[med-svn] [Git][med-team/toil][master] 7 commits: routine-update: Packaging update
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Jun 23 14:18:35 BST 2022
Andreas Tille pushed to branch master at Debian Med / toil
Commits:
2f760910 by Andreas Tille at 2022-06-23T10:34:56+02:00
routine-update: Packaging update
- - - - -
09814dcc by Andreas Tille at 2022-06-23T10:34:57+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
c6f86691 by Andreas Tille at 2022-06-23T10:35:00+02:00
routine-update: Remove trailing whitespace in debian/changelog
- - - - -
1f71871c by Andreas Tille at 2022-06-23T10:35:01+02:00
Drop unnecessary dependency on build-essential.
Changes-By: lintian-brush
Fixes: lintian: build-depends-on-build-essential
See-also: https://lintian.debian.org/tags/build-depends-on-build-essential.html
- - - - -
86d043e4 by Andreas Tille at 2022-06-23T12:36:01+02:00
Cleanup changelog
- - - - -
13b122e7 by Andreas Tille at 2022-06-23T12:48:07+02:00
Make sure the doc applies to Debian installations with Python3
- - - - -
1b731ffe by Andreas Tille at 2022-06-23T12:51:17+02:00
Update lintian-overrides
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/python3_in_doc.patch
- debian/patches/series
- debian/toil.lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+toil (5.6.0-7) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Packaging update
+ * Standards-Version: 4.6.1 (routine-update)
+ * Remove trailing whitespace in debian/changelog (routine-update)
+ * Drop unnecessary dependency on build-essential.
+ * Make sure the doc applies to Debian installations with Python3
+ * Update lintian-overrides
+
+ -- Andreas Tille <tille at debian.org> Thu, 23 Jun 2022 10:34:56 +0200
+
toil (5.6.0-6) unstable; urgency=medium
* Team Upload.
@@ -40,7 +52,7 @@ toil (5.6.0-1) unstable; urgency=medium
* Refresh patches, retiring cwl_test_path, spelling, and
test_with_less_memory
* Skip the py-tes dependency for now.
- * Skip testVirtualEnv
+ * Skip testVirtualEnv
-- Michael R. Crusoe <crusoe at debian.org> Wed, 19 Jan 2022 14:23:52 +0100
=====================================
debian/control
=====================================
@@ -22,10 +22,9 @@ Build-Depends: debhelper-compat (= 13),
python3-stubserver <!nocheck>,
rsync <!nocheck>,
python3-yaml <!nocheck>,
-# documentation
python3-urllib3,
python3-sphinx
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/toil
Vcs-Git: https://salsa.debian.org/med-team/toil.git
Homepage: https://github.com/BD2KGenomics/toil
=====================================
debian/patches/python3_in_doc.patch
=====================================
@@ -0,0 +1,275 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 23 Jun 2022 10:34:56 +0200
+Description: Make sure the doc applies to Debian installations with Python3
+
+--- a/docs/gettingStarted/install.rst
++++ b/docs/gettingStarted/install.rst
+@@ -35,7 +35,7 @@ package directly, untar the file, create
+ $ curl -O https://pypi.python.org/packages/d4/0c/9840c08189e030873387a73b90ada981885010dd9aea134d6de30cd24cb8/virtualenv-15.1.0.tar.gz
+ $ tar xvfz virtualenv-15.1.0.tar.gz
+ $ cd virtualenv-15.1.0
+- $ python virtualenv.py ~/venv
++ $ python3 virtualenv.py ~/venv
+
+ Now that you've created your virtualenv, activate your virtual environment::
+
+--- a/docs/gettingStarted/quickStart.rst
++++ b/docs/gettingStarted/quickStart.rst
+@@ -16,7 +16,7 @@ A Toil workflow can be run with just two
+
+ 2. Specify the name of the :ref:`job store <jobStoreOverview>` and run the workflow::
+
+- python helloWorld.py file:my-job-store
++ python3 helloWorld.py file:my-job-store
+
+ Congratulations! You've run your first Toil workflow using the default :ref:`Batch System <batchsysteminterface>`, ``singleMachine``,
+ using the ``file`` job store.
