:: :iconify:`devicon:anaconda` conda - >> make docupdate + .. code-block:: bash + + >> make docupdate + + .. tab-item:: :iconify:`material-icon-theme:uv` uv + + .. code-block:: bash + + >> make docupdate_uv .. _Performance: @@ -232,7 +302,6 @@ These are an option for an environment without ``conda`` that needs Intel MKL wi ``intel-numpy`` and ``intel-scipy`` not only link against Intel MKL, but also substitute NumPy and SciPy FFTs with `Intel MKL FFT `_. - Multithreading ============== It is important to ensure that your environment variable which sets threads is @@ -295,15 +364,13 @@ other libraries that you have in your system, we have decided to build some of t of PyLops in such a way that if an *optional* dependency is not present in your Python environment, a safe fallback to one of the required dependencies will be enforced. -When available in your system, we recommend using the Conda package manager and install all the -required and some of the optional dependencies of PyLops at once using the command: +When using the Conda package manager, all of the required dependencies (and some of the +optional ones - namely ) are installed using the command: .. code-block:: bash >> conda install --channel conda-forge pylops -in this case all dependencies will be installed from their Conda distributions. - Alternatively, from version ``1.4.0`` some of the optional dependencies can also be installed as part of the pip installation via: @@ -329,6 +396,7 @@ More details about the installation process for the different optional dependenc in the following (an asterisc is used to indicate those dependencies that are automatically installed when installing PyLops from conda-forge or via ``pip install pylops[advanced]``): + ASTRA ----- `ASTRA `_ is library used to perform computerized @@ -337,16 +405,18 @@ tomography. It is used in PyLops in the operator :py:class:`pylops.medical.CT2D` To use this library, install it manually either via ``conda``: .. code-block:: bash + >> conda install --channel astra-toolbox astra-toolbox or via pip: .. code-block:: bash + >> pip install astra-toolbox -dtcwt* ------- +dtcwt +----- `dtcwt `_ is a library used to implement the DT-CWT operators. @@ -374,8 +444,8 @@ Install it via ``pip`` with >> pip install devito -FFTW* and MKL-FFT ------------------ +FFTW and MKL-FFT +---------------- Four different "engines" are provided by the :py:class:`pylops.signalprocessing.FFT` operator: ``engine="numpy"`` (default), ``engine="scipy"``, ``engine="fftw"`` and ``engine="mkl_fft"``. Similarly, the :py:class:`pylops.signalprocessing.FFT2D` and @@ -520,8 +590,8 @@ or via ``pip`` with OSX users may experience a ``CompileError`` error when using PyTensor. This can be solved by adding ``pytensor.config.gcc__cxxflags = "-Wno-c++11-narrowing"`` after ``import pytensor``. -PyWavelets* ------------ +PyWavelets +---------- `PyWavelets `_ is used to implement the wavelet operators. Install it via ``conda`` with: @@ -536,8 +606,8 @@ or via ``pip`` with >> pip install PyWavelets -scikit-fmm* ------------ +scikit-fmm +---------- `scikit-fmm `_ is a library which implements the fast marching method. It is used in PyLops to compute traveltime tables in the initialization of :py:class:`pylops.waveeqprocessing.Kirchhoff` @@ -555,8 +625,8 @@ or with ``pip`` via >> pip install scikit-fmm -SPGL1* ------- +SPGL1 +----- `SPGL1 `_ is used to solve sparsity-promoting basis pursuit, basis pursuit denoise, and Lasso problems in :py:func:`pylops.optimization.sparsity.SPGL1` solver. diff --git a/docs/source/papers.rst b/docs/source/papers.rst index c4774e8b..0637a76f 100755 --- a/docs/source/papers.rst +++ b/docs/source/papers.rst @@ -1,7 +1,8 @@ .. _papers: -Papers using PyLops -=================== +|:bookmark:| Papers using PyLops +################################ + This section lists various conference abstracts and papers using the PyLops framework. If you publish a paper using PyLops, `we'd love to hear about it `_! diff --git a/docs/source/roadmap.rst b/docs/source/roadmap.rst index 96833346..0dbd2cd4 100755 --- a/docs/source/roadmap.rst +++ b/docs/source/roadmap.rst @@ -3,8 +3,8 @@ .. role:: strike :class: strike -Roadmap -======= +|:construction:| Roadmap +######################## This roadmap is aimed at providing an high-level overview on the bug fixes, improvements and new functionality that are planned for the PyLops library. @@ -17,7 +17,7 @@ such a fix/addition. with more details regarding how this task has been carried out. Library structure ------------------ +***************** * Create a child repository and python library called ``geolops`` (just a suggestion) where geoscience-related operators and examples are moved across, keeping the core @@ -25,8 +25,8 @@ Library structure `Issue #22 `_. -Code cleaning -------------- +Code style +********** * :strike:`Change all ``np.flatten()``` :strike:`into ``np.ravel()``` - `Issue #24 `_. @@ -38,7 +38,7 @@ Code cleaning Code optimization ------------------ +***************** * Investigate speed-up given by decorating ``_matvec`` and ``_rmatvec`` methods with `numba `_ ``@jit`` and ``@stencil`` decorators - @@ -50,16 +50,17 @@ Code optimization Modules -------- +******* avo -~~~ +=== * Add possibility to choose different damping factors for each elastic parameter to invert for in :py:class:`pylops.avo.prestack.PrestackInversion` - `Issue #25 `_. + basicoperators -~~~~~~~~~~~~~~ +============== * :strike:`Create Kronecker operator` - `Issue #28 `_. @@ -67,15 +68,16 @@ basicoperators * :strike:`Deal with edges in FirstDerivative and SecondDerivative operators` - `Issue #34 `_. + optimization -~~~~~~~~~~~~ +============ * :strike:`Sparse solvers` - `Issue #44 `_. signalprocessing -~~~~~~~~~~~~~~~~ +================ * :strike:`Compare performance in FTT operator of performing np.swap+np.fft.fft(..., axis=-1) versus np.fft.fft(..., axis=chosen)` @@ -90,14 +92,15 @@ signalprocessing * :strike:`Fredholm2 operators applying Fredholm integrals of second kind` - `Issue #31 `_. + utils -~~~~~ +===== Nothing so far waveeqprocessing -~~~~~~~~~~~~~~~~ +================ * :strike:`numpy.matmul as a way to speed up integral computation (i.e., inner for loop) in MDC operator` - `Issue #32 `_. diff --git a/environment-dev-arm.yml b/environment-dev-arm.yml index 4b5c80d1..041c3cd2 100644 --- a/environment-dev-arm.yml +++ b/environment-dev-arm.yml @@ -33,11 +33,14 @@ dependencies: - jax - pytest-runner - setuptools_scm - - pydata-sphinx-theme - - pooch + - shibuya + - sphinx-design - sphinx-gallery + - sphinx-iconify + - pooch - nbsphinx - sphinxemoji - image - flake8 - mypy + - coverage diff --git a/environment-dev-gpu.yml b/environment-dev-gpu.yml index cb19a0b5..90bfa013 100644 --- a/environment-dev-gpu.yml +++ b/environment-dev-gpu.yml @@ -26,11 +26,14 @@ dependencies: - torch - pytest-runner - setuptools_scm - - pydata-sphinx-theme - - pooch + - shibuya + - sphinx-design - sphinx-gallery + - sphinx-iconify + - pooch - nbsphinx - sphinxemoji - image - flake8 - mypy + - coverage diff --git a/environment-dev-intel-mkl.yml b/environment-dev-intel-mkl.yml index 4895288c..959b3b1f 100644 --- a/environment-dev-intel-mkl.yml +++ b/environment-dev-intel-mkl.yml @@ -36,11 +36,14 @@ dependencies: - jax - pytest-runner - setuptools_scm - - pydata-sphinx-theme - - pooch + - shibuya + - sphinx-design - sphinx-gallery + - sphinx-iconify + - pooch - nbsphinx - sphinxemoji - image - flake8 - mypy + - coverage diff --git a/environment-dev.yml b/environment-dev.yml index f719e8d9..3ac6fbe2 100644 --- a/environment-dev.yml +++ b/environment-dev.yml @@ -34,11 +34,14 @@ dependencies: - jax - pytest-runner - setuptools_scm - - pydata-sphinx-theme - - pooch + - shibuya + - sphinx-design - sphinx-gallery + - sphinx-iconify + - pooch - nbsphinx - sphinxemoji - image - flake8 - mypy + - coverage diff --git a/examples/README.txt b/examples/README.txt index 5d98186b..6c3ef5c4 100755 --- a/examples/README.txt +++ b/examples/README.txt @@ -1,6 +1,6 @@ .. _general_examples: -Gallery -------- +|:framed_picture:| Gallery +-------------------------- Below is a gallery of examples which use PyLops operators and utilities. diff --git a/requirements-dev-arm.txt b/requirements-dev-arm.txt index 985ac7b1..fe022a68 100644 --- a/requirements-dev-arm.txt +++ b/requirements-dev-arm.txt @@ -18,7 +18,8 @@ setuptools_scm docutils<0.18 Sphinx pooch -pydata-sphinx-theme +shibuya +sphinx-design sphinx-gallery sphinxemoji numpydoc diff --git a/requirements-dev-gpu.txt b/requirements-dev-gpu.txt index 6d011e53..703e713c 100644 --- a/requirements-dev-gpu.txt +++ b/requirements-dev-gpu.txt @@ -13,7 +13,8 @@ setuptools_scm docutils<0.18 Sphinx pooch -pydata-sphinx-theme +shibuya +sphinx-design sphinx-gallery sphinxemoji numpydoc diff --git a/requirements-dev.txt b/requirements-dev.txt index f10a4002..eb2d166a 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -17,7 +17,8 @@ setuptools_scm docutils<0.18 Sphinx pooch -pydata-sphinx-theme +shibuya +sphinx-design sphinx-gallery sphinxemoji numpydoc diff --git a/requirements-doc.txt b/requirements-doc.txt index 64c12e39..4ea0d12c 100644 --- a/requirements-doc.txt +++ b/requirements-doc.txt @@ -18,7 +18,8 @@ setuptools_scm docutils<0.18 Sphinx pooch -pydata-sphinx-theme +shibuya +sphinx-design sphinx-gallery sphinxemoji numpydoc diff --git a/tutorials/README.txt b/tutorials/README.txt index cc1d3777..13b88920 100755 --- a/tutorials/README.txt +++ b/tutorials/README.txt 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9687dbb8eda108d238d3a8578f53964d793d6d07 Mon Sep 17 00:00:00 2001 From: mrava87 Date: Thu, 12 Mar 2026 23:09:10 +0000 Subject: [PATCH 3/5] minor: added missing sphinx dependency to req files --- pyproject.toml | 4 ++-- requirements-dev-arm.txt | 1 + requirements-dev-gpu.txt | 1 + requirements-dev.txt | 1 + requirements-doc.txt | 1 + uv.lock | 8 +++----- 6 files changed, 9 insertions(+), 7 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 67ab6fe9..f8cd80f0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,11 +45,11 @@ advanced = [ "scikit-fmm", "spgl1", "dtcwt", - "astra-toolbox; sys_platform == 'linux'" + "astra-toolbox; sys_platform == 'linux'", + "devito" ] deep = ["torch", "jax"] stat = ["pytensor", "pymc"] -seis = ["devito"] [dependency-groups] dev = [ diff --git a/requirements-dev-arm.txt b/requirements-dev-arm.txt index fe022a68..3f78c9a7 100644 --- a/requirements-dev-arm.txt +++ b/requirements-dev-arm.txt @@ -21,6 +21,7 @@ pooch shibuya sphinx-design sphinx-gallery +sphinx-iconify sphinxemoji numpydoc nbsphinx diff --git a/requirements-dev-gpu.txt b/requirements-dev-gpu.txt index 703e713c..731bc845 100644 --- a/requirements-dev-gpu.txt +++ b/requirements-dev-gpu.txt @@ -16,6 +16,7 @@ pooch shibuya sphinx-design sphinx-gallery +sphinx-iconify sphinxemoji numpydoc nbsphinx diff --git a/requirements-dev.txt b/requirements-dev.txt index eb2d166a..70f3b2f5 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -20,6 +20,7 @@ pooch shibuya sphinx-design sphinx-gallery +sphinx-iconify sphinxemoji numpydoc nbsphinx diff --git a/requirements-doc.txt b/requirements-doc.txt index 4ea0d12c..5d954a86 100644 --- a/requirements-doc.txt +++ b/requirements-doc.txt @@ -21,6 +21,7 @@ pooch shibuya sphinx-design sphinx-gallery +sphinx-iconify sphinxemoji numpydoc nbsphinx diff --git a/uv.lock b/uv.lock index b830036b..4b768815 100644 --- a/uv.lock +++ b/uv.lock @@ -2849,6 +2849,7 @@ dependencies = [ [package.optional-dependencies] advanced = [ { name = "astra-toolbox", marker = "sys_platform == 'linux'" }, + { name = "devito" }, { name = "dtcwt" }, { name = "llvmlite" }, { name = "numba" }, @@ -2865,9 +2866,6 @@ deep = [ { name = "torch", version = "2.10.0", source = { registry = "https://download.pytorch.org/whl/cpu" }, marker = "sys_platform == 'darwin'" }, { name = "torch", version = "2.10.0+cpu", source = { registry = "https://download.pytorch.org/whl/cpu" }, marker = "sys_platform != 'darwin'" }, ] -seis = [ - { name = "devito" }, -] stat = [ { name = "pymc", version = "5.25.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, { name = "pymc", version = "5.28.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, @@ -2904,7 +2902,7 @@ doc = [ [package.metadata] requires-dist = [ { name = "astra-toolbox", marker = "sys_platform == 'linux' and extra == 'advanced'" }, - { name = "devito", marker = "extra == 'seis'" }, + { name = "devito", marker = "extra == 'advanced'" }, { name = "dtcwt", marker = "extra == 'advanced'" }, { name = "jax", marker = "extra == 'deep'" }, { name = "llvmlite", marker = "extra == 'advanced'" }, @@ -2919,7 +2917,7 @@ requires-dist = [ { name = "spgl1", marker = "extra == 'advanced'" }, { name = "torch", marker = "extra == 'deep'", index = "https://download.pytorch.org/whl/cpu" }, ] -provides-extras = ["advanced", "deep", "stat", "seis"] +provides-extras = ["advanced", "deep", "stat"] [package.metadata.requires-dev] dev = [ From 652923d2c4cebeae50ce42d7d8344c2b1987fd3f Mon Sep 17 00:00:00 2001 From: mrava87 Date: Thu, 12 Mar 2026 23:14:38 +0000 Subject: [PATCH 4/5] doc: removed unmantained roadmap --- CONTRIBUTING.md | 4 -- docs/source/contributing.rst | 3 - docs/source/index.rst | 1 - docs/source/roadmap.rst | 112 ----------------------------------- 4 files changed, 120 deletions(-) delete mode 100755 docs/source/roadmap.rst diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 58ce812c..dd690a56 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -6,10 +6,6 @@ The best way to get in touch with the core developers and maintainers is to join the [PyLops slack channel](https://pylops.slack.com/) as well as open new *Issues* directly from the GitHub repo. -Moreover, take a look at the [Roadmap](https://pylops.readthedocs.io/en/stable/roadmap.html) -page for a list of current ideas for improvements and additions to the PyLops library. - - ## Welcomed contributions ### Bug reports diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index b5140625..82a30720 100755 