From 14b50bf1eb1d20523889ddc3a27bdd0edf352cab Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Mon, 27 Apr 2015 16:55:19 +0200 Subject: [PATCH 1/9] Add docopt installation --- scripts/docopt.py | 590 -------------------------------------- scripts/install_docopt.sh | 21 ++ setup_environment.sh | 3 + 3 files changed, 24 insertions(+), 590 deletions(-) delete mode 100755 scripts/docopt.py create mode 100755 scripts/install_docopt.sh diff --git a/scripts/docopt.py b/scripts/docopt.py deleted file mode 100755 index 59830d53..00000000 --- a/scripts/docopt.py +++ /dev/null @@ -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, , 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 "", and values are the - parsed values of those elements. - - Example - ------- - >>> from docopt import docopt - >>> doc = ''' - ... Usage: - ... my_program tcp [--timeout=] - ... my_program serial [--baud=] [--timeout=] - ... my_program (-h | --help | --version) - ... - ... Options: - ... -h, --help Show this screen and exit. - ... --baud= Baudrate [default: 9600] - ... ''' - >>> argv = ['tcp', '127.0.0.1', '80', '--timeout', '30'] - >>> docopt(doc, argv) - {'--baud': '9600', - '--help': False, - '--timeout': '30', - '--version': False, - '': '127.0.0.1', - '': '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() diff --git a/scripts/install_docopt.sh b/scripts/install_docopt.sh new file mode 100755 index 00000000..7edf2377 --- /dev/null +++ b/scripts/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 + print "The QPACKAGE_ROOT environment variable is not set." + print "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} \ No newline at end of file diff --git a/setup_environment.sh b/setup_environment.sh index be4bae64..e650a273 100755 --- a/setup_environment.sh +++ b/setup_environment.sh @@ -57,6 +57,9 @@ ${QPACKAGE_ROOT}/scripts/install_curl.sh | tee install_curl.log echo "${BLUE}===== Installing M4 ===== ${BLACK}" ${QPACKAGE_ROOT}/scripts/install_m4.sh | tee install_m4.log +echo "${BLUE}===== Installing Docopt ===== ${BLACK}" +${QPACKAGE_ROOT}/scripts/install_docopt.sh | tee install_docopt.log + echo "${BLUE}===== Installing EMSL Basis set library ===== ${BLACK}" ${QPACKAGE_ROOT}/scripts/install_emsl.sh | tee install_emsl.log From 24c5e1aa57b7a5e2dd208453c7834b36c2f13508 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Mon, 27 Apr 2015 17:10:25 +0200 Subject: [PATCH 2/9] Change print into echo for install_* --- scripts/install_curl.sh | 4 ++-- scripts/install_docopt.sh | 4 ++-- scripts/install_emsl.sh | 4 ++-- scripts/install_ezfio.sh | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/scripts/install_curl.sh b/scripts/install_curl.sh index 20033f77..b2e47481 100755 --- a/scripts/install_curl.sh +++ b/scripts/install_curl.sh @@ -8,8 +8,8 @@ CURL_URL="http://qmcchem.ups-tlse.fr/files/scemama/${CURL}.tar.bz2" if [[ -z ${QPACKAGE_ROOT} ]] then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." exit -1 fi diff --git a/scripts/install_docopt.sh b/scripts/install_docopt.sh index 7edf2377..6f799c47 100755 --- a/scripts/install_docopt.sh +++ b/scripts/install_docopt.sh @@ -8,8 +8,8 @@ DOCOPT_URL="https://raw.githubusercontent.com/docopt/docopt/master/${DOCOPT}" if [[ -z ${QPACKAGE_ROOT} ]] then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." exit -1 fi diff --git a/scripts/install_emsl.sh b/scripts/install_emsl.sh index dff002a1..b01afb6e 100755 --- a/scripts/install_emsl.sh +++ b/scripts/install_emsl.sh @@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz" if [[ -z ${QPACKAGE_ROOT} ]] then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." exit -1 fi diff --git a/scripts/install_ezfio.sh b/scripts/install_ezfio.sh index 0f7a6505..c0033ca8 100755 --- a/scripts/install_ezfio.sh +++ b/scripts/install_ezfio.sh @@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz" if [[ -z ${QPACKAGE_ROOT} ]] then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." exit -1 fi From c1c3285ceca0bd0192ade4710c157cb7d31735d2 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Mon, 27 Apr 2015 17:10:25 +0200 Subject: [PATCH 3/9] Move install script into install folder --- scripts/{ => install}/install_curl.sh | 4 ++-- scripts/{ => install}/install_docopt.sh | 4 ++-- scripts/{ => install}/install_emsl.sh | 4 ++-- scripts/{ => install}/install_ezfio.sh | 4 ++-- scripts/{ => install}/install_irpf90.sh | 0 scripts/{ => install}/install_m4.sh | 0 scripts/{ => install}/install_ocaml.sh | 0 scripts/{ => install}/install_resultsFile.sh | 0 scripts/{ => install}/install_zlib.sh | 0 scripts/upgrade_ezfio.sh | 2 +- scripts/upgrade_irpf90.sh | 2 +- setup_environment.sh | 18 +++++++++--------- 12 files changed, 19 insertions(+), 19 deletions(-) rename scripts/{ => install}/install_curl.sh (83%) rename scripts/{ => install}/install_docopt.sh (70%) rename scripts/{ => install}/install_emsl.sh (79%) rename scripts/{ => install}/install_ezfio.sh (77%) rename scripts/{ => install}/install_irpf90.sh (100%) rename scripts/{ => install}/install_m4.sh (100%) rename scripts/{ => install}/install_ocaml.sh (100%) rename scripts/{ => install}/install_resultsFile.sh (100%) rename scripts/{ => install}/install_zlib.sh (100%) diff --git a/scripts/install_curl.sh b/scripts/install/install_curl.sh similarity index 83% rename from scripts/install_curl.sh rename to scripts/install/install_curl.sh index 20033f77..b2e47481 100755 --- a/scripts/install_curl.sh +++ b/scripts/install/install_curl.sh @@ -8,8 +8,8 @@ CURL_URL="http://qmcchem.ups-tlse.fr/files/scemama/${CURL}.tar.bz2" if [[ -z ${QPACKAGE_ROOT} ]] then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." exit -1 fi diff --git a/scripts/install_docopt.sh b/scripts/install/install_docopt.sh similarity index 70% rename from scripts/install_docopt.sh rename to scripts/install/install_docopt.sh index 7edf2377..6f799c47 100755 --- a/scripts/install_docopt.sh +++ b/scripts/install/install_docopt.sh @@ -8,8 +8,8 @@ DOCOPT_URL="https://raw.githubusercontent.com/docopt/docopt/master/${DOCOPT}" if [[ -z ${QPACKAGE_ROOT} ]] then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." exit -1 fi diff --git a/scripts/install_emsl.sh b/scripts/install/install_emsl.sh similarity index 79% rename from scripts/install_emsl.sh rename to scripts/install/install_emsl.sh index dff002a1..b01afb6e 100755 --- a/scripts/install_emsl.sh +++ b/scripts/install/install_emsl.sh @@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz" if [[ -z ${QPACKAGE_ROOT} ]] then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." exit -1 fi diff --git a/scripts/install_ezfio.sh b/scripts/install/install_ezfio.sh similarity index 77% rename from scripts/install_ezfio.sh rename to scripts/install/install_ezfio.sh index 0f7a6505..c0033ca8 100755 --- a/scripts/install_ezfio.sh +++ b/scripts/install/install_ezfio.sh @@ -8,8 +8,8 @@ URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz" if [[ -z ${QPACKAGE_ROOT} ]] then - print "The QPACKAGE_ROOT environment variable is not set." - print "Please reload the quantum_package.rc file." + echo "The QPACKAGE_ROOT environment variable is not set." + echo "Please reload the quantum_package.rc file." exit -1 fi diff --git a/scripts/install_irpf90.sh b/scripts/install/install_irpf90.sh similarity index 100% rename from scripts/install_irpf90.sh rename to scripts/install/install_irpf90.sh diff --git a/scripts/install_m4.sh b/scripts/install/install_m4.sh similarity index 100% rename from scripts/install_m4.sh rename to scripts/install/install_m4.sh diff --git a/scripts/install_ocaml.sh b/scripts/install/install_ocaml.sh similarity index 100% rename from scripts/install_ocaml.sh rename to scripts/install/install_ocaml.sh diff --git a/scripts/install_resultsFile.sh b/scripts/install/install_resultsFile.sh similarity index 100% rename from scripts/install_resultsFile.sh rename to scripts/install/install_resultsFile.sh diff --git a/scripts/install_zlib.sh b/scripts/install/install_zlib.sh similarity index 100% rename from scripts/install_zlib.sh rename to scripts/install/install_zlib.sh diff --git a/scripts/upgrade_ezfio.sh b/scripts/upgrade_ezfio.sh index 4a9af403..c35a2dbd 100755 --- a/scripts/upgrade_ezfio.sh +++ b/scripts/upgrade_ezfio.sh @@ -12,7 +12,7 @@ fi cd -- ${QPACKAGE_ROOT} mv -- ${QPACKAGE_ROOT}/EZFIO ${QPACKAGE_ROOT}/EZFIO.old -${QPACKAGE_ROOT}/scripts/install_ezfio.sh +${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh if [[ $? -eq 0 ]] then diff --git a/scripts/upgrade_irpf90.sh b/scripts/upgrade_irpf90.sh index 5735754f..dea48014 100755 --- a/scripts/upgrade_irpf90.sh +++ b/scripts/upgrade_irpf90.sh @@ -12,7 +12,7 @@ fi cd -- ${QPACKAGE_ROOT} mv -f -- ${QPACKAGE_ROOT}/irpf90 ${QPACKAGE_ROOT}/irpf90.old -${QPACKAGE_ROOT}/scripts/install_irpf90.sh +${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh if [[ $? -eq 0 ]] then diff --git a/setup_environment.sh b/setup_environment.sh index e650a273..cc6dd570 100755 --- a/setup_environment.sh +++ b/setup_environment.sh @@ -28,7 +28,7 @@ EOF source quantum_package.rc echo "${BLUE}===== Installing IRPF90 ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_irpf90.sh | tee install_irpf90.log +${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh | tee install_irpf90.log if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]] then echo $RED "Error in IRPF90 installation" $BLACK @@ -49,19 +49,19 @@ fi echo "${BLUE}===== Installing Zlib ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_zlib.sh | tee install_zlib.log +${QPACKAGE_ROOT}/scripts/install/install_zlib.sh | tee install_zlib.log echo "${BLUE}===== Installing Curl ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_curl.sh | tee install_curl.log +${QPACKAGE_ROOT}/scripts/install/install_curl.sh | tee install_curl.log echo "${BLUE}===== Installing M4 ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_m4.sh | tee install_m4.log +${QPACKAGE_ROOT}/scripts/install/install_m4.sh | tee install_m4.log echo "${BLUE}===== Installing Docopt ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_docopt.sh | tee install_docopt.log +${QPACKAGE_ROOT}/scripts/install/install_docopt.sh | tee install_docopt.log echo "${BLUE}===== Installing EMSL Basis set library ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_emsl.sh | tee install_emsl.log +${QPACKAGE_ROOT}/scripts/install/install_emsl.sh | tee install_emsl.log if [[ ! -d ${QPACKAGE_ROOT}/EMSL_Basis ]] then @@ -71,7 +71,7 @@ fi echo "${BLUE}===== Installing EZFIO ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_ezfio.sh | tee install_ezfio.log +${QPACKAGE_ROOT}/scripts/install/install_ezfio.sh | tee install_ezfio.log if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]] then echo $RED "Error in EZFIO installation" $BLACK @@ -81,7 +81,7 @@ fi echo "${BLUE}===== Installing Ocaml compiler and libraries ===== ${BLACK}" rm -f -- ocaml/Qptypes.ml -${QPACKAGE_ROOT}/scripts/install_ocaml.sh | tee install_ocaml.log +${QPACKAGE_ROOT}/scripts/install/install_ocaml.sh | tee install_ocaml.log if [[ ! -f ${QPACKAGE_ROOT}/ocaml/Qptypes.ml ]] then @@ -90,7 +90,7 @@ then fi echo "${BLUE}===== Installing resultsFile Python library ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install_resultsFile.sh +${QPACKAGE_ROOT}/scripts/install/install_resultsFile.sh if [[ ! -d ${QPACKAGE_ROOT}/resultsFile ]] then echo $RED "Error in resultsFile installation" $BLACK From 281dd89c25c76fd0408da6542b9d15d00150ebcb Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Thu, 30 Apr 2015 14:10:41 +0200 Subject: [PATCH 4/9] Move create script into create folder --- ocaml/Makefile | 2 +- scripts/build_modules.sh | 4 ++-- scripts/{ => create}/create_Makefile.sh | 0 scripts/{ => create}/create_Makefile_depend.sh | 0 scripts/{ => create}/create_Needed_modules.sh | 0 scripts/{ => create}/create_executables_list.sh | 0 scripts/{ => create}/create_gitignore.sh | 0 scripts/{ => create}/create_module.sh | 6 +++--- scripts/{ => create}/create_rst_templates.sh | 0 scripts/run_Makefile_common.sh | 4 ++-- src/Makefile.common | 2 +- 11 files changed, 9 insertions(+), 9 deletions(-) rename scripts/{ => create}/create_Makefile.sh (100%) rename scripts/{ => create}/create_Makefile_depend.sh (100%) rename scripts/{ => create}/create_Needed_modules.sh (100%) rename scripts/{ => create}/create_executables_list.sh (100%) rename scripts/{ => create}/create_gitignore.sh (100%) rename scripts/{ => create}/create_module.sh (88%) rename scripts/{ => create}/create_rst_templates.sh (100%) diff --git a/ocaml/Makefile b/ocaml/Makefile index eaa8e382..ce932bfc 100644 --- a/ocaml/Makefile +++ b/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 diff --git a/scripts/build_modules.sh b/scripts/build_modules.sh index c3e0cda5..44c8183a 100755 --- a/scripts/build_modules.sh +++ b/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 +${QPACKAGE_ROOT}/scripts/create/create_executables_list.sh diff --git a/scripts/create_Makefile.sh b/scripts/create/create_Makefile.sh similarity index 100% rename from scripts/create_Makefile.sh rename to scripts/create/create_Makefile.sh diff --git a/scripts/create_Makefile_depend.sh b/scripts/create/create_Makefile_depend.sh similarity index 100% rename from scripts/create_Makefile_depend.sh rename to scripts/create/create_Makefile_depend.sh diff --git a/scripts/create_Needed_modules.sh b/scripts/create/create_Needed_modules.sh similarity index 100% rename from scripts/create_Needed_modules.sh rename to scripts/create/create_Needed_modules.sh diff --git a/scripts/create_executables_list.sh b/scripts/create/create_executables_list.sh similarity index 100% rename from scripts/create_executables_list.sh rename to scripts/create/create_executables_list.sh