From 4fedc7274907a87b3b74a0b4ac299523366e2a6e Mon Sep 17 00:00:00 2001
From: Thomas Applencourt <t.applencourt@gmail.com>
Date: Fri, 5 Jun 2015 22:33:19 +0200
Subject: [PATCH] First try of new setup

---
 doc/code_architecture/Script.md               |   2 +
 install/scripts/build.sh                      |  10 ++
 .../scripts}/fetch_from_web.py                |   0
 install/scripts/install_curl.sh               |  19 +++
 install/scripts/install_docopt.sh             |  10 ++
 install/scripts/install_emsl.sh               |  10 ++
 install/scripts/install_ezfio.sh              |  16 +++
 install/scripts/install_irpf90.sh             |  24 ++++
 install/scripts/install_m4.sh                 |  15 +++
 install/scripts/install_ninja.sh              |  14 +++
 install/scripts/install_ocaml.sh              |  41 +++++++
 install/scripts/install_patch.sh              |  19 +++
 install/scripts/install_resultsFile.sh        |  11 ++
 install/scripts/install_zlib.sh               |  16 +++
 scripts/cache_compile.py                      |  62 ----------
 scripts/compilation/qp_create_ninja.py        |  28 +++--
 scripts/install/install_curl.sh               |  31 -----
 scripts/install/install_docopt.sh             |  21 ----
 scripts/install/install_emsl.sh               |  23 ----
 scripts/install/install_ezfio.sh              |  24 ----
 scripts/install/install_irpf90.sh             |  29 -----
 scripts/install/install_m4.sh                 |  31 -----
 scripts/install/install_ninja.sh              |  23 ----
 scripts/install/install_ocaml.sh              |  67 ----------
 scripts/install/install_resultsFile.sh        |  24 ----
 scripts/install/install_zlib.sh               |  38 ------
 setup_environment.sh                          | 116 ------------------
 27 files changed, 225 insertions(+), 499 deletions(-)
 create mode 100755 install/scripts/build.sh
 rename {scripts/install => install/scripts}/fetch_from_web.py (100%)
 create mode 100755 install/scripts/install_curl.sh
 create mode 100755 install/scripts/install_docopt.sh
 create mode 100755 install/scripts/install_emsl.sh
 create mode 100755 install/scripts/install_ezfio.sh
 create mode 100755 install/scripts/install_irpf90.sh
 create mode 100755 install/scripts/install_m4.sh
 create mode 100755 install/scripts/install_ninja.sh
 create mode 100755 install/scripts/install_ocaml.sh
 create mode 100755 install/scripts/install_patch.sh
 create mode 100755 install/scripts/install_resultsFile.sh
 create mode 100755 install/scripts/install_zlib.sh
 delete mode 100755 scripts/cache_compile.py
 delete mode 100755 scripts/install/install_curl.sh
 delete mode 100755 scripts/install/install_docopt.sh
 delete mode 100755 scripts/install/install_emsl.sh
 delete mode 100755 scripts/install/install_ezfio.sh
 delete mode 100755 scripts/install/install_irpf90.sh
 delete mode 100755 scripts/install/install_m4.sh
 delete mode 100755 scripts/install/install_ninja.sh
 delete mode 100755 scripts/install/install_ocaml.sh
 delete mode 100755 scripts/install/install_resultsFile.sh
 delete mode 100755 scripts/install/install_zlib.sh
 delete mode 100755 setup_environment.sh

diff --git a/doc/code_architecture/Script.md b/doc/code_architecture/Script.md
index b5c19dcd..c348aca5 100644
--- a/doc/code_architecture/Script.md
+++ b/doc/code_architecture/Script.md
@@ -23,6 +23,8 @@ It have some usefull property:
     - The dict of the root
     - The list reduced tree (For a list of module in input return only the root)
 
+For tree syntax you can check http://en.wikipedia.org/wiki/Tree_%28data_structure%29#Terminologies_used_in_Trees
+
 In the cli mode:
     - From a `NEEDED_CHILDREN_MODULE` file you can have all the descendant, and a png
     representation who correspond.
