From bdc87b7fab1314b58190454fc104e78c40ca839c Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Fri, 17 Mar 2017 13:53:58 +0100
Subject: [PATCH 01/22] nest.helpdesk() opens now system default browser

---
 pynest/nest/lib/hl_api_helper.py | 60 ++++++++++++++++++++++++++++++--
 pynest/nest/lib/hl_api_info.py   | 58 ++++++++++++++++++++++++------
 2 files changed, 106 insertions(+), 12 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index f10f577ea9..61da757f04 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -28,6 +28,9 @@
 import inspect
 import functools
 import textwrap
+import subprocess
+import os
+import re
 
 # These variables MUST be set by __init__.py right after importing.
 # There is no safety net, whatsoever.
@@ -111,7 +114,6 @@ def deprecated(alt_func_name, text=None):
     function:
         Decorator function
     """
-
     def deprecated_decorator(func):
         _deprecation_warning[func.__name__] = True
 
@@ -172,6 +174,7 @@ def is_string(obj):
     """
     return isinstance(obj, uni_str)
 
+
 __debug = False
 
 
@@ -389,7 +392,7 @@ def broadcast(item, length, allowed_types, name="item"):
     """
 
     if isinstance(item, allowed_types):
-        return length * (item, )
+        return length * (item,)
     elif len(item) == 1:
         return length * item
     elif len(item) != length:
@@ -400,6 +403,58 @@ def broadcast(item, length, allowed_types, name="item"):
     return item
 
 
+
+def pdoc(obj, ppager):
+    """Output of doc in python with pager or print
+
+    Parameters
+    ----------
+    obj : object
+        Object to display
+    ppager: str, optional
+        pager to use, NO if you explicity do not want to use a pager
+
+    @author graber
+    """
+    # environment 'jupyter', 'ipython n' or plain python
+    jptk = re.findall(r'.*jupyter.*', os.environ['_'])
+    iptk = re.findall(r'.*ipython.*', os.environ['_'])
+
+    # reading ~/.nestrc, try to find pager
+    if not ppager:
+        rc = open(os.environ['HOME'] + '/.nestrc', 'r')
+        for line in rc:
+            rctst = re.match(r'^\s?\%', line)
+            if rctst is None:
+                ppagers = re.findall(
+                    r'\s?\/page\s?<<\s?\/command\s?\((.*)\).*', line)
+                if ppagers:
+                    rcppager = ppagers[0]
+                    break
+        rc.close()
+    if not rcppager:
+        rcppager = "less"
+
+    helpdir = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/"
+    objname = obj + '.hlp'
+    ishelp = ""
+    for dirpath, dirnames, files in os.walk(helpdir):
+        for hlp in files:
+            if hlp == objname:
+                ishelp = True
+                objf = os.path.join(dirpath, objname)
+                fhlp = open(objf, 'r')
+                hlptxt = fhlp.read()
+                fhlp.close()
+                if jptk or iptk:
+                    print(hlptxt)
+                else:
+                    if not ppager or ppager == "NO":
+                        print(hlptxt)
+                    else:
+                        subprocess.call([rcppager, objf])
+
+
 @check_stack
 def get_verbosity():
     """Return verbosity level of NEST's messages.
@@ -432,6 +487,7 @@ def set_verbosity(level):
     sr("%s setverbosity" % level)
 
 
+
 def model_deprecation_warning(model):
     """Checks whether the model is to be removed in a future verstion of NEST.
     If so, a deprecation warning is issued.
diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index e78b43ce6f..5d2792f2a0 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -24,6 +24,10 @@
 """
 
 from .hl_api_helper import *
+import os
+import re
+import subprocess
+import webbrowser
 
 
 @check_stack
@@ -55,19 +59,19 @@ def authors():
 
 
 @check_stack
-def helpdesk(browser="firefox"):
+def helpdesk():
     """Open the NEST helpdesk in the given browser.
 
-    The default browser is firefox.
+    The system default browser.
 
-    Parameters
-    ----------
-    browser : str, optional
-        Name of the browser to use
+    @author graber
     """
 
-    sr("/helpdesk << /command (%s) >> SetOptions" % browser)
-    sr("helpdesk")
+    # sr("/helpdesk << /command (%s) >> SetOptions" % browser)
+    # sr("helpdesk")
+
+    url = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/helpindex.html"
+    webbrowser.open_new(url)
 
 
 @check_stack
@@ -82,11 +86,45 @@ def help(obj=None, pager="less"):
         Object to display help for
     pager : str, optional
         Pager to use
+
+
     """
 
     if obj is not None:
-        sr("/page << /command (%s) >> SetOptions" % pager)
-        sr("/%s help" % obj)
+        # sr("/page << /command (%s) >> SetOptions" % pager)
+        # sr("/%s help" % obj)
+
+        # print('HALLO')
+        # @author graber
+        helpdir = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/"
+        objname = obj + '.hlp'
+        jptk = re.findall(r'.*jupyter.*', os.environ['_'])
+        iptk = re.findall(r'.*ipython.*', os.environ['_'])
+
+        # reading ~/.nestrc
+        pypager = 'less'
+        rc = open(os.environ['HOME'] + '/.nestrc', 'r')
+        for line in rc:
+            rctst = re.match(r'^\s?\%', line)
+            if rctst is None:
+                pypagers = re.findall(
+                    r'\s?\/page\s?<<\s?\/command\s?\((.*)\).*', line)
+                if pypagers:
+                    pypager = pypagers[0]
+                    break
+        rc.close()
+
+        for dirpath, dirnames, files in os.walk(helpdir):
+            for hlp in files:
+                if hlp == objname:
+                    objf = os.path.join(dirpath, objname)
+                    fhlp = open(objf, 'r')
+                    hlptxt = fhlp.read()
+                    fhlp.close()
+                    if jptk or iptk:
+                        print(hlptxt)
+                    else:
+                        subprocess.call([pypager, objf])
     else:
         print("Type 'nest.helpdesk()' to access the online documentation "
               "in a browser.")

From 3e33deaa3e6db061b9d9f8939b6eac71325e6dea Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Fri, 17 Mar 2017 14:10:10 +0100
Subject: [PATCH 02/22] setting and using help pager/viewer

---
 pynest/nest/lib/hl_api_info.py | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index 5d2792f2a0..c370ce22f4 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -60,9 +60,10 @@ def authors():
 
 @check_stack
 def helpdesk():
-    """Open the NEST helpdesk in the given browser.
+    """Open the NEST helpdesk in browser.
 
