Merge pull request #69 from TApplencourt/master

Ninja build

.travis.yml

@@ -10,7 +10,7 @@ before_script:
   - sudo apt-get install graphviz
 
 script: 
-  - ./setup_environment.sh --robot 
+  - ./setup_environment.py
   - source ./quantum_package.rc
   - qp_create_ninja.py --production ./config/gfortran_example.cfg
   - ninja

COMPILE_RUN.md

@@ -12,11 +12,11 @@ The script to create the dependencies file (aka `build.ninja`) is `create_ninja_
 
 ## Compilation Flag
 
-You need to specify all the flag useful for the compilation:   like the optimization one, the mkl one .``$QPACKAGE_ROOT/config`` contains ``ifort.cfg`` and ``gfortran.cfg`` files which have the compiler flags that will be used to compile the code. You can edit these files to modify the compiling option. Put the file path when calling `create_ninja_build.py`
+You need to specify all the flag useful for the compilation:   like the optimization one, the mkl one .``$QP_ROOT/config`` contains ``ifort.cfg`` and ``gfortran.cfg`` files which have the compiler flags that will be used to compile the code. You can edit these files to modify the compiling option. Put the file path when calling `create_ninja_build.py`
 
 ## Example to create the Ninja file
 
-`create_ninja_build.py --production $QPACKAGE_ROOT/config/ifort.cfg`
+`create_ninja_build.py --production $QP_ROOT/config/ifort.cfg`
 
 # WARNING
 
@@ -24,8 +24,8 @@ For now reload this command if you add a `IRP.f90` or `EZFIO.cfg` file or modify
 
 ## Compile
 
-Just type `ninja` if you are in `$QPACKAGE_ROOT` (or `ninja -f $QPACKAGE_ROOT/build.ninja` elsewhere). The compilation will take approximately 3 min.
+Just type `ninja` if you are in `$QP_ROOT` (or `ninja -f $QP_ROOT/build.ninja` elsewhere). The compilation will take approximately 3 min.
 
 If you have set the `--developement` flag in a specific module you can go in the corresponding IRPF90_temp and run `ninja` to only make the module and submodule binaries. (You can use the `-f` option too)
 
-Now go in `$QPACKAGE_ROOT/ocaml` and type `make`
+Now go in `$QP_ROOT/ocaml` and type `make`

data/Makefile

@@ -1,7 +0,0 @@
-all: executables
-
-.PHONY: executables
-
-executables: 
-	cd  $(QPACKAGE_ROOT)/src ; $(MAKE) executables 
-	mv $(QPACKAGE_ROOT)/src/executables .

doc/code_architecture/Script.md

@@ -1,17 +1,17 @@
 # `ei_handler.py`
 
-This script in located in `$QPACKAGE_ROOT/scripts/ezfio_interface/`.
+This script in located in `$QP_ROOT/scripts/ezfio_interface/`.
 It provide all the resource need to deal with the `EZFIO.cfg` files :
-    - The creation of `$MODULE_LOWER_ezfio_config` in `$QPACKAGE_ROOT/ezfio/config`
+    - The creation of `$MODULE_LOWER_ezfio_config` in `$QP_ROOT/ezfio/config`
     - The `ezfio_interface.irp.f` who containt all the provider associate (in `$MODULE/`)
-    - The `$MODULE_LOWER_ezfio_defaults` in `$QPACKAGE_ROOT/data/`
+    - The `$MODULE_LOWER_ezfio_defaults` in `$QP_ROOT/data/`
     - The `Input_$MODULE_LOWER.ml` for the *qp_edit*
 
 For more information you can type `ei_handler.py -h`
 
 # `module_handler.py`
 
-This script in located in `$QPACKAGE_ROOT/scripts/module/`.
+This script in located in `$QP_ROOT/scripts/module/`.
 It provide all the resource related to the tree dependancy of the modules.
 If more useful as a librairy than a cli.
 
@@ -23,19 +23,21 @@ 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.
 
 
 # `qp_install_module.py`
-This script is located in `$QPACKAGE_ROOT/scripts/module/`.
+This script is located in `$QP_ROOT/scripts/module/`.
 
 It is usefull when you need to install a new module. (From the soon to come repo or from scratch).
 
 # `qp_create_ninja.py`
 
-This script is located in `$QPACKAGE_ROOT/scripts/compilation/`.
+This script is located in `$QP_ROOT/scripts/compilation/`.
 It will create the `build.ninja` file. It will use intersifly the `module_handler.py` module.
 
 To read all the flag for the compilation the module `read_compilation_cfg.py` is used. 

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

install/scripts/install_curl.sh

@@ -0,0 +1,19 @@
+#!/bin/bash -x
+TARGET=curl
+
+function _install()
+{
+  cd ..
+  QP_ROOT=$PWD
+  cd -
+  cd ${BUILD} || return 1
+  mv curl.ermine ${QP_ROOT}/bin/curl || return 1
+}
+
+BUILD=_build/${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

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

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

install/scripts/install_ezfio.sh

@@ -0,0 +1,16 @@
+#!/bin/bash -x
+
+TARGET=ezfio
+
+function _install()
+{
+  cd ..
+  QP_ROOT=$PWD
+  cd -
+  rm -rf ${QP_ROOT}/EZFIO
+  cd ${BUILD}/config || return 1
+  cd -
+  mv ${BUILD} ${QP_ROOT}/install/EZFIO || return 1
+}
+
+source scripts/build.sh

install/scripts/install_irpf90.sh

@@ -0,0 +1,24 @@
+#!/bin/bash -x
+
+TARGET=irpf90
+function _install()
+{
+  cd ..
+  QP_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 ${QP_ROOT}/install/irpf90/bin/irpf90 $@' > ../bin/irpf90 || return 1
+  echo 'exec ${QP_ROOT}/install/irpf90/bin/irpman $@' > ../bin/irpman || return 1
+  chmod +x ../bin/irpf90 ../bin/irpman || return 1
+  return 0
+}
+
+source scripts/build.sh
+
+

install/scripts/install_m4.sh

@@ -0,0 +1,15 @@
+#!/bin/bash -x
+
+TARGET=m4
+
+function _install()
+{
+  cd ..
+  QP_ROOT=$PWD
+  cd -
+  cd ${BUILD}
+  ./configure && make || exit 1 
+  ln -sf ${PWD}/src/m4 ${QP_ROOT}/bin || exit 1 
+}
+
+source scripts/build.sh

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

install/scripts/install_ocaml.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+cd ..
+QP_ROOT=$PWD
+cd -
+
+# Normal installation
+PACKAGES="core cryptokit ocamlfind sexplib"
+
+declare -i i
+i=$(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
+
+if [[ -d ${HOME}/.opam ]]
+then
+  source ${HOME}/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true
+fi
+
+cd Downloads || exit 1
+chmod +x  ocaml.sh || exit 1
+
+echo N | ./ocaml.sh ${QP_ROOT}/bin/ || exit 1
+
+${QP_ROOT}/bin/opam config setup -a -q || exit 1
+
+export LD_LIBRARY_PATH=${QP_ROOT}/lib:${LD_LIBRARY_PATH}
+export LIBRARY_PATH=${QP_ROOT}/lib:${LIBRARY_PATH}
+export C_INCLUDE_PATH=${QP_ROOT}/lib:${C_INCLUDE_PATH}
+source ${HOME}/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true
+
+${QP_ROOT}/bin/opam install ${PACKAGES} -y -q || exit 1
+rm -f ../_build/ocaml.log
+exit 0
+
+

install/scripts/install_patch.sh

@@ -0,0 +1,19 @@
+#!/bin/bash -x
+
+TARGET=patch
+
+function _install()
+{  
+  mkdir ${TARGET}
+  cd ..
+  QP_ROOT=$PWD
+  cd -
+  cd ${BUILD}
+  ./configure --prefix=${QP_ROOT}/install/${TARGET} && make || exit 1
+  make install || exit 1
+  cd -
+  cp ${TARGET}/bin/${TARGET} ${QP_ROOT}/bin || exit 1
+  rm -R -- ${TARGET} || exit 1
+}
+
+source scripts/build.sh