diff --git a/install/scripts/build.sh b/install/scripts/build.sh
new file mode 100755
index 00000000..6b7fc80a
--- /dev/null
+++ b/install/scripts/build.sh
@@ -0,0 +1,10 @@
+#!/bin/bash -x
+# This script should be included
+
+BUILD=_build/${TARGET}
+rm -rf -- ${BUILD}
+mkdir ${BUILD} || exit 1
+tar -zxf Downloads/${TARGET}.tar.gz --strip-components=1 --directory=${BUILD} || exit 1
+_install || exit 1
+rm -rf -- ${BUILD} _build/${TARGET}.log
+exit 0
\ No newline at end of file
diff --git a/scripts/install/fetch_from_web.py b/install/scripts/fetch_from_web.py
similarity index 100%
rename from scripts/install/fetch_from_web.py
rename to install/scripts/fetch_from_web.py
diff --git a/install/scripts/install_curl.sh b/install/scripts/install_curl.sh
new file mode 100755
index 00000000..a8ce9724
--- /dev/null
+++ b/install/scripts/install_curl.sh
@@ -0,0 +1,19 @@
+#!/bin/bash -x
+TARGET=curl
+
+function _install()
+{
+  cd ..
+  QPACKAGE_ROOT=$PWD
+  cd -
+  cd ${BUILD} || return 1
+  mv curl.ermine ${QPACKAGE_ROOT}/bin/curl || return 1
+}
+
+BUILD=_build/${TARGET}
+rm -rf -- ${BUILD}
+mkdir ${BUILD} || exit 1
+tar -xvjf Downloads/${TARGET}.tar.bz2 --strip-components=1 --directory=${BUILD} || exit 1
+_install || exit 1
+rm -rf -- ${BUILD} _build/${TARGET}.log
+exit 0
\ No newline at end of file
diff --git a/install/scripts/install_docopt.sh b/install/scripts/install_docopt.sh
new file mode 100755
index 00000000..d632ebd6
--- /dev/null
+++ b/install/scripts/install_docopt.sh
@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+TARGET=docopt
+
+function _install()
+{
+  cp -R ${BUILD} . || exit 1
+}
+
+source scripts/build.sh
diff --git a/install/scripts/install_emsl.sh b/install/scripts/install_emsl.sh
new file mode 100755
index 00000000..a87f91ec
--- /dev/null
+++ b/install/scripts/install_emsl.sh
@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+TARGET=emsl
+
+function _install()
+{
+  cp -R ${BUILD} . || exit 1
+}
+
+source scripts/build.sh
diff --git a/install/scripts/install_ezfio.sh b/install/scripts/install_ezfio.sh
new file mode 100755
index 00000000..9b7b8c59
--- /dev/null
+++ b/install/scripts/install_ezfio.sh
@@ -0,0 +1,16 @@
+#!/bin/bash -x
+
+TARGET=ezfio
+
+function _install()
+{
+  cd ..
+  QPACKAGE_ROOT=$PWD
+  cd -
+  rm -rf ${QPACKAGE_ROOT}/EZFIO
+  cd ${BUILD}/config || return 1
+  cd -
+  mv ${BUILD} ${QPACKAGE_ROOT}/install/EZFIO || return 1
+}
+
+source scripts/build.sh
diff --git a/install/scripts/install_irpf90.sh b/install/scripts/install_irpf90.sh
new file mode 100755
index 00000000..00dd7675
--- /dev/null
+++ b/install/scripts/install_irpf90.sh
@@ -0,0 +1,24 @@
+#!/bin/bash -x
+
+TARGET=irpf90
+function _install()
+{
+  cd ..
+  QPACKAGE_ROOT=$PWD
+  cd -
+
+  make -C ${BUILD} || return 1
+  rm -rf -- ./irpf90 
+  mv ${BUILD} .  || return 1
+  [[ -x ./irpf90/bin/irpf90 ]] || return 1
+  [[ -x ./irpf90/bin/irpman ]] || return 1
+  rm -rf -- ../bin/irpf90 ../bin/irpman
+  echo 'exec ${QMCCHEM_PATH}/install/irpf90/bin/irpf90 $@' > ../bin/irpf90 || return 1
+  echo 'exec ${QMCCHEM_PATH}/install/irpf90/bin/irpman $@' > ../bin/irpman || return 1
+  chmod +x ../bin/irpf90 ../bin/irpman || return 1
+  return 0
+}
+
+source scripts/build.sh
+
+
diff --git a/install/scripts/install_m4.sh b/install/scripts/install_m4.sh
new file mode 100755
index 00000000..db65aa15
--- /dev/null
+++ b/install/scripts/install_m4.sh
@@ -0,0 +1,15 @@
+#!/bin/bash -x
+
+TARGET=m4
+
+function _install()
+{
+  cd ..