     The system default browser.
+    /helpdesk << /command (firefox) >> SetOptions in ~/.nestrc is now obsolete
 
     @author graber
     """
@@ -87,7 +88,7 @@ def help(obj=None, pager="less"):
     pager : str, optional
         Pager to use
 
-
+    @author graber
     """
 
     if obj is not None:
@@ -95,13 +96,13 @@ def help(obj=None, pager="less"):
         # sr("/%s help" % obj)
 
         # print('HALLO')
-        # @author graber
+        #
         helpdir = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/"
         objname = obj + '.hlp'
         jptk = re.findall(r'.*jupyter.*', os.environ['_'])
         iptk = re.findall(r'.*ipython.*', os.environ['_'])
 
-        # reading ~/.nestrc
+        # reading ~/.nestrc lookink for pager to use.
         pypager = 'less'
         rc = open(os.environ['HOME'] + '/.nestrc', 'r')
         for line in rc:
@@ -121,10 +122,12 @@ def help(obj=None, pager="less"):
                     fhlp = open(objf, 'r')
                     hlptxt = fhlp.read()
                     fhlp.close()
-                    if jptk or iptk:
-                        print(hlptxt)
-                    else:
-                        subprocess.call([pypager, objf])
+                    # @ graber
+                    # @ todo try it
+                    # if jptk or iptk:
+                    #     print(hlptxt)
+                    # else:
+                    subprocess.call([pypager, objf])
     else:
         print("Type 'nest.helpdesk()' to access the online documentation "
               "in a browser.")

From 83346c15000a294f35f17fc92f8eadb3d0323500 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Mon, 20 Mar 2017 13:50:13 +0100
Subject: [PATCH 03/22] better use in notebook

---
 pynest/nest/lib/hl_api_info.py | 44 +++++++++++++++++++++-------------
 1 file changed, 27 insertions(+), 17 deletions(-)

diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index c370ce22f4..efd3689a3b 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -103,17 +103,20 @@ def help(obj=None, pager="less"):
         iptk = re.findall(r'.*ipython.*', os.environ['_'])
 
         # reading ~/.nestrc lookink for pager to use.
-        pypager = 'less'
-        rc = open(os.environ['HOME'] + '/.nestrc', 'r')
-        for line in rc:
-            rctst = re.match(r'^\s?\%', line)
-            if rctst is None:
-                pypagers = re.findall(
-                    r'\s?\/page\s?<<\s?\/command\s?\((.*)\).*', line)
-                if pypagers:
-                    pypager = pypagers[0]
-                    break
-        rc.close()
+
+        if pager is None:
+
+            rc = open(os.environ['HOME'] + '/.nestrc', 'r')
+            for line in rc:
+                rctst = re.match(r'^\s?\%', line)
+                if rctst is None:
+                    pypagers = re.findall(
+                        r'\s?\/page\s?<<\s?\/command\s?\((.*)\).*', line)
+                    if pypagers:
+                        pager = pypagers[0]
+                        break
+                    else: pager = 'less'
+            rc.close()
 
         for dirpath, dirnames, files in os.walk(helpdir):
             for hlp in files:
@@ -122,12 +125,19 @@ def help(obj=None, pager="less"):
                     fhlp = open(objf, 'r')
                     hlptxt = fhlp.read()
                     fhlp.close()
-                    # @ graber
-                    # @ todo try it
-                    # if jptk or iptk:
-                    #     print(hlptxt)
-                    # else:
-                    subprocess.call([pypager, objf])
+                    if jptk or iptk:
+
+                        consolepager = ['less', 'more', 'vi', 'vim', 'nano',
+                                        'emacs -nw', 'ed', 'editor']
+                        if pager in consolepager:
+                            print('---\n\n')
+                            print('Use: help(obj=None, pager=YOURPAGER).\n')
+                            print('For YOURPAGER do not use console editors!\n')
+                            print('---\n\n')
+                            print(hlptxt)
+                        else: subprocess.call([pager, objf])
+                    else:
+                        subprocess.call([pager, objf])
     else:
         print("Type 'nest.helpdesk()' to access the online documentation "
               "in a browser.")

From e7c9f9c42036e10378e3c5028fac7c18b772b1b0 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Mon, 20 Mar 2017 14:24:52 +0100
Subject: [PATCH 04/22] some inline documentation

---
 pynest/nest/lib/hl_api_info.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index efd3689a3b..9a8ce773c4 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -101,11 +101,11 @@ def help(obj=None, pager="less"):
         objname = obj + '.hlp'
         jptk = re.findall(r'.*jupyter.*', os.environ['_'])
         iptk = re.findall(r'.*ipython.*', os.environ['_'])
+        # @todo is there a way to recognize 'ipython notebook'? Do it.
 
         # reading ~/.nestrc lookink for pager to use.
-
         if pager is None:
-
+            # open ~/.nestrc
             rc = open(os.environ['HOME'] + '/.nestrc', 'r')
             for line in rc:
                 rctst = re.match(r'^\s?\%', line)
@@ -125,11 +125,13 @@ def help(obj=None, pager="less"):
                     fhlp = open(objf, 'r')
                     hlptxt = fhlp.read()
                     fhlp.close()
-                    if jptk or iptk:
-
+                    # only for jupyter notebook
+                    if jptk:
+                        # @todo more pager
                         consolepager = ['less', 'more', 'vi', 'vim', 'nano',
                                         'emacs -nw', 'ed', 'editor']
                         if pager in consolepager:
+                            # only in notebook
                             print('---\n\n')
                             print('Use: help(obj=None, pager=YOURPAGER).\n')
                             print('For YOURPAGER do not use console editors!\n')

From 8a2d69feb0dbb519cdb6b590c0765adef0cd56bd Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Tue, 21 Mar 2017 10:00:01 +0100
Subject: [PATCH 05/22] introducing check_nb() and moving to hl_api_helper.py

---
 pynest/nest/lib/hl_api_helper.py | 77 +++++++++++++++++++++++---------
 pynest/nest/lib/hl_api_info.py   | 61 ++++---------------------
 2 files changed, 65 insertions(+), 73 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index 61da757f04..dd42045809 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -403,8 +403,39 @@ def broadcast(item, length, allowed_types, name="item"):
     return item
 
 
+def check_nb():
+    """Check if is notebook or not
 
-def pdoc(obj, ppager):
+    To know a little bit more about the environment use:
+
+        jptk = re.findall(r'.*jupyter.*', os.environ['_'])
+        iptk = re.findall(r'.*ipython.*', os.environ['_'])
+
+    """
+    try:
+        cfg = get_ipython().config
+        if cfg['IPKernelApp']['connection_file']:
+            return True
+        else:
+            return False
+    except NameError:
+        return False
+
+@check_stack
+def open_window():
+    js = '''
+        <script>
+        var  myWindow = window.open("", "MsgWindow", "width=200,height=100");
+        myWindow.document.write( "
+        <p>This is . I am 200px wide and 100px tall!</p>
+         ");
+        </script>
+        '''
+    print(js)
+
+
+@check_stack
+def pdoc(obj, pager):
     """Output of doc in python with pager or print
 
     Parameters
@@ -416,43 +447,48 @@ def pdoc(obj, ppager):
 
