galaxy-commits January 2019

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[galaxyproject/galaxy] cbcd36: Allow passing unused keywords to container resolve...
by GitHub 07 Jan '19

07 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cbcd3627f3833ada31b58863d5504666bb98b956 https://github.com/galaxyproject/galaxy/commit/cbcd3627f3833ada31b58863d550… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Allow passing unused keywords to container resolver Commit: 8f8642aa33e4c25e9f3bdff28b37a334af97b89c https://github.com/galaxyproject/galaxy/commit/8f8642aa33e4c25e9f3bdff28b37… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge container resolver with high-level dependency manager Commit: b505fe37eac6b0331c20b26b7a0cddc49942a38a https://github.com/galaxyproject/galaxy/commit/b505fe37eac6b0331c20b26b7a0c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Introduce a ContainerDependency class Commit: 360e605be965be5c414ca9ead34c536dd4003fd9 https://github.com/galaxyproject/galaxy/commit/360e605be965be5c414ca9ead34c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Adjust _requirements_to_dependencies_dict to also report available containers in the manage dependencies menu Commit: 40d8a38108fca6c21efc72f66660b3a1a7c42caa https://github.com/galaxyproject/galaxy/commit/40d8a38108fca6c21efc72f66660… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Augment NullDependency with version and always record incoming null dependencies, since the container resolvers don't return NullDependency objects. Commit: f2128692a4f42da2254a53b69cbf1931e74c10dc https://github.com/galaxyproject/galaxy/commit/f2128692a4f42da2254a53b69cbf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Fix matching single package mulled docker containers An image like `quay.io/biocontainers/ucsc-liftover:357--1` would otherwise have the package name `quay.io/biocontainers/ucsc-liftover` instead of `ucsc-liftover` Commit: fa6cca0224fd2b0239160df565a58507b05ac00f https://github.com/galaxyproject/galaxy/commit/fa6cca0224fd2b0239160df565a5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/views.py Log Message: ----------- Only walk through enabled container resolvers Commit: 541f0ebf3d754f5a8eb4a3d8a56d0c197c29c5cb https://github.com/galaxyproject/galaxy/commit/541f0ebf3d754f5a8eb4a3d8a56d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dependencies.py Log Message: ----------- Avoid circular imports by moving {App,Job,Tool} Info classes to dependencies.py Commit: 3b4b510ad01f48253587db1bcd87400237709673 https://github.com/galaxyproject/galaxy/commit/3b4b510ad01f48253587db1bcd87… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py Log Message: ----------- Add `can_uninstall_dependencies` attribute to ContainerResolver Commit: a4f18d8f601c83826a451d63af2fa67d319f58a7 https://github.com/galaxyproject/galaxy/commit/a4f18d8f601c83826a451d63af2f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/container_classes.py M lib/galaxy/tools/deps/views.py Log Message: ----------- Make DependencyManager container & destination-aware This will allow us to use the proper parameters when pulling containers. Commit: 2d3ab4ce1205aec24664225d74b2a851cb94b2b0 https://github.com/galaxyproject/galaxy/commit/2d3ab4ce1205aec24664225d74b2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Allow specifying resolver index and resolver_type when installing dependencies via tools API Commit: 7ca17e2b83d45e3c5a63643cc59785f6162803c5 https://github.com/galaxyproject/galaxy/commit/7ca17e2b83d45e3c5a63643cc597… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Drop NullDependency only when not skipping resolver Commit: 59c56b8f563fd4298d37d40af0b0f429761c4392 https://github.com/galaxyproject/galaxy/commit/59c56b8f563fd4298d37d40af0b0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Mention index and resolver_type in API docstring Commit: 2aab490807245c30935389001605c170bbebbf98 https://github.com/galaxyproject/galaxy/commit/2aab490807245c30935389001605… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/container_classes.