+  QPACKAGE_ROOT=$PWD
+  cd -
+  cd ${BUILD}
+  ./configure && make || exit 1 
+  ln -sf ${PWD}/src/m4 ${QPACKAGE_ROOT}/bin || exit 1 
+}
+
+source scripts/build.sh
diff --git a/install/scripts/install_ninja.sh b/install/scripts/install_ninja.sh
new file mode 100755
index 00000000..2aab6edd
--- /dev/null
+++ b/install/scripts/install_ninja.sh
@@ -0,0 +1,14 @@
+#!/bin/bash -x
+
+TARGET=ninja
+
+function _install()
+{
+  cd ${BUILD} || return 1
+  ./configure.py --bootstrap || return 1
+  cd -
+  mv ${BUILD}/ninja ../bin/ || return 1
+  return 0 
+}
+
+source scripts/build.sh
\ No newline at end of file
diff --git a/install/scripts/install_ocaml.sh b/install/scripts/install_ocaml.sh
new file mode 100755
index 00000000..caa49c19
--- /dev/null
+++ b/install/scripts/install_ocaml.sh
@@ -0,0 +1,41 @@
+#!/bin/bash -x
+
+PACKAGES="core cryptokit ocamlfind sexplib"
+
+declare -i i
+i=$(gcc -dumpversion | cut -d '.' -f 2)
+if [[ i -lt 6 ]]
+then
+   echo "GCC version $(gcc -dumpversion) too old. GCC >= 4.6 required."
+   exit 1
+fi
+
+cd ..
+QPACKAGE_ROOT=$PWD
+cd -
+
+cd Downloads || exit 1
+chmod +x  ocaml.sh || exit 1
+
+if [[ -d ${HOME}/.opam ]]
+then
+  source ${HOME}/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true
+fi
+
+echo N | ./ocaml.sh ${QPACKAGE_ROOT}/bin/ || exit 1
+if [[ ! -f ${QPACKAGE_ROOT}/bin/opam ]]
+then
+   echo "Installation of OPAM failed"
+   exit 2
+fi
+${QPACKAGE_ROOT}/bin/opam config setup -a --dot-profile ${QPACKAGE_ROOT}/qmcchemrc || exit 1
+touch ${QPACKAGE_ROOT}/bin/opam
+
+export LD_LIBRARY_PATH=${QPACKAGE_ROOT}/lib:${LD_LIBRARY_PATH}
+export LIBRARY_PATH=${QPACKAGE_ROOT}/lib:${LIBRARY_PATH}
+export C_INCLUDE_PATH=${QPACKAGE_ROOT}/lib:${C_INCLUDE_PATH}
+opam install ${PACKAGES} || exit 1
+rm -f ../_build/ocaml.log
+exit 0
+
+
diff --git a/install/scripts/install_patch.sh b/install/scripts/install_patch.sh
new file mode 100755
index 00000000..53eda01c
--- /dev/null
+++ b/install/scripts/install_patch.sh
@@ -0,0 +1,19 @@
+#!/bin/bash -x
+
+TARGET=patch
+
+function _install()
+{  
+  mkdir ${TARGET}
+  cd ..
