Refortorisation of update_readme

plugins/Full_CI/.gitignore

@@ -22,7 +22,6 @@ Properties
 Pseudo
 Selectors_full
 Utils
-exc_degree
 ezfio_interface.irp.f
 full_ci
 full_ci_no_skip

plugins/Full_CI/README.rst

@@ -4,10 +4,22 @@ Full_CI Module
 
 Performs a perturbatively selected Full-CI.
 
+Needed Modules
+==============
+
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+.. image:: tree_dependency.png
+
+* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
+* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
+* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
+
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `full_ci <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/full_ci_no_skip.irp.f#L1>`_
@@ -153,15 +165,3 @@ Documentation
 `var_pt2_ratio_run <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI/var_pt2_ratio.irp.f#L1>`_
   Undocumented
 
-Needed Modules
-==============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
-

plugins/Generators_full/README.rst

@@ -5,10 +5,21 @@ Generators_full Module
 All the determinants of the wave function are generators. In this way, the Full CI
 space is explored.
 
+Needed Modules
+==============
+
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `degree_max_generators <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L43>`_
@@ -37,14 +48,3 @@ Documentation
 `size_select_max <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full/generators.irp.f#L58>`_
   Size of the select_max array
 
-Needed Modules
-==============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-

plugins/Hartree_Fock/README.rst

@@ -7,7 +7,7 @@ From the 140 molecules of the G2 set, only LiO, ONa don't converge well.
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
@@ -18,7 +18,7 @@ Needed Modules
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `ao_bi_elec_integral_alpha <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/Fock_matrix.irp.f#L102>`_

plugins/Perturbation/README.rst

@@ -67,10 +67,21 @@ Assumptions
     pt2_....
 
 
+Needed Modules
+==============
+
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+.. image:: tree_dependency.png
+
+* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `do_pt2_end <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation/ezfio_interface.irp.f#L6>`_
@@ -350,14 +361,3 @@ Documentation
   The selection process stops when the energy ratio variational/(variational+PT2)
   is equal to var_pt2_ratio
 
-Needed Modules
-==============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Properties <http://github.com/LCPQ/quantum_package/tree/master/src/Properties>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-

plugins/Properties/README.rst

@@ -2,10 +2,20 @@
 Properties Module
 =================
 
+Needed Modules
+==============
+
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `ao_integrated_delta_rho_all_points <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/delta_rho.irp.f#L61>`_
@@ -142,13 +152,3 @@ Documentation
 `z_one_point <http://github.com/LCPQ/quantum_package/tree/master/src/Properties/ezfio_interface.irp.f#L6>`_
   z point on which the integrated delta rho is calculated
 
-Needed Modules
-==============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-

plugins/Selectors_full/README.rst

@@ -2,10 +2,21 @@
 Selectors_full Module
 =====================
 
+Needed Modules
+==============
+
+.. Do not edit this section It was auto-generated
+.. by the `update_README.py` script.
+
+.. image:: tree_dependency.png
+
+* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
+* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
+
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `coef_hf_selector <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/e_corr_selectors.irp.f#L28>`_
@@ -175,14 +186,3 @@ Documentation
 `psi_selectors_size <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full/selectors.irp.f#L3>`_
   Undocumented
 
-Needed Modules
-==============
-
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-.. image:: tree_dependency.png
-
-* `Determinants <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-

scripts/compilation/qp_create_ninja.py

@@ -23,12 +23,11 @@ except ImportError:
                                       "..",
                                       "..",
                                       "quantum_package.rc"))
-    print """
+
-Error:
+    print "\n".join(["", "Error:", "source %s" % f, ""])
- source %s
-""" % f
     sys.exit(1)
 
+
 #  __
 # /__ |  _  |_   _. |       _. ._ o  _. |_  |  _   _
 # \_| | (_) |_) (_| |   \/ (_| |  | (_| |_) | (/_ _>
@@ -516,7 +515,7 @@ def ninja_readme_rule():
     For not dealted the readme when ninja -t clean and the generator option
     """
     l_string = ["rule build_readme",
-                "   command = cd $module_abs ; update_README.py $module_root",
+                "   command = qp_update_readme.py $module_abs --root_module $module_root",
                 "   description = update_README $module_rel",
                 "   generator = 1", ""]
 
