Merge tag 'fix_new_module_tag_error' into develop

Clean before unistall

plugins/Hartree_Fock/.gitignore

@@ -21,4 +21,5 @@ MOGuess
 Nuclei
 Utils
 Huckel_guess
+test
 SCF

plugins/Hartree_Fock/README.rst

@@ -29,7 +29,17 @@ Documentation
   Alpha Fock matrix in AO basis set
 
 
-`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L8>`_
+`big <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/test.irp.f#L1>`_
+  Produce `Huckel` MO orbital
+  output:  mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
+  Produce `Hartree_Fock` MO orbital
+  output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
+  output: hartree_fock.energy
+  input: mo_basis.mo_coef
+  Run SCF calculation
+
+
+`create_guess <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L13>`_
   Create an MO guess if no MOs are present in the EZFIO directory
 
 
@@ -139,12 +149,15 @@ Documentation
   Maximum number of SCF iterations
 
 
-`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L33>`_
+`run <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L38>`_
   Run SCF calculation
 
 
-`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L2>`_
+`scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/SCF.irp.f#L1>`_
-  Undocumented
+  Produce `Hartree_Fock` MO orbital
+  output: mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
+  output: hartree_fock.energy
+  optional: mo_basis.mo_coef
 
 
 `thresh_scf <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock/ezfio_interface.irp.f#L46>`_

scripts/compilation/qp_create_ninja.py

@@ -26,7 +26,7 @@ except ImportError:
     print """
 Error:
  source %s
-"""%f
+""" % f
     sys.exit(1)
 
 header = r"""#
@@ -313,8 +313,11 @@ def ninja_symlink_build(path_module, l_symlink):
     if not l_symlink:
         return []
 
-    l_string = ["build l_symlink_{0} : phony {1}".format(
+    l_folder = [s.destination for s in l_symlink]
-        path_module.rel, " ".join([s.destination for s in l_symlink])), ""]
+
+    l_string = ["build l_symlink_{0} : phony {1}".format(path_module.rel,
+                                                         " ".join(l_folder)),
+                ""]
 
     for symlink in l_symlink:
         l_string += ["build {0}: build_symlink {1}".format(symlink.destination,
@@ -336,20 +339,22 @@ def ninja_gitignore_rule():
             "  description = Create gitignore for $module_rel", ""]
 
 
-def ninja_gitignore_build(path_module, d_binaries):
+def ninja_gitignore_build(path_module, d_binaries, l_symlink):
     """
     """
 
     path_gitignore = join(path_module.abs, ".gitignore")
 
     l_b = [i.abs for i in d_binaries[path_module]]
-    l_sym = [i.destination for i in l_symlink]
 
-    l_string = ["build {0}: build_gitignore {1} || l_symlink_{2}".format(path_gitignore,
+    root = "build {0}: build_gitignore {1}".format(path_gitignore,
-                                                                         " ".join(l_b),
+                                                   " ".join(l_b))
-                                                                         path_module.rel),
+    if l_symlink:
-                "   module_rel = {0}".format(path_module.rel),
+        l_string = ["{0} || l_symlink_{1}".format(root, path_module.rel)]
-                ""]
+    else:
+        l_string = ["{0}".format(root)]
+
+    l_string.extend(("   module_rel = {0}".format(path_module.rel), ""))
 
     return l_string
 
@@ -911,7 +916,8 @@ if __name__ == "__main__":
         l_string += ninja_binaries_build(module_to_compile, l_children,
                                          d_binaries)
 
-        l_string += ninja_gitignore_build(module_to_compile, d_binaries)
+        l_string += ninja_gitignore_build(module_to_compile, d_binaries,
+                                          l_symlink)
 
     with open(join(QP_ROOT, "config", "build.ninja"), "w+") as f:
         f.write(header)

scripts/module/qp_install_module.py

@@ -16,6 +16,7 @@ Options:
 
 import sys
 import os
+import subprocess
 
 try:
     from docopt import docopt
@@ -152,6 +153,11 @@ if __name__ == '__main__':
                     except OSError:
                         print "Your src directory is broken. Please remove %s" % des
                         raise
+            try:
+                import subprocess
+                subprocess.check_call(["qp_create_ninja.py", "update"])
+            except:
+                raise
             print "Done"
             print "You can now compile as usual"
 
@@ -164,24 +170,29 @@ if __name__ == '__main__':
         l_name = arguments["<name>"]
 
         l_failed = [name for name in l_name if name not in d_local]
+
         if l_failed:
             print "Modules not installed:"
             for name in sorted(l_failed):
                 print "* %s" % name
             sys.exit(1)
-        else:
+
         if arguments["--and_ancestor"]:
 
             l_name_to_remove = l_name + [module for module in m_instance.l_module for name in l_name if name in d_descendant[module]]
             print "You will remove all of:"
             print l_name_to_remove
-
         else:
             l_name_to_remove = l_name
 
-            def unlink(x):
+        for module in l_name_to_remove:
+
             try:
-                    os.unlink(os.path.join(QP_SRC, x))
+                subprocess.check_call(["module_handler.py", "clean", module])
+            except:
+                raise
+
+            try:
+                os.unlink(os.path.join(QP_SRC, module))
             except OSError:
                 print "%s is a core module which can not be renmoved" % x
-            map(unlink, l_name_to_remove)

src/MOGuess/README.rst

@@ -37,3 +37,7 @@ Documentation
   Produce `H_core` MO orbital
   output:  mo_basis.mo_tot_num mo_basis.mo_label mo_basis.ao_md5 mo_basis.mo_coef mo_basis.mo_occ
 
+
+`hcore_guess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess/h_core_guess_routine.irp.f#L1>`_
+  Produce `H_core` MO orbital
+