+  QPACKAGE_ROOT=$PWD
+  cd -
+  cd ${BUILD}
+  ./configure --prefix=${QPACKAGE_ROOT}/install/${TARGET} && make || exit 1
+  make install || exit 1
+  cd -
+  cp ${TARGET}/bin/${TARGET} ${QPACKAGE_ROOT}/bin || exit 1
+  rm -R -- ${TARGET} || exit 1
+}
+
+source scripts/build.sh
\ No newline at end of file
diff --git a/install/scripts/install_resultsFile.sh b/install/scripts/install_resultsFile.sh
new file mode 100755
index 00000000..d4238d5f
--- /dev/null
+++ b/install/scripts/install_resultsFile.sh
@@ -0,0 +1,11 @@
+#!/bin/bash -x
+
+TARGET=resultsFile
+
+function _install()
+{
+  cp -R ${BUILD} . || exit 1
+}
+
+source scripts/build.sh
+
diff --git a/install/scripts/install_zlib.sh b/install/scripts/install_zlib.sh
new file mode 100755
index 00000000..7cd66d76
--- /dev/null
+++ b/install/scripts/install_zlib.sh
@@ -0,0 +1,16 @@
+#!/bin/bash -x
+
+TARGET=zlib
+
+function _install()
+{
+  mkdir ${TARGET} || exit 1
+  cd ..
+  QPACKAGE_ROOT=$PWD
+  cd -
+  cd ${BUILD}
+  ./configure && make || exit 1
+  make install prefix=$QPACKAGE_ROOT/install/${TARGET} || exit 1
+}
+
+source scripts/build.sh
\ No newline at end of file
diff --git a/scripts/cache_compile.py b/scripts/cache_compile.py
deleted file mode 100755
index 9898eae5..00000000
--- a/scripts/cache_compile.py
+++ /dev/null
@@ -1,62 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import shelve
-import hashlib
-import re
-
-r = re.compile(ur'-c\s+(\S+\.[fF]90)\s+-o\s+(\S+\.o)')
-p = re.compile(ur'-I IRPF90_temp/\S*\s+')
-mod = re.compile(ur'module\s+(?P<mod>\S+).+end\s?module\s+(?P=mod)?', re.MULTILINE | re.IGNORECASE)
-
-TMPDIR="/tmp/qp_compiler/"
-
-def main():
-    # Create temp directory
-    if "qp_compiler" not in os.listdir("/tmp"):
-      os.mkdir("/tmp/qp_compiler/")
-
-    line = sys.argv[1:]
-    command = " ".join(line)
-    command_clean = p.sub('',command)
-
-    try:
-      match = r.search(command_clean)
-      input  = match.group(1)
-      output = match.group(2)
-    except:
-      os.system(command)
-      return
-    m = hashlib.md5()
-
-    # Fread : read input
-    with open(input,'r') as file:
-      fread = file.read()
-      m.update( " ".join( [ command, fread ] ))
-
-    # Md5 Key containing command + content of Fread
-    key = TMPDIR+m.hexdigest()
-    try:
-        # Try to return the content of the .o file
-        with open(key,'r') as file:
-            result = file.read()
-    except IOError:
-        # Compile the file -> .o
-        os.system(command)
-        # Read the .o
-        with open(output,'r') as file:
-            result = file.read()
-        # Copy the .o in database
-        if not mod.search(fread.replace('\n',' ')):
-            with open(key,'w') as file:
-                file.write(result)
-        else:
-            print input+' -> module'
-    else:
-        # Write the .o file
-        with open(output,'w') as file:
-            file.write(result)
-
-if __name__ == '__main__':
-    main()
diff --git a/scripts/compilation/qp_create_ninja.py b/scripts/compilation/qp_create_ninja.py
index 343ccd89..62f4758d 100755
--- a/scripts/compilation/qp_create_ninja.py
+++ b/scripts/compilation/qp_create_ninja.py
@@ -296,7 +296,7 @@ def ninja_symlink_build(path_module, l_symlink):
 # o ._ ._ _|_ (_| / \   ._ _   _. |   _
 # | |  |_) |    | \_/ o | | | (_| |< (/_
 #      |
-def get_l_file_for_module(path_module_abs):
+def get_l_file_for_module(path_module):
     '''
     return the list of irp.f in a module
     '''
@@ -306,17 +306,17 @@ def get_l_file_for_module(path_module_abs):
 
     l_template = []
 
-    for f in os.listdir(path_module_abs):
+    for f in os.listdir(path_module.abs):
         if f.lower().endswith(tuple([".template.f", ".include.f"])):
-            l_template.append(join(path_module_abs, f))
