| HEAD | 615dacc | Remove unused CI test (#4843) | 16 March 2024, 00:19:23 UTC |
| refs/heads/2623/delete-redun-tests | 81315b2 | Added back the needed AWSencrypted test and need_ecnryption tag | 20 June 2019, 17:22:06 UTC |
| refs/heads/abstract_grid_types | 509562e | start typing AbstractGridEngine and friends | 02 March 2023, 17:11:44 UTC |
| refs/heads/adamnovak-giraffe-graph-build | edb0e58 | Complain about recursion for services jobs | 04 June 2020, 18:15:18 UTC |
| refs/heads/adamnovak-toil-vg | 46f0b22 | Fit scheduler config format and replicate kubeadm's overridden flag settings | 30 April 2021, 01:26:07 UTC |
| refs/heads/agc-integration | 62cf105 | Fix #4066 by printing locations in the destBucket in output | 16 March 2022, 19:37:22 UTC |
| refs/heads/auto-update | 4da7b59 | Add workflow to automatically update PRs when other PRs merge | 30 January 2024, 17:32:58 UTC |
| refs/heads/avoid_boto_imports | 1b1418a | Merge master into avoid_boto_imports | 31 January 2024, 21:27:21 UTC |
| refs/heads/cwl_test_cwl_1.2.1 | 804d6a2 | cwl: use the latest commit from the proposed CWL v1.2.1 branch match the changes in cwltest ("id" field instead of "label") likewise for CWL v1.0 & v1.1 | 16 August 2023, 18:21:46 UTC |
| refs/heads/cwltoil_types | 5270e38 | other type fixes | 20 July 2021, 10:57:40 UTC |
| refs/heads/cwltool_3.1.20230601100705 | 00fb975 | upgrade to cwltool 3.1.20230601100705 Highlights: `--leave-tmpdir` includes the input staging directories by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1674 https://github.com/common-workflow-language/cwltool/pull/1840 use importlib instead of the deprecated pkg_resources by @mr-c in https://github.com/common-workflow-language/cwltool/pull/1844 | 15 June 2023, 15:04:06 UTC |
| refs/heads/cwltool_3.1.20231206180100 | 7fbb170 | upgrade to cwltool 3.1.20231207110929 | 06 December 2023, 18:33:54 UTC |
| refs/heads/dev | 992d3b5 | Weird linting error? | 13 November 2023, 20:55:02 UTC |
| refs/heads/gh-pages | fb0643c | Update statement about CWL support. (#4387) | 22 February 2023, 15:31:16 UTC |
| refs/heads/gitlab-test | 2c91bd6 | Merge remote-tracking branch 'upstream/master' into issues/2589-construct-error-right | 02 May 2019, 17:11:16 UTC |
| refs/heads/gridengine-testing | bd020f2 | Base docker file | 02 September 2022, 18:55:02 UTC |
| refs/heads/hprc | 134d918 | Remove some environment logging | 15 April 2023, 01:07:10 UTC |
| refs/heads/issue/3884-descriptive-hpc-jobName | b7843dc | fix: merge conflicts from latest main | 23 November 2021, 20:21:10 UTC |
| refs/heads/issue/3917-toil-kill-find-pid-log | 7abfd02 | Merge branch 'master' into issue/3917-toil-kill-find-pid-log | 23 November 2021, 20:21:41 UTC |
| refs/heads/issues/1695-promise-indexing | 827bf30 | Make promises indexable with more path components to fix #1695 | 07 October 2020, 18:04:26 UTC |
| refs/heads/issues/1704-better-error-logging | 2aca6b8 | Merge master into issues/1704-better-error-logging | 16 March 2024, 00:21:30 UTC |
| refs/heads/issues/1812-makefile-and-pyproj | 9d4fbfe | Re-add tool.poetry.build with script | 01 November 2021, 20:33:14 UTC |
| refs/heads/issues/1951-update-aws-spot-documentation | 15e4055 | Merge branch 'master' into issues/1951-update-aws-spot-documentation | 30 January 2023, 21:54:29 UTC |
| refs/heads/issues/2088-toil-zipping-everything | 9f32741 | Fixed minor issues requested by Adam | 05 July 2019, 18:46:26 UTC |
| refs/heads/issues/2103-scaler-overhead | 8f8e500 | Merge branch 'master' into issues/2103-scaler-overhead | 04 November 2022, 20:12:36 UTC |
| refs/heads/issues/2232-handle-more-os-link-errors | ee9b57b | Merge branch 'master' into issues/2232-handle-more-os-link-errors | 05 December 2022, 16:14:33 UTC |
| refs/heads/issues/2234-fix_s3_import | 2150ab6 | Added cwl https import test (resolves #2234) | 08 February 2019, 16:28:37 UTC |
| refs/heads/issues/2355-fix-workdir-tmpfiles-permissions | a820032 | Add missing parentheses | 18 September 2020, 18:58:11 UTC |
