diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..fdfc501
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,83 @@
+MAKESELF:=makeself
+VERSION:=$(shell git describe|sed 's/-\([[:digit:]]\+\)-.*/\.post\1/')
+SETUPFILE:=MsSpec-$(VERSION).setup
+
+
+VERBOSE:=0
+ifeq ($(VERBOSE),0)
+	SUPPRESS_OUPUT:=1>/dev/null 2>/dev/null
+	MAKEFLAGS += --no-print-directory
+else
+	SUPPRESS_OUPUT:=
+endif
+
+
+.PHONY: clean version selfex venv doc
+
+
+selfex: results
+	@echo "Creating the self-extractible setup program... "
+#	copy the src folder and purge it
+	@cp -r src src_
+	@+$(MAKE) -C ./src_ purge
+#	update the version
+	@echo "$(VERSION)" > ./src_/VERSION
+#	distribute the README.md file
+	@cp README.md ./src_/
+#	create the package folder
+	@mkdir -p package
+#	create the *.lsm file
+	@echo "Begin4" > msspec.lsm
+	@echo "Title: Python MsSpec" >> msspec.lsm
+	@echo "Version: $(VERSION)" >> msspec.lsm
+	@echo "Entered-date: `date +%Y-%m-%d`" >> msspec.lsm
+	@echo "Description: A multiple scattering package for spectroscopies using electrons to probe materials" >> msspec.lsm
+	@echo "Keywords: " >> msspec.lsm
+	@echo "Author: sylvain.tricot@univ-rennes1.fr (Sylvain Tricot), didier.sebilleau@univ-rennes1.fr (Didier Sébilleau)" >> msspec.lsm
+	@echo "Maintained-by: sylvain.tricot@univ-rennes1.fr (Sylvain Tricot)" >> msspec.lsm
+	@echo "Primary-site: https://msspec.cnrs.fr" >> msspec.lsm
+	@echo "Alternate-site:" >> msspec.lsm
+	@echo "Original-site:" >> msspec.lsm
+	@echo "Platforms:" >> msspec.lsm
+	@echo "Copying-policy: Gnu Library General Public License (GLPL) 2.0" >> msspec.lsm
+	@echo "End" >> msspec.lsm
+#	create the self-extractible archive
+	@$(MAKESELF) --license "./license.txt" --lsm ./msspec.lsm ./src_ package/$(SETUPFILE) "Python MsSpec"  ./install.sh $(SUPPRESS_OUPUT)
+#	remove *.lsm file and src_
+	@rm ./msspec.lsm
+	@rm -rf ./src_
+
+
+version:
+	@python ./CI/update_version.py
+
+
+clean:
+	@echo "Cleaning all..."
+	@find ./src -type f -name '*.pyc' -exec rm -f {} +
+	@find ./src -type d -name '__pycache__' -exec rm -rf {} +
+	@rm -rf src/dist
+	@rm -rf src/*.egg*
+	@+$(MAKE) -C src/ clean $(SUPPRESS_OUPUT)
+	@+$(MAKE) -C doc/ clean $(SUPPRESS_OUPUT)
+	@rm -rf package
+
+purge: clean
+	@echo "Removing also shared objects..."
+	@find ./src -type f -name '*.so' -exec rm -f {} +
+
+results:
+	@+$(MAKE) -C src results
+
+
+venv:
+	@virtualenv --python=python3 --system-site-packages ci_venv $(SUPPRESS_OUPUT)
+	@. "./ci_venv/bin/activate" && pip install --upgrade pip && pip install --upgrade -r requirements.txt $(SUPPRESS_OUPUT)
+
+doc:
+	@echo "Building pdf and html documentation..."
+	@mkdir -p package/
+	@+$(MAKE) -C doc/ latexpdf $(SUPPRESS_OUPUT)
+	@rm -rf package/*.pdf
+	@cp "doc/build/latex/MsSpec-python.pdf" "./package/MsSpec-${VERSION}.pdf"
+	@+$(MAKE) -C doc/ html $(SUPPRESS_OUPUT)
diff --git a/src/Makefile b/src/Makefile
new file mode 100644
index 0000000..598e623
--- /dev/null
+++ b/src/Makefile
@@ -0,0 +1,36 @@
+include options.mk
+
+.PHONY: pybinding results clean 
+
+pybinding:
+	@echo "Building Python binding for phagen and spec..."