diff --git a/scripts/create_gitignore.sh b/scripts/create/create_gitignore.sh similarity index 100% rename from scripts/create_gitignore.sh rename to scripts/create/create_gitignore.sh diff --git a/scripts/create_module.sh b/scripts/create/create_module.sh similarity index 88% rename from scripts/create_module.sh rename to scripts/create/create_module.sh index dbddc3d3..90c6586b 100755 --- a/scripts/create_module.sh +++ b/scripts/create/create_module.sh @@ -117,7 +117,7 @@ debug "Module directory is created." # Create the Makefile -"${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 diff --git a/scripts/create_rst_templates.sh b/scripts/create/create_rst_templates.sh similarity index 100% rename from scripts/create_rst_templates.sh rename to scripts/create/create_rst_templates.sh diff --git a/scripts/run_Makefile_common.sh b/scripts/run_Makefile_common.sh index 82e898ac..153fa948 100755 --- a/scripts/run_Makefile_common.sh +++ b/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 diff --git a/src/Makefile.common b/src/Makefile.common index eddaa481..4df805ce 100644 --- a/src/Makefile.common +++ b/src/Makefile.common @@ -45,7 +45,7 @@ include irpf90.make endif .gitignore: - $(QPACKAGE_ROOT)/scripts/create_gitignore.sh + $(QPACKAGE_ROOT)/scripts/create/create_gitignore.sh # Frequent typos clena: clean From 57f2050fb8404646d3b1f6da40dd62c7d220dac9 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Thu, 30 Apr 2015 14:20:08 +0200 Subject: [PATCH 5/9] Move upgrade script into upgrade folder --- scripts/run_Makefile_global.sh | 4 ++-- scripts/{ => upgrade}/upgrade_ezfio.sh | 0 scripts/{ => upgrade}/upgrade_irpf90.sh | 0 3 files changed, 2 insertions(+), 2 deletions(-) rename scripts/{ => upgrade}/upgrade_ezfio.sh (100%) rename scripts/{ => upgrade}/upgrade_irpf90.sh (100%) diff --git a/scripts/run_Makefile_global.sh b/scripts/run_Makefile_global.sh index fc9e168a..869172a2 100755 --- a/scripts/run_Makefile_global.sh +++ b/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" diff --git a/scripts/upgrade_ezfio.sh b/scripts/upgrade/upgrade_ezfio.sh similarity index 100% rename from scripts/upgrade_ezfio.sh rename to scripts/upgrade/upgrade_ezfio.sh diff --git a/scripts/upgrade_irpf90.sh b/scripts/upgrade/upgrade_irpf90.sh similarity index 100% rename from scripts/upgrade_irpf90.sh rename to scripts/upgrade/upgrade_irpf90.sh From 5d29f3c8d9e10a93304e3bf4d23199c8a96fd827 Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Thu, 30 Apr 2015 14:27:32 +0200 Subject: [PATCH 6/9] Put prepare_ezfio.sh in ezfio_interface/ --- scripts/{ => ezfio_interface}/prepare_ezfio.sh | 0 scripts/run_Makefile_common.sh | 2 +- src/Makefile | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename scripts/{ => ezfio_interface}/prepare_ezfio.sh (100%) diff --git a/scripts/prepare_ezfio.sh b/scripts/ezfio_interface/prepare_ezfio.sh similarity index 100% rename from scripts/prepare_ezfio.sh rename to scripts/ezfio_interface/prepare_ezfio.sh diff --git a/scripts/run_Makefile_common.sh b/scripts/run_Makefile_common.sh index 153fa948..c0e88a1e 100755 --- a/scripts/run_Makefile_common.sh +++ b/scripts/run_Makefile_common.sh @@ -65,4 +65,4 @@ fi ${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 diff --git a/src/Makefile b/src/Makefile index 237b3ae4..0757825b 100644 --- a/src/Makefile +++ b/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)" ;\ $(MAKE) ;\ From 08aa4d2a7511fa36332c36a7acfce73b92ed8d9b Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Thu, 30 Apr 2015 14:36:40 +0200 Subject: [PATCH 7/9] Add recursif path into quantum_package.rc --- setup_environment.sh | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/setup_environment.sh b/setup_environment.sh index cc6dd570..ce522099 100755 --- a/setup_environment.sh +++ b/setup_environment.sh @@ -17,8 +17,10 @@ export QPACKAGE_ROOT=\$( cd \$(dirname "\${BASH_SOURCE}") ; pwd -P ) export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH} export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH} export C_INCLUDE_PATH="\${QPACKAGE_ROOT}"/include:\${C_INCLUDE_PATH} -export PYTHONPATH=\${PYTHONPATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface -export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/scripts:"\${QPACKAGE_ROOT}"/scripts/ezfio_interface + +export PYTHONPATH=${PYTHONPATH}$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p") + +export PATH=${PATH}$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p") export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null From 013c9b9a0d774ab061ff47babab43f143314f74d Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Thu, 30 Apr 2015 14:44:14 +0200 Subject: [PATCH 8/9] Cleaning --- setup_environment.sh | 38 +++++++++++++------------------------- 1 file changed, 13 insertions(+), 25 deletions(-) diff --git a/setup_environment.sh b/setup_environment.sh index ce522099..657573c0 100755 --- a/setup_environment.sh +++ b/setup_environment.sh @@ -18,9 +18,9 @@ export LD_LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LD_LIBRARY_PATH} export LIBRARY_PATH="\${QPACKAGE_ROOT}"/lib:\${LIBRARY_PATH} export C_INCLUDE_PATH="\${QPACKAGE_ROOT}"/include:\${C_INCLUDE_PATH} -export PYTHONPATH=${PYTHONPATH}$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p") +export PYTHONPATH=\${PYTHONPATH}\$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p") -export PATH=${PATH}$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p") +export PATH=\${PATH}\$(find "${QPACKAGE_ROOT}"/scripts -type d -printf ":%p") export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/bin export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null @@ -30,40 +30,29 @@ EOF source quantum_package.rc echo "${BLUE}===== Installing IRPF90 ===== ${BLACK}" -${QPACKAGE_ROOT}/scripts/install/install_irpf90.sh | tee install_irpf90.log -if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]] -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 ${QPACKAGE_ROOT}/bin/irpman ]] +${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 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 install_docopt.log +${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 ${QPACKAGE_ROOT}/EMSL_Basis ]] then @@ -73,7 +62,7 @@ fi echo "${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" $BLACK @@ -83,7 +72,7 @@ fi echo "${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 @@ -111,8 +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 From acb6b7b16af7a39924c3bc204fda4dd509e9f73c Mon Sep 17 00:00:00 2001 From: Thomas Applencourt Date: Thu, 30 Apr 2015 17:36:36 +0200 Subject: [PATCH 9/9] Add NEED_CHILDREN_MODULE to replace NEEDED_MODULES --- scripts/check_dependencies.sh | 4 +- scripts/clean_modules.sh | 2 +- .../module/only_children_to_all_genealogy.py | 108 ++++++++++++++++++ scripts/qp_include.sh | 4 +- scripts/update_README.py | 2 +- src/AOs/NEEDED_CHILDREN_MODULES | 1 + src/AOs/NEEDED_MODULES | 2 - src/AOs/README.rst | 3 - src/Bielec_integrals/NEEDED_CHILDREN_MODULES | 1 + src/Bielec_integrals/NEEDED_MODULES | 1 - src/Bielec_integrals/README.rst | 9 +- src/Bitmask/NEEDED_CHILDREN_MODULES | 1 + src/Bitmask/NEEDED_MODULES | 1 - src/Bitmask/README.rst | 6 - src/CAS_SD/NEEDED_CHILDREN_MODULES | 1 + src/CAS_SD/NEEDED_MODULES | 2 - src/CAS_SD/README.rst | 16 +-- src/CID/NEEDED_CHILDREN_MODULES | 1 + src/CID/NEEDED_MODULES | 3 - src/CID/README.rst | 13 --- src/CID_SC2_selected/NEEDED_CHILDREN_MODULES | 1 + src/CID_SC2_selected/NEEDED_MODULES | 2 - src/CID_SC2_selected/README.rst | 20 +--- src/CID_selected/NEEDED_CHILDREN_MODULES | 1 + src/CID_selected/NEEDED_MODULES | 2 - src/CID_selected/README.rst | 18 +-- src/CIS/NEEDED_CHILDREN_MODULES | 1 + src/CIS/NEEDED_MODULES | 2 - src/CIS/README.rst | 13 --- src/CISD/NEEDED_CHILDREN_MODULES | 1 + src/CISD/NEEDED_MODULES | 2 - src/CISD/README.rst | 13 --- src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES | 1 + src/CISD_SC2_selected/NEEDED_MODULES | 2 - src/CISD_SC2_selected/README.rst | 18 --- src/CISD_selected/NEEDED_CHILDREN_MODULES | 1 + src/CISD_selected/NEEDED_MODULES | 2 - src/CISD_selected/README.rst | 18 +-- src/DDCI_selected/NEEDED_CHILDREN_MODULES | 1 + src/DDCI_selected/NEEDED_MODULES | 2 - src/DDCI_selected/README.rst | 16 +-- src/Determinants/NEEDED_CHILDREN_MODULES | 1 + src/Determinants/NEEDED_MODULES | 1 - src/Determinants/README.rst | 9 -- src/Electrons/NEEDED_CHILDREN_MODULES | 1 + src/Electrons/NEEDED_MODULES | 1 - src/Electrons/README.rst | 2 - .../NEEDED_CHILDREN_MODULES} | 0 src/Ezfio_files/NEEDED_MODULES | 0 src/Ezfio_files/README.rst | 1 + src/FCIdump/NEEDED_CHILDREN_MODULES | 1 + src/FCIdump/NEEDED_MODULES | 1 - src/FCIdump/README.rst | 10 -- src/Full_CI/NEEDED_CHILDREN_MODULES | 1 + src/Full_CI/NEEDED_MODULES | 2 - src/Full_CI/README.rst | 16 +-- src/Generators_CAS/NEEDED_CHILDREN_MODULES | 1 + src/Generators_CAS/NEEDED_MODULES | 1 - src/Generators_CAS/README.rst | 10 -- src/Generators_full/NEEDED_CHILDREN_MODULES | 1 + src/Generators_full/NEEDED_MODULES | 2 - src/Generators_full/README.rst | 11 -- .../NEEDED_CHILDREN_MODULES | 1 + src/Generators_restart/NEEDED_MODULES | 1 - src/Hartree_Fock/NEEDED_CHILDREN_MODULES | 1 + src/Hartree_Fock/NEEDED_MODULES | 1 - src/Hartree_Fock/README.rst | 9 -- src/MOGuess/NEEDED_CHILDREN_MODULES | 1 + src/MOGuess/NEEDED_MODULES | 1 - src/MOGuess/README.rst | 7 -- src/MOs/NEEDED_CHILDREN_MODULES | 1 + src/MOs/NEEDED_MODULES | 3 - src/MOs/README.rst | 4 - src/MP2/NEEDED_CHILDREN_MODULES | 1 + src/MP2/NEEDED_MODULES | 2 - src/MP2/README.rst | 14 --- src/MRCC/NEEDED_CHILDREN_MODULES | 1 + src/MRCC/NEEDED_MODULES | 2 - src/MRCC/README.rst | 16 +-- src/Makefile.common | 8 +- src/Molden/NEEDED_CHILDREN_MODULES | 1 + src/Molden/NEEDED_MODULES | 1 - src/Molden/README.rst | 6 - src/MonoInts/NEEDED_CHILDREN_MODULES | 1 + src/MonoInts/NEEDED_MODULES | 1 - src/MonoInts/README.rst | 6 - src/Nuclei/NEEDED_CHILDREN_MODULES | 1 + src/Nuclei/NEEDED_MODULES | 1 - src/Nuclei/README.rst | 2 - src/Output/NEEDED_CHILDREN_MODULES | 1 + src/Output/NEEDED_MODULES | 1 - src/Output/README.rst | 2 +- src/Perturbation/NEEDED_CHILDREN_MODULES | 1 + src/Perturbation/NEEDED_MODULES | 2 - src/Properties/NEEDED_CHILDREN_MODULES | 1 + src/Properties/NEEDED_MODULES | 1 - src/Selectors_full/NEEDED_CHILDREN_MODULES | 1 + src/Selectors_full/NEEDED_MODULES | 2 - src/Selectors_full/README.rst | 11 -- .../NEEDED_CHILDREN_MODULES | 1 + src/Selectors_no_sorted/NEEDED_MODULES | 1 - src/SingleRefMethod/NEEDED_CHILDREN_MODULES | 1 + src/SingleRefMethod/NEEDED_MODULES | 1 - src/Utils/NEEDED_CHILDREN_MODULES | 1 + 104 files changed, 162 insertions(+), 351 deletions(-) create mode 100755 scripts/module/only_children_to_all_genealogy.py create mode 100644 src/AOs/NEEDED_CHILDREN_MODULES delete mode 100644 src/AOs/NEEDED_MODULES create mode 100644 src/Bielec_integrals/NEEDED_CHILDREN_MODULES delete mode 100644 src/Bielec_integrals/NEEDED_MODULES create mode 100644 src/Bitmask/NEEDED_CHILDREN_MODULES delete mode 100644 src/Bitmask/NEEDED_MODULES create mode 100644 src/CAS_SD/NEEDED_CHILDREN_MODULES delete mode 100644 src/CAS_SD/NEEDED_MODULES create mode 100644 src/CID/NEEDED_CHILDREN_MODULES delete mode 100644 src/CID/NEEDED_MODULES create mode 100644 src/CID_SC2_selected/NEEDED_CHILDREN_MODULES delete mode 100644 src/CID_SC2_selected/NEEDED_MODULES create mode 100644 src/CID_selected/NEEDED_CHILDREN_MODULES delete mode 100644 src/CID_selected/NEEDED_MODULES create mode 100644 src/CIS/NEEDED_CHILDREN_MODULES delete mode 100644 src/CIS/NEEDED_MODULES create mode 100644 src/CISD/NEEDED_CHILDREN_MODULES delete mode 100644 src/CISD/NEEDED_MODULES create mode 100644 src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES delete mode 100644 src/CISD_SC2_selected/NEEDED_MODULES create mode 100644 src/CISD_selected/NEEDED_CHILDREN_MODULES delete mode 100644 src/CISD_selected/NEEDED_MODULES create mode 100644 src/DDCI_selected/NEEDED_CHILDREN_MODULES delete mode 100644 src/DDCI_selected/NEEDED_MODULES create mode 100644 src/Determinants/NEEDED_CHILDREN_MODULES delete mode 100644 src/Determinants/NEEDED_MODULES create mode 100644 src/Electrons/NEEDED_CHILDREN_MODULES delete mode 100644 src/Electrons/NEEDED_MODULES rename src/{Utils/NEEDED_MODULES => Ezfio_files/NEEDED_CHILDREN_MODULES} (100%) delete mode 100644 src/Ezfio_files/NEEDED_MODULES create mode 100644 src/FCIdump/NEEDED_CHILDREN_MODULES delete mode 100644 src/FCIdump/NEEDED_MODULES create mode 100644 src/Full_CI/NEEDED_CHILDREN_MODULES delete mode 100644 src/Full_CI/NEEDED_MODULES create mode 100644 src/Generators_CAS/NEEDED_CHILDREN_MODULES delete mode 100644 src/Generators_CAS/NEEDED_MODULES create mode 100644 src/Generators_full/NEEDED_CHILDREN_MODULES delete mode 100644 src/Generators_full/NEEDED_MODULES create mode 100644 src/Generators_restart/NEEDED_CHILDREN_MODULES delete mode 100644 src/Generators_restart/NEEDED_MODULES create mode 100644 src/Hartree_Fock/NEEDED_CHILDREN_MODULES delete mode 100644 src/Hartree_Fock/NEEDED_MODULES create mode 100644 src/MOGuess/NEEDED_CHILDREN_MODULES delete mode 100644 src/MOGuess/NEEDED_MODULES create mode 100644 src/MOs/NEEDED_CHILDREN_MODULES delete mode 100644 src/MOs/NEEDED_MODULES create mode 100644 src/MP2/NEEDED_CHILDREN_MODULES delete mode 100644 src/MP2/NEEDED_MODULES create mode 100644 src/MRCC/NEEDED_CHILDREN_MODULES delete mode 100644 src/MRCC/NEEDED_MODULES create mode 100644 src/Molden/NEEDED_CHILDREN_MODULES delete mode 100644 src/Molden/NEEDED_MODULES create mode 100644 src/MonoInts/NEEDED_CHILDREN_MODULES delete mode 100644 src/MonoInts/NEEDED_MODULES create mode 100644 src/Nuclei/NEEDED_CHILDREN_MODULES delete mode 100644 src/Nuclei/NEEDED_MODULES create