The four main commands are

Check the help screen for usage info:

$ cln help
Computational Lab Notebooks


CLI to help you manage a lab notbook with git and git-annex.

=== subcommands ===

  init     Initialize a new project
  prepare  Prepare an action
  remove   Remove a pending action
  run      Run an action
  version  print version information
  help     explain a given subcommand (perhaps recursively)

Initialize a new project

To initialize a new project/lab notebook use cln init. The cln app is a wrapper on git and git-annex, so your project lives in a certain directory. That directory is the one in which you run the cln init command!

There is nothing magical about the cln init command. It sets up the required directories, makes a file, and then sets up a new git and git-annex repository.

After you run cln init, you are ready to start getting some real work done!


To view the usage screen, run cln help init or cln init -help.

$ cln help init
Initialize a new project

  cln init PROJECT_NAME

=== info ===

Initialize a new computational lab notebook project using git and

For more info, see

=== flags ===

  [-help]  print this help text and exit
           (alias: -?)


First make a new directory and cd into it.

$ mkdir my_project && cd my_project

Then initialize a new project called My Project.

$ cln init 'My Project'

Notice how I put the My Project bit inside single quote characters (')? If your project name has spaces, you need to remember to quote it!


  • If you run cln init in a directory that already has a git repository, you will get an error.

Prepare an action

To prepare an action or command to run, use the cln prepare command.

This creates a new action file (i.e., bash script) and a git commit template in the <project_root>/.actions/pending directory.

When I say "action", I just mean, something (e.g., a shell script) that will change the state of the repository (aka your lab notebook). The reason we formalize these things as actions is that it makes it a lot easier to figure out what happened in your project/repository a couple of months down the line when you come back to it.


To vier the usage screen, run cln help prepare or cln prepare -help.

$ cln help prepare
Prepare an action

  cln prepare ACTION

=== info ===

Generates an action file and a git commit template in the
'<project_root>/.actions/pending' directory.

For more info, see

=== flags ===

  [-help]  print this help text and exit
           (alias: -?)


Prepare a shell command to run:

$ cln prepare 'echo "hello, world" > hello.txt'

Rather than running echo "hello, world" > hello.txt yourself, "preparing" the command sets it up so that you have a way to run the command that makes it easier to remember what you did a few months/years down the line.

What files were created?

Action file

You have the action file (aka bash script):

$ cat .actions/pending/
/usr/bin/echo "hello, world" > hello.txt

The first weird number in the file name is a hash code representing the contents of the file. The second is the date and time in which you prepared the command.

Commit template

And you have the git commit template. Git commit templates are a nice way to help you write good commit messages with as little annoyance as possible.

$ cat .actions/pending/action__262765981__2021-04-09_14:54:48.gc_template.txt

== Details ==

== Command(s) ==
/usr/bin/echo "hello, world" > hello.txt

== Action file ==

Notice how the prepared action and the action file are automatically included in the commit template? This is really helpful for when you're going back searching through the commit logs. It will give you context of the exact command that was run connected with the exact changes it produced in any of the files included in your repository.

After you run the action, add the changes to git and then go to actually commit the changes, you can use the commit template like this:

$ git commit -t .actions/pending/action__262765981__2021-04-09_14:54:48.gc_template.txt

This will open up a text editor with the contents of that file. Then you just have to edit the summary message and the details. For the summary, just put a short < 50 character explanation of what you did. For the details, try and put as much info and context as you will need to figure out what you did and why you did it. Basically, you should put the sort of things here that you would be putting in your lab notebook anyway.


If you try and prepare an action when there is already a pending action, you will get an error. It's set up this way to encourage you to set up a single action, run it (which then changes the state of your repository, then commit those changes to the repository. So it's like 1 action <=> 1 commit.

Run an action

To run an action, use the cln run command.

This will look for a valid pending action, and if it finds one, runs it with bash. If it succeeds, then the program will also move the action into the <project_root>/.actions/completed directory.

  • You will get an error if there are no pending actions.
  • If there are more than one pending action, you will also get an error.
  • The cln prepare command won't let you make more than one pending action.
  • But even if you make an extra "by-hand" with the format exactly correct, the cln run command still won't let you run it if there are more than one.

