From 1a350ec5ebb177949291b4acbce2d236dc6b1965 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Fri, 18 Nov 2022 21:34:27 -0600
Subject: [PATCH 01/17] enh: set up conan, re-setup tests

---
 .gitignore                        |  1 +
 CMakeLists.txt                    | 38 ++++++++++++++++----------
 conanfile.txt                     |  9 +++++++
 {src => include/trx}/trx.h        |  0
 scripts/fetch_test.sh             | 24 +++++++++++++++++
 src/trx.cpp                       |  2 +-
 tests/CMakeLists.txt              | 44 +++++--------------------------
 tests/{ => src}/test_trx_mmap.cpp |  8 +++++-
 8 files changed, 73 insertions(+), 53 deletions(-)
 create mode 100644 conanfile.txt
 rename {src => include/trx}/trx.h (100%)
 create mode 100755 scripts/fetch_test.sh
 rename tests/{ => src}/test_trx_mmap.cpp (98%)

diff --git a/.gitignore b/.gitignore
index 94a144d..88cb477 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,4 @@
 libtrx.a
 tests/data
 .vscode
+data
\ No newline at end of file
diff --git a/CMakeLists.txt b/CMakeLists.txt
index b3a8300..4ccddf1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,29 +1,39 @@
+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)
+project(${LOCAL_PROJECT_NAME} VERSION ${LOCAL_PROJECT_VERSION})
 set (CMAKE_CXX_STANDARD 11)
 
+include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake)
+conan_basic_setup()
+
 #set(CMAKE_BUILD_TYPE RelWithDebInfo)
 set(CMAKE_BUILD_TYPE Debug)
 
-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)
+add_library(${LOCAL_PROJECT_NAME} src/trx.cpp src/trx.tpp)
 
-TARGET_LINK_LIBRARIES(trx
-	PRIVATE
-	nlohmann_json::nlohmann_json
-	libzip::zip
-	Eigen3::Eigen
-    spdlog::spdlog
-    spdlog::spdlog_header_only
+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
 )
 
+target_link_libraries(
+    ${LOCAL_PROJECT_NAME}
+    PRIVATE ${CONAN_LIBS}
+)
 
 set(CPACK_PROJECT_NAME ${PROJECT_NAME})
 set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
 include(CPack)
+
+option(PACKAGE_TESTS "Build the tests" ON)
+if(PACKAGE_TESTS)
+    add_subdirectory(tests)
+endif()
\ No newline at end of file
diff --git a/conanfile.txt b/conanfile.txt
new file mode 100644
index 0000000..15120e8
--- /dev/null
+++ b/conanfile.txt
@@ -0,0 +1,9 @@
+[requires]
+eigen/3.4.0@#3bc2bf84eff697283b6bd64d8262c423
+spdlog/1.10.0@#bd2bfacf219f212f2874313ebd74da23
+nlohmann_json/3.11.2@#a35423bb6e1eb8f931423557e282c7ed
+libzip/1.8.0@#5a0a692ec9d7d8a4337eb79e55869639
+gtest/cci.20210126
+
+[generators]
+cmake
\ No newline at end of file
diff --git a/src/trx.h b/include/trx/trx.h
similarity index 100%
rename from src/trx.h
rename to include/trx/trx.h
diff --git a/scripts/fetch_test.sh b/scripts/fetch_test.sh
new file mode 100755
index 0000000..5a50a11
--- /dev/null
+++ b/scripts/fetch_test.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+SCRIPT_DIR=$( 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)
diff --git a/src/trx.cpp b/src/trx.cpp
index e65ff2d..8010572 100644
--- a/src/trx.cpp
+++ b/src/trx.cpp
@@ -1,4 +1,4 @@
-#include "trx.h"
+#include <trx/trx.h>
 #include <fstream>
 #include <typeinfo>
 #include <errno.h>
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 847dc83..0282af1 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -1,41 +1,11 @@
-cmake_minimum_required(VERSION 3.0.0)
-cmake_policy(SET CMP0074 NEW)
-cmake_policy(SET CMP0079 NEW)
-project(trx)
-set (CMAKE_CXX_STANDARD 11)
-
-set(PROJECT_BINARY_DIR ../../builds)
-set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/build/tests)
-set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/build/tests)
-set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
-
-set(CMAKE_BUILD_TYPE Debug)
-
-find_package(libzip REQUIRED)
-find_package (Eigen3 CONFIG REQUIRED)
-find_package(nlohmann_json CONFIG REQUIRED)
-find_package(spdlog CONFIG REQUIRED)
-find_package(GTest CONFIG REQUIRED)
+include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake)
+include_directories(${PROJECT_SOURCE_DIR}/src)
 
 enable_testing()
+find_package(GTest REQUIRED)
+include(GoogleTest)
 
-include_directories(../src)
-add_executable(test_mmap test_trx_mmap.cpp ../src/trx.h ../src/trx.tpp ../src/trx.cpp)
-
-
-TARGET_LINK_LIBRARIES(test_mmap
-	nlohmann_json::nlohmann_json
-	Eigen3::Eigen
-	libzip::zip
-	GTest::gtest
-	GTest::gtest_main
-	spdlog::spdlog
-	spdlog::spdlog_header_only
-)
-
+add_executable(tests src/test_trx_mmap.cpp)
+target_link_libraries(tests PRIVATE ${CONAN_LIBS} ${LOCAL_PROJECT_NAME})
 