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -9,9 +9,6 @@ The best way to get in touch with the core developers and maintainers is to join the `PyLops slack channel `_ as well as open new *Issues* directly from the `GitHub repo `_. -Moreover, take a look at the :ref:`roadmap` page for a list of current ideas -for improvements and additions to the PyLops library. - Welcomed contributions ********************** diff --git a/docs/source/index.rst b/docs/source/index.rst index 0f085cfb..ecc28e50 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -103,7 +103,6 @@ PyLops is a `NUMFOCUS `_. - - -Code style -********** - -* :strike:`Change all ``np.flatten()``` :strike:`into ``np.ravel()``` - - `Issue #24 `_. -* Fix all ``if: return ... else: ...`` statements to enforce a single return - with the same number of outputs - - `Issue #26 `_. -* Protected attributes and @property attributes in linear operator classes? - - `Issue #27 `_. - - -Code optimization -***************** - -* Investigate speed-up given by decorating ``_matvec`` and ``_rmatvec`` methods with - `numba `_ ``@jit`` and ``@stencil`` decorators - - `Issue #23 `_. - -* :strike:`Replace np.fft.* routines used in several submodules with double engine, - numpy and pyFFTW` - - `Issue #20 `_. - - -Modules -******* - -avo -=== - -* Add possibility to choose different damping factors for each elastic parameter to invert for in - :py:class:`pylops.avo.prestack.PrestackInversion` - `Issue #25 `_. - - -basicoperators -============== - -* :strike:`Create Kronecker operator` - - `Issue #28 `_. - -* :strike:`Deal with edges in FirstDerivative and SecondDerivative operators` - - `Issue #34 `_. - - -optimization -============ - -* :strike:`Sparse solvers` - - `Issue #44 `_. - - -signalprocessing -================ - -* :strike:`Compare performance in FTT operator of performing - np.swap+np.fft.fft(..., axis=-1) versus np.fft.fft(..., axis=chosen)` - - `Issue #33 `_. - -* :strike:`Add Wavelet operator performing the wavelet transform` - - `Issue #21 `_. - -* :strike:`Fredholm1 operator applying Fredholm integrals - of first kind` - `Issue #31 `_. - -* :strike:`Fredholm2 operators applying Fredholm integrals - of second kind` - `Issue #31 `_. - - -utils -===== - -Nothing so far - - -waveeqprocessing -================ - -* :strike:`numpy.matmul as a way to speed up integral computation (i.e., inner for loop) - in MDC operator` - `Issue #32 `_. - -* ``NMO`` operator performing NMO modelling - - `Issue #29 `_. - -* :strike:`WavefieldDecomposition operator performing acoustic wavefield separation - by inversion` - `Issue #30 `_. From b95e6dc85604be4fba5515ad67eab8857f52cfd1 Mon Sep 17 00:00:00 2001 From: mrava87 Date: Fri, 13 Mar 2026 18:26:07 +0000 Subject: [PATCH 5/5] bug: switch to np.trapezoid in dublurring tutorial (np.trapz deprecated) --- tutorials/deblurring.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tutorials/deblurring.py b/tutorials/deblurring.py index a397805b..ebc6e71e 100755 --- a/tutorials/deblurring.py +++ b/tutorials/deblurring.py @@ -28,8 +28,8 @@ nh = [15, 25] hz = np.exp(-0.1 * np.linspace(-(nh[0] // 2), nh[0] // 2, nh[0]) ** 2) hx = np.exp(-0.03 * np.linspace(-(nh[1] // 2), nh[1] // 2, nh[1]) ** 2) -hz /= np.trapz(hz) # normalize the integral to 1 -hx /= np.trapz(hx) # normalize the integral to 1 +hz /= np.trapezoid(hz) # normalize the integral to 1 +hx /= np.trapezoid(hx) # normalize the integral to 1 h = hz[:, np.newaxis] * hx[np.newaxis, :] fig, ax = plt.subplots(1, 1, figsize=(5, 3))