phepex 0.1.0__tar.gz

phepex-0.1.0/.gitignore

@@ -0,0 +1,10 @@
+.DS_Store
+__pycache__
+build
+dist/
+dist_wheel/
+docs/_build/
+docs/_doxygen/
+docs/Doxyfile
+include/phepex/version.hpp
+wheelhouse/

phepex-0.1.0/CMakeLists.txt

@@ -0,0 +1,138 @@
+# SPDX-License-Identifier: MPL-2.0
+# Copyright (c) 2026 Max-Planck-Institut für Kernphysik
+#
+# This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0.
+# If a copy of the MPL was not distributed with this file, You can obtain one at
+# https://mozilla.org/MPL/2.0/.
+
+cmake_minimum_required(VERSION 3.15...3.30)
+
+# Derive the version from the git tag (see cmake/GitVersion.cmake). This must run before
+# project(), which needs a numeric MAJOR.MINOR.PATCH; PHEPEX_VERSION_STRING carries the full
+# `git describe` string for display (the C++ PHEPEX_VERSION macro).
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+include(GitVersion)
+
+project(phepex VERSION ${PHEPEX_VERSION} LANGUAGES CXX
+        DESCRIPTION "Photo-electron pulse extraction kernels")
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  set(CMAKE_BUILD_TYPE Release)
+endif()
+
+include(GNUInstallDirs)
+include(CMakePackageConfigHelpers)
+
+# Generate the public version header from the git-derived version into the build tree.
+configure_file(
+    "${CMAKE_CURRENT_SOURCE_DIR}/include/phepex/version.hpp.in"
+    "${CMAKE_CURRENT_BINARY_DIR}/include/phepex/version.hpp"
+    @ONLY)
+
+# When built as a Python wheel (scikit-build-core defines SKBUILD), build the bindings and
+# skip the C++ dev-install (headers/lib/cmake/pc) that only matters for C++ consumers.
+if(DEFINED SKBUILD)
+  set(_phepex_python_default ON)
+else()
+  set(_phepex_python_default OFF)
+endif()
+option(PHEPEX_BUILD_PYTHON "Build the nanobind Python module (phepex._core)" ${_phepex_python_default})
+option(PHEPEX_BUILD_EXAMPLES "Build the C++ example" OFF)
+option(PHEPEX_BUILD_TESTS "Build the standalone C++ unit tests (vendored Catch2)" OFF)
+
+# libphepex: built as both shared (libphepex.so) and static (libphepex.a)
+set(PHEPEX_SOURCES
+    src/deconvolve.cpp
+    src/preprocess.cpp
+    src/clip.cpp
+    src/neighbor.cpp
+    src/extract.cpp
+    src/generate.cpp)
+
+add_library(phepex SHARED ${PHEPEX_SOURCES})
+add_library(phepex_static STATIC ${PHEPEX_SOURCES})
+add_library(phepex::phepex ALIAS phepex)
+add_library(phepex::phepex_static ALIAS phepex_static)
+
+foreach(tgt phepex phepex_static)
+  target_include_directories(${tgt} PUBLIC
+      $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+      $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/include>
+      $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
+  target_compile_features(${tgt} PUBLIC cxx_std_17)
+  target_compile_options(${tgt} PRIVATE -O3)
+  set_target_properties(${tgt} PROPERTIES
+      OUTPUT_NAME phepex
+      POSITION_INDEPENDENT_CODE ON)
+endforeach()
+set_target_properties(phepex PROPERTIES VERSION ${PROJECT_VERSION} SOVERSION ${PROJECT_VERSION_MAJOR})
+
+# Python bindings (phepex._core), statically linking libphepex into the module
+if(PHEPEX_BUILD_PYTHON)
+  # ${SKBUILD_SABI_COMPONENT} is set by scikit-build-core to "Development.SABIModule" when
+  # building a stable-ABI (abi3) wheel and is empty otherwise. It must be requested here so
+  # FindPython creates the Python::SABIModule target that nanobind's STABLE_ABI build links
+  # against; without it nanobind silently falls back to a version-specific module while the
+  # wheel is still tagged abi3 (a broken, mis-tagged wheel).
+  find_package(Python 3.10 REQUIRED
+               COMPONENTS Interpreter Development.Module ${SKBUILD_SABI_COMPONENT})
+  execute_process(
+    COMMAND "${Python_EXECUTABLE}" -c "import nanobind; print(nanobind.cmake_dir())"
+    OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE nanobind_ROOT)
+  find_package(nanobind CONFIG REQUIRED)
+  nanobind_add_module(_core STABLE_ABI NB_STATIC src/bindings.cpp)
+  target_link_libraries(_core PRIVATE phepex_static)
+  install(TARGETS _core LIBRARY DESTINATION phepex)
+endif()
+
+# C++ example (optional)
+if(PHEPEX_BUILD_EXAMPLES)
+  add_executable(phepex_example examples/example.cpp)
+  target_link_libraries(phepex_example PRIVATE phepex::phepex)
+endif()
+
+# Standalone C++ unit tests (vendored Catch2 v3)
+if(PHEPEX_BUILD_TESTS)
+  enable_testing()
+  add_executable(phepex_tests
+      tests/cpp/test_phepex.cpp
+      third_party/catch2/catch_amalgamated.cpp)
+  target_include_directories(phepex_tests PRIVATE third_party/catch2)
+  target_link_libraries(phepex_tests PRIVATE phepex::phepex)
+  add_test(NAME phepex_tests COMMAND phepex_tests)
+endif()
+
+# Install the C++ library (headers, targets, CMake package config, pkg-config)
+if(NOT DEFINED SKBUILD)
+  install(TARGETS phepex phepex_static EXPORT phepexTargets
+          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
+  install(DIRECTORY include/phepex DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+          PATTERN "version.hpp.in" EXCLUDE)
+  # version.hpp is generated (git-derived); install the generated copy, not the template.
+  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/include/phepex/version.hpp"
+          DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/phepex")
+
+  install(EXPORT phepexTargets NAMESPACE phepex::
+          DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/phepex)
+  configure_package_config_file(
+      cmake/phepexConfig.cmake.in
+      "${CMAKE_CURRENT_BINARY_DIR}/phepexConfig.cmake"
+      INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/phepex)
+  write_basic_package_version_file(
+      "${CMAKE_CURRENT_BINARY_DIR}/phepexConfigVersion.cmake"
+      VERSION ${PROJECT_VERSION} COMPATIBILITY SameMajorVersion)
+  install(FILES
+          "${CMAKE_CURRENT_BINARY_DIR}/phepexConfig.cmake"
+          "${CMAKE_CURRENT_BINARY_DIR}/phepexConfigVersion.cmake"
+          DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/phepex)
+
+  # pkg-config for Makefile-based consumers
+  configure_file(phepex.pc.in "${CMAKE_CURRENT_BINARY_DIR}/phepex.pc" @ONLY)
+  install(FILES "${CMAKE_CURRENT_BINARY_DIR}/phepex.pc"
+          DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+endif()