-set(CPACK_PROJECT_NAME ${PROJECT_NAME})
-set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
-include(CPack)
-include(GoogleTest)
-gtest_discover_tests(test_mmap)
+gtest_discover_tests(tests)
diff --git a/tests/test_trx_mmap.cpp b/tests/src/test_trx_mmap.cpp
similarity index 98%
rename from tests/test_trx_mmap.cpp
rename to tests/src/test_trx_mmap.cpp
index d381731..2cf3c3a 100644
--- a/tests/test_trx_mmap.cpp
+++ b/tests/src/test_trx_mmap.cpp
@@ -1,5 +1,7 @@
+#include <filesystem>
+#include <iostream>
 #include <gtest/gtest.h>
-#include "../src/trx.h"
+#include <trx/trx.h>
 #include <typeinfo>
 
 using namespace Eigen;
@@ -204,6 +206,10 @@ TEST(TrxFileMemmap, __create_memmap)
 
 TEST(TrxFileMemmap, load_header)
 {
+
+    if(const char* env_p = std::getenv("DATA_DIR"))
+        std::cout << "Your PATH is: " << env_p << '\n';
+
 	std::string path = "data/small.trx";
 	int *errorp;
 	zip_t *zf = zip_open(path.c_str(), 0, errorp);

From 3bfffe4735f90d2ff78e81cfcb5a46a19cfa6e65 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Fri, 18 Nov 2022 22:23:51 -0600
Subject: [PATCH 02/17] enh: set data dir

---
 tests/CMakeLists.txt        |  2 ++
 tests/src/test_trx_mmap.cpp | 17 +++++++----------
 2 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 0282af1..ed43d92 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -5,6 +5,8 @@ enable_testing()
 find_package(GTest REQUIRED)
 include(GoogleTest)
 
+add_definitions(-DDATA_DIR="${CMAKE_CURRENT_SOURCE_DIR}/data")
+
 add_executable(tests src/test_trx_mmap.cpp)
 target_link_libraries(tests PRIVATE ${CONAN_LIBS} ${LOCAL_PROJECT_NAME})
 
diff --git a/tests/src/test_trx_mmap.cpp b/tests/src/test_trx_mmap.cpp
index 2cf3c3a..431252d 100644
--- a/tests/src/test_trx_mmap.cpp
+++ b/tests/src/test_trx_mmap.cpp
@@ -206,11 +206,8 @@ TEST(TrxFileMemmap, __create_memmap)
 
 TEST(TrxFileMemmap, load_header)
 {
+	std::string path = DATA_DIR "/small.trx";
 
-    if(const char* env_p = std::getenv("DATA_DIR"))
-        std::cout << "Your PATH is: " << env_p << '\n';
-
-	std::string path = "data/small.trx";
 	int *errorp;
 	zip_t *zf = zip_open(path.c_str(), 0, errorp);
 	json root = trxmmap::load_header(zf);
@@ -253,7 +250,7 @@ TEST(TrxFileMemmap, load_header)
 
 TEST(TrxFileMemmap, load_zip)
 {
-	trxmmap::TrxFile<half> *trx = trxmmap::load_from_zip<half>("data/small.trx");
+	trxmmap::TrxFile<half> *trx = trxmmap::load_from_zip<half>(DATA_DIR "/small.trx");
 	EXPECT_GT(trx->streamlines->_data.size(), 0);
 }
 
@@ -274,7 +271,7 @@ TEST(TrxFileMemmap, TrxFile)
 
 	EXPECT_EQ(trx->header, expected);
 
-	std::string path = "data/small.trx";
+	std::string path = DATA_DIR "/small.trx";
 	int *errorp;
 	zip_t *zf = zip_open(path.c_str(), 0, errorp);
 	json root = trxmmap::load_header(zf);
@@ -296,13 +293,13 @@ TEST(TrxFileMemmap, TrxFile)
 
 	EXPECT_EQ(root_init->header, init_as);
 	EXPECT_EQ(trx_init->streamlines->_data.size(), 33886 * 3);
-	EXPECT_EQ(trx_init->streamlines->_offsets.size(), 1000);
+	EXPECT_EQ(trx_init->streamlines->_offsets.size(), 1001);
 	EXPECT_EQ(trx_init->streamlines->_lengths.size(), 1000);
 }
 
 TEST(TrxFileMemmap, deepcopy)
 {
-	trxmmap::TrxFile<half> *trx = trxmmap::load_from_zip<half>("data/small.trx");
+	trxmmap::TrxFile<half> *trx = trxmmap::load_from_zip<half>(DATA_DIR "/small.trx");
 	trxmmap::TrxFile<half> *copy = trx->deepcopy();
 
 	EXPECT_EQ(trx->header, copy->header);
@@ -313,13 +310,13 @@ TEST(TrxFileMemmap, deepcopy)
 
 TEST(TrxFileMemmap, resize)
 {
-	trxmmap::TrxFile<half> *trx = trxmmap::load_from_zip<half>("data/small.trx");
+	trxmmap::TrxFile<half> *trx = trxmmap::load_from_zip<half>(DATA_DIR "/small.trx");
 	trx->resize();
 	trx->resize(10);
 }
 TEST(TrxFileMemmap, save)
 {
-	trxmmap::TrxFile<half> *trx = trxmmap::load_from_zip<half>("data/small.trx");
+	trxmmap::TrxFile<half> *trx = trxmmap::load_from_zip<half>(DATA_DIR "/small.trx");
 	trxmmap::save(*trx, (std::string) "testsave");
 	trxmmap::save(*trx, (std::string) "testsave.trx");
 

From 2b0fb27d182e4c124494c3326fb49a192cfbc577 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Fri, 18 Nov 2022 22:24:20 -0600
Subject: [PATCH 03/17] enh: n+1 offset

