2024.10.14

What's Changed

• updated NOTICE.txt by @thecaffiend in #13
• Get to baseline of datalake demo with ResourceComponent architecture changes by @thecaffiend in #14
• Add Public stack for easy infrastructure creation by @mehalter in #20
• ci: add necessary permissions for pull request creation by @mehalter in #21
• Update public pulumi stack configuration by @github-actions in #23
• Add unit testing by @mehalter in #19
• Added README.md by @thecaffiend in #25
• docs: add configuration for prettier by @mehalter in #26
• fixed bad parental relations by @thecaffiend in #27
• First cut private VPC by @thecaffiend in #29
• Add descriptive tags and fix/shorten resource names by @thecaffiend in #35
• Update public pulumi stack configuration by @github-actions in #30
• Updates to get genomics tributary in by @thecaffiend in #36
• Update public pulumi stack configuration by @github-actions in #37
• Moved inline policy docs to module by @thecaffiend in #39
• added get_inline_role function by @thecaffiend in #42
• changed crawlers from event driven to scheduled by @thecaffiend in #43
• added sub readme for push vs pull queuing by @thecaffiend in #47
• 46 implement push based queuing for etl by @thecaffiend in #48
• changed genomics crawler to run hourly by @thecaffiend in #51
• Update public pulumi stack configuration by @github-actions in #44
• feat(private): add vm subnet by @mehalter in #53
• Modified swimlane VPCs for egress to internet by @thecaffiend in #56
• Update public pulumi stack configuration by @github-actions in #59
• start of simple api spec for data analysis pipelines by @thecaffiend in #60
• linked all TODOs in code to specific issues for tracking by @thecaffiend in #73
• Add AWS Batch Compute Environments by @mehalter in #74
• Update public pulumi stack configuration by @github-actions in #79
• chore: add .vscode with basic configuration by @mehalter in #82
• Markdown formatting by @mehalter in #83
• Implement a few new configuration options by @mehalter in #80
• foundation for job submission to head node by @thecaffiend in #90
• Update public pulumi stack configuration by @github-actions in #85
• 87 need to pass region into lambdas that need it as an env var by @edpg-cp-24 in #93
• feat(etl): add GPHL sequencing PDF ETL script by @mehalter in #52
• Update public pulumi stack configuration by @github-actions in #94
• updated etl (tnl, gphl-cre) scripts from their respective repos by @thecaffiend in #96
• Formalize our usage of the Pulumi configuration by @mehalter in #81
• added a config value for type of deployment by @thecaffiend in #91
• Update public pulumi stack configuration by @github-actions in #97
• fix(config): ignore keys that resolve to None by @mehalter in #98
• chore(vscode): configure pytest for project by @mehalter in #103
• Add testing badge by @mehalter in #104
• added private swimlane vpn by @thecaffiend in #102
• Update public pulumi stack configuration by @github-actions in #108
• ci: add release workflow by @mehalter in #110
• 107 separate tracked and non tracked assets by @thecaffiend in #111
• Update public pulumi stack configuration by @github-actions in #113
• Get AWS Batch working by @mehalter in #116
• use versioning for CI/CD by @mehalter in #117
• changed the default schedule for all crawlers to be 0200 daily by @thecaffiend in #121
• ci: add pre-commit configuration for safer development by @mehalter in #123
• fix(batch): update AMI environment ID by @mehalter in #124
• plumbing for private s3 hosted web forms by @thecaffiend in #119
• fix(batch): update image AMI for analysis pipeline by @mehalter in #137
• add baseline cape analysis UI application to repo by @thecaffiend in #139
• list pipelines api endpoint and api static app permissions by @thecaffiend in #140
• temporary handling of output s3 buckets for data analysis pipeline output by @thecaffiend in #149
• remove cape frontend from repo, will deploy manually by @mehalter in #154
• get nextflow head node running commands from lambda by @thecaffiend in #160
• add a second bactopia version for testing purposes by @mehalter in #157
• update bactopia pipeline parameters by @thecaffiend in #161
• fix: add support for v3.0.1 by @mehalter in #162
• EC2 Instance tagging for pipeline executors by @mehalter in #163
• fix integrationHttpMethod always showing change for options endpoints by @thecaffiend in #164
• implement real bactopia output etl by @thecaffiend in #165
• Update public pulumi stack configuration by @github-actions in #122

New Contributors

• @thecaffiend made their first contribution in #13
• @mehalter made their first contribution in #20
• @github-actions made their first contribution in #23
• @edpg-cp-24 made their first contribution in #93

Full Changelog: https://github.com/cape-ph/cape-cod/commits/2024.10.14