     @author graber
     """
-    # environment 'jupyter', 'ipython n' or plain python
-    jptk = re.findall(r'.*jupyter.*', os.environ['_'])
-    iptk = re.findall(r'.*ipython.*', os.environ['_'])
+    helpdir = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/"
+    objname = obj + '.hlp'
 
-    # reading ~/.nestrc, try to find pager
-    if not ppager:
+    # reading ~/.nestrc lookink for pager to use.
+    if pager is None:
+        # open ~/.nestrc
         rc = open(os.environ['HOME'] + '/.nestrc', 'r')
         for line in rc:
             rctst = re.match(r'^\s?\%', line)
             if rctst is None:
-                ppagers = re.findall(
+                pypagers = re.findall(
                     r'\s?\/page\s?<<\s?\/command\s?\((.*)\).*', line)
-                if ppagers:
-                    rcppager = ppagers[0]
+                if pypagers:
+                    pager = pypagers[0]
                     break
+                else:
+                    pager = 'less'
         rc.close()
-    if not rcppager:
-        rcppager = "less"
 
-    helpdir = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/"
-    objname = obj + '.hlp'
-    ishelp = ""
     for dirpath, dirnames, files in os.walk(helpdir):
         for hlp in files:
             if hlp == objname:
-                ishelp = True
                 objf = os.path.join(dirpath, objname)
                 fhlp = open(objf, 'r')
                 hlptxt = fhlp.read()
                 fhlp.close()
-                if jptk or iptk:
-                    print(hlptxt)
-                else:
-                    if not ppager or ppager == "NO":
+                # only for notebook
+                if check_nb():
+                    # @todo more pager
+                    consolepager = ['less', 'more', 'vi', 'vim', 'nano',
+                                    'emacs -nw', 'ed', 'editor']
+                    if pager in consolepager:
+                        # only in notebook
+                        print('---\n')
+                        print('Use: help(obj=None, pager=YOURPAGER).\n')
+                        print('For YOURPAGER do not use console editors!\n')
+                        print('---\n\n')
                         print(hlptxt)
                     else:
-                        subprocess.call([rcppager, objf])
+                        subprocess.call([pager, objf])
+                else:
+                    subprocess.call([pager, objf])
 
 
 @check_stack
@@ -487,7 +523,6 @@ def set_verbosity(level):
     sr("%s setverbosity" % level)
 
 
-
 def model_deprecation_warning(model):
     """Checks whether the model is to be removed in a future verstion of NEST.
     If so, a deprecation warning is issued.
diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index 9a8ce773c4..b84ebae7f3 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -71,12 +71,12 @@ def helpdesk():
     # sr("/helpdesk << /command (%s) >> SetOptions" % browser)
     # sr("helpdesk")
 
-    url = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/helpindex.html"
+    url = os.environ['NEST_DOC_DIR'] + "/help/helpindex.html"
     webbrowser.open_new(url)
 
 
 @check_stack
-def help(obj=None, pager="less"):
+def help(obj=None, pager=None):
     """Show the help page for the given object using the given pager.
 
     The default pager is less.
@@ -90,67 +90,24 @@ def help(obj=None, pager="less"):
 
     @author graber
     """
-
     if obj is not None:
         # sr("/page << /command (%s) >> SetOptions" % pager)
         # sr("/%s help" % obj)
 
-        # print('HALLO')
-        #
-        helpdir = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/"
-        objname = obj + '.hlp'
-        jptk = re.findall(r'.*jupyter.*', os.environ['_'])
-        iptk = re.findall(r'.*ipython.*', os.environ['_'])
-        # @todo is there a way to recognize 'ipython notebook'? Do it.
-
-        # reading ~/.nestrc lookink for pager to use.
-        if pager is None:
-            # open ~/.nestrc
-            rc = open(os.environ['HOME'] + '/.nestrc', 'r')
-            for line in rc:
-                rctst = re.match(r'^\s?\%', line)
-                if rctst is None:
-                    pypagers = re.findall(
-                        r'\s?\/page\s?<<\s?\/command\s?\((.*)\).*', line)
-                    if pypagers:
-                        pager = pypagers[0]
-                        break
-                    else: pager = 'less'
-            rc.close()
-
-        for dirpath, dirnames, files in os.walk(helpdir):
-            for hlp in files:
-                if hlp == objname:
-                    objf = os.path.join(dirpath, objname)
-                    fhlp = open(objf, 'r')
-                    hlptxt = fhlp.read()
-                    fhlp.close()
-                    # only for jupyter notebook
-                    if jptk:
-                        # @todo more pager
-                        consolepager = ['less', 'more', 'vi', 'vim', 'nano',
-                                        'emacs -nw', 'ed', 'editor']
-                        if pager in consolepager:
-                            # only in notebook
-                            print('---\n\n')
-                            print('Use: help(obj=None, pager=YOURPAGER).\n')
-                            print('For YOURPAGER do not use console editors!\n')
-                            print('---\n\n')
-                            print(hlptxt)
-                        else: subprocess.call([pager, objf])
-                    else:
-                        subprocess.call([pager, objf])
+        pdoc(obj, pager)
+
+
     else:
-        print("Type 'nest.helpdesk()' to access the online documentation "
-              "in a browser.")
+        print("\nType 'nest.helpdesk()' to access the online documentation "
+              "in a browser.\n")
         print("Type 'nest.help(object)' to get help on a NEST object or "
               "command.\n")
         print("Type 'nest.Models()' to see a list of available models "
               "in NEST.\n")
         print("Type 'nest.authors()' for information about the makers "
-              "of NEST.")
+              "of NEST.\n")
         print("Type 'nest.sysinfo()' to see details on the system "
-              "configuration.")
+              "configuration.\n")
         print("Type 'nest.version()' for information about the NEST "
               "version.\n")
         print("For more information visit http://www.nest-simulator.org.")

From 64f18a5de67a299f0589a154ffe40b8e01e82b97 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Tue, 21 Mar 2017 15:49:31 +0100
Subject: [PATCH 06/22] introducing modal window in notebook

---
 pynest/nest/lib/hl_api_helper.py | 99 ++++++++++++++++++++++----------
 pynest/nest/lib/hl_api_info.py   |  9 ++-
 2 files changed, 74 insertions(+), 34 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index dd42045809..e0e8ce53da 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -26,6 +26,7 @@
 
 import warnings
 import inspect
+import json
 import functools
 import textwrap
 import subprocess
@@ -406,35 +407,67 @@ def broadcast(item, length, allowed_types, name="item"):
 def check_nb():
     """Check if is notebook or not
 
+    Parameters
+    ----------
+       
+
     To know a little bit more about the environment use:
 
         jptk = re.findall(r'.*jupyter.*', os.environ['_'])
         iptk = re.findall(r'.*ipython.*', os.environ['_'])
 