Dry run

To do a "dry run", i.e., to have the cln prepare program just tell you what it will do without actually running any actions, you can use the -dry-run flag. Here is an example:

$ cln run -dry-run

You will see some useful output. Check it out and make sure it looks good. If so, then you can run the action.

While the -dry-run is totally optional, I recommend that you do a dry run before running the action so you can check that you haven't made any obvious mistakes!

A note on exit codes

To determine wether an action has failed or succeeded, we check the exit codes.

  • Exit code of 0 means success.
  • Any other exit code means failure.

Let's say that you prepared an action to run some bash script that you have written like this:

printf "Starting script!\n"

## This command will fail.
cat this_file_doesnt_exist.txt > new_file.txt

## But the script will keep going and run this, which will succeed.
printf "All done!\n"

If you ran this at the command line with bash, you would get this:

$ bash
Starting script!
cat: this_file_doesnt_exist.txt: No such file or directory
All done!

Do you think it "succeeded"? Let's check the exit code.

$ echo $?

According to the exit code, yes, the script as a whole succeeded. But if you check the contents of new_file.txt you will see that it is empty, which is probably not what you wanted! So what happened is that an intermediate command failed, but given the way the script was written, the script as a whole succeeded.

How to fix it

This is something you will want to watch out for. If this were run as an action by cln run, the cln program would consider this program a success and move the action into the completed directory.

If you have scripts like this that run lots of commands, you should consider breaking them up. That way you stick to the one action, one commit principal mentioned above.

If you really want a multi-command bash script

In some cases, you may need more than one command, e.g., when something only makes sense if something succeeds first. In that case, you can join the commands with &&. Let's try that on the previous example.

printf "Starting script!\n" && \
  cat this_file_doesnt_exist.txt > new_file.txt && \
  printf "All done!\n"

And run that.

$ bash
Starting script!
cat: this_file_doesnt_exist.txt: No such file or directory

See how the last printf command was not run? Let's check the exit code again.

$ echo $?

That's a failing exit code. So, the cln run program would consider that script to have failed.

Remove an action

Sometimes you need to remove pending actions:

  • You made a mistake when prepping the action.
  • You don't need that action anymore.
  • There was an error when running the action.
  • Whatever!

The point is that you sometimes will want to delete actions! The way that the cln program currently works is that you can only ever have one pending action at a time. So if you have messed something up and need to get rid of the action, you will need to remove it. To do this, we use the cln remove program.

Deleting, failing, or ignoring actions

There are three ways to "remove" a pending action:

  • Deleting it
  • Marking it as "failed" (aka failing the action)
  • Marking it as "ignored" (aka ignoring the action)

Of these three only deleting truly deletes the action data. (And even then, if you've already checked it into your git repository you will still be able to get it back.)

"Failing" an action means moving the action (and its associated git commit template) out of the .actions/pending directory and into the .actions/failed directory.

"Ignoring" an action is similar to "failing" an action except that the pending action is moved to the .actions/ignored directory rather than the .actions/failed directory.

The reason for this distinction is to help you when you're going back through your history and commit logs. I.e., it will give you more context as to why a pending action was no longer necessary.

Specifying the method

You specify the method you want to use with the -method flag like this

  • Delete: cln remove -method delete
  • Fail: cln remove -method fail
  • Ignore: cln remove -method ignore

Saving the results in the git repo

After you run the cln remove command you will see some output suggesting how to proceed. You may see something like this:

~~~ * Check which files have changed:
~~~     $ git status
~~~ * Add actions and commit templates (I know it says add--it means "track this change with git"):
~~~     $ git add .actions
~~~ * After "adding" files, commit changes:
~~~     $ git commit

As you can see, you still need to let git know that you have moved the actions around and commit the changes.

Manually removing actions

Like many of the cln commands, you could just do this "by-hand". Currently, the cln remove command is a pretty thin wrapper around what you would probably do by hand, but it does give you some nice messages on what you may want to do next and it does some sanity checking on your pending actions to make sure nothing has gotten crazy in the meantime.