Fix merge issue

ocaml/Makefile

@@ -35,7 +35,7 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore
 executables: $(QPACKAGE_ROOT)/data/executables
 
 $(QPACKAGE_ROOT)/data/executables:
-	$(QPACKAGE_ROOT)/scripts/create_executables_list.sh
+	$(QPACKAGE_ROOT)/scripts/create/create_executables_list.sh
 
 external_libs:
 	opam install cryptokit core

scripts/build_modules.sh

@@ -30,7 +30,7 @@ Build failed for module $MODULE
 "
     fi
   fi
-  ${QPACKAGE_ROOT}/scripts/create_gitignore.sh
+  ${QPACKAGE_ROOT}/scripts/create/create_gitignore.sh
   cd ${OLDPWD}
 done
-${QPACKAGE_ROOT}/scripts/create_executables_list.sh
+${QPACKAGE_ROOT}/scripts/create/create_executables_list.sh

scripts/check_dependencies.sh

@@ -25,7 +25,7 @@ fi
 
 if [[ $1 == "-" ]]
 then
-  COMMAND_LINE=$(cat NEEDED_MODULES)
+  COMMAND_LINE=$(only_children_to_all_genealogy.py NEEDED_MODULES)
 else
   COMMAND_LINE=$(unique_list $@)
 fi
@@ -44,7 +44,7 @@ DEPS_LONG=""
 for i in $COMMAND_LINE
 do
   DEPS_LONG+=" $i "
-  DEPS_LONG+=$(cat "${QPACKAGE_ROOT}/src/${i}/NEEDED_MODULES")
+  DEPS_LONG+=$(only_children_to_all_genealogy.py "${QPACKAGE_ROOT}/src/${i}/NEEDED_MODULES")
 done
 
 DEPS=$(unique_list $DEPS_LONG)

scripts/clean_modules.sh

@@ -13,7 +13,7 @@ source ${QPACKAGE_ROOT}/scripts/qp_include.sh
 function do_clean()
 {
   rm -rf -- \
-    IRPF90_temp IRPF90_man Makefile.depend $(cat NEEDED_MODULES) include \
+    IRPF90_temp IRPF90_man Makefile.depend $(only_children_to_all_genealogy.py) include \
     ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe) *.mod
 }
 

scripts/create/create_module.sh

@@ -117,7 +117,7 @@ debug "Module directory is created."
 
 
 # Create the Makefile
-"${QPACKAGE_ROOT}/scripts/create_Makefile.sh" || fail "Unable to create Makefile"
+"${QPACKAGE_ROOT}/scripts/create/create_Makefile.sh" || fail "Unable to create Makefile"
 if [[ ! -f Makefile ]]
 then
   fail "Makefile was not created"
@@ -125,7 +125,7 @@ fi
 debug "Makefile created"
 
 # Create the NEEDED_MODULES file
-"${QPACKAGE_ROOT}/scripts/create_Needed_modules.sh" ${NEEDED_MODULES} || fail "Unable to create the NEEDED_MODULES file"
+"${QPACKAGE_ROOT}/scripts/create/create_Needed_modules.sh" ${NEEDED_MODULES} || fail "Unable to create the NEEDED_MODULES file"
 if [[ ! -f NEEDED_MODULES ]]
 then
   fail "NEEDED_MODULES was not created"
@@ -135,7 +135,7 @@ debug "NEEDED_MODULES created"
 
 
 # Create rst templates
-"${QPACKAGE_ROOT}/scripts/create_rst_templates.sh" || fail "Unable to create rst templates"
+"${QPACKAGE_ROOT}/scripts/create/create_rst_templates.sh" || fail "Unable to create rst templates"
 
