.gitignore

@@ -6,6 +6,7 @@
 __pycache__
 .eggs/
 .cache/
+.idea/
 /test-report.xml
 /test-report-*.xml
 /venv/

LICENSE

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+
+   Copyright 2011 UCSC Computational Genomics Lab
+   Original Contributors: Benedict Paten, Hannes Schmidt, John Vivian,
+   Christopher Ketchum, Joel Armstrong and co-authors (benedictpaten@gmail.com)
+   
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
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+
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+
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+   limitations under the License.

LICENSE.txt

-Copyright (C) 2011-15 by UCSC Computational Genomics Lab
-
-Contributors: Benedict Paten, Hannes Schmidt, John Vivian,
-Christopher Ketchum, Joel Armstrong and co-authors (benedictpaten@gmail.com)
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-    http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
\ No newline at end of file

Makefile

-# Copyright (C) 2015 UCSC Computational Genomics Lab
+# Copyright (C) 2015-2018 UCSC Computational Genomics Lab
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -26,7 +26,7 @@ immediately affect the virtualenv. Set the 'extras' variable to ensure that the
 installs support for extras. Consult setup.py for the list of supported extras. To install Toil
 in develop mode with all extras, run
 
-	make develop extras=[mesos,aws,google,azure,cwl,encryption]
+	make develop extras=[all]
 
 The 'sdist' target creates a source distribution of Toil. It is used for some unit tests and for
 installing the currently checked out version of Toil into the appliance image.
@@ -74,7 +74,7 @@ requires the TOIL_DOCKER_REGISTRY variable to be set to a value other than the d
 accidentally pushing to the official Docker registry for Toil.
 
 The TOIL_DOCKER_NAME environment variable can be set to customize the appliance image name that
-is created by the 'docker' target and pushed by the 'push_docker' target. The Toil team's
+is created by the 'docker' target and pushed by the 'push_docker' target. The Toil team\'s
 continuous integration system overrides this variable to avoid conflicts between concurrently
 executing builds for the same revision, e.g. toil-pr and toil-it.
 
@@ -99,19 +99,13 @@ sdist_name:=toil-$(dist_version).tar.gz
 docker_tag:=$(shell $(python) version_template.py dockerTag)
 default_docker_registry:=$(shell $(python) version_template.py dockerRegistry)
 docker_path:=$(strip $(shell which docker))
-ifdef docker_path
+
 ifdef docker_registry
     export TOIL_DOCKER_REGISTRY?=$(docker_registry)
 else
     export TOIL_DOCKER_REGISTRY?=$(default_docker_registry)
 endif
-else
-    $(warning Cannot find 'docker' executable. Docker-related targets will be skipped.)
-    export TOIL_DOCKER_REGISTRY:=
-endif
 export TOIL_DOCKER_NAME?=$(shell $(python) version_template.py dockerName)
-# Note that setting TOIL_DOCKER_REGISTRY to an empty string yields an invalid TOIL_APPLIANCE_SELF
-# which will coax the @needs_appliance decorator to skip the test.
 export TOIL_APPLIANCE_SELF:=$(TOIL_DOCKER_REGISTRY)/$(TOIL_DOCKER_NAME):$(docker_tag)
 
 ifndef BUILD_NUMBER
@@ -121,7 +115,6 @@ red=\033[0;31m
 cyan=\033[0;36m
 endif
 
-
 develop: check_venv
 	$(pip) install -e .$(extras)
 clean_develop: check_venv
@@ -150,7 +143,7 @@ test_offline: check_venv check_build_reqs
 	TOIL_SKIP_DOCKER=True \
 		$(python) -m pytest $(pytest_args_local) $(tests_local)
 
-# The hot deployment test needs the docker appliance
+# The auto-deployment test needs the docker appliance
 test: check_venv check_build_reqs docker
 	TOIL_APPLIANCE_SELF=$(docker_registry)/$(docker_base_name):$(docker_tag) \
 	    $(python) -m pytest $(pytest_args_local) $(tests)
@@ -270,11 +263,10 @@ check_build_reqs:
 
 prepare: check_venv
 	$(pip) install sphinx==1.5.5 mock==1.0.1 pytest==2.8.3 stubserver==1.0.1 \
-		pytest-timeout==1.2.0
+		pytest-timeout==1.2.0 cwltest
 
 
 check_venv:
-
 	@$(python) -c 'import sys; sys.exit( int( not (hasattr(sys, "real_prefix") or ( hasattr(sys, "base_prefix") and sys.base_prefix != sys.prefix ) ) ) )' \
 		|| ( printf "$(red)A virtualenv must be active.$(normal)\n" ; false )
 