@@ -552,7 +551,8 @@ def ninja_readme_build(path_module, d_irp, dict_root_path):
 #                 /
 def get_binaries(path_module):
     """
-    Return the list of binaries (Path= namedtuple('Path', ['abs', 'rel']) for a module
+    Return the list of binaries
+    (Path= namedtuple('Path', ['abs', 'rel']) for a module
     """
     import subprocess
 
@@ -729,7 +729,7 @@ def ninja_dot_tree_build(path_module, l_module):
 # |\/|  _   _|     |  _
 # |  | (_) (_| |_| | (/_
 #
-def create_build_ninja_module(path_module):
+def save_subninja_file(path_module):
     l_string = ["builddir = {0}".format(os.path.dirname(ROOT_BUILD_NINJA)),
                 ""]
 
@@ -929,9 +929,6 @@ if __name__ == "__main__":
 
     for module_to_compile in l_module:
 
-        if arguments["--development"]:
-            create_build_ninja_module(module_to_compile)
-
         # ~#~#~#~#~#~#~#~ #
         #  S y m l i n k  #
         # ~#~#~#~#~#~#~#~ #
@@ -946,19 +943,18 @@ if __name__ == "__main__":
         l_string += ninja_irpf90_make_build(module_to_compile, l_children,
                                             d_irp)
 
-        if arguments["--development"]:
+        l_string += ninja_binaries_build(module_to_compile, l_children,
-            l_string += ninja_binaries_build(module_to_compile, l_children,
+                                         d_binaries)
-                                             d_binaries)
 
-        elif arguments["--production"]:
+        if arguments["--development"]:
-            l_string += ninja_binaries_build(module_to_compile, l_children,
-                                             d_binaries)
 
             l_string += ninja_module_build(module_to_compile, d_binaries)
 
             l_string += ninja_gitignore_build(module_to_compile, d_binaries,
                                               l_symlink)
 
+            save_subninja_file(module_to_compile)
+
     # ~#~#~#~#~ #
     # S a v e s #
     # ~#~#~#~#~ #

scripts/module/module_handler.py

@@ -30,7 +30,6 @@ except ImportError:
     raise
 
 
-# Canot cache for namedtuple are not hashable
 def is_module(path_module):
     return os.path.isfile(os.path.join(QP_SRC, path_module,
                                        "NEEDED_CHILDREN_MODULES"))
@@ -290,4 +289,3 @@ if __name__ == '__main__':
                     l_text = l_dir + l_file + l_symlink + l_exe
                     l_text.sort()
                     f.write("\n".join(l_text))
-