 
 # Update module list in main NEEDED_MODULES

scripts/docopt.py

@@ -1,590 +0,0 @@
-"""Pythonic command-line interface parser that will make you smile.
-
- * http://docopt.org
- * Repository and issue-tracker: https://github.com/docopt/docopt
- * Licensed under terms of MIT license (see LICENSE-MIT)
- * Copyright (c) 2013 Vladimir Keleshev, vladimir@keleshev.com
-
-"""
-import sys
-import re
-
-
-__all__ = ['docopt']
-__version__ = '0.6.1'
-
-
-class DocoptLanguageError(Exception):
-
-    """Error in construction of usage-message by developer."""
-
-
-class DocoptExit(SystemExit):
-
-    """Exit in case user invoked program with incorrect arguments."""
-
-    usage = ''
-
-    def __init__(self, message=''):
-        SystemExit.__init__(self, (message + '\n' + self.usage).strip())
-
-
-class Pattern(object):
-
-    def __eq__(self, other):
-        return repr(self) == repr(other)
-
-    def __hash__(self):
-        return hash(repr(self))
-
-    def fix(self):
-        self.fix_identities()
-        self.fix_repeating_arguments()
-        return self
-
-    def fix_identities(self, uniq=None):
-        """Make pattern-tree tips point to same object if they are equal."""
-        if not hasattr(self, 'children'):
-            return self
-        uniq = list(set(self.flat())) if uniq is None else uniq
-        for i, child in enumerate(self.children):
-            if not hasattr(child, 'children'):
-                assert child in uniq
-                self.children[i] = uniq[uniq.index(child)]
-            else:
-                child.fix_identities(uniq)
-
-    def fix_repeating_arguments(self):
-        """Fix elements that should accumulate/increment values."""
-        either = [list(child.children) for child in transform(self).children]
-        for case in either:
-            for e in [child for child in case if case.count(child) > 1]:
-                if isinstance(
-                        e,
-                        Argument) or isinstance(
-                        e,
-                        Option) and e.argcount:
-                    if e.value is None:
-                        e.value = []
-                    elif not isinstance(e.value, list):
-                        e.value = e.value.split()
-                if isinstance(
-                        e,
-                        Command) or isinstance(
-                        e,
-                        Option) and e.argcount == 0:
-                    e.value = 0
-        return self
-
-
-def transform(pattern):
-    """Expand pattern into an (almost) equivalent one, but with single Either.
-
-    Example: ((-a | -b) (-c | -d)) => (-a -c | -a -d | -b -c | -b -d)
-    Quirks: [-a] => (-a), (-a...) => (-a -a)
-
-    """
-    result = []
-    groups = [[pattern]]
-    while groups:
-        children = groups.pop(0)
-        parents = [Required, Optional, OptionsShortcut, Either, OneOrMore]
-        if any(t in map(type, children) for t in parents):
-            child = [c for c in children if type(c) in parents][0]
-            children.remove(child)
-            if isinstance(child, Either):
-                for c in child.children:
-                    groups.append([c] + children)
-            elif isinstance(child, OneOrMore):
-                groups.append(child.children * 2 + children)
-            else:
-                groups.append(child.children + children)
-        else:
-            result.append(children)
-    return Either(*[Required(*e) for e in result])
-
-
-class LeafPattern(Pattern):
-
-    """Leaf/terminal node of a pattern tree."""
-
-    def __init__(self, name, value=None):
-        self.name, self.value = name, value
-
-    def __repr__(self):
-        return '%s(%r, %r)' % (self.__class__.__name__, self.name, self.value)
-
-    def flat(self, *types):
-        return [self] if not types or type(self) in types else []
-
-    def match(self, left, collected=None):
-        collected = [] if collected is None else collected
-        pos, match = self.single_match(left)
-        if match is None:
-            return False, left, collected
-        left_ = left[:pos] + left[pos + 1:]
-        same_name = [a for a in collected if a.name == self.name]
-        if type(self.value) in (int, list):
-            if isinstance(self.value, int):
-                increment = 1
-            else:
-                increment = ([match.value] if isinstance(match.value, str)
-                             else match.value)
-            if not same_name:
-                match.value = increment
-                return True, left_, collected + [match]
-            same_name[0].value += increment
-            return True, left_, collected
-        return True, left_, collected + [match]
-
-
-class BranchPattern(Pattern):
-
-    """Branch/inner node of a pattern tree."""
-
-    def __init__(self, *children):
-        self.children = list(children)
-
-    def __repr__(self):
-        return '%s(%s)' % (self.__class__.__name__,
-                           ', '.join(repr(a) for a in self.children))
-
-    def flat(self, *types):
-        if type(self) in types:
-            return [self]
