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tpeulentpeulen
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Fix CI build failures across Linux, Windows, and macOS jobs
- SWIG >= 4.4 resolves int64_t to 'long long' unless SWIGWORDSIZE64 is defined; glibc defines it as 'long', so the generated wrappers mixed vector<long long> with the library's vector<long> and failed to compile (Conda/Pip/Bioconda Linux builds). Pass -DSWIGWORDSIZE64 to SWIG on Linux for all bindings and instantiate the int64_t-based container templates there for Python-list conversion parity with Windows/macOS. - Commit recipes/docs, referenced by the Docs Build job but never added, which made rattler-build parse an empty recipe. - Anchor the build/ gitignore pattern to the repository root: rattler-build's path source copy honors .gitignore, and the unanchored pattern dropped the tracked thirdparty/libtiff/build/ directory, breaking the bundled-libtiff configure on Windows (add_subdirectory(build) not found). - Raise the macOS deployment floor from 10.13 to 10.15: TTTR.cpp uses std::filesystem and path::u8string, unavailable before 10.15 (ImageJ darwin builds). - Disable LTO on MinGW: its linker fails to resolve symbols from LTO bitcode in static archives (undefined TIFFSetErrorHandler from the bundled libtiff.a in the ImageJ win32 build).
1 parent ac48f10 commit c78afa1

6 files changed

Lines changed: 131 additions & 11 deletions

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‎.gitignore‎

Lines changed: 3 additions & 1 deletion
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@@ -1,5 +1,7 @@
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# Build outputs
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build/
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# Root-anchored: rattler-build's path source copy honors .gitignore, and an
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# unanchored build/ would drop the tracked thirdparty/libtiff/build/ directory.
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/build/
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bld-dir/
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dist/
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dist

‎CMakeLists.txt‎

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@@ -155,11 +155,16 @@ ELSEIF (CMAKE_BUILD_TYPE STREQUAL "Release")
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-funroll-loops # Unroll loops
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-finline-functions # Inline functions
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-fomit-frame-pointer # Omit frame pointer
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-flto # Link-time optimization
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-w # Disable all warnings in Release builds
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)
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SET(CMAKE_EXE_LINKER_FLAGS_RELEASE "${CMAKE_EXE_LINKER_FLAGS_RELEASE} -flto")
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SET(CMAKE_SHARED_LINKER_FLAGS_RELEASE "${CMAKE_SHARED_LINKER_FLAGS_RELEASE} -flto")
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# LTO everywhere except MinGW: MinGW's ld fails to resolve symbols from
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# LTO bitcode inside static archives (e.g. TIFFSetErrorHandler from the
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# bundled libtiff.a), producing undefined references at link time.
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IF(NOT MINGW)
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ADD_COMPILE_OPTIONS(-flto)
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SET(CMAKE_EXE_LINKER_FLAGS_RELEASE "${CMAKE_EXE_LINKER_FLAGS_RELEASE} -flto")
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SET(CMAKE_SHARED_LINKER_FLAGS_RELEASE "${CMAKE_SHARED_LINKER_FLAGS_RELEASE} -flto")
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ENDIF()
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ENDIF()
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ENDIF ()
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@@ -174,17 +179,18 @@ ENDIF (MSVC)
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if(APPLE)
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FIND_PACKAGE(Threads)
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# comatibility with older systems
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set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -mmacosx-version-min=10.13")
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mmacosx-version-min=10.13")
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set(CMAKE_LFLAGS "${CMAKE_LFLAGS} -mmacosx-version-min=10.13")
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# Compatibility with older systems. 10.15 is the floor: the sources use
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# std::filesystem and std::filesystem::path::u8string, which Apple's SDK
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# marks unavailable before macOS 10.15.
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set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -mmacosx-version-min=10.15")
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mmacosx-version-min=10.15")
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set(CMAKE_LFLAGS "${CMAKE_LFLAGS} -mmacosx-version-min=10.15")
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SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
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SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -pthread")
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# explicit link to libc++ for recent osx versions
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MESSAGE(STATUS "Explicitly link to libc++ on modern osx versions")
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ADD_DEFINITIONS(-stdlib=libc++)
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SET(CMAKE_LFLAGS "${CMAKE_LFLAGS} -mmacosx-version-min=10.9")
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# Don't set MACOSX_RPATH by default
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# https://github.com/conda/conda/issues/3624
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if(DEFINED ENV{CONDA_PREFIX})

