2. Unit testing added to repository and increased to 100% code coverage.
Badges have also been implemented so users can monitor success rate.
Codecoverage is picked up from travis and compiled at
https://coveralls.io/github/HECBioSim/Longbow.
3. Automated running of code quality checks is now triggered via github
pushes and is done at https://landscape.io/github/HECBioSim/Longbow
The actual changes to the code are:
1. Added in some extra commonly found naming for GROMACS executables
(gmx_mpi and gmx_mpi_d).
2. Bugs detected in shellwrappers.py during unit test writing have now
been fixed.
3. Fixed formatting issue with logging in staging.py -
stage_downstream()
4. Removed import statements for relative imports, this eliminated the
need for the try/except imports at the top of each code module.
5. The parameter "frequency" has been split into two parameters
"polling-frequency" and "staging-frequency". This enables the user to
have Longbow poll jobs without staging all the time.
6. The timing mechanism for timing between polling events has now been
changed from a disruptive wait() to a timestamp comparison. This stops
the process being "blocked" by wait() and in future will allow the
addition of other features that can happen on different timelines to
polling.
7. There are now two steps to job completion, instead of marking a job
as finished when it is finished on the remote host and results
downloaded, Longbow will now mark at as finished as it is finished on
the remote host and then once staging has happened it will then be
marked as complete.
8. Fixed glitch in applications.py processjobs() where the wrong
comparitor was used on the if statement to construct the upload include
list
9. Huge refactoring of code to break down larger methods into smaller
easier to test methods. All new methods are private methods (starting
with "_") these should not be used by people making use of Longbow in
their own code, unless they know what they are doing!
10. Moved all code for Longbow entrypoints out of the executable and
into corelibs/entrypoints.py, this allows more options for integration
and also simplifies it somewhat since the library top level can now be
imported from the library (otherwise hooking against the executable or
copying the code into a project was the only way).
11. The plugin framework no longer has a complicated path such as
plugins/apps/gromacs.py, now two directories "apps" and "schedulers" sit
at the same level as corelibs in the library. This removed most of the
complexity in the import system, now it is a very simple and elegant way
to provide plugins for these two categories.
12. Fixed the problem of returning information upon job submission
error, this was a typo in each of the scheduler plugins.
13. Fix for strange job status glitch when jobid appeard in say a
timestamp or some other parameter in the output of qstat etc, this has
been fixed across all schedulers.
14. Fixed spacing problem in some generated job submit files.
15. Modification into the way command-lines are parsed, this is so that
the detection of executables and their commands as well as Longbow
commands is much more robust and can now handle arbitrary executables.
16. Addition of --nochecks command-line flag, this will disable testing
whether the application is available on the remote host. In some
circumstances it is very difficult to get Longbow to recognise an
application is installed. This is aimed at advanced users only.
17. all parameters in the main entry point that were previous passed
into longbow have now all been assimilated into one dictionary
"parameters" this then allowed refactoring all the switch cases for
command-line parameters into a much neater single method.
18. Fix for problem detected during unit test writing for
configurations.py saveconfigs() where if used incorrectly would blow up.
19. Fixed problem in applications.py causing failed run under python 3.2
20. Fix for filenaming glitch when using global files in replicates.
21. Fixed problem where if required files were not found this was
ignored but should have been flagged up.
22. Fixed a number of bad initialisers that would cause filenames to go
missing.
23. legacy code in status method in all schedulers removed.
24. Fixed freezing glitch when all jobs failed to submit.
25. Fixed bad parameter in substitutions.