---
 src/trx.tpp | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/trx.tpp b/src/trx.tpp
index 92eebdc..8ead332 100644
--- a/src/trx.tpp
+++ b/src/trx.tpp
@@ -285,7 +285,7 @@ TrxFile<DT> *_initialize_empty_trx(int nb_streamlines, int nb_vertices, const Tr
 	std::tuple<int, int> shape_off = std::make_tuple(nb_streamlines, 1);
 
 	trx->streamlines->mmap_off = trxmmap::_create_memmap(offsets_filename, shape_off, "w+", offsets_dtype);
-	new (&(trx->streamlines->_offsets)) Map<Matrix<uint64_t, Dynamic, 1>>(reinterpret_cast<uint64_t *>(trx->streamlines->mmap_off.data()), std::get<0>(shape_off), std::get<1>(shape_off));
+	new (&(trx->streamlines->_offsets)) Map<Matrix<uint64_t, Dynamic, 1>>(reinterpret_cast<uint64_t *>(trx->streamlines->mmap_off.data()), std::get<0>(shape_off) + 1, std::get<1>(shape_off));
 
 	trx->streamlines->_lengths.resize(nb_streamlines);
 
@@ -343,7 +343,7 @@ TrxFile<DT> *_initialize_empty_trx(int nb_streamlines, int nb_vertices, const Tr
 				new (&(trx->data_per_vertex[x.first]->_data)) Map<Matrix<double, Dynamic, Dynamic>>(reinterpret_cast<double *>(trx->data_per_vertex[x.first]->mmap_pos.data()), rows, cols);
 			}
 
-			new (&(trx->data_per_vertex[x.first]->_offsets)) Map<Matrix<uint64_t, Dynamic, Dynamic>>(trx->streamlines->_offsets.data(), int(trx->streamlines->_offsets.rows()), int(trx->streamlines->_offsets.cols()));
+			new (&(trx->data_per_vertex[x.first]->_offsets)) Map<Matrix<uint64_t, Dynamic, Dynamic>>(trx->streamlines->_offsets.data(), int(trx->streamlines->_offsets.rows()) + 1, int(trx->streamlines->_offsets.cols()));
 			trx->data_per_vertex[x.first]->_lengths = trx->streamlines->_lengths;
 		}
 
@@ -481,16 +481,16 @@ TrxFile<DT> *TrxFile<DT>::_create_trx_from_pointer(json header, std::map<std::st
 
 		else if (base.compare("offsets") == 0 && (folder.compare("") == 0 || folder.compare(".") == 0))
 		{
-			if (size != int(trx->header["NB_STREAMLINES"]) || dim != 1)
+			int nb_streamlines = int(trx->header["NB_STREAMLINES"]);
+			if (size != nb_streamlines + 1 || dim != 1)
 			{
-
 				throw std::invalid_argument("Wrong offsets size/dimensionality");
 			}
 
 			std::tuple<int, int> shape = std::make_tuple(trx->header["NB_STREAMLINES"], 1);
 			trx->streamlines->mmap_off = trxmmap::_create_memmap(filename, shape, "r+", ext, mem_adress);
 
-			new (&(trx->streamlines->_offsets)) Map<Matrix<uint64_t, Dynamic, 1>>(reinterpret_cast<uint64_t *>(trx->streamlines->mmap_off.data()), std::get<0>(shape), std::get<1>(shape));
+			new (&(trx->streamlines->_offsets)) Map<Matrix<uint64_t, Dynamic, 1>>(reinterpret_cast<uint64_t *>(trx->streamlines->mmap_off.data()), std::get<0>(shape) + 1, std::get<1>(shape));
 
 			// TODO : adapt compute_lengths to accept a map
 			Matrix<uint64_t, Dynamic, 1> offsets;
@@ -617,7 +617,7 @@ TrxFile<DT> *TrxFile<DT>::_create_trx_from_pointer(json header, std::map<std::st
 			spdlog::error("{} is not part of a valid structure.", elem_filename);
 		}
 	}
-	if (trx->streamlines->_data.size() == 0 || trx->streamlines->_offsets.size() == 0)
+	if (trx->streamlines->_data.size() == 0 || trx->streamlines->_offsets.size() <= 1)
 	{
 
 		throw std::invalid_argument("Missing essential data.");
@@ -650,7 +650,7 @@ TrxFile<DT> *TrxFile<DT>::deepcopy()
 
 	if (!this->_copy_safe)
 	{
-		tmp_header["NB_STREAMLINES"] = to_dump->_offsets.size();
+		tmp_header["NB_STREAMLINES"] = to_dump->_offsets.size() - 1;
 		tmp_header["NB_VERTICES"] = to_dump->_data.size() / 3;
 	}
 	if (out_json.is_open())
@@ -813,7 +813,7 @@ std::tuple<int, int> TrxFile<DT>::_copy_fixed_arrays_from(TrxFile<DT> *trx, int
 		return std::make_tuple(strs_start, pts_start);
 
 	this->streamlines->_data(seq(pts_start, pts_end - 1), all) = trx->streamlines->_data(seq(0, curr_pts_len - 1), all);
-	this->streamlines->_offsets(seq(strs_start, strs_end - 1), all) = (trx->streamlines->_offsets(seq(0, curr_strs_len - 1), all).array() + pts_start).matrix();
+	this->streamlines->_offsets(seq(strs_start, strs_end), all) = (trx->streamlines->_offsets(seq(0, curr_strs_len), all).array() + pts_start).matrix();
 	this->streamlines->_lengths(seq(strs_start, strs_end - 1), all) = trx->streamlines->_lengths(seq(0, curr_strs_len - 1), all);
 
 	for (auto const &x : this->data_per_vertex)