+	@+$(MAKE) -C msspec/phagen/fortran all
+	@+$(MAKE) -C msspec/spec/fortran all
+
+results: msspec/results.txt
+
+msspec/results.txt: pybinding
+	@echo "Generating results for unittests"
+	@coverage run --source=./ --omit=msspec/es/*,msspec/msspecgui/* msspec/create_tests_results.py
+#	create the html coverage report
+	@coverage html -d ../doc/source/htmlcov
+	@rm .coverage
+
+tests: pybinding
+	@echo "Runing unittests"
+	@python -m msspec.tests 1>/dev/null
+
+clean:
+	@echo "Cleaning all..."
+	@find ./ -type f -name '*.pyc' -exec rm -f {} +
+	@find ./ -type d -name '__pycache__' -exec rm -rf {} +
+	@+$(MAKE) -C msspec/spec/fortran clean
+	@+$(MAKE) -C msspec/phagen/fortran clean
+#	remove previous sdist
+	@rm -rf dist
+	@rm -rf *.egg*
+
+
+help:
+	@echo "help message"
+
diff --git a/src/Makefile.old b/src/Makefile.old
new file mode 100644
index 0000000..a7cc556
--- /dev/null
+++ b/src/Makefile.old
@@ -0,0 +1,60 @@
+VERSION:=$(shell python -c "import msspec; print(msspec.__version__)")
+
+VERBOSE:=0
+ifeq ($(VERBOSE),0)
+	SUPPRESS_OUPUT:=1>/dev/null 2>/dev/null
+	MAKEFLAGS += --no-print-directory --silent
+else
+	SUPPRESS_OUPUT:=
+endif
+
+
+install: sdist
+	@echo "Installing the newly created Python package..."
+	@pip install dist/msspec-*.tar.gz $(SUPPRESS_OUPUT)
+
+sdist: install_deps
+	@echo "Creating Python source distribution..."
+#	Create the source distrib
+	@python setup.py sdist $(SUPPRESS_OUPUT)
+
+install_deps: pybinding
+	@echo "Installing Python dependencies..."
+#	Install dependencies with pip
+	@pip install --upgrade -r requirements.txt $(SUPPRESS_OUPUT)
+
+pybinding:
+	@echo "Building Python binding for phagen and spec..."
+	@+$(MAKE) -C msspec/spec/fortran pybinding $(SUPPRESS_OUPUT)
+	@+$(MAKE) -C msspec/phagen/fortran pybinding $(SUPPRESS_OUPUT)
+
+results: msspec/results.txt
+
+msspec/results.txt: pybinding
+	@echo "Generating results for unittests"
+	@coverage run --source=./ --omit=msspec/es/*,msspec/msspecgui/* msspec/create_tests_results.py 1>/dev/null
+#	create the html coverage report
+	@coverage html -d ../doc/source/htmlcov
+	@rm .coverage
+
+tests: pybinding
+	@echo "Runing unittests"
+	@python -m msspec.tests 1>/dev/null
+
+clean:
+	@echo "Cleaning all..."
+	@find ./ -type f -name '*.pyc' -exec rm -f {} +
+	@find ./ -type d -name '__pycache__' -exec rm -rf {} +
+	@+$(MAKE) -C msspec/spec/fortran clean $(SUPPRESS_OUPUT)
+	@+$(MAKE) -C msspec/phagen/fortran clean $(SUPPRESS_OUPUT)
+#	remove previous sdist
+	@rm -rf dist
+	@rm -rf *.egg*
+
+purge: clean
+	@echo "Removing also shared objects..."
