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Changelog

0.7.17 (unreleased)

  • Nothing changed yet.

0.7.16 (2024-09-20)

  • Fixed circus dependencies

0.7.15 (2024-09-19)

  • Added prompt to confirm overwrite if qa-report already exists

0.7.14 (2022-03-09)

  • Updated Datomic download source to Wormbase bucket (datomic free download no longer supported by Datomic)
  • Added new upload-result subcommand to upload migration results to the Wormbase S3 bucket (instead of requiring manual upload)
  • Updated release process to use GH personal access tokens
  • Security improvements and dependency bumping

0.7.13 (2020-11-23)

  • Bumped pseudoace dependency version to bugfix migrate-homol DB naming (mismatch between pseudoace and azanium)
  • Corrected ws_release_tag git tag availability check
  • Changed WB release name parsing strategy, now tag-based rather than FTP-path based (#41)
  • Github authorization update (fix #40)
  • Fixed release creation vs tagging mismatch (fix #42)

0.7.12 (2020-09-22)

  • Updated & completed docs
  • Bugfixed migrate-homol DB name and DB backup file generation
  • Minor logging and code improvements

0.7.11 (2020-07-16)

  • Updated pseudoace dependency version

0.7.10 (2020-07-09)

  • Cleanup downloaded artefacts in /tmp

0.7.9 (2020-07-08)

  • Specify release tag when configuring.
  • Source annotated models from a configured github release tag.

0.7.8 (2020-06-23)

  • Fixed backup-db step for homology migration.

0.7.7 (2020-06-22)

  • Bump version of pseudoace.

0.7.6 (2020-06-19)

  • Increase transactor start wait time.

0.7.5 (2020-06-19)

  • Configure and start transactor before homol migration run.
  • Fixed slack notify invocation at end of main migration.

0.7.4 (2020-06-16)

  • Fixed temp directory cleanup in installers.

0.7.3 (2020-06-16)

  • Bumped version of pseudoace to 0.7.3 (bring in CLI fix).

0.7.2 (2020-06-15)

  • Added separate top-level command for running homology migration.
  • Bumped version of pseudoace to 0.7.2 to bring in fixes for homology command.

0.7.1 (2020-06-07)

  • Bring in pseudoace 0.7.1 for import-logs command line bug fix.

0.7.0 (2020-04-06)

  • Bumped version of pseduoace for CLI homology command fix.

0.60 (2020-03-19)

  • Bumped version of pseudoace to bring in bug-fix for homology pipeline.

0.59 (2020-03-13)

  • Fixed issue with datomic_free installer not being re-entrant.

0.58 (2020-03-13)

  • Ensured error messages are echoed to console during preliminary checks.

0.57 (2020-01-20)

  • Fixed recording/resetting of current step.
  • Fixed click integration for homology import command.

0.56 (2020-01-09)

  • Fixed command to populate homology db.

0.55 (2020-01-06)

  • Provide default for db_name when invoking Context.datomic_url.

0.54 (2019-12-03)

  • Apply retry logic when restarting datomic transactor.
  • Bumped version of pseudoace.
  • Added two new steps to the migration process (produce homology database).

0.53 (2019-10-08)

  • Bumped version of pseudoace for bug fixes.

0.52 (2019-09-09)

  • Pull in new version of pseudoace for bugfix.

0.51 (2019-09-03)

  • Bumped version of pseudoace to pull in bugfix.

0.50 (2019-09-03)

  • Bumped version of pseudoace to pull in bugfix.

0.49 (2019-08-30)

  • Bumped version of pseudoace.

0.48 (2019-08-29)

  • Fixed locating of pseudoace release archive.

0.47 (2019-07-18)

  • Modify the way pseudoace is invoked via java jar file.
  • Apply any patches from the PATCHES directory on the FTP site.

0.46 (2018-12-11)

  • Addressed github-reported security vulnerability in package dependencies.

0.45 (2018-12-11)

  • Bumped versions of datomic and pseudoace.

0.44 (2018-10-24)

  • Updated to latest version of pseudoace.
  • Fixed typo (#35)
  • Added missing requriement.

0.43 (2018-06-26)

  • Configuration of WormBase FTP URL an Slack URL done via configure command.
  • Made slack configuration optional, persistent across migration runs.
  • Downloading of ACeDB data moved from install step as the first migration step.
  • Various bug fixes around the configuration command.
  • Updated documentation to match changes to commands.

0.41 (2018-06-19)

  • Fixed bootstrapping issue.

0.40 (2018-06-19)

  • The FTP URL is now passed to the azanium configure command, rather than partially parameterised in install commmand(s).
  • Fixed bugs with configuration code and logging.