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
+

install/scripts/install_zlib.sh

@@ -0,0 +1,19 @@
+#!/bin/bash -x
+
+TARGET=zlib
+
+function _install()
+{
+  rm -rf -- ${TARGET}
+  mkdir ${TARGET} || exit 1
+  cd ..
+  QP_ROOT=$PWD
+  cd -
+  cd ${BUILD}
+  ./configure && make || exit 1
+  make install prefix=$QP_ROOT/install/${TARGET} || exit 1
+  ln -s -f $QP_ROOT/install/${TARGET}/lib/libz.so $QP_ROOT/lib || exit 1
+  ln -s -f $QP_ROOT/install/${TARGET}/lib/libz.a $QP_ROOT/lib || exit 1
+}
+
+source scripts/build.sh

ocaml/Makefile

@@ -1,9 +1,9 @@
 .NOPARALLEL:
 
-# Check if QPACKAGE_ROOT is defined
+# Check if QP_ROOT is defined
-ifndef QPACKAGE_ROOT
+ifndef QP_ROOT
 $(info  -------------------- Error --------------------)
-$(info  QPACKAGE_ROOT undefined. Source the quantum_package.rc script)
+$(info  QP_ROOT undefined. Source the quantum_package.rc script)
 $(info  -----------------------------------------------)
 $(error )
 endif
@@ -32,10 +32,10 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore
 	   echo $$i ; \
 	done > .gitignore
 
-executables: $(QPACKAGE_ROOT)/data/executables
+executables: $(QP_ROOT)/data/executables
 
-$(QPACKAGE_ROOT)/data/executables:
+$(QP_ROOT)/data/executables:
-	$(QPACKAGE_ROOT)/scripts/module/create_executables_list.sh
+	$(QP_ROOT)/scripts/module/create_executables_list.sh
 
 external_libs:
 	opam install cryptokit core
@@ -62,8 +62,8 @@ qp_run.native: $(MLFILES) $(MLIFILES) executables
 	$(OCAMLBUILD) $*.native -use-ocamlfind $(PKGS)
 	ln -s $*.native $*
 
-ezfio.ml: ${QPACKAGE_ROOT}/EZFIO/Ocaml/ezfio.ml
+ezfio.ml: ${QP_ROOT}/install/EZFIO/Ocaml/ezfio.ml
-	cp ${QPACKAGE_ROOT}/EZFIO/Ocaml/ezfio.ml .
+	cp ${QP_ROOT}/install/EZFIO/Ocaml/ezfio.ml .
 
 qptypes_generator.byte: qptypes_generator.ml
 	$(OCAMLBUILD) qptypes_generator.byte  -use-ocamlfind 
@@ -71,8 +71,8 @@ qptypes_generator.byte: qptypes_generator.ml
 Qptypes.ml: qptypes_generator.byte
 	./qptypes_generator.byte > Qptypes.ml
 
-${QPACKAGE_ROOT}/EZFIO/Ocaml/ezfio.ml: 
+${QP_ROOT}/install/EZFIO/Ocaml/ezfio.ml: 
-	$(MAKE) -C ${QPACKAGE_ROOT}/src ezfio
+	$(MAKE) -C ${QP_ROOT}/install/src ezfio
 
 Input_auto_generated.ml qp_edit.ml:
 	ei_handler.py ocaml_global

ocaml/Qpackage.ml

@@ -5,8 +5,8 @@ open Qputils;;
 (** Variables related to the quantum package installation *)
 
 let root = 
-  match (Sys.getenv "QPACKAGE_ROOT") with
+  match (Sys.getenv "QP_ROOT") with
-  | None -> failwith "QPACKAGE_ROOT environment variable is not set.
+  | None -> failwith "QP_ROOT environment variable is not set.
 Please source the quantum_package.rc file."
   | Some x -> x 
 ;;
@@ -59,7 +59,7 @@ let executables = lazy (
            |> List.filter ~f:(fun x -> x <> "")
          in
          match e with
-         | [a;b] -> (a,String.substr_replace_all ~pattern:"$QPACKAGE_ROOT" ~with_:root b)
+         | [a;b] -> (a,String.substr_replace_all ~pattern:"$QP_ROOT" ~with_:root b)
          | _ -> ("","")
      )
   in

scripts/cache_compile.py

@@ -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()

scripts/compilation/cache_compile.py

@@ -104,5 +104,5 @@ if __name__ == '__main__':
 
     try:
         cache_utility(command)
-    except:
+    except OSError:
         process = subprocess.Popen(command, shell=True)

scripts/compilation/qp_create_ninja.py

@@ -24,11 +24,11 @@ except ImportError:
 # \_| | (_) |_) (_| |   \/ (_| |  | (_| |_) | (/_ _>
 #
 
-QPACKAGE_ROOT = os.environ['QPACKAGE_ROOT']
+QP_ROOT = os.environ['QP_ROOT']
-QPACKAGE_ROOT_SRC = join(QPACKAGE_ROOT, 'src')
+QP_ROOT_SRC = join(QP_ROOT, 'src')
-QPACKAGE_ROOT_EZFIO = join(QPACKAGE_ROOT, 'EZFIO')
+QP_ROOT_EZFIO = join(QP_ROOT, 'install', 'EZFIO')
 
-EZFIO_LIB = join(QPACKAGE_ROOT_EZFIO, "lib", "libezfio.a")
+EZFIO_LIB = join(QP_ROOT, "lib", "libezfio.a")
 
 #
 # |\ |  _. ._ _   _   _|   _|_     ._  |  _
@@ -57,8 +57,7 @@ def ninja_create_env_variable(pwd_config_file):
         l_string.append(str_)
 
     lib_lapack = get_compilation_option(pwd_config_file, "LAPACK_LIB")
-    lib_ezfio = join(QPACKAGE_ROOT_EZFIO, "lib", "libezfio_irp.a")
+    l_string.append("{0} = {1} {2}".format("LIB", lib_lapack, EZFIO_LIB))
-    l_string.append("{0} = {1} {2}".format("LIB", lib_lapack, lib_ezfio))
 
     l_string.append("")
 
@@ -76,14 +75,14 @@ def dict_module_genelogy_path(d_module_genelogy):
     """
     d = dict()
     for module_rel, l_children_rel in d_module_genelogy.iteritems():
-        module_abs = join(QPACKAGE_ROOT_SRC, module_rel)
+        module_abs = join(QP_ROOT_SRC, module_rel)
 
         p = Path(module_abs, module_rel)
         try:
-            d[p] = Path(join(QPACKAGE_ROOT_SRC, l_children_rel),
+            d[p] = Path(join(QP_ROOT_SRC, l_children_rel),
                         l_children_rel)
         except:
-            d[p] = [Path(join(QPACKAGE_ROOT_SRC, children), children)
+            d[p] = [Path(join(QP_ROOT_SRC, children), children)
                     for children in l_children_rel]
 
     return d
@@ -100,7 +99,7 @@ def get_l_module_with_ezfio_cfg():
     """
     from os import listdir
     from os.path import isfile, join
-    qp_src = QPACKAGE_ROOT_SRC
+    qp_src = QP_ROOT_SRC
 
     return [join(qp_src, m) for m in listdir(qp_src)
             if isfile(join(qp_src, m, "EZFIO.cfg"))]
@@ -113,10 +112,10 @@ def get_l_ezfio_config():
 
     l = []
 