@@ -303,10 +295,12 @@ check_docker_registry:
 	$(default_docker_registry) and ensure that you have permissions to push \
 	to that registry. Only CI builds should push to $(default_docker_registry).$(normal)\n' ; false )
 
+
 check_cpickle:
 	# fail if cPickle.dump(s) called without HIGHEST_PROTOCOL
 	# https://github.com/BD2KGenomics/toil/issues/1503
-	! find . -iname '*.py' | xargs grep 'cPickle.dump' | grep --invert-match HIGHEST_PROTOCOL
+	! find src -iname '*.py' | xargs grep 'cPickle.dump' | grep --invert-match HIGHEST_PROTOCOL
+
 
 .PHONY: help \
 		prepare \
@@ -323,4 +317,3 @@ check_cpickle:
 		check_running_on_jenkins \
 		check_build_reqs \
 		docker clean_docker push_docker
-

attic/toil-sort-example.py

@@ -17,7 +17,7 @@ def setup(job, input_file_id, n, down_checkpoints):
     return job.addChildJobFn(down,
                              input_file_id, n,
                              down_checkpoints=down_checkpoints,
-                             memory='1000M').rv()
+                             memory='600M').rv()
 
 
 def down(job, input_file_id, n, down_checkpoints):
@@ -45,10 +45,10 @@ def down(job, input_file_id, n, down_checkpoints):
 
         # Call the down function recursively
         return job.addFollowOnJobFn(up, job.addChildJobFn(down, job.fileStore.writeGlobalFile(t1), n,
-                                    down_checkpoints=down_checkpoints, memory='1000M').rv(),
+                                    down_checkpoints=down_checkpoints, memory='600M').rv(),
                                     job.addChildJobFn(down, job.fileStore.writeGlobalFile(t2), n,
                                                       down_checkpoints=down_checkpoints,
-                                                      memory='1000M').rv()).rv()
+                                                      memory='600M').rv()).rv()
     else:
         # We can sort this bit of the file
         job.fileStore.logToMaster("Sorting file: %s of size: %s"
@@ -163,7 +163,7 @@ def main():
         sort_file_url = 'file://' + os.path.abspath('file_to_sort.txt')
         if not toil.options.restart:
             sort_file_id = toil.importFile(sort_file_url)
-            sorted_file_id = toil.start(Job.wrapJobFn(setup, sort_file_id, int(options.N), False, memory='1000M'))
+            sorted_file_id = toil.start(Job.wrapJobFn(setup, sort_file_id, int(options.N), False, memory='600M'))
         else:
             sorted_file_id = toil.restart()
         toil.exportFile(sorted_file_id, sort_file_url)

dashboard/prometheus/Dockerfile

-FROM prom/prometheus
+FROM prom/prometheus:v2.0.0
 
 COPY ./prometheus.yml /etc/prometheus/prometheus.yml
 COPY ./run.sh /opt/run.sh

dashboard/prometheus/run.sh

@@ -5,4 +5,4 @@
 
 sed -i "s/^\([[:blank:]]*\) regex: CLUSTER_NAME/\1 regex: \'${1}\'/g" /etc/prometheus/prometheus.yml
 
-exec /bin/prometheus -config.file=/etc/prometheus/prometheus.yml -storage.local.path=/prometheus -web.console.libraries=/usr/share/prometheus/console_libraries -web.console.templates=/usr/share/prometheus/consoles
+exec /bin/prometheus --config.file=/etc/prometheus/prometheus.yml --storage.tsdb.path=/prometheus --web.console.libraries=/usr/share/prometheus/console_libraries --web.console.templates=/usr/share/prometheus/consoles

debian/changelog

+toil (3.16.0-1) experimental; urgency=medium
+
+  * New upstream version.
+    - No dependency on db2k any more -> python3 compatibility
+  * debian/control
+    - compliance with policy 4.1.4
+    - adjusted paths to repository
+  * Initial release to experimental for initial feedback from the
+    community (Closes: #851365)
+    - need to clarify if to depend on python2 or python3
+    - need to clarify essential and recommended runtime dependencies
+    - extra binaries installed
+    - documentation should be built beyond man page,
+      demanded virtualenv for doc-building unclear
+    - missing some optional modules like python-htcondor
+
+ -- Steffen Moeller <moeller@debian.org>  Thu, 14 Jun 2018 00:10:51 +0200
+
 toil (3.14.0-1) UNRELEASED; urgency=medium
 
   [ Steffen Moeller ]
-  * Initial release (Closes: #851365)
+  * Initial packaging.
 