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dockerfiles.py Log Message: ----------- Move Container classes into container_classes to avoid circular imports Commit: 55f989c23650e94e1f28a3ac60d10931dfd70076 https://github.com/galaxyproject/galaxy/commit/55f989c23650e94e1f28a3ac60d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Make mulled docker containers installable Commit: 19bc4985c91c14295d7c2048355a0bf71d4ec1cd https://github.com/galaxyproject/galaxy/commit/19bc4985c91c14295d7c2048355a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Allow selecting resolver when uninstalling through tools API Commit: 50d8e3079d873fe4161149b00365cf0d5702eb56 https://github.com/galaxyproject/galaxy/commit/50d8e3079d873fe4161149b00365… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Add integration test for un/install with resolver_type Commit: 66a3f556abeb410fd59f1b408efae94f168699d8 https://github.com/galaxyproject/galaxy/commit/66a3f556abeb410fd59f1b408efa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/container_classes.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/singularity_util.py Log Message: ----------- Use singularity build with biocontainers This makes it possible to pull a container from quay.io/biocontainers and to convert it to singularity format for later execution (via the CachedMulledSingularityContainerResolver). This is nicely integrated with the DependencyManager view, so you can (as for conda or docker) do: ``` requests.post(galaxy_url+'/api/tools/deseq2/dependencies', {'key': API_KEY, 'resolver_type': 'mulled_singularity'}) ``` This is quite lightweight, the resulting image is significantly smaller than the conda env (since it is compressed), and the install process is much faster. Commit: 1fcbd971c8aa743b3e035ddc27a4ea78e01bac0a https://github.com/galaxyproject/galaxy/commit/1fcbd971c8aa743b3e035ddc27a4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M config/container_resolvers_conf.xml.sample M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Try cached resolver before non-cached Commit: b41d969d681e3d427fd9f42ca9502c91634f061d https://github.com/galaxyproject/galaxy/commit/b41d969d681e3d427fd9f42ca950… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/singularity_util.py A test/integration/singularity_job_conf.xml A test/integration/test_containerized_jobs.py R test/integration/test_dockerized_jobs.py Log Message: ----------- Add integration test for singularity resolution Commit: fd4b009089d226e05a6191c3067fad560c5a77c8 https://github.com/galaxyproject/galaxy/commit/fd4b009089d226e05a6191c3067f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M test/base/integration_util.py M test/integration/test_containerized_jobs.py Log Message: ----------- Skip singualrity integration tests if singularity not available Commit: 2d6863067554f38ac05625bee1b81663a7973a1a https://github.com/galaxyproject/galaxy/commit/2d6863067554f38ac05625bee1b8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Add MulledSingularityContainerResolver to __all__ Otherwise speicifying the resolver in containers_conf.xml fails. Commit: 337bddfd4841d51291f940effc99a4622f10649a https://github.com/galaxyproject/galaxy/commit/337bddfd4841d51291f940effc99… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Pass in user, fixes dependency install for data manager tools Commit: 83473f075d9e8cce04dc775d37b44b87baca9931 https://github.com/galaxyproject/galaxy/commit/83473f075d9e8cce04dc775d37b4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh R test/docker/base/start_mysql.sh Log Message: ----------- Update testing docker image; drop mysql tests, add singularity Commit: 6b25cace916de7a694b0e83ee640d7170c24cd10 https://github.com/galaxyproject/galaxy/commit/6b25cace916de7a694b0e83ee640… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Do run through build_mulled resolver if install is set Commit: 0d86c9098c032742b091d4691634ada81da980f0 https://github.com/galaxyproject/galaxy/commit/0d86c9098c032742b091d4691634… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Make NullDependencyManager a class with empty non-container dependencies Commit: 13592e5e85195cb0c457457fb1a350fa8df213d4 https://github.com/galaxyproject/galaxy/commit/13592e5e85195cb0c457457fb1a3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Fix __str__ for BuildSingularityContainerResolver Commit: ccb8429a84e8d4a63f57e320510b5de2524eb5e6 https://github.com/galaxyproject/galaxy/commit/ccb8429a84e8d4a63f57e320510b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Download a binary that works on OSX Commit: 4ef3460c041f210b0c0513a3786b186bac7a05e9 https://github.com/galaxyproject/galaxy/commit/4ef3460c041f210b0c0513a3786b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- DependencyManager lint fix Commit: ac5e7d994912b292fb3d3464e4e5e58859070bc9 https://github.com/galaxyproject/galaxy/commit/ac5e7d994912b292fb3d3464e4e5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Make `resolver` methods respect enabled_container_types Commit: 62863e8991728a1fe4b92cf42cd9d1e825ff1a02 