+	@find ./ -type f -name '*.so' -exec rm -f {} +
+
+help:
+	@echo "help message"
+
diff --git a/src/msspec/phagen/fortran/Makefile b/src/msspec/phagen/fortran/Makefile
new file mode 100644
index 0000000..a00c241
--- /dev/null
+++ b/src/msspec/phagen/fortran/Makefile
@@ -0,0 +1,6 @@
+
+SRCS   = phagen_scf_2.1_dp.f
+MAIN_F = main.f
+SO     = libphagen.so
+
+include ../../../options.mk
diff --git a/src/msspec/spec/fortran/Makefile b/src/msspec/spec/fortran/Makefile
new file mode 100644
index 0000000..f7def44
--- /dev/null
+++ b/src/msspec/spec/fortran/Makefile
@@ -0,0 +1,25 @@
+.PHONY: all phd_se phd_mi eig_mi eig_pw comp_curve clean
+
+all: phd_se phd_mi eig_mi eig_pw comp_curve
+
+phd_se:
+	@+$(MAKE) -f phd_se_noso_nosp_nosym.mk all
+
+phd_mi:
+	@+$(MAKE) -f phd_mi_noso_nosp_nosym.mk all
+
+eig_mi:
+	@+$(MAKE) -f eig_mi.mk all
+
+eig_pw:
+	@+$(MAKE) -f eig_pw.mk all
+
+comp_curve:
+	@+$(MAKE) -f comp_curve.mk all
+
+clean:
+	@+$(MAKE) -f phd_se_noso_nosp_nosym.mk $@
+	@+$(MAKE) -f phd_mi_noso_nosp_nosym.mk $@
+	@+$(MAKE) -f eig_mi.mk $@
+	@+$(MAKE) -f eig_pw.mk $@
+	@+$(MAKE) -f comp_curve.mk $@
diff --git a/src/msspec/spec/fortran/comp_curve.mk b/src/msspec/spec/fortran/comp_curve.mk
new file mode 100644
index 0000000..616e9ba
--- /dev/null
+++ b/src/msspec/spec/fortran/comp_curve.mk
@@ -0,0 +1,5 @@
+SRCS   = treatment/comp_curves.f
+MAIN_F = treatment/main.f
+SO     = comp_curves.so
+
+include ../../../options.mk
diff --git a/src/msspec/spec/fortran/eig_mi.mk b/src/msspec/spec/fortran/eig_mi.mk
new file mode 100644
index 0000000..c9be31d
--- /dev/null
+++ b/src/msspec/spec/fortran/eig_mi.mk
@@ -0,0 +1,12 @@
+memalloc_src               := memalloc/dim_mod.f memalloc/modules.f memalloc/allocation.f 
+cluster_gen_src            := $(wildcard cluster_gen/*.f)
+common_sub_src             := $(wildcard common_sub/*.f)
+renormalization_src        := $(wildcard renormalization/*.f)
+eig_common_src             := $(wildcard eig/common/*.f)
+eig_mi_src                 := $(wildcard eig/mi/*.f)
+
+SRCS   = $(memalloc_src) $(cluster_gen_src) $(common_sub_src) $(renormalization_src) $(eig_mi_src)
+MAIN_F = eig/mi/main.f
+SO     = _eig_pw.so
+
+include ../../../options.mk
diff --git a/src/msspec/spec/fortran/eig_pw.mk b/src/msspec/spec/fortran/eig_pw.mk
new file mode 100644
index 0000000..dd7f2a3
--- /dev/null
+++ b/src/msspec/spec/fortran/eig_pw.mk
@@ -0,0 +1,12 @@
+memalloc_src               := memalloc/dim_mod.f memalloc/modules.f memalloc/allocation.f 
+cluster_gen_src            := $(wildcard cluster_gen/*.f)
+common_sub_src             := $(wildcard common_sub/*.f)
+renormalization_src        := $(wildcard renormalization/*.f)
+eig_common_src             := $(wildcard eig/common/*.f)
+eig_pw_src                 := $(wildcard eig/pw/*.f)
+
+SRCS   = $(memalloc_src) $(cluster_gen_src) $(common_sub_src) $(renormalization_src) $(eig_pw_src)
+MAIN_F = eig/pw/main.f
+SO     = _eig_pw.so
+
+include ../../../options.mk
diff --git a/src/msspec/spec/fortran/phd_mi_noso_nosp_nosym.mk b/src/msspec/spec/fortran/phd_mi_noso_nosp_nosym.mk
new file mode 100644
index 0000000..2179c68
--- /dev/null
+++ b/src/msspec/spec/fortran/phd_mi_noso_nosp_nosym.mk
@@ -0,0 +1,11 @@
+memalloc_src               := memalloc/dim_mod.f memalloc/modules.f memalloc/allocation.f 
+cluster_gen_src            := $(wildcard cluster_gen/*.f)
+common_sub_src             := $(wildcard common_sub/*.f)
+renormalization_src        := $(wildcard renormalization/*.f)
+phd_mi_noso_nosp_nosym_src := $(wildcard phd_mi_noso_nosp_nosym/*.f)
+
+SRCS   = $(memalloc_src) $(cluster_gen_src) $(common_sub_src) $(renormalization_src) $(phd_mi_noso_nosp_nosym_src)
+MAIN_F = phd_mi_noso_nosp_nosym/main.f
+SO     = _phd_mi_noso_nosp_nosym.so
+
+include ../../../options.mk
diff --git a/src/msspec/spec/fortran/phd_se_noso_nosp_nosym.mk b/src/msspec/spec/fortran/phd_se_noso_nosp_nosym.mk