| refs/heads/issues/2370-trackInstances | 0489e66 | Merge branch 'master' into issues/2370-trackInstances | 11 March 2019, 03:01:11 UTC |
| refs/heads/issues/2373-no-workdir-batch | b1c0270 | Support providing multiple work directories | 19 January 2023, 20:19:03 UTC |
| refs/heads/issues/2428-shift-tests-to-travis | 518630d | Revised indent error | 06 June 2019, 19:17:19 UTC |
| refs/heads/issues/2501-file-store-case-insensitive | cdf19b0 | Merge branch 'master' into issues/2501-file-store-case-insensitive | 24 June 2022, 21:17:55 UTC |
| refs/heads/issues/2504-ignored-nodes-for-some-reason | b58da2f | Propagate eager ignored node removals to batch system | 08 January 2019, 00:45:43 UTC |
| refs/heads/issues/2509-fix-job-throttling | 1fb78cf | Merge branch 'master' into issues/2509-fix-job-throttling | 08 May 2023, 16:11:10 UTC |
| refs/heads/issues/2534-make-cwl-use-symlinks | b76ec8e | Merge branch 'master' into issues/2534-make-cwl-use-symlinks | 22 February 2021, 10:29:25 UTC |
| refs/heads/issues/2549-fix-boto3-credentials | 7a84970 | Fix boto3 credentials for permanent credentials. | 18 March 2019, 21:31:05 UTC |
| refs/heads/issues/2551-optimize-filestore-links | 6b649cf | Allow symlinks to be created between devices when reading fileJobStore file | 25 March 2019, 23:47:56 UTC |
| refs/heads/issues/2553-cross-device-issue | 06a514c | Update fileJobStore to resolve symlinks before creating a hard link | 19 March 2019, 23:08:13 UTC |
| refs/heads/issues/2555-warn-diff-cwltool-version | 6ef611c | Add docstring | 03 August 2021, 16:25:48 UTC |
| refs/heads/issues/2558-add-missing-imports | 54fbffc | Add missing imports to toil/__init__.py. | 20 March 2019, 16:48:39 UTC |
| refs/heads/issues/2561-add-support-for-running-custom-init-commands-in-docker | 12e84f9 | Add docs for TOIL_CUSTOM_DOCKER_INIT_COMMAND. | 21 March 2019, 17:25:26 UTC |
| refs/heads/issues/2563-make-the-build-reproducible | 91cde6f | Make the build reproducible Whilst working on the Reproducible Builds effort [0], we noticed that toil could not be built reproducibly. This is due to the documentation embedding the year when the software was built. This was originally filed in Debian as #925191 [1]. [0] https://reproducible-builds.org/ [1] https://bugs.debian.org/925191 Signed-off-by: Chris Lamb <lamby@debian.org> | 21 March 2019, 02:42:41 UTC |
| refs/heads/issues/2568-private-ip-support | 8b21f8d | Add private IP support to node operations. | 25 March 2019, 20:09:20 UTC |
| refs/heads/issues/2576-fix-tmpdir-prefix | 31958a8 | Merge remote-tracking branch 'upstream/master' into issues/2576-fix-tmpdir-prefix | 23 May 2019, 17:41:06 UTC |
| refs/heads/issues/2585-save-toil-docker-registry | 49c6233 | Ensure TOIL_DOCKER_REGISTRY variable is in version_template. | 05 April 2019, 20:42:14 UTC |
| refs/heads/issues/2586-allow-enabling-caching | 99bc9e7 | Set defaultCaching back to True, but add =False option. | 08 April 2019, 19:57:27 UTC |
| refs/heads/issues/2606-improve-pr-import | 00aa222 | Rename example Github user | 18 April 2019, 20:08:17 UTC |
| refs/heads/issues/2608-update-copyrights | 9cadd6b | Merge branch 'master' of https://github.com/BD2KGenomics/toil into nonfunctionalChanges | 29 October 2018, 22:13:10 UTC |
| refs/heads/issues/2643-fix-StatsAndLogging-py3-before-3.6 | c8b3919 | jobStoreTest.py: add test for StatsAndLogging.writeLogFiles() | 24 April 2019, 08:54:26 UTC |
| refs/heads/issues/2648-changed-logging-output | a7440b2 | Updated log to say 'Job Ended' instead of '...ended successfully' | 05 July 2019, 17:00:10 UTC |
| refs/heads/issues/2649-log-file-access | f524012 | Implement file logging via requirements on AbstractFileStore implementations | 29 October 2020, 19:07:19 UTC |
| refs/heads/issues/2650-redesign-file-layout | aa7f5cf | Don't look for job ID in a service | 23 May 2019, 20:01:06 UTC |
