Remove boost::filesystem dependency

Author: alonyado

Internal/AlgoMarker/AlgoMarker/AlgoMarkerInternal.cpp

@@ -2,7 +2,7 @@
 #include "AlgoMarkerErr.h"
 #include <Logger/Logger/Logger.h>
 #include <boost/algorithm/string.hpp>
-#include <boost/filesystem.hpp>
+#include <filesystem>
 #define LOCAL_SECTION LOG_APP
 #define LOCAL_LEVEL	LOG_DEF_LEVEL
 
@@ -284,7 +284,7 @@ int InputSanityTester::read_config(const string &f_conf)
 
 	if (!inf)
 		return -1;
-	string base_path = boost::filesystem::path(f_conf.c_str()).parent_path().string();
+	string base_path = std::filesystem::path(f_conf).parent_path().string();
 
 	//MLOG("initializing sanity tester from file %s\n", f_conf.c_str());
 	string curr_line;

Internal/InfraMed/InfraMed/MedConvert.cpp

@@ -18,7 +18,7 @@
 #include <boost/algorithm/string/split.hpp>
 #include <boost/algorithm/string.hpp>
 #include <boost/algorithm/string/replace.hpp>
-#include <boost/filesystem.hpp>
+#include <filesystem>
 
 using namespace boost;
 
@@ -266,7 +266,7 @@ int MedConvert::prep_sids_to_load()
 void get_rel_filename(vector<string> &paths) {
 	for (size_t i = 0; i < paths.size(); i++)
 	{
-		boost::filesystem::path pt(paths[i]);
+		std::filesystem::path pt(paths[i]);
 		paths[i] = pt.filename().string();
 	}
 }
@@ -386,8 +386,8 @@ int MedConvert::read_all(const string &config_fname)
 	for (string d : dict_fnames)
 	{
 		add_path_to_name_IM(out_path, d);
-		boost::filesystem::path pt_dict(d);
-		boost::filesystem::create_directories(pt_dict.parent_path().string());
+		std::filesystem::path pt_dict(d);
+		std::filesystem::create_directories(pt_dict.parent_path().string());
 	}
 	if (copy_files_IM(path, out_path, dict_fnames) < 0)
 		MTHROW_AND_ERR("MedConvert : read_all() : failed copying files from in to out directory\n");

Internal/InfraMed/InfraMed/Utils.cpp

@@ -9,7 +9,7 @@
 #define _LARGE_FILE_SOURCE
 #define _FILE_OFFSET_BITS 64
 #include <cstdio>
-#include <boost/filesystem.hpp>
+#include <filesystem>
 
 #define LOCAL_SECTION LOG_INFRA
 #define LOCAL_LEVEL	LOG_DEF_LEVEL
@@ -19,7 +19,7 @@ extern MedLogger global_logger;
 //-----------------------------------------------------------------------------
 bool file_exists_IM(const string &fname)
 {
-	return boost::filesystem::exists(fname);
+	return std::filesystem::exists(fname);
 }
 
 //----------------------------------------------------------------------------
@@ -91,7 +91,7 @@ int copy_file_IM(const string& in_file, const string& out_file) {
 int copy_files_IM(const string &in_path, const string &out_path, vector<string>& fnames) {
 
 	if (in_path != out_path) {
-		boost::filesystem::create_directories(out_path);
+		std::filesystem::create_directories(out_path);
 		for (unsigned int i=0; i<fnames.size(); i++) {
 			if (fnames[i].size() > 0 && fnames[i][0] == '/') {
 				MLOG("not copying [%s] as its absolute path\n", fnames[i].c_str());

Internal/MedProcessTools/MedProcessTools/MedModel.cpp

@@ -6,7 +6,7 @@
 #include <boost/foreach.hpp>
 #include <boost/algorithm/string/predicate.hpp>
 #include <boost/algorithm/string/find.hpp>
-#include <boost/filesystem.hpp>
+#include <filesystem>
 #include <boost/regex.hpp>
 #include <boost/algorithm/string/regex.hpp>
 #include <cmath>
@@ -1176,7 +1176,7 @@ void MedModel::fill_list_from_file(const string& fname, vector<string>& list) {
 
 }
 string MedModel::make_absolute_path(const string& main_file, const string& small_file, bool use_cwd) {
-	boost::filesystem::path p(main_file);
+	std::filesystem::path p(main_file);
 	string main_file_path = p.parent_path().string();
 	if (use_cwd)
 		main_file_path = run_current_path;
@@ -1309,9 +1309,9 @@ string MedModel::json_file_to_string(int recursion_level, const string& main_fil
 		}
 		out_string += orig.substr(last_char, it->position() - last_char);
 		if (add_change_path) {
-			boost::filesystem::path json_p(small_file_inc);
-			boost::filesystem::path json_par(fname);
-			string pth = boost::filesystem::absolute(json_p.parent_path(), json_par.parent_path()).string();
+			std::filesystem::path json_p(small_file_inc);
+			std::filesystem::path json_par(fname);
+			string pth = std::filesystem::absolute(json_par.parent_path() / json_p.parent_path()).string();
 			snprintf(buff, sizeof(buff), "{\"action_type\":\"change_path:%s\"},\n", pth.c_str());
 			add_path = string(buff);
 			out_string += add_path;