https://github.com/galaxyproject/galaxy/commit/62863e8991728a1fe4b92cf42cd9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Don't fail if build exists and also don't remove build dir if it already exists Commit: 4a307ac5bea000d097e8488017f437e678a97a7f https://github.com/galaxyproject/galaxy/commit/4a307ac5bea000d097e8488017f4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Add ExplicitSingularityContainerResolver Commit: a6a186a64251f206294f2fd3416fb08db4234f47 https://github.com/galaxyproject/galaxy/commit/a6a186a64251f206294f2fd3416f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Make containers list, map can only be iterated once Commit: 44d73f72c8967b114114d662ddb42098514026ee https://github.com/galaxyproject/galaxy/commit/44d73f72c8967b114114d662ddb4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Update Dockefile and run_test_wrapper.sh We use the Galaxy users' home dir for HOME. Otherwise os.environ.get('HOME') would return '/home/galaxy', but jobs run would see /galaxy. Commit: c0b63a18c7a2fa7d7fb45ffbddfcef5aa4c00c67 https://github.com/galaxyproject/galaxy/commit/c0b63a18c7a2fa7d7fb45ffbddfc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/integration/test_containerized_jobs.py Log Message: ----------- Fix container integration tests Commit: a0bd7072adf7f03a82adfddf3216b15ce7105c87 https://github.com/galaxyproject/galaxy/commit/a0bd7072adf7f03a82adfddf3216… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Use bash for mulled ContainerDescriptions The base mulled container contains bash, and unfortunately bashisms such as <(cat bla) are very common in widely used Galaxy wrappers. So I think it makes sense to default to bash here. Commit: 99a0ab03e90d2f9355c130403b1a0f5cb1ca5706 https://github.com/galaxyproject/galaxy/commit/99a0ab03e90d2f9355c130403b1a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M run_tests.sh Log Message: ----------- Temporarily test from mvdbeek/testing-base Commit: a056f1746069a38b43bd0cc62bbe12d96aaa5145 https://github.com/galaxyproject/galaxy/commit/a056f1746069a38b43bd0cc62bbe… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Document and use mulled_channels option Commit: 93622f026bacef4328e2415aad72f521d92192c9 https://github.com/galaxyproject/galaxy/commit/93622f026bacef4328e2415aad72… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Only parse build if build in name Otherwise this fails with ``` Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 277, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/web/framework/decorators.py", line 101, in decorator return func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/tools.py", line 239, in install_dependencies tool._view.install_dependencies(tool.requirements, **kwds) File "lib/galaxy/tools/deps/views.py", line 107, in install_dependencies return self._dependency_manager._requirements_to_dependencies_dict(requirements, **kwds) File "lib/galaxy/tools/deps/__init__.py", line 190, in _requirements_to_dependencies_dict **kwds) File "lib/galaxy/tools/deps/container_resolvers/mulled.py", line 343, in resolve name = targets_to_mulled_name(targets=targets, hash_func=self.hash_func, namespace=self.namespace) File "lib/galaxy/tools/deps/container_resolvers/mulled.py", line 278, in targets_to_mulled_name version, build = split_tag(tag) File "lib/galaxy/tools/deps/mulled/util.py", line 69, in split_tag build = tag.split('--', 1)[1] IndexError: list index out of range ``` if a single-target image was build with a build_mulled resolver. Commit: b3af5176d35b0a1e818975c263018fb7ea800bcd https://github.com/galaxyproject/galaxy/commit/b3af5176d35b0a1e818975c26301… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Replace deprecated singularity import with build And upgrade singularity build image to 2.4.6 (latest on biocontainers). Overall this is necessary because singularity import 2.3X doesn't work behind proxies. The change from `Singularity` to `Singularity.def` is necessary because the script uses the `file` command if the Singularity file doesn't end in .def or is not exactly Singularity (it is `/import/Singularity` in our case). `file` isn't available in the biocontainers image. Commit: 5f389dd11ea3da935b382871305bf0a7c1e2d3d4 https://github.com/galaxyproject/galaxy/commit/5f389dd11ea3da935b382871305b… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M config/container_resolvers_conf.xml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix spelling in resolver docs Co-Authored-By: mvdbeek <m.vandenbeek(a)gmail.com> Commit: 0343d3d87f438bdb669959bc5141030169cc01ba