Merge branch 'notebook_interface' into develop

Author: ptooley

bin/ipynb_to_report

@@ -9,6 +9,7 @@ output_filename="$(echo ${report_nb} | sed 's/ /_/g' | sed 's/.ipynb$//').tex"
 export TEXINPUTS="${template_dir}//:"
 
 jupyter nbconvert "${report_nb}" \
+                  --execute \
                   --to latex \
                   --template=${template_dir}/pop_report.tplx \
                   --output=${output_filename}

ipython_templates/pop_report.tplx

@@ -26,7 +26,7 @@
 ## Input necessary details from ipynb metadata
 ((* block maketitle *))
 
-  ((* for item in ['reprefnum', 'title', 'servicelevel', 'author', 'contributors'] *))
+  ((* for item in ['reprefnum', 'title', 'author', 'contributors'] *))
     \((( item ))){((( nb.metadata.get("pop_metadata", {}).get(item, '\color{{red}} pop\_metadata.{} NOT SET'.format(item))
                   )))}
   ((* endfor *))

pypop/__init__.py

@@ -12,8 +12,6 @@
 
 from .version import get_version
 
-__all__ = ['__version__']
+__all__ = ["__version__"]
 
 __version__ = get_version()
-
-

pypop/cli.py

@@ -5,8 +5,19 @@
 """CLI Analysis scripts"""
 
 from os import getcwd
-from os.path import expanduser, join as path_join, normpath
+from os.path import (
+    exists as path_exists,
+    expanduser,
+    isabs,
+    join as path_join,
+    normpath,
+    realpath,
+    relpath,
+)
+from pkg_resources import resource_filename
 from shutil import copytree, Error as shutil_error
+from webbrowser import open_new_tab
+import sys
 
 from matplotlib import use
 
@@ -17,10 +28,31 @@
 from pypop.dimemas import dimemas_idealise
 from pypop.config import set_dimemas_path, set_paramedir_path, set_tmpdir_path
 from pypop.examples import examples_directory
+from pypop.server import get_notebook_server_instance, construct_nb_url
 
 from argparse import ArgumentParser
 from tqdm import tqdm
 
+import nbformat
+
+latest_nbformat = getattr(nbformat, "v{}".format(nbformat.current_nbformat))
+new_nb = latest_nbformat.new_notebook
+code_cell = latest_nbformat.new_code_cell
+md_cell = latest_nbformat.new_markdown_cell
+
+GUI_MSG = """
+        PyPOP GUI Ready:
+        If the gui does not open automatically, please go to the following url
+        in your web browser:
+
+        {}
+"""
+
+OWN_SERVER_MSG = """
+        A new notebook server was started for this PyPOP session.  When you are finished,
+        press CTRL-C in this window to shut down the server.
+"""
+
 
 def _dimemas_idealise_parse_args():
 
@@ -133,6 +165,10 @@ def _preprocess_traces_parse_args():
     parser.add_argument(
         "--dimemas-path", type=str, metavar="PATH", help="Path to Dimemas executable"
     )
+
+    parser.add_argument(
+        "--tag", type=str, metavar="TAG", help="Tag to apply to trace(s)"
+    )
     parser.add_argument(
         "--outfile-path",
         type=str,
@@ -274,6 +310,7 @@ def preprocess_traces():
         force_recalculation=config.force_recalculation,
         chop_to_roi=config.chop_to_roi,
         outpath=config.outfile_path,
+        tag=config.tag,
     )
 