   [ Michael R. Crusoe ]
   * Python 2 version only as upstream is not ready for Py3

debian/control

@@ -2,26 +2,39 @@ Source: toil
 Section: net
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller@debian.org>, Michael R. Crusoe <michael.crusoe@gmail.com>
+Uploaders: Steffen Moeller <moeller@debian.org>,
+           Michael R. Crusoe <michael.crusoe@gmail.com>
 Build-Depends: debhelper (>= 10),
                dh-python,
                python-all,
                python-setuptools,
                python-docker,
-               python-bd2k,
                python-galaxy-lib,
-               cwltool
-Standards-Version: 3.9.8
+               cwltool,
+# documentation
+               python-urllib3,
+               python-chardet,
+               python-sphinx
+Standards-Version: 4.1.4
 Homepage: https://github.com/BD2KGenomics/toil
 X-Python-Version: >= 2.6
 #X-Python3-Version: >= 3.2
-Vcs-Git: https://anonscm.debian.org/git/debian-med/toil.git
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/toil.git
+Vcs-Git: https://salsa.debian.org/med-team/toil.git
+Vcs-Browser: https://salsa.debian.org/med-team/toil
 #Testsuite: autopkgtest-pkg-python
 
 Package: toil
 Architecture: all
-Depends: ${python:Depends}, ${misc:Depends}, python-cgcloud-lib, cwltool
+Depends: ${python:Depends}, ${misc:Depends},
+         python-cgcloud-lib,
+         python-schema-salad,
+         cwltool
+Recommends:
+         python-boto, python-boto3,
+         python-protobuf,
+         python-futures,
+         python-libcloud
+Suggests: python-azure, python-azure-storage
 #Suggests: python-toil-doc
 Description: cross-platform workflow engine
  Toil is a scalable, efficient, cross-platform and easy-to-use workflow

debian/manpages

+docs/_build/man/toil.1

debian/patches/bd2k_as_short_name.patch

---- toil.orig/setup.py
-+++ toil/setup.py
-@@ -70,7 +70,7 @@
-         classifiers=["License :: OSI Approved :: Apache Software License"],
-         license="Apache License v2.0",
-         install_requires=[
--            'bd2k-python-lib>=1.14a1.dev35',
-+            'bd2k>=1.14a1.dev35',
-             'dill==0.2.5',
-             'six>=1.10.0',
-             'future',
-

debian/patches/no_virtualenv_to_create_manpages.patch

+Index: toil/docs/conf.py
+===================================================================
+--- toil.orig/docs/conf.py
++++ toil/docs/conf.py
+@@ -35,8 +35,8 @@ def fetch_parent_dir(filepath, n=1):
+         filepath = os.path.dirname(filepath)
+     return os.path.basename(filepath)
+ 
+-if not hasattr(sys, 'real_prefix'):
+-    raise RuntimeError('A virtualenv must be active and Sphinx must be installed in it')
++#if not hasattr(sys, 'real_prefix'):
++#    raise RuntimeError('A virtualenv must be active and Sphinx must be installed in it')
+ path_to_dir = os.path.dirname(os.path.abspath(__file__))
+ 
+ # Example of toil.version.__file__ on sphinx:

debian/patches/series

-bd2k_as_short_name.patch
 version.patch
+no_virtualenv_to_create_manpages.patch
+setting_version.patch

debian/patches/setting_version.patch

+Description: Fixing version.py that is variable and required
+Author: Steffen Moeller <moeller@debian.org>
+Bug-Debian: https://bugs.debian.org/851365
+Forwarded: not-needed
+Last-Update: 2018-06-14
+---
+
+Index: toil/src/toil/version.py
+===================================================================
+--- /dev/null
++++ toil/src/toil/version.py
+@@ -0,0 +1 @@
++distVersion="3.16.0"

