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dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\r\n\r\n* bugfix/server-pip-redis-conf (#443)\r\n\r\n* add *.conf to the MANIFEST file so pip will grab the redis.conf file\r\n\r\n* add note explaining how to fix a hanging merlin server start\r\n\r\n* modify CHANGELOG\r\n\r\n* add second export option to docs and fix typo\r\n\r\n* bump to version 1.10.3 (#444)\r\n\r\n---------\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\r\n\r\n* change hardcoded sphinx requirement\r\n\r\n* update CHANGELOG\r\n\r\n---------\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\r\n\r\n* feature/vlauncher (#447)\r\n\r\n* fix file naming error for iterative workflows\r\n\r\n* fixed small bug with new filepath naming\r\n\r\n* add VLAUNCHER functionality\r\n\r\n* add docs for VLAUNCHER and modify changelog\r\n\r\n* re-word docs and fix table format\r\n\r\n* add a test for vlauncher\r\n\r\n* run fix-style and add a test for vlauncher\r\n\r\n* Add the find_vlaunch_var and setup_vlaunch functions.\r\nThe numeric value of the shell variables may not be defined until run\r\ntime, so replace with variable strings instead of values.\r\nConsolidate the commands into one function.\r\n\r\n* Add variable set for (t)csh.\r\n\r\n* Run fix-style\r\n\r\n* make step settings the defaults and ignore commented lines\r\n\r\n* add some additional tests\r\n\r\n* remove regex library import\r\n\r\n---------\r\n\r\nCo-authored-by: Joseph M. Koning <koning1@llnl.gov>\r\n\r\n* release/1.11.0 (#448)\r\n\r\n* bugfix/skewed-sample-hierarchy (#450)\r\n\r\n* add patch for skewed sample hierarchy/additional samples\r\n\r\n* update changelog\r\n\r\n* catch narrower range of exceptions\r\n\r\n* bugfix/lsf-gpu-typo (#453)\r\n\r\n* fix typo in batch.py that causes a bug\r\n\r\n* change print statements to log statements\r\n\r\n* release/1.11.1 (#454)\r\n\r\n* Add Pytest Fixtures to Test Suite (#456)\r\n\r\n* begin work on integration refactor; create fixtures and initial tests\r\n\r\n* update CHANGELOG and run fix-style\r\n\r\n* add pytest fixtures and README explaining them\r\n\r\n* add tests to demonstrate how to use the fixtures\r\n\r\n* move/rename some files and modify integration's README\r\n\r\n* add password change to redis.pass file\r\n\r\n* fix lint issues\r\n\r\n* modify redis pwd for test server to be constant for each test\r\n\r\n* fix lint issue only caught on github ci\r\n\r\n* Bugfix for WEAVE CI (#457)\r\n\r\n* begin work on integration refactor; create fixtures and initial tests\r\n\r\n* update CHANGELOG and run fix-style\r\n\r\n* add pytest fixtures and README explaining them\r\n\r\n* add tests to demonstrate how to use the fixtures\r\n\r\n* move/rename some files and modify integration's README\r\n\r\n* add password change to redis.pass file\r\n\r\n* fix lint issues\r\n\r\n* modify redis pwd for test server to be constant for each test\r\n\r\n* fix lint issue only caught on github ci\r\n\r\n* add fix for merlin server startup\r\n\r\n* update CHANGELOG\r\n\r\n* bugfix/monitor-shutdown (#452)\r\n\r\n* add celery query to see if workers still processing tasks\r\n\r\n* fix merlin status when using redis as broker\r\n\r\n* fix consumer count bug and run fix-style\r\n\r\n* fix linter issues\r\n\r\n* update changelog\r\n\r\n* update docs for monitor\r\n\r\n* remove unused exception I previously added\r\n\r\n* first attempt at using pytest fixtures for monitor tests\r\n\r\n* (partially) fix launch_workers fixture so it can be used in multiple classes\r\n\r\n* fix linter issues and typo on pytest decorator\r\n\r\n* update black's python version and fix style issue\r\n\r\n* remove print statements from celeryadapter.py\r\n\r\n* workers manager is now allowed to be used as a context manager\r\n\r\n* add one thing to changelog and remove print statement\r\n\r\n* Add the missing restart keyword to the specification docs. (#459)\r\n\r\n* docs/conversion-to-mkdocs (#460)\r\n\r\n* remove a merge conflict statement that was missed\r\n\r\n* add base requirements for mkdocs\r\n\r\n* set up configuration for API docs\r\n\r\n* start work on porting user guide to mkdocs\r\n\r\n* add custom styling and contact page\r\n\r\n* begin work on porting tutorial to mkdocs\r\n\r\n* add new examples page\r\n\r\n* move old sphinx docs to their own folder (*delete later*)\r\n\r\n* modify some admonitions to be success\r\n\r\n* modify hello examples page and port step 3 of tutorial to mkdocs\r\n\r\n* fix typo in hello example\r\n\r\n* finish porting step 4 of tutorial to mkdocs\r\n\r\n* port part 5 of the tutorial to mkdocs\r\n\r\n* copy faq and contributing from old docs\r\n\r\n* port step 6 of tutorial to mkdocs\r\n\r\n* remove unused prereq\r\n\r\n* port step 7 of tutorial to mkdocs\r\n\r\n* add more detailed instructions on contributing\r\n\r\n* move venv page into installation and add spack instructions too\r\n\r\n* add configuration docs\r\n\r\n* add content to user guide landing page\r\n\r\n* port celery page to mkdocs\r\n\r\n* rearrange configuration pages to add in merlin server configuration instructions\r\n\r\n* port command line page to mkdocs\r\n\r\n* finish new landing page\r\n\r\n* change size of merlin logo\r\n\r\n* port variables page to mkdocs\r\n\r\n* fix broken links to configuration page\r\n\r\n* port FAQ to mkdocs\r\n\r\n* fix incorrect requirement name\r\n\r\n* update CHANGELOG\r\n\r\n* attempt to get docs to build through readthedocs\r\n\r\n* port docker page to mkdocs\r\n\r\n* port contributing guide to mkdocs\r\n\r\n* add new 'running studies' page\r\n\r\n* add path changes to images\r\n\r\n* add a page on how to interpret study output\r\n\r\n* add page on the spec file\r\n\r\n* remove old sphinx docs that are no longer needed\r\n\r\n* added README to docs and updated CHANGELOG\r\n\r\n* fix copyright and hello_samples tree\r\n\r\n* rearrange images/stylesheets and statements that use them\r\n\r\n* add suggestions from Luc and Joe\r\n\r\n* add tcsh instructions for venv activation\r\n\r\n* add Charle's suggestions for the landing page\r\n\r\n* change tcsh mentions to csh\r\n\r\n* openfoam tutorial modifications (#463)\r\n\r\n* feature/revamped status (#464)\r\n\r\n* feature/new-status (#442)\r\n\r\n* add backend functionality for merlin status\r\n\r\n* add frontend functionality for merlin status\r\n\r\n* add tests for merlin status\r\n\r\n* run fix-style and remove import of deprecated function\r\n\r\n* update CHANGELOG\r\n\r\n* add more logging statements, make better use of glob\r\n\r\n* run fix-style\r\n\r\n* clean up test files a bit\r\n\r\n* fix test suite after step_name_map mod\r\n\r\n* add avg/std dev run time calculations to status\r\n\r\n* modify status tests to accommodate new avg/std dev calculations\r\n\r\n* fix linter issues\r\n\r\n* fix lint issue and add test for avg/std dev calc\r\n\r\n* feature/detailed-status (#451)\r\n\r\n* Version/1.11.0 (#449)\r\n\r\n* fix default worker bug with all steps\r\n\r\n* version bump and requirements fix\r\n\r\n* Bugfix/filename-special-vars (#425)\r\n\r\n* fix file naming bug\r\n\r\n* fix filename bug with variable as study name\r\n\r\n* add tests for the file name special vars changes\r\n\r\n* modify changelog\r\n\r\n* implement Luc's suggestions\r\n\r\n* remove replace line\r\n\r\n* Create dependabot-changelog-updater.yml\r\n\r\n* testing outputs of modifying changelog\r\n\r\n* delete dependabot-changelog-updater\r\n\r\n* feature/pdf-docs (#427)\r\n\r\n* first attempt at adding pdf\r\n\r\n* fixing build error\r\n\r\n* modify changelog to show docs changes\r\n\r\n* fix errors Luc found in the build logs\r\n\r\n* trying out removal of latex\r\n\r\n* reverting latex changes back\r\n\r\n* uncommenting the latex_elements settings\r\n\r\n* adding epub to see if latex will build\r\n\r\n* adding a latex engine variable to conf\r\n\r\n* fix naming error with latex_engine\r\n\r\n* attempting to add a logo to