-    cmd = "{0}/*/*.ezfio_config".format(QPACKAGE_ROOT_SRC)
+    cmd = "{0}/*/*.ezfio_config".format(QP_ROOT_SRC)
     for path_in_module in glob.glob(cmd):
         name_lower = os.path.split(path_in_module)[1].lower()
-        path_in_ezfio = join(QPACKAGE_ROOT_EZFIO, "config", name_lower)
+        path_in_ezfio = join(QP_ROOT_EZFIO, "config", name_lower)
         l.append(EZ_config_path(path_in_module, path_in_ezfio))
 
     return l
@@ -147,7 +146,7 @@ def get_children_of_ezfio_cfg(l_module_with_ezfio_cfg):
     """
     From a module list of ezfio_cfg return all the stuff create by him
     """
-    config_folder = join(QPACKAGE_ROOT_EZFIO, "config")
+    config_folder = join(QP_ROOT_EZFIO, "config")
 
     l_util = dict()
 
@@ -223,8 +222,9 @@ def ninja_ezfio_rule():
     l_flag = ["export {0}='${0}'".format(flag)
               for flag in ["FC", "FCFLAGS", "IRPF90"]]
 
-    l_cmd = ["cd {0}".format(QPACKAGE_ROOT_EZFIO)
+    l_cmd = ["cd {0}".format(QP_ROOT_EZFIO)
-             ] + l_flag + ["ninja"]
+             ] + l_flag + ["ninja && ln -f {0} {1}".format(join(QP_ROOT, 'install', 'EZFIO',"lib","libezfio.a"),
+                                                          EZFIO_LIB)]
 
     l_string = ["rule build_ezfio",
                 "   command = {0}".format(" ; ".join(l_cmd)),
@@ -245,7 +245,7 @@ def ninja_ezfio_build(l_ezfio_config, l_util):
 
     str_ = " ".join(l_ezfio_config + l_ezfio_from_cfg)
 
-    ezfio_make_config = join(QPACKAGE_ROOT_EZFIO,"make.config")
+    ezfio_make_config = join(QP_ROOT_EZFIO, "make.config")
     l_string = ["build {0} {1}: build_ezfio {2}".format(EZFIO_LIB,
                                                         ezfio_make_config,
                                                         str_), ""]
@@ -262,7 +262,7 @@ def get_source_destination(path_module, l_needed_molule):
     Return a list of Sym_link = namedtuple('Sym_link', ['source', 'destination'])
     for a module
     """
-    return [Sym_link(m.abs, join(QPACKAGE_ROOT_SRC, path_module.rel, m.rel))
+    return [Sym_link(m.abs, join(QP_ROOT_SRC, path_module.rel, m.rel))
             for m in l_needed_molule]
 
 
@@ -296,29 +296,30 @@ 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
     '''
-    l_irp = []
+    l_depend = []
     l_src = []
     l_obj = []
 
     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_depend.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_depend.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_depend.append(join(path_module.abs, "ezfio_interface.irp.f"))
 
-    d = {"l_irp": l_irp,
+    d = {"l_depend": l_depend,
          "l_src": l_src,
          "l_obj": l_obj,
          "l_template": l_template}
@@ -334,11 +335,21 @@ 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():
+            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
@@ -388,24 +399,24 @@ def ninja_irpf90_make_build(path_module, l_needed_molule, d_irp):
 
     l_creation = [join(path_module.abs, i)
                   for i in ["irpf90.make", "irpf90_entities", "tags",
-                            "IRPF90_temp/build.ninja"]]
+                            "build.ninja"]]
     str_creation = " ".join(l_creation)
 
     # ~#~#~#~#~#~#~#~#~#~ #
     # D e p e n d a n c y #
     # ~#~#~#~#~#~#~#~#~#~ #
 
-    l_irp_need = d_irp[path_module]["l_irp"]
+    l_depend = d_irp[path_module]["l_depend"]
     l_src = d_irp[path_module]["l_src"]
     l_obj = d_irp[path_module]["l_obj"]
     l_template = d_irp[path_module]["l_template"]
 
     if l_needed_molule:
-        l_destination = ["l_symlink_{0}".format(path_module.rel)]
+        l_symlink = ["l_symlink_{0}".format(path_module.rel)]
     else:
-        l_destination = []
+        l_symlink = []
 
-    str_depend = " ".join(l_irp_need + l_destination + l_src + l_template)
+    str_depend = " ".join(l_depend + l_symlink + l_template)
 
     # ~#~#~#~#~#~#~#~#~#~#~ #
     # N i n j a _ b u i l d #
@@ -521,7 +532,7 @@ def ninja_binaries_rule():
     # c m d #
     # ~#~#~ #
 
-    l_cmd = ["cd $module/IRPF90_temp", "ninja"]
+    l_cmd = ["cd $module", "ninja"]
 
     # ~#~#~#~#~#~ #
     # s t r i n g #
@@ -543,7 +554,7 @@ def ninja_binaries_build(path_module, l_children, d_binaries):
     # c m d #
     # ~#~#~ #
 
-    ninja_module_path = join(path_module.abs, "IRPF90_temp", "build.ninja")
+    ninja_module_path = join(path_module.abs, "build.ninja")
     l_abs_bin = [binary.abs for binary in d_binaries[path_module]]
 
     # ~#~#~#~#~#~ #
@@ -694,5 +705,5 @@ if __name__ == "__main__":
         l_string += ninja_binaries_build(module_to_compile, l_children,
                                          d_binaries_production)
 
-    with open(join(QPACKAGE_ROOT, "build.ninja"), "w+") as f:
+    with open(join(QP_ROOT, "build.ninja"), "w+") as f:
         f.write("\n".join(l_string))

scripts/compilation/read_compilation_cfg.py

@@ -36,7 +36,7 @@ def get_compilation_option(pwd_cfg, flag_name):
 
 if __name__ == '__main__':
 
-    qpackage_root = os.environ['QPACKAGE_ROOT']
+    qpackage_root = os.environ['QP_ROOT']
     pwd_cfg = os.path.join(qpackage_root, "config/gfortran_example.cfg")
 
     print get_compilation_option(pwd_cfg, "FC")

scripts/ezfio_interface/ei_handler.py

@@ -21,11 +21,11 @@ Options:
                              (aka all with the `interface: input` parameter)
                              in `${pwd}`
     --ezfio_config     Create the `${module_lower}_ezfio_interface_config` in
-                             `${QPACKAGE_ROOT}/EZFIO/config/`
+                             `${QP_ROOT}/EZFIO/config/`
                        This file is needed by *EZFIO* to create the `libezfio.so`
     --ocaml            Create the `Input_module.lower.ml` for the *qp_edit*
     --ezfio_default    Create the `${module_lower}_ezfio_interface_default` in
-                             `${QPACKAGE_ROOT}/data/ezfio_defaults` needed by
+                             `${QP_ROOT}/data/ezfio_defaults` needed by
                              the ocaml
     ocaml_global       Create the qp_edit
 
@@ -100,7 +100,7 @@ def get_type_dict():
     # ~#~#~#~#~ #
     # P i c l e #
     # ~#~#~#~#~ #
-    qpackage_root = os.environ['QPACKAGE_ROOT']
+    qpackage_root = os.environ['QP_ROOT']
 
     # ~#~#~#~ #
     # I n i t #
@@ -325,7 +325,7 @@ def save_ezfio_provider(path_head, dict_code_provider):
     path = "{0}/ezfio_interface.irp.f".format(path_head)
 
     l_output = ["! DO NOT MODIFY BY HAND",
-                "! Created by $QPACKAGE_ROOT/scripts/ezfio_interface.py",
+                "! Created by $QP_ROOT/scripts/ezfio_interface.py",
                 "! from file {0}/EZFIO.cfg".format(path_head),
                 "\n"]
 
@@ -368,7 +368,7 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
                     if begin[0] == '-':
                         a_size_raw.append("{0}+{1}+1".format(end, begin[1:]))
                     else:
-                       a_size_raw.append("{0}-{1}+1".format(end, begin))
+                        a_size_raw.append("{0}-{1}+1".format(end, begin))
 
             size_raw = ",".join(a_size_raw)
 
