# Recipes¶

This is a collection of recipes on how to solve typical problems using signac.

## How to migrate (change) the data space schema.¶

Oftentimes, one discovers at a later stage that important keys are missing from the metadata schema. For example, in the tutorial we are modeling a gas using the ideal gas law, but we might discover later that important effects are not captured using this overly simplistic model and decide to replace it with the van der Waals equation:

$\left(p + \frac{N^2 a}{V^2}\right) \left(V - Nb \right) = N k_B T$

Since the ideal gas law can be considered a special case of the equation above with $$a=b=0$$, we could migrate all jobs with:

>>> for job in project:
...     job.sp.setdefault('a', 0)
...     job.sp.setdefault('b', 0)
...


The setdefault() function sets the value for $$a$$ and $$b$$ to 0 in case that they are not already present.

• To delete a key use del job.sp['key_to_be_removed'].
• To rename a key, use job.sp.new_name = job.sp.pop('old_name').

Note

The job.sp and job.doc attributes provide all basic functions of a regular Python dict.

### Initializing Jobs with Replica Indices¶

If you want to initialize your workspace with multiple instances of the same statepoint, you may want to include a replica_index or random_seed parameter in the statepoint.

num_reps = 3
for i in range(num_reps) :
for p in range(1, 11):
sp = {'p': p, 'kT': 1.0, 'N': 1000, "replica_index": i}
job = project.open_job(sp)
job.init()


### Apply document-wide changes¶

The safest approach to apply multiple document-wide changes is to replace the document in one operation. Here is an example on how we could recursively replace all dot (.)-characters with the underscore-character in all keys [1]:

import signac
from collections.abc import Mapping

def migrate(doc):
if isinstance(doc, Mapping):
return {k.replace('.', '_'): migrate(v) for k, v in doc.items()}
else:
return doc

for job in signac.get_project():
job.sp = migrate(job.sp)
job.doc = migrate(job.doc)


This approach makes it also easy to compare the pre- and post-migration states before actually applying them.

 [1] The use of dots in keys is deprecated. Dots will be exclusively used to denote nested keywords in the future.

## How to initialize with replica indices¶

We often require multiple jobs with the same statepoint to collect enough information to make statistical inferences about the data. Instead of creating multiple projects to handle this, we can simply add a replica_index to the statepoint. For example, we can use the following code to generate 3 copies of each statepoint in a workspace:

# init.py
import signac

project = signac.init_project('ideal-gas-project')
num_reps = 3

## How to run in containerized environments¶

Using signac-flow in combination with container systems such as docker or singularity is easily achieved by modifying the executable directive. For example, assuming that we wanted to use a singularity container named software.simg, which is placed within the project root directory, we use the following directive to specify that a given operation is to be executed within then container:

@Project.operation
@flow.directives(executable='singularity exec software.simg python')
def containerized_operation(job):
pass


If you are using the run command for execution, simply execute the whole script in the container:

\$ singularity exec software.simg python project.py run


Attention

Many cluster environments will not allow you to submit jobs to the scheduler using the container image. This means that the actual submission, (e.g. python project.py submit or similar) will need to be executed with a local Python executable.

To avoid issues with dependencies that are only available in the container image, move imports into the operation function. Condition functions will be executed during the submission process to determine what to submit, so depedencies for those must be installed into the local environment as well.

Tip

You can define a decorator that can be reused like this:

def on_container(func):
return flow.directives(executable='singularity exec software.simg python')(func)

@on_container
@Project.operation
def containerized_operation(job):
pass