debian/patches/version.patch

---- /dev/null
-+++ toil/src/toil/version.py
-@@ -0,0 +1,13 @@
-+dockerShortTag = '3.14.0-b91dbf9'
-+baseVersion = '3.14.0'
-+dockerTag = '3.14.0-b91dbf9bf6116879952f0a70f9a2fbbcae7e51b6'
-+dockerName = 'toil'
-+buildNumber = '12345'
-+cgcloudVersion = '1.6.0a1.dev393'
-+version = '3.14.0-b91dbf9bf6116879952f0a70f9a2fbbcae7e51b6'
-+dirty = False
-+shortVersion = '3.14.0-b91dbf9'
-+currentCommit = 'b91dbf9bf6116879952f0a70f9a2fbbcae7e51b6'
-+dockerMinimalTag = '3.14.0'
-+distVersion = '3.14.0'
-+dockerRegistry = 'quay.io/ucsc_cgl'
+Index: toil/setup.py
+===================================================================
 --- toil.orig/setup.py
 +++ toil/setup.py
-@@ -31,10 +31,9 @@
-     azureCosmosdbTable = 'azure-cosmosdb-table==0.37.1'
-     pynacl = 'pynacl==1.1.2'
+@@ -34,9 +34,9 @@ def runSetup():
      gcs = 'google-cloud-storage==1.6.0'
--    cwltool = 'cwltool==1.0.20180130110340'
-+    cwltool = 'cwltool>=1.0.20180130110340'
+     gcs_oauth2_boto_plugin = 'gcs_oauth2_boto_plugin==1.14'
+     apacheLibcloud = 'apache-libcloud==2.2.1'
+-    cwltool = 'cwltool==1.0.20180518123035'
++    cwltool = 'cwltool>=1.0.20180518123035'
      schemaSalad = 'schema-salad >= 2.6, < 3'
 -    galaxyLib = 'galaxy-lib==17.9.3'
--    cwltest = 'cwltest>=1.0.20180130081614'
 +    galaxyLib = 'galaxy-lib>=17.9.3'
      htcondor = 'htcondor>=8.6.0'
  
      mesos_reqs = [
-@@ -55,8 +54,7 @@
-     cwl_reqs = [
-                   cwltool,
-                   schemaSalad,
--                  galaxyLib,
--                  cwltest]
-+                  galaxyLib]
-     wdl_reqs = []
-     htcondor_reqs = [
-                   htcondor]
-@@ -116,33 +114,6 @@
+@@ -137,33 +137,6 @@ def importVersion():
      required.
      """
      import imp

debian/rules

@@ -11,6 +11,10 @@ export PYBUILD_DISABLE_python3=1
 %:
 	dh $@ --with python2 --buildsystem=pybuild
 
+override_dh_auto_build:
+	dh_auto_build
+	$(MAKE) -C docs man
+
 
 # If you need to rebuild the Sphinx documentation
 # Add spinxdoc to the dh --with line
@@ -20,4 +24,6 @@ export PYBUILD_DISABLE_python3=1
 #	PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bman  docs/ build/man  # Manpage generator
 
 override_dh_auto_clean:
-
+	rm -rf .pybuild
+	rm -rf docs/_build
+	find . -name "*.pyc" -delete

docker/Dockerfile.py

@@ -41,13 +41,11 @@ def heredoc(s):
 
 motd = heredoc('''
 
-    This is the Toil appliance. You can run your Toil script directly on the appliance, but only
-    in single-machine mode. Alternatively, create a Toil cluster with `toil launch-cluster`,
-    log into the leader of that cluster with `toil ssh-cluster` and run your Toil script there.
-
+    This is the Toil appliance. You can run your Toil script directly on the appliance. 
+    Run toil <workflow>.py --help to see all options for running your workflow.
     For more information see http://toil.readthedocs.io/en/latest/
 
-    Copyright (C) 2015-2016 Regents of the University of California
+    Copyright (C) 2015-2018 Regents of the University of California
 
     Version: {applianceSelf}
 
@@ -117,7 +115,7 @@ print(heredoc('''
 
     # This component changes most frequently and keeping it last maximizes Docker cache hits.
     COPY {sdistName} .
-    RUN pip install {sdistName}[aws,mesos,encryption,cwl]
+    RUN pip install {sdistName}[all]
     RUN rm {sdistName}
 
     # We intentionally inherit the default ENTRYPOINT and CMD from the base image, to the effect