Fix failing unit tests.

[joaander]

Description

Use a for loop to run nbconvert once in each directory.

For unknown reasons, the behavior of nbconvert changed preventing the use of **/*.ipynb in one call. It reported:

ValueError: Conversion would override an already generated output. This is probably due to --output or output_base configuration leading to non-unique output names. Output notebook names were: ['00-index', '01-The-Simulation-Object', '02-Performing-Hard-Particle-Monte-Carlo-Simulations', '03-Initializing-the-System-State', '04-Randomizing-the-System', '05-Compressing-the-System', '06-Equilibrating-the-System', '07-Analyzing-Trajectories', '00-index', '01-Molecular-Dynamics-Simulations', '02-Initializing-a-Random-System', '03-Compressing-the-System', '00-index', '01-Logging-to-a-GSD-file', '02-Saving-Array-Quantities', '03-Storing-Particle-Shape', '04-Writing-Formatted-Output', '00-index', '01-Introduction-to-MPI', '02-Domain-Decomposition', '03-Accessing-System-Configurations-With-MPI', '04-Running-Multiple-Simulations-With-Partitions', '00-index', '01-What-are-Actions', '02-An-Initial-Custom-Action', '03-Custom-Action-Features', '04-Custom-Updater', '05-Custom-Writer', '06-Improving-Performance', '00-index', '01-Organizing-Data', '02-Executing-Simulations', '03-Continuing-Simulations', '04-Submitting-Cluster-Jobs', '00-index', '01-Introduction-to-Rigid-Bodies', '02-Running-Rigid-Body-Simulations', '03-Preparing-a-General-Body', '00-index', '01-Kern-Frenkel-Model', '02-Simulating-a-System-of-Patchy-Particles', 'create-figures']

Checklist:

• [x] I have reviewed the Contributor Guidelines.
• [x] I agree with the terms of the HOOMD-blue Contributor Agreement.
• [x] My name is on the list of authors.

[joaander]

Indeed. I have tested the signac tutorials on trunk-major and they execute successfully. I will leave trunk alone for now as we will soon release HOOMD v4.0 and merge trunk-major into trunk.