mode 100644 src/Output/NEEDED_CHILDREN_MODULES delete mode 100644 src/Output/NEEDED_MODULES create mode 100644 src/Perturbation/NEEDED_CHILDREN_MODULES delete mode 100644 src/Perturbation/NEEDED_MODULES create mode 100644 src/Properties/NEEDED_CHILDREN_MODULES delete mode 100644 src/Properties/NEEDED_MODULES create mode 100644 src/Selectors_full/NEEDED_CHILDREN_MODULES delete mode 100644 src/Selectors_full/NEEDED_MODULES create mode 100644 src/Selectors_no_sorted/NEEDED_CHILDREN_MODULES delete mode 100644 src/Selectors_no_sorted/NEEDED_MODULES create mode 100644 src/SingleRefMethod/NEEDED_CHILDREN_MODULES delete mode 100644 src/SingleRefMethod/NEEDED_MODULES create mode 100644 src/Utils/NEEDED_CHILDREN_MODULES diff --git a/scripts/check_dependencies.sh b/scripts/check_dependencies.sh index f21dbc40..e1149d2d 100755 --- a/scripts/check_dependencies.sh +++ b/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) diff --git a/scripts/clean_modules.sh b/scripts/clean_modules.sh index 452724f2..e51bbede 100755 --- a/scripts/clean_modules.sh +++ b/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 } diff --git a/scripts/module/only_children_to_all_genealogy.py b/scripts/module/only_children_to_all_genealogy.py new file mode 100755 index 00000000..ecc6054e --- /dev/null +++ b/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) diff --git a/scripts/qp_include.sh b/scripts/qp_include.sh index 467baca8..04cc6a17 100644 --- a/scripts/qp_include.sh +++ b/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 diff --git a/scripts/update_README.py b/scripts/update_README.py index 0f32404d..177d57a4 100755 --- a/scripts/update_README.py +++ b/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() diff --git a/src/AOs/NEEDED_CHILDREN_MODULES b/src/AOs/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..2c80725f --- /dev/null +++ b/src/AOs/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Nuclei diff --git a/src/AOs/NEEDED_MODULES b/src/AOs/NEEDED_MODULES deleted file mode 100644 index 9f7ccbcc..00000000 --- a/src/AOs/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -Ezfio_files Nuclei Output Utils - diff --git a/src/AOs/README.rst b/src/AOs/README.rst index f9f81f5f..1507d56c 100644 --- a/src/AOs/README.rst +++ b/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 `_ * `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/Bielec_integrals/NEEDED_CHILDREN_MODULES b/src/Bielec_integrals/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..24979463 --- /dev/null +++ b/src/Bielec_integrals/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +MonoInts Bitmask diff --git a/src/Bielec_integrals/NEEDED_MODULES b/src/Bielec_integrals/NEEDED_MODULES deleted file mode 100644 index 5f709ce4..00000000 --- a/src/Bielec_integrals/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bitmask Electrons Ezfio_files MOs Nuclei Output Utils MonoInts diff --git a/src/Bielec_integrals/README.rst b/src/Bielec_integrals/README.rst index 38dc9e96..6e17f2b7 100644 --- a/src/Bielec_integrals/README.rst +++ b/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 `_ -* `Bitmask `_ -* `Electrons `_ -* `Ezfio_files `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ * `MonoInts `_ +* `Bitmask `_ Documentation ============= diff --git a/src/Bitmask/NEEDED_CHILDREN_MODULES b/src/Bitmask/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..b936db90 --- /dev/null +++ b/src/Bitmask/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +MOs diff --git a/src/Bitmask/NEEDED_MODULES b/src/Bitmask/NEEDED_MODULES deleted file mode 100644 index 190f8c6e..00000000 --- a/src/Bitmask/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Electrons Ezfio_files MOs Nuclei Output Utils diff --git a/src/Bitmask/README.rst b/src/Bitmask/README.rst index b8e3aa57..395efc52 100644 --- a/src/Bitmask/README.rst +++ b/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 `_ -* `Electrons `_ -* `Ezfio_files `_ * `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/CAS_SD/NEEDED_CHILDREN_MODULES b/src/CAS_SD/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..f7264a0f --- /dev/null +++ b/src/CAS_SD/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation Selectors_full Generators_CAS diff --git a/src/CAS_SD/NEEDED_MODULES b/src/CAS_SD/NEEDED_MODULES deleted file mode 100644 index f20d16a0..00000000 --- a/src/CAS_SD/NEEDED_MODULES +++ /dev/null @@ -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 - diff --git a/src/CAS_SD/README.rst b/src/CAS_SD/README.rst index 0b3293d5..2e56e56e 100644 --- a/src/CAS_SD/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Generators_CAS `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ * `Selectors_full `_ -* `Utils `_ +* `Generators_CAS `_ diff --git a/src/CID/NEEDED_CHILDREN_MODULES b/src/CID/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..afc8cfd4 --- /dev/null +++ b/src/CID/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Selectors_full SingleRefMethod diff --git a/src/CID/NEEDED_MODULES b/src/CID/NEEDED_MODULES deleted file mode 100644 index f7a1831f..00000000 --- a/src/CID/NEEDED_MODULES +++ /dev/null @@ -1,3 +0,0 @@ -AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils - - diff --git a/src/CID/README.rst b/src/CID/README.rst index 47cbc40b..5d2fa851 100644 --- a/src/CID/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Selectors_full `_ * `SingleRefMethod `_ -* `Utils `_ Documentation ============= diff --git a/src/CID_SC2_selected/NEEDED_CHILDREN_MODULES b/src/CID_SC2_selected/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..7be053d7 --- /dev/null +++ b/src/CID_SC2_selected/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +CID_selected diff --git a/src/CID_SC2_selected/NEEDED_MODULES b/src/CID_SC2_selected/NEEDED_MODULES deleted file mode 100644 index 67f77e87..00000000 --- a/src/CID_SC2_selected/NEEDED_MODULES +++ /dev/null @@ -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 - diff --git a/src/CID_SC2_selected/README.rst b/src/CID_SC2_selected/README.rst index 37680ebb..ec9e7a3f 100644 --- a/src/CID_SC2_selected/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `CISD `_ -* `CISD_selected `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Perturbation `_ -* `Properties `_ -* `Selectors_full `_ -* `SingleRefMethod `_ -* `Utils `_ +* `CID_selected `_ diff --git a/src/CID_selected/NEEDED_CHILDREN_MODULES b/src/CID_selected/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..1e0c52c2 --- /dev/null +++ b/src/CID_selected/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation CID diff --git a/src/CID_selected/NEEDED_MODULES b/src/CID_selected/NEEDED_MODULES deleted file mode 100644 index ca89c5f3..00000000 --- a/src/CID_selected/NEEDED_MODULES +++ /dev/null @@ -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 - diff --git a/src/CID_selected/README.rst