phepex-0.1.0/LICENSE

@@ -0,0 +1,373 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at https://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.

phepex-0.1.0/PKG-INFO

@@ -0,0 +1,66 @@
+Metadata-Version: 2.4
+Name: phepex
+Version: 0.1.0
+Summary: Photo-electron pulse extraction: fast PMT/SiPM waveform charge & timing extraction for Python.
+Keywords: waveform,charge-extraction,PMT,SiPM,Cherenkov,signal-processing,DSP
+Author: Max-Planck-Institut für Kernphysik
+Author-Email: Felix Werner <felix.werner@mpi-hd.mpg.de>
+License-Expression: MPL-2.0
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: C++
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS
+Project-URL: Homepage, https://github.com/phepex/phepex
+Project-URL: Documentation, https://phepex.github.io/phepex
+Project-URL: Repository, https://github.com/phepex/phepex
+Project-URL: Issues, https://github.com/phepex/phepex/issues
+Requires-Python: >=3.10
+Requires-Dist: numpy
+Provides-Extra: bench
+Requires-Dist: ctapipe>=0.31; extra == "bench"
+Description-Content-Type: text/markdown
+
+# phepex — photo-electron pulse extraction
+
+Fast numeric kernels for extracting charge and timing from digitised PMT/SiPM
+waveforms (e.g. Cherenkov telescopes or Water Cherenkov Detectors): pole-zero
+deconvolution + upsampling, neighbour-sum peak finding, soft clipping, window
+integration and leading-edge timing — plus a fast waveform generator for testing.
+
+The heavy lifting runs in a compiled extension; `import phepex` needs only numpy.
+
+## Install
+
+```bash
+pip install phepex
+```
+
+## Usage
+
+```python
+import phepex
+# phepex.deconvolve, phepex.pos_soft_clip, phepex.neighbor_peak_indices,
+# phepex.extract_around_peak, phepex.adaptive_centroid, phepex.generate_waveforms
+```
+
+The ctapipe-integrated `phepex.extractor.FastFlashCamExtractor` — a drop-in
+accelerating ctapipe's `FlashCamExtractor` (typically ~5× faster end-to-end, with
+bit-exact / ~1e-7 agreement on signal pixels) — lives in a separate submodule
+imported on demand. It needs the `bench` extra:
+
+```bash
+pip install phepex[bench]      # pulls in ctapipe
+```
+
+## Documentation
+
+Full API documentation is published to **https://phepex.github.io/phepex/**.
+
+## License
+
+phepex is licensed under the **Mozilla Public License 2.0**.
+Copyright © 2026 Max-Planck-Institut für Kernphysik.