Improved qp completion

configure

@@ -70,7 +70,7 @@ while true : ; do
             exit 0;;
         --) shift ; break ;;
         *)
-            error "unknown option $1, try --help"
+            error $(basename $0)": unknown option $1, try --help"
             exit 2;;
     esac
 done

etc/ezfio.rc

@@ -5,8 +5,8 @@ export QP_EZFIO=${QP_ROOT}/external/ezfio
 
 function source_if_exists() {
   if [[ -f $1 ]]; then
-        source $1
+        cd $(dirname $1) ; source $(basename $1) ; cd -
-  fi
+  fi &> /dev/null
 } 
 
 source ${QP_ROOT}/etc/autocomplete.rc

etc/irpf90.rc

@@ -8,10 +8,11 @@ export IRPF90=${IRPF90_PATH}/bin/irpf90
 
 function source_if_exists() {
   if [[ -f $1 ]]; then
-     source $1
+        cd $(dirname $1) ; source $(basename $1) ; cd -
-  fi
+  fi &> /dev/null
 } 
 
+
 source ${QP_ROOT}/etc/autocomplete.rc
 source_if_exists "${IRPF90_PATH}/irpman-completions.bash"
   

etc/qp.rc

@@ -20,23 +20,20 @@ Usage:
   qp set         DIRECTORY   ITEM         : Array values read from stdin
 
   qp run         PROGRAM
+  qp man         PROGRAM   
   qp srun        PROGRAM
   qp mpirun      PROGRAM
 
   qp set_frozen_core
-  qp create_ezfio_from_xyz    --help
+
-  qp convert_output_to_ezfio  --help
+  qp create_ezfio_from_xyz 
-  qp set_mo_class             --help
+  qp convert_output_to_ezfio
+  qp update
+  qp set_mo_class
+  qp plugins
 "
 }
 
-#function test_ezfio()
-#{
-#      if [[ ! -d ${EZFIO_FILE} ]] ; then
-#        echo "qp: cannot access ${EZFIO_FILE}: No such file or directory"
-#        return 1
-#      fi
-#}
 
 function qp()
 {
@@ -52,13 +49,22 @@ function qp()
 
     "create_ezfio_from_xyz")
       shift
-      NAME=$(qp_create_ezfio_from_xyz "$@")
+      # Replace ':' by spaces
+      for arg in $@ ; do
+        if [[ $arg =~ -* ]] ; then
+          _ARGS+=("\"${arg//:/ }\"")
+        else
+          _ARGS+=("${arg}")
+        fi
+      done
+      NAME=$(eval "qp_create_ezfio_from_xyz ${_ARGS}")
       if [[ -d $NAME ]] ; then
         [[ -d $EZFIO_FILE ]] && ezfio unset_file
         ezfio set_file $NAME
       else
         echo $NAME | more
       fi
+      unset _ARGS
       ;;
 
     "convert_output_to_ezfio")
@@ -105,10 +111,19 @@ function qp()
           printf "\e[0;31m|${EZFIO_FILE}>\e[m"
         fi
       }
-#      PS1="${PS1%\\\$ } \$(_check_ezfio) $ "
       PS1="\$(_check_ezfio)\n$PS1"
       ;;
       
+    "plugins")
+      shift
+      qp_plugins $@
+      ;;
+
+    "update")
+      shift
+      qp_update $@
+      ;;
+
     *)
       _qp_usage
       ;;
@@ -117,60 +132,144 @@ function qp()
 }
 
 
+function _get_basis_sets () {
+  ( qp_create_ezfio_from_xyz -b show \
+  | tr ' ' ':' \
+  | while IFS= read -r LINE ; do
+      printf '%s\n' ${LINE}
+    done
+  (cd ~/quantum_package/data/basis/ ; \ls)
+  ) | sort | uniq
+}
+
+
+
 _Complete()
 {
   local cur
 
   COMPREPLY=()
   cur="${COMP_WORDS[COMP_CWORD]}"
+  first="${COMP_WORDS[1]}"
   prev="${COMP_WORDS[COMP_CWORD-1]}"
   prev2="${COMP_WORDS[COMP_CWORD-2]}"
 
