Installation using Anaconda and Git

Using Anaconda Prompt (Windows) or Terminal (Mac)...

> git clone https://github.com/asmith-whoi/cg_inst_automation.git

A new folder will be created with the required files and folder structure.

> cd cg_inst_automation

Set up the software environment...

> conda env create -f instruments.yml

Activate the new environment...

> conda activate instruments

If you encounter any problems during the installation or setup, try updating conda.

Usage

Calling the program from the command line is the best way to run the program. If using Anaconda, be sure the instruments environment is configured and activated.

(instruments) cg_inst_automation> python main.py

Adding Instruments

A new instrument may be added to the program as either a python package or a module. A package is best for supporting many varied actions and procedures, but is more complex to create. A module may be easier if very little code will be required.

Templates for both are located in the cg_inst_automation/instruments folder.

The module template

Duplicate _inst_mod_template.py and rename it to {instrument}.py with the name of the instrument, e.g. dosta.py for a DOSTA instrument. Use all lower case letters, with no spaces. The name you give the file will be used to automatically generate the program's interactive menus.

Common code

To access the program's common code, uncomment the common and instrumentbase import statements...

from common import common
from instrumentbase import Instrument

If you will be assigning your instrument to one of the program's existing instrument subclasses, uncomment the subclass import statement and replace {subclass} with the name of the desired subclass...

from common.{subclass}_common import {subclass}_instrument

Define a new class for the new instrument. Uncomment the following lines, and replace _Template with the name of the instrument, exactly as you named the file with the first letter capitalized, e.g. class Dosta(Instrument) for a DOSTA instrument. If you chose to make the new instrument part of an existing subclass above, replace Instrument with the subclass name as used in the import statement...

class _Template(Instrument):
    # class variables common to all {instrument}
    proctypes = ['{proc1}', '{proc2}'...]

Edit the proctypes list in the above block to include all the procedures for the new instrument that will appear in the program's interactive menus. Replace {proc1}, etc. with the names of these procedures.

Add your code to define these procedures as methods of the new class.

The package template

Duplicate the _inst_pkg_template directory and rename it to {instrument} with the name of the instrument, e.g. dosta for a DOSTA instrument. Use all lower case letters, with no spaces. The name you give the directory will be used to automatically generate the program's interactive menus.

The init.py file

The init.py file must be present in the new instrument's directory. Edit this file's contents, replacing {instrument} with the name of the instrument, as above. Replace {Instrument}, capitalizing the first letter.

The _inst_template.py file

Rename the _inst_template.py file exactly as you named the package, e.g. dosta.py for a DOSTA instrument.

To access the program's common code, uncomment the common and instrumentbase import statements...

from common import common
from instrumentbase import Instrument

If you will be assigning your instrument to one of the program's existing instrument subclasses, uncomment the subclass import statement and replace {subclass} with the name of the desired subclass...

from common.{subclass}_common import {subclass}_instrument

Define a new class for the new instrument. Uncomment the following lines, and replace _Template with the name of the instrument, exactly as you named the file with the first letter capitalized, e.g. class Dosta(Instrument) for a DOSTA instrument. If you chose to make the new instrument part of an existing subclass above, replace Instrument with the subclass name as used in the import statement...

class _Template(Instrument):
    # class variables common to all {instrument}
    proctypes = ['{proc1}', '{proc2}'...]

Edit the proctypes list in the above block to include all the procedures for the new instrument that will appear in the program's interactive menus. Replace {proc1}, etc. with the names of these procedures.

Add your code to define these procedures as methods of the new class.

You may create separate modules to contain your code for each procedure. To do this, name the modules exactly as you named the corresponding procedure in the proctypes list. Uncomment and edit the last import statement at the top of the template file to import the modules when the package is loaded.

You may add as many modules to the package as you wish. They do not need to be added to the proctypes list unless you wish for them to appear in the program's interactive menus.