@@ -452,12 +452,10 @@ def create_ezfio_config(dict_ezfio_cfg):
 def save_ezfio_config(module_lower, str_ezfio_config):
     """
     Write the str_ezfio_config in
-    "$QPACKAGE_ROOT/EZFIO/{0}.ezfio_interface_config".format(module_lower)
+    "$QP_ROOT/EZFIO/{0}.ezfio_interface_config".format(module_lower)
     """
-
+    name = "{0}.ezfio_interface_config".format(module_lower)
-    root_ezfio = "{0}/EZFIO".format(os.environ['QPACKAGE_ROOT'])
+    path = os.path.join(os.environ['QP_EZFIO'], "config", name)
-    path = "{0}/config/{1}.ezfio_interface_config".format(root_ezfio,
-                                                          module_lower)
 
     with open(path, "w+") as f:
         f.write(str_ezfio_config)
@@ -471,11 +469,11 @@ def create_ezfio_default(dict_ezfio_cfg):
 def save_ezfio_default(module_lower, str_ezfio_default):
     """
     Write the str_ezfio_config in
-    "$QPACKAGE_ROOT/data/ezfio_defaults/{0}.ezfio_interface_default".format(module_lower)
+    "$QP_ROOT/data/ezfio_defaults/{0}.ezfio_interface_default".format(module_lower)
     """
 
     root_ezfio_default = "{0}/data/ezfio_defaults/".format(
-        os.environ['QPACKAGE_ROOT'])
+        os.environ['QP_ROOT'])
     path = "{0}/{1}.ezfio_interface_default".format(root_ezfio_default,
                                                     module_lower)
     with open(path, "w+") as f:
@@ -580,10 +578,10 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
 def save_ocaml_input(module_lower, str_ocaml_input):
     """
     Write the str_ocaml_input in
-    $QPACKAGE_ROOT/ocaml/Input_{0}.ml".format(module_lower)
+    $QP_ROOT/ocaml/Input_{0}.ml".format(module_lower)
     """
 
-    path = "{0}/ocaml/Input_{1}.ml".format(os.environ['QPACKAGE_ROOT'],
+    path = "{0}/ocaml/Input_{1}.ml".format(os.environ['QP_ROOT'],
                                            module_lower)
 
     with open(path, "w+") as f:
@@ -600,7 +598,7 @@ def get_l_module_with_auto_generate_ocaml_lower():
     # I n i t #
     # ~#~#~#~ #
 
-    mypath = "{0}/src".format(os.environ['QPACKAGE_ROOT'])
+    mypath = "{0}/src".format(os.environ['QP_ROOT'])
 
     # ~#~#~#~#~#~#~#~ #
     # L _ f o l d e r #
@@ -641,7 +639,7 @@ def create_ocaml_input_global(l_module_with_auto_generate_ocaml_lower):
 
     from ezfio_generate_ocaml import EZFIO_ocaml
 
-    qpackage_root = os.environ['QPACKAGE_ROOT']
+    qpackage_root = os.environ['QP_ROOT']
     path = qpackage_root + "/scripts/ezfio_interface/qp_edit_template"
 
     with open(path, "r") as f:
@@ -663,10 +661,10 @@ def create_ocaml_input_global(l_module_with_auto_generate_ocaml_lower):
 def save_ocaml_input_auto(str_ocaml_input_global):
     """
     Write the str_ocaml_input in
-    $QPACKAGE_ROOT/ocaml/Input_auto_generated.ml
+    $QP_ROOT/ocaml/Input_auto_generated.ml
     """
 
-    path = "{0}/ocaml/Input_auto_generated.ml".format(os.environ['QPACKAGE_ROOT'])
+    path = "{0}/ocaml/Input_auto_generated.ml".format(os.environ['QP_ROOT'])
 
     with open(path, "w+") as f:
         f.write(str_ocaml_input_global)
@@ -675,10 +673,10 @@ def save_ocaml_input_auto(str_ocaml_input_global):
 def save_ocaml_qp_edit(str_ocaml_qp_edit):
     """
     Write the str_ocaml_qp_edit in
-    $QPACKAGE_ROOT/ocaml/qp_edit.ml
+    $QP_ROOT/ocaml/qp_edit.ml
     """
 
-    path = "{0}/ocaml/qp_edit.ml".format(os.environ['QPACKAGE_ROOT'])
+    path = "{0}/ocaml/qp_edit.ml".format(os.environ['QP_ROOT'])
 
     with open(path, "w+") as f:
         f.write(str_ocaml_qp_edit)
@@ -773,7 +771,7 @@ if __name__ == "__main__":
     #  G e t _ l _ d i c t _ e z f i o _ c f g #
     # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
 
-    qpackage_root_src = join(os.environ['QPACKAGE_ROOT'], "src")
+    qpackage_root_src = join(os.environ['QP_ROOT'], "src")
 
     l_module_with_ezfio = []
 

scripts/ezfio_interface/qp_convert_output_to_ezfio.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 """
-This function acceep
+convert output of gamess/GAU$$IAN to ezfio
 
 Usage:
     qp_convert_output_to_ezfio.py <file.out> [--ezfio=<folder.ezfio>]
@@ -24,14 +24,14 @@ from functools import reduce
 
 
 try:
-    QPACKAGE_ROOT = os.environ["QPACKAGE_ROOT"]
+    QP_ROOT = os.environ["QP_ROOT"]
 except:
-    print "Error: QPACKAGE_ROOT environment variable not found."
+    print "Error: QP_ROOT environment variable not found."
     sys.exit(1)
 else:
-    sys.path = [QPACKAGE_ROOT + "/EZFIO/Python",
+    sys.path = [QP_ROOT + "/install/EZFIO/Python",
-                QPACKAGE_ROOT + "/resultsFile",
+                QP_ROOT + "/resultsFile",
-                QPACKAGE_ROOT + "/scripts"] + sys.path
+                QP_ROOT + "/scripts"] + sys.path
 
 # ~#~#~#~#~#~ #
 # I m p o r t #

scripts/ezfio_interface/qp_edit_template

@@ -260,7 +260,7 @@ Edit input data
        | Assert_failure (file, line, ch) as e ->
          begin
            Printf.eprintf "=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-\n\n";
-           Printf.eprintf "Assert error in file $QPACKAGE_ROOT/ocaml/%s, line %d, character %d\n\n" file line ch;
+           Printf.eprintf "Assert error in file $QP_ROOT/ocaml/%s, line %d, character %d\n\n" file line ch;
            Printf.eprintf "=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-\n\n";
            (* restore_backup ezfio_file; *)
            raise e

scripts/generate_h_apply.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 import os
-file = open(os.environ["QPACKAGE_ROOT"]+'/src/Determinants/H_apply.template.f','r')
+file = open(os.environ["QP_ROOT"]+'/src/Determinants/H_apply.template.f','r')
 template = file.read()
 file.close()
 

scripts/get_basis.sh

@@ -8,15 +8,14 @@
 # Prints in stdout the name of a temporary file containing the basis set.
 #
 
-if [[ -z ${QPACKAGE_ROOT} ]]
+if [[ -z ${QP_ROOT} ]]
 then
-  print "The QPACKAGE_ROOT environment variable is not set."
+  print "The QP_ROOT environment variable is not set."
   print "Please reload the quantum_package.rc file."
   exit -1
 fi
 
