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1.7.2 #264

Merged
merged 69 commits into from
Aug 4, 2020
Merged

1.7.2 #264

merged 69 commits into from
Aug 4, 2020

Commits on May 18, 2020

  1. locked maestro version

    ben-bay committed May 18, 2020
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  2. incremented to 1.5.3

    ben-bay committed May 18, 2020
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  3. Update CHANGELOG.md

    ben-bay authored May 18, 2020
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  4. resolved conflict

    ben-bay committed May 18, 2020
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  6. Feature/koning/vhost no leading slash (#217)

    * The broker name can now be amqps (with ssl) or amqp (without ssl).
    The default rabbitmq vhost is now <user> instead of /<user>.
    
    * Undo fix typos.
    
    * Fix spacing.
    
    * Add amqps conn for self doc.
    koning authored May 18, 2020
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Commits on May 19, 2020

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Commits on May 26, 2020

  1. updated timeout (#223)

    * updated default task timeout
    
    * Added to CHANGELOG
    ben-bay authored May 26, 2020
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Commits on May 27, 2020

  1. Feature/koning/create encrypt key init (#219)

    * Add init_key to create the encryption key when merlin config is run.
    
    * Move import to point of use for encryption.
    koning authored May 27, 2020
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Commits on May 28, 2020

  1. Feature/koning/monitor upgrade (#221)

    * Fix sleep variable.
    
    * Change another sleep variable.
    
    * Change brackets.
    
    * Fix clarity for jobs but no consumers condition.
    
    * Fix comment.
    
    * Update comment.
    
    * Move check_merlin_status to router.
    
    * Run fix-style.
    koning authored May 28, 2020
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Commits on May 29, 2020

  1. Bugfix/ben/expand name (#220)

    * working on bugfix
    
    * achieved desired behavior
    
    * made expansion anf filewriting conditional
    
    * fixed style
    
    * updated CHANGELOG
    
    * fixed samples and restart
    
    * fixed style
    
    * used variable
    
    * added name expansion test
    
    * temporarily commented out one test
    
    * fixed style
    
    * added debug block
    
    * changes
    
    * corrected bug
    
    * updated example; scripts are now copied into merlin_info
    ben-bay authored May 29, 2020
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Commits on Jun 2, 2020

  1. Feature/ben/expose visibility timeout (#224)

    * exposed visibility timeout in config file
    
    * added visibility timeouts to default config files
    
    * fixed style
    
    * added seconds to clarify name
    
    * fixed attribute name
    
    * locked celery version at 4.4.2
    
    * updated CHANGELOG
    ben-bay authored Jun 2, 2020
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  2. v1.5.4

    ben-bay committed Jun 2, 2020
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  3. adjusted CHANGELOG

    ben-bay committed Jun 2, 2020
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  4. adjusted CHANGELOG

    ben-bay committed Jun 2, 2020
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  5. Feature/koning/info conn timeout (#226)

    * Add a timeout check for the merlin info kombu connection test. The redis
    server will not comply with the connection_timeout config.
    
    * Update docs.
    koning authored Jun 2, 2020
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  6. 1.6.0

    ben-bay committed Jun 2, 2020
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Commits on Jun 3, 2020

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  2. 1.6.1

    ben-bay committed Jun 3, 2020
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Commits on Jun 11, 2020

  1. bugfix (#232)

    * bugfix
    
    * removed repetition in logic
    ben-bay authored Jun 11, 2020
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Commits on Jun 16, 2020

  1. Log sample generation to merlin_info (#234)

    * sample generation is now logged to merlin_info
    
    * Added to CHANGELOG
    
    * fixed style
    ben-bay authored Jun 16, 2020
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Commits on Jun 18, 2020