+  case "${first}" in
+      update)
+        COMPREPLY=( $(compgen -W "-h" -- $cur ) )
+        return 0
+        ;;
+      man)
+        COMPREPLY=( $(compgen -W "$(cd ${QP_ROOT}/man ; \ls | sed 's/\.1//')" -- $cur ) )
+        return 0
+        ;;
+      convert_output_to_ezfio)
+        COMPREPLY=( $(compgen -W "-o $(\ls)" -- ${cur} ) )
+        return 0
+        ;;
+      create_ezfio_from_xyz)
+        case "${prev}" in
+          create_ezfio_from_xyz)
+            COMPREPLY=( $(compgen -W "-b -a -c -d -h -m -o -p -x" -- $cur ) )
+            return 0
+            ;;
+          -m|-d|-c)
+            COMPREPLY=( $(compgen -W "" -- $cur ) )
+            return 0;;
+          -b)
+            for iter in $(_get_basis_sets); do
+              if [[ $iter =~ ^$cur ]]; then
+                 COMPREPLY+=( "${iter}" )
+              fi
+            done;
+            return 0
+            ;;
+          -p)
+            COMPREPLY=( $(compgen -W "$(cd ~/quantum_package/data/pseudo ; \ls)" -- $cur ) )
+            return 0
+            ;;
+          *)
+            COMPREPLY=( $(compgen -W "-b -a -c -d -h -m -o -p -x $(\ls)" -- $cur ) )
+            return 0
+            ;;
+        esac;;
+      plugins)
+        case "${prev}" in
+          plugins)
+            COMPREPLY=( $(compgen -W "list download install uninstall create" -- $cur ) )
+            return 0
+            ;;
+          list)
+            COMPREPLY=( $(compgen -W "-i -u -q" -- $cur ) )
+            return 0;;
+          download)
+            COMPREPLY=( $(compgen -W "http:// git@github.com: git@gitlab.com: " -- $cur ) )
+            return 0;;
+          install)
+            COMPREPLY=( $(compgen -W "$(qp_plugins list -u)" -- $cur ) )
+            return 0;;
+          uninstall)
+            COMPREPLY=( $(compgen -W "$(qp_plugins list -i)" -- $cur ) )
+            return 0;;
+          create) 
+            COMPREPLY=( $(compgen -W "-n " -- $cur ) )
+            return 0;;
+          *)
+            COMPREPLY=( $(compgen -W "$( \ls ; cd ~/quantum_package/src ; \ls )" -- $cur ) )
+            return 0
+            ;;
+        esac;;
+      *)
+        COMPREPLY=( $(compgen -W 'plugins \
+                                   man \
+                                   create_ezfio_from_xyz \
+                                   convert_output_to_ezfio \
+                                   -h update' -- $cur ) )
+
+  esac
+
   if [[ -n ${EZFIO_FILE} && -d ${EZFIO_FILE} ]]
   then
 
     case "${prev2}" in
       "set"|has|get)
         if [[ ${prev} == "qp" ]] ; then
-          COMPREPLY=( $(compgen -W "set set_frozen_core set_mo_class" -- $cur ) )
+          COMPREPLY=( $(compgen -W "plugins set set_frozen_core set_mo_class" -- $cur ) )
         elif [[ ! -d ${EZFIO_FILE}/${prev} ]] ; then
           COMPREPLY=( $(compgen -W "" -- $cur ) )
         else
-          COMPREPLY=( $(compgen -W "$(cd ${EZFIO_FILE}/${prev} ; ls | sed 's/\.gz//' )" -- $cur ) )
+          COMPREPLY=( $(compgen -W "$(cd ${EZFIO_FILE}/${prev} ; \ls | sed 's/\.gz//' )" -- $cur ) )
         fi
         return 0
         ;;
-       *)
-          COMPREPLY=( $(compgen -W "$(\ls)" -- $cur ) )
     esac
 
-    case "${prev}" in
+    case "${first}" in
       run|srun|mpirun)
-        COMPREPLY=( $(compgen -W "$(cat ${QP_ROOT}/data/executables | cut -d ' ' -f 1)" -- $cur ) )
+        COMPREPLY=( $(compgen -W "-h $(cat ${QP_ROOT}/data/executables | cut -d ' ' -f 1)" -- $cur ) )
         return 0
         ;;
-      unset_file|edit|set_frozen_core)
+      unset_file|set_frozen_core)
         COMPREPLY=()
         return 0
         ;;
       set_mo_class)
-        COMPREPLY=( $(compgen -W "-h -core -inact -act -virt -del" -- $cur ) )
+        COMPREPLY=( $(compgen -W "-h -c -i -a -v -d -q" -- $cur ) )
-        return 0
-        ;;
-      man)
-        COMPREPLY=( $(compgen -W "$(cd ${QP_ROOT}/man ; \ls | sed '/\.[1-9] / /')" -- $cur ) )
         return 0
         ;;
       set|has|get)
         COMPREPLY=( $(compgen -W "$(cd ${EZFIO_FILE} ; \ls -d */ | sed 's|/||g')" -- $cur ) )
         return 0
         ;;
+      edit)
+        COMPREPLY=( $(compgen -W "-h -c -n -s" -- $cur ) )
+        return 0
+        ;;
       *)
-        COMPREPLY=( $(compgen -W 'has get set unset_file edit \
+        COMPREPLY+=( $(compgen -W 'has get set unset_file edit \
                                   run srun mpirun set_frozen_core \
-                                  set_mo_class create_ezfio_from_xyz \
+                                  set_mo_class ' \
-                                  convert_output_to_ezfio \
+                                  -- $cur ) )
-                                  -h' -- $cur ) )
         return 0
         ;;
     esac
@@ -178,24 +277,12 @@ _Complete()
   else
 