https://github.com/galaxyproject/galaxy/commit/0343d3d87f438bdb669959bc5141… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/mulled/util.py Log Message: ----------- Cache requests to mulled registry for 5 minutes When going through the resolvers we can easily exceed the allowed API request rate. Commit: 9051c10cba8360bc5a4ee199ff01657c3fda3b20 https://github.com/galaxyproject/galaxy/commit/9051c10cba8360bc5a4ee199ff01… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M run_tests.sh Log Message: ----------- More docker debug Commit: a03f8bdffd272e0195a6bf88931fb17b6e428d13 https://github.com/galaxyproject/galaxy/commit/a03f8bdffd272e0195a6bf88931f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Test singularity exec as Galaxy user Commit: 658816264a8e84bacfdf83e9c9029338b2e1f85d https://github.com/galaxyproject/galaxy/commit/658816264a8e84bacfdf83e9c902… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/tools/deps/singularity_util.py Log Message: ----------- Explicitly pass home dir to singularity command Commit: 06f5abe1bc16eccf750baf7a754d48dfdedaaf5a https://github.com/galaxyproject/galaxy/commit/06f5abe1bc16eccf750baf7a754d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Install singularity 3.0.1 from source Commit: bed8b54af604a2caf9161a5265953c90ae5a6c8a https://github.com/galaxyproject/galaxy/commit/bed8b54af604a2caf9161a526595… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M .ci/jenkins/integration-py3/run_tests.sh M .ci/jenkins/integration/run_tests.sh M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Only run integration tests with --privileged Commit: 9517871b4af27c9647436d84ea2bfe76bb242ca8 https://github.com/galaxyproject/galaxy/commit/9517871b4af27c9647436d84ea2b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M run_tests.sh Log Message: ----------- Bump image to use Commit: 6b3af3b2ffa8d90946a6b2d9b803779df35e19fd https://github.com/galaxyproject/galaxy/commit/6b3af3b2ffa8d90946a6b2d9b803… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py Log Message: ----------- Make dependency_shell_commands a property If we know we use a container we don't need to pass through the dependency resolver. Commit: 8a34101089085c6203cdd11468de4a0866922534 https://github.com/galaxyproject/galaxy/commit/8a34101089085c6203cdd11468de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M config/container_resolvers_conf.xml.sample M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Introduce `auto_install` ContainerResolver flag If set to True (thats's the default), the container resolvers that can pull or build images will do that, if they are enabled. You can set this to `False` and instead pass through the DependencyManager to use these resolvers to pull or build images. Commit: 03b363a1ef92e696ba07050e2a4832c15c8a8964 https://github.com/galaxyproject/galaxy/commit/03b363a1ef92e696ba07050e2a48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M .ci/jenkins/integration-py3/run_tests.sh M .ci/jenkins/integration/run_tests.sh M config/container_resolvers_conf.xml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/container_classes.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/config_schema.yml M run_tests.sh M test/base/integration_util.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh R test/docker/base/start_mysql.sh M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml A test/integration/singularity_job_conf.xml A test/integration/test_containerized_jobs.py R test/integration/test_dockerized_jobs.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #7125 from mvdbeek/MulledSingularityContainerResolver Use singularity build / exec with biocontainers Compare: https://github.com/galaxyproject/galaxy/compare/952af6b6fde1...03b363a1ef92 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 7ca739: Document ``message_box_class`` option
by GitHub 07 Jan '19

07 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ca7394c7d1e19ec5a42dae526b5bc20f33c3ac9 https://github.com/galaxyproject/galaxy/commit/7ca7394c7d1e19ec5a42dae526b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Document ``message_box_class`` option Reported by @vazovn Commit: 952af6b6fde107c9769f3393beb44032f36e9827 https://github.com/galaxyproject/galaxy/commit/952af6b6fde107c9769f3393beb4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Merge pull request #7174 from nsoranzo/message_box_class Document ``message_box_class`` option Compare: https://github.com/galaxyproject/galaxy/compare/128af8f9ba21...952af6b6fde1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c5dbd7: Do not use default value in workflow execution for...