+    @author graber
     """
+    # test if notebook in ipython
     try:
         cfg = get_ipython().config
-        if cfg['IPKernelApp']['connection_file']:
-            return True
-        else:
-            return False
+        iptnk = cfg['IPKernelApp']['parent_appname']
     except NameError:
+        iptnk = ''
+    # test if jupyther notebook
+    jpnk = re.findall(r'.*jupyter.*', os.environ['_'])
+    if iptnk == 'ipython-notebook':
+        return True
+    elif jpnk:
+        return True
+    else:
         return False
 
-@check_stack
-def open_window():
-    js = '''
-        <script>
-        var  myWindow = window.open("", "MsgWindow", "width=200,height=100");
-        myWindow.document.write( "
-        <p>This is . I am 200px wide and 100px tall!</p>
-         ");
-        </script>
-        '''
-    print(js)
+
+def open_window(objname, hlptxt):
+    """Open modal window with help text
+
+    Parameters
+    ----------
+    objname :   str
+            filename
+    hlptxt  :   str
+            Full text
+
+    @author graber
+    """
+    hlptxt = json.dumps(hlptxt)
+    style = "<style>.modal-body p { display: block;unicode-bidi: embed; " \
+            "font-family: monospace; white-space: pre; }</style>"
+
+    from IPython.display import HTML, Javascript, display
+    display(HTML(style))
+    display(Javascript("""
+    require(
+        ["base/js/dialog"],
+        function(dialog) {
+            dialog.modal({
+                title: '%s',
+                body: %s,
+                buttons: {
+                    'close': {}
+                }
+            });
+        }
+    );
+    """ % (objname, hlptxt)))
 
 
-@check_stack
 def pdoc(obj, pager):
     """Output of doc in python with pager or print
 
@@ -449,16 +482,20 @@ def pdoc(obj, pager):
     """
     helpdir = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/"
     objname = obj + '.hlp'
+    htmlname = obj + '.html'
+    # @todo more pager
+    consolepager = ['less', 'more', 'vi', 'vim', 'nano', 'emacs -nw',
+                    'ed', 'editor']
 
     # reading ~/.nestrc lookink for pager to use.
     if pager is None:
         # open ~/.nestrc
         rc = open(os.environ['HOME'] + '/.nestrc', 'r')
         for line in rc:
-            rctst = re.match(r'^\s?\%', line)
+            rctst = re.match(r'^\s?%', line)
             if rctst is None:
                 pypagers = re.findall(
-                    r'\s?\/page\s?<<\s?\/command\s?\((.*)\).*', line)
+                    r'\s?/page\s?<<\s?/command\s?\((.*)\).*', line)
                 if pypagers:
                     pager = pypagers[0]
                     break
@@ -475,20 +512,24 @@ def pdoc(obj, pager):
                 fhlp.close()
                 # only for notebook
                 if check_nb():
-                    # @todo more pager
-                    consolepager = ['less', 'more', 'vi', 'vim', 'nano',
-                                    'emacs -nw', 'ed', 'editor']
                     if pager in consolepager:
-                        # only in notebook
-                        print('---\n')
-                        print('Use: help(obj=None, pager=YOURPAGER).\n')
-                        print('For YOURPAGER do not use console editors!\n')
-                        print('---\n\n')
-                        print(hlptxt)
+                        htf = os.path.join(dirpath, htmlname)
+                        fht = open(htf, 'r')
+                        htmltxt = fht.read()
+                        fht.close()
+                        # only in notebook open modal window
+                        open_window(objname, hlptxt)
+                        break
                     else:
-                        subprocess.call([pager, objf])
+                        proc = subprocess.Popen([pager, objf])
+                        break
                 else:
-                    subprocess.call([pager, objf])
+                    if pager in consolepager:
+                        subprocess.call([pager, objf])
+                        break
+                    else:
+                        proc = subprocess.Popen([pager, objf])
+                        break
 
 
 @check_stack
diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index b84ebae7f3..21888f02f4 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -96,18 +96,17 @@ def help(obj=None, pager=None):
 
         pdoc(obj, pager)
 
-
     else:
-        print("\nType 'nest.helpdesk()' to access the online documentation "
-              "in a browser.\n")
+        print("Type 'nest.helpdesk()' to access the online documentation "
+              "in a browser.")
         print("Type 'nest.help(object)' to get help on a NEST object or "
               "command.\n")
         print("Type 'nest.Models()' to see a list of available models "
               "in NEST.\n")
         print("Type 'nest.authors()' for information about the makers "
-              "of NEST.\n")
+              "of NEST.")
         print("Type 'nest.sysinfo()' to see details on the system "
-              "configuration.\n")
+              "configuration.")
         print("Type 'nest.version()' for information about the NEST "
               "version.\n")
         print("For more information visit http://www.nest-simulator.org.")

From 7a3b8f8c06e0d46cb048157952c79df26eab3bbc Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Wed, 22 Mar 2017 07:55:55 +0100
Subject: [PATCH 07/22] better help on pure python level

---
 pynest/nest/lib/hl_api_helper.py | 9 ++++++---
 pynest/nest/lib/hl_api_info.py   | 7 ++++---
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index e0e8ce53da..bb3addf77a 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -426,10 +426,13 @@ def check_nb():
         iptnk = ''
     # test if jupyther notebook
     jpnk = re.findall(r'.*jupyter.*', os.environ['_'])
+    ipjptk = re.findall(r'.*ipython.*', os.environ['_'])
     if iptnk == 'ipython-notebook':
         return True
     elif jpnk:
         return True
+    elif ipjptk:
+        return True
     else:
         return False
 
@@ -468,7 +471,7 @@ def open_window(objname, hlptxt):
     """ % (objname, hlptxt)))
 
 
-def pdoc(obj, pager):
+def pdoc(hlpobj, pager):
     """Output of doc in python with pager or print
 
     Parameters
@@ -481,8 +484,8 @@ def pdoc(obj, pager):
     @author graber
     """
     helpdir = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/"
-    objname = obj + '.hlp'
-    htmlname = obj + '.html'
+    objname = hlpobj + '.hlp'
+    htmlname = hlpobj + '.html'
     # @todo more pager
     consolepager = ['less', 'more', 'vi', 'vim', 'nano', 'emacs -nw',
                     'ed', 'editor']
diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index 21888f02f4..72a5c16c4b 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -90,11 +90,12 @@ def help(obj=None, pager=None):
 
     @author graber
     """
-    if obj is not None:
+    hlpobj = obj
+    if hlpobj is not None:
         # sr("/page << /command (%s) >> SetOptions" % pager)
         # sr("/%s help" % obj)
 
-        pdoc(obj, pager)
+        pdoc(hlpobj, pager)
 
     else:
         print("Type 'nest.helpdesk()' to access the online documentation "
@@ -102,7 +103,7 @@ def help(obj=None, pager=None):
         print("Type 'nest.help(object)' to get help on a NEST object or "
               "command.\n")
         print("Type 'nest.Models()' to see a list of available models "
-              "in NEST.\n")
+              "in NEST.")
         print("Type 'nest.authors()' for information about the makers "
               "of NEST.")
         print("Type 'nest.sysinfo()' to see details on the system "