  1. Maestro 1.1.8+ update (#233)

    * working on adding maestro's schema validation to merlin
    
    * updated schemas
    
    * adding merlin_schema to spec logic
    
    * added debug prints
    
    * added print
    
    * fixing vestigial Maestro calls
    
    * adjusted merlin_schemas
    
    * fixed json file
    
    * validation progress
    
    * added from_dict replacement logic
    
    * adjusted maestrowf version req
    
    * fixed string
    
    * schema improvements
    
    * merlinsection schema updates
    
    * merlin section error parsing appears to work
    
    * updated CHANGELOG
    
    * fixed merge error
    
    * Added walltime to json schema
    ben-bay authored Jun 18, 2020
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  2. Add the bank and walltime keywords to the batch slurm launch, these (#…

    …236)
    
    will not alter the lsf launch.
    koning authored Jun 18, 2020
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  3. Bugfix for new celery versions (#231)

    * Change the expand_tasks_with_samples task to use an immutable signature,
    no return code is neccessary.
    
    * Change only expand_tasks_with_samples to si()
    
    * Increase celery version requirement to the latest (4.4.5).
    
    * Update CHANGELOG.
    
    Co-authored-by: Benjamin Bay <[email protected]>
    koning and ben-bay authored Jun 18, 2020
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  4. hidden test specs (#237)

    * added tests to run_tests.py
    
    * updated merlinsection schema
    
    * added full_spec test
    
    * added to CHANGELOG
    ben-bay authored Jun 18, 2020
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Commits on Jun 22, 2020

  1. merlinspec change

    ben-bay committed Jun 22, 2020
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Commits on Jun 29, 2020

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Commits on Jul 1, 2020

  1. use regex to find variable tokens (#239)

    * now using regex to find variable tokens
    
    * added shell ref function
    ben-bay authored Jul 1, 2020
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  2. added to CHANGELOG

    ben-bay committed Jul 1, 2020
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Commits on Jul 2, 2020

  1. Revert maestro 1.1.8 support (#241)

    * reverted support of Maestro 1.1.8
    
    * removed tests that use maestro validation
    
    * fixed style
    ben-bay authored Jul 2, 2020
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  2. fixed cli tests, reactivated 3 old ones (#242)

    * fixed cli tests, reactivated 3 old ones
    
    * added to CHANGELOG
    ben-bay authored Jul 2, 2020
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  3. More provenance specs + logic improvements (#240)

    * added orig.yaml and expanded.yaml
    
    * added partial provenance spec
    
    * fixed style
    
    * added to CHANGELOG
    
    * removed comments
    
    * made env replacement more precise
    
    * fixed restart bug
    
    * changed provenance file names
    
    * logic update
    
    * fixed style
    
    * expansion now working
    
    * added cli test logic to test all 3 provenance file types
    
    * updated CHANGELOG
    
    * expansion sans io (#243)
    
    * reverted support of Maestro 1.1.8
    
    * removed tests that use maestro validation
    
    * fixed style
    
    * added sections property to spec
    
    * reducing number of file writes and reads
    
    * provenance specs are correct
    
    * fixed style
    
    * removed unused imports
    
    * cleaning up logic
    
    * fixed style
    
    * final logic improvements
    
    * removed unused property
    
    * updated CHANGELOG
    ben-bay authored Jul 2, 2020
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  4. v1.6.2

    ben-bay committed Jul 2, 2020
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  5. 1.6.2

    ben-bay committed Jul 2, 2020
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Commits on Jul 3, 2020

  1. debugging study

    ben-bay committed Jul 3, 2020
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  2. added provenance tests

    ben-bay committed Jul 3, 2020
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  3. fixed path in test

    ben-bay committed Jul 3, 2020
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Commits on Jul 6, 2020

  1. 1.6.2 changes

    ben-bay committed Jul 6, 2020
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Commits on Jul 9, 2020

  1. Docs/ben/level max dirs (#250)

    * added to documentation
    
    * added to CHANGELOG
    
    * added default
    ben-bay authored Jul 9, 2020
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Commits on Jul 14, 2020

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Commits on Jul 15, 2020

  1. Feature/ben/pgen (#248)

    * added basic pgen support
    
    * added to CHANGELOG
    
    * pgen, pargs, and env appear to work
    
    * added to CHANGELOG
    
    * fixed typo
    
    * added pgen cli test
    
    * added faq entry on pgen
    ben-bay authored Jul 15, 2020
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Commits on Jul 16, 2020

