The signac-flow package follows semantic versioning.

Version 0.6

Major changes

  1. The generation of execution and submission scripts is now based on the jinja2 templating system.
  2. The new decorator API for the definition of a FlowProject class largely reduces the amount of boiler plate code needed to implement FlowProjects. It also removes the necessity to have at least two modules, e.g., one and one module.
  3. Serial execution is now the default for all project sub commands, that includes run, script, and submit. Parallel execution must be explicitly enabled with the --parallel option.
  4. The run command executes all eligible operations, that means you don’t have to run the command multiple times to “cycle” through all pending operations. Accidental infinite loops are automatically avoided.
  5. Execution scripts generated with the script option are always bundled. The previous behavior, where the script command would print multiple scripts to screen unless the --bundle option was provided did not make much sense.

See the full changelog below for detailed information on all changes.

How to migrate existing projects

If your project runs with flow 0.5 without any DeprecationWarnings (that means no messages when running Python with the -W flag), then you don’t have to do anything. Version 0.6 is mostly backwards compatible to 0.5, with the execption of custom script templating.

Since 0.6 uses jinja2 to generate execution and submission scripts, the previous method of generating custom scripts by overloading the FlowProject.write_script*() methods is now deprecated. That means that if you overloaded any of these functions, the new templating system is disabled, and flow will fallback to the old templating system and you won’t be able to use jinja2 templates.

If you decide to migrate to the new API, those are the steps you most likely have to take:

  1. Replace all write_script*() methods and replace them with a custom template script, e.g., templates/ within your project root directory.
  2. Optionally, use the new decorator API instead of FlowProject.add_operation to add operations to your FlowProject.
  3. Optionally, use the new decorator API to define label functions for your FlowProject.
  4. Execute your project with the Python -w option to make DeprecationWarnings visible and address all issues.

We recommend to go through the tutorial on signac-docs to learn how to best take advantage of flow 0.6.

[0.6.4] – 2018-12-28

  • Add the @with_job decorator that allows the definition of operations to take place within the job context. Works with @cmd.
  • Add the not_ condition prefix to negate condition functions.
  • Add the false condition prefix as analogue to the true condition prefix.
  • Add support for the Summit supercomputer (U.S. DOE, Oak Ridge National Laboratory) and Ascent testing cluster.
  • Add support for the IBM LSF scheduler.
  • Add warning about explicitly set, but unused directives during submission.
  • Add official support for Python version 3.7.
  • Fix issue where the status sub-command ignored the –show-traceback option.
  • Fix SLURM scheduler driver to show full error message in case that submission with squeue failed.
  • Better specification of (optional) dependencies in and requirements.txt.
  • Overall revision of all cluster submission templates; improved structure and abstraction of logic.
  • The serialization of operations was improved to optimize execution speed for local runs.
  • The evaluation of pre- and post-conditions was optimized for optimally lazy evaluation: cheaper conditions should be placed above more expensive conditions for maximal performance.
  • When gathering operations, signac will automatically use the buffered mode when config value ‘flow.use_buffered_mode’ is set to True (requires signac >= 0.9.3).
  • Improved documentation for developers and contributors.

[0.6.3] – 2018-08-22

  • Fix issue related to dynamic data spaces, that means data spaces where jobs are either added, removed, or changed during the execution of the workflow. Specifically, flow will now execute operations also for jobs that were added during execution.
  • Fix issue where command line options would be ignored when provided before the sub-command.
  • Fix issue where the table symbols in the –stack –pretty view were swapped.

[0.6.2] – 2018-08-11

  • Increase performance of condition evaluation (switch from eager to lazy evaluation). Speeds up detailed status update and run/script/submit sub commands.
  • Fix issue with the detailed status update failing on older Python versions (#29).
  • Fix issue with the XSEDE Bridges template in combination with GPU operations.

[0.6.1] – 2018-07-01

  • Add the -v/--verbosity and --show-traceback option to the project interface, which allows for more fine-grained control over the message verbosity. The --debug option is now equivalent to -vv --show-traceback.
  • The message verbosity of the project class was overall reduced.
  • Global options including (--debug and --verbose) can be used at any place within the project command and must no longer be placed before the sub command, e.g., the following commands are equivalent: $ python run --debug and $ python --debug run.
  • Implement the -p/--parallel option for the project run command.
  • Use cloudpickle when encountering pickling issues during parallel execution (when installed).
  • Implement the status --ignore-errors option.
  • Handle changes to the project data space during running execution, e.g., removed jobs.
  • Print the operation.cmd attribute to screen in run --pretend mode, not repr(operation).
  • Show progressbar while gathering pending operations.

[0.6.0] – 2018-05-24

Major updates and new features

  • Use jinja2 as templating engine for the generation of execution and submission scripts.
  • Add decorator API for the definition of FlowProject operations and label functions.
  • Revise the status view to render on a per job-operation basis, not on a per job basis.
  • The <project> run function executes all pending operations, not just the next pending ones.
  • The <project> script function no longer supports explicit bundling, all operations are bundled by default.
  • The default execution mode for script and submission script bundling is serial, not parallel.
  • Add the operations directive parameter, which provides a more generalized interface to specify required resources or other execution related metadata.
  • Add support for XSEDE Stampede2.
  • Add simple-scheduler, for local testing of scheduled workflows.
  • Allow the override of the detected environment with the SIGNAC_FLOW_ENVIRONMENT variable.
  • The $ flow init commad initializes the signac project if not project is found.