From 41c5f1dd3f6a40155d5ccbb122c9b3c06e49ccf3 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Sun, 20 Nov 2022 16:19:10 -0600
Subject: [PATCH 04/17] enh: handle temp dir using envvars

---
 include/trx/trx.h           |  3 +++
 src/trx.cpp                 | 34 ++++++++++++++++++++++++++++++----
 src/trx.tpp                 | 12 ++----------
 tests/src/test_trx_mmap.cpp | 13 +++++++------
 4 files changed, 42 insertions(+), 20 deletions(-)

diff --git a/include/trx/trx.h b/include/trx/trx.h
index 4cf112a..cbca831 100644
--- a/include/trx/trx.h
+++ b/include/trx/trx.h
@@ -282,6 +282,8 @@ 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 +293,7 @@ namespace trxmmap
 	int rm_dir(const char *d);
 
 	std::string rm_root(std::string root, const std::string path);
+
 #include "trx.tpp"
 
 }
diff --git a/src/trx.cpp b/src/trx.cpp
index 8010572..0b04441 100644
--- a/src/trx.cpp
+++ b/src/trx.cpp
@@ -78,6 +78,32 @@ namespace trxmmap
 		}
 		closedir(dir);
 	}
+	std::string get_extraction_dir()
+	{
+		std::string dir_template = "/tmp/trx_XXXXXX";
+		char* extraction_dir;
+
+		if (const char* trx_tmp_dir = std::getenv("TRX_TMPDIR")) {
+			std::string trx_tmp_dir_s(trx_tmp_dir);
+			if (trx_tmp_dir_s.compare("use_working_dir") == 0) {
+				dir_template = "./trx_XXXXXX";
+			} else {
+				dir_template = trx_tmp_dir_s + "/trx_XXXXXX";
+			}
+		}
+		extraction_dir = mkdtemp(&dir_template[0]);
+		if (extraction_dir == NULL) {
+			spdlog::error("Could not create temporary directory {}", dir_template);
+			exit(1);
+		}
+		return std::string(extraction_dir);
+	}
+
+	int free_extraction_dir(std::string extraction_dir)
+	{
+		return rm_dir(extraction_dir.c_str());
+	}
+
 	std::string get_base(const std::string &delimiter, const std::string &str)
 	{
 		std::string token;
@@ -425,7 +451,7 @@ namespace trxmmap
 		{
 			if (entry->d_type == DT_DIR)
 			{
-				char path[1024];
+				char path[PATH_MAX];
 				if (strcmp(entry->d_name, ".") == 0 || strcmp(entry->d_name, "..") == 0)
 					continue;
 				snprintf(path, sizeof(path), "%s%s%s", d, SEPARATOR.c_str(), entry->d_name);
@@ -433,7 +459,7 @@ namespace trxmmap
 			}
 			else
 			{
-				char fn[1024];
+				char fn[PATH_MAX];
 				snprintf(fn, sizeof(fn), "%s%s%s", d, SEPARATOR.c_str(), entry->d_name);
 				if (remove(fn) != 0)
 				{
@@ -458,7 +484,7 @@ namespace trxmmap
 		{
 			if (entry->d_type == DT_DIR)
 			{
-				char path[1024];
+				char path[PATH_MAX];
 				if (strcmp(entry->d_name, ".") == 0 || strcmp(entry->d_name, "..") == 0)
 					continue;
 				snprintf(path, sizeof(path), "%s%s%s", directory.c_str(), SEPARATOR.c_str(), entry->d_name);
@@ -471,7 +497,7 @@ namespace trxmmap
 			else
 			{
 				std::string fn;
-				char fullpath[1024];
+				char fullpath[PATH_MAX];
 
 				snprintf(fullpath, sizeof(fullpath), "%s%s%s", directory.c_str(), SEPARATOR.c_str(), entry->d_name);
 				fn = rm_root(root, std::string(fullpath));
diff --git a/src/trx.tpp b/src/trx.tpp
index 8ead332..dea138c 100644
--- a/src/trx.tpp
+++ b/src/trx.tpp
@@ -223,11 +223,7 @@ TrxFile<DT> *_initialize_empty_trx(int nb_streamlines, int nb_vertices, const Tr
 {
 	TrxFile<DT> *trx = new TrxFile<DT>();
 
-	char *dirname;
-	char t[] = "/tmp/trx_XXXXXX";
-	dirname = mkdtemp(t);
-
-	std::string tmp_dir(dirname);
+	std::string tmp_dir = get_extraction_dir();
 
 	spdlog::info("Temporary folder for memmaps: {}", tmp_dir);
 
@@ -630,11 +626,7 @@ TrxFile<DT> *TrxFile<DT>::_create_trx_from_pointer(json header, std::map<std::st
 template <typename DT>
 TrxFile<DT> *TrxFile<DT>::deepcopy()
 {
-	char *dirname;
-	char t[] = "/tmp/trx_XXXXXX";
-	dirname = mkdtemp(t);
-
-	std::string tmp_dir(dirname);
+	std::string tmp_dir = get_extraction_dir();
 
 	std::string header = tmp_dir + SEPARATOR + "header.json";
 	std::ofstream out_json(header);
diff --git a/tests/src/test_trx_mmap.cpp b/tests/src/test_trx_mmap.cpp
index 431252d..10f35c2 100644
--- a/tests/src/test_trx_mmap.cpp
+++ b/tests/src/test_trx_mmap.cpp
@@ -173,13 +173,10 @@ TEST(TrxFileMemmap, __dichotomic_search)
 
 TEST(TrxFileMemmap, __create_memmap)
 {
+	setenv("TRX_TMPDIR", DATA_DIR, 1);
 