scripts/module/qp_update_readme.py

@@ -0,0 +1,196 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Updates the README.rst of a module
+Usage:
+       qp_update_readme.py [<module_path>...] [--root_module=<module_path>]
+
+Options:
+    path_readme: All the absolute path you want to update.
+                 By default is the cwd
+    --root_module: Is the path of the root module who containt the tags file.
+                   By default is the cwd
+"""
+
+import sys
+
+try:
+    from docopt import docopt
+except:
+    print "Please check if you have sourced the .quantum_package.rc"
+    print "(`source .quantum_package.rc`)"
+    print sys.exit(1)
+
+import os
+from collections import namedtuple
+from collections import defaultdict
+
+
+def header_format(str_):
+    return "{0}\n{1}\n".format(str_, "=" * len(str_))
+
+
+D_KEY = {"needed_module": header_format("Needed Modules"),
+         "documentation": header_format("Documentation")}
+
+
+URL = "http://github.com/LCPQ/quantum_package/tree/master/src"
+
+HEADER = "\n".join([".. Do not edit this section It was auto-generated",
+                    ".. by the `update_README.py` script."])
+
+# d[Path] ={humain, needed_module, documentation}
+d_readme = defaultdict(dict)
+
+
+def fetch_splitted_data(l_module_readme):
+    """Read the README.rst file and split it in strings:
+    * The documentation
+    * The needed modules
+    The result is given as a list of strings
+    """
+
+    sentinel = "@@$%&@@"
+
+    for path_readme in l_module_readme:
+        with open(os.path.join(path_readme, "README.rst"), 'r') as f:
+            data = f.read()
+
+        # Place sentinels
+
+        for v in D_KEY.values():
+            data = data.replace(v, sentinel + v)
+
+        # Now Split data using the sentinels
+        d_readme[path_readme] = {"human": data.split(sentinel)[0]}
+
+
+def update_needed(d_readme):
+    """Read the NEEDED_CHILDREN_MODULES file, and replace the data with it.
+    Create the links to the GitHub pages."""
+
+    header_image = ".. image:: tree_dependency.png"
+
+    for path in d_readme:
+
+        with open(os.path.join(path, 'NEEDED_CHILDREN_MODULES'), 'r') as f:
+            modules = f.read()
+
+        if modules.strip():
+            l_module = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name))
+                        for name in modules.split()]
+
+            l_module_section = [D_KEY["needed_module"],
+                                HEADER, '',
+                                header_image, '',
+                                '\n'.join(l_module), '', '']
+        else:
+            l_module_section = ""
+
+        d_readme[path]["needed_module"] = "\n".join(l_module_section)
+
+
+def extract_doc(item):
+    """Extracts the documentation contained in IRPF90_man file"""
+
+    path = os.path.join(ROOT_module, "IRPF90_man/%s.l" % (item))
+    with open(path, 'r') as f:
+        l_line = f.readlines()
+
+    result = []
+    inside = False
+    for line in l_line:
+        if not inside:
+            inside = line.startswith(".SH Description")
+        else:
+            if line.startswith(".SH"):
+                break
+            result.append("  {0}".format(line.strip()))
+
+    if not result:
+        result = ["  Undocumented"]
+
+    return "\n".join(result) + "\n"
+
+
+def update_documentation(ROOT_module, d_readme):
+    """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
+
+    IRP_info = namedtuple('IRP_info', ["module", "file", "provider", "line"])
+
+    # If the file does not exist, don't do anything
+    path = os.path.join(ROOT_module, "tags")
+
+    with open(path, 'r') as f:
+        dump = f.readlines()
+
+    d_info = defaultdict(list)
+
+    for i in dump:
+        # i =
+        # output_cpu_time_0  Ezfio_files/output.irp.f    2
+        provider, irp_file_raw, ligne = i.split()
+
+        for path in d_readme:
+
+            if ROOT_module == path and "/" not in irp_file_raw:
+                d_info[path].append(IRP_info(os.path.basename(path),
+                                             irp_file_raw,
+                                             provider,
+                                             ligne))
+
+            elif "/" in irp_file_raw and os.path.dirname(irp_file_raw) in path:
+
+                module, irp_file = os.path.split(irp_file_raw)
+                d_info[path].append(IRP_info(module, irp_file, provider, ligne))
+
+    for path in d_readme:
+
+        l_doc = []
+
+        for irp in d_info[path]:
+            url = os.path.join(URL, os.path.basename(path), irp.file)
+            doc = extract_doc(irp.provider)
+
+            l_doc += ["`{0} <{1}#L{2}>`_".format(irp.provider, url, irp.line),
+                      doc,
+                      ""]
+
+        l_doc_section = [D_KEY["documentation"],
+                         HEADER, '',
+                         "\n".join(l_doc)]
+
+        d_readme[path]["documentation"] = "\n".join(l_doc_section)
+
+if __name__ == '__main__':
+    arguments = docopt(__doc__)
+
+    if arguments["--root_module"]:
+        ROOT_module = os.path.realpath(arguments["--root_module"])
+    else:
+        ROOT_module = os.getcwd()
+
+    if not arguments["<module_path>"]:
+        l_module_readme = [os.path.join(os.getcwd())]
+    else:
+        l_module_readme = arguments["<module_path>"]
+
+    try:
+        fetch_splitted_data(l_module_readme)
+    except IOError:
+        print l_module_readme, "is not a module and/or",
+        print "have not a `README.rst` file inside"
+        print "Abort..."
+        sys.exit(1)
+
+    update_needed(d_readme)
+    update_documentation(ROOT_module, d_readme)
+
+    for path, d in d_readme.iteritems():
+
+        with open(os.path.join(path, "README.rst"), 'w') as f:
+            for k in ["human",
+                      "needed_module",
+                      "documentation"]:
+
+                f.write(d[k])