0.39 (2018-06-18)

  • Removed all AWS specific code, documentation and configuration.

0.38 (2018-06-12)

  • Fixed dependency issue with awscli.
  • Improved docs.

0.37 (2018-06-12)

  • Updated versions for the next migration run.

0.36 (2018-04-24)

  • Added admin script for adding new AWS IAM and EC2-host linux user.
  • Updated documentation for multi-user migration.

0.35 (2018-04-19)

  • Use FTP staging area to obtain ACeDB release and class report.
  • Improved docs.

0.34 (2018-04-19)

  • Bumped software versions.
  • Updated notification docs.
  • Fixed syntax errors.

0.33 (2018-03-06)

  • Split migration into two stages to speed up the process.
  • Fix issue with upgrading package dependencies on install (docs)
  • Updated documentation.

0.32 (2018-03-05)

  • Bumped versions for corresponding versions in pseudoace (WS264 + datomic).

0.31 (2017-12-18)

  • Release to fix release-script malfunction (!).

0.30 (2017-12-18)

  • Updated python requirements.

0.29.un-released (2017-12-18)

  • Bump versions for next migration run.

0.28 (2017-10-30)

  • Addition of new command "reset-to-step".
  • clean-previous-state command now removes app state file.
  • Bump versions for next migration run.

0.27 (2017-09-11)

  • Source annotated models from release-tag in the Wormbase/wormbase-pipeline repository
  • Fixed issue with notifications configuration where configuration could potentially be overridden.
  • Bumped versions for next migration run.

0.26 (2017-07-07)

  • Bumped version of pseudoace.
  • Bumped version of datomic-free.
  • Bumped release version.
  • Removed excise-tmp-data step.

0.25 (2017-05-19)

  • Bumped version of pseudoace.
  • Allow migrate command to work with existing ACeDB database and corresponding pre-gzipped output.

0.24 (2017-04-27)

  • Bumped data release and pseudoace versions.

0.23 (2017-02-16)

  • Bumped data release version.

0.22 (2017-02-16)

  • Bumped versions.

0.21 (2016-11-19)

  • Bumped versions.

0.20 (2016-11-19)

  • Download the annotated models file separately (Fixes #8).
  • Fix last step (backup and transfer to S3)

0.19 (2016-10-11)

  • Fixed issue in cleaning up previous migration.
  • Allow Datomic URI to be overridden via environment variable.
  • Minor fixes to docs.
  • Bump data release version to WS256.
  • Use the AWS_DEFAULT_PROFILE environment variable rather requiring user to specify with --profile.

0.18 (2016-08-10)

  • Cleanup data from any previous migration before starting a new one.
  • Keep datomic backup directory on disk after S3 upload of tarfile to enable DDB restore.
  • Reflect change in pseudoace 0.4.10 (Location of annotated ACeDB models file)
  • Fixed issue with wrong path to QA id catalog input path.
  • Fixed bucket S3 path for Datomic db backup.
  • datomic-free does not support direct s3 upload - work around that with local back and upload via AWS APIs.
  • Updates to reflect switch to non-ephemeral instance.
  • Bump data version to WS255.

0.17 (2016-06-27)

  • Minor updates to docs.

0.16 (2016-06-27)

  • Update install instructions in docs.

0.15 (2016-06-27)

  • Tweaks to documentation.

0.14 (2016-06-24)

  • Store application logfile in S3 at the end of each build step.
  • Improved docs.

0.13 (2016-06-23)

  • Updated documentation to match release procedure changes.

0.12 (2016-06-23)

  • Fix name of entry point zest.releaser uses.

0.11 (2016-06-23)

  • Fix bug with release hook.

0.10 (2016-06-23)

  • Fix dependencies.
  • Added zest.releaser hook to deploy code/docs to github/github-pages.
  • Made the migrate command re-entrant.

0.9 (2016-06-23)

  • Make this changelog show up in the docs.

0.8 (2016-06-23)

  • Re-worked documentation to use ghp-import instead of travis-sphinx.
  • Add post-release hook to deploy documentation via make-file.

0.7 (2016-06-22)

  • Pass correct flags to travis-sphinx to get HTML docs built and deployed.

0.6 (2016-06-22)

  • Fix typo in Sphinx configuration.

0.5 (2016-06-22)

  • Use Sphinx's builtin githubpages extension.

0.4 (2016-06-22)

  • Fixed issue with sphinx build (missing docs/_static)

0.3 (2016-06-22)

  • Fix docs-build on travis.

0.2 (2016-06-22)

  • Unified documentation.
  • Unified all build steps into a single command azanium migrate.
  • Add slack notifications for build progress.
  • Prepare automation of documentation build to github pages.

0.1 (2016-06-22)

  • Initial version.