+            l_template.append(join(path_module.abs, f))
         elif f.endswith(".irp.f"):
-            l_irp.append(join(path_module_abs, f))
+            l_irp.append(join(path_module.abs, f))
         elif f.lower().endswith(tuple([".f", ".f90", ".c", ".cpp", ".cxx"])):
-            l_src.append(join(path_module_abs, f))
+            l_src.append(f)
             obj = '{0}.o'.format(os.path.splitext(f)[0])
-            l_obj.append(join(path_module_abs, obj))
+            l_obj.append(obj)
         elif f == "EZFIO.cfg":
-            l_irp.append(join(path_module_abs, "ezfio_interface.irp.f"))
+            l_irp.append(join(path_module.abs, "ezfio_interface.irp.f"))
 
     d = {"l_irp": l_irp,
          "l_src": l_src,
@@ -334,12 +334,20 @@ def get_file_dependency(d_info_module):
 
     for module, l_children in d_info_module.iteritems():
 
-        for key, values in get_l_file_for_module(module.abs).iteritems():
+        for key, values in get_l_file_for_module(module).iteritems():
+            if key in ["l_src"]:
+		values = [join(module.abs,o) for o in values]
+	    if key in ["l_obj"]:
+              	values = [join(module.abs,"IRPF90_temp",o) for o in values]
             d_irp[module][key] = values
 
         for children in l_children:
-            for key, values in get_l_file_for_module(children.abs).iteritems():
-                d_irp[module][key].extend(values)
+            for key, values in get_l_file_for_module(children).iteritems():
+		 if key in ["l_src"]:
+		      values = [join(module.abs,children.rel,o) for o in values]
+		 if key in ["l_obj"]:
+		      values = [join(module.abs,"IRPF90_temp",children.rel,o) for o in values]
+                 d_irp[module][key].extend(values)
 
     return d_irp
 
diff --git a/scripts/install/install_curl.sh b/scripts/install/install_curl.sh
deleted file mode 100755
index 5f32e384..00000000
--- a/scripts/install/install_curl.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/bin/bash
-#
-# Installs curl for ocaml
-# Mon Jan 12 18:52:48 CET 2015
-
-CURL="curl-7.30.0.ermine"
-CURL_URL="http://qmcchem.ups-tlse.fr/files/scemama/${CURL}.tar.bz2"
-
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit -1
-fi
-
-cd ${QPACKAGE_ROOT}
-
-curl -kL "https://github.com/LCPQ/quantum_package" &> /dev/null
-if [[ $? -eq 0 ]]
-then
-  exit 0
-fi
-
-rm -f -- ${QPACKAGE_ROOT}/bin/curl
-${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${CURL_URL} CURL.tar.bz2
-tar -jxf CURL.tar.bz2 && rm CURL.tar.bz2 ||exit 1
-cd ${CURL} || exit 1 
-mv curl.ermine ${QPACKAGE_ROOT}/bin/curl
-cd ${QPACKAGE_ROOT}
-rm -rf -- ${CURL}
-
diff --git a/scripts/install/install_docopt.sh b/scripts/install/install_docopt.sh
deleted file mode 100755
index 862e61cd..00000000
--- a/scripts/install/install_docopt.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/bash
-#
-# Installs docopt
-# lundi 27 avril 2015, 16:51:34 (UTC+0200)
-
-DOCOPT="docopt.py"
-DOCOPT_URL="https://raw.githubusercontent.com/docopt/docopt/master/${DOCOPT}"
-
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit -1
-fi
-
-cd ${QPACKAGE_ROOT}
-
-rm -f -- scripts/${DOCOPT}{,c}
-${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${DOCOPT_URL} ${DOCOPT}
-
-mv ${DOCOPT} scripts/utility/${DOCOPT}
diff --git a/scripts/install/install_emsl.sh b/scripts/install/install_emsl.sh
deleted file mode 100755
index b0bbc820..00000000
--- a/scripts/install/install_emsl.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-#
-# Installs EMSL_Basis_Set_Exchange_Local
-# Mon Jan 12 12:57:19 CET 2015
-
-BASE="EMSL_Basis_Set_Exchange_Local"
-URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
-
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit -1
-fi
-
-cd ${QPACKAGE_ROOT}
-
-${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
-tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
-rm -rf EMSL_Basis
-mv ${BASE}-master EMSL_Basis
-
-
diff --git a/scripts/install/install_ezfio.sh b/scripts/install/install_ezfio.sh
deleted file mode 100755
index 7e9a39e2..00000000
--- a/scripts/install/install_ezfio.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/bash
-#
-# Installs EZFIO
-# Mon Jan 12 16:06:44 CET 2015
-
-BASE="ezfio"
-URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
-
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit -1
-fi
-
-cd ${QPACKAGE_ROOT}
-
-rm -rf -- EZFIO
-${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
-tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
-mv EZFIO-master EZFIO
-
-
-
diff --git a/scripts/install/install_irpf90.sh b/scripts/install/install_irpf90.sh
deleted file mode 100755
index 251cd9f3..00000000
--- a/scripts/install/install_irpf90.sh
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/bin/bash
-#
-# Installs irpf90
-# Mon Jan 12 16:00:20 CET 2015
-
-BASE="irpf90"
-URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
-
-# Check the QPACKAGE_ROOT directory
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit 1
-fi
-
-cd ${QPACKAGE_ROOT}
-
-
-${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
-tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
-mv ${BASE}-master irpf90
-make -C irpf90
-rm -rf -- bin/irpf90 bin/irpman
-echo '${QPACKAGE_ROOT}/irpf90/bin/irpf90 $@' > bin/irpf90
-echo '${QPACKAGE_ROOT}/irpf90/bin/irpman $@' > bin/irpman
-chmod +x bin/irpf90 bin/irpman
-
-
diff --git a/scripts/install/install_m4.sh b/scripts/install/install_m4.sh
deleted file mode 100755
index 6495b82e..00000000
--- a/scripts/install/install_m4.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/bin/bash
-#
-# Installs m4 for ocaml
-# Thu Oct 23 22:02:08 CEST 2014
-
-M4_URL="http://ftp.gnu.org/gnu/m4/m4-latest.tar.gz"
-M4=$(which m4)
-
-# Check the QPACKAGE_ROOT directory
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit 1
-fi
-
-cd ${QPACKAGE_ROOT}
-
-rm -f l${QPACKAGE_ROOT}/bin/m4
-if [[ -z ${M4} ]] 
-then 
-    rm -f -- bin/m4
-    ${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${M4_URL} M4.tar.gz 
-    tar -zxf M4.tar.gz && rm M4.tar.gz ||exit 1
-    cd m4* || exit 1 
-    ./configure && make || exit 1 
-    ln -s ${PWD}/src/m4 ${QPACKAGE_ROOT}/bin 
-else
-    ln -s ${M4} ${QPACKAGE_ROOT}/bin/m4
-fi
-
diff --git a/scripts/install/install_ninja.sh b/scripts/install/install_ninja.sh
deleted file mode 100755
index e54c5366..00000000
--- a/scripts/install/install_ninja.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-#
-# Installs the ninja build system
-# Thu May 28 13:21:16 CEST 2015
-
-BASE="ninja"
-URL="https://github.com/martine/ninja/archive/master.tar.gz"
-
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit -1
-fi
-
-cd ${QPACKAGE_ROOT}
-
-${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
-tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
-rm -rf ${BASE}
-mv ${BASE}-master ${BASE}
-cd ${BASE}
-./configure.py --bootstrap
diff --git a/scripts/install/install_ocaml.sh b/scripts/install/install_ocaml.sh
deleted file mode 100755
index fe02e9df..00000000
--- a/scripts/install/install_ocaml.sh
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/bin/bash
-#
-# Downloads and installs ocaml, opam and core library
-# Thu Oct 23 21:58:40 CEST 2014
-
-PACKAGES="core cryptokit"
-OPAM_BASE=$HOME/.opam
-
-# Check the QPACKAGE_ROOT directory
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit 1
-fi
-
-cd ${QPACKAGE_ROOT}
-
-
-if [[ -f quantum_package.rc ]]
-then
-  source quantum_package.rc
-fi
-make -C ocaml Qptypes.ml &> /dev/null
-
-if [[ $? -ne 0 ]]
-then
-
-  if [[ -d ${OPAM_BASE} ]]
-  then
-    echo "${OPAM_BASE} exists."
