Initial commit, migrating content from the core.

.gitignore

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+build/
+*.swp
+docs/html
+docs/latex

CMakeLists.txt

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+cmake_minimum_required(VERSION 3.14)
+
+project(tatami_hdf5
+    VERSION 1.0.0
+    DESCRIPTION "tatami bindings for HDF5"
+    LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+
+add_library(tatami_hdf5 INTERFACE)
+
+add_subdirectory(extern)
+
+# Switch between include directories depending on whether the downstream is
+# using the build directly or is using the installed package.
+target_include_directories(tatami_hdf5 
+    INTERFACE 
+    "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
+    "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
+)
+
+# Building the test-related machinery, if we are compiling this library directly.
+if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
+    option(INSTALL_GTEST OFF)
+    include(CTest)
+    if(BUILD_TESTING)
+        add_subdirectory(tests)
+    endif() 
+endif()

LICENSE

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+MIT License
+
+Copyright (c) 2023 Aaron Lun
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# tatami for HDF5 matrices
+
+![Unit tests](https://github.com/tatami-inc/tatami_hdf5/actions/workflows/run-tests.yaml/badge.svg)
+![Gallery](https://github.com/tatami-inc/tatami_hdf5/actions/workflows/run-gallery.yaml/badge.svg)
+![Documentation](https://github.com/tatami-inc/tatami_hdf5/actions/workflows/doxygenate.yaml/badge.svg)
+[![Codecov](https://codecov.io/gh/tatami-inc/tatami_hdf5/branch/master/graph/badge.svg?token=Z189ORCLLR)](https://codecov.io/gh/tatami-inc/tatami_hcdf5)
+
+This repository implements [**tatami**](https://github.com/tatami-inc/tatami) bindings for HDF5-backed matrices,
+allowing some level of random access without loading the entire dataset into memory.
+Matrices can be conventionally stored as 2-dimensional HDF5 datasets,
+or in a compressed sparse format with a 1-dimensional dataset for each component (data, indices, pointers).

extern/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.14 FATAL_ERROR)
+
+include(FetchContent)
+
+FetchContent_Declare(
+  tatami
+  GIT_REPOSITORY https://github.com/LTLA/tatami
+  GIT_TAG eddc3350b290adcd69a226ffb18bcf3bfe0020ef
+)
+
+FetchContent_MakeAvailable(tatami)