Steffen Möller pushed to branch master at Debian Med / toil
Commits: 2532f726 by Steffen Möller at 2019-07-29T18:26:27Z Delete spelling - - - - - 1 changed file: - − debian/patches/spelling Changes: ===================================== debian/patches/spelling deleted ===================================== @@ -1,108 +0,0 @@ -From: Michael R. Crusoe <[email protected]> -Subject: Lintian-inspired spelling fixes ---- toil.orig/docs/running/cloud/amazon.rst -+++ toil/docs/running/cloud/amazon.rst -@@ -165,7 +165,7 @@ - - When using the Toil provisioner, the appliance image will be automatically chosen - based on the pip-installed version of Toil on your system. That choice can be -- overriden by setting the environment variables ``TOIL_DOCKER_REGISTRY`` and ``TOIL_DOCKER_NAME`` or -+ overridden by setting the environment variables ``TOIL_DOCKER_REGISTRY`` and ``TOIL_DOCKER_NAME`` or - ``TOIL_APPLIANCE_SELF``. See :ref:`envars` for more information on these variables. If - you are developing with autoscaling and want to test and build your own - appliance have a look at :ref:`appliance_dev`. ---- toil.orig/docs/running/cloud/gce.rst -+++ toil/docs/running/cloud/gce.rst -@@ -32,7 +32,7 @@ - - $ chmod 400 ~/.ssh/id_rsa ~/.ssh/id_rsa.pub - --#. Add your newly formated public key to Google. To do this, log into your Google Cloud account -+#. Add your newly formatted public key to Google. To do this, log into your Google Cloud account - and go to `metadata`_ section under the Compute tab. - - .. image:: googleScreenShot.png ---- toil.orig/docs/running/cwl.rst -+++ toil/docs/running/cwl.rst -@@ -33,7 +33,7 @@ - ------------------------------------ - - A CWL workflow can be run indirectly in a native Toil script. However, this is not the :ref:`standard <cwl>` way to run --CWL workflows with Toil and doing so comes at the cost of job efficency. For some use cases, such as running one process on -+CWL workflows with Toil and doing so comes at the cost of job efficiency. For some use cases, such as running one process on - multiple files, it may be useful. For example, if you want to run a CWL workflow with 3 YML files specifying different - samples inputs, it could look something like:: - ---- toil.orig/docs/running/wdl.rst -+++ toil/docs/running/wdl.rst -@@ -117,7 +117,7 @@ - A cromwell.jar file is needed in order to run a WDL workflow. - - A WDL workflow can be run indirectly in a native Toil script. However, this is not the :ref:`standard <wdl>` way to run --WDL workflows with Toil and doing so comes at the cost of job efficency. For some use cases, such as running one process on -+WDL workflows with Toil and doing so comes at the cost of job efficiency. For some use cases, such as running one process on - multiple files, it may be useful. For example, if you want to run a WDL workflow with 3 JSON files specifying different - samples inputs, it could look something like:: - ---- toil.orig/src/toil/jobStores/abstractJobStore.py -+++ toil/src/toil/jobStores/abstractJobStore.py -@@ -758,7 +758,7 @@ - def jobs(self): - """ - Best effort attempt to return iterator on all jobs in the store. The iterator may not -- return all jobs and may also contain orphaned jobs that have already finished succesfully -+ return all jobs and may also contain orphaned jobs that have already finished successfully - and should not be rerun. To guarantee you get any and all jobs that can be run instead - construct a more expensive ToilState object - ---- toil.orig/src/toil/lib/threading.py -+++ toil/src/toil/lib/threading.py -@@ -39,7 +39,7 @@ - class ExceptionalThread(threading.Thread): - """ - A thread whose join() method re-raises exceptions raised during run(). While join() is -- idempotent, the exception is only during the first invocation of join() that succesfully -+ idempotent, the exception is only during the first invocation of join() that successfully - joined the thread. If join() times out, no exception will be re reraised even though an - exception might already have occured in run(). - ---- toil.orig/src/toil/job.py -+++ toil/src/toil/job.py -@@ -273,11 +273,11 @@ - exhausting all their retries, remove any successor jobs and rerun this job to restart the - subtree. Job must be a leaf vertex in the job graph when initially defined, see - :func:`toil.job.Job.checkNewCheckpointsAreCutVertices`. -- :type cores: int or string convertable by toil.lib.humanize.human2bytes to an int -- :type disk: int or string convertable by toil.lib.humanize.human2bytes to an int -+ :type cores: int or string convertible by toil.lib.humanize.human2bytes to an int -+ :type disk: int or string convertible by toil.lib.humanize.human2bytes to an int - :type preemptable: bool -- :type cache: int or string convertable by toil.lib.humanize.human2bytes to an int -- :type memory: int or string convertable by toil.lib.humanize.human2bytes to an int -+ :type cache: int or string convertible by toil.lib.humanize.human2bytes to an int -+ :type memory: int or string convertible by toil.lib.humanize.human2bytes to an int - """ - requirements = {'memory': memory, 'cores': cores, 'disk': disk, - 'preemptable': preemptable} ---- toil.orig/docs/appendices/environment_vars.rst -+++ toil/docs/appendices/environment_vars.rst -@@ -28,7 +28,7 @@ - | TOIL_DOCKER_REGISTRY | The URL of the registry of the Toil Appliance | - | | image you wish to use. Docker will use Dockerhub | - | | by default, but the quay.io registry is also | --| | very popular and easily specifiable by settting | -+| | very popular and easily specifiable by setting | - | | this option to ``quay.io``. | - +------------------------+----------------------------------------------------+ - | TOIL_DOCKER_NAME | The name of the Toil Appliance image you | ---- toil.orig/docs/developingWorkflows/developing.rst -+++ toil/docs/developingWorkflows/developing.rst -@@ -559,7 +559,7 @@ - - Just like regular promises, the return value must be determined prior to - scheduling any job that depends on the return value. In our example above, notice -- how the dependant jobs were follow ons to the parent while promising jobs are -+ how the dependent jobs were follow ons to the parent while promising jobs are - children of the parent. This ordering ensures that all promises are - properly fulfilled. - View it on GitLab: https://salsa.debian.org/med-team/toil/commit/2532f726bf8795142aa282837dca98c0a0c6973d -- View it on GitLab: https://salsa.debian.org/med-team/toil/commit/2532f726bf8795142aa282837dca98c0a0c6973d You're receiving this email because of your account on salsa.debian.org.
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