Longbow

Latest version: v1.5.2

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1.3.0

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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.

1.2.1

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1. Fix for annoying error in pip when not using http on urls.

2. Modified recovery mode to use recovery files that are signed by a time stamp
rather than using a single file, this preserves the ability to have multiple
Longbow instances.

1.2.0

-------------

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.

1.1.6

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1. Fix for issue on install through pip where it was complaining about the
missing README.rst.

2. A manifest file was added to make sure that the setuptools picks up the
extra files.

1.1.5

-------------

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.

1.1.4

-------------

1. The saveconfigs method would overwrite entries within the hosts config with
potentially blank entries if it was triggered and parameters existed in such
a state (perhaps via overrides).

2. There was a missing clause on one of the if statements that prevented
parameters at the hosts level from overriding internal defaults. This
has now been added in.

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