diff --git a/README.rst b/README.rst index c458a6f..18cc713 100644 --- a/README.rst +++ b/README.rst @@ -17,7 +17,7 @@ environment! +---------+----------------------------------------------------+ | License | MIT License, property of Stanford, use as you wish | +---------+----------------------------------------------------+ -| Version | 0.6.1-beta.6 | +| Version | 0.6.1-beta.7 | +---------+----------------------------------------------------+ .. image:: https://readthedocs.org/projects/fyrd/badge/?version=latest @@ -39,7 +39,7 @@ techniques to avoid overwhelming the queue and to catch bugs on the fly. It is routinely tested on Mac OS and Linux with slurm and torque clusters, or in the absence of a cluster, on Python versions `2.7.10`, `2.7.11`, `2.7.12`, -`3.3.0`, `3.4.0`, `3.5.2`, `3.6-dev`, and `3.7-dev`. The full test suite is +`3.3.0`, `3.4.0`, `3.5.2`, `3.6.2`, and `3.7-dev`. The full test suite is available in the `tests` folder. Fyrd is pronounced 'feared' (sort of), it is an Anglo-Saxon term for an army, diff --git a/docs/fyrd_manual.pdf b/docs/fyrd_manual.pdf index 8b3599e..e34888c 100644 Binary files a/docs/fyrd_manual.pdf and b/docs/fyrd_manual.pdf differ diff --git a/docs/sphinx/advanced_usage.rst b/docs/sphinx/advanced_usage.rst index e843193..ff7637d 100644 --- a/docs/sphinx/advanced_usage.rst +++ b/docs/sphinx/advanced_usage.rst @@ -259,6 +259,7 @@ The method can actually be simply accessed as a function instead of needing the `Queue` class: .. code:: python + fyrd.wait([1,2,3]) To generate a `Queue` object, do the following: diff --git a/docs/sphinx/api.rst b/docs/sphinx/api.rst index d7b303a..3909d72 100644 --- a/docs/sphinx/api.rst +++ b/docs/sphinx/api.rst @@ -41,7 +41,7 @@ Methods .. automethod:: fyrd.queue.Queue.update -.. automethod:: fyrd.queue.Queue.QueueJob +.. autoclass:: fyrd.queue.Queue.QueueJob .. autoexception:: fyrd.queue.QueueError @@ -354,9 +354,9 @@ fyrd.local.job_runner fyrd.run -------- -.. automodule:: fyrd.local.run +.. automodule:: fyrd.run :members: - "show-inheritance: + :show-inheritance: fyrd.logme ---------- diff --git a/docs/sphinx/conf.py b/docs/sphinx/conf.py index dcc7340..1e538b8 100644 --- a/docs/sphinx/conf.py +++ b/docs/sphinx/conf.py @@ -9,7 +9,7 @@ copyright = '2016, Michael Dacre ' author = 'Michael Dacre ' version = '0.6' -release = '0.6.1-beta.6' +release = '0.6.1-beta.7' language = 'en' # Add any paths that contain templates here, relative to this directory. diff --git a/docs/sphinx/index.rst b/docs/sphinx/index.rst index e1ba114..1232b56 100644 --- a/docs/sphinx/index.rst +++ b/docs/sphinx/index.rst @@ -8,7 +8,7 @@ Python job submission on torque and slurm clusters with dependency tracking. +---------+----------------------------------------------------+ | License | MIT License, property of Stanford, use as you wish | +---------+----------------------------------------------------+ -| Version | 0.6.1-beta.6 | +| Version | 0.6.1-beta.7 | +---------+----------------------------------------------------+ .. only:: html @@ -27,7 +27,7 @@ techniques to avoid overwhelming the queue and to catch bugs on the fly. It is routinely tested on Mac OS and Linux with slurm and torque clusters, or in the absence of a cluster, on Python versions 2.7.10, 2.7.11, 2.7.12, 3.3.0, 3.4.0, -3.5.2, 3.6-dev, and 3.7-dev. The full test suite is available in the `tests` folder. +3.5.2, 3.6.2, and 3.7-dev. The full test suite is available in the `tests` folder. Fyrd is pronounced 'feared' (sort of), it is an Anglo-Saxon term for an army, particularly an army of freemen (in