Longbow v1.5.2

The changes in this release are summarised below:

1. Bug fix - OMP environment variable added to all schedulers to fix a specific
   set of user reported issues (issue #114).

2. Bug fix - Further PBS and NAMD SMP issues relating to under subscription,
   users had to do a hacky way by dropping the corespernode parameter to under
   subscribe which resulted in errors from the scheduler. Now users wishing to
   do this should set mpiprocs in their job or host conf files to do this (issue #105).

3. Bug fix - The memory parameter only worked with the PBS scheduler, this has
   now been extended to work in all schedulers (issue #98).

4. Bug fix - The --maxtime parameter went missing from the --help output (issue #96).

5. Doc fix - The documentation for the recovery mode was incorrect (issue #102).

6. New feature - An update mode has been added so that users doing
   disconnectable sessions can simply run an update to get the current
   simulation status and download a snapshot of the data (issue #61).

7. New feature - Move documentation to be under version control, using sphinx
   and readthedocs for auto documentation assembly. Documentation can then
   become part of the CI cycle and thus be enforced on code contribution (issue #90).

8. Enhancement - users can now explicitly set the filenames of stderr and
   stdout from the scheduler script using the parameters "stdout = filename"
   and "stderr = filename" in their host of job conf files (issue #108).

9. Enhancement - Users can now make use of existing job scripts, by providing
   the name of the script to the parameter "subfile" in their host or job conf
   files. This mode is mainly aimed at advanced users that understand the short
   falls of doing this and the problems that could occur (issue #77).

10. Enhancement - Users can now set the naming scheme of the replicate
    directories. Instead of having to provide directories of the form
    rep1, rep2, ...., repx. Users can now set the name of the "rep" part by
    setting the "replicate-naming" parameter. So "replicate-naming = foo"
    would need directories named foo1, foo2, ...., foox (issue #92).

11. Enhancement - Documentation for the examples have been cleaned up and added
    to the new sphinx docs (issue #10).

12. Enhancement - Refactor the exception code in the top level API methods to
    remove duplication (issue #44).

13. Removed support for Python versions 2.6, 3.2 and 3.3 due to these versions
    being old unsupported versions and various python packages such as
    pip/ci-tools withdrawing support. Longbow may still work for these versions
    but this is no longer guaranteed (issue #113).

Longbow v1.5.1

The changes in this release are summarised below:

1. Bug fix - a number of parameters that are only used in specific scheduler or application plugins have been renamed to include the plugin name prefix (issue #54)

2. Bug fix - executables expressed as absolute paths for supported plugins would cause a crash due to searching for a module with that key. (issue #63)

3. Bug fix - wrong error message was displayed when an executable didn't exist on HPC machine (issue #65)

4. Bug fix - fix for crash when using NAMD SMP builds, the commandline parameters beginning with "+" would trigger the crash (issue #66)

5. Bug fix - fixed misleading error messages about missing files and flags (issue #67)

6. Bug fix - fixed problem where the newly added bash autocomplete did not allow filenames on disk to autocomplete (issue #68)

7. Bug fix - fixed a problem when a large number of short jobs that trigger job subqueuing would cause a crash (issue #72)

8. Bug fix - fixed user reported bug with strange looking error messages concealing a further absolute path bug (issue #75)

9. New feature - Added support for the slurm gres flag so users can do something like this "slurm-gres = gpu:1" in their host or job conf files (issue #76)

10. Bug fix - Restored the ability to issue --maxtime on the commandline (issue #78)

11. New feature - support added for the upcoming release of python chemshell (issue #80)

12. Bug fix - fix for problem where parameters in configuration files containing the "=" sign would cause the input file parser to misread them (issue #81)

13. Bug fix - fix for problem with LAMMPS jobs where files provided with "include" or as part of other parameters would not be transferred, thanks to Anders Johansson for suggesting some ideas and solutions (issue #86)

14. The structure of the Longbow API has been simplified, the source files no longer reside in a subdirectory called "core" within the installation directory. This has made importing much simpler and imports shorter

15. Examples have been restructured and the how to run instructions updated. The actual run files remain the same, there are still incompatibilities with these and newer versions of MD codes but this will be addressed in the next version

Longbow v1.5.0

The changes in this release are summarised below:

1. Change of license from GPLv2 to the BSD 3 clause license. This will resolve
   the copy-left issues a number of projects are having (Issue #30).

2. Fix for problem where environment is not properly loaded on some machines,
   this is a non-login shell related problem (Issue #4).