From 3edd66e8ce70615f2257dec185c8486617a52395 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Wed, 22 Mar 2017 08:07:11 +0100
Subject: [PATCH 08/22] minor helptext edits

---
 pynest/nest/lib/hl_api_helper.py | 23 +++++------------------
 pynest/nest/lib/hl_api_info.py   |  9 +--------
 2 files changed, 6 insertions(+), 26 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index bb3addf77a..bcd9e05c5b 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -406,19 +406,8 @@ def broadcast(item, length, allowed_types, name="item"):
 
 def check_nb():
     """Check if is notebook or not
-
-    Parameters
-    ----------
-       
-
-    To know a little bit more about the environment use:
-
-        jptk = re.findall(r'.*jupyter.*', os.environ['_'])
-        iptk = re.findall(r'.*ipython.*', os.environ['_'])
-
-    @author graber
     """
-    # test if notebook in ipython
+
     try:
         cfg = get_ipython().config
         iptnk = cfg['IPKernelApp']['parent_appname']
@@ -446,9 +435,8 @@ def open_window(objname, hlptxt):
             filename
     hlptxt  :   str
             Full text
-
-    @author graber
     """
+
     hlptxt = json.dumps(hlptxt)
     style = "<style>.modal-body p { display: block;unicode-bidi: embed; " \
             "font-family: monospace; white-space: pre; }</style>"
@@ -476,13 +464,12 @@ def pdoc(hlpobj, pager):
 
     Parameters
     ----------
-    obj : object
+    hlpobj : object
         Object to display
-    ppager: str, optional
+    pager: str, optional
         pager to use, NO if you explicity do not want to use a pager
-
-    @author graber
     """
+
     helpdir = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/"
     objname = hlpobj + '.hlp'
     htmlname = hlpobj + '.html'
diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index 72a5c16c4b..073964537a 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -68,9 +68,6 @@ def helpdesk():
     @author graber
     """
 
-    # sr("/helpdesk << /command (%s) >> SetOptions" % browser)
-    # sr("helpdesk")
-
     url = os.environ['NEST_DOC_DIR'] + "/help/helpindex.html"
     webbrowser.open_new(url)
 
@@ -87,14 +84,9 @@ def help(obj=None, pager=None):
         Object to display help for
     pager : str, optional
         Pager to use
-
-    @author graber
     """
     hlpobj = obj
     if hlpobj is not None:
-        # sr("/page << /command (%s) >> SetOptions" % pager)
-        # sr("/%s help" % obj)
-
         pdoc(hlpobj, pager)
 
     else:
@@ -125,6 +117,7 @@ def get_argv():
     tuple:
         Argv, as seen by NEST.
     """
+
     sr('statusdict')
     statusdict = spp()
     return statusdict['argv']

From 6fe70e5a69d21309debcbd44a732aefe931dcffa Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Thu, 23 Mar 2017 11:19:38 +0100
Subject: [PATCH 09/22] Better check for notebooks

---
 pynest/nest/lib/hl_api_helper.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index bcd9e05c5b..60fa41541b 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -415,6 +415,8 @@ def check_nb():
         iptnk = ''
     # test if jupyther notebook
     jpnk = re.findall(r'.*jupyter.*', os.environ['_'])
+
+    # todo
     ipjptk = re.findall(r'.*ipython.*', os.environ['_'])
     if iptnk == 'ipython-notebook':
         return True
@@ -426,6 +428,13 @@ def check_nb():
         return False
 
 
+def check_nb():
+    try:
+        return get_ipython().__class__.__name__.startswith('ZMQ')
+    except NameError:
+        return False
+
+
 def open_window(objname, hlptxt):
     """Open modal window with help text
 

From 3e710ae97d7bfe423a4844a8c6f0f6cc9a564b01 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Thu, 23 Mar 2017 13:10:35 +0100
Subject: [PATCH 10/22] private functions

---
 pynest/nest/lib/hl_api_helper.py | 98 ++++++++++++--------------------
 pynest/nest/lib/hl_api_info.py   |  2 +-
 2 files changed, 37 insertions(+), 63 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index 60fa41541b..4e02f5d920 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -33,6 +33,8 @@
 import os
 import re
 
+from string import Template
+
 # These variables MUST be set by __init__.py right after importing.
 # There is no safety net, whatsoever.
 sps = spp = sr = pcd = kernel = None
@@ -233,11 +235,11 @@ def stack_checker_func(*args, **kwargs):
         if not get_debug():
             return f(*args, **kwargs)
         else:
-            sr('count')
-            stackload_before = spp()
+            sr
+            stackload_before = spp
             result = f(*args, **kwargs)
-            sr('count')
-            num_leftover_elements = spp() - stackload_before
+            sr
+            num_leftover_elements = spp - stackload_before
             if num_leftover_elements != 0:
                 eargs = (f.__name__, num_leftover_elements)
                 etext = "Function '%s' left %i elements on the stack."
@@ -397,45 +399,21 @@ def broadcast(item, length, allowed_types, name="item"):
     elif len(item) == 1:
         return length * item
     elif len(item) != length:
-        raise TypeError("'%s' must be a single value, a list with " +
-                        "one element or a list with %i elements."
-                        % (name, length))
-
+        raise TypeError("'{0}' must be a single value, a list with " +
+                        "one element or a list with {1} elements.".format(
+                            name, length))
     return item
 
 
-def check_nb():
-    """Check if is notebook or not
-    """
-
-    try:
-        cfg = get_ipython().config
-        iptnk = cfg['IPKernelApp']['parent_appname']
-    except NameError:
-        iptnk = ''
-    # test if jupyther notebook
-    jpnk = re.findall(r'.*jupyter.*', os.environ['_'])
-
-    # todo
-    ipjptk = re.findall(r'.*ipython.*', os.environ['_'])
-    if iptnk == 'ipython-notebook':
-        return True
-    elif jpnk:
-        return True
-    elif ipjptk:
-        return True
-    else:
-        return False
-
-
-def check_nb():
+def __check_nb():
+    """Return true if called from a Jupyter notebook."""
     try:
         return get_ipython().__class__.__name__.startswith('ZMQ')
     except NameError:
         return False
 
 
-def open_window(objname, hlptxt):
+def __show_help_in_modal_window(objname, hlptxt):
     """Open modal window with help text
 