by GitHub 06 Jan '19

06 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5dbd78af6ae4c7738a05708ffb01e444ee92a2b https://github.com/galaxyproject/galaxy/commit/c5dbd78af6ae4c7738a05708ffb0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-12-26 (Wed, 26 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Do not use default value in workflow execution form for runtime values Commit: 128af8f9ba21a56f3021791affc2a539f74fc1fb https://github.com/galaxyproject/galaxy/commit/128af8f9ba21a56f3021791affc2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-06 (Sun, 06 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #7157 from guerler/workflow_runtime_default_value Do not use default values for runtime values in workflow execution form Compare: https://github.com/galaxyproject/galaxy/compare/1222f80ae99d...128af8f9ba21 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 548d0c: WIP job assignment using database transaction isol...
by GitHub 05 Jan '19

05 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 548d0cb2c9e38594f747c17e57939eca2344353f https://github.com/galaxyproject/galaxy/commit/548d0cb2c9e38594f747c17e5793… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/util/handlers.py Log Message: ----------- WIP job assignment using database transaction isolation Commit: b067fd194b2a3a28c23900eb45ace726aa842d78 https://github.com/galaxyproject/galaxy/commit/b067fd194b2a3a28c23900eb45ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/handler.py Log Message: ----------- Rename job assigner to job grabber and clean up, also add support for (preferable) FOR UPDATE ... SKIP LOCKED Commit: 34eb8a45c1e4e069ca6d91965aa1985eb444da83 https://github.com/galaxyproject/galaxy/commit/34eb8a45c1e4e069ca6d91965aa1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Integrate DB serialization methods with new handler assignment process Commit: 473210714e719f4c36d77b49281a82567b294c8e https://github.com/galaxyproject/galaxy/commit/473210714e719f4c36d77b49281a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/workflow/scheduling_manager.py M scripts/galaxy-main Log Message: ----------- Add support for dynamic handlers when using DB serialization handler assignment Commit: 602b86ef9ee0efddb3614f03c19d5772ab5bdf0d https://github.com/galaxyproject/galaxy/commit/602b86ef9ee0efddb3614f03c19d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- SQLAlchemize the grabber query and fold grabber directly into JobHandlerQueue Commit: 2c73ac3e22f608a3049f5bafc477b1a199d25c33 https://github.com/galaxyproject/galaxy/commit/2c73ac3e22f608a3049f5bafc477… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-18 (Tue, 18 Dec 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- No longer using trace logging Commit: b0691089eafd303cc0a31b589f465f552a90c40a https://github.com/galaxyproject/galaxy/commit/b0691089eafd303cc0a31b589f46… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-04 (Fri, 04 Jan 2019) Changed paths: M test/unit/jobs/test_job_configuration.py Log Message: ----------- Unit tests for new DB serialization handler assignment methods Commit: df7f8b425d16ddb54d4acb181f9a4ee415b510ea https://github.com/galaxyproject/galaxy/commit/df7f8b425d16ddb54d4acb181f9a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-04 (Fri, 04 Jan 2019) Changed paths: M test/base/integration_util.py A test/integration/handler_template_job_conf.xml A test/integration/test_handler_assignment_methods.py M test/integration/test_scripts.py Log Message: ----------- Integration tests for handler assignment methods Commit: 1222f80ae99da18f6361bbad6234bfba65e278f5 https://github.com/galaxyproject/galaxy/commit/1222f80ae99da18f6361bbad6234… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-05 (Sat, 05 Jan 2019) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/workflow/scheduling_manager.py M scripts/galaxy-main M test/base/integration_util.py A test/integration/handler_template_job_conf.xml A test/integration/test_handler_assignment_methods.py M test/integration/test_scripts.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge pull request #7129 from natefoo/serializable-job-assignment Perform job assignment using DB serialization techniques Compare: https://github.com/galaxyproject/galaxy/compare/fa071b3c4fca...1222f80ae99d **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9e7fa2: Lower provider name
