[ENH] Dev-ops, N+1 offset, temporary directory

.github/workflows/test.yml

@@ -0,0 +1,46 @@
+on: [push, pull_request]
+
+env:
+  BUILD_TYPE: Debug
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest]
+        include:
+          - os: macos-latest
+          - os: ubuntu-latest
+
+    steps:
+
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      - name: Install Conan
+        run: pip install conan pytest && conan --version
+
+      - name: Setup cmake
+        uses: jwlawson/[email protected]
+        with:
+          cmake-version: '3.22.x'
+
+      - name: Build
+        run: |
+          mkdir build && cd build
+          conan profile new ./.conan --detect
+          conan profile update settings.compiler.libcxx=libstdc++11 ./.conan
+          conan install --profile ./.conan ..
+          cmake -S .. -B . && make
+
+      - name: Test
+        run: |
+          build/bin/tests
+        env:
+          TRX_TMPDIR: ${{ runner.temp }}

.gitignore

@@ -9,3 +9,4 @@
 libtrx.a
 tests/data
 .vscode
+data

CMakeLists.txt

@@ -1,29 +1,27 @@
+set(LOCAL_PROJECT_NAME "trx")
+set(LOCAL_PROJECT_VERSION "0.1.0")
+
 cmake_minimum_required(VERSION 3.0.0)
 cmake_policy(SET CMP0074 NEW)
 cmake_policy(SET CMP0079 NEW)
-project(trx VERSION 0.1.0)
-set (CMAKE_CXX_STANDARD 11)
+project(${LOCAL_PROJECT_NAME} VERSION ${LOCAL_PROJECT_VERSION})
+set(CMAKE_CXX_STANDARD 11)
+
+option(TRX_USE_CONAN "Should Conan package manager be used?" ON)
 
 #set(CMAKE_BUILD_TYPE RelWithDebInfo)
 set(CMAKE_BUILD_TYPE Debug)
+#set(CMAKE_BUILD_TYPE Release)
 
-find_package(libzip REQUIRED)
-find_package (Eigen3 CONFIG REQUIRED)
-find_package(nlohmann_json CONFIG REQUIRED)
-find_package(spdlog CONFIG REQUIRED)
-
-add_library(trx src/trx.cpp src/trx.tpp src/trx.h)
-
-TARGET_LINK_LIBRARIES(trx
-	PRIVATE
-	nlohmann_json::nlohmann_json
-	libzip::zip
-	Eigen3::Eigen
-    spdlog::spdlog
-    spdlog::spdlog_header_only
-)
+add_library(${LOCAL_PROJECT_NAME} src/trx.cpp src/trx.tpp)
 
+include(cmake/ConanSetup.cmake)
 
 set(CPACK_PROJECT_NAME ${PROJECT_NAME})
 set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
 include(CPack)
+
+option(TRX_TESTS "Build the tests" ON)
+if(TRX_TESTS)
+    add_subdirectory(tests)
+endif()

README.md

@@ -3,16 +3,48 @@
 The C++ implementations to the memory-mapped tractography file format.
 
 ## Installation
+
+The project requires `gcc`, `make` and `cmake`. Please refer to your OS instructions
+for proper installation.
+
 ### Dependencies
-- c++11 compiler / cmake
-- libzip
-- nlohmann::json
-- Eigen3
-- spdlog
-- GTest (optional)
 
-### Installing
-`cmake . && make`
+The project dependencies are handled using [Conan](https://conan.io/).
+Its installation can be found in their [documentation](https://docs.conan.io/en/latest/installation.html).
+TL;DR: It is basically `pip install conan`, and works for Python >= 3.6.
+
+To install the dependencies, run the following:
+```bash
+# Fresh build
+rm -Rf build && mkdir build && cd build
+
+# Creates a Conan profile relative to the project
+conan profile new ./.conan --detect && conan profile update settings.compiler.libcxx=libstdc++11 ./.conan
+
+# Install dependencies
+conan install --build=missing --settings=build_type=Debug --profile ./.conan ..
+
+# Build
+cmake -S .. -B . && make
+```
+### Running tests
+
+In `./build`:
+```bash
+bin/tests
+```
+
+### Iterating the code with new changes
+
+In `./build`:
+```bash
+make && bin/tests
+```
 