new file mode 100644
index 0000000..9769213
--- /dev/null
+++ b/src/msspec/spec/fortran/phd_se_noso_nosp_nosym.mk
@@ -0,0 +1,11 @@
+memalloc_src               := memalloc/dim_mod.f memalloc/modules.f memalloc/allocation.f 
+cluster_gen_src            := $(wildcard cluster_gen/*.f)
+common_sub_src             := $(wildcard common_sub/*.f)
+renormalization_src        := $(wildcard renormalization/*.f)
+phd_se_noso_nosp_nosym_src := $(wildcard phd_se_noso_nosp_nosym/*.f)
+
+SRCS   = $(memalloc_src) $(cluster_gen_src) $(common_sub_src) $(renormalization_src) $(phd_se_noso_nosp_nosym_src)
+MAIN_F = phd_se_noso_nosp_nosym/main.f
+SO     = _phd_se_noso_nosp_nosym.so
+
+include ../../../options.mk
diff --git a/src/options.mk b/src/options.mk
new file mode 100644
index 0000000..d3e7187
--- /dev/null
+++ b/src/options.mk
@@ -0,0 +1,97 @@
+FC       = gfortran
+F2PY     = f2py3
+
+DEBUG    = 0
+VERBOSE  = 0
+BUILDDIR = ./build
+
+
+################################################################################
+# GFORTRAN CONFIGURATION                                                       #
+################################################################################
+GFORTRAN_FFLAGS      = -O2 -ffast-math
+GFORTRAN_FFLAGS_DBG  = -g -Wall -Wextra -Warray-temporaries -Wconversion 
+GFORTRAN_FFLAGS_DBG += -fbacktrace -ffree-line-length-0 -fcheck=all
+GFORTRAN_FFLAGS_DBG += -ffpe-trap=zero,overflow,underflow -finit-real=nan
+################################################################################
+
+################################################################################
+# IFORT CONFIGURATION                                                          #
+################################################################################
+IFORT_FFLAGS     = 
+IFORT_FFLAGS_DBG =
+################################################################################
+
+################################################################################
+# F2PY CONFIGURATION                                                           #
+################################################################################
+F2PYFLAGS     = --opt=-O2
+F2PYFLAGS_DBG = --debug-capi --debug
+################################################################################
+
+
+
+################################################################################
+# /!\ DO NOT EDIT BELOW THAT LINE (unlesss you know what you're doing...)      #
+# CORE CONFIGURATION                                                           #
+################################################################################
+VERSION:=$(shell python -c "import msspec; print(msspec.__version__)")
+
+ifeq ($(VERBOSE),0)
+	OUPUT_REDIRECTION := 1>/dev/null 2>/dev/null
+	MAKEFLAGS = -s --no-print-directory
+else
+	OUPUT_REDIRECTION:=
+	MAKEFLAGS += --debug=b
+endif
+
+PREFIX=
+SUFFIX=
+
+ifeq ($(FC),gfortran)
+	PREFIX = GFORTRAN
+endif
+
+ifeq ($(FC),IFORT)
+	PREFIX = IFORT
+endif
+
+ifeq ($(DEBUG),1)
+	SUFFIX = _DBG
+endif
+
+FFLAGS = $($(PREFIX)_FFLAGS$(SUFFIX))
+
+OBJS = $(addprefix $(BUILDDIR)/, $(patsubst %.f,%.o, $(filter-out $(MAIN_F), $(SRCS))))
+
+.PHONY: clean obj all compilation_info
+
+compilation_info:
+	@echo "Compiler used: $(FC)"
+	@echo "fortran flags: $(FFLAGS)"
+	@echo "f2py flags: $(FFLAGS)"
+
+
+all: $(SO)
+
+
+obj: $(OBJS)
+
+
+clean:
+	@echo "Cleaning..."
+	rm -rf $(BUILDDIR)
+	rm -rf $(SO)
+
+
+$(BUILDDIR)/%.o: %.f
+	@echo "Compiling $@..."
+	mkdir -p $(basename $@)
+	$(FC) $(FFLAGS) -J $(BUILDDIR) -I $(BUILDDIR) -fPIC -o $@ -c $^ $(OUPUT_REDIRECTION)
+
+
+$(SO): $(OBJS) $(MAIN_F)
+	@echo "building Python binding $@..."      
+	mkdir -p $(BUILDDIR)
+	$(F2PY) $(F2PYFLAGS) -I$(BUILDDIR) -m $(basename $@) -c $(OBJS) $(MAIN_F) $(OUPUT_REDIRECTION)
+	mv $(basename $@).*.so $@