ciak 0.1.0.dev0

Run executables according to a configuration file

README/DOCUMENTATION IS WORK IN PROGRESS

ciak is a Python program that runs executables according to a configuration file (a ciakfile) that optional contains user-declared variables which can be adjusted at runtime.

A ciakfile is a simple text file that describes a nested tree using asterisks and that has placeholders for runtime-controllable variables, supporting defaults. Thanks to the nested tree structure, the amount of typing required is drastically reduced when the same commands have to be executed multiple times but with different arguments. On the other hand, support for placeholders allows for code reuse and the same ciakfile can be used for different situations. This is facilitated by the fact that if you define an environmental variable CIAKFILE_DIR, ciak will know where to look for your ciakfiles, so you can call them from anywhere in your system. Finally, in ciakfiles, every line that does not start with an asterisk (up to leading spaces) is treated as a comment. With this feature, one can write extensive commentaries that perfectly blend in with the configuration itself.

For an example of use case, see the section "Complete explanation of a specific use case" [TODO: Add link here]. See below for an example of what a configuration file looks like.

Installation

ciak is available on PyPI. You can install it with pip:

pip3 install ciak

ciak requires Python3.9 and has no external dependency. See ciak36 [TODO: ADD LINK HERE] for compatibility with previous versions of Python.

Why should I use ciak instead of a shell script?

At a first glance, ciak may seem just a convoluted way to write a shell script. This is not the case: ciak enables workflows that are impractical with shell script. The main advantages of ciak are:

• Simplify repeated arguments across multiple scripts
• Use keyword arguments
• Have parallelization with no effort
• Strong emphasis on self-documentation

However, by design, ciak does not support any shell feature (like input/output redirection, for loops, variable assignment, ...).

ciak36

ciak uses features available only with Python3.9 or later versions. For convenience, an executable ciak36 is provided, compatible with Python3.6. There is no difference in features available between ciak and ciak36. ciak36 is automatically generated by ciak with the generate_ciak36.sh script. ciak36 will be dropped in the future.

The ciakfile configuration syntax

Valid ciakfiles are text files with the following characteristics:

• Lines that do no start with asterisk (up to initial spaces) are considered comments.
• The number of asterisks defines the level in the three and the parent of an item is the first item with fewer asterisk above it.
• Executables have to be on the first level of the tree.
• Placeholders can be defined with the syntax {{key::default_value}}. These will be substituted at runtime with values specified via command-line or with the default value.
• Indentation, leading/trailing spaces, and file extension do not matter.

Examples

A simple ciakfile is

* ls {{pwd::/tmp}}

Assuming we save the file to ciak1.org, we can then run

ciak -c ciak1.org --pwd $HOME

This will execute the command ls $HOME. If we were to run

ciak -c ciak1.org

then the default value for pwd is used and the command ls /tmp is run instead.

In a more slightly interesting example, we want to compress different files. This can be achieved with

* gzip
** file1
** file2
** file3
** file4

Saving this as ciak2.org, running

ciak -c ciak2.org --parallel

will correspond to running gzip file1, gzip file2, ..., using as many processes as the number of cores available, as requested by the --parallel flag.

ciak and org-mode

ciak borrows its syntax from GNU Emacs's org-mode . As such, if you save your ciakfiles with extension .org and you open them with Emacs, you gain access to a large number of additional features (e.g., automatic coloring and indentation, subtree folding, tables, exporting to different formats, ...). This is what an example of a ciakfile will look like in (customized) Emacs

Using org-mode greatly enhances ciak's self-documenting capabilities.

Options

--fail-fast, if enabled, ciak stops as soon as a non-zero return code is found.

--parellel, if enabled, the commands are executed in parallel with a number of workers that is equal to the number of available cores on the machine.

Development

We use:

• Poetry to manage dependencies, build, and publish motionpicture.
• Black for formatting the code (with 89 columns).
• pytest for unit tests (with pytest-cov for test coverage).
• mypy for static type analysis.
• GitHub actions for continuous integration.

We are happy to accept contributions.

What does ciak mean?

In Italian, the word ciak is an onomatopoeia that indicates the sound of the clapperboard used by movie directors to kick off the recording of a scene. Along the same lines, when you use this program, you are the script-writer and the director: you define what needs to be run in the ciakfile and you start and control its execution with ciak, your clapperboard.

Going over a specific use case

ciak was developed to run analysis of Einstein Toolkit simulations using kuibit. ciak solves four problems:

1. Simplification in writing the analysis
2. Reuse of the code
3. Reproducibility and self-documentation in the analysis
4. Parallelization of analysis

Normally, one runs several simulations of the same kind when only a few parameters are changed.

Distributing the ciakfile along with the scripts that are called allows other people to easily reproduce the analysis. The comments in the ciakfile are helpful to explain what is going on and why certain values are set at the values they are set.