 ## How to use
 COMING SOON
+
+Examples to set up:
+- Adding to my project without cmake?
+- Adding to my project without conan
+- Adding to my project with conan

conanfile.py

@@ -0,0 +1,19 @@
+from conans import ConanFile, CMake
+
+
+class TRX(ConanFile):
+    name = "trx"
+    version = "1.0.0"
+    description = "TRX (tee-ar-ex), a community-oriented unified tractography file"
+    license = "BSD-2-Clause"
+    url = "https://tee-ar-ex.github.io/"
+    settings = "os", "arch", "compiler", "build_type"
+    generators = "cmake"
+    requires = [
+        "eigen/3.4.0@#3bc2bf84eff697283b6bd64d8262c423",
+        "spdlog/1.10.0@#1e0f4eb6338d05e4bd6fcc6bf4734172",
+        "nlohmann_json/3.11.2@#a35423bb6e1eb8f931423557e282c7ed",
+        "libzip/1.8.0@#5a0a692ec9d7d8a4337eb79e55869639",
+        "mio/cci.20201220",
+        "gtest/cci.20210126",
+    ]

examples/install-using-conan/CMakeLists.txt

@@ -0,0 +1,30 @@
+cmake_minimum_required(VERSION 3.0.0)
+cmake_policy(SET CMP0074 NEW)
+cmake_policy(SET CMP0079 NEW)
+project(trx_example)
+
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_BUILD_TYPE Debug)
+
+add_executable(load_trx load_trx.cpp)
+
+include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake)
+conan_basic_setup()
+
+# target_link_libraries(
+#     ${LOCAL_PROJECT_NAME}
+#     PRIVATE ${CONAN_LIBS}
+# )
+
+# target_include_directories(${LOCAL_PROJECT_NAME}
+#     PUBLIC
+#         $<INSTALL_INTERFACE:include>
+#         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+#     PRIVATE
+#         ${CMAKE_CURRENT_SOURCE_DIR}/src
+#         ${CMAKE_CURRENT_BINARY_DIR}/gen-private-include
+#         ${CONAN_INCLUDE_DIRS}
+# )
+
+set(CPACK_PROJECT_NAME ${PROJECT_NAME})
+set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})

examples/install-using-conan/README.md

@@ -0,0 +1,11 @@
+
+```bash
+conan editable add ../.. trx/1.0.0@user/channel
+```
+
+```bash
+cd .. && rm -Rf build && mkdir build && cd build
+conan profile new ./.conan --detect && conan profile update settings.compiler.libcxx=libstdc++11 ./.conan
+conan install --build=missing --settings=build_type=Debug --profile ./.conan ..
+cmake -S .. -B . && make
+```

examples/install-using-conan/conanfile.txt

@@ -0,0 +1,5 @@
+[requires]
+trx/1.0.0@user/channel
+
+[generators]
+cmake

examples/load_trx.cpp → examples/install-using-conan/load_trx.cpp

@@ -1,4 +1,4 @@
-#include "../src/trx.h"
+#include <trx/trx.h>
 
 using namespace trxmmap;
 int main(int argc, char **argv)

examples/install-using-vendor/CMakeLists.txt

@@ -0,0 +1,13 @@
+cmake_minimum_required(VERSION 3.0.0)
+project(trx_example)
+
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_BUILD_TYPE Debug)
+
+add_executable(load_trx load_trx.cpp)
+
+set(TRX_USE_CONAN OFF)
+add_subdirectory(vendor/trx)
+
+set(CPACK_PROJECT_NAME ${PROJECT_NAME})
+set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})