| refs/heads/issues/2665-collect-logs | 924447c | Add command-line option --noStdOutErr - This forces Toil to discard all standard output and error from batch system jobs (i.e. redirect to /dev/null) should that be desirable - Implement option in common.py - BatchSystemSupport.formatStdOutErrPath() now returns os.devnull if noStdOutErr config option is true - Document this option in cliOptions.rst and hpcEnvironments.rst - Also document in hpcEnvironments.rst that in order to capture standard output and error --workDir will need to be on a shared filesystem | 08 May 2019, 06:44:26 UTC |
| refs/heads/issues/2683-update-to-ubuntu18.04 | de1dca9 | Remove commented-out package | 06 June 2019, 16:39:10 UTC |
| refs/heads/issues/2691-revise-caching | 54972d4 | Merge remote-tracking branch 'upstream/master' into issues/2691-revise-caching | 20 June 2019, 19:19:25 UTC |
| refs/heads/issues/2694-run-aws-jobstore-tests | d0ceaa4 | Python3 jobstore tests working. | 09 August 2019, 04:20:05 UTC |
| refs/heads/issues/2704-boto3-upload/download | 0f2b048 | updated jobstore | 22 August 2019, 17:41:33 UTC |
| refs/heads/issues/2711-truncating-fileName | 9a7864b | Added comment and updated len check | 02 August 2019, 22:26:45 UTC |
| refs/heads/issues/2717-k8-batch-system | a5801b5 | Merge remote-tracking branch 'upstream/issues/2717-k8-batch-system' into issues/2717-k8-batch-system | 24 October 2019, 19:34:08 UTC |
| refs/heads/issues/2721-pass-wdl-args | 9c53405 | rename toil-wdl-runner outputdir argument | 26 October 2019, 18:36:57 UTC |
| refs/heads/issues/2724-support-new-lsf | bc5866f | Merge branch 'master' into master | 01 July 2019, 17:09:27 UTC |
| refs/heads/issues/2725-un-hard-code-architecture | 57d1796 | Remove X86_64 type requirement from lsf support | 27 June 2019, 16:49:04 UTC |
| refs/heads/issues/2735-document-debug | cc5c74d | Don't use code role for link | 15 July 2019, 03:50:30 UTC |
| refs/heads/issues/2742-match-appliance | 697957d | Keep using Python 2 to do the docker login | 23 January 2020, 01:13:21 UTC |
| refs/heads/issues/2759-fix-wdl-builtin-basename | 0ccf7ec | Merge branch 'master' into issues/2759-fix-wdl-builtin-basename | 16 April 2021, 17:16:52 UTC |
| refs/heads/issues/2767-expose-docker-timeout | 9582e1f | Apply extended timeout to other connections to the Docker daemon | 19 August 2019, 15:49:20 UTC |
| refs/heads/issues/2808-head-object-404 | 8f676c0 | Add wait_until_exists before calling head_object, resolves #2808 | 04 October 2019, 19:44:34 UTC |
| refs/heads/issues/2808-head-object-404_with-encryption | 4f6032d | Re-add wait_until_exists, this time with encryption args as necessary, resolves #2808 | 12 November 2019, 21:31:23 UTC |
| refs/heads/issues/2811-robust-space | 333c5ec | Use argparse Namespace because setattr on Object doesn't always work in the tests | 23 October 2019, 17:37:16 UTC |
| refs/heads/issues/2820-split-long-commands | 4cc9674 | spacing | 13 August 2020, 07:22:05 UTC |
| refs/heads/issues/2821-mock-with-namespace | d215043 | Use argparse Namespace because setattr on Object doesn't always work in the tests | 23 October 2019, 17:37:16 UTC |
| refs/heads/issues/2827-use-coreos-family | 14be5d6 | Try to use coreos-stable family | 30 October 2019, 03:21:20 UTC |
| refs/heads/issues/2832-deduplicate-examples | e4b5adc | Make examples a symlink to make examples discoverable | 31 October 2019, 18:11:22 UTC |
| refs/heads/issues/2835-de-spookify-names | 6eaab02 | Turn usernames into non-spooky Kubernetes name components | 31 October 2019, 18:27:45 UTC |
| refs/heads/issues/2837-configure-kubernetes | c58d0d2 | Add missing colon I think I changed this line as a result of a review and never actually tested it. Now it will be under CI though. | 02 January 2020, 20:30:48 UTC |
| refs/heads/issues/2839-botoadapter | 133fec4 | Merge remote-tracking branch 'upstream/master' into issues/2839-botoadapter | 17 January 2020, 18:15:26 UTC |
| refs/heads/issues/2850-try-service-account | e98a7bd | Don't log every time we poll a scheduled pod | 12 November 2019, 21:28:24 UTC |
| refs/heads/issues/2858-watch-for-oom | fb9b36f | Merge branch 'master' into issues/2858-watch-for-oom | 23 December 2019, 21:38:17 UTC |
