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Anvil update #474

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wants to merge 64 commits into from
Closed

Anvil update #474

wants to merge 64 commits into from

Commits on Aug 13, 2021

  1. Changes for not mounting entire NFS to each job 

    friends with galaxyproject/galaxy#12345
    @almahmoud
    almahmoud authored Aug 13, 2021
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Commits on Aug 30, 2021

  1. Separate data and working dir pvcs

    @almahmoud
    almahmoud authored Aug 30, 2021
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Commits on Dec 20, 2021

  1. Removed unnecessary mounts and made inputs read only

    @nuwang
    nuwang committed Dec 20, 2021
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Commits on Feb 9, 2024

  1. Remove spaces that makes helm lint unhappy

    @ksuderman
    ksuderman committed Feb 9, 2024
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  2. First pass at defining cron jobs in the values.yaml file.

    @ksuderman
    ksuderman committed Feb 9, 2024
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Commits on Feb 13, 2024

  1. Fix command formatting and quoting

    @ksuderman
    ksuderman committed Feb 13, 2024
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  2. Remove nodeSelector

    @ksuderman
    ksuderman committed Feb 13, 2024
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Commits on Feb 16, 2024

  1. Tmp cleanup and maintenance scripts are treated as special cases.

    @ksuderman
    ksuderman committed Feb 16, 2024
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  2. Update the name of the container used to run the maintenance script.

    @ksuderman
    ksuderman committed Feb 16, 2024
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Commits on Feb 19, 2024

  1. Define all cron jobs in the values.yaml file again, but allows time d… 

    …urations to be parameterized.
    @ksuderman
    ksuderman committed Feb 19, 2024
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Commits on Feb 20, 2024

  1. Use walltime limit for cleanup and other minor tweaks

    @nuwang
    nuwang committed Feb 20, 2024
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  2. Change find units from seconds to days

    @nuwang
    nuwang committed Feb 20, 2024
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Commits on Feb 21, 2024

  1. Parameterize the nodeSelector

    @ksuderman
    ksuderman committed Feb 21, 2024
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  2. Remove the chown cron job

    @ksuderman
    ksuderman committed Feb 21, 2024
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  3. Reverting my revert

    @ksuderman
    ksuderman committed Feb 21, 2024
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Commits on Feb 28, 2024

  1. Add extraFileMappings for cron jobs

    @ksuderman
    ksuderman committed Feb 28, 2024
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  2. Start documenting cron jobs

    @ksuderman
    ksuderman committed Feb 28, 2024
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Commits on Mar 8, 2024

  1. Make the galaxy.yml file available in a configmap for the maintenance… 

    … cronjob
    @ksuderman
    ksuderman committed Mar 8, 2024
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  2. Update galaxy/values.yaml 

    Co-authored-by: Nuwan Goonasekera <[email protected]>
    @ksuderman @nuwang
    ksuderman and nuwang authored Mar 8, 2024
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Commits on Mar 12, 2024

  1. Add helper to calculate the postgres connection string

    @ksuderman
    ksuderman committed Mar 12, 2024
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  2. Add cron job documentation and remove Galaxy versions section

    @ksuderman
    ksuderman committed Mar 12, 2024
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  3. Add env definitions

    @ksuderman
    ksuderman committed Mar 12, 2024
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  4. Maintenace job should include default env vars

    @ksuderman
    ksuderman committed Mar 12, 2024
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  5. Update galaxy/values.yaml 

    Co-authored-by: Nuwan Goonasekera <[email protected]>
    @ksuderman @nuwang
    ksuderman and nuwang authored Mar 12, 2024
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  6. Update galaxy/values.yaml 

    Co-authored-by: Nuwan Goonasekera <[email protected]>
    @ksuderman @nuwang
    ksuderman and nuwang authored Mar 12, 2024
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  7. Parameterize Docker image for cron jobs

    @ksuderman
    ksuderman committed Mar 12, 2024
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Commits on Mar 13, 2024

  1. Allow mode (permissions) to be defined on extraFileMappings

    @ksuderman
    ksuderman committed Mar 13, 2024
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  2. Add YAML document separators (triple dashes) to the start of yaml tem… 

    …plates.
    @ksuderman
    ksuderman committed Mar 13, 2024
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  3. Add example cron job

    @ksuderman
    ksuderman committed Mar 13, 2024
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  4. Additional documentation for cron jobs

    @ksuderman
    ksuderman committed Mar 13, 2024
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Commits on Mar 14, 2024

  1. Comment out the example cron job. Examples should not add arbitrary c… 

    …ode to clusters.
    @ksuderman
    ksuderman committed Mar 14, 2024
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Commits on Mar 17, 2024

  1. Run extraEnv values through the template engine

    @ksuderman
    ksuderman committed Mar 17, 2024
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Commits on Mar 21, 2024

  1. Run tests with 1.28, and add missing tool versions to sanitize allowlist

    @afgane
    afgane committed Mar 21, 2024
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Commits on Apr 16, 2024

  1. Merge branch 'master' into data_pvc

    @nuwang
    nuwang authored Apr 16, 2024
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  2. Merge pull request galaxyproject#314 from galaxyproject/data_pvc 

    Changes for not mounting entire NFS to each job
    @afgane
    afgane authored Apr 16, 2024
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  3. Automatic Version Bumping from 5.9.0 to 5.10.0

    @actions-user
    actions-user committed Apr 16, 2024
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  4. Add plotly tools to allow list

    @afgane
    afgane committed Apr 16, 2024
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Commits on Apr 17, 2024

  1. Add checkout set to the tag-and-release step.

    @ksuderman
    ksuderman committed Apr 17, 2024
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  2. Update .github/workflows/packaging.yml 

    Use latest version of the checkout action.