examples/install-using-vendor/load_trx.cpp

@@ -0,0 +1,33 @@
+#include <trx/trx.h>
+
+using namespace trxmmap;
+int main(int argc, char **argv)
+{
+	trxmmap::TrxFile<half> *trx = trxmmap::load_from_zip<half>(argv[1]);
+
+	std::cout << "Vertices: " << trx->streamlines->_data.size() / 3 << "\n";
+	std::cout << "First vertex (x,y,z): " << trx->streamlines->_data(0, 0)
+		  << "," << trx->streamlines->_data(0, 1)
+		  << "," << trx->streamlines->_data(0, 2) << "\n";
+	std::cout << "Streamlines: " << trx->streamlines->_offsets.size() << "\n";
+	std::cout << "Vertices in first streamline: " << trx->streamlines->_offsets(1) - trx->streamlines->_offsets(0) << "\n";
+	std::cout << "dpg (data_per_group) items: " << trx->data_per_group.size() << "\n";
+	std::cout << "dps (data_per_streamline) items: " << trx->data_per_streamline.size() << "\n";
+
+	for (auto const &x : trx->data_per_streamline)
+	{
+		std::cout << "'" << x.first << "' items: "
+			  << x.second->_matrix.size()
+			  << "\n";
+	}
+
+	std::cout << "dpv (data_per_vertex) items:" << trx->data_per_vertex.size() << "\n";
+	for (auto const &x : trx->data_per_vertex)
+	{
+		std::cout << "'" << x.first << "' items: "
+			  << x.second->_data.size()
+			  << "\n";
+	}
+
+	std::cout << *trx << std::endl;
+}

src/trx.h → include/trx/trx.h

@@ -17,6 +17,9 @@
 #include <mio/mmap.hpp>
 #include <mio/shared_mmap.hpp>
 
+#ifndef SPDLOG_FMT_EXTERNAL
+#define SPDLOG_FMT_EXTERNAL
+#endif
 #include "spdlog/spdlog.h"
 
 using namespace Eigen;
@@ -282,6 +285,8 @@ namespace trxmmap
 	 */
 	void zip_from_folder(zip_t *zf, const std::string root, const std::string directory, zip_uint32_t compression_standard = ZIP_CM_STORE);
 
+	std::string get_extraction_dir();
+	int free_extraction_dir(std::string extraction_dir);
 	std::string get_base(const std::string &delimiter, const std::string &str);
 	std::string get_ext(const std::string &str);
 	void populate_fps(const char *name, std::map<std::string, std::tuple<long long, long long>> &file_pointer_size);
@@ -291,6 +296,7 @@ namespace trxmmap
 	int rm_dir(const char *d);
 
 	std::string rm_root(std::string root, const std::string path);
+
 #include "trx.tpp"
 
 }

scripts/fetch_test.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+cd $SCRIPT_DIR/..
+
+function hashcheck() {
+  MD5=$(md5sum "$1" | cut -d " " -f1)
+  if [[ $MD5 != $2 ]]
+  then
+    echo "md5sum for $1 does not match. Please remove the file to download it again."
+    exit 1
+  fi
+}
+
+mkdir -p data
+
+curl -L https://figshare.com/ndownloader/files/37624154 --output data/DSI.zip
+hashcheck data/DSI.zip b847f053fc694d55d935c0be0e5268f7 # V1 (27.09.2022)
+
+curl -L https://figshare.com/ndownloader/files/37624148 --output data/memmap_test_data.zip
+hashcheck data/memmap_test_data.zip 03f7651a0f9e3eeabee9aed0ad5f69e1 # V2 (27.09.2022)
+
+curl -L https://figshare.com/ndownloader/files/37624151 --output data/trx_from_scratch.zip
+hashcheck data/trx_from_scratch.zip d9f220a095ce7f027772fcd9451a2ee5 # V2 (27.09.2022)