3. Removal of capitalisation from around the whole project for convenience
   (Issues #26 #28 #46 #47).

4. Longbow will now clean out recovery files upon successful completion of the
   session (Issue #24).

5. Bash autocomplete creation added to the setup.py (Issue #23 #49).

6. Fix for bad exit from recovery mode when user issues a keyboard interrupt
   (ctrl-c) (Issue #25).

7. Fix for monitoring phase causing CPU to be spun up to 100% (Issue #35).

8. Fix for bug when examples are downloaded in app, the original zip archive
   is not removed after extraction (Issue #34).

9. Fixed a bug in setup script with the python version check code (Issue #32).

10. Python 3.6 added to supported versions (Issue #33).

11. All public methods in the Longbow API can now be accessed from a single
    import, (ie "import longbow" then "longbow.somemethod()") (Issue #27).

Longbow v1.4.0

This release is a rather large release with a lot of changes to the code
and also to the way things are being done.

This project is moving towards using CI tools more and more, and in this
release and all future releases tools for automated unit testing and
code quality checks will be used. In this release the following changes
have been made in this regard:

1. Travis-CI is now used to automate testing for all versions of python
   2.6 through 3.5 https://travis-ci.org/HECBioSim/Longbow

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.

Longbow v1.3.2

The changes for this release are summarised below:

1. Fix for new gromacs packaging where the gmx mdrun CLI would not be
   recognised.

2. Fix for case in gromacs where if input file -s and -deffnm would be
   provided together and a file was a global file in a replicate job that
   all files would be set to output global.

3. Can now use -deffnm with gromacs on replicate jobs with global files
   without having to also set -s.

4. Fix for missing space in sge replicate script generator

5. Added the ability for emails to be sent to the user, these are
   invoked by providing the email address in a submit file by
   'email-address = blah@blah.com' and also to set the email flags, these
   flags should be the same ones and same format you use in your submit
   script for example 'email-flags = -M' or 'email-flags = ib'.

6. New common executable naming schemes added for things like cuda.

7. Fixed some missing newline characters from the job submit script
   generator.

8. Recovery system broken by renaming the method to same as a variable,
   this has now been resolved.

9. Rewrites to the applications.py module, it was too unwield to add to.
   This has now been split down to allow future expansion in a much easier
   fashion.

Longbow v1.3.1

The changes in this release are summarised below:

1. For machines running SGE a new parameter to control the flag used on
   the -pe directive has been implemented. This parameter is "sge-peflag"
   and has a default value of "mpi", if your cluster requires something
   different then use this parameter in a configuration file to set it.

2. Some cases on SGE clusters, it can be set that even if a job needs
   only 1 core that the -pe mpi #cores must be set. A new flag called
   "sge-peoverride" will make this happen, just provide "sge-peoverride =
   true" in a configuration file to enable.

3. Fixed a problem where Longbow would exit when no jobs are running,
   this was fixed in PBS but not in other schedulers. It is now fixed in
   all supported schedulers.

4. The import statements that looked pretty nasty across the library
   have been changed for nicer more pythonic ones.

5. Some refactoring to get rid of pylint warnings about not using lazy
   logging.

6. Ability to add script calls into the job submission script that is
   created by Longbow. The parameter "scripts" should be used, for multiple
   script references then a comma separated list should be provided. Just
   add something like this to your configuration file "scripts = source
   /some/file" or "scripts = source /first/file, source /second/file"

7. Fix a problem when using job configuration files and not referencing
   a resource, what should have happened is that Longbow should choose the
   default (top one in hosts.conf). But it crashed with a KeyError
   exception, this is now fixed.

Longbow v1.3.0

The changes in this release are summarised below:

1. Fix for recovery file bug where the file name was mangled by
   misplaced comma in os.path.join()

2. Fix for bug where the recovery file was not being recognised from the
   command-line

3. Hydra MPI support was added to the LSF plugin, to get this to work a
   user needs to supply mpiexec.hydra as the handler parameter in
   hosts.conf

4. Some bad file keywords have been removed from the NAMD plugin, more
   files have been added to the list and some corrections to bad case in
   list.

5. Fix for required parameters for staging not being written into the
   recovery file.

6. GROMACS files added to NAMD plugin

7. A disconnect feature has been implemented, users supplying
   --disconnect on the command-line will have Longbow disconnect after
   submitting jobs, these can be reconnected by using the recovery file.

8. Small change to the executable, all code moved from the if name
   == "main": to main() and all code previously in main() moved to
   longbowmain() so unit tests can be made for this part of the
   application.

Longbow v1.2.1

The changes in this release are summarised below:

1. pip now complains if http:// is not on the front of a URL, the setup.py has been fixed for this.

2. recovery files now have time stamps in their name so it is possible to select a recovery file if running multiple concurrent instances of Longbow.