     case "${prev}" in
-      man)
-        COMPREPLY=( $(compgen -W "$(cd ${QP_ROOT}/man ; echo * | sed 's|\.[1-9] | |g')" -- $cur ) )
-        return 0
-        ;;
       set_file)
         COMPREPLY=( $(compgen -W "$(\ls -d */ | sed 's|/||g')" -- ${cur} ) )
         return 0
         ;;
-      convert_output_to_ezfio|create_ezfio_from_xyz)
-        COMPREPLY=( $(compgen -W "$(\ls)" -- ${cur} ) )
-        return 0
-        ;;
       *)
-        COMPREPLY=( $(compgen -W 'set_file \
+        COMPREPLY+=( $(compgen -W "set_file" -- $cur ) )
-                                  man \
-                                  create_ezfio_from_xyz \
-                                  convert_output_to_ezfio \
-                                  -h' -- $cur ) )
         return 0
         ;;
     esac

ocaml/Command_line.mli

@@ -8,6 +8,8 @@ let () =
   let open Command_line in
   begin
     set_header_doc (Sys.argv.(0) ^ " - quantum_package command");
+    set_description_doc
+      "Opens a text editor to edit the parameters of an EZFIO directory.";
 
     [ { short='c'; long="check"; opt=Optional;
         doc="Checks the input data";
@@ -25,8 +27,6 @@ let () =
     ]
     |> set_specs ;
 
-    set_description_doc
-      "Opens a text editor to edit the parameters of a EZFIO directory.";
   end;
 
 

ocaml/Makefile

@@ -82,6 +82,8 @@ git:
 ${QP_EZFIO}/Ocaml/ezfio.ml: 
 	$(NINJA) -C ${QP_EZFIO}
 
+qp_edit.ml: ../scripts/ezfio_interface/qp_edit_template
+
 Input_auto_generated.ml qp_edit.ml: $(filter-out Input_auto_generated.ml, $(wildcard Input_*.ml))
 	ei_handler.py ocaml_global
 

scripts/ezfio_interface/qp_edit_template

@@ -9,7 +9,7 @@ open Core
 (** Interactive editing of the input.
 
 WARNING 
-This file is autogenerad by
+This file is automatically generated by
 `${{QP_ROOT}}/scripts/ezfio_interface/ei_handler.py`
 *)
 
@@ -265,24 +265,33 @@ let restore_backup ezfio_filename =
 
 
 
-
 let () =
-  (* Command-line specs *)
+  let open Command_line in
-  Command_line.set_header_doc "Opens a text editor to edit the parameters of a EZFIO directory.";
+  begin
+    set_header_doc (Sys.argv.(0) ^ " - quantum_package command");
+    set_description_doc
+      "Opens a text editor to edit the parameters of an EZFIO directory.";
 
-  [ ( 'c', "check", "Checks the input data", Command_line.Without_arg);
+    [ {{ short='c'; long="check"; opt=Optional;
-    ( 'n', "ndet", "<int> Truncate the wavefunction to the target number of determinants",
+        doc="Checks the input data";
-      Command_line.With_arg);
+        arg=Without_arg; }};
-    ( 's', "state", "<range> Extract selected states, for example \"[1,3-5]\"", Command_line.With_arg);
-    Command_line.anonymous "<EZFIO_FILE>" "EZFIO directory";
-  ]
-  |> Command_line.set_specs ;
 
+      {{ short='n'; long="ndet"; opt=Optional;
+        doc="Truncates the wavefunction to the target number of determinants";
+        arg=With_arg "<int>"; }};
+
+      {{
+        short='s'; long="state"; opt=Optional;
+        doc="Extracts selected states, for example \"[1,3-5]\"";
+        arg=With_arg "<range>"; }};
+
+      anonymous "EZFIO_DIR" Mandatory "EZFIO directory";
+    ]
+    |> set_specs ;
+
+  end;
 
   (*  Handle options *)
-  if Command_line.show_help () then
-    exit 0;
-
   let ndet =
     match Command_line.get "ndet" with
     | None -> None
@@ -296,16 +305,12 @@ let () =
             with _ -> failwith "[-s|--state] expects a range")
   in
 