the pdf build\r\n\r\n* testing an override to the searchtools file\r\n\r\n* revert back to not using searchtools override\r\n\r\n* update changelog\r\n\r\n* bugfix/openfoam_singularity_issues (#426)\r\n\r\n* fix openfoam_singularity issues\r\n\r\n* update requirements and descriptions for openfoam examples\r\n\r\n* bugfix/output-path-substitution (#430)\r\n\r\n* fix bug with output_path and variable substitution\r\n\r\n* add tests for cli substitutions\r\n\r\n* bugfix/scheduler-permission-error (#436)\r\n\r\n* Release/1.10.2 (#437)\r\n\r\n* bump version to 1.10.2\r\n\r\n* bump version in CHANGELOG\r\n\r\n* resolve develop to main merge issues (#439)\r\n\r\n* fix default worker bug with all steps\r\n\r\n* version bump and requirements fix\r\n\r\n* dependabot/certifi-requests-pygments (#441)\r\n\r\n* Bump certifi from 2022.12.7 to 2023.7.22 in /docs\r\n\r\nBumps [certifi](https://github.com/certifi/python-certifi) from 2022.12.7 to 2023.7.22.\r\n- [Commits](https://github.com/certifi/python-certifi/compare/2022.12.07...2023.07.22)\r\n\r\n---\r\nupdated-dependencies:\r\n- dependency-name: certifi\r\n  dependency-type: direct:production\r\n...\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\n\r\n* add all dependabot changes and update CHANGELOG\r\n\r\n---------\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\r\n\r\n* bugfix/server-pip-redis-conf (#443)\r\n\r\n* add *.conf to the MANIFEST file so pip will grab the redis.conf file\r\n\r\n* add note explaining how to fix a hanging merlin server start\r\n\r\n* modify CHANGELOG\r\n\r\n* add second export option to docs and fix typo\r\n\r\n* bump to version 1.10.3 (#444)\r\n\r\n* bugfix/sphinx-5.3.0-requirement (#446)\r\n\r\n* Version/1.10.3 (#445)\r\n\r\n* fix default worker bug with all steps\r\n\r\n* version bump and requirements fix\r\n\r\n* Bugfix/filename-special-vars (#425)\r\n\r\n* fix file naming bug\r\n\r\n* fix filename bug with variable as study name\r\n\r\n* add tests for the file name special vars changes\r\n\r\n* modify changelog\r\n\r\n* implement Luc's suggestions\r\n\r\n* remove replace line\r\n\r\n* Create dependabot-changelog-updater.yml\r\n\r\n* testing outputs of modifying changelog\r\n\r\n* delete dependabot-changelog-updater\r\n\r\n* feature/pdf-docs (#427)\r\n\r\n* first attempt at adding pdf\r\n\r\n* fixing build error\r\n\r\n* modify changelog to show docs changes\r\n\r\n* fix errors Luc found in the build logs\r\n\r\n* trying out removal of latex\r\n\r\n* reverting latex changes back\r\n\r\n* uncommenting the latex_elements settings\r\n\r\n* adding epub to see if latex will build\r\n\r\n* adding a latex engine variable to conf\r\n\r\n* fix naming error with latex_engine\r\n\r\n* attempting to add a logo to the pdf build\r\n\r\n* testing an override to the searchtools file\r\n\r\n* revert back to not using searchtools override\r\n\r\n* update changelog\r\n\r\n* bugfix/openfoam_singularity_issues (#426)\r\n\r\n* fix openfoam_singularity issues\r\n\r\n* update requirements and descriptions for openfoam examples\r\n\r\n* bugfix/output-path-substitution (#430)\r\n\r\n* fix bug with output_path and variable substitution\r\n\r\n* add tests for cli substitutions\r\n\r\n* bugfix/scheduler-permission-error (#436)\r\n\r\n* Release/1.10.2 (#437)\r\n\r\n* bump version to 1.10.2\r\n\r\n* bump version in CHANGELOG\r\n\r\n* resolve develop to main merge issues (#439)\r\n\r\n* fix default worker bug with all steps\r\n\r\n* version bump and requirements fix\r\n\r\n* dependabot/certifi-requests-pygments (#441)\r\n\r\n* Bump certifi from 2022.12.7 to 2023.7.22 in /docs\r\n\r\nBumps [certifi](https://github.com/certifi/python-certifi) from 2022.12.7 to 2023.7.22.\r\n- [Commits](https://github.com/certifi/python-certifi/compare/2022.12.07...2023.07.22)\r\n\r\n---\r\nupdated-dependencies:\r\n- dependency-name: certifi\r\n  dependency-type: direct:production\r\n...