-export EMSL_API_ROOT="${QPACKAGE_ROOT}"/EMSL_Basis/
+export EMSL_API_ROOT="${QP_ROOT}"/install/emsl
-export PYTHONPATH="${EMSL_API_ROOT}":${PYTHONPATH}
 
 tmpfile="$1"
 shift

scripts/install/install_curl.sh

@@ -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}
-

scripts/install/install_docopt.sh

@@ -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}

scripts/install/install_emsl.sh

@@ -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
-
-

scripts/install/install_ezfio.sh

@@ -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
-
-
-

scripts/install/install_irpf90.sh

@@ -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
-
-

scripts/install/install_m4.sh

@@ -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
-

scripts/install/install_ninja.sh

@@ -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

scripts/install/install_ocaml.sh

@@ -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 
-

scripts/install/install_resultsFile.sh

@@ -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
-
-

scripts/install/install_zlib.sh

@@ -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}
-

scripts/make_binary.sh

@@ -6,15 +6,15 @@
 #
 
 
-# Check the QPACKAGE_ROOT directory
+# Check the QP_ROOT directory
-if [[ -z ${QPACKAGE_ROOT} ]]
+if [[ -z ${QP_ROOT} ]]
 then
-  echo "The QPACKAGE_ROOT environment variable is not set."
+  echo "The QP_ROOT environment variable is not set."
   echo "Please reload the quantum_package.rc file."
   exit 1
 fi
 
-cd ${QPACKAGE_ROOT}
+cd ${QP_ROOT}
 if [[ -f quantum_package.rc \
    && -f README.md \
    && -d src  \
@@ -35,7 +35,7 @@ fi
 
 
 # Build all sources
-for dir in ${QPACKAGE_ROOT}/{src,ocaml}
+for dir in ${QP_ROOT}/{src,ocaml}
 do
   make -C ${dir}
   if [[ $? -ne 0 ]]
@@ -46,7 +46,7 @@ done
 
 
 # Copy the files in the static directory
-QPACKAGE_STATIC=${QPACKAGE_ROOT}/quantum_package_static
+QPACKAGE_STATIC=${QP_ROOT}/quantum_package_static
 
 function find_libs ()
 {
@@ -58,7 +58,7 @@ function find_libs ()
 
 function find_exec ()
 {
-  find ${QPACKAGE_ROOT}/$1 -perm /u+x -type f
+  find ${QP_ROOT}/$1 -perm /u+x -type f
 }
 
 
@@ -111,12 +111,12 @@ cd -
 for i in ${FORTRAN_EXEC}
 do
   i=$(basename $i)
-  echo $i \$QPACKAGE_ROOT/bin/$i
+  echo $i \$QP_ROOT/bin/$i
 done >> ${QPACKAGE_STATIC}/data/executables
 
-cp ${QPACKAGE_ROOT}/data/ezfio_defaults ${QPACKAGE_STATIC}/data
+cp ${QP_ROOT}/data/ezfio_defaults ${QPACKAGE_STATIC}/data
 mkdir -p ${QPACKAGE_STATIC}/src/Bitmask
-cp ${QPACKAGE_ROOT}/src/Bitmask/bitmasks_module.f90 ${QPACKAGE_STATIC}/src/Bitmask
+cp ${QP_ROOT}/src/Bitmask/bitmasks_module.f90 ${QPACKAGE_STATIC}/src/Bitmask
 
 #
 echo "Copying dynamic libraries"
@@ -143,10 +143,10 @@ cp -- ${QPACKAGE_STATIC}/extra_lib/lib{[gi]omp*,mkl*,lapack*,blas*,z*} ${QPACKAG
 echo "Copying EMSL_Basis directory"
 #     ---------------------------- 
 
-cp -r -- ${QPACKAGE_ROOT}/EMSL_Basis ${QPACKAGE_STATIC}/
+cp -r -- ${QP_ROOT}/EMSL_Basis ${QPACKAGE_STATIC}/
 if [[ $? -ne 0 ]] ;
 then
-  echo 'cp -r -- ${QPACKAGE_ROOT}/EMSL_Basis ${QPACKAGE_STATIC}/'
+  echo 'cp -r -- ${QP_ROOT}/EMSL_Basis ${QPACKAGE_STATIC}/'
   exit 1
 fi
 
@@ -155,10 +155,10 @@ fi
 echo "Copying scripts directory"
 #     ------------------------- 
 
-cp -r -- ${QPACKAGE_ROOT}/scripts ${QPACKAGE_STATIC}/
+cp -r -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/
 if [[ $? -ne 0 ]] ;
 then
-  echo 'cp -r -- ${QPACKAGE_ROOT}/scripts ${QPACKAGE_STATIC}/'
+  echo 'cp -r -- ${QP_ROOT}/scripts ${QPACKAGE_STATIC}/'
   exit 1
 fi
 
@@ -168,13 +168,13 @@ echo "Creating quantum_package.rc"
 #     ---------------------------
 
 cat << EOF > ${QPACKAGE_STATIC}/quantum_package.rc
-export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}")  ; pwd -P )
+export QP_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}")  ; pwd -P )
-export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH}
+export LD_LIBRARY_PATH="\${QP_ROOT}"/lib:\${LD_LIBRARY_PATH}
-export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH}
+export LIBRARY_PATH="\${QP_ROOT}"/lib:\${LIBRARY_PATH}
-export PYTHONPATH="\${QPACKAGE_ROOT}"/scripts:\${PYTHONPATH}
+export PYTHONPATH="\${QP_ROOT}"/scripts:\${PYTHONPATH}
-export PATH="\${QPACKAGE_ROOT}"/scripts:\${PATH}
+export PATH="\${QP_ROOT}"/scripts:\${PATH}
-export PATH="\${QPACKAGE_ROOT}"/bin:\${PATH}
+export PATH="\${QP_ROOT}"/bin:\${PATH}
-export PATH="\${QPACKAGE_ROOT}"/ocaml:\${PATH}
+export PATH="\${QP_ROOT}"/ocaml:\${PATH}
 EOF
 
 #exit 0

scripts/module/clean_modules.sh

@@ -2,13 +2,13 @@
 #
 # Cleans a module directory 
 
-if [[ -z ${QPACKAGE_ROOT} ]]
+if [[ -z ${QP_ROOT} ]]
 then
-  print "The QPACKAGE_ROOT environment variable is not set."
+  print "The QP_ROOT environment variable is not set."
   print "Please reload the quantum_package.rc file."
   exit -1
 fi
-source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+source ${QP_ROOT}/scripts/qp_include.sh
 
 function do_clean()
 {

scripts/module/create_executables_list.sh

@@ -2,20 +2,20 @@
 #
 # Thu Mar 26 01:27:14 CET 2015
 
-if [[ -z ${QPACKAGE_ROOT} ]]
+if [[ -z ${QP_ROOT} ]]
 then
-  print "The QPACKAGE_ROOT environment variable is not set."
+  print "The QP_ROOT environment variable is not set."
   print "Please reload the quantum_package.rc file."
   exit -1
 fi
 
-cd ${QPACKAGE_ROOT}/data
+cd ${QP_ROOT}/data
 rm -f executables
-EXES=$(find ${QPACKAGE_ROOT}/src -perm /u+x -type f | grep -e "${QPACKAGE_ROOT}/src/[^/]*/[^/]*$" |sort ) 
+EXES=$(find ${QP_ROOT}/src -perm /u+x -type f | grep -e "${QP_ROOT}/src/[^/]*/[^/]*$" |sort ) 
 
 for EXE in $EXES
 do
-   printf "%-30s %s\n" $(basename $EXE) $EXE | sed "s|${QPACKAGE_ROOT}|\$QPACKAGE_ROOT|g" >> executables 
+   printf "%-30s %s\n" $(basename $EXE) $EXE | sed "s|${QP_ROOT}|\$QP_ROOT|g" >> executables 
 done
 