-  let c =
+  let c = Command_line.get_bool "check" in
-    match Command_line.get "check" with
-    | None -> false
-    | _ -> true
-  in
 
   let ezfio_filename =
     match Command_line.anon_args () with
     | [x] -> x
-    | _ -> (Command_line.help () ; failwith "EZFIO_FILE is missing")
+    | _ -> (Command_line.help () ; failwith "EZFIO_DIR is missing")
   in
 
   at_exit (fun () -> remove_backup ezfio_filename);

scripts/qp_mpirun

@@ -7,6 +7,15 @@ function error() {
 
 set -e
 
+PROG=$1
+INPUT=$2
+
+case ${PROG} in 
+  -h|--help)
+        exec qp_run --help
+  ;;
+esac
+
 NODES=($(mpirun hostname))
 
 # Test that there is one MPI process per node
@@ -28,8 +37,7 @@ In your SLURM script file, use:
   exit -1
 fi
 
-PROG=$1
+        
-INPUT=$2
 
 # Check if quantum_package.rc is sourced
 

scripts/qp_plugins

@@ -94,8 +94,8 @@ def main(arguments):
     arguments["<name>"] = [os.path.normpath(name) for name in arguments["<name>"]]
 
     if arguments["list"]:
-        if arguments["-q"]:
+        if arguments["--repositories"]:
-            l_result = [f for f in os.path.listdir(QP_PLUGINS) if f not in [".gitignore", "local"]]
+            l_result = [f for f in os.listdir(QP_PLUGINS) if f not in [".gitignore", "local"]]
 
         else:
             # Search in src all directories with a NEED file
@@ -113,20 +113,20 @@ def main(arguments):
             l_plugins = [module for module in m_instance.l_module]
             l_result = l_plugins
 
-            if arguments["-i"] or arguments["-u"]:
+            if arguments["--installed"] or arguments["--uninstalled"]:
                 # Search in src all symbolic links that are modules
-                l_installed = [f for f in os.path.listdir(QP_SRC) \
+                l_installed = [f for f in os.listdir(QP_SRC) \
                                if (os.path.islink(os.path.join(QP_SRC, f)) \
                                and f != ".gitignore")]
 
-            if arguments["-i"]:
+            if arguments["--installed"]:
                 l_result = [f for f in l_plugins if f in l_installed]
 
-            elif arguments["-u"]:
+            elif arguments["--uninstalled"]:
                 l_result = [f for f in l_plugins if f not in l_installed]
 
         for module in sorted(l_result):
-            print "* {0}".format(module)
+            print module
 
     if arguments["create"]:
         m_instance = ModuleHandler([QP_SRC])
@@ -135,8 +135,8 @@ def main(arguments):
 
         name = arguments["<name>"][0]
 
-        if arguments["-r"]:
+        if arguments["--repository"]:
-            repository = arguments["-r"]
+            repository = arguments["--repository"]
         else:
             repository = "local"
 
@@ -266,7 +266,7 @@ def main(arguments):
         if l_failed:
             print "Plugins not installed:"
             for name in sorted(l_failed):
-                print "* %s" % name
+                print "%s" % name
             sys.exit(1)
 
         l_name_to_remove = l_name + \

scripts/qp_srun

@@ -7,6 +7,15 @@ function error() {
 
 set -e
 
+PROG=$1
+INPUT=$2
+
+case ${PROG} in  
+  -h|--help)
+        exec qp_run --help
+  ;;
+esac
+
 NODES=($(srun hostname))
 
 # Test that there is one MPI process per node
@@ -28,8 +37,6 @@ In your SLURM script file, use:
   exit -1
 fi
 
-PROG=$1
-INPUT=$2
 
 # Check if quantum_package.rc is sourced
 

scripts/qp_update

@@ -0,0 +1,67 @@
+#!/bin/bash
+#
+# Updates the current version of QP
+#
+# Mon Jan 14 21:51:08 CET 2019
+#
+
+function help() {
+  cat << EOF
+Updates the current version of QP.
+
+Usage:
+
+    $(basename $0) [-h|--help]
+
+Options:
+
+    -h    --help    Prints the help message
+
+EOF
+  exit 0
+}
+
+function error() {
+    >&2 echo "$(basename $0): $@"
+    exit 2
+}
+
+
+TEMP=`getopt -o h -l help -n $0 -- "$@"` || exit 1
+
+while true ; do
+    case "$1" in
+        ""|--) shift ; break ;;
+        -h|-help|--help)
+            help
+            shift
+            exit 0;;
+        *)
+            echo $(basename $0)": unknown option $1, try --help"
+            exit 2;;
+    esac
+done
+
+# Check the QP_ROOT directory
+if [[ -z ${QP_ROOT} ]] ; then
+  echo "The QP_ROOT environment variable is not set."
+  echo "Please reload the quantum_package.rc file."
+  exit 1
+fi
+
+read -r -p "Are you sure you want to update QP? [y/N] " response
+case "$response" in
+    [yY][eE][sS]|[yY]) 
+        :
+        ;;
+    *)
+        exit 0
+        ;;
+esac
+
+cd ${QP_ROOT}
+ninja clean
+git pull origin master
+ninja
+
+