scripts/module/update_README.py

@@ -1,188 +0,0 @@
-#!/usr/bin/env python
-"""Updates the README.rst file as the include directive is disabled on GitHub."""
-__date__ = "Thu Apr  3 23:06:18 CEST 2014"
-__author__ = "Anthony Scemama<scemama@irsamc.ups-tlse.fr>  & TApplencourt "
-
-README = "README.rst"
-Assum_key = "Assumptions\n===========\n"
-Needed_key = "Needed Modules\n==============\n"
-Doc_key = "Documentation\n=============\n"
-Sentinel = "@@$%&@@"
-URL = "http://github.com/LCPQ/quantum_package/tree/master/src/"
-
-import os
-import subprocess
-from collections import namedtuple
-import sys
-
-"""
-NEED to call in a module
-First arg can be the root parent
-"""
-try:
-    ROOT_module = os.path.realpath(sys.argv[1])
-except:
-    ROOT_module = os.getcwd()
-
-if ROOT_module != os.getcwd():
-    change = True
-else:
-    change = False
-
-MODULE_NAME = os.path.basename(os.getcwd())
-
-
-header = """
-.. Do not edit this section. It was auto-generated from the
-.. by the `update_README.py` script.
-
-"""
-
-
-def fetch_splitted_data():
-    """Read the README.rst file and split it in strings:
-    * The documentation
-    * The needed modules
-    The result is given as a list of strings
-    """
-
-    with open(README, 'r') as f:
-        data = f.read()
-
-    # Place sentinels
-    data = data.replace(Doc_key, Sentinel + Doc_key)
-    data = data.replace(Needed_key, Sentinel + Needed_key)
-
-    # Now Split data using the sentinels
-    result = data.split(Sentinel)
-
-    return result
-
-
-def update_needed(data):
-    """Read the NEEDED_CHILDREN_MODULES file, and replace the data with it.
-    Create the links to the GitHub pages."""
-
-    with open('NEEDED_CHILDREN_MODULES', 'r') as f:
-        modules = f.read()
-
-    header_image = ".. image:: tree_dependency.png\n\n"
-
-    if modules.strip():
-        modules = ['* `{0} <{1}>`_'.format(name, os.path.join(URL, name))
-                   for name in modules.split()]
-        modules = "\n".join(modules)
-        modules = Needed_key + header + header_image + modules + '\n\n'
-
-    has_modules = False
-    for i in range(len(data)):
-        if data[i].startswith(Needed_key):
-            has_modules = True
-            data[i] = modules
-
-    if not has_modules:
-        data.append(modules)
-
-    return data
-
-
-def extract_doc(item):
-    """Extracts the documentation contained in IRPF90_man file"""
-
-    path = os.path.join(ROOT_module, "IRPF90_man/%s.l" % (item))
-    with open(path, 'r') as f:
-        l_line = f.readlines()
-
-    result = []
-    inside = False
-    for line in l_line:
-        if not inside:
-            inside = line.startswith(".SH Description")
-        else:
-            if line.startswith(".SH"):
-                break
-            result.append("  {0}".format(line.strip()))
-
-    if not result:
-        result = ["  Undocumented"]
-
-    return "\n".join(result) + '\n'
-
-
-def update_documentation(data):
-    """Reads the BEGIN_DOC ... END_DOC blocks and builds the documentation"""
-
-    IRP_info = namedtuple('IRP_info', ["name", "file", "line"])
-
-    # If the file does not exist, don't do anything
-
-    path = os.path.join(ROOT_module, "tags")
-
-    with open(path, 'r') as f:
-        dump = f.readlines()
-
-    l_info = []
-    for i in dump:
-        name, f, ligne = i.split()
-
-        if not change and "/" not in i:
-            l_info.append(IRP_info(name, f, ligne))
-        elif change and MODULE_NAME in i:
-            l_info.append(IRP_info(name, f.split("/")[-1], ligne))
-
-    l_line = []
-
-    for irp in l_info:
-        url = os.path.join(URL, MODULE_NAME, irp.file)
-        doc = extract_doc(irp.name)
-
-        l_line += ["`{0} <{1}#L{2}>`_".format(irp.name, url, irp.line), doc,
-                   ""]
-
-    documentation = Doc_key + header + "\n".join(l_line)
-
-    has_doc = False
-    for i in range(len(data)):
-        if data[i].startswith(Doc_key):
-            has_doc = True
-            data[i] = documentation
-
-    if not has_doc:
-        data.append(documentation)
-
-    return data
-
-
-def git_add():
-    """Executes:
-    git add README.rst
-    throw an error if git is not precent"""
-
-    try:
-        # pipe output to /dev/null for silence
-        null = open("/dev/null", "w")
-        subprocess.Popen("git add README.rst", stdout=null, stderr=null)
-        null.close()
-
-    except OSError:
-        raise
-
-
-def main():
-    data = fetch_splitted_data()
-
-    data = update_documentation(data)
-    data = update_needed(data)
-    output = ''.join(data)
-
-    with open(README, 'w') as f:
-        f.write(output)
-
-    try:
-        git_add()
-    except OSError:
-        pass
-
-
-if __name__ == '__main__':
-    main()

src/AO_Basis/README.rst

@@ -33,7 +33,7 @@ Assumptions
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
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 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
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 .. by the `update_README.py` script.
 