-	char *dirname;
-	char t[] = "/tmp/trx_XXXXXX";
-	dirname = mkdtemp(t);
-
-	std::string path(dirname);
-	path += "/offsets.int16";
+	std::string dir = get_extraction_dir();
+	std::string path = dir + "/offsets.int16";
 
 	std::tuple<int, int> shape = std::make_tuple(3, 4);
 
@@ -202,6 +199,10 @@ TEST(TrxFileMemmap, __create_memmap)
 	Map<Matrix<half, 3, 4>> real_m(reinterpret_cast<half *>(filled_mmap.data()), std::get<0>(shape), std::get<1>(shape));
 
 	EXPECT_EQ(expected_m, real_m);
+
+	free_extraction_dir(dir);
+
+	unsetenv("TRX_TMPDIR");
 }
 
 TEST(TrxFileMemmap, load_header)

From b8940636e74906787af581d8bce0c17691cc6ac0 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Wed, 7 Dec 2022 12:28:10 -0600
Subject: [PATCH 05/17] enh: some install info

---
 README.md | 34 ++++++++++++++++++++++++++--------
 1 file changed, 26 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 5809b04..b782fc2 100644
--- a/README.md
+++ b/README.md
@@ -4,15 +4,33 @@ The C++ implementations to the memory-mapped tractography file format.
 
 ## 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).
+It is basically `pip install conan`, for Python >= 3.6.
+
+To install the dependencies, run the following:
+```bash
+mkdir build && cd build
+conan install ..
+```
+
+### Building
+
+In `./build`:
+```bash
+cmake . && make
+```
+
+### Running tests
+```bash
+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

From 768c485b344fdacc99c5807237ccc749d1e9649a Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Fri, 6 Jan 2023 20:50:46 -0600
Subject: [PATCH 06/17] fix: cmake target

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index b782fc2..2ffe195 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,7 @@ conan install ..
 
 In `./build`:
 ```bash
-cmake . && make
+cmake .. && make
 ```
 
 ### Running tests

From eda4b662595e9f156cffb928ea5d27ca8901d204 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Fri, 6 Jan 2023 20:57:08 -0600
Subject: [PATCH 07/17] enh: add context

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 2ffe195..5d2a67e 100644
--- a/README.md
+++ b/README.md
@@ -23,6 +23,8 @@ cmake .. && make
 ```
 
 ### Running tests
+
+In `./build`:
 ```bash
 bin/tests
 ```

From 2b400ab1e993cb872058ab4554c864da1c5da655 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Mon, 9 Jan 2023 11:25:28 -0600
Subject: [PATCH 08/17] enh: ci

---
 .github/workflows/test.yml | 39 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..c63082e
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,39 @@
+on: [push, pull_request]
+
+env:
+  BUILD_TYPE: Release
+
+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/actions-setup-cmake@v1.13
+        with:
+          cmake-version: '3.22.x'
+    
+      - name: Run Tests
+        run: |
+          mkdir build && cd build
+          conan install ..
+          cmake .. && make
+          bin/tests

From fb4f8d15e348659453f0da277025212b6e3e5a69 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Mon, 9 Jan 2023 13:28:19 -0600
Subject: [PATCH 09/17] fix: install mio

---
 conanfile.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conanfile.txt b/conanfile.txt
index 15120e8..497437e 100644
--- a/conanfile.txt
+++ b/conanfile.txt
@@ -3,6 +3,7 @@ eigen/3.4.0@#3bc2bf84eff697283b6bd64d8262c423
 spdlog/1.10.0@#bd2bfacf219f212f2874313ebd74da23
 nlohmann_json/3.11.2@#a35423bb6e1eb8f931423557e282c7ed
 libzip/1.8.0@#5a0a692ec9d7d8a4337eb79e55869639
+mio/cci.20201220
 gtest/cci.20210126
 
 [generators]

From 1ee138f4c792d98c26b1863c50aef96b5d84912a Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Sat, 21 Jan 2023 16:54:40 -0600
Subject: [PATCH 10/17] enh: update instructions for conan and gcc

---
 .github/workflows/test.yml |  2 +-
 CMakeLists.txt             | 14 ++++++++------
 README.md                  | 28 ++++++++++++++++++++--------
 conanfile.txt              |  2 +-
 4 files changed, 30 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index c63082e..491148f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,7 +1,7 @@
 on: [push, pull_request]
 
 env:
-  BUILD_TYPE: Release
+  BUILD_TYPE: Debug
 
 jobs:
   test:
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4ccddf1..1218e99 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -12,9 +12,15 @@ conan_basic_setup()
 
 #set(CMAKE_BUILD_TYPE RelWithDebInfo)
 set(CMAKE_BUILD_TYPE Debug)
+#set(CMAKE_BUILD_TYPE Release)
 
 add_library(${LOCAL_PROJECT_NAME} src/trx.cpp src/trx.tpp)
 
+target_link_libraries(
+    ${LOCAL_PROJECT_NAME}
+    PRIVATE ${CONAN_LIBS}
+)
+
 target_include_directories(${LOCAL_PROJECT_NAME}
     PUBLIC
         $<INSTALL_INTERFACE:include>
@@ -22,11 +28,7 @@ target_include_directories(${LOCAL_PROJECT_NAME}
     PRIVATE
         ${CMAKE_CURRENT_SOURCE_DIR}/src
         ${CMAKE_CURRENT_BINARY_DIR}/gen-private-include
-)
-
-target_link_libraries(
-    ${LOCAL_PROJECT_NAME}
-    PRIVATE ${CONAN_LIBS}
+        ${CONAN_INCLUDE_DIRS}
 )
 
 set(CPACK_PROJECT_NAME ${PROJECT_NAME})
@@ -36,4 +38,4 @@ include(CPack)
 option(PACKAGE_TESTS "Build the tests" ON)
 if(PACKAGE_TESTS)
     add_subdirectory(tests)
-endif()
\ No newline at end of file
+endif()
diff --git a/README.md b/README.md
index 5d2a67e..953b8e9 100644
--- a/README.md
+++ b/README.md
@@ -3,30 +3,42 @@
 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
 
 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).
-It is basically `pip install conan`, for Python >= 3.6.
+TL;DR: It is basically `pip install conan`, and works for Python >= 3.6.
 
 To install the dependencies, run the following:
 ```bash
-mkdir build && cd build
-conan install ..
-```
+# 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 ..
 