     Parameters
@@ -449,26 +427,28 @@ def open_window(objname, hlptxt):
     hlptxt = json.dumps(hlptxt)
     style = "<style>.modal-body p { display: block;unicode-bidi: embed; " \
             "font-family: monospace; white-space: pre; }</style>"
+    s = Template("""
+       require(
+           ["base/js/dialog"],
+           function(dialog) {
+               dialog.modal({
+                   title: '$jstitle',
+                   body: $jstext,
+                   buttons: {
+                       'close': {}
+                   }
+               });
+           }
+       );
+       """)
 
     from IPython.display import HTML, Javascript, display
     display(HTML(style))
-    display(Javascript("""
-    require(
-        ["base/js/dialog"],
-        function(dialog) {
-            dialog.modal({
-                title: '%s',
-                body: %s,
-                buttons: {
-                    'close': {}
-                }
-            });
-        }
-    );
-    """ % (objname, hlptxt)))
-
-
-def pdoc(hlpobj, pager):
+
+    display(Javascript(s.substitute(jstitle=objname, jstext=hlptxt)))
+
+
+def show_help_with_pager(hlpobj, pager):
     """Output of doc in python with pager or print
 
     Parameters
@@ -481,7 +461,6 @@ def pdoc(hlpobj, pager):
 
     helpdir = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/"
     objname = hlpobj + '.hlp'
-    htmlname = hlpobj + '.html'
     # @todo more pager
     consolepager = ['less', 'more', 'vi', 'vim', 'nano', 'emacs -nw',
                     'ed', 'editor']
@@ -508,16 +487,11 @@ def pdoc(hlpobj, pager):
                 objf = os.path.join(dirpath, objname)
                 fhlp = open(objf, 'r')
                 hlptxt = fhlp.read()
-                fhlp.close()
                 # only for notebook
-                if check_nb():
+                if __check_nb():
                     if pager in consolepager:
-                        htf = os.path.join(dirpath, htmlname)
-                        fht = open(htf, 'r')
-                        htmltxt = fht.read()
-                        fht.close()
                         # only in notebook open modal window
-                        open_window(objname, hlptxt)
+                        __show_help_in_modal_window(objname, hlptxt)
                         break
                     else:
                         proc = subprocess.Popen([pager, objf])
@@ -543,8 +517,8 @@ def get_verbosity():
 
     # Defined in hl_api_helper to avoid circular inclusion problem with
     # hl_api_info.py
-    sr('verbosity')
-    return spp()
+    sr
+    return spp
 
 
 @check_stack
@@ -560,7 +534,7 @@ def set_verbosity(level):
 
     # Defined in hl_api_helper to avoid circular inclusion problem with
     # hl_api_info.py
-    sr("%s setverbosity" % level)
+    sr
 
 
 def model_deprecation_warning(model):
diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index 073964537a..4426fd47e4 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -87,7 +87,7 @@ def help(obj=None, pager=None):
     """
     hlpobj = obj
     if hlpobj is not None:
-        pdoc(hlpobj, pager)
+        show_help_with_pager(hlpobj, pager)
 
     else:
         print("Type 'nest.helpdesk()' to access the online documentation "

From fc66fe263f49248a8a09df685e8235b4ff777e44 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Mon, 3 Apr 2017 10:12:59 +0200
Subject: [PATCH 11/22] Secure environment setting

---
 pynest/nest/lib/hl_api_helper.py | 14 ++++++++++----
 pynest/nest/lib/hl_api_info.py   |  2 --
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index 4e02f5d920..9414fd271d 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -458,8 +458,14 @@ def show_help_with_pager(hlpobj, pager):
     pager: str, optional
         pager to use, NO if you explicity do not want to use a pager
     """
-
-    helpdir = os.environ['NEST_INSTALL_DIR'] + "/share/doc/nest/help/"
+    if 'NEST_INSTALL_DIR' not in os.environ:
+        print(
+            'NEST help needs to know where NEST is installed.'
+            'Please source nest_vars.sh or define NEST_INSTALL_DIR manually.')
+        return
+
+    helpdir = os.path.join(os.environ['NEST_INSTALL_DIR'],
+                           "/share/doc/nest/help/")
     objname = hlpobj + '.hlp'
     # @todo more pager
     consolepager = ['less', 'more', 'vi', 'vim', 'nano', 'emacs -nw',
@@ -494,14 +500,14 @@ def show_help_with_pager(hlpobj, pager):
                         __show_help_in_modal_window(objname, hlptxt)
                         break
                     else:
-                        proc = subprocess.Popen([pager, objf])
+                        subprocess.Popen([pager, objf])
                         break
                 else:
                     if pager in consolepager:
                         subprocess.call([pager, objf])
                         break
                     else:
-                        proc = subprocess.Popen([pager, objf])
+                        subprocess.Popen([pager, objf])
                         break
 
 
diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index 4426fd47e4..16e5a13625 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -25,8 +25,6 @@
 
 from .hl_api_helper import *
 import os
-import re
-import subprocess
 import webbrowser
 
 

From 508c008993a5f2ee9c8768de90ec83b451a9d10c Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Fri, 21 Apr 2017 15:39:13 +0200
Subject: [PATCH 12/22] change from review

---
 pynest/nest/lib/hl_api_helper.py |  8 ++++----
 pynest/nest/lib/hl_api_info.py   | 13 ++++++++-----
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index 9414fd271d..6b96617d55 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -464,8 +464,8 @@ def show_help_with_pager(hlpobj, pager):
             'Please source nest_vars.sh or define NEST_INSTALL_DIR manually.')
         return
 
-    helpdir = os.path.join(os.environ['NEST_INSTALL_DIR'],
-                           "/share/doc/nest/help/")
+    helpdir = os.path.join(os.environ['NEST_INSTALL_DIR'], "share", "doc",
+                           "nest", "help")
     objname = hlpobj + '.hlp'
     # @todo more pager
     consolepager = ['less', 'more', 'vi', 'vim', 'nano', 'emacs -nw',
@@ -500,14 +500,14 @@ def show_help_with_pager(hlpobj, pager):
                         __show_help_in_modal_window(objname, hlptxt)
                         break
                     else:
-                        subprocess.Popen([pager, objf])
+                        subprocess.call([pager, objf])
                         break
                 else:
                     if pager in consolepager:
                         subprocess.call([pager, objf])
                         break
                     else:
-                        subprocess.Popen([pager, objf])
+                        subprocess.call([pager, objf])
                         break
 
 
diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index 16e5a13625..ee61dacb55 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -24,6 +24,7 @@
 """
 
 from .hl_api_helper import *
+import sys
 import os
 import webbrowser
 
@@ -62,12 +63,14 @@ def helpdesk():
 
     The system default browser.
     /helpdesk << /command (firefox) >> SetOptions in ~/.nestrc is now obsolete
-
-    @author graber
     """
-
-    url = os.environ['NEST_DOC_DIR'] + "/help/helpindex.html"
-    webbrowser.open_new(url)
+    url = os.path.join(os.environ['NEST_DOC_DIR'] + "help", "helpindex.html")
+    if sys.platform[:3] == "win":
+        os.startfile(url)
+    if sys.platform[:3] == "dar":
+        webbrowser.get('safari').open_new(url)
+    else:
+        webbrowser.open_new(url)
 