+@@ -28,7 +28,7 @@ local machine. Once validated, try runni
+ Toil supports many different batch systems such as `Apache Mesos`_ and Grid Engine; its versatility makes it
+ easy to run your workflow in all kinds of places.
+
+-Toil is totally customizable! Run ``python helloWorld.py --help`` to see a complete list of available options.
++Toil is totally customizable! Run ``python3 helloWorld.py --help`` to see a complete list of available options.
+
+ For something beyond a "Hello, world!" example, refer to :ref:`runningDetail`.
+
+@@ -140,7 +140,7 @@ Running the example
+
+ #. Run it with the default settings::
+
+- $ python sort.py file:jobStore
++ $ python3 sort.py file:jobStore
+
+ The workflow created a file called ``sortedFile.txt`` in your current directory.
+ Have a look at it and notice that it contains a whole lot of sorted lines!
+@@ -157,7 +157,7 @@ Running the example
+
+ 3. Run with custom options::
+
+- $ python sort.py file:jobStore \
++ $ python3 sort.py file:jobStore \
+ --numLines=5000 \
+ --lineLength=10 \
+ --overwriteOutput=True \
+@@ -262,7 +262,7 @@ Mesos the worker processes will typicall
+ boilerplate ensures that the pipeline is only started once---on the leader---but
+ not when its job functions are imported and executed on the individual workers.
+
+-Typing ``python sort.py --help`` will show the complete list of
++Typing ``python3 sort.py --help`` will show the complete list of
+ arguments for the workflow which includes both Toil's and ones defined inside
+ ``sort.py``. A complete explanation of Toil's arguments can be
+ found in :ref:`commandRef`.
+@@ -276,7 +276,7 @@ in addition to messages from the batch s
+ with the ``--logLevel`` flag. For example, to only log ``CRITICAL`` level
+ messages to the screen::
+
+- $ python sort.py file:jobStore \
++ $ python3 sort.py file:jobStore \
+ --logLevel=critical \
+ --overwriteOutput=True
+
+@@ -302,7 +302,7 @@ example (the first line of ``down()``):
+
+ When we run the pipeline, Toil will show a detailed failure log with a traceback::
+
+- $ python sort.py file:jobStore
++ $ python3 sort.py file:jobStore
+ ...
+ ---TOIL WORKER OUTPUT LOG---
+ ...
+@@ -324,13 +324,13 @@ that a job store of the same name alread
+ failure, the job store is preserved so that the workflow can be restarted,
+ starting from the previously failed jobs. We can restart the pipeline by running ::
+
+- $ python sort.py file:jobStore \
++ $ python3 sort.py file:jobStore \
+ --restart \
+ --overwriteOutput=True
+
+ We can also change the number of times Toil will attempt to retry a failed job::
+
+- $ python sort.py file:jobStore \
++ $ python3 sort.py file:jobStore \
+ --retryCount 2 \
+ --restart \
+ --overwriteOutput=True
+@@ -344,7 +344,7 @@ line 30, or remove it, and then run
+
+ ::
+
+- $ python sort.py file:jobStore \
++ $ python3 sort.py file:jobStore \
+ --restart \
+ --overwriteOutput=True
+
+@@ -393,7 +393,7 @@ Also! Remember to use the :ref:`destroy
+
+ #. Run the Toil script in the cluster::
+
+- $ python /tmp/helloWorld.py aws:us-west-2:my-S3-bucket
++ $ python3 /tmp/helloWorld.py aws:us-west-2:my-S3-bucket
+
+ In this particular case, we create an S3 bucket called ``my-S3-bucket`` in
+ the ``us-west-2`` availability zone to store intermediate job results.