-        return sum([child.flat(*types) for child in self.children], [])
-
-
-class Argument(LeafPattern):
-
-    def single_match(self, left):
-        for n, pattern in enumerate(left):
-            if isinstance(pattern, Argument):
-                return n, Argument(self.name, pattern.value)
-        return None, None
-
-    @classmethod
-    def parse(class_, source):
-        name = re.findall('(<\S*?>)', source)[0]
-        value = re.findall('\[default: (.*)\]', source, flags=re.I)
-        return class_(name, value[0] if value else None)
-
-
-class Command(Argument):
-
-    def __init__(self, name, value=False):
-        self.name, self.value = name, value
-
-    def single_match(self, left):
-        for n, pattern in enumerate(left):
-            if isinstance(pattern, Argument):
-                if pattern.value == self.name:
-                    return n, Command(self.name, True)
-                else:
-                    break
-        return None, None
-
-
-class Option(LeafPattern):
-
-    def __init__(self, short=None, long=None, argcount=0, value=False):
-        assert argcount in (0, 1)
-        self.short, self.long, self.argcount = short, long, argcount
-        self.value = None if value is False and argcount else value
-
-    @classmethod
-    def parse(class_, option_description):
-        short, long, argcount, value = None, None, 0, False
-        options, _, description = option_description.strip().partition('  ')
-        options = options.replace(',', ' ').replace('=', ' ')
-        for s in options.split():
-            if s.startswith('--'):
-                long = s
-            elif s.startswith('-'):
-                short = s
-            else:
-                argcount = 1
-        if argcount:
-            matched = re.findall('\[default: (.*)\]', description, flags=re.I)
-            value = matched[0] if matched else None
-        return class_(short, long, argcount, value)
-
-    def single_match(self, left):
-        for n, pattern in enumerate(left):
-            if self.name == pattern.name:
-                return n, pattern
-        return None, None
-
-    @property
-    def name(self):
-        return self.long or self.short
-
-    def __repr__(self):
-        return 'Option(%r, %r, %r, %r)' % (self.short, self.long,
-                                           self.argcount, self.value)
-
-
-class Required(BranchPattern):
-
-    def match(self, left, collected=None):
-        collected = [] if collected is None else collected
-        l = left
-        c = collected
-        for pattern in self.children:
-            matched, l, c = pattern.match(l, c)
-            if not matched:
-                return False, left, collected
-        return True, l, c
-
-
-class Optional(BranchPattern):
-
-    def match(self, left, collected=None):
-        collected = [] if collected is None else collected
-        for pattern in self.children:
-            m, left, collected = pattern.match(left, collected)
-        return True, left, collected
-
-
-class OptionsShortcut(Optional):
-
-    """Marker/placeholder for [options] shortcut."""
-
-
-class OneOrMore(BranchPattern):
-
-    def match(self, left, collected=None):
-        assert len(self.children) == 1
-        collected = [] if collected is None else collected
-        l = left
-        c = collected
-        l_ = None
-        matched = True
-        times = 0
-        while matched:
-            # could it be that something didn't match but changed l or c?
-            matched, l, c = self.children[0].match(l, c)
-            times += 1 if matched else 0
-            if l_ == l:
-                break
-            l_ = l
-        if times >= 1:
-            return True, l, c
-        return False, left, collected
-
-
-class Either(BranchPattern):
-
-    def match(self, left, collected=None):
-        collected = [] if collected is None else collected
-        outcomes = []
-        for pattern in self.children:
-            matched, _, _ = outcome = pattern.match(left, collected)
-            if matched:
-                outcomes.append(outcome)
-        if outcomes:
-            return min(outcomes, key=lambda outcome: len(outcome[1]))
-        return False, left, collected
-
-
-class Tokens(list):
-
-    def __init__(self, source, error=DocoptExit):
-        self += source.split() if hasattr(source, 'split') else source
-        self.error = error
-
-    @staticmethod
-    def from_pattern(source):
-        source = re.sub(r'([\[\]\(\)\|]|\.\.\.)', r' \1 ', source)
-        source = [s for s in re.split('\s+|(\S*<.*?>)', source) if s]
-        return Tokens(source, error=DocoptLanguageError)
-
-    def move(self):
-        return self.pop(0) if len(self) else None
-
-    def current(self):
-        return self[0] if len(self) else None
-
-
-def parse_long(tokens, options):
-    """long ::= '--' chars [ ( ' ' | '=' ) chars ] ;"""
-    long, eq, value = tokens.move().partition('=')
-    assert long.startswith('--')
-    value = None if eq == value == '' else value
-    similar = [o for o in options if o.long == long]
-    if tokens.error is DocoptExit and similar == []:  # if no exact match