\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\n\r\n* add all dependabot changes and update CHANGELOG\r\n\r\n---------\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\r\n\r\n* bugfix/server-pip-redis-conf (#443)\r\n\r\n* add *.conf to the MANIFEST file so pip will grab the redis.conf file\r\n\r\n* add note explaining how to fix a hanging merlin server start\r\n\r\n* modify CHANGELOG\r\n\r\n* add second export option to docs and fix typo\r\n\r\n* bump to version 1.10.3 (#444)\r\n\r\n---------\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\r\n\r\n* change hardcoded sphinx requirement\r\n\r\n* update CHANGELOG\r\n\r\n---------\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\r\n\r\n* feature/vlauncher (#447)\r\n\r\n* fix file naming error for iterative workflows\r\n\r\n* fixed small bug with new filepath naming\r\n\r\n* add VLAUNCHER functionality\r\n\r\n* add docs for VLAUNCHER and modify changelog\r\n\r\n* re-word docs and fix table format\r\n\r\n* add a test for vlauncher\r\n\r\n* run fix-style and add a test for vlauncher\r\n\r\n* Add the find_vlaunch_var and setup_vlaunch functions.\r\nThe numeric value of the shell variables may not be defined until run\r\ntime, so replace with variable strings instead of values.\r\nConsolidate the commands into one function.\r\n\r\n* Add variable set for (t)csh.\r\n\r\n* Run fix-style\r\n\r\n* make step settings the defaults and ignore commented lines\r\n\r\n* add some additional tests\r\n\r\n* remove regex library import\r\n\r\n---------\r\n\r\nCo-authored-by: Joseph M. Koning <koning1@llnl.gov>\r\n\r\n* release/1.11.0 (#448)\r\n\r\n* bugfix/skewed-sample-hierarchy (#450)\r\n\r\n* add patch for skewed sample hierarchy/additional samples\r\n\r\n* update changelog\r\n\r\n* catch narrower range of exceptions\r\n\r\n---------\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\r\nCo-authored-by: Joseph M. Koning <koning1@llnl.gov>\r\n\r\n* add functionality for the detailed-status command\r\n\r\n* add tests for detailed-status\r\n\r\n* fix linter issues\r\n\r\n* update changelog\r\n\r\n* general cleanup and add log statements\r\n\r\n* slightly modify two tests\r\n\r\n* default status renderer now uses json status format\r\n\r\n* remove inaccurate comment\r\n\r\n* bugfix/lsf-gpu-typo (#453)\r\n\r\n* fix typo in batch.py that causes a bug\r\n\r\n* change print statements to log statements\r\n\r\n* release/1.11.1 (#454)\r\n\r\n* Add Pytest Fixtures to Test Suite (#456)\r\n\r\n* begin work on integration refactor; create fixtures and initial tests\r\n\r\n* update CHANGELOG and run fix-style\r\n\r\n* add pytest fixtures and README explaining them\r\n\r\n* add tests to demonstrate how to use the fixtures\r\n\r\n* move/rename some files and modify integration's README\r\n\r\n* add password change to redis.pass file\r\n\r\n* fix lint issues\r\n\r\n* modify redis pwd for test server to be constant for each test\r\n\r\n* fix lint issue only caught on github ci\r\n\r\n* Bugfix for WEAVE CI (#457)\r\n\r\n* begin work on integration refactor; create fixtures and initial tests\r\n\r\n* update CHANGELOG and run fix-style\r\n\r\n* add pytest fixtures and README explaining them\r\n\r\n* add tests to demonstrate how to use the fixtures\r\n\r\n* move/rename some files and modify integration's README\r\n\r\n* add password change to redis.pass file\r\n\r\n* fix lint issues\r\n\r\n* modify redis pwd for test server to be constant for each test\r\n\r\n* fix lint issue only caught on github ci\r\n\r\n* add fix for merlin server startup\r\n\r\n* update CHANGELOG\r\n\r\n* bugfix/monitor-shutdown (#452)\r\n\r\n* add celery query to see if workers still processing tasks\r\n\r\n* fix merlin status when using redis as broker\r\n\r\n* fix consumer count bug and run fix-style\r\n\r\n* fix linter issues\r\n\r\n* update changelog\r\n\r\n* update docs for monitor\r\n\r\n* remove unused exception I previously added\r\n\r\n* first attempt at using pytest fixtures for monitor tests\r\n\r\n* (partially) fix launch_workers fixture