by GitHub 05 Jan '19

05 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e7fa2f0e98afc252bda91852063ee2b38e276a4 https://github.com/galaxyproject/galaxy/commit/9e7fa2f0e98afc252bda91852063… Author: Marcus Christie <machrist(a)iu.edu> Date: 2019-01-02 (Wed, 02 Jan 2019) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Lower provider name The keys of the oidc_backends_config dict are created by lowercasing the provider names in oidc_backends_config.xml file so we need to lower the provider name given in the request in order to find the backend config. Commit: fa071b3c4fca24caed2d9a258e31ae87851a0da2 https://github.com/galaxyproject/galaxy/commit/fa071b3c4fca24caed2d9a258e31… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2019-01-05 (Sat, 05 Jan 2019) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Merge pull request #7166 from machristie/lower-provider-name Lower provider name Compare: https://github.com/galaxyproject/galaxy/compare/b8f445556abf...fa071b3c4fca **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 403d0a: Stricter ``process_key`` tests
by GitHub 04 Jan '19

04 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 403d0a9361ca5fcc400eed6500415d288bf04903 https://github.com/galaxyproject/galaxy/commit/403d0a9361ca5fcc400eed650041… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-04 (Fri, 04 Jan 2019) Changed paths: M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Stricter ``process_key`` tests Commit: 31e5fced00778cf469b98dc05eb5f3221fc0caa6 https://github.com/galaxyproject/galaxy/commit/31e5fced00778cf469b98dc05eb5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-04 (Fri, 04 Jan 2019) Changed paths: M lib/galaxy/tools/parameters/meta.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Fix nesting and test Commit: b8f445556abf8469b022afd9b59fa0a14b45dad9 https://github.com/galaxyproject/galaxy/commit/b8f445556abf8469b022afd9b59f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-04 (Fri, 04 Jan 2019) Changed paths: M lib/galaxy/tools/parameters/meta.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Merge pull request #7169 from mvdbeek/fix_process_key_unordered_elements Fix process_key test and deal with unordered repeat elements Compare: https://github.com/galaxyproject/galaxy/compare/55e539d1e943...b8f445556abf **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] cd8b12: Fix test_test_data_download
by GitHub 04 Jan '19

04 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd8b129b8e462eaf281ea0ef5cbd02d50dc32e66 https://github.com/galaxyproject/galaxy/commit/cd8b129b8e462eaf281ea0ef5cbd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-04 (Fri, 04 Jan 2019) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix test_test_data_download This contains 5 items after https://github.com/galaxyproject/galaxy-test-data/pull/2 had been merged. Commit: 55e539d1e943805634ec290eadb412e86a27571a https://github.com/galaxyproject/galaxy/commit/55e539d1e943805634ec290eadb4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-04 (Fri, 04 Jan 2019) Changed paths: M test/api/test_tools.py Log Message: ----------- Merge pull request #7171 from mvdbeek/fix_test_data_download_api_test Fix test_test_data_download Compare: https://github.com/galaxyproject/galaxy/compare/0d221b33e6b8...55e539d1e943 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 97bf8b: Remove unnecessary split
by GitHub 04 Jan '19