 

scripts/module/create_gitignore.sh

@@ -5,13 +5,13 @@
 # Tue Jan 13 14:18:05 CET 2015
 #
 
-if [[ -z ${QPACKAGE_ROOT} ]]
+if [[ -z ${QP_ROOT} ]]
 then
-  print "The QPACKAGE_ROOT environment variable is not set."
+  print "The QP_ROOT environment variable is not set."
   print "Please reload the quantum_package.rc file."
   exit -1
 fi
-source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+source ${QP_ROOT}/scripts/qp_include.sh
 
 
 function do_gitingore()

scripts/module/module_handler.py

@@ -30,13 +30,13 @@ except ImportError:
 
 # Canot cache for namedtuple are not hashable
 def get_dict_child():
-    """Loop over MODULE in  QPACKAGE_ROOT/src, open all the NEEDED_CHILDREN_MODULES
+    """Loop over MODULE in  QP_ROOT/src, open all the NEEDED_CHILDREN_MODULES
     and create a dict[MODULE] = [sub module needed, ...]
     """
     d_ref = dict()
 
-    qpackage_root = os.environ['QPACKAGE_ROOT']
+    qp_root = os.environ['QP_ROOT']
-    dir_ = os.path.join(qpackage_root, 'src')
+    dir_ = os.path.join(qp_root, 'src')
 
     for o in os.listdir(dir_):
 

scripts/module/qp_install_module.py

@@ -61,7 +61,7 @@ if __name__ == '__main__':
     elif arguments["create"]:
         l_children = arguments["<children_module>"]
 
-        qpackage_root = os.environ['QPACKAGE_ROOT']
+        qpackage_root = os.environ['QP_ROOT']
         path = os.path.join(qpackage_root, "src", arguments["<name>"])
 
         print "You will create the module:"

scripts/perturbation.py

@@ -2,7 +2,7 @@
 
 import os
 
-Pert_dir = os.environ["QPACKAGE_ROOT"]+"/src/Perturbation/"
+Pert_dir = os.environ["QP_ROOT"]+"/src/Perturbation/"
 
 perturbations = []
 

scripts/pseudo/put_pseudo_in_ezfio.py

@@ -17,9 +17,9 @@ from docopt import docopt
 
 from subprocess import Popen, PIPE
 
-qpackage_root = os.environ['QPACKAGE_ROOT']
+qpackage_root = os.environ['QP_ROOT']
 
-EZFIO = "{0}/EZFIO".format(qpackage_root)
+EZFIO = "{0}/install/EZFIO".format(qpackage_root)
 sys.path = [EZFIO + "/Python"] + sys.path
 
 from ezfio import ezfio
@@ -51,7 +51,7 @@ def get_pseudo_str(l_atom):
         10.11238853 0   1.14052020  |1><1|
     """
 
-    EMSL_root = "{0}/EMSL_Basis/".format(qpackage_root)
+    EMSL_root = "{0}/install/emsl/".format(qpackage_root)
     EMSL_path = "{0}/EMSL_api.py".format(EMSL_root)
     db_path = "{0}/db/Pseudo.db".format(EMSL_root)
 

scripts/qp_include.sh

@@ -13,23 +13,23 @@ function unique_list()
 
 function check_current_dir_is_src()
 {
-  if [[ "${PWD}" == "${QPACKAGE_ROOT}/src" ]]
+  if [[ "${PWD}" == "${QP_ROOT}/src" ]]
   then
      return 0
   else
-     echo "Current directory should be \$QPACKAGE_ROOT/src"
+     echo "Current directory should be \$QP_ROOT/src"
      exit -1
   fi
 }
 
 function check_current_dir_is_module()
 {
-  # If the prefix ${QPACKAGE_ROOT}/src/ can be removed from $PWD, it means that
+  # If the prefix ${QP_ROOT}/src/ can be removed from $PWD, it means that
-  # $PWD is somewhere below ${QPACKAGE_ROOT}/src/ so it is a module.
+  # $PWD is somewhere below ${QP_ROOT}/src/ so it is a module.
-  # If the prefix ${QPACKAGE_ROOT}/src/ can not be removed from $PWD, then
+  # If the prefix ${QP_ROOT}/src/ can not be removed from $PWD, then
-  # "${PWD##${QPACKAGE_ROOT}/src/}" == "$PWD".
+  # "${PWD##${QP_ROOT}/src/}" == "$PWD".
 
-  if [[ "${PWD##${QPACKAGE_ROOT}/src/}" != "$PWD" ]]
+  if [[ "${PWD##${QP_ROOT}/src/}" != "$PWD" ]]
   then
      return 0
   else

scripts/qp_set_frozen_core.py

@@ -3,7 +3,7 @@
 import os
 import sys
 
-sys.path = [ os.environ["QPACKAGE_ROOT"]+"/EZFIO/Python" ] + sys.path
+sys.path = [ os.environ["QP_ROOT"]+"/EZFIO/Python" ] + sys.path
 from ezfio import ezfio
 
 ezfio.set_filename(sys.argv[1])

scripts/save_current_mos.sh

@@ -4,9 +4,9 @@
 # directory, where xxx is the corresponding mo_label.
 # Wed Apr  2 14:35:15 CEST 2014
 
-if [[ -z ${QPACKAGE_ROOT} ]]
+if [[ -z ${QP_ROOT} ]]
 then
-  print "The QPACKAGE_ROOT environment variable is not set."
+  print "The QP_ROOT environment variable is not set."
   print "Please reload the quantum_package.rc file."
   exit -1
 fi

scripts/upgrade/upgrade_ezfio.sh

@@ -3,24 +3,24 @@
 # Upgrades the EZFIO library from the web.
 # Tue Nov  4 00:53:13 CET 2014
 
-if [[ -z ${QPACKAGE_ROOT} ]]
+if [[ -z ${QP_ROOT} ]]
 then
-  print "The QPACKAGE_ROOT environment variable is not set."
+  print "The QP_ROOT environment variable is not set."
   print "Please reload the quantum_package.rc file."
 fi
 
-cd -- ${QPACKAGE_ROOT}
+cd -- ${QP_ROOT}
-mv -- ${QPACKAGE_ROOT}/EZFIO ${QPACKAGE_ROOT}/EZFIO.old
+mv -- ${QP_ROOT}/EZFIO ${QP_ROOT}/EZFIO.old
 
-${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh
+${QP_ROOT}/scripts/install/install_ezfio.sh
 
 if [[ $? -eq 0 ]]
 then
-  rm -rf -- ${QPACKAGE_ROOT}/EZFIO.old
+  rm -rf -- ${QP_ROOT}/EZFIO.old
   echo "Successfully updated EZFIO"
 else
-  rm -rf -- ${QPACKAGE_ROOT}/EZFIO
+  rm -rf -- ${QP_ROOT}/EZFIO
-  mv --  ${QPACKAGE_ROOT}/EZFIO.old ${QPACKAGE_ROOT}/EZFIO
+  mv --  ${QP_ROOT}/EZFIO.old ${QP_ROOT}/EZFIO
   echo "Failed to update EZFIO"
 fi
 

scripts/upgrade/upgrade_irpf90.sh

@@ -3,23 +3,23 @@
 # Upgrades IRPF90 from the web.
 # Wed Mar 25 11:41:04 CET 2015
 
-if [[ -z ${QPACKAGE_ROOT} ]]
+if [[ -z ${QP_ROOT} ]]
 then
-  print "The QPACKAGE_ROOT environment variable is not set."
+  print "The QP_ROOT environment variable is not set."
   print "Please reload the quantum_package.rc file."
 fi
 
-cd -- ${QPACKAGE_ROOT}
+cd -- ${QP_ROOT}
-mv -f -- ${QPACKAGE_ROOT}/irpf90 ${QPACKAGE_ROOT}/irpf90.old
+mv -f -- ${QP_ROOT}/irpf90 ${QP_ROOT}/irpf90.old
 