so it can be used in multiple classes\r\n\r\n* fix linter issues and typo on pytest decorator\r\n\r\n* update black's python version and fix style issue\r\n\r\n* remove print statements from celeryadapter.py\r\n\r\n* workers manager is now allowed to be used as a context manager\r\n\r\n* add one thing to changelog and remove print statement\r\n\r\n* Add the missing restart keyword to the specification docs. (#459)\r\n\r\n* add Jeremy's suggestion to change vars option to output-path\r\n\r\n* remove unnecessary lines from CHANGELOG\r\n\r\n---------\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\r\nCo-authored-by: Joseph M. Koning <koning1@llnl.gov>\r\nCo-authored-by: Joe Koning <koning@users.noreply.github.com>\r\n\r\n* feature/queue info (#461)\r\n\r\n* remove a merge conflict statement that was missed\r\n\r\n* add queue-info functionality\r\n\r\n* add tests for queue-info\r\n\r\n* update CHANGELOG\r\n\r\n* add try/except for forceful termination of test workers\r\n\r\n* change github workflow to use py38 with black instead of py36\r\n\r\n* run fix-style with py 3.12 and fix a typo in a test\r\n\r\n* add filetype check for dump option\r\n\r\n* add banner print statement\r\n\r\n* docs/revamped status (#462)\r\n\r\n* fix broken image link in README\r\n\r\n* add new commands to the command line page\r\n\r\n* add monitoring docs layout and complete status cmds page\r\n\r\n* fix bug with dumping queue-info to files\r\n\r\n* add docs for queue-info\r\n\r\n* add documentation for 'query-workers'\r\n\r\n* add reference to new query-workers docs and split a paragraph\r\n\r\n* fix small bug with --steps option of monitor\r\n\r\n* add documentation for monitor command\r\n\r\n* update CHANGELOG\r\n\r\n* fix dump-csv image for queue-info\r\n\r\n---------\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\r\nCo-authored-by: Joseph M. Koning <koning1@llnl.gov>\r\nCo-authored-by: Joe Koning <koning@users.noreply.github.com>\r\n\r\n* release/1.12.0 (#465)\r\n\r\n* remove a merge conflict statement that was missed\r\n\r\n* bump version to 1.12.0\r\n\r\n* feature/retry_priority (#468)\r\n\r\n* remove a merge conflict statement that was missed\r\n\r\n* add a 'pip freeze' call in github workflow to view reqs versions\r\n\r\n* add new retry priority as highest task priority\r\n\r\n* update CHANGELOG\r\n\r\n* add in MID priority\r\n\r\n* change default priority to use priority map MID value\r\n\r\n* docs/server-cross-node (#470)\r\n\r\n* remove a merge conflict statement that was missed\r\n\r\n* add a 'pip freeze' call in github workflow to view reqs versions\r\n\r\n* rename the merlin server config page\r\n\r\n* add instructions for running a cross-node workflow w/ containerized server\r\n\r\n* update CHANGELOG\r\n\r\n* bugfix/initial-status-issues (#471)\r\n\r\n* remove a merge conflict statement that was missed\r\n\r\n* add a 'pip freeze' call in github workflow to view reqs versions\r\n\r\n* fix bug with dry run status\r\n\r\n* set MANPAGER for detailed-status\r\n\r\n* fix bug with 1 sample removing the status file\r\n\r\n* add support for multiple workers on one step in status files\r\n\r\n* update test suite to accommodate changes to workers in status files\r\n\r\n* add catch and potential fix for JSONDecodeError\r\n\r\n* fix docstring of a test\r\n\r\n* update CHANGELOG.md\r\n\r\n* run fix style and add Luc's suggestions\r\n\r\n* run fix-style with python 3.12\r\n\r\n* added additional check for status file while condensing\r\n\r\n* add try/except to catch an error for dumping statuses\r\n\r\n* release/1.12.1 (#472)\r\n\r\n* remove a merge conflict statement that was missed\r\n\r\n* add a 'pip freeze' call in github workflow to view reqs versions\r\n\r\n* bump version to 1.12.1\r\n\r\n* fix a lint issue that somehow slipped through the cracks\r\n\r\n---------\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\r\nCo-authored-by: Joseph M. 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