-        similar = [o for o in options if o.long and o.long.startswith(long)]
-    if len(similar) > 1:  # might be simply specified ambiguously 2+ times?
-        raise tokens.error('%s is not a unique prefix: %s?' %
-                           (long, ', '.join(o.long for o in similar)))
-    elif len(similar) < 1:
-        argcount = 1 if eq == '=' else 0
-        o = Option(None, long, argcount)
-        options.append(o)
-        if tokens.error is DocoptExit:
-            o = Option(None, long, argcount, value if argcount else True)
-    else:
-        o = Option(similar[0].short, similar[0].long,
-                   similar[0].argcount, similar[0].value)
-        if o.argcount == 0:
-            if value is not None:
-                raise tokens.error('%s must not have an argument' % o.long)
-        else:
-            if value is None:
-                if tokens.current() in [None, '--']:
-                    raise tokens.error('%s requires argument' % o.long)
-                value = tokens.move()
-        if tokens.error is DocoptExit:
-            o.value = value if value is not None else True
-    return [o]
-
-
-def parse_shorts(tokens, options):
-    """shorts ::= '-' ( chars )* [ [ ' ' ] chars ] ;"""
-    token = tokens.move()
-    assert token.startswith('-') and not token.startswith('--')
-    left = token.lstrip('-')
-    parsed = []
-    while left != '':
-        short, left = '-' + left[0], left[1:]
-        similar = [o for o in options if o.short == short]
-        if len(similar) > 1:
-            raise tokens.error('%s is specified ambiguously %d times' %
-                               (short, len(similar)))
-        elif len(similar) < 1:
-            o = Option(short, None, 0)
-            options.append(o)
-            if tokens.error is DocoptExit:
-                o = Option(short, None, 0, True)
-        else:  # why copying is necessary here?
-            o = Option(short, similar[0].long,
-                       similar[0].argcount, similar[0].value)
-            value = None
-            if o.argcount != 0:
-                if left == '':
-                    if tokens.current() in [None, '--']:
-                        raise tokens.error('%s requires argument' % short)
-                    value = tokens.move()
-                else:
-                    value = left
-                    left = ''
-            if tokens.error is DocoptExit:
-                o.value = value if value is not None else True
-        parsed.append(o)
-    return parsed
-
-
-def parse_pattern(source, options):
-    tokens = Tokens.from_pattern(source)
-    result = parse_expr(tokens, options)
-    if tokens.current() is not None:
-        raise tokens.error('unexpected ending: %r' % ' '.join(tokens))
-    return Required(*result)
-
-
-def parse_expr(tokens, options):
-    """expr ::= seq ( '|' seq )* ;"""
-    seq = parse_seq(tokens, options)
-    if tokens.current() != '|':
-        return seq
-    result = [Required(*seq)] if len(seq) > 1 else seq
-    while tokens.current() == '|':
-        tokens.move()
-        seq = parse_seq(tokens, options)
-        result += [Required(*seq)] if len(seq) > 1 else seq
-    return [Either(*result)] if len(result) > 1 else result
-
-
-def parse_seq(tokens, options):
-    """seq ::= ( atom [ '...' ] )* ;"""
-    result = []
-    while tokens.current() not in [None, ']', ')', '|']:
-        atom = parse_atom(tokens, options)
-        if tokens.current() == '...':
-            atom = [OneOrMore(*atom)]
-            tokens.move()
-        result += atom
-    return result
-
-
-def parse_atom(tokens, options):
-    """atom ::= '(' expr ')' | '[' expr ']' | 'options'
-             | long | shorts | argument | command ;
-    """
-    token = tokens.current()
-    result = []
-    if token in '([':
-        tokens.move()
-        matching, pattern = {'(': [')', Required], '[': [']', Optional]}[token]
-        result = pattern(*parse_expr(tokens, options))
-        if tokens.move() != matching:
-            raise tokens.error("unmatched '%s'" % token)
-        return [result]
-    elif token == 'options':
-        tokens.move()
-        return [OptionsShortcut()]
-    elif token.startswith('--') and token != '--':
-        return parse_long(tokens, options)
-    elif token.startswith('-') and token not in ('-', '--'):
-        return parse_shorts(tokens, options)
-    elif token.startswith('<') and token.endswith('>') or token.isupper():
-        return [Argument(tokens.move())]
-    else:
-        return [Command(tokens.move())]
-
-
-def parse_argv(tokens, options, options_first=False):
-    """Parse command-line argument vector.
-
-    If options_first:
-        argv ::= [ long | shorts ]* [ argument ]* [ '--' [ argument ]* ] ;
-    else:
-        argv ::= [ long | shorts | argument ]* [ '--' [ argument ]* ] ;
-
-    """
-    parsed = []
-    while tokens.current() is not None:
-        if tokens.current() == '--':
-            return parsed + [Argument(None, v) for v in tokens]
-        elif tokens.current().startswith('--'):
-            parsed += parse_long(tokens, options)
-        elif tokens.current().startswith('-') and tokens.current() != '-':