API changes (breaking)

  • The method arguments were changed [1]; the old API is better supported by the new FlowProject.run_operations() function.
  • The FlowProject.submit() and .submit_operations() method arguments were changed [1].
  • The JobOperation constructor arguments were changed; the old API ist still supported.

API changes (non-breaking)

  • Unify the job and operation selection API for the run/script/submit commands.
  • Add FlowProject.operation() decorator function.
  • Add FlowProject.label() docorator function.
  • The FlowProject.write_human_readable_statepoints() method is deprecated.
  • All FlowProject methods relating to the old templating system are deprecated, that includes all write_script*() methods.
  • Add flow.cmd decorator function.
  • Add flow.directives decorator function.

[1] A reasonable attempt to support legacy API use is made, but may fail under some circumstances.

Version 0.5

[0.5.6] – 2018-02-22

  • Fix issue, where operations with spaces in their name would not be accepted by the SLURM scheduler.
  • Add environment profile for XSEDE Bridges.
  • Update the environment profile for XSEDE comet to use the shared queue by default and provide options to specify the memory allocation.
  • Improve performance of the project update status function.

[0.5.5] – 2017-10-05

  • Fix issue with the SLURM scheduler, where the queue status could not be parsed.

[0.5.4] – 2017-08-01

  • Fix issue with <project> run, where operation commands consist of multiple shell commands.
  • Fix issue where the <project> status output showed negative values for the number of lines omitted (issue #12).
  • Raise error when trying to provide a timeout for <project> run in serial execution in combination with Python 2.7; this mode of execution is not supported for Python versions 2.7.x.
  • Enforce that the <project> status –overview-max-lines (-m) argument is positive.

[0.5.3] – 2017-07-18

  • Fix issue where the return value of FlowProject.next_operation() is ignored in combination with the <project> submit / run / script interface.

[0.5.2] – 2017-07-12

  • Fix bug in detailed status output in combination with unhashable types.
  • Do not fork when executing only a single operation with
  • Run all next operations for each job with instead of only one of the next operations.
  • Gather all next operations when submitting, instead of only one of the nex operations for each job.

[0.5.1] – 2017-06-08

  • Exclude private functions, that means functions with a name that start with an underscore, from the operations listing when using
  • Forward all extra submit arguments into the write_script() methods.
  • Fix an issue with $flow init/flow.init() in combination with Python 2.7.

[0.5.0] – 2017-05-24

Major updates and new features

  • The documentation has been completely revised; most components are now covered by a reference documentation; the reference documentation serves also as basic tutorial.
  • The signac-flow package now officially supports Python version 2.7 in addition to versions 3.4+; the support for version 3.3 has been dropped.
  • Add comand line interface for instances of FlowProject, to be accessed via the FlowProject.main() function. This makes it easier to interact with specific workflow implementations on the command line, for example to view the project’s status, execute operations or submit them to a scheduler.
  • The $ flow init command initializes a new very lean workflow module that replaces the need to use project templates. Setting up a workflow with signac-flow is now much easier; template projects are no longer needed. The $ flow init command can be invoked with an optional -t/–template argument to initialize project modules with example code.
  • Add the function to turn python modules that implement functions to be used as data space operations into executables. Executing the function opens a command line interface that can be used to execute operations defined within the same module directly from the command line in serial and parallel.
  • The definition of operations on the project level is now possible via the FlowProject.operations dictionary; operations can either be added directly or via the FlowProject.add_operation() function.
  • Environment with torque or slurm scheduler are now immediately supported via a default environment profile.
  • The submission process is generally streamlined and it is easier to forward arguments to the underlying scheduler; this is is supposed to enable the user to directly submit scripts and operations without the need to setup a custom environment profile.
  • Some environment profiles for large cluster environments are bundled with the package; it is no longer needed to install external packages to be able to use profiles on some HPC resources.

API changes (breaking)

  • The use of JobScript.write_cmd() with an np argument is pending deprecation, the adjustment of commands to the local environment is moved to an earlier stage (for instance, during project instance construction).
  • The official project template is still functional via a legacy API layer, however it is recommended that users update projects to use with this version; the update process is described in the README document.
  • Most of the environment specific command line arguments are now directly provided by the environment profile via profile specific add_parser_args() functions; that means that existing environment might be require some tweaking to work with this version.

Version 0.4

[0.4.2] – 2017-02-28

  • Fix issue in the submit legacy mode, the write_header() method was previously ignored.

[0.4.1] – 2017-02-24

  • Fix ppn issue when submitting in legacy mode.
  • Enable optional parallelization during submit.

[0.4.0] – 2017-02-23

Major revision to the job-operation submission function.

  • The write_user() function has been replaced by submit_user() with slightly adjusted API.
  • The header and environment module have been merged into a single environment module.
  • All submit logic has been removed from the scheduler drivers.
  • Any submit logic implemented as part of the environment module has been reduced to the bare minimum.
  • The submission flow has been refactored to be based on JobOperations.
  • An attempt is made to detect the use of the deprecated API which will trigger the use of a legacy code path and the emission of warnings.
  • Improved testing capabilities for unknown environments.
  • The determination of present environments is deterministic and based on reversed definition order.
  • Add the label decorators, allowing a more concise definition of methods which are to be used for classification.
  • Add the FlowGraph, which allows the user to implement workflows in form of a graph.
  • Implement unit tests for all core functionalities.