+--- a/docs/running/cloud/amazon.rst
++++ b/docs/running/cloud/amazon.rst
+@@ -135,7 +135,7 @@ all you need to do is specify the prefix
+
+ To run the sort example :ref:`sort example <sortExample>` with the AWS job store you would type ::
+
+- $ python sort.py aws:us-west-2:my-aws-sort-jobstore
++ $ python3 sort.py aws:us-west-2:my-aws-sort-jobstore
+
+ .. _installProvisioner:
+
+@@ -284,7 +284,7 @@ Autoscaling leverages Mesos containers t
+
+ #. Run the script as an autoscaling workflow: ::
+
+- $ python /root/sort.py aws:us-west-2:<my-jobstore-name> \
++ $ python3 /root/sort.py aws:us-west-2:<my-jobstore-name> \
+ --provisioner aws \
+ --nodeTypes c3.large \
+ --maxNodes 2 \
+@@ -311,7 +311,7 @@ Autoscaling leverages Mesos containers t
+
+ For more information on other autoscaling (and other) options have a look at :ref:`workflowOptions` and/or run ::
+
+- $ python my-toil-script.py --help
++ $ python3 my-toil-script.py --help
+
+ .. important::
+
+--- a/docs/running/cloud/gce.rst
++++ b/docs/running/cloud/gce.rst
+@@ -58,7 +58,7 @@ To use the Google Job Store you will nee
+
+ Then to run the sort example with the Google job store you would type ::
+
+- $ python sort.py google:my-project-id:my-google-sort-jobstore
++ $ python3 sort.py google:my-project-id:my-google-sort-jobstore
+
+ Running a Workflow with Autoscaling
+ -----------------------------------
+@@ -93,7 +93,7 @@ need to explicitly specify the ``--provi
+
+ #. Run the workflow::
+
+- $ python /root/sort.py google:<PROJECT-ID>:<JOBSTORE-NAME> \
++ $ python3 /root/sort.py google:<PROJECT-ID>:<JOBSTORE-NAME> \
+ --provisioner gce \
+ --batchSystem mesos \
+ --nodeTypes n1-standard-2 \
+--- a/docs/appendices/deploy.rst
++++ b/docs/appendices/deploy.rst
+@@ -70,7 +70,7 @@ both Python and Toil are assumed to be p
+
+ We can now run our workflow::
+
+- $ python main.py --batchSystem=mesos …
++ $ python3 main.py --batchSystem=mesos …
+
+ .. important::
+
+@@ -79,9 +79,9 @@ We can now run our workflow::
+
+ .. warning::
+
+- Neither ``python setup.py develop`` nor ``pip install -e .`` can be used in
++ Neither ``python3 setup.py develop`` nor ``pip install -e .`` can be used in
+ this process as, instead of copying the source files, they create ``.egg-link``
+- files that Toil can't auto-deploy. Similarly, ``python setup.py install``
++ files that Toil can't auto-deploy. Similarly, ``python3 setup.py install``
+ doesn't work either as it installs the project as a Python ``.egg`` which is
+ also not currently supported by Toil (though it `could be`_ in the future).
+
+@@ -143,7 +143,7 @@ The following shell session illustrates
+ └── main.py
+
+ 3 directories, 5 files
+- $ python -m workflow.main --batchSystem=mesos …
++ $ python3 -m workflow.main --batchSystem=mesos …
+
+ .. _package: https://docs.python.org/2/tutorial/modules.html#packages
+
+@@ -151,7 +151,7 @@ Here the user module ``main.py`` does no
+ is part of a package called ``util``, in a subdirectory of the current
+ directory. Additional functionality is in a separate module called
+ ``util.sort.quick`` which corresponds to ``util/sort/quick.py``. Because we
+-invoke the user module via ``python -m workflow.main``, Toil can determine the
++invoke the user module via ``python3 -m workflow.main``, Toil can determine the
+ root directory of the hierarchy–``my_project`` in this case–and copy all Python
+ modules underneath it to each worker. The ``-m`` option is documented `here`_
+
+@@ -160,7 +160,7 @@ modules underneath it to each worker. Th
+ When ``-m`` is passed, Python adds the current working directory to
+ ``sys.path``, the list of root directories to be considered when resolving a
+ module name like ``workflow.main``. Without that added convenience we'd have to
+-run the workflow as ``PYTHONPATH="$PWD" python -m workflow.main``. This also
++run the workflow as ``PYTHONPATH="$PWD" python3 -m workflow.main``. This also
+ means that Toil can detect the root directory of the user module's package
+ hierarchy even if it isn't the current working directory. In other words we
+ could do this::
+@@ -168,7 +168,7 @@ could do this::
+ $ cd my_project
+ $ export PYTHONPATH="$PWD"
+ $ cd /some/other/dir
+- $ python -m workflow.main --batchSystem=mesos …
++ $ python3 -m workflow.main --batchSystem=mesos …
+
+ Also note that the root directory itself must not be package, i.e. must not
+ contain an ``__init__.py``.