 
 @check_stack

From 5d47a8032aa0119b219b25f50eadc269a94d41a2 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Thu, 4 May 2017 09:47:22 +0200
Subject: [PATCH 13/22] Right URL for nest.helpdesk()

---
 pynest/nest/lib/hl_api_info.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index ee61dacb55..7231a38b61 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -64,7 +64,7 @@ def helpdesk():
     The system default browser.
     /helpdesk << /command (firefox) >> SetOptions in ~/.nestrc is now obsolete
     """
-    url = os.path.join(os.environ['NEST_DOC_DIR'] + "help", "helpindex.html")
+    url = os.path.join(os.environ['NEST_DOC_DIR'] + "/help", "helpindex.html")
     if sys.platform[:3] == "win":
         os.startfile(url)
     if sys.platform[:3] == "dar":

From 4e124a39dcb1cec87c86c1db5eaf9f3fbffb72d6 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Wed, 31 May 2017 13:00:15 +0200
Subject: [PATCH 14/22] Drop todo

pager list seems to be complete
---
 pynest/nest/lib/hl_api_helper.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index 6b96617d55..4e07d6369a 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -467,7 +467,6 @@ def show_help_with_pager(hlpobj, pager):
     helpdir = os.path.join(os.environ['NEST_INSTALL_DIR'], "share", "doc",
                            "nest", "help")
     objname = hlpobj + '.hlp'
-    # @todo more pager
     consolepager = ['less', 'more', 'vi', 'vim', 'nano', 'emacs -nw',
                     'ed', 'editor']
 

From 13caa6487231fc0e64ab8158ef27f977cd3c5cf3 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Wed, 31 May 2017 13:01:11 +0200
Subject: [PATCH 15/22] Insert  inline documentation

---
 pynest/nest/lib/hl_api_info.py | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index 7231a38b61..2e99b8ed85 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -61,12 +61,25 @@ def authors():
 def helpdesk():
     """Open the NEST helpdesk in browser.
 
-    The system default browser.
-    /helpdesk << /command (firefox) >> SetOptions in ~/.nestrc is now obsolete
+    Use the system default browser.
     """
+    if 'NEST_DOC_DIR' not in os.environ:
+        print(
+            'NEST help needs to know where NEST is installed.'
+            'Please source nest_vars.sh or define NEST_DOC_DIR manually.')
+        return
+
     url = os.path.join(os.environ['NEST_DOC_DIR'] + "/help", "helpindex.html")
+    """
+    Under Windows systems webbrowser.open is incomplete 
+    <https://bugs.python.org/issue8232>
+    """
     if sys.platform[:3] == "win":
         os.startfile(url)
+    """
+    Under MacOs we need to ask for the browser explicitly. 
+    See <https://bugs.python.org/issue30392>.
+    """
     if sys.platform[:3] == "dar":
         webbrowser.get('safari').open_new(url)
     else:

From 89a5abe7e6492f20e8464beccaded2dd29691cf2 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Wed, 31 May 2017 13:11:59 +0200
Subject: [PATCH 16/22] Set default browser to 'more'

---
 pynest/nest/lib/hl_api_helper.py | 2 +-
 pynest/nest/lib/hl_api_info.py   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index 4e07d6369a..0e0f672685 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -483,7 +483,7 @@ def show_help_with_pager(hlpobj, pager):
                     pager = pypagers[0]
                     break
                 else:
-                    pager = 'less'
+                    pager = 'more'
         rc.close()
 
     for dirpath, dirnames, files in os.walk(helpdir):
diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index 2e99b8ed85..1dca2a7bbc 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -90,7 +90,7 @@ def helpdesk():
 def help(obj=None, pager=None):
     """Show the help page for the given object using the given pager.
 
-    The default pager is less.
+    The default pager is more.
 
     Parameters
     ----------

From 148fdb585d9f26c642e2511bdf21c68066a7830f Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Wed, 31 May 2017 15:04:16 +0200
Subject: [PATCH 17/22] Better .nesrc handling

---
 pynest/nest/lib/hl_api_helper.py | 31 ++++++++++++++++++-------------
 1 file changed, 18 insertions(+), 13 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index 0e0f672685..66cefd2a92 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -472,19 +472,24 @@ def show_help_with_pager(hlpobj, pager):
 
     # reading ~/.nestrc lookink for pager to use.
     if pager is None:
-        # open ~/.nestrc
-        rc = open(os.environ['HOME'] + '/.nestrc', 'r')
-        for line in rc:
-            rctst = re.match(r'^\s?%', line)
-            if rctst is None:
-                pypagers = re.findall(
-                    r'\s?/page\s?<<\s?/command\s?\((.*)\).*', line)
-                if pypagers:
-                    pager = pypagers[0]
-                    break
-                else:
-                    pager = 'more'
-        rc.close()
+        # check if .netsrc exist
+        rc_file = Path(os.environ['HOME'] + '/.nestrc')
+        if os.path.isfile(rc_file):
+            # open ~/.nestrc
+            rc = open(os.environ['HOME'] + '/.nestrc', 'r')
+            for line in rc:
+                rctst = re.match(r'^\s?%', line)
+                if rctst is None:
+                    pypagers = re.findall(
+                        r'^\s?/page\s?<<\s?/command\s?\((\S*)', line)
+                    if pypagers:
+                        pager = pypagers[0]
+                        break
+                    else:
+                        pager = 'more'
+            rc.close()
+        else:
+            pager = 'more'
 
     for dirpath, dirnames, files in os.walk(helpdir):
         for hlp in files:

From 4642c8df860296eaa6613589b00ae0da666681d5 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Thu, 1 Jun 2017 09:56:23 +0200
Subject: [PATCH 18/22] Better inline documentation

---
 pynest/nest/lib/hl_api_info.py | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index 1dca2a7bbc..448da950fc 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -70,16 +70,14 @@ def helpdesk():
         return
 
     url = os.path.join(os.environ['NEST_DOC_DIR'] + "/help", "helpindex.html")
-    """
-    Under Windows systems webbrowser.open is incomplete 
-    <https://bugs.python.org/issue8232>
-    """
+
+    # Under Windows systems webbrowser.open is incomplete
+    # See <https://bugs.python.org/issue8232>
     if sys.platform[:3] == "win":
         os.startfile(url)
-    """
-    Under MacOs we need to ask for the browser explicitly. 
-    See <https://bugs.python.org/issue30392>.
-    """
+
+    # Under MacOs we need to ask for the browser explicitly.
+    # See <https://bugs.python.org/issue30392>.
     if sys.platform[:3] == "dar":
         webbrowser.get('safari').open_new(url)
     else:

From ee5b97dd79a51dddc9ee901e996d733e02fed47a Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Thu, 1 Jun 2017 10:00:31 +0200
Subject: [PATCH 19/22] Improvement of calling the help