-${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh
+${QP_ROOT}/scripts/install/install_irpf90.sh
 
 if [[ $? -eq 0 ]]
 then
-  rm -rf -- ${QPACKAGE_ROOT}/irpf90.old
+  rm -rf -- ${QP_ROOT}/irpf90.old
   echo "Successfully updated IRPF90"
 else
-  rm -rf -- ${QPACKAGE_ROOT}/irpf90
+  rm -rf -- ${QP_ROOT}/irpf90
-  mv --  ${QPACKAGE_ROOT}/irpf90.old ${QPACKAGE_ROOT}/irpf90
+  mv --  ${QP_ROOT}/irpf90.old ${QP_ROOT}/irpf90
   echo "Failed to update IRPF90"
 fi

setup_environment.py

@@ -0,0 +1,383 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import subprocess
+import os
+import sys
+import pprint
+
+from os.path import join
+
+#  __                           _
+# /__ |   _  |_   _. |   o ._ _|_ _
+# \_| |_ (_) |_) (_| |   | | | | (_)
+#
+
+QP_ROOT = os.getcwd()
+QP_ROOT_BIN = join(QP_ROOT, "bin")
+QP_ROOT_INSTALL = join(QP_ROOT, "install")
+
+d_dependancy = {
+    "ocaml": ["m4", "curl", "zlib", "patch", "gcc"],
+    "m4": ["make"],
+    "curl": ["make"],
+    "zlib": ["gcc", "make"],
+    "patch": ["make"],
+    "ezfio": ["irpf90"],
+    "irpf90": ["python"],
+    "docopt": ["python"],
+    "resultsFile": ["python"],
+    "emsl": ["python"],
+    "gcc": [],
+    "python": [],
+    "ninja": ["gcc", "python"],
+    "make": []
+}
+
+from collections import namedtuple
+
+Info = namedtuple("Info", ["url", "description", "default_path"])
+
+path_github = {"head": "http://github.com/", "tail": "archive/master.tar.gz"}
+
+ocaml = Info(
+    url='http://raw.github.com/ocaml/opam/master/shell/opam_installer.sh',
+    description=' ocaml (it will take some time roughly 20min)',
+    default_path=join(QP_ROOT_BIN, "opam"))
+
+m4 = Info(
+    url="http://ftp.gnu.org/gnu/m4/m4-latest.tar.gz",
+    description=" m4",
+    default_path=join(QP_ROOT_BIN, "m4"))
+
+curl = Info(
+    url="http://qmcchem.ups-tlse.fr/files/scemama/curl-7.30.0.ermine.tar.bz2",
+    description=" curl",
+    default_path=join(QP_ROOT_BIN, "curl"))
+
+zlib = Info(
+    url='http://zlib.net/zlib-1.2.8.tar.gz',
+    description=' zlib',
+    default_path=join(QP_ROOT_INSTALL, "zlib"))
+
+path = Info(
+    url='ftp://ftp.gnu.org/gnu/patch/patch-2.7.5.tar.gz',
+    description=' path',
+    default_path=join(QP_ROOT_BIN, "patch"))
+
+irpf90 = Info(
+    url='{head}/scemama/irpf90/archive/v1.6.6.tar.gz'.format(**path_github),
+    description=' irpf90',
+    default_path=join(QP_ROOT_BIN, "irpf90"))
+
+docopt = Info(
+    url='{head}/docopt/docopt/{tail}'.format(**path_github),
+    description=' docop',
+    default_path=join(QP_ROOT_INSTALL, "docopt"))
+
+resultsFile = Info(
+    url='{head}/LCPQ/resultsFile/{tail}'.format(**path_github),
+    description=' resultsFile',
+    default_path=join(QP_ROOT_INSTALL, "resultsFile"))
+
+ninja = Info(
+    url='{head}/martine/ninja/{tail}'.format(**path_github),
+    description=' nina',
+    default_path=join(QP_ROOT_BIN, "ninja"))
+
+emsl = Info(
+    url='{head}/LCPQ/EMSL_Basis_Set_Exchange_Local/{tail}'.format(**
+                                                                  path_github),
+    description=' emsl',
+    default_path=join(QP_ROOT_INSTALL, "emsl"))
+
+ezfio = Info(
+    url='{head}/LCPQ/EZFIO/{tail}'.format(**path_github),
+    description=' EZFIO',
+    default_path=join(QP_ROOT_INSTALL, "EZFIO"))
+
+d_info = dict()
+
+for m in ["ocaml", "m4", "curl", "zlib", "path", "irpf90", "docopt",
+          "resultsFile", "ninja", "emsl", "ezfio"]:
+    exec ("d_info['{0}']={0}".format(m))
+
+l_need = []
+
+
+#  _
+# |_    ._   _ _|_ o  _  ._
+# | |_| | | (_  |_ | (_) | |
+#
+def check_output(*popenargs, **kwargs):
+    """Run command with arguments and return its output as a byte string.
+
+    Backported from Python 2.7 as it's implemented as pure python on stdlib.
+
+    >>> check_output(['/usr/bin/python', '--version'])
+    Python 2.6.2
+    """
+    process = subprocess.Popen(stdout=subprocess.PIPE, *popenargs, **kwargs)
+    output, unused_err = process.communicate()
+    retcode = process.poll()
+    if retcode:
+        cmd = kwargs.get("args")
+        if cmd is None:
+            cmd = popenargs[0]
+        error = subprocess.CalledProcessError(retcode, cmd)
+        error.output = output
+        raise error
+    return output
+
+
+def check_python():
+    req_version = (2, 6)
+    cur_version = sys.version_info
+
+    # Check python
+    if cur_version >= req_version:
+        l_installed["python"] = ""
+    else:
+        print "To old version (need >2.5). Abort"
+        sys.exit(1)
+
+
+def check_avabiliy(binary):
+
+    if binary == "python":
+        check_python()
+
+    try:
+        return check_output(["which", binary])
+    except subprocess.CalledProcessError:
+        default_path = d_info[binary].default_path
+        if os.path.exists(default_path):
+            return default_path
+        else:
+            return 0
+
+
+def splitext(path):
+    for ext in ['.tar.gz', '.tar.bz2']:
+        if path.endswith(ext):
+            return path[:-len(ext)], path[-len(ext):]
+    return os.path.splitext(path)
+
+
+l_installed = dict()
+
+print """
+  _
+ /  |_   _   _ |  o ._   _
+ \_ | | (/_ (_ |< | | | (_|
+                         _|
+"""
+
+# Check all the other
+for i in d_dependancy.keys():
+    print "Checking if you have {0} avalaible...".format(i),
+
+    r = check_avabiliy(i)
+    if r:
+        print "OK"
+        l_installed[i] = r.strip()
+    else:
+        print "We will try to compile if from source in a few moment"
+        l_need.append(i)
+
+# Expend the need_stuff for all the genealogy
+
+d_need_genealogy = dict()
+
+for need in l_need:
+    d_need_genealogy[need] = None
+    for childen in d_dependancy[need]:
+        if childen not in l_installed:
+            d_need_genealogy[childen] = None
+
+l_need_genealogy = d_need_genealogy.keys()
+
+print """
+  __
+ (_      ._ _  ._ _   _. ._
+ __) |_| | | | | | | (_| | \/
+                           /
+"""
+
+print "You have already installed :"
+def f( (a1,a2), (key,value) ): 
+    return tuple(max(x,len(y)) for (x,y) in [(a1,key), (a2,value)] )
+fmt_tuple =reduce(f, l_installed.iteritems(), (0,0))
+for k,v in l_installed.iteritems():
+    fmt = "{0:<%d} : {1:<%d}"%fmt_tuple
+    print fmt.format( k, v )
+
+print """
+ ___
+  |  ._   _ _|_  _. | |  _. _|_ o  _  ._
+ _|_ | | _>  |_ (_| | | (_|  |_ | (_) | |
+
+"""
+
+if l_need_genealogy:
+    print "You need to install"
+    pprint.pprint(l_need_genealogy)
+else:
+    print "Nothing to do"
+    sys.exit()
+
+if "ninja" in l_need_genealogy:
+
+    print """
+# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
+# I n s t a l l _ n i n j a #
+# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
+"""
+    url = d_info["ninja"].url
+    extension = splitext(url)[1]
+    path_archive = "Downloads/{0}{1}".format("ninja", extension)
+
+    l_cmd = ["cd install &&",
+             "wget {0} -O {1} -o /dev/null &&".format(url, path_archive),
+             "./scripts/install_ninja.sh 2> /dev/null &&", "cd -"]
+
+    check_output(" ".join(l_cmd), shell=True)
+
+    print "Done"
+    l_need_genealogy.remove("ninja")
+
+print """
+# ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+# C r e a t i n g _ n i n j a #
+# ~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+"""
+
+
+def create_rule():
+
+    l_rules = [
+        "rule download", "  command = wget ${url} -O ${out} -o /dev/null",
+        "  description = Downloading ${descr}", "", "rule install",
+        "  command = ./scripts/install_${target}.sh > _build/${target}.log 2>&1",
+        "  description = Installing ${descr}", ""
+    ]
+
+    return l_rules
+
+l_string = create_rule()
+
+l_build = []
+
+for need in l_need_genealogy:
+
+    if need == "ocaml":
+        continue
+
+    url = d_info[need].url
+    extension = splitext(url)[1]
+
+    archive_path = "Downloads/{0}{1}".format(need, extension)
+
+    descr = d_info[need].description
+
+    # Build to dowload
+    l_build += ["build {0}: download".format(archive_path),
+                "   url = {0}".format(url),
+                "   descr = {0}".format(descr), ""]
+
+    # Build to install
+    l_dependancy = [d_info[i].default_path for i in d_dependancy[need] if i in l_need_genealogy]
+
+    l_build += ["build {0}: install {1} {2}".format(d_info[need].default_path,
+                                                    archive_path,
+                                                    " ".join(l_dependancy)),
+                "   target = {0}".format(need),
+                "   descr = {0}".format(descr), ""]
+
+l_string += l_build
+
+path = join(QP_ROOT_INSTALL, "build.ninja")
+with open(path, "w+") as f:
+    f.write("\n".join(l_string))
+
+print "Done"
+print "You can check at {0}".format(path)
+
+print """
+# ~#~#~#~#~#~#~#~#~ #
+# R u n _ n i n j a #
+# ~#~#~#~#~#~#~#~#~ #
+"""
+
+if [i for i in l_need_genealogy if i not in "ocaml"]:
+    subprocess.check_call("./bin/ninja -C install", shell=True)
+
+print "Done"
+
+if "ocaml" in l_need_genealogy:
+
+    print """
+# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
+# I n s t a l l _ o c a m l #
+# ~#~#~#~#~#~#~#~#~#~#~#~#~ #
+"""
+    url = d_info["ocaml"].url
+    extension = splitext(url)[1]
+    path_archive = "Downloads/{0}{1}".format("ocaml", extension)
+
+    l_cmd = ["cd install &&",
+             "wget {0} -O {1} -o /dev/null &&".format(url, path_archive),
+             "./scripts/install_ocaml.sh --fast"]
+
+    os.system(" ".join(l_cmd))
+
+    print "Done"
+    l_need_genealogy.remove("ocaml")
+
+
+print """
+# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+# C r e a t e   q u a n t u m _ p a c k a g e . r c
+# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
+"""
+
+python_path = [join(QP_ROOT, "scripts"), join(QP_ROOT, "install")]
+
+l_python = [join(QP_ROOT, "scripts")]
+for dir_ in python_path:
+    for folder in os.listdir(dir_):
+        path = join(dir_, folder)
+        if os.path.isdir(path):
+            l_python.append(path)
+
+
+def find_path(bin_):
+    try:
+        locate = l_installed[bin_]
+    except KeyError:
+        locate = d_info[bin_].default_path
+    return locate
+
+
+l_rc = [
+    'export QP_ROOT={0}'.format(QP_ROOT),
+    'export QP_EZFIO={0}'.format(find_path('ezfio')),
+    'export IRPF90={0}'.format(find_path("irpf90")),
+    'export NINJA={0}'.format(find_path("ninja")),
+    'export QP_PYTHON={0}'.format(":".join(l_python)),
+    "",
+    'export PYTHONPATH="${PYTHONPATH}":"${QP_PYTHON}"',
+    'export PATH="${PATH}":"${QP_PYTHON}":"${QP_ROOT}"/bin:"${QP_ROOT}"/ocaml',
+    'export LD_LIBRARY_PATH="${QP_ROOT}"/lib:"${LD_LIBRARY_PATH}"',
+    'export LIBRARY_PATH="${QP_ROOT}"/lib:"${LIBRARY_PATH}"', ""
+    'source ${HOME}/.opam/opam-init/init.sh > /dev/null 2> /dev/null || true',
+    ""
+]
+
+path = join(QP_ROOT, "quantum_package.rc")
+with open(path, "w+") as f:
+    f.write("\n".join(l_rc))
+
+print "Done"
+print "You can check at {0}".format(path)
+print "Don't forget to source it"