+--- a/docs/running/cliOptions.rst
++++ b/docs/running/cliOptions.rst
+@@ -17,8 +17,8 @@ The Job Store
+ Running toil scripts requires a filepath or url to a centralizing location for all of the files of the workflow.
+ This is Toil's one required positional argument: the job store. To use the :ref:`quickstart <quickstart>` example,
+ if you're on a node that has a large **/scratch** volume, you can specify that the jobstore be created there by
+-executing: ``python HelloWorld.py /scratch/my-job-store``, or more explicitly,
+-``python HelloWorld.py file:/scratch/my-job-store``.
++executing: ``python3 HelloWorld.py /scratch/my-job-store``, or more explicitly,
++``python3 HelloWorld.py file:/scratch/my-job-store``.
+
+ Syntax for specifying different job stores:
+
+@@ -351,7 +351,7 @@ the logging module:
+ Restart Option
+ --------------
+ In the event of failure, Toil can resume the pipeline by adding the argument ``--restart`` and rerunning the
+-python script. Toil pipelines can even be edited and resumed which is useful for development or troubleshooting.
++Python3 script. Toil pipelines can even be edited and resumed which is useful for development or troubleshooting.
+
+ Running Workflows with Services
+ -------------------------------
+--- a/docs/running/cloud/clusterUtils.rst
++++ b/docs/running/cloud/clusterUtils.rst
+@@ -58,7 +58,7 @@ that toil does not delete the job store,
+
+ An example of this would be running the following::
+
+- python discoverfiles.py file:my-jobstore --stats
++ python3 discoverfiles.py file:my-jobstore --stats
+
+ Where ``discoverfiles.py`` is the following:
+
+@@ -112,7 +112,7 @@ Status Command
+
+ Continuing the example from the stats section above, if we ran our workflow with the command ::
+
+- python discoverfiles.py file:my-jobstore --stats
++ python3 discoverfiles.py file:my-jobstore --stats
+
+ We could interrogate our jobstore with the status command, for example::
+
+--- a/docs/contributing/contributing.rst
++++ b/docs/contributing/contributing.rst
+@@ -66,7 +66,7 @@ Often it is simpler to use pytest direct
+ This usually works as expected, but some tests need some manual preparation. To run a specific test with pytest,
+ use the following::
+
+- python -m pytest src/toil/test/sort/sortTest.py::SortTest::testSort
++ python3 -m pytest src/toil/test/sort/sortTest.py::SortTest::testSort
+
+ For more information, see the `pytest documentation`_.
+
=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ soften-pydocker-dep
ship_tests
skip_py_tes_dep
atomic_copy_as_alternative.patch
+python3_in_doc.patch
=====================================
debian/toil.lintian-overrides
=====================================
@@ -1,4 +1,5 @@
# false positive
-toil: repeated-path-segment lib usr/lib/python3/dist-packages/toil/lib*
+toil: repeated-path-segment lib
# false positive
-toil: python-traceback-in-manpage usr/share/man/man1/toil.1.gz
+toil: python-traceback-in-manpage
+toil: mismatched-override python-traceback-in-manpage usr/share/man/man1/toil.1.gz
View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/2ff109b158bf420919ce9042292057fa95839833...1b731ffe8b392161dc5894f9aec1496c083511d7
--
View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/2ff109b158bf420919ce9042292057fa95839833...1b731ffe8b392161dc5894f9aec1496c083511d7
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20220623/211bd2d6/attachment-0001.htm>
More information about the debian-med-commit
mailing list