-            parsed += parse_shorts(tokens, options)
-        elif options_first:
-            return parsed + [Argument(None, v) for v in tokens]
-        else:
-            parsed.append(Argument(None, tokens.move()))
-    return parsed
-
-
-def parse_defaults(doc):
-    defaults = []
-    for s in parse_section('options:', doc):
-        # FIXME corner case "bla: options: --foo"
-        _, _, s = s.partition(':')  # get rid of "options:"
-        split = re.split('\n[ \t]*(-\S+?)', '\n' + s)[1:]
-        split = [s1 + s2 for s1, s2 in zip(split[::2], split[1::2])]
-        options = [Option.parse(s) for s in split if s.startswith('-')]
-        defaults += options
-    return defaults
-
-
-def parse_section(name, source):
-    pattern = re.compile('^([^\n]*' + name + '[^\n]*\n?(?:[ \t].*?(?:\n|$))*)',
-                         re.IGNORECASE | re.MULTILINE)
-    return [s.strip() for s in pattern.findall(source)]
-
-
-def formal_usage(section):
-    _, _, section = section.partition(':')  # drop "usage:"
-    pu = section.split()
-    return '( ' + ' '.join(') | (' if s == pu[0] else s for s in pu[1:]) + ' )'
-
-
-def extras(help, version, options, doc):
-    if help and any((o.name in ('-h', '--help')) and o.value for o in options):
-        print(doc.strip("\n"))
-        sys.exit()
-    if version and any(o.name == '--version' and o.value for o in options):
-        print(version)
-        sys.exit()
-
-
-class Dict(dict):
-
-    def __repr__(self):
-        return '{%s}' % ',\n '.join('%r: %r' % i for i in sorted(self.items()))
-
-
-def docopt(doc, argv=None, help=True, version=None, options_first=False):
-    """Parse `argv` based on command-line interface described in `doc`.
-
-    `docopt` creates your command-line interface based on its
-    description that you pass as `doc`. Such description can contain
-    --options, <positional-argument>, commands, which could be
-    [optional], (required), (mutually | exclusive) or repeated...
-
-    Parameters
-    ----------
-    doc : str
-        Description of your command-line interface.
-    argv : list of str, optional
-        Argument vector to be parsed. sys.argv[1:] is used if not
-        provided.
-    help : bool (default: True)
-        Set to False to disable automatic help on -h or --help
-        options.
-    version : any object
-        If passed, the object will be printed if --version is in
-        `argv`.
-    options_first : bool (default: False)
-        Set to True to require options precede positional arguments,
-        i.e. to forbid options and positional arguments intermix.
-
-    Returns
-    -------
-    args : dict
-        A dictionary, where keys are names of command-line elements
-        such as e.g. "--verbose" and "<path>", and values are the
-        parsed values of those elements.
-
-    Example
-    -------
-    >>> from docopt import docopt
-    >>> doc = '''
-    ... Usage:
-    ...     my_program tcp <host> <port> [--timeout=<seconds>]
-    ...     my_program serial <port> [--baud=<n>] [--timeout=<seconds>]
-    ...     my_program (-h | --help | --version)
-    ...
-    ... Options:
-    ...     -h, --help  Show this screen and exit.
-    ...     --baud=<n>  Baudrate [default: 9600]
-    ... '''
-    >>> argv = ['tcp', '127.0.0.1', '80', '--timeout', '30']
-    >>> docopt(doc, argv)
-    {'--baud': '9600',
-     '--help': False,
-     '--timeout': '30',
-     '--version': False,
-     '<host>': '127.0.0.1',
-     '<port>': '80',
-     'serial': False,
-     'tcp': True}
-
-    See also
-    --------
-    * For video introduction see http://docopt.org
-    * Full documentation is available in README.rst as well as online
-      at https://github.com/docopt/docopt#readme
-
-    """
-    argv = sys.argv[1:] if argv is None else argv
-
-    usage_sections = parse_section('usage:', doc)
-    if len(usage_sections) == 0:
-        raise DocoptLanguageError('"usage:" (case-insensitive) not found.')
-    if len(usage_sections) > 1:
-        raise DocoptLanguageError('More than one "usage:" (case-insensitive).')
-    DocoptExit.usage = usage_sections[0]
-
-    options = parse_defaults(doc)
-    pattern = parse_pattern(formal_usage(DocoptExit.usage), options)
-    # [default] syntax for argument is disabled
-    # for a in pattern.flat(Argument):
-    #    same_name = [d for d in arguments if d.name == a.name]
-    #    if same_name:
-    #        a.value = same_name[0].value
-    argv = parse_argv(Tokens(argv), list(options), options_first)
-    pattern_options = set(pattern.flat(Option))
-    for options_shortcut in pattern.flat(OptionsShortcut):
-        doc_options = parse_defaults(doc)
-        options_shortcut.children = list(set(doc_options) - pattern_options)
-        # if any_options:
-        #    options_shortcut.children += [Option(o.short, o.long, o.argcount)
-        #                    for o in argv if type(o) is Option]
-    extras(help, version, argv, doc)
-    matched, left, collected = pattern.fix().match(argv)
-    if matched and left == []:  # better error message if left?
-        return Dict((a.name, a.value) for a in (pattern.flat() + collected))
-    raise DocoptExit()

