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Python3 includes the venv module for virtual environments. We should use this to simplify installation.

See #48

There are significant differences between the ConfigParser for Python 2.7 and Python 3.X. The handling of multiple values is one of them. The v3 ConfigParser first reads in the values and then resets them using _join_multiline_values(). This interferes with the proxy Section used in Pyre to set paths and track the location of settings. Currently, we overwrite this method in pyre.inventory.cfg.Parser and raise an exception if we encounter a value that is a list.

The way to resolve this is to reimplement _join_multiline_values() so that it handles the multiline values without messing up the registry that tracks the paths and location of where values were set.

Create unit tests for Pyre inventory.

See #5.

Inventory

• bool
• int
• float
• string
• dimensional
• list
• InputFile
• OutputFile
• facility
• array of facilities

Functionality

• defaults
• override defaults using command line arguments
• override defaults using .cfg file
• override defaults using pml file

pryre_doc [--short] MODULE|CLASS

For modules show module help and help on class of same name if it exists. For a class show help for properties and facilities if corresponding methods exist.

Create unit tests for Pyre application.

See #5.

Create unit tests for journal.

See #5.

Before converting code to Python 3, we need unit tests for the functionality that we use, so that we can verify the conversion doesn't break anything.

Functionality that needs unit tests:

• Journal
• MPI
• Pyre units
• Pyre inventory
• Pyre application
• Pyre schedulers

Python packaging continues to undergo significant changes. The "new" preferred mechanism (PEP 517) puts all packages into the destination directory. As a result, all pythia packages (pyre, journal, mpi, etc) are not listed under a pythia directory. This could result in naming conflicts, for example multiple mpi or journal packages.

Proposed change: Move all current packages under a top-level pythia directory so that they become submodules of the pythia package.

This alleviates the dependency of the tests on nemesis/mpinemesis.

Preparation for conversion to Python 3 (Issue #4).

The factory keyword is used to bind a default component to a facilityArray. Within a .cfg file or on the command line, we can assign an array of components, but we cannot assign a single component acting as the array.

Example

A materials array with a default factory creating an array with one facility.

Ok: Use the default

materials.homogeneous = materials.Elastic

Ok: Create array of two materials.

materials = [one, two]
materials.one = materials.Elastic
materials.two = materials.Plastic

Fails: Replace default factory with another factory.

materials = materials.ElasticPlastic

# This is interpreted as materials = [materials.ElasticPlastic]

Create unit tests for Pyre units.

See #5.

Create unit tests for Pyre schedulers.

See #5.

Create unit tests for Python/MPI interface.

See #5.

Need to convert to Python 3 before end of life for Python v2.

Pyre currently has implementations for the LSF, PBS, and SGE batch schedulers. We should also have an implementation for the SLURM batch scheduler.

The schedulers are in the pyre/schedulers directory.

Having an inadvertent space at the beginning of a line in a .cfg file specifying a facility (not a property) generates a very vague, difficult to understand error message:

 >> {command line}::
 >> pyre.inventory(error)
 -- 'str' object has no attribute 'append'
pylithapp: configuration error(s)

This could be an error in generating the error message.