---
 pynest/nest/lib/hl_api_helper.py | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index 66cefd2a92..98b7e5603c 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -473,7 +473,7 @@ def show_help_with_pager(hlpobj, pager):
     # reading ~/.nestrc lookink for pager to use.
     if pager is None:
         # check if .netsrc exist
-        rc_file = Path(os.environ['HOME'] + '/.nestrc')
+        rc_file = os.environ['HOME'] + '/.nestrc'
         if os.path.isfile(rc_file):
             # open ~/.nestrc
             rc = open(os.environ['HOME'] + '/.nestrc', 'r')
@@ -481,19 +481,24 @@ def show_help_with_pager(hlpobj, pager):
                 rctst = re.match(r'^\s?%', line)
                 if rctst is None:
                     pypagers = re.findall(
-                        r'^\s?/page\s?<<\s?/command\s?\((\S*)', line)
+                        r'^\s?/page\s?<<\s?/command\s?\((\w*)', line)
                     if pypagers:
-                        pager = pypagers[0]
+                        for pa in pypagers:
+                            if pa:
+                                pager = pa
+                            else:
+                                pager = 'more'
                         break
                     else:
                         pager = 'more'
             rc.close()
         else:
             pager = 'more'
-
+    hlperror = True
     for dirpath, dirnames, files in os.walk(helpdir):
         for hlp in files:
             if hlp == objname:
+                hlperror = False
                 objf = os.path.join(dirpath, objname)
                 fhlp = open(objf, 'r')
                 hlptxt = fhlp.read()
@@ -502,17 +507,23 @@ def show_help_with_pager(hlpobj, pager):
                     if pager in consolepager:
                         # only in notebook open modal window
                         __show_help_in_modal_window(objname, hlptxt)
+                        fhlp.close()
                         break
                     else:
                         subprocess.call([pager, objf])
+                        fhlp.close()
                         break
                 else:
                     if pager in consolepager:
                         subprocess.call([pager, objf])
+                        fhlp.close()
                         break
                     else:
                         subprocess.call([pager, objf])
+                        fhlp.close()
                         break
+    if hlperror == True:
+        print("Sorry, there is no help for '" + hlpobj + "'!")
 
 
 @check_stack

From 42da7c34b4fc6d0d5650ea58d3de9ba1cd162952 Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Thu, 1 Jun 2017 10:22:10 +0200
Subject: [PATCH 20/22] PEP 8

---
 pynest/nest/lib/hl_api_helper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index 98b7e5603c..29d5c77ef4 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -522,7 +522,7 @@ def show_help_with_pager(hlpobj, pager):
                         subprocess.call([pager, objf])
                         fhlp.close()
                         break
-    if hlperror == True:
+    if hlperror is True:
         print("Sorry, there is no help for '" + hlpobj + "'!")
 
 

From b82fa50502457995f2dd118a2918c61993d4d57c Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Wed, 7 Jun 2017 15:19:47 +0200
Subject: [PATCH 21/22] Documentation

---
 pynest/nest/lib/hl_api_helper.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index 29d5c77ef4..198115616e 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -476,10 +476,17 @@ def show_help_with_pager(hlpobj, pager):
         rc_file = os.environ['HOME'] + '/.nestrc'
         if os.path.isfile(rc_file):
             # open ~/.nestrc
-            rc = open(os.environ['HOME'] + '/.nestrc', 'r')
+            rc = open(rc_file, 'r')
+            # The loop goes through the .nestrc line by line and checks
+            # it for the definition of a pager. Whether a pager is
+            # found or not, this pager is used or the standard pager 'more'.
             for line in rc:
+                # the re checks if there are lines beginning with '%'
                 rctst = re.match(r'^\s?%', line)
                 if rctst is None:
+                    # the next re checks for a sth. like
+                    # '/page << /command (more)'
+                    # and returns the given pager.
                     pypagers = re.findall(
                         r'^\s?/page\s?<<\s?/command\s?\((\w*)', line)
                     if pypagers:
@@ -495,6 +502,8 @@ def show_help_with_pager(hlpobj, pager):
         else:
             pager = 'more'
     hlperror = True
+    # Searching the given object in all helpfiles, check the environment
+    # and display the helptext in the pager.
     for dirpath, dirnames, files in os.walk(helpdir):
         for hlp in files:
             if hlp == objname:
@@ -522,7 +531,7 @@ def show_help_with_pager(hlpobj, pager):
                         subprocess.call([pager, objf])
                         fhlp.close()
                         break
-    if hlperror is True:
+    if hlperror:
         print("Sorry, there is no help for '" + hlpobj + "'!")
 
 

From a86a32cf75c7fbc46f1d744782054a8a6b29f7cc Mon Sep 17 00:00:00 2001
From: steffen <s.graber@fz-juelich.de>
Date: Fri, 9 Jun 2017 10:54:05 +0200
Subject: [PATCH 22/22] Removed string concatenation

Minor Fix.
---
 pynest/nest/lib/hl_api_helper.py | 2 +-
 pynest/nest/lib/hl_api_info.py   | 9 +++++----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/pynest/nest/lib/hl_api_helper.py b/pynest/nest/lib/hl_api_helper.py
index 198115616e..4ad8a798ba 100644
--- a/pynest/nest/lib/hl_api_helper.py
+++ b/pynest/nest/lib/hl_api_helper.py
@@ -473,7 +473,7 @@ def show_help_with_pager(hlpobj, pager):
     # reading ~/.nestrc lookink for pager to use.
     if pager is None:
         # check if .netsrc exist
-        rc_file = os.environ['HOME'] + '/.nestrc'
+        rc_file = os.path.join(os.environ['HOME'], '.nestrc')
         if os.path.isfile(rc_file):
             # open ~/.nestrc
             rc = open(rc_file, 'r')
diff --git a/pynest/nest/lib/hl_api_info.py b/pynest/nest/lib/hl_api_info.py
index 448da950fc..9d3da1db75 100644
--- a/pynest/nest/lib/hl_api_info.py
+++ b/pynest/nest/lib/hl_api_info.py
@@ -69,19 +69,20 @@ def helpdesk():
             'Please source nest_vars.sh or define NEST_DOC_DIR manually.')
         return
 
-    url = os.path.join(os.environ['NEST_DOC_DIR'] + "/help", "helpindex.html")
+    helpfile = os.path.join(os.environ['NEST_DOC_DIR'], 'help',
+                            'helpindex.html')
 
     # Under Windows systems webbrowser.open is incomplete
     # See <https://bugs.python.org/issue8232>
     if sys.platform[:3] == "win":
-        os.startfile(url)
+        os.startfile(helpfile)
 
     # Under MacOs we need to ask for the browser explicitly.
     # See <https://bugs.python.org/issue30392>.
     if sys.platform[:3] == "dar":
-        webbrowser.get('safari').open_new(url)
+        webbrowser.get('safari').open_new(helpfile)
     else:
-        webbrowser.open_new(url)
+        webbrowser.open_new(helpfile)
 
 
 @check_stack