scripts/install/install_curl.sh

@@ -8,8 +8,8 @@ CURL_URL="http://qmcchem.ups-tlse.fr/files/scemama/${CURL}.tar.bz2"
 
 if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  print "The QPACKAGE_ROOT environment variable is not set."
+  echo "The QPACKAGE_ROOT environment variable is not set."
-  print "Please reload the quantum_package.rc file."
+  echo "Please reload the quantum_package.rc file."
   exit -1
 fi
 

scripts/install/install_docopt.sh

@@ -0,0 +1,21 @@
+#!/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/fetch_from_web.py ${DOCOPT_URL} ${DOCOPT}
+
+mv ${DOCOPT} scripts/${DOCOPT}

scripts/install/install_emsl.sh

@@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
 
 if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  print "The QPACKAGE_ROOT environment variable is not set."
+  echo "The QPACKAGE_ROOT environment variable is not set."
-  print "Please reload the quantum_package.rc file."
+  echo "Please reload the quantum_package.rc file."
   exit -1
 fi
 

scripts/install/install_ezfio.sh

@@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
 
 if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  print "The QPACKAGE_ROOT environment variable is not set."
+  echo "The QPACKAGE_ROOT environment variable is not set."
-  print "Please reload the quantum_package.rc file."
+  echo "Please reload the quantum_package.rc file."
   exit -1
 fi
 

scripts/module/only_children_to_all_genealogy.py

@@ -0,0 +1,108 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+import os.path
+
+dir_ = '/home/razoa/quantum_package/src'
+
+
+def get_dict_genealogy(all_children=False):
+
+    d_ref = dict()
+
+    for o in os.listdir(dir_):
+
+        try:
+            with open(os.path.join(dir_, o, "NEEDED_CHILDREN_MODULES"), "r") as f:
+                l_children = f.read().split()
+        except IOError:
+            pass
+        else:
+            d_ref[o] = l_children
+
+    if all_children:
+        for module in d_ref:
+            d_ref[module] = get_all_children(d_ref, d_ref[module], [])
+
+    return d_ref
+
+
+def module_children_to_all(d_ref,path):
+
+    if not path:
+        dir_ = os.getcwd()
+        path = os.path.join(dir_, "NEEDED_CHILDREN_MODULES")
+
+    try:
+        with open(path, "r") as f:
+            l_children = f.read().split()
+    except IOError:
+        return []
+    else:
+        needed_module = l_children
+        for module in l_children:
+
+            for children in get_all_children(d_ref, d_ref[module], []):
+                if children not in needed_module:
+                    needed_module.append(children)
+
+        return needed_module
+
+
+def get_all_children(d_ref, l_module, l=[]):
+    """
+    From a d_ref (who containt all the data --flatter or not-- create
+        an flatten list who contain all the children
+    """
+    for module in l_module:
+        if module not in l:
+            l.append(module)
+            get_all_children(d_ref, d_ref[module], l)
+
+    return list(set(l))
+
+
+def reduce_(d_ref, name):
+
+    """
+    Take a big list and try to find the lower parent
+    available
+    """
+    import itertools
+
+    a = sorted(get_all_children(d_ref[name]))
+
+    for i in xrange(len(d_ref)):
+        for c in itertools.combinations(d_ref, i):
+
+                l = []
+                b = sorted(get_all_children(c, l))
+
+                if a == b:
+                    return c
+
+#for i in sorted(d_ref):
+#    print i, reduce_(i)
+#
+
+if __name__ == '__main__':
+    import sys
+
+    try:
+        path = sys.argv[1]
+    except IndexError:
+        path = None
+
+    d_ref = get_dict_genealogy()
+
+    l_all_needed_molule = module_children_to_all(d_ref, path)
+    print " ".join(sorted(l_all_needed_molule))
+
+#    print d_ref
+#
+#    d_ref = get_dict_genealogy(True)
+#
+#    print d_ref
+#
+#    module_hl_to_ll(d_ref)

scripts/qp_include.sh

@@ -35,9 +35,9 @@ function check_current_dir_is_module()
      exit -1
   fi
 }
-if [[ -f NEEDED_MODULES ]]
+if [[ -f NEEDED_CHILDREN_MODULES ]]
 then
-  NEEDED_MODULES=$(cat NEEDED_MODULES)
+  NEEDED_MODULES=$(only_children_to_all_genealogy.py)
 fi
 
 # List of executables in the current directory

scripts/run_Makefile_common.sh

@@ -28,7 +28,7 @@ fi
 # Check if README.rst exists
 if [[ ! -f README.rst ]] 
 then
-  ${QPACKAGE_ROOT}/scripts/create_rst_templates.sh
+  ${QPACKAGE_ROOT}/scripts/create/create_rst_templates.sh
   error "
 README.rst was not present, so I created a
 default one for you.
@@ -62,7 +62,7 @@ then
 fi
 
 # Update Makefile.depend
-${QPACKAGE_ROOT}/scripts/create_Makefile_depend.sh
+${QPACKAGE_ROOT}/scripts/create/create_Makefile_depend.sh
 
 # Update EZFIO interface
-  ${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py
+${QPACKAGE_ROOT}/scripts/ezfio_interface/ei_handler.py

scripts/run_Makefile_global.sh

@@ -52,7 +52,7 @@ ${IRPF90_VERSION}.
 