 
@@ -322,3 +359,127 @@ def copy_examples():
     except shutil_error as err:
         print("Copy failed: {}".format(str(err)))
         return -1
+
+
+def _gui_launcher_parse_args():
+
+    # make an argument parser
+    parser = ArgumentParser(description="Launch the PyPOP GUI and Notebook server")
+
+    # First define collection of traces
+    parser.add_argument(
+        "nb_path",
+        type=str,
+        nargs="?",
+        metavar="NB_PATH",
+        help="GUI Notebook name/path default is $PWD/pypop_gui.ipynb",
+    )
+    parser.add_argument(
+        "-n",
+        "--notebookdir",
+        type=str,
+        metavar="NB_DIR",
+        help="Notebook server root directory (default is $PWD or inferred from "
+        "NB_PATH), ignored if an existing server is used",
+    )
+    parser.add_argument(
+        "-f",
+        "--force-overwrite",
+        action="store_true",
+        help="Overwrite existing file when creating GUI notebook.",
+    )
+
+    return parser.parse_args()
+
+
+def _gui_exit(msg, own_server):
+    print(msg, file=sys.stderr)
+    if own_server:
+        own_server.kill()
+    sys.exit(-1)
+
+
+def pypop_gui():
+    """Entrypoint for launching Jupyter Notebook GUI
+    """
+
+    config = _gui_launcher_parse_args()
+
+    notebookdir = getcwd()
+    nb_name = "pypop_gui.ipynb"
+    if config.notebookdir:
+        notebookdir = realpath(notebookdir)
+
+    nb_path = realpath(path_join(notebookdir, nb_name))
+    if config.nb_path:
+        if isabs(config.nb_path):
+            if relpath(realpath(config.nb_path), notebookdir):
+                gui_exit(
+                    "Requested gui notebook file path is not in the notebook server "
+                    "directory ({}).".format(config.nb_path, notebookdir),
+                    None,
+                )
+            nb_path = os.realpath(config.nb_path)
+        else:
+            nb_name = os.realpath(join(notebookdir, config.nb_path))
+
+    server_info, own_server = get_notebook_server_instance()
+
+    real_nbdir = realpath(server_info["notebook_dir"])
+    if relpath(nb_path, real_nbdir).startswith(".."):
+        _gui_exit(
+            "Requested gui notebook file path {} is not in the root of the "
+            "notebook server ({}). You may need to specify a different working "
+            "directory, change the server config, or allow PyPOP to start its own "
+            "server.".format(nb_path, real_nbdir),
+            own_server,
+        )
+
+    if not path_exists(nb_path) or config.force_overwrite:
+        try:
+            write_gui_nb(nb_path)
+        except:
+            _gui_exit("Failed to create gui notebook", own_server)
+
+    nb_url = construct_nb_url(server_info, nb_path)
+
+    open_new_tab(nb_url)
+
+    print(GUI_MSG.format(nb_url))
+
+    if own_server:
+        print(OWN_SERVER_MSG)
+        try:
+            own_server.wait()
+        except KeyboardInterrupt:
+            own_server.terminate()
+
+
+def hidden_code_cell(*args, **kwargs):
+
+    hidden_cell = {"hide_input": True}
+
+    if "metadata" in kwargs:
+        kwargs["metadata"].update(hidden_cell)
+    else:
+        kwargs["metadata"] = hidden_cell
+
+    return code_cell(*args, **kwargs)
+
+
+def write_gui_nb(gui_nb_path):
+
+    gui_nb = new_nb(metadata={})
+
+    gui_code = """\
+from pypop.notebook_interface import MetricsWizard
+from pypop.metrics import MPI_OpenMP_Metrics
+gui = MetricsWizard(MPI_OpenMP_Metrics)
+display(gui)\
+    """
+    gui_cells = [(gui_code, hidden_code_cell)]
+
+    for cell_text, cell_ctr in gui_cells:
+        gui_nb.cells.append(cell_ctr(cell_text))
+
+    nbformat.write(gui_nb, gui_nb_path)

pypop/config.py

@@ -7,7 +7,7 @@
 
 from os.path import normpath, expanduser
 
-__all__ = ['set_paramedir_path', 'set_dimemas_path', 'set_tmpdir_path']
+__all__ = ["set_paramedir_path", "set_dimemas_path", "set_tmpdir_path"]
 
 _dimemas_path = None
 _paramedir_path = None

pypop/dimemas.py

@@ -59,9 +59,7 @@ def dimemas_idealise(tracefile, outpath=None):
 
     # Pass trace, run config and path to idealisation skeleton config and let
     # dimemas_analyze work its subtle magic(k)s
-    return dimemas_analyse(
-        tracefile, IDEAL_CONF_PATH, outpath, subs
-    )
+    return dimemas_analyse(tracefile, IDEAL_CONF_PATH, outpath, subs)
 
 
 def dimemas_analyse(tracefile, configfile, outpath=None, substrings=None):
@@ -93,7 +91,7 @@ def dimemas_analyse(tracefile, configfile, outpath=None, substrings=None):
 
     # Perform all work in a tempdir with predictable names,
     # this works around a series of weird dimemas bugs
-    
+
     # Make sure config._tmpdir_path exists before using it
     if config._tmpdir_path:
         try:
@@ -142,7 +140,7 @@ def dimemas_analyse(tracefile, configfile, outpath=None, substrings=None):
     # Now create the dim file for dimemas
     tmp_dim = os.path.join(workdir, splitext(basename(tmp_prv))[0] + ".dim")
 
-    prv2dim_binpath = 'prv2dim'
+    prv2dim_binpath = "prv2dim"
     if config._dimemas_path:
         prv2dim_binpath = os.path.join(config._dimemas_path, prv2dim_binpath)
 
@@ -165,7 +163,7 @@ def dimemas_analyse(tracefile, configfile, outpath=None, substrings=None):
     except Exception as err:
         raise RuntimeError("prv2dim execution_failed: {}".format(err))
 
-    dimemas_binpath = 'Dimemas'
+    dimemas_binpath = "Dimemas"
     if config._dimemas_path:
         dimemas_binpath = os.path.join(config._dimemas_path, dimemas_binpath)
 
@@ -228,4 +226,4 @@ def dimemas_analyse(tracefile, configfile, outpath=None, substrings=None):
     shutil.rmtree(workdir, ignore_errors=True)
 
     # finally return outpath as promised
-    return os.path.join(outpath,filestem + ".sim.prv")
+    return os.path.join(outpath, filestem + ".sim.prv")