this case an army of compute nodes). The diff --git a/docs/sphinx/simple_index.rst b/docs/sphinx/simple_index.rst index 5f324b7..d459431 100644 --- a/docs/sphinx/simple_index.rst +++ b/docs/sphinx/simple_index.rst @@ -17,7 +17,7 @@ techniques to avoid overwhelming the queue and to catch bugs on the fly. It is routinely tested on Mac OS and Linux with slurm and torque clusters, or in the absence of a cluster, on Python versions 2.7.10, 2.7.11, 2.7.12, 3.3.0, 3.4.0, -3.5.2, 3.6-dev, and 3.7-dev. The full test suite is available in the `tests` folder. +3.5.2, 3.6.2, and 3.7-dev. The full test suite is available in the `tests` folder. For complete documentation see `the documentation site `_ and the `Fyrd.pdf `_ document in this repository. diff --git a/fyrd/__init__.py b/fyrd/__init__.py index 4d61d79..c7067c5 100644 --- a/fyrd/__init__.py +++ b/fyrd/__init__.py @@ -6,9 +6,9 @@ AUTHOR: Michael D Dacre, mike.dacre@gmail.com ORGANIZATION: Stanford University LICENSE: MIT License, property of Stanford, use as you wish - VERSION: 0.6.1-beta.6 + VERSION: 0.6.1-beta.7 CREATED: 2015-12-11 22:19 - Last modified: 2016-11-28 14:06 + Last modified: 2017-08-02 11:43 =============== =================================================== Allows simple job submission with *dependency tracking and queue waiting* with @@ -143,7 +143,7 @@ import atexit as _atexit # Version Number -__version__ = '0.6.1-beta.6' +__version__ = '0.6.1-beta.7' ################################################# # Currently configured job submission systems # diff --git a/fyrd/__main__.py b/fyrd/__main__.py index 9370051..d4c9664 100644 --- a/fyrd/__main__.py +++ b/fyrd/__main__.py @@ -7,7 +7,7 @@ Author Michael D Dacre Organization Stanford University License MIT License, use as you wish -Version 0.6.2-beta.6 +Version 0.6.2-beta.7 ============ ====================================== """ from __future__ import print_function diff --git a/fyrd/helpers.py b/fyrd/helpers.py index fad094d..cdf1d02 100644 --- a/fyrd/helpers.py +++ b/fyrd/helpers.py @@ -299,7 +299,8 @@ def splitrun(jobs, infile, inheader, command, args=None, kwargs=None, with the jobs argument, and run command on each. Accepts exactly the same arguments as the Job class, with the exception of - the first three and last four arguments, which are: + the first three and last four arguments, which are:: + - the number of jobs - the file to work on - whether the input file has a header @@ -357,10 +358,12 @@ def splitrun(jobs, infile, inheader, command, args=None, kwargs=None, Returns: Primary return value varies and is decided in this order: + If outfile: the absolute path to that file If merge_func: the result of merge_func(list), where list is the list of outputs. Else: a list of results + If direct is False, this function returns a fyrd.job.Job object which will return the results described above on get(). """ diff --git a/fyrd/run.py b/fyrd/run.py index d4f2a12..45d3d0e 100644 --- a/fyrd/run.py +++ b/fyrd/run.py @@ -686,6 +686,7 @@ def get_imports(function, mode='string'): """Build a list of potentially useful imports from a function handle. Gets: + - All modules from globals() - All modules from the function's globals() - All functions from the function's globals() diff --git a/setup.py b/setup.py index 2c57b18..b089a0a 100755 --- a/setup.py +++ b/setup.py @@ -54,7 +54,7 @@ def run_tests(self): setup( name='fyrd', - version='0.6.1-beta.6', + version='0.6.1-beta.7', description=('Submit functions and shell scripts to torque, slurm, ' + 'or local machines'), long_description=long_description,