 IRPF90 version >= ${IRPF90_REQUIRED_VERSION} is required.
 To upgrade IRPF90, run :                       
-  ${QPACKAGE_ROOT}/scripts/upgrade_irpf90.sh   
+  ${QPACKAGE_ROOT}/scripts/upgrade/upgrade_irpf90.sh   
 "
 else
   info "irpf90 version is OK"
@@ -75,7 +75,7 @@ then
 Current EZFIO version : ${EZFIO_VERSION}
 EZFIO version >= ${EZFIO_REQUIRED_VERSION} is required.
 To upgrade EZFIO, run :                       
-  ${QPACKAGE_ROOT}/scripts/upgrade_ezfio.sh   
+  ${QPACKAGE_ROOT}/scripts/upgrade/upgrade_ezfio.sh   
 "
 else
   info "EZFIO version is OK"

scripts/update_README.py

@@ -83,7 +83,7 @@ def update_needed(data):
     """Read the NEEDED_MODULES file, and replace the data with it.
     Create the links to the GitHub pages."""
 
-    file = open('NEEDED_MODULES', 'r')
+    file = open('NEEDED_CHILDREN_MODULES', 'r')
     modules = file.read()
     file.close()
 

setup_environment.sh

@@ -17,10 +17,10 @@ export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}")  ; pwd -P )
 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}:"\${QPACKAGE_ROOT}"/scripts
+
-export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface
+export PYTHONPATH=\${PYTHONPATH}\$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
-export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts/pseudo
+
-export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface
+export PATH=\${PATH}\$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p")
 export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin
 export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml
 source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null
@@ -30,37 +30,29 @@ EOF
 source quantum_package.rc
 
 echo "${BLUE}===== Installing IRPF90 ===== ${BLACK}"
-${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh     | tee install_irpf90.log
+${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh     | tee ${QPACKAGE_ROOT}/install_logs/install_irpf90.log
-if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]]
+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
-
-if [[ ! -x ${QPACKAGE_ROOT}/bin/irpf90 ]]
-then
-  echo $RED "Error in IRPF90 installation" $BLACK
-  exit 1
-fi
-
-if [[ ! -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 Zlib ===== ${BLACK}"
-${QPACKAGE_ROOT}/scripts/install/install_zlib.sh       | tee install_zlib.log
+${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 install_curl.log
+${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 install_m4.log
+${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 install_emsl.log
+${QPACKAGE_ROOT}/scripts/install/install_emsl.sh       | tee ${QPACKAGE_ROOT}/install_logs/install_emsl.log
 
 if [[ ! -d ${QPACKAGE_ROOT}/EMSL_Basis ]]
 then
@@ -70,7 +62,7 @@ fi
 
 echo "${BLUE}===== Installing EZFIO ===== ${BLACK}"
 
-${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh | tee install_ezfio.log
+${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
@@ -80,7 +72,7 @@ fi
 
 echo "${BLUE}===== Installing Ocaml compiler and libraries ===== ${BLACK}"
 rm -f -- ocaml/Qptypes.ml
-${QPACKAGE_ROOT}/scripts/install/install_ocaml.sh | tee install_ocaml.log
+${QPACKAGE_ROOT}/scripts/install/install_ocaml.sh | tee ${QPACKAGE_ROOT}/install_logs/install_ocaml.log
 
 if [[ ! -f ${QPACKAGE_ROOT}/ocaml/Qptypes.ml ]]
 then
@@ -108,8 +100,7 @@ source ${QPACKAGE_ROOT}/quantum_package.rc
 " $BLACK
 
 
-mkdir -p ${QPACKAGE_ROOT}/install_logs
+
-mv ${QPACKAGE_ROOT}/*.log ${QPACKAGE_ROOT}/install_logs/
 
 if [[ $1 == "--robot" ]] ; 
 then

src/AOs/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Nuclei

src/AOs/NEEDED_MODULES

@@ -1,2 +0,0 @@
-Ezfio_files Nuclei Output Utils
-

src/AOs/README.rst

@@ -39,10 +39,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============

src/Bielec_integrals/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+MonoInts Bitmask

src/Bielec_integrals/NEEDED_MODULES

@@ -1 +0,0 @@
-AOs Bitmask Electrons Ezfio_files MOs Nuclei Output Utils MonoInts

src/Bielec_integrals/README.rst

@@ -16,15 +16,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
+* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 
 Documentation
 =============

src/Bitmask/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+MOs

src/Bitmask/NEEDED_MODULES

@@ -1 +0,0 @@
-AOs Electrons Ezfio_files MOs Nuclei Output Utils

src/Bitmask/README.rst

@@ -40,13 +40,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============

src/CAS_SD/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Perturbation Selectors_full Generators_CAS

src/CAS_SD/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
-

src/CAS_SD/README.rst

@@ -24,21 +24,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
 

src/CID/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Selectors_full SingleRefMethod

src/CID/NEEDED_MODULES

@@ -1,3 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils
-
-

src/CID/README.rst

@@ -15,21 +15,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============

src/CID_SC2_selected/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+CID_selected

src/CID_SC2_selected/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask CISD CISD_selected Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
-