Co-authored-by: Nuwan Goonasekera <[email protected]>
    @ksuderman @nuwang
    ksuderman and nuwang authored Apr 17, 2024
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  3. Update all checkout actions to v4

    @ksuderman
    ksuderman committed Apr 17, 2024
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  4. Merge pull request galaxyproject#463 from ksuderman/482-release-notes 

    Fix release notes generation
    @nuwang
    nuwang authored Apr 17, 2024
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  5. Merge pull request galaxyproject#458 from ksuderman/document-separators 

    Add YAML document separators
    @nuwang
    nuwang authored Apr 17, 2024
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  6. Automatic Version Bumping from 5.10.0 to 5.10.1

    @actions-user
    actions-user committed Apr 17, 2024
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  7. Merge pull request galaxyproject#460 from galaxyproject/encouraging-s… 

    …callop

Run tests with 1.28, and add missing tool versions to sanitize allowlist
    @nuwang
    nuwang authored Apr 17, 2024
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  8. Automatic Version Bumping from 5.10.1 to 5.11.0

    @actions-user
    actions-user committed Apr 17, 2024
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  9. Set user.name and user.email for the GitHub bot

    @ksuderman
    ksuderman committed Apr 17, 2024
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Commits on Apr 18, 2024

  1. Merge branch 'master' into 408-maintenance

    @ksuderman
    ksuderman authored Apr 18, 2024
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  2. Add newline to the end of the file.

    @ksuderman
    ksuderman committed Apr 18, 2024
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  3. Merge pull request galaxyproject#466 from ksuderman/465-bot-email 

    Set committer info for the GitHub bot
    @nuwang
    nuwang authored Apr 18, 2024
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  4. Merge pull request galaxyproject#448 from ksuderman/408-maintenance 

    Cron job maintenance
    @nuwang
    nuwang authored Apr 18, 2024
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  5. Automatic Version Bumping from 5.11.0 to 5.12.0

    @actions-user
    actions-user committed Apr 18, 2024
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  6. Add enabled flag to the actions

    @ksuderman
    ksuderman committed Apr 18, 2024
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Commits on Apr 19, 2024

  1. Update galaxy/templates/cronjob-maintenance.yaml 

    Co-authored-by: Nuwan Goonasekera <[email protected]>
    @ksuderman @nuwang
    ksuderman and nuwang authored Apr 19, 2024
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Commits on Apr 20, 2024

  1. Merge pull request galaxyproject#468 from ksuderman/408-maintenance-e… 

    …nable

Add enable flag to cron jobs
    @nuwang
    nuwang authored Apr 20, 2024
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Commits on Apr 21, 2024

  1. Update README.md

    @nuwang @ksuderman
    nuwang authored and ksuderman committed Apr 21, 2024
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Commits on Apr 23, 2024

  1. Document enabled flag for cron jobs

    @ksuderman
    ksuderman committed Apr 23, 2024
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  2. Persist credentials and set GH_TOKEN for the GitHub command line tool

    @ksuderman
    ksuderman committed Apr 23, 2024
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Commits on Apr 24, 2024

  1. Merge pull request galaxyproject#470 from ksuderman/462-release-notes 

    Persist credentials and set GH_TOKEN for the GitHub command line tool
    @nuwang
    nuwang authored Apr 24, 2024
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  2. Automatic Version Bumping from 5.12.0 to 5.12.1

    @actions-user
    actions-user committed Apr 24, 2024
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  3. Merge pull request galaxyproject#469 from ksuderman/408-readme 

    Document enabled flag for cron jobs
    @nuwang
    nuwang authored Apr 24, 2024
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  4. Automatic Version Bumping from 5.12.1 to 5.13.0

    @actions-user
    actions-user committed Apr 24, 2024
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Commits on Apr 26, 2024

  1. Ensure tag-and-release checks out the latest commits make by the helm… 

    …-ci action.
    @ksuderman
    ksuderman committed Apr 26, 2024
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  2. Merge pull request galaxyproject#473 from ksuderman/472-checkout-latest 

    Checkout latest commit made by helm-ci action
    @nuwang
    nuwang authored Apr 26, 2024
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Commits on May 7, 2024

  1. Updating AnVIL branch to latest Galaxy Helm

    @ksuderman
    ksuderman committed May 7, 2024
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