[med-svn] [Git][med-team/toil][master] Delete spelling
Steffen Möller
gitlab at salsa.debian.org
Mon Jul 29 19:26:53 BST 2019
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 <michael.crusoe at gmail.com>
-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
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