== Tutorial to aid adding a new e2program to the e2projectmanager.py ==
This tutorial covers the necessary steps to incorporate a e2program into the projectmanager.
=== Modifications to the e2program itself ===
Canonical e2programs must maintain the following standards
 1. Options are handled via EMArgumentParser, which is a subclass of Python's argparse module (version 2.7 and higher). For more information on argparse, see the python documentation. [[http://docs.python.org/dev/library/argparse.html]]
 1. Arguments are handled via EMArgumentParser.
 1. A line usage = """blah, blah, blah...""" must be present to give help info on the e2program
 1. A line progname = os.path.basename(sys.argv[0]) must be present

To illustrate what an e2program should look like, here is an example program: 
{{{#!highlight python
#!/usr/bin/env python
#
# GPL licensing info goes here
#

from EMAN2 import *

def main():
    progname = os.path.basename(sys.argv[0])
    usage = """prog arg1, arg2, [options] 
            This is an example program """

    parser = EMArgumentParser(usage=usage,version=EMANVERSION)
    parser.add_argument("--option1",type=str,help="This is the first option",default="myvalue")
    parser.add_argument("--option2",type=int,help="This is the second option",default=1)
    parser.add_argument("--option3",type=float,help="This is the third option",default=3.14)
    parser.add_argument("--option4",action="store_true",help="This is the fourth option",default=False)

    (options, args) = parser.parse_args()

    print "Arguments are", args
    print "Options are", options

if __name__ == __main__:
    main()
}}}

To enable this program to be integrated into the GUI the following item must be implemented:
 1. For each argument you must add the method: parser.add_pos_argument()
 1. To add dividing lines with help info into the GUI, add the method: parser.add_header()
 1. The option PPID must be added to enable cross platform PPID support
 1. To all parser  'add' methods the following keyword arguments must be added
 1. guitype="", this specifies what type of widget we want to use for this GUI
 1. row="", this specifies what row the widget should appear in
 1. col="", this specifies what column the widget should appear in
 1. rowspan="", this specifies how many rows the widget should span
 1. colspan="", this specifies how many columns the widget should span
 1. browser="", if the widget represents and option that refers to a file, this keyword argument lists a filebrowser to use.

To illustrate how to integrate the above example e2program int the GUI, the following example is given:
{{{#!highlight python
#!/usr/bin/env python
#
# GPL licensing info goes here
#

from EMAN2 import *

def main():
    progname = os.path.basename(sys.argv[0])
    usage = """prog arg1, arg2, [options] 
            This is an example program """

    parser = EMArgumentParser(usage=usage,version=EMANVERSION)
    #For the add_pos_Argument() and add_header() methods, you must add the name="" keyword argument. For the add_argument() method, the 'name' is taken from the --option argument
    parser.add_pos_argument(name="argument1",help="First argument, this will be a file", default="", guitype='filetype', browser="EMBrowserWidget(withmodal=True,multiselect=True)", row=0, col=0,rowspan=1,colspan=2)
    parser.add_header(name="header1", help="Use the header to display useful info in the GUI", title="### Actual info goes here ###", row=1, col=0,rowspan=1,colspan=2)
    parser.add_argument("--option1",type=str,help="This is the first option",default="myvalue",guitype='strbox', row=2,col=0,rowspan=1,colspan=1)
    parser.add_argument("--option2",type=int,help="This is the second option",default=1,guitype='intbox',row=2,col=1,rowspan=1,colspan=1)
    parser.add_argument("--option3",type=float,help="This is the third option",default=3.14,guitype='floatbox',row=3,col=0,rowspan=1,colspan=1)
    parser.add_argument("--option4",action="store_true",help="This is the fourth option",default=False,guitype='boolbox',row=3,col=1,rowspan=1,colspan=1)
    # This is needed by all e2programs that run on the GUI
    parser.add_argument("--ppid",type=int,help="Set the PID of the parent process, used for cross platform PPID",default=-1)
    (options, args) = parser.parse_args()

    print "Arguments are", args
    print "Options are", options

if __name__ == __main__:
    main()
}}}

=== Modification of the workflow JSON file ===
If your program is for single particle applications, modify the spr.json file found in /libEM/pmconfig. If your program is for tomographic applications, modify tomo.json file.

For example the spr.json will look something like this.
{{{#!highlight python
  {
    "ICON": "ctf", 
    "TABLE": "EMCTFcorrectedParticlesTable(withmodal=False,multiselect=True)", 
    "NAME": "CTF", 
    "CHILDREN": [
      {
        "ICON": "ctf", 
        "PROGRAM": "e2ctf.py",
        "MODE": "autofit",
        "WIKIPAGE": "http://blake.bcm.tmc.edu/emanwiki/EMAN2/Programs/e2ctf",
        "NAME": "Automated Fitting -e2ctf", 
	"NOTELEVEL": "1",
        "CHILDREN": []
      }, 
      {
        "ICON": "ctf", 
        "PROGRAM": "e2ctf.py",
	"MODE": "tuning", 
        "WIKIPAGE": "http://blake.bcm.tmc.edu/emanwiki/EMAN2/Programs/e2ctf",
        "NAME": "Interactive Tuning -e2ctf", 
        "CHILDREN": []
      }, 
      {
        "ICON": "ctf", 
        "PROGRAM": "e2ctf.py", 
        "MODE": "genoutp",
        "WIKIPAGE": "http://blake.bcm.tmc.edu/emanwiki/EMAN2/Programs/e2ctf",
        "NAME": "Generate Output - e2ctf", 
	"NOTELEVEL": "1",
        "CHILDREN": []
      }, 
      {
        "ICON": "ctf", 
        "PROGRAM": "e2ctf.py", 
        "MODE": "gensf",
        "WIKIPAGE": "http://blake.bcm.tmc.edu/emanwiki/EMAN2/Programs/e2ctf",
        "NAME": "Generate Structure Factor - e2ctf", 
	"NOTELEVEL": "1",
        "CHILDREN": []
      }
    ]
  },
}}}

Adding your new e2program is quite straight forward. To the JSON file just add(as a child in a CHILDREN list), in the appropriate location:
{{{#!highlight python
      {
        "ICON": "single boxes", 
        "PROGRAM": "e2myprogram.py", 
        "NAME": "Do some stuff - e2myprogram", 
        "CHILDREN": []
      }
}}}

There are multiple other options, such as Wizard, Expert, etc. For a list and explanation see: [[EMAN2/Programs/e2projectmanager]]