b/src/CID_selected/README.rst index d8f054ac..50cc701f 100644 --- a/src/CID_selected/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `CISD `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ -* `Selectors_full `_ -* `SingleRefMethod `_ -* `Utils `_ +* `CID `_ diff --git a/src/CIS/NEEDED_CHILDREN_MODULES b/src/CIS/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..afc8cfd4 --- /dev/null +++ b/src/CIS/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Selectors_full SingleRefMethod diff --git a/src/CIS/NEEDED_MODULES b/src/CIS/NEEDED_MODULES deleted file mode 100644 index 5cdee2e5..00000000 --- a/src/CIS/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils - diff --git a/src/CIS/README.rst b/src/CIS/README.rst index 59558a31..e3b2478a 100644 --- a/src/CIS/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Selectors_full `_ * `SingleRefMethod `_ -* `Utils `_ diff --git a/src/CISD/NEEDED_CHILDREN_MODULES b/src/CISD/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..afc8cfd4 --- /dev/null +++ b/src/CISD/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Selectors_full SingleRefMethod diff --git a/src/CISD/NEEDED_MODULES b/src/CISD/NEEDED_MODULES deleted file mode 100644 index 5cdee2e5..00000000 --- a/src/CISD/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full SingleRefMethod Utils - diff --git a/src/CISD/README.rst b/src/CISD/README.rst index bcf7aee2..68ab4cfb 100644 --- a/src/CISD/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Selectors_full `_ * `SingleRefMethod `_ -* `Utils `_ Documentation ============= diff --git a/src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES b/src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..fa61747b --- /dev/null +++ b/src/CISD_SC2_selected/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +CISD_selected diff --git a/src/CISD_SC2_selected/NEEDED_MODULES b/src/CISD_SC2_selected/NEEDED_MODULES deleted file mode 100644 index 67f77e87..00000000 --- a/src/CISD_SC2_selected/NEEDED_MODULES +++ /dev/null @@ -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 - diff --git a/src/CISD_SC2_selected/README.rst b/src/CISD_SC2_selected/README.rst index 915c85f1..b4f4fac1 100644 --- a/src/CISD_SC2_selected/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `CISD `_ * `CISD_selected `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Perturbation `_ -* `Properties `_ -* `Selectors_full `_ -* `SingleRefMethod `_ -* `Utils `_ diff --git a/src/CISD_selected/NEEDED_CHILDREN_MODULES b/src/CISD_selected/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..2b104007 --- /dev/null +++ b/src/CISD_selected/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation CISD diff --git a/src/CISD_selected/NEEDED_MODULES b/src/CISD_selected/NEEDED_MODULES deleted file mode 100644 index ca89c5f3..00000000 --- a/src/CISD_selected/NEEDED_MODULES +++ /dev/null @@ -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 - diff --git a/src/CISD_selected/README.rst b/src/CISD_selected/README.rst index e2b6989e..a72c5a21 100644 --- a/src/CISD_selected/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `CISD `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ -* `Selectors_full `_ -* `SingleRefMethod `_ -* `Utils `_ +* `CISD `_ diff --git a/src/DDCI_selected/NEEDED_CHILDREN_MODULES b/src/DDCI_selected/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..f7264a0f --- /dev/null +++ b/src/DDCI_selected/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation Selectors_full Generators_CAS diff --git a/src/DDCI_selected/NEEDED_MODULES b/src/DDCI_selected/NEEDED_MODULES deleted file mode 100644 index f20d16a0..00000000 --- a/src/DDCI_selected/NEEDED_MODULES +++ /dev/null @@ -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 - diff --git a/src/DDCI_selected/README.rst b/src/DDCI_selected/README.rst index 2b5823c7..9cfdbefa 100644 --- a/src/DDCI_selected/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Generators_CAS `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ * `Selectors_full `_ -* `Utils `_ +* `Generators_CAS `_ diff --git a/src/Determinants/NEEDED_CHILDREN_MODULES b/src/Determinants/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..afc397de --- /dev/null +++ b/src/Determinants/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Bielec_integrals diff --git a/src/Determinants/NEEDED_MODULES b/src/Determinants/NEEDED_MODULES deleted file mode 100644 index 824c75ed..00000000 --- a/src/Determinants/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/Determinants/README.rst b/src/Determinants/README.rst index 445c8b5e..039238c8 100644 --- a/src/Determinants/README.rst +++ b/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 `_ * `Bielec_integrals `_ -* `Bitmask `_ -* `Electrons `_ -* `Ezfio_files `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/Electrons/NEEDED_CHILDREN_MODULES b/src/Electrons/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..83260f86 --- /dev/null +++ b/src/Electrons/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Output diff --git a/src/Electrons/NEEDED_MODULES b/src/Electrons/NEEDED_MODULES deleted file mode 100644 index e9594555..00000000 --- a/src/Electrons/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -Ezfio_files Output Utils diff --git a/src/Electrons/README.rst b/src/Electrons/README.rst index ffd6d21b..e71a552d 100644 --- a/src/Electrons/README.rst +++ b/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 `_ * `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/Utils/NEEDED_MODULES b/src/Ezfio_files/NEEDED_CHILDREN_MODULES similarity index 100% rename from src/Utils/NEEDED_MODULES rename to src/Ezfio_files/NEEDED_CHILDREN_MODULES diff --git a/src/Ezfio_files/NEEDED_MODULES b/src/Ezfio_files/NEEDED_MODULES deleted file mode 100644 index e69de29b..00000000 diff --git a/src/Ezfio_files/README.rst b/src/Ezfio_files/README.rst index 274eff11..e0ef23da 100644 --- a/src/Ezfio_files/README.rst +++ b/src/Ezfio_files/README.rst @@ -30,3 +30,4 @@ Documentation + diff --git a/src/FCIdump/NEEDED_CHILDREN_MODULES b/src/FCIdump/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..aae89501 --- /dev/null +++ b/src/FCIdump/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants diff --git a/src/FCIdump/NEEDED_MODULES b/src/FCIdump/NEEDED_MODULES deleted file mode 100644 index c5e6c2d3..00000000 --- a/src/FCIdump/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/FCIdump/README.rst b/src/FCIdump/README.rst index bf39955b..8a467b16 100644 --- a/src/FCIdump/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ * `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ diff --git a/src/Full_CI/NEEDED_CHILDREN_MODULES b/src/Full_CI/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..04ce9e78 --- /dev/null +++ b/src/Full_CI/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation Selectors_full Generators_full diff --git a/src/Full_CI/NEEDED_MODULES b/src/Full_CI/NEEDED_MODULES deleted file mode 100644 index f225090c..00000000 --- a/src/Full_CI/NEEDED_MODULES +++ /dev/null @@ -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 - diff --git a/src/Full_CI/README.rst b/src/Full_CI/README.rst index 53fdc1d5..51bb05d2 100644 --- a/src/Full_CI/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Generators_full `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ * `Selectors_full `_ -* `Utils `_ +* `Generators_full `_ diff --git a/src/Generators_CAS/NEEDED_CHILDREN_MODULES b/src/Generators_CAS/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..aae89501 --- /dev/null +++ b/src/Generators_CAS/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants diff --git a/src/Generators_CAS/NEEDED_MODULES b/src/Generators_CAS/NEEDED_MODULES deleted file mode 100644 index c5e6c2d3..00000000 --- a/src/Generators_CAS/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/Generators_CAS/README.rst b/src/Generators_CAS/README.rst index 3fca0916..b729212c 100644 --- a/src/Generators_CAS/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ * `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ diff --git a/src/Generators_full/NEEDED_CHILDREN_MODULES b/src/Generators_full/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..54f54203 --- /dev/null +++ b/src/Generators_full/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants Hartree_Fock diff --git a/src/Generators_full/NEEDED_MODULES b/src/Generators_full/NEEDED_MODULES deleted file mode 100644 index a848a687..00000000 --- a/src/Generators_full/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Utils - diff --git a/src/Generators_full/README.rst b/src/Generators_full/README.rst index 79f4037c..e558f48b 100644 --- a/src/Generators_full/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ * `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ * `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ diff --git a/src/Generators_restart/NEEDED_CHILDREN_MODULES b/src/Generators_restart/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..aae89501 --- /dev/null +++ b/src/Generators_restart/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants diff --git a/src/Generators_restart/NEEDED_MODULES b/src/Generators_restart/NEEDED_MODULES deleted file mode 100644 index c5e6c2d3..00000000 --- a/src/Generators_restart/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/Hartree_Fock/NEEDED_CHILDREN_MODULES b/src/Hartree_Fock/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..b779faec --- /dev/null +++ b/src/Hartree_Fock/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Bielec_integrals MOGuess diff --git a/src/Hartree_Fock/NEEDED_MODULES b/src/Hartree_Fock/NEEDED_MODULES deleted file mode 100644 index 8f7f21c6..00000000 --- a/src/Hartree_Fock/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Electrons Ezfio_files MonoInts MOGuess MOs Nuclei Output Utils diff --git a/src/Hartree_Fock/README.rst b/src/Hartree_Fock/README.rst index a1030e4a..2b470e9f 100644 --- a/src/Hartree_Fock/README.rst +++ b/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 `_ * `Bielec_integrals `_ -* `Bitmask `_ -* `Electrons `_ -* `Ezfio_files `_ -* `MonoInts `_ * `MOGuess `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/MOGuess/NEEDED_CHILDREN_MODULES b/src/MOGuess/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..88d7352e --- /dev/null +++ b/src/MOGuess/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +MonoInts diff --git a/src/MOGuess/NEEDED_MODULES b/src/MOGuess/NEEDED_MODULES deleted file mode 100644 index 59b334d4..00000000 --- a/src/MOGuess/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/MOGuess/README.rst b/src/MOGuess/README.rst index cb1702ab..771825ee 100644 --- a/src/MOGuess/README.rst +++ b/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 `_ -* `Electrons `_ -* `Ezfio_files `_ * `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/MOs/NEEDED_CHILDREN_MODULES b/src/MOs/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..4692ec21 --- /dev/null +++ b/src/MOs/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +AOs Electrons diff --git a/src/MOs/NEEDED_MODULES b/src/MOs/NEEDED_MODULES deleted file mode 100644 index 5ca73603..00000000 --- a/src/MOs/NEEDED_MODULES +++ /dev/null @@ -1,3 +0,0 @@ -AOs Electrons Ezfio_files Nuclei Output Utils - - diff --git a/src/MOs/README.rst b/src/MOs/README.rst index d7a15219..78d3d96e 100644 --- a/src/MOs/README.rst +++ b/src/MOs/README.rst @@ -24,10 +24,6 @@ Needed Modules * `AOs `_ * `Electrons `_ -* `Ezfio_files `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/MP2/NEEDED_CHILDREN_MODULES b/src/MP2/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..d26e4dee --- /dev/null +++ b/src/MP2/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation Selectors_full SingleRefMethod diff --git a/src/MP2/NEEDED_MODULES b/src/MP2/NEEDED_MODULES deleted file mode 100644 index b7a006c3..00000000 --- a/src/MP2/NEEDED_MODULES +++ /dev/null @@ -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 - diff --git a/src/MP2/README.rst b/src/MP2/README.rst index 74db8039..f68d5936 100644 --- a/src/MP2/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ * `Selectors_full `_ * `SingleRefMethod `_ -* `Utils `_ diff --git a/src/MRCC/NEEDED_CHILDREN_MODULES b/src/MRCC/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..04ce9e78 --- /dev/null +++ b/src/MRCC/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Perturbation Selectors_full Generators_full diff --git a/src/MRCC/NEEDED_MODULES b/src/MRCC/NEEDED_MODULES deleted file mode 100644 index f225090c..00000000 --- a/src/MRCC/NEEDED_MODULES +++ /dev/null @@ -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 - diff --git a/src/MRCC/README.rst b/src/MRCC/README.rst index f96f329f..38137667 100644 --- a/src/MRCC/README.rst +++ b/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 `_ -* `Bielec_integrals `_ -* `Bitmask `_ -* `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ -* `Generators_full `_ -* `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ * `Perturbation `_ -* `Properties `_ * `Selectors_full `_ -* `Utils `_ +* `Generators_full `_ Documentation ============= diff --git a/src/Makefile.common b/src/Makefile.common index 4df805ce..cd98329e 100644 --- a/src/Makefile.common +++ b/src/Makefile.common @@ -18,8 +18,8 @@ default: all .gitignore # Include the user's config include $(QPACKAGE_ROOT)/src/Makefile.config -# Create the NEEDED_MODULES variable, needed for IRPF90 -NEEDED_MODULES=$(shell cat NEEDED_MODULES) +# Create the NEEDED_CHILDREN_MODULES variable, needed for IRPF90 +NEEDED_CHILDREN_MODULES=$(shell only_children_to_all_genealogy.py) # Check and update dependencies include Makefile.depend @@ -28,7 +28,7 @@ include