Internal/MedProcessTools/MedProcessTools/MedModelInitFromJson.cpp

@@ -6,7 +6,7 @@
 #include <boost/foreach.hpp>
 #include <boost/algorithm/string/predicate.hpp>
 #include <boost/algorithm/string/find.hpp>
-#include <boost/filesystem.hpp>
+#include <filesystem>
 #include <boost/regex.hpp>
 #include <boost/algorithm/string/regex.hpp>
 #include <string>
@@ -140,7 +140,7 @@ void MedModel::parse_action(basic_ptree<string, string>& action, vector<vector<s
 }
 
 void MedModel::init_from_json_file_with_alterations(const string &fname, vector<string>& alterations) {
-	run_current_path = boost::filesystem::path(fname).parent_path().string();
+	run_current_path = std::filesystem::path(fname).parent_path().string();
 	string json_contents = json_file_to_string(0, fname, alterations, "", true);
 
 	if (init_from_json_string(json_contents, fname) == 1)
@@ -403,7 +403,7 @@ void MedModel::replace_predictor_with_json_predictor(string f_json)
 {
 	// open the json file, transfer it to string
 	vector<string> alternations;
-	run_current_path = boost::filesystem::path(f_json).parent_path().string();
+	run_current_path = std::filesystem::path(f_json).parent_path().string();
 	string json_contents = json_file_to_string(0, f_json, alternations, "", true);
 
 	istringstream no_comments_stream(json_contents);

Internal/MedPyExport/README.md

@@ -1,5 +1,10 @@
 # Medial Python Binding
 
+## Relase Notes - 1.0.6
+* Fix code to compile in ARM computer
+* Removed ipython dependency
+* Readme fixes
+
 ## Relase Notes - 1.0.5
 * Adjustments to compile with Alpine/Musl library
 * Bugfix issue #5

Internal/MedPyExport/generate_binding/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "medpython"
-version = "1.0.5"
+version = "1.0.6"
 description = "Medial EarlySign Python"
 readme = "README.md"
 license = "MIT"
@@ -26,7 +26,6 @@ dependencies = [
     "numpy>=1.21.0",
     "pandas", 
     "plotly", 
-    "ipython"
 ]
 
 [project.urls]

Internal/MedUtils/MedUtils/MedPlot.cpp

@@ -4,8 +4,7 @@
 #include <ctime>
 #include <iostream>
 #include <algorithm>
-#include <boost/filesystem/path.hpp>
-#include <boost/filesystem.hpp>
+#include <filesystem>
 
 #ifdef _WIN32
 //define something for Windows
@@ -147,8 +146,8 @@ void createScatterHtmlGraph(const string &outPath, const vector<vector<pair<floa
 		y_name = "values";
 	}
 
-	boost::filesystem::path p(outPath);
-	boost::filesystem::path outDir = p.parent_path();
+	std::filesystem::path p(outPath);
+	std::filesystem::path outDir = p.parent_path();
 
 	string content = template_str;
 	if (template_str.empty())
@@ -473,7 +472,7 @@ void plotAUC(const vector<vector<float>> &all_preds, const vector<vector<float>>
 	vector<float> false_rate;
 	vector<float> ppv, pr;
 
-	boost::filesystem::create_directories(baseOut.data());
+	std::filesystem::create_directories(baseOut);
 	vector<map<float, float>> allData;
 	vector<map<float, float>> allPPV;
 	vector<map<float, float>> allSensPPV;

Internal/MedUtils/MedUtils/MedRegistry.cpp

@@ -10,7 +10,7 @@
 #include <MedProcessTools/MedProcessTools/MedModel.h>
 #include <boost/algorithm/string.hpp>
 #include <boost/math/distributions/chi_squared.hpp>
-#include <boost/filesystem.hpp>
+#include <filesystem>
 #include <omp.h>
 #include <MedMat/MedMat/MedMat.h>
 
@@ -269,7 +269,7 @@ RegistrySignalSet::RegistrySignalSet(const string &sigName, int durr_time, int b
 	outcome_value = outcome_val;
 	channel = chan;
 	repo = &rep;
-	boost::filesystem::path p(path_to_cfg_file);
+	std::filesystem::path p(path_to_cfg_file);
 	base_cfg_path = p.parent_path().string();
 	if (!sigName.empty()) {
 		int sid = rep.sigs.sid(sigName);
@@ -378,7 +378,7 @@ RegistrySignalSet::RegistrySignalSet(const string &init_string, MedRepository &r
 	repo = &rep;
 	init_from_string(init_string);
 	outcome_value = outcome_val;
-	boost::filesystem::path p(path_to_cfg_file);
+	std::filesystem::path p(path_to_cfg_file);
 	base_cfg_path = p.parent_path().string();
 	if (!sets.empty()) {
 		int section_id = rep.dict.section_id(signalName);
@@ -457,7 +457,7 @@ RegistrySignalDrug::RegistrySignalDrug(MedRepository &rep, const string &path_to
 	buffer_duration = 0;
 	take_only_first = false;
 	outcome_value = 1;
-	boost::filesystem::path p(path_to_cfg_file);
+	std::filesystem::path p(path_to_cfg_file);
 	base_path = p.parent_path().string();
 }
 

README.md

@@ -48,7 +48,14 @@ To install the python module:
 pip install medpython
 ```
 
+Build from source:
+```bash
+apt install libboost-all-dev
+python -m pip install -v "medpython @ git+https://github.com/Medial-EarlySign/medpython.git/#subdirectory=Internal/MedPyExport/generate_binding"
+```
+
 To explore the code:
 
 * `Internal/MedPython` - for the python module. The folder `generate_bindings` contains the `setup.py` to install the module.
 * `Internal/AlgoMarker` - the folder to compile the minimal shared library for production and running it in distroless container.
+