‎ext/CMakeLists.txt‎

Lines changed: 12 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,16 @@ MESSAGE(STATUS "SWIG_VERSION: ${SWIG_VERSION}")
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INCLUDE(${SWIG_USE_FILE})
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INCLUDE_DIRECTORIES(.)
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# glibc on LP64 Linux defines int64_t as 'long', but SWIG's stdint.i typedefs
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# (applied by SWIG >= 4.4 whenever stdint.i is included) resolve int64_t to
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# 'long long' unless SWIGWORDSIZE64 is defined. Without this flag the
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# generated wrappers mix std::vector<long long> with the library's
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# std::vector<long> and do not compile on Linux.
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IF(UNIX AND NOT APPLE AND CMAKE_SIZEOF_VOID_P EQUAL 8)
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SET(TTTRLIB_SWIG_INT64_FLAG "-DSWIGWORDSIZE64")
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LIST(APPEND CMAKE_SWIG_FLAGS ${TTTRLIB_SWIG_INT64_FLAG})
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ENDIF()
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IF(BUILD_PYTHON_INTERFACE)
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IF(BUILD_PYTHON_DOCS)
@@ -199,7 +209,7 @@ IF(BUILD_R_INTERFACE)
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SWIG_MODULE_NAME tttrlib)
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# r/tttrlib.i re-includes the shared fragments that live in ext/python.
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SET(CMAKE_SWIG_FLAGS -I${CMAKE_CURRENT_SOURCE_DIR}/python)
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SET(CMAKE_SWIG_FLAGS -I${CMAKE_CURRENT_SOURCE_DIR}/python ${TTTRLIB_SWIG_INT64_FLAG})
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# Rerun SWIG when any shared fragment, the R module, or the R array library changes.
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file(GLOB R_SWIG_DEPS
@@ -250,7 +260,7 @@ IF(BUILD_JAVA_INTERFACE)
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SET_SOURCE_FILES_PROPERTIES(java/tttrlib.i PROPERTIES
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CPLUSPLUS ON
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SWIG_MODULE_NAME tttrlib)
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SET(CMAKE_SWIG_FLAGS -package ${J_PACKAGE} -I${CMAKE_CURRENT_SOURCE_DIR}/python)
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SET(CMAKE_SWIG_FLAGS -package ${J_PACKAGE} -I${CMAKE_CURRENT_SOURCE_DIR}/python ${TTTRLIB_SWIG_INT64_FLAG})
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SET(CMAKE_SWIG_OUTDIR ${J_OUTDIR})
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file(GLOB J_SWIG_DEPS

‎ext/python/misc_types.i‎

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@@ -1,4 +1,5 @@
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// SPDX-License-Identifier: BSD-3-Clause
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%include "stdint.i";
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%include "stl.i";
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%include "typemaps.i";
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%include "std_string.i";
@@ -74,6 +75,16 @@ $result = swig::from($1);
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// Pair templates
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%template(VectorPairInt) std::vector<std::pair<int,int>>;
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%template(VectorPairInt64) std::vector<std::pair<long long, long long>>;
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79+
// With SWIGWORDSIZE64 (Linux, see ext/CMakeLists.txt) int64_t is 'long' and
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// therefore a different type than the 'long long' containers above.
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// Instantiate the int64_t-based containers there so the APIs spelled with
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// int64_t (BurstFilter, BurstFeatureExtractor) convert to/from native lists
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// just like they do on Windows/macOS, where int64_t is 'long long'.
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#ifdef SWIGWORDSIZE64
85+
%template(VectorInt64T) std::vector<int64_t>;
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%template(VectorPairInt64T) std::vector<std::pair<int64_t, int64_t>>;
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#endif
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%template(PairVectorDouble) std::pair<std::vector<double>, std::vector<double>>;
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%template(PairVectorInt64) std::pair<std::vector<unsigned long long>, std::vector<unsigned long long>>;
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‎recipes/docs/build.sh‎