04 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97bf8b7d738b0f40725cc5abcf5d1b783eb820cb https://github.com/galaxyproject/galaxy/commit/97bf8b7d738b0f40725cc5abcf5d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-03 (Thu, 03 Jan 2019) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Remove unnecessary split Commit: c242842b7e0e5032b08532fedd362c30a7f00866 https://github.com/galaxyproject/galaxy/commit/c242842b7e0e5032b08532fedd36… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-04 (Fri, 04 Jan 2019) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Use dict ``setdefault()`` Commit: 5a6f489276d9c5d3732948f7050b080004b84c11 https://github.com/galaxyproject/galaxy/commit/5a6f489276d9c5d3732948f7050b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-04 (Fri, 04 Jan 2019) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Remove mailto link from error reports `email_str` is often not a simple email address. Commit: 0d221b33e6b86611d09da8fa275d1e087dcf0c78 https://github.com/galaxyproject/galaxy/commit/0d221b33e6b86611d09da8fa275d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-01-04 (Fri, 04 Jan 2019) Changed paths: M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/meta.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Merge pull request #7168 from nsoranzo/misc Misc fixes Compare: https://github.com/galaxyproject/galaxy/compare/cf01e9e7ac87...0d221b33e6b8 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ab8fd9: Fixes toolshed and reports styling that was previo...
by GitHub 02 Jan '19

02 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab8fd9bc95b3e40eb3efc294408330954aa0220a https://github.com/galaxyproject/galaxy/commit/ab8fd9bc95b3e40eb3efc2944083… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-20 (Thu, 20 Dec 2018) Changed paths: M client/galaxy/style/scss/base.scss M templates/base/base_panels.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/admin/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/index.mako Log Message: ----------- Fixes toolshed and reports styling that was previously applied at the mako template level. We'll want to update the look here, I think, but this is an incremental step that correctly uses the background image, bundled via webpack. Commit: cf01e9e7ac8722d2e90fd5a6a6534b654aa89f0a https://github.com/galaxyproject/galaxy/commit/cf01e9e7ac8722d2e90fd5a6a653… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-01-02 (Wed, 02 Jan 2019) Changed paths: M client/galaxy/style/scss/base.scss M templates/base/base_panels.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/admin/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/index.mako Log Message: ----------- Merge pull request #7146 from dannon/fix_toolshed_styles Fixes toolshed and reports styling that was previously applied at the… Compare: https://github.com/galaxyproject/galaxy/compare/14ed1e78377b...cf01e9e7ac87 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] aae7c9: Fix TestDataResolver.get_filecontent
by GitHub 02 Jan '19

02 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aae7c9bb8457da24e45790b17464db0656b08746 https://github.com/galaxyproject/galaxy/commit/aae7c9bb8457da24e45790b17464… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-02 (Wed, 02 Jan 2019) Changed paths: M lib/galaxy/tools/verify/test_data.py Log Message: ----------- Fix TestDataResolver.get_filecontent Commit: 14ed1e78377b1945eebd967d08537bc931cf79e1 https://github.com/galaxyproject/galaxy/commit/14ed1e78377b1945eebd967d0853… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-02 (Wed, 02 Jan 2019) Changed paths: M lib/galaxy/tools/verify/test_data.py Log Message: ----------- Merge pull request #7165 from mvdbeek/remote_test_data_followup Fix TestDataResolver.get_filecontent Compare: https://github.com/galaxyproject/galaxy/compare/e906ca1ffdd9...14ed1e78377b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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