-    echo  "Re-install ? [y/N]"
-    while read -r -n 1 -s answer; do
-      if [[ $answer = [YyNn] ]]; then
-         if [[ $answer = [Yy] ]] ; then
-           echo "  - Remove your directory ${OPAM_BASE}"
-           echo "  - Restart setup"
-           exit 1
-         fi
-         if [[ $answer = [Nn] ]] ; then
-           make -C ocaml Qptypes.ml
-           exit 0
-         fi
-      fi
-    done
-  fi
-fi
-${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py \
-   "https://raw.github.com/ocaml/opam/master/shell/opam_installer.sh" opam_installer.sh
-chmod +x opam_installer.sh
-echo N | ./opam_installer.sh ${QPACKAGE_ROOT}/bin 
-
-if [[ ! -f ${QPACKAGE_ROOT}/bin/opam ]]
-then
-   echo "Installation of OPAM failed"
-   exit 2
-fi
-rm -f opam_installer.sh
-${QPACKAGE_ROOT}/bin/opam config setup -a --dot-profile ${QPACKAGE_ROOT}/quantum_package.rc 
-
-source ${QPACKAGE_ROOT}/quantum_package.rc
-echo Y | opam install ${PACKAGES}
-
-make -C ocaml Qptypes.ml
-
-exit 0 
-
diff --git a/scripts/install/install_resultsFile.sh b/scripts/install/install_resultsFile.sh
deleted file mode 100755
index dc5c5d11..00000000
--- a/scripts/install/install_resultsFile.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/bash
-#
-# Installs the resultsFile Python library
-# Mon Jan 19 15:08:18 CET 2015
-
-URL="https://github.com/LCPQ/resultsFile/archive/master.tar.gz"
-
-# Check the QPACKAGE_ROOT directory
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit 1
-fi
-
-cd ${QPACKAGE_ROOT}
-
-
-rm -rf resultsFile-master
-${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/resultsFile.tar.gz
-tar -zxf resultsFile.tar.gz && rm resultsFile.tar.gz ||exit 1
-mv resultsFile-master resultsFile
-
-
diff --git a/scripts/install/install_zlib.sh b/scripts/install/install_zlib.sh
deleted file mode 100755
index 30f0055b..00000000
--- a/scripts/install/install_zlib.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/bin/bash
-#
-# Installs zlib for ocaml cryptokit
-# Mon Jan 12 18:52:48 CET 2015
-
-ZLIB="zlib-1.2.8"
-ZLIB_URL="http://zlib.net/${ZLIB}.tar.gz"
-
-# Check the QPACKAGE_ROOT directory
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit 1
-fi
-
-cd ${QPACKAGE_ROOT}
-
-
-cat > /tmp/main.c << EOF
-int main () {}
-EOF
-gcc /tmp/main.c -lz
-if [[ $? -eq 0 ]]
-then
-  rm /tmp/main.c "a.out"
-  exit 0
-fi
-rm /tmp/main.c
-
-${QPACKAGE_ROOT}/scripts/install/fetch_from_web.py ${ZLIB_URL} ZLIB.tar.gz
-tar -zxf ZLIB.tar.gz && rm ZLIB.tar.gz ||exit 1
-cd ${ZLIB} || exit 1 
-./configure && make
-make install prefix=$QPACKAGE_ROOT
-cd ${QPACKAGE_ROOT}
-rm -rf -- ${ZLIB}
-
diff --git a/setup_environment.sh b/setup_environment.sh
deleted file mode 100755
index 0eb5e20d..00000000
--- a/setup_environment.sh
+++ /dev/null
@@ -1,116 +0,0 @@
-#!/bin/bash
-#
-# Setup script. Downloads dependencies if they are not already present
-# in the current installation.