Longbow v1.2.0

The changes in this release are summarised below:

1. Simplification of the whole Longbow library. This means lots of changes have
   been made to the source code and thus developers making use of Longbow in
   their code might be affected, those that simply wrap the executable will be
   largely unaffected by this, but may be affected by the below changes. The
   main change as part of the API re-write is that the hosts and jobs
   structures have simply been merged into a single structure called jobs, the
   library is now much more simple to use since all parameters are passed
   around in this single structure, so no more checking which data structure a
   parameter belongs to.

2. Extend informative error messages to all schedulers. This is issue is all
   about trying to get information from the scheduler as to why a job
   submission has failed.

   Error messages from PBS/Torque now passed to the Longbow logging system.
   Error messages from LSF now passed to the Longbow logging system.
   Error messages from SGE now passed to the Longbow logging system.
   Error messages from slurm now passed to the Longbow logging system.
   Error messages from SoGE now passed to the Longbow logging system.
   Fixed vague error that occurs during staging if bad path is used.

3. Longbow can now detect queue size limits dynamically. Machines such as
   ARCHER that only allow a certain number of jobs in the queued state at any
   one time would mean users have to use multiple Longbow sessions to do larger
   numbers of jobs. This improvement now means that a single Longbow instance
   can now submit a number of jobs larger than this limit and Longbow will hold
   back any that cannot get onto the queue in the first submit instance, as
   jobs complete, further jobs will be submitted.

4. A new recovery mode has been introduced that can recover a Longbow session
   if for some reason it gets disconnected. See documentation for more details
   on this.

5. Removal of the logging module and explicit error handling configuration
   within the top level of the library, this issue has ramifications mainly for
   developers using Longbow within their applications, users of Longbow won't
   be affected much.

   The console output messages have been aligned to 80 character widths for
   portability (users might notice this).
   Removal of the internal logging module from within Longbow (affects
   developers).

   Logging for Longbow is now configured and instantiated at the entry point
   of the application (affects developers).
   For developers using Longbow as a library now have the ability to specify
   how logging happens themselves each Longbow module logs to its own log,
   these can then be controlled by the developer allowing for deeper
   integration (affects developers).

   The top level longbow method main() has had all unnecessary code and
   parameters stripped out, this has all been moved to the application entry
   point. This now provides developers with a very high level integration point
   for simple integrations (affects developers).

6. Bad comment on the configuration method fixed (developers only).

7. API comments have been updated to be more accurate with latest changes.

8. Fix for unicode/byte string problem between Python2.x and Python3.x which
   would garble outputs from subprocess.

9. Rename the scheduler plugin "sge_arc2" to "soge" (Son of Grid Engine).

10. All Longbow command-line arguments now support both GNU standard and non
    standard forms for convenience (eg. --version and -version would be valid),
    although future versions might phase out the non-standard -param in favour
    of --param but keeping the single letter -h, -V etc as these are part of
    the standard.

Longbow v1.1.5

The changes in this release are summarised below:

1. Longbow would not install under python 3 using either pip or by running the
   setup script manually. This has now been fixed by using print statements of
   the format print("text"), this form will work in all versions of python.

2. Fix for user reported annoyance of installing the hosts.conf in secret, and
   also leaving the archive that is downloaded in $home. This has now been
   replaced with a warning during install, and also the file is created locally
   and not downloaded.

3. Removed padding from version numbers so v1.01.005 > v1.1.5.

4. Changed the README.md from markdown format to reStructured text, so now the
   README is README.rst, this is to make Longbow more pip friendly whilst still
   being bitbucket and possibly github (in case in future we move).

5. setup.py modified to eliminate the python 3 issues, and also the long
   description is now the README.rst, this means that users will see something
   standard between the pip page and the bitbucket page, this will also tie in
   with new pages on the HECBioSim website which will push pip as the preferred
   way to install more prominently.

6. hosts.conf file has been removed from the development version since this is
   now created on install for new users using pip, this will be marked as
   deprecated on the website for a while so users on old versions can still get
   it. Documentation will need to be updated to reflect this change and provide
   the quickstart example that users can grab a copy of if they are doing a more
   manual install. However pip will be the encouraged way to install.

7. Parameters specified within the configuration files had to be specified in a
   very strict format (param = value), users that omitted the spaces would find
   that Longbow would crash. The code has now been fixed to use regular
   expression to read in and parse for the equals sign, this can now handle
   cases where users specify cases such as:

       param1 = value1
       param2 =value2
       param3= value3
       param4=value4
   

8. Added python version to logging.

9. Added longbow version to logging.

10. Moved version to the top of the longbow file.

11. Added the paper citation to the logging and readme.