 `ao_coef <http://github.com/LCPQ/quantum_package/tree/master/src/AO_Basis/ezfio_interface.irp.f#L24>`_

src/Bitmask/README.rst

@@ -37,7 +37,7 @@ Assumptions
 Needed Modules
 ==============
 
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 .. image:: tree_dependency.png
@@ -47,7 +47,7 @@ Needed Modules
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `bitstring_to_hexa <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask/bitmasks_routines.irp.f#L98>`_

src/Determinants/README.rst

@@ -29,7 +29,7 @@ Assumptions
 Needed Modules
 ==============
 
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 .. image:: tree_dependency.png
@@ -40,7 +40,7 @@ Needed Modules
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `a_operator <http://github.com/LCPQ/quantum_package/tree/master/src/Determinants/slater_rules.irp.f#L962>`_

src/Electrons/README.rst

@@ -21,7 +21,7 @@ Assumptions
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
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 .. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
@@ -31,7 +31,7 @@ Needed Modules
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `elec_alpha_num <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons/ezfio_interface.irp.f#L28>`_

src/Integrals_Bielec/README.rst

@@ -13,7 +13,7 @@ MO integral, use ``get_mo_bielec_integral(i,j,k,l,mo_integrals_map)`` or
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
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 .. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
@@ -24,7 +24,7 @@ Needed Modules
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `add_integrals_to_map <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Bielec/mo_bi_integrals.irp.f#L42>`_

src/Integrals_Monoelec/README.rst

@@ -1,7 +1,7 @@
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
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 .. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
@@ -12,7 +12,7 @@ Needed Modules
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `ao_deriv2_x <http://github.com/LCPQ/quantum_package/tree/master/src/Integrals_Monoelec/kin_ao_ints.irp.f#L1>`_

src/MOGuess/README.rst

@@ -5,7 +5,7 @@ MOGuess Module
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
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 .. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
@@ -15,7 +15,7 @@ Needed Modules
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `ao_ortho_lowdin_coef <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/mo_ortho_lowdin.irp.f#L2>`_

src/MO_Basis/README.rst

@@ -33,7 +33,7 @@ ASSUMPTONS
 Needed Modules
 ==============
 
-.. Do not edit this section. It was auto-generated from the
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 .. by the `update_README.py` script.
 
 .. image:: tree_dependency.png
@@ -44,7 +44,7 @@ Needed Modules
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `ao_to_mo <http://github.com/LCPQ/quantum_package/tree/master/src/MO_Basis/mos.irp.f#L136>`_

src/Nuclei/README.rst

@@ -9,7 +9,7 @@ The coordinates are expressed in atomic units.
 Needed Modules
 ==============
 
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 .. image:: tree_dependency.png
@@ -20,7 +20,7 @@ Needed Modules
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `element_name <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei/nuclei.irp.f#L172>`_

src/Pseudo/README.rst

@@ -5,7 +5,7 @@ Pseudo Module
 Needed Modules
 ==============
 
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 .. image:: tree_dependency.png
@@ -15,7 +15,7 @@ Needed Modules
 Documentation
 =============
 
-.. Do not edit this section. It was auto-generated from the
+.. Do not edit this section It was auto-generated
 .. by the `update_README.py` script.
 
 `do_pseudo <http://github.com/LCPQ/quantum_package/tree/master/src/Pseudo/ezfio_interface.irp.f#L248>`_

src/Utils/README.rst

@@ -7,7 +7,7 @@ Contains general purpose utilities.
 Documentation
 =============
 
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 `a_coef <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/need.irp.f#L252>`_
@@ -634,4 +634,3 @@ Documentation
 `write_git_log <http://github.com/LCPQ/quantum_package/tree/master/src/Utils/util.irp.f#L243>`_
   Write the last git commit in file iunit.
 
-