  1. Update Dockerfile (#254)

    fixdocker authored Jul 16, 2020
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  2. Update CHANGELOG.md

    ben-bay authored Jul 16, 2020
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  3. pretty yaml (#252)

    * starting
    
    * building pretty_dump function
    
    * updates
    
    * fixed style
    
    * tweaks
    
    * valid yaml
    
    * added yaml_sections
    
    * added to CHANGELOG
    
    * removed old yaml representer code
    
    * added cli test for equality of provenance specs
    
    * fixed pgen test
    
    * disabled test while not working
    
    * fixed yaml lists for source, paths, git
    
    * tweaks / fixes
    ben-bay authored Jul 16, 2020
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  4. env variable bugfix (#247)

    * removed expansion of env variables in provenance specs
    
    * added to CHANGELOG
    
    * corrected unit tests
    
    * added todos
    
    * working on expand_env_var function
    
    * fixed type bug
    
    * removed comments, prints, fixed style
    
    * added to CHANGELOG
    
    * tweaks
    
    * fixed output path
    
    * allowed study name to use env vars
    
    * fixed style
    
    * added to CHANGELOG, added support for 'restart'
    
    * Update CHANGELOG.md
    
    * added docs strings
    
    * added to docs
    
    * updated comment
    
    * fixed CHANGELOG
    ben-bay authored Jul 16, 2020
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  5. removed debug print

    ben-bay committed Jul 16, 2020
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Commits on Jul 20, 2020

  1. flux examples fix (#253)

    * Update flux example workflows to use new kvs query methods.
    
    * Update CHANGELOG with fix info.
    
    * Add coker fix comment.
    koning authored Jul 20, 2020
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  2. Update CHANGELOG.md

    ben-bay authored Jul 20, 2020
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Commits on Jul 21, 2020

  1. added gitlab ci file

    ben-bay committed Jul 21, 2020
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  2. improved gitlab ci setup

    ben-bay committed Jul 21, 2020
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  3. renamed file

    ben-bay committed Jul 21, 2020
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Commits on Jul 22, 2020

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  2. redis update (#255)

    * Update redis to new version with TLS support.
    
    * Add changelog.
    koning authored Jul 22, 2020
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Commits on Jul 23, 2020

  1. expose celery (#245)

    * added default app.yaml, still in progress...
    
    * added celery defaults
    
    * Update app.yaml
    
    * config override appears to be working
    
    * corrected value name
    
    * shifted some properties to be optional defaults
    
    * removed unneeded file
    
    * improvements
    
    * fixed style
    
    * fixed style
    
    * hid 'no override' message
    
    * tweaked var names
    
    * added 2 tests for celery app (#246)
    
    * fixed test
    
    * fixed workers bug
    
    * fixed unit tests for running offline
    
    * removed 2 unit tests
    
    * fixed CHANGELOG
    
    * added info print of all celery configurations being overridden
    ben-bay authored Jul 23, 2020
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  2. 1.7.0

    ben-bay committed Jul 23, 2020
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  3. 1.7.0

    ben-bay committed Jul 23, 2020
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Commits on Jul 28, 2020

  1. copy samplesfile to merlin_info (#259)

    * copy samplesfile to merlin_info
    
    * added to CHANGELOG
    ben-bay authored Jul 28, 2020
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Commits on Aug 3, 2020

  1. Bugfix/koning/process exceptions (#260)

    * Add bugfix log.
    
    * Add an exception catcher for the multiprocessing Process class.
    koning authored Aug 3, 2020
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  2. fixed style

    ben-bay committed Aug 3, 2020
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  3. 1.7.1

    ben-bay committed Aug 3, 2020
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  4. 1.7.1

    ben-bay committed Aug 3, 2020
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Commits on Aug 4, 2020

  1. hotfix

    ben-bay committed Aug 4, 2020
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  2. fix

    ben-bay committed Aug 4, 2020
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  3. 1.7.2

    ben-bay committed Aug 4, 2020
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