src/CID_SC2_selected/README.rst

@@ -19,23 +19,5 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
+* `CID_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CID_selected>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
-* `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/CID_selected/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Perturbation CID

src/CID_selected/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask CISD Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
-

src/CID_selected/README.rst

@@ -22,22 +22,6 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `CID <http://github.com/LCPQ/quantum_package/tree/master/src/CID>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/CIS/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Selectors_full SingleRefMethod

src/CIS/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils
-

src/CIS/README.rst

@@ -31,19 +31,6 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/CISD/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Selectors_full SingleRefMethod

src/CISD/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils
-

src/CISD/README.rst

@@ -15,21 +15,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============

src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+CISD_selected

src/CISD_SC2_selected/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask CISD CISD_selected Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
-

src/CISD_SC2_selected/README.rst

@@ -19,23 +19,5 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
 * `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/CISD_selected/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Perturbation CISD

src/CISD_selected/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask CISD Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
-

src/CISD_selected/README.rst

@@ -28,22 +28,6 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/DDCI_selected/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Perturbation Selectors_full Generators_CAS

src/DDCI_selected/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Generators_CAS Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
-

src/DDCI_selected/README.rst

@@ -19,21 +19,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+* `Generators_CAS <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_CAS>`_
 

src/Determinants/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Bielec_integrals

src/Determinants/NEEDED_MODULES

@@ -1 +0,0 @@
-AOs Bielec_integrals Bitmask Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

src/Determinants/README.rst

@@ -32,16 +32,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
 * `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============

src/Electrons/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Output

src/Electrons/NEEDED_MODULES

@@ -1 +0,0 @@
-Ezfio_files Output Utils

src/Electrons/README.rst

@@ -24,9 +24,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============

src/Ezfio_files/README.rst

@@ -30,3 +30,4 @@ Documentation
 
 
 
+

src/FCIdump/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Determinants

src/FCIdump/NEEDED_MODULES

@@ -1 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

src/FCIdump/README.rst

@@ -21,15 +21,5 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/Full_CI/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Perturbation Selectors_full Generators_full

src/Full_CI/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
-

src/Full_CI/README.rst

@@ -24,21 +24,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
 

src/Generators_CAS/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Determinants

src/Generators_CAS/NEEDED_MODULES

@@ -1 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

src/Generators_CAS/README.rst

@@ -43,15 +43,5 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/Generators_full/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Determinants Hartree_Fock

src/Generators_full/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Utils
-

src/Generators_full/README.rst

@@ -40,17 +40,6 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
 * `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/Generators_restart/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Determinants

src/Generators_restart/NEEDED_MODULES

@@ -1 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

src/Hartree_Fock/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Bielec_integrals MOGuess

src/Hartree_Fock/NEEDED_MODULES

@@ -1 +0,0 @@
-AOs Bielec_integrals Bitmask Electrons Ezfio_files MonoInts MOGuess MOs Nuclei Output Utils 

src/Hartree_Fock/README.rst

@@ -10,17 +10,8 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
 * `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
 * `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============

src/MOGuess/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+MonoInts

src/MOGuess/NEEDED_MODULES

@@ -1 +0,0 @@
-AOs Electrons Ezfio_files MonoInts MOs Nuclei Output Utils

src/MOGuess/README.rst

@@ -8,14 +8,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
 * `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============

src/MOs/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+AOs Electrons

src/MOs/NEEDED_MODULES

@@ -1,3 +0,0 @@
-AOs Electrons Ezfio_files Nuclei Output Utils
-
-

src/MOs/README.rst

@@ -24,10 +24,6 @@ Needed Modules
 
 * `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
 * `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 
 Documentation
 =============

src/MP2/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Perturbation Selectors_full SingleRefMethod

src/MP2/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full SingleRefMethod Utils
-

src/MP2/README.rst

@@ -19,21 +19,7 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
 * `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
 

src/MRCC/NEEDED_CHILDREN_MODULES

@@ -0,0 +1 @@
+Perturbation Selectors_full Generators_full

src/MRCC/NEEDED_MODULES

@@ -1,2 +0,0 @@
-AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Perturbation Properties Selectors_full Utils
-

src/MRCC/README.rst

@@ -8,23 +8,9 @@ Needed Modules
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `Bielec_integrals <http://github.com/LCPQ/quantum_package/tree/master/src/Bielec_integrals>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
 * `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
 * `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
+* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
 
 Documentation
 =============

src/Makefile

@@ -26,7 +26,7 @@ $(ALL_MODULES): ezfio
 
 # Define the EZFIO rules
 $(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/EZFIO.cfg)
-	$(QPACKAGE_ROOT)/scripts/prepare_ezfio.sh
+	$(QPACKAGE_ROOT)/scripts/ezfio_interface/prepare_ezfio.sh
 	cd $(EZFIO_DIR);\
 	export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ;\
 	$(MAKE) ;\