-### Building
+# Build
+cmake -S .. -B . && make
+```
+### Running tests
 
 In `./build`:
 ```bash
-cmake .. && make
+bin/tests
 ```
 
-### Running tests
+### Iterating the code with new changes
 
 In `./build`:
 ```bash
-bin/tests
+make && bin/tests
 ```
 
 ## How to use
diff --git a/conanfile.txt b/conanfile.txt
index 497437e..70fd93c 100644
--- a/conanfile.txt
+++ b/conanfile.txt
@@ -1,6 +1,6 @@
 [requires]
 eigen/3.4.0@#3bc2bf84eff697283b6bd64d8262c423
-spdlog/1.10.0@#bd2bfacf219f212f2874313ebd74da23
+spdlog/1.10.0@#1e0f4eb6338d05e4bd6fcc6bf4734172
 nlohmann_json/3.11.2@#a35423bb6e1eb8f931423557e282c7ed
 libzip/1.8.0@#5a0a692ec9d7d8a4337eb79e55869639
 mio/cci.20201220

From 71f44977f41cacf56a434d6af9cc1cccad6820eb Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Sat, 21 Jan 2023 16:56:46 -0600
Subject: [PATCH 11/17] fix: add profile set up

---
 .github/workflows/test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 491148f..1107e45 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -34,6 +34,8 @@ jobs:
       - name: Run Tests
         run: |
           mkdir build && cd build
+          conan profile new ./.conan --detect
+          conan profile update settings.compiler.libcxx=libstdc++11 ./.conan
           conan install ..
           cmake .. && make
           bin/tests

From 2bbaf40fb57ba418e121b78e6bd8afe210e79963 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Sat, 21 Jan 2023 17:03:16 -0600
Subject: [PATCH 12/17] fix: actually use profile

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 1107e45..9cca178 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -36,6 +36,6 @@ jobs:
           mkdir build && cd build
           conan profile new ./.conan --detect
           conan profile update settings.compiler.libcxx=libstdc++11 ./.conan
-          conan install ..
+          conan install --profile ./.conan ..
           cmake .. && make
           bin/tests

From 4fb2aa1db9b2d1f5b71081f8fba6c5aea724dcd7 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Sat, 21 Jan 2023 17:22:40 -0600
Subject: [PATCH 13/17] enh: break in two steps, set temp dir

---
 .github/workflows/test.yml | 11 ++++++++---
 src/trx.cpp                |  1 +
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 9cca178..92250cb 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -31,11 +31,16 @@ jobs:
         with:
           cmake-version: '3.22.x'
     
-      - name: Run Tests
+      - 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 .. && make
-          bin/tests
+          cmake -S .. -B . && make
+
+      - name: Test
+        run: |
+          build/bin/tests
+        env:
+          TRX_TMPDIR: ${{ runner.temp }}
diff --git a/src/trx.cpp b/src/trx.cpp
index 0b04441..feae848 100644
--- a/src/trx.cpp
+++ b/src/trx.cpp
@@ -78,6 +78,7 @@ namespace trxmmap
 		}
 		closedir(dir);
 	}
+
 	std::string get_extraction_dir()
 	{
 		std::string dir_template = "/tmp/trx_XXXXXX";

From d8a828c1cb0a7c93d8e6bc0d0fd38a4d0808bcc4 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Wed, 25 Jan 2023 22:57:28 -0600
Subject: [PATCH 14/17] fix: zip not setting compression mode/lvl

---
 src/trx.cpp                 | 13 ++++++++-----
 src/trx.tpp                 |  7 ++++---
 tests/src/test_trx_mmap.cpp |  7 +++----
 3 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/src/trx.cpp b/src/trx.cpp
index feae848..0e3541a 100644
--- a/src/trx.cpp
+++ b/src/trx.cpp
@@ -298,6 +298,7 @@ namespace trxmmap
 
 	mio::shared_mmap_sink _create_memmap(std::string &filename, std::tuple<int, int> &shape, std::string mode, std::string dtype, long long offset)
 	{
+
 		if (dtype.compare("bool") == 0)
 		{
 			std::string ext = "bit";
@@ -314,10 +315,7 @@ namespace trxmmap
 			allocate_file(filename, filesize);
 		}
 
-		// std::error_code error;
-
 		mio::shared_mmap_sink rw_mmap(filename, offset, filesize);
-
 		return rw_mmap;
 	}
 
@@ -504,12 +502,17 @@ namespace trxmmap
 				fn = rm_root(root, std::string(fullpath));
 
 				zip_source_t *s;
+				zip_int64_t idx;
 