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@@ -0,0 +1,27 @@
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#!/usr/bin/env bash
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set -euxo pipefail
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# 1. Build & install tttrlib into the host python (needed for autodoc/gallery).
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export CMAKE_ARGS="-DWITH_AVX=OFF"
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"${PYTHON}" -m pip install . --no-deps --no-build-isolation -vv
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# 2. Reference data for the example gallery (examples are NOT executed).
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export TTTRLIB_DATA="${SRC_DIR}/tttr-data"
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export TTTRLIB_DOCS_EXECUTE_EXAMPLES=0
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"${PYTHON}" -m pip install --no-build-isolation pooch tqdm || true
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"${PYTHON}" test/download_test_data.py --output-dir "${TTTRLIB_DATA}" --quiet || \
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echo "warning: reference data download failed; gallery thumbnails may be missing"
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# 3. Build the HTML documentation.
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export BUILD_TIER="${BUILD_TIER:-4}"
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cd doc
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mkdir -p _build/api
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"${PYTHON}" -m sphinx -T -b html -d _build/doctrees . _build/html/stable
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"${PYTHON}" ../tools/check_docs_pages.py _build/html/stable || true
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rm -rf _build/html/stable/api
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[ -d _build/api ] && cp -r _build/api _build/html/stable/ || true
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cd ..
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25+
# 4. Install the built HTML into the package.
26+
mkdir -p "${PREFIX}/share/doc/tttrlib"
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cp -r doc/_build/html/stable "${PREFIX}/share/doc/tttrlib/html"

‎recipes/docs/recipe.yaml‎

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# rattler-build recipe that builds the tttrlib HTML documentation (Sphinx +
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# Doxygen) reproducibly and packages it under share/doc/tttrlib/html.
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# Build with: rattler-build build --recipe recipes/docs -c conda-forge
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context:
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version: ${{ env.get("PKG_VERSION", default="0.27.0") }}
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package:
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name: tttrlib-docs
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version: ${{ version }}
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source:
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path: ../..
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build:
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number: 0
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# Documentation is built on Linux.
17+
skip: ${{ not linux }}
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19+
requirements:
20+
build:
21+
- ${{ compiler('c') }}
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- ${{ compiler('cxx') }}
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- cmake
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- ninja
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- make
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- swig >=4.1
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- doxygen
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- pandoc
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- graphviz
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host:
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- python
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- pip
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- scikit-build-core
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- numpy
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- hdf5
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- highfive
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- nlohmann_json
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# Sphinx documentation stack (mirrors the CI docs dependencies)
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- sphinx
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- sphinx-copybutton
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- sphinx-design
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- sphinxext-opengraph
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- numpydoc
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- nbsphinx
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- matplotlib-base
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- ipython
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- sphinxcontrib-bibtex
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- sphinx-gallery
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- pydata-sphinx-theme
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- scikit-image
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- phconvert
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- numba
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- imagecodecs
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about:
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homepage: https://github.com/fluorescence-tools/tttrlib
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summary: HTML documentation for tttrlib (Sphinx + Doxygen).
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license: BSD-3-Clause
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license_file: LICENSE.txt
60+
repository: https://github.com/fluorescence-tools/tttrlib
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extra:
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recipe-maintainers:
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- tpeulen

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