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Dev - #5477

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hanars merged 187 commits into
masterfrom
dev
Jun 10, 2026
Merged

Dev#5477
hanars merged 187 commits into
masterfrom
dev

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@hanars

@hanars hanars commented Jun 10, 2026 •
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  • All unit test are passing and coverage has not substantively dropped
  • No new dependency vulnerabilities have been introduced
  • Any changes to the docker image have been vetted for potential vulnerabilities and privacy implications
  • If any python requirements are updated, they are noted and here and will be updated before deploying:
  • Any database migrations are noted here, and will be run before deploying:
  • All major changes are recorded in the changelog, and the changelog has been updated to reflect the latest release
  • Any new endpoints are explicitly tested to ensure they are only accessible to correctly permissioned users
  • No secrets have been committed
  • Any changes to environment variables or secrets are noted here, and will properly configured before deploying:
  • The following charts will be updated as part of this release:
    • seqr
    • vlm

hanars added 30 commits May 20, 2026 14:07
@hanars
update test requirements
0ca6025
@hanars
use django for db setup
b95b675
@hanars
update requiremnts
fe4dd34
@hanars
use seqr requiremnts
068833f
@hanars
use venv
809a6d3
@hanars
no seqr app migrations
261cdd0
@hanars
fix venv
f115f20
@hanars
split setup steps
62eec9a
@hanars
remove venv for now
13d8176
@hanars
add postgres
74fa807
@hanars
Merge branch 'vlm-no-hail' of https://github.com/broadinstitute/seqr …
e0e4e1f 
…into vlm-shared-test-db
@hanars
depndency install order
a606624
@hanars
psycopg setup
79f1531
@hanars
add clickhous eports
d2c1aaa
@hanars
env reset
7381323
@hanars
fix clcikhouse host
203aa1e
@hanars
explicitly create database
8bd7a87
@hanars
use default github actions docker
a0f6eb6
@hanars
fix clickhouse hostname
81766d7
@hanars
remove extra psycopg
2601e0c
@hanars
test setup order
4e68be2
@hanars
add clikhouse data dirs
f4029bb
@hanars
use venv
1781696
@hanars
reload users
168372b
@hanars
setup order
9da4a70
@hanars
run all db migrations
0c25271
@hanars
install postrgres db too
9ee12e9
@hanars
postgres db setup
17c64ac
@hanars
use pytest for test db creation
0c8add8
@hanars
depndency install
cb28176
hanars and others added 28 commits May 29, 2026 16:13
@hanars
update gnomad constartint citation
0d3ac44
@hanars
fix linting
71d8608
@hanars
Merge pull request #5469 from broadinstitute/gnomad-constraint-citation
2e5be0c 
update gnomad constartint citation
@hanars
sync tag updates to postgres dicts
227b2a3
@hanars
reload metadata on project update
0498c89
@hanars
family update reload
1386778
@hanars
individual update reloads
a5fabc3
@hanars
log user with relaods
622fc4c
@hanars
fix tests
5722238
@hanars
fix saved variant data tests
0b7806b
@hanars
test family updte metadata
74d5a58
@hanars
individual tests
5034717
@hanars
test project updates
6a452a5
@hanars
test saved variant relaod
262deb8
@hanars
fix tests
9aaa4b9
@hanars
pr feedback
0bafd43
@hanars
Merge pull request #5456 from broadinstitute/clickhouse-bump-unit-tes…
fabf64e 
…t-version

clickhouse official docker for tests
@hanars
Merge branch 'dev' of https://github.com/broadinstitute/seqr into vlm…
6d5072e 
…-shared-test-db
@hanars
actually merge dev
692e3ff
@hanars
update for newwer verrsion
5738357
@hanars
clean up db config for clickhouse
0d7c2cc
@hanars
fix settings vars
5aef707
@dependabot
Bump shell-quote from 1.8.1 to 1.8.4 in /ui
3e44ff6 
Bumps [shell-quote](https://github.com/ljharb/shell-quote) from 1.8.1 to 1.8.4.
- [Changelog](https://github.com/ljharb/shell-quote/blob/main/CHANGELOG.md)
- [Commits](ljharb/shell-quote@v1.8.1...v1.8.4)

---
updated-dependencies:
- dependency-name: shell-quote
  dependency-version: 1.8.4
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
@hanars
Merge pull request #5475 from broadinstitute/dependabot/npm_and_yarn/…
d9684c5 
…ui/shell-quote-1.8.4

Bump shell-quote from 1.8.1 to 1.8.4 in /ui
@hanars
Merge pull request #5472 from broadinstitute/postgres-dict-reloads
d9be882 
sync tag updates to postgres dicts
@hanars
Merge pull request #5474 from broadinstitute/db-config-cleanup
a825833 
clean up db config for clickhouse
@hanars
Merge pull request #5448 from broadinstitute/vlm-shared-test-db
b8e95c6 
Vlm shared test db
@hanars
correctly mock response in tests
71c12ef
@hanars
hanars marked this pull request as ready for review June 10, 2026 17:24
@hanars
hanars merged commit 75ec42b into master Jun 10, 2026
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@hanars