-				if ((s = zip_source_file(zf, fullpath, 0, 0)) == NULL ||
-				    zip_file_add(zf, fn.c_str(), s, ZIP_FL_ENC_UTF_8) < 0)
+				if (
+					(s = zip_source_file(zf, fullpath, 0, 0)) == NULL ||
+					(idx = zip_file_add(zf, fn.c_str(), s, ZIP_FL_ENC_UTF_8)) < 0
+				)
 				{
 					zip_source_free(s);
 					spdlog::error("error adding file {}: {}", fn, zip_strerror(zf));
+				} else {
+					zip_set_file_compression(zf, idx, compression_standard, 0);
 				}
 			}
 		}
diff --git a/src/trx.tpp b/src/trx.tpp
index dea138c..f46b61f 100644
--- a/src/trx.tpp
+++ b/src/trx.tpp
@@ -529,9 +529,10 @@ TrxFile<DT> *TrxFile<DT>::_create_trx_from_pointer(json header, std::map<std::st
 		{
 			std::tuple<int, int> shape;
 			trx->data_per_vertex[base] = new ArraySequence<DT>();
-			int nb_scalar = size / int(trx->header["NB_VERTICES"]);
+			int nb_vertices = int(trx->header["NB_VERTICES"]);
+			int nb_scalar = size / nb_vertices;
 
-			if (size % int(trx->header["NB_VERTICES"]) != 0 || nb_scalar != dim)
+			if (size % nb_vertices != 0 || nb_scalar != dim)
 			{
 
 				throw std::invalid_argument("Wrong dpv size/dimensionality");
@@ -647,7 +648,7 @@ TrxFile<DT> *TrxFile<DT>::deepcopy()
 	}
 	if (out_json.is_open())
 	{
-		out_json << std::setw(4) << tmp_header << std::endl;
+		out_json << tmp_header << std::endl;
 		out_json.close();
 	}
 
diff --git a/tests/src/test_trx_mmap.cpp b/tests/src/test_trx_mmap.cpp
index 10f35c2..7a76aaf 100644
--- a/tests/src/test_trx_mmap.cpp
+++ b/tests/src/test_trx_mmap.cpp
@@ -318,11 +318,10 @@ TEST(TrxFileMemmap, resize)
 TEST(TrxFileMemmap, save)
 {
 	trxmmap::TrxFile<half> *trx = trxmmap::load_from_zip<half>(DATA_DIR "/small.trx");
-	trxmmap::save(*trx, (std::string) "testsave");
-	trxmmap::save(*trx, (std::string) "testsave.trx");
+	trxmmap::save(*trx, "/testsave.trx");
+	trxmmap::TrxFile<half> *saved = trxmmap::load_from_zip<half>("/testsave.trx");
 
-	// trxmmap::TrxFile<half> *saved = trxmmap::load_from_zip<half>("testsave.trx");
-	//  EXPECT_EQ(saved->data_per_vertex["color_x.float16"]->_data, trx->data_per_vertex["color_x.float16"]->_data);
+	EXPECT_EQ(saved->data_per_vertex["color_x"]->_data, trx->data_per_vertex["color_x"]->_data);
 }
 
 int main(int argc, char **argv)

From 0d841f752a7ee7bce05569a320c9707a44380fe1 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Mon, 30 Jan 2023 23:38:46 -0600
Subject: [PATCH 15/17] enh: optional conan dependencies

---
 CMakeLists.txt       | 24 +++++-------------------
 conanfile.py         | 11 +++++++++++
 include/trx/trx.h    |  3 +++
 tests/CMakeLists.txt | 11 +++++++++--
 4 files changed, 28 insertions(+), 21 deletions(-)
 create mode 100644 conanfile.py

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1218e99..ed15b0d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -5,10 +5,9 @@ cmake_minimum_required(VERSION 3.0.0)
 cmake_policy(SET CMP0074 NEW)
 cmake_policy(SET CMP0079 NEW)
 project(${LOCAL_PROJECT_NAME} VERSION ${LOCAL_PROJECT_VERSION})
-set (CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 11)
 
-include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake)
-conan_basic_setup()
+option(TRX_USE_CONAN "Should Conan package manager be used?" ON)
 
 #set(CMAKE_BUILD_TYPE RelWithDebInfo)
 set(CMAKE_BUILD_TYPE Debug)
@@ -16,26 +15,13 @@ set(CMAKE_BUILD_TYPE Debug)
 
 add_library(${LOCAL_PROJECT_NAME} src/trx.cpp src/trx.tpp)
 
-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}
-)
+include(cmake/ConanSetup.cmake)
 
 set(CPACK_PROJECT_NAME ${PROJECT_NAME})
 set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
 include(CPack)
 
-option(PACKAGE_TESTS "Build the tests" ON)
-if(PACKAGE_TESTS)
+option(TRX_TESTS "Build the tests" ON)
+if(TRX_TESTS)
     add_subdirectory(tests)
 endif()
diff --git a/conanfile.py b/conanfile.py
new file mode 100644
index 0000000..f7a4a5f
--- /dev/null
+++ b/conanfile.py
@@ -0,0 +1,11 @@
+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"
diff --git a/include/trx/trx.h b/include/trx/trx.h
index cbca831..288fb33 100644
--- a/include/trx/trx.h
+++ b/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;
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index ed43d92..267552e 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -1,4 +1,7 @@
-include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake)
+if(TRX_USE_CONAN)
+    include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake)
+endif()
+
 include_directories(${PROJECT_SOURCE_DIR}/src)
 
 enable_testing()
@@ -8,6 +11,10 @@ include(GoogleTest)
 add_definitions(-DDATA_DIR="${CMAKE_CURRENT_SOURCE_DIR}/data")
 
 add_executable(tests src/test_trx_mmap.cpp)
-target_link_libraries(tests PRIVATE ${CONAN_LIBS} ${LOCAL_PROJECT_NAME})
+if(TRX_USE_CONAN)
+    target_link_libraries(tests PRIVATE ${CONAN_LIBS} ${LOCAL_PROJECT_NAME})
+else()
+    target_link_libraries(tests PRIVATE GTest::GTest GTest::Main)
+endif()
 
 gtest_discover_tests(tests)