| refs/heads/issues/2864-k8s-queue-jobs | 77d0687 | protect `_getIssuedNonLocalBatchJobIDs` | 14 February 2023, 17:35:36 UTC |
| refs/heads/issues/2864-k8s-resource-restriction-options | b5ee7f2 | Fix mypy | 10 January 2023, 07:49:40 UTC |
| refs/heads/issues/2865-kubernetes-owner-name | 7b825d8 | Revise variable description. | 21 November 2019, 18:12:46 UTC |
| refs/heads/issues/2867-constantly-reload-kubernetes | 116852a | Use a with to clearly close our namespace file | 20 December 2019, 00:38:22 UTC |
| refs/heads/issues/2873-fix-aws-jobstore-test | 2530608 | Do integration tests last again | 05 December 2019, 22:11:32 UTC |
| refs/heads/issues/2876-change-kubernetes-sizing | 4e576c1 | Change Kubernetes job sizing logic This will fix #2876 by not floor-ing the CPU requirement. It now uses the same requirements and limits, to make our admins happy, and also now adds half a gig of memory and storage for Toil overhead (like the hot-deployed user scripts, or the logs), instead of using that as a minimum job size, which didn't quite make sense. | 05 December 2019, 18:30:03 UTC |
| refs/heads/issues/2879-increase-disk-to-default | e4937bb | Up the disk to the default as well as the memory | 06 December 2019, 00:12:52 UTC |
| refs/heads/issues/2882-schlep-numbers | 0a61a12 | Report more info from and robustify the ToyService Maybe this will make it not fail and fix #2882? | 06 December 2019, 19:35:55 UTC |
| refs/heads/issues/2884-crypticKubEnd | e4106ae | fixed the problems | 30 March 2020, 23:29:34 UTC |
| refs/heads/issues/2893-tolerate-missing-bucket | 5bd06fd | Use status to properly get the HTTP status code from boto | 22 January 2020, 20:43:30 UTC |
| refs/heads/issues/2897-atomic-jobstore | 032ccc2 | used atomic creation when reading from aws/google job stores | 09 January 2020, 19:59:28 UTC |
| refs/heads/issues/2897-atomic-jobstore-diekhans | 7d4cbc8 | added function to do atomic install on posix filesystems added atomic copying for file jobstore (addresses #2897) | 24 December 2019, 05:07:16 UTC |
| refs/heads/issues/2907-default-vars | c742347 | Set Docker vars back to ?= This will fix #2907. | 08 January 2020, 17:41:36 UTC |
| refs/heads/issues/2910-commit-giveaway | 4adf3a0 | Make sure to commit when giving away files This might help with #2910. | 09 January 2020, 23:23:46 UTC |
| refs/heads/issues/2910-test-caching-sync | 1609ba5 | Except into e instead of trying to match type e | 07 February 2020, 19:01:30 UTC |
| refs/heads/issues/2915-fix-aws-size-polling | f15bfb1 | Actually call the implemented size polling method | 10 January 2020, 23:00:21 UTC |
| refs/heads/issues/2919-robustify-kubernetes | d22384e | Improve Kubernetes job timing The Kubernetes batch system should now always produce positive runtimes, even when pods behave strangely. It also does a bit more work to come up with meaningful runtimes for cases where pods don't formally end. | 15 January 2020, 18:47:28 UTC |
| refs/heads/issues/2923-reuse-pods | e923d7b | Start on a wrapping version of the local batch system support | 15 January 2020, 23:24:31 UTC |
| refs/heads/issues/2924-require-new-http-parser | cbacf14 | Use an http-parser for pymesos that builds on 3.7+ | 22 January 2020, 19:17:03 UTC |
| refs/heads/issues/2925-intermittentFailure | b5bb1db | increased badWorkedFailInterval and added more failure attempts | 22 January 2020, 20:55:28 UTC |
| refs/heads/issues/2928-reduce-granularity | 1da749a | Raise default min CPU size of single machine jobs This should stop us spawning quite so many threads on single machine, and help with #2928. The cost is that jobs that ask for less than a core will get an entire core to themselves. A real solution without all these placeholder threads would address that, but this change is easy and should be a good stopgap. | 19 February 2020, 19:29:32 UTC |
| refs/heads/issues/2929-restrict-deferred-names | 0779163 | Exclude .nfs files from deferred function search | 21 January 2020, 18:45:16 UTC |