setup_environment.sh

@@ -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
-

src/Ezfio_files/output.irp.f

@@ -10,7 +10,7 @@ END_PROVIDER
  
 BEGIN_SHELL [ /bin/bash ]
  
- for NAME in $(\ls -d ${QPACKAGE_ROOT}/src/*/)
+ for NAME in $(\ls -d ${QP_ROOT}/src/*/)
  do
  NAME=$(basename ${NAME})
  cat << EOF

src/MOs/utils.irp.f

@@ -3,7 +3,7 @@ subroutine save_mos
   double precision, allocatable  :: buffer(:,:)
   integer                        :: i,j
   
-  call system('$QPACKAGE_ROOT/scripts/save_current_mos.sh '//trim(ezfio_filename))
+  call system('$QP_ROOT/scripts/save_current_mos.sh '//trim(ezfio_filename))
   
   call ezfio_set_mo_basis_mo_tot_num(mo_tot_num)
   call ezfio_set_mo_basis_mo_label(mo_label)

src/Perturbation/perturbation.irp.f

@@ -2,7 +2,7 @@ BEGIN_SHELL [ /usr/bin/env python ]
 from perturbation import perturbations
 import os
 
-filename = os.environ["QPACKAGE_ROOT"]+"/src/Perturbation/perturbation.template.f"
+filename = os.environ["QP_ROOT"]+"/src/Perturbation/perturbation.template.f"
 file = open(filename,'r')
 template = file.read()
 file.close()

src/README.rst

@@ -31,7 +31,7 @@ Creating a new module
 =====================
 
 Every new module should be created using the interactive ``create_module.sh``
-script located in the ``${QPACKAGE_ROOT}/scripts`` directory. This will create
+script located in the ``${QP_ROOT}/scripts`` directory. This will create
 all the required files with correct templates.
 
 
@@ -88,7 +88,7 @@ HTML, man, etc.
 Creating a shell script
 =======================
 
-Shell scripts should be located in the ``${QPACKAGE_ROOT}/scripts`` directory.
+Shell scripts should be located in the ``${QP_ROOT}/scripts`` directory.
 Relative paths should be avoided as much as possible, and the result of commands
 should be always checked. For example, when creating a directory the existence
 of the directory has to be checked.

testing_no_regression/unit_test.py

@@ -5,9 +5,9 @@ import subprocess
 import os
 import sys
 
-qpackage_root = os.environ['QPACKAGE_ROOT']
+qpackage_root = os.environ['QP_ROOT']
 
-EZFIO = "{0}/EZFIO".format(qpackage_root)
+EZFIO = "{0}/install/EZFIO".format(qpackage_root)
 sys.path = [EZFIO + "/Python"] + sys.path
 
 from ezfio import ezfio