Makefile.depend # Define the Makefile common variables EZFIO_DIR=$(QPACKAGE_ROOT)/EZFIO EZFIO=$(EZFIO_DIR)/lib/libezfio_irp.a -INCLUDE_DIRS=$(NEEDED_MODULES) include +INCLUDE_DIRS=$(NEEDED_CHILDREN_MODULES) include clean_links: rm -f $(INCLUDE_DIRS) $$(basename $$PWD) @@ -36,7 +36,7 @@ clean_links: LIB+=$(EZFIO) $(MKL) IRPF90+=$(patsubst %, -I %, $(INCLUDE_DIRS)) $(IRPF90_FLAGS) -irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_MODULES $(wildcard *.py) +irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp.f) $(wildcard *.inc.f) Makefile $(EZFIO) NEEDED_CHILDREN_MODULES $(wildcard *.py) - $(IRPF90) - update_README.py diff --git a/src/Molden/NEEDED_CHILDREN_MODULES b/src/Molden/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..b936db90 --- /dev/null +++ b/src/Molden/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +MOs diff --git a/src/Molden/NEEDED_MODULES b/src/Molden/NEEDED_MODULES deleted file mode 100644 index 190f8c6e..00000000 --- a/src/Molden/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Electrons Ezfio_files MOs Nuclei Output Utils diff --git a/src/Molden/README.rst b/src/Molden/README.rst index d0e2343d..128a020a 100644 --- a/src/Molden/README.rst +++ b/src/Molden/README.rst @@ -31,11 +31,5 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Electrons `_ -* `Ezfio_files `_ * `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ diff --git a/src/MonoInts/NEEDED_CHILDREN_MODULES b/src/MonoInts/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..b936db90 --- /dev/null +++ b/src/MonoInts/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +MOs diff --git a/src/MonoInts/NEEDED_MODULES b/src/MonoInts/NEEDED_MODULES deleted file mode 100644 index 67230c44..00000000 --- a/src/MonoInts/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Electrons Ezfio_files MOs Nuclei Output Utils diff --git a/src/MonoInts/README.rst b/src/MonoInts/README.rst index fdbb086b..6ac65919 100644 --- a/src/MonoInts/README.rst +++ b/src/MonoInts/README.rst @@ -4,13 +4,7 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Electrons `_ -* `Ezfio_files `_ * `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ Documentation ============= diff --git a/src/Nuclei/NEEDED_CHILDREN_MODULES b/src/Nuclei/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..83260f86 --- /dev/null +++ b/src/Nuclei/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Output diff --git a/src/Nuclei/NEEDED_MODULES b/src/Nuclei/NEEDED_MODULES deleted file mode 100644 index 516a2a11..00000000 --- a/src/Nuclei/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -Ezfio_files Utils Output diff --git a/src/Nuclei/README.rst b/src/Nuclei/README.rst index b21d02ee..aaad706d 100644 --- a/src/Nuclei/README.rst +++ b/src/Nuclei/README.rst @@ -12,8 +12,6 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `Ezfio_files `_ -* `Utils `_ * `Output `_ Documentation diff --git a/src/Output/NEEDED_CHILDREN_MODULES b/src/Output/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..dcdb5f86 --- /dev/null +++ b/src/Output/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Ezfio_files Utils diff --git a/src/Output/NEEDED_MODULES b/src/Output/NEEDED_MODULES deleted file mode 100644 index f684b5aa..00000000 --- a/src/Output/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -Utils Ezfio_files diff --git a/src/Output/README.rst b/src/Output/README.rst index 7b510fc1..5fe93f50 100644 --- a/src/Output/README.rst +++ b/src/Output/README.rst @@ -31,8 +31,8 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `Utils `_ * `Ezfio_files `_ +* `Utils `_ Documentation ============= diff --git a/src/Perturbation/NEEDED_CHILDREN_MODULES b/src/Perturbation/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..e29a6721 --- /dev/null +++ b/src/Perturbation/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Properties Hartree_Fock diff --git a/src/Perturbation/NEEDED_MODULES b/src/Perturbation/NEEDED_MODULES deleted file mode 100644 index 4e0f218e..00000000 --- a/src/Perturbation/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Properties Utils - diff --git a/src/Properties/NEEDED_CHILDREN_MODULES b/src/Properties/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..aae89501 --- /dev/null +++ b/src/Properties/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants diff --git a/src/Properties/NEEDED_MODULES b/src/Properties/NEEDED_MODULES deleted file mode 100644 index 62dbbe42..00000000 --- a/src/Properties/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/Selectors_full/NEEDED_CHILDREN_MODULES b/src/Selectors_full/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..54f54203 --- /dev/null +++ b/src/Selectors_full/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants Hartree_Fock diff --git a/src/Selectors_full/NEEDED_MODULES b/src/Selectors_full/NEEDED_MODULES deleted file mode 100644 index a848a687..00000000 --- a/src/Selectors_full/NEEDED_MODULES +++ /dev/null @@ -1,2 +0,0 @@ -AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files Hartree_Fock MOGuess MonoInts MOs Nuclei Output Utils - diff --git a/src/Selectors_full/README.rst b/src/Selectors_full/README.rst index 2ca9380a..11286fce 100644 --- a/src/Selectors_full/README.rst +++ b/src/Selectors_full/README.rst @@ -165,17 +165,6 @@ Needed Modules .. Do not edit this section. It was auto-generated from the .. NEEDED_MODULES file. -* `AOs `_ -* `Bielec_integrals `_ -* `Bitmask `_ * `Determinants `_ -* `Electrons `_ -* `Ezfio_files `_ * `Hartree_Fock `_ -* `MOGuess `_ -* `MonoInts `_ -* `MOs `_ -* `Nuclei `_ -* `Output `_ -* `Utils `_ diff --git a/src/Selectors_no_sorted/NEEDED_CHILDREN_MODULES b/src/Selectors_no_sorted/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..aae89501 --- /dev/null +++ b/src/Selectors_no_sorted/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Determinants diff --git a/src/Selectors_no_sorted/NEEDED_MODULES b/src/Selectors_no_sorted/NEEDED_MODULES deleted file mode 100644 index c5e6c2d3..00000000 --- a/src/Selectors_no_sorted/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bielec_integrals Bitmask Determinants Electrons Ezfio_files MonoInts MOs Nuclei Output Utils diff --git a/src/SingleRefMethod/NEEDED_CHILDREN_MODULES b/src/SingleRefMethod/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..bf459a13 --- /dev/null +++ b/src/SingleRefMethod/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +Bitmask diff --git a/src/SingleRefMethod/NEEDED_MODULES b/src/SingleRefMethod/NEEDED_MODULES deleted file mode 100644 index bdcbdf7d..00000000 --- a/src/SingleRefMethod/NEEDED_MODULES +++ /dev/null @@ -1 +0,0 @@ -AOs Bitmask Electrons Ezfio_files MOs Nuclei Output Utils diff --git a/src/Utils/NEEDED_CHILDREN_MODULES b/src/Utils/NEEDED_CHILDREN_MODULES new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/src/Utils/NEEDED_CHILDREN_MODULES @@ -0,0 +1 @@ +