From fc58961e04fe3dfe1c960dcee50e17d461ae8837 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Mon, 30 Jan 2023 23:48:34 -0600
Subject: [PATCH 16/17] enh: conan requirements in python

---
 conanfile.py  |  8 ++++++++
 conanfile.txt | 10 ----------
 2 files changed, 8 insertions(+), 10 deletions(-)
 delete mode 100644 conanfile.txt

diff --git a/conanfile.py b/conanfile.py
index f7a4a5f..2f6b509 100644
--- a/conanfile.py
+++ b/conanfile.py
@@ -9,3 +9,11 @@ class TRX(ConanFile):
     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",
+    ]
diff --git a/conanfile.txt b/conanfile.txt
deleted file mode 100644
index 70fd93c..0000000
--- a/conanfile.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-[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
-
-[generators]
-cmake
\ No newline at end of file

From 671a73ea121495cb9c1df1025c8458ad91b503d8 Mon Sep 17 00:00:00 2001
From: Anibal <anibalsolon@gmail.com>
Date: Wed, 8 Feb 2023 13:40:26 -0600
Subject: [PATCH 17/17] enh: reformatting examples

---
 examples/CMakeLists.txt                       | 28 ----------------
 examples/install-using-conan/CMakeLists.txt   | 30 +++++++++++++++++
 examples/install-using-conan/README.md        | 11 +++++++
 examples/install-using-conan/conanfile.txt    |  5 +++
 .../{ => install-using-conan}/load_trx.cpp    |  2 +-
 examples/install-using-vendor/CMakeLists.txt  | 13 ++++++++
 examples/install-using-vendor/load_trx.cpp    | 33 +++++++++++++++++++
 7 files changed, 93 insertions(+), 29 deletions(-)
 delete mode 100644 examples/CMakeLists.txt
 create mode 100644 examples/install-using-conan/CMakeLists.txt
 create mode 100644 examples/install-using-conan/README.md
 create mode 100644 examples/install-using-conan/conanfile.txt
 rename examples/{ => install-using-conan}/load_trx.cpp (97%)
 create mode 100644 examples/install-using-vendor/CMakeLists.txt
 create mode 100644 examples/install-using-vendor/load_trx.cpp

diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
deleted file mode 100644
index 22e116c..0000000
--- a/examples/CMakeLists.txt
+++ /dev/null
@@ -1,28 +0,0 @@
-cmake_minimum_required(VERSION 3.0.0)
-cmake_policy(SET CMP0074 NEW)
-cmake_policy(SET CMP0079 NEW)
-project(trx)
-set (CMAKE_CXX_STANDARD 11)
-
-set(CMAKE_BUILD_TYPE Debug)
-
-find_package(libzip REQUIRED)
-find_package (Eigen3 CONFIG REQUIRED)
-find_package(nlohmann_json CONFIG REQUIRED)
-find_package(spdlog CONFIG REQUIRED)
-
-include_directories(../src)
-add_executable(load_trx load_trx.cpp ../src/trx.h ../src/trx.tpp ../src/trx.cpp)
-
-
-TARGET_LINK_LIBRARIES(load_trx
-	nlohmann_json::nlohmann_json
-	Eigen3::Eigen
-	libzip::zip
-	spdlog::spdlog
-	spdlog::spdlog_header_only
-)
-
-
-set(CPACK_PROJECT_NAME ${PROJECT_NAME})
-set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
diff --git a/examples/install-using-conan/CMakeLists.txt b/examples/install-using-conan/CMakeLists.txt
new file mode 100644
index 0000000..cb8af49
--- /dev/null
+++ b/examples/install-using-conan/CMakeLists.txt
@@ -0,0 +1,30 @@
+cmake_minimum_required(VERSION 3.0.0)
+cmake_policy(SET CMP0074 NEW)
+cmake_policy(SET CMP0079 NEW)
+project(trx_example)
+
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_BUILD_TYPE Debug)
+
+add_executable(load_trx load_trx.cpp)
+
+include(${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})
diff --git a/examples/install-using-conan/README.md b/examples/install-using-conan/README.md
new file mode 100644
index 0000000..e5c2d03
--- /dev/null
+++ b/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
+```
diff --git a/examples/install-using-conan/conanfile.txt b/examples/install-using-conan/conanfile.txt
new file mode 100644
index 0000000..1aa8816
--- /dev/null
+++ b/examples/install-using-conan/conanfile.txt
@@ -0,0 +1,5 @@
+[requires]
+trx/1.0.0@user/channel
+
+[generators]
+cmake
\ No newline at end of file
diff --git a/examples/load_trx.cpp b/examples/install-using-conan/load_trx.cpp
similarity index 97%
rename from examples/load_trx.cpp
rename to examples/install-using-conan/load_trx.cpp
index 0f41601..de2e99b 100644
--- a/examples/load_trx.cpp
+++ b/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)
diff --git a/examples/install-using-vendor/CMakeLists.txt b/examples/install-using-vendor/CMakeLists.txt
new file mode 100644
index 0000000..5d95187
--- /dev/null
+++ b/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})
diff --git a/examples/install-using-vendor/load_trx.cpp b/examples/install-using-vendor/load_trx.cpp
new file mode 100644
index 0000000..de2e99b
--- /dev/null
+++ b/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;
+}
\ No newline at end of file