-# Thu Oct 23 22:02:08 CEST 2014
-
-BLUE=""
-RED=""
-BLACK="(B"
-
-QPACKAGE_ROOT="$( cd "$(dirname "$BASH_SOURCE")"  ; pwd -P )"
-
-
-cat << EOF > quantum_package.rc
-export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}")  ; pwd -P )
-export IRPF90="\${QPACKAGE_ROOT}/bin/irpf90"
-export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH}
-export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH}
-export C_INCLUDE_PATH="\${QPACKAGE_ROOT}"/include:\${C_INCLUDE_PATH}
-
-export PYTHONPATH=\${PYTHONPATH}\$(find "\${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
-
-export PATH=\${PATH}\$(find "\${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
-export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin
-export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml
-export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ninja
-source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null
-EOF
-
-
-source quantum_package.rc
-mkdir -p install_logs
-echo "${BLUE}===== Installing IRPF90 ===== ${BLACK}"
-${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh     | tee ${QPACKAGE_ROOT}/install_logs/install_irpf90.log
-if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]]  ||  [[ ! -x ${QPACKAGE_ROOT}/bin/irpf90 ]] ||  [[ ! -x ${QPACKAGE_ROOT}/bin/irpman ]]
-then
-  echo $RED "Error in IRPF90 installation" $BLACK
-  exit 1
-fi
-
-mkdir -p ${QPACKAGE_ROOT}/install_logs
-
-echo "${BLUE}===== Installing Ninja ===== ${BLACK}"
-${QPACKAGE_ROOT}/scripts/install/install_ninja.sh       | tee ${QPACKAGE_ROOT}/install_logs/install_ninja.log
-
-echo "${BLUE}===== Installing Zlib ===== ${BLACK}"
-${QPACKAGE_ROOT}/scripts/install/install_zlib.sh       | tee ${QPACKAGE_ROOT}/install_logs/install_zlib.log
-
-echo "${BLUE}===== Installing Curl ===== ${BLACK}"
-${QPACKAGE_ROOT}/scripts/install/install_curl.sh       | tee ${QPACKAGE_ROOT}/install_logs/install_curl.log
-
-echo "${BLUE}===== Installing M4 ===== ${BLACK}"
-${QPACKAGE_ROOT}/scripts/install/install_m4.sh         | tee ${QPACKAGE_ROOT}/install_logs/install_m4.log
-
-echo "${BLUE}===== Installing Docopt ===== ${BLACK}"
-${QPACKAGE_ROOT}/scripts/install/install_docopt.sh     | tee ${QPACKAGE_ROOT}/install_logs/install_docopt.log
-
-echo "${BLUE}===== Installing EMSL Basis set library ===== ${BLACK}"
-${QPACKAGE_ROOT}/scripts/install/install_emsl.sh       | tee ${QPACKAGE_ROOT}/install_logs/install_emsl.log
-
-if [[ ! -d ${QPACKAGE_ROOT}/EMSL_Basis ]]
-then
-  echo $RED "Error in EMSL Basis set library installation" $BLACK
-  exit 1
-fi
-
-echo "${BLUE}===== Installing EZFIO ===== ${BLACK}"
-
-${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh | tee ${QPACKAGE_ROOT}/install_logs/install_ezfio.log
-if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]]
-then
-  echo $RED "Error in EZFIO installation" $BLACK
-  exit 1
-fi
-
-
-echo "${BLUE}===== Installing Ocaml compiler and libraries ===== ${BLACK}"
-rm -f -- ocaml/Qptypes.ml
-${QPACKAGE_ROOT}/scripts/install/install_ocaml.sh | tee ${QPACKAGE_ROOT}/install_logs/install_ocaml.log
-
-if [[ ! -f ${QPACKAGE_ROOT}/ocaml/Qptypes.ml ]]
-then
-  echo $RED "Error in Ocaml installation" $BLACK
-  exit 1
-fi
-
-echo "${BLUE}===== Installing resultsFile Python library ===== ${BLACK}"
-${QPACKAGE_ROOT}/scripts/install/install_resultsFile.sh
-if [[ ! -d ${QPACKAGE_ROOT}/resultsFile ]]
-then
-  echo $RED "Error in resultsFile installation" $BLACK
-  exit 1
-fi
-
-
-echo $RED "
-=======================================================
-To complete the installation, add the following line to
-your ~/.bashrc:
-
-source ${QPACKAGE_ROOT}/quantum_package.rc
-
-=======================================================
-" $BLACK
-
-
-
-
-if [[ $1 == "--robot" ]] ; 
-then
-  exit 0
-else
-  source quantum_package.rc
-  exec bash
-fi
-