daniel-goldstein

Daniel Goldstein daniel-goldstein

12 followers · 6 following

Broad Institute of MIT and Harvard
Boston, MA
danielgoldstein.dev

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Pinned

hail-is/hail Public

Cloud-native genomic dataframes and batch computing

Python 889 232
tskit-dev/tskit Public

Population-scale genomics

Python 123 63
envoyproxy/envoy Public

Cloud-native high-performance edge/middle/service proxy

C++ 22.8k 4.5k
tskit-dev/msprime Public

Simulate genealogical trees and genomic sequence data using population genetic models

Python 155 82
pawprints-web Public archive

Web app for managing and uploading clue locations for Husky Hunt

JavaScript 1
racket-fun Public

Fun snippets I like to share with my Fundamentals 1 class to really blow their minds.

Racket 2

1,073 contributions in the last year

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Activity overview

Contributed to hail-is/hail, daniel-goldstein/zmk-config, daniel-goldstein/bookclub and 7 other repositories

Contribution activity

September 2023

Created 59 commits in 3 repositories

Created a pull request in hail-is/hail that received 17 comments

Sep 19

[devbin] Add a script for running a database locally

I picked this refactor off of my terra branch and took it the last ten yards such that now you can run make batch-db and get a full local instance …

+294 −173 • 17 comments

Opened 51 other pull requests in 1 repository

hail-is/hail 6 open 45 merged

[pytest] Stop and reinitialize hail between QoB tests Sep 28
[linting] Catch unintended errors in check-sql.sh Sep 28
[humanizex] Run humanize tests and fix microseconds bug Sep 28
[batch] Ignore client_job attribute in test_callback test Sep 28
Gateway return 503 on failed auth check Sep 27
[batch] Allow image Env to be None Sep 27
[services] Use AsyncExitStack on app cleanup Sep 26
[query] Remove unused dependency on google-cloud-storage Sep 26
[website] Make better use of make when building docs locally for the website Sep 26
[batch] Report duration ms in batch and job records Sep 22
[deploy] Update PyPI assertion to not use more than 20GiB at PyPI Sep 21
[hailctl] Fixes for first time init Sep 21
[batch] Support container images with nonexistent users Sep 20
[batch] Account for JVM containers when allocating network namespaces Sep 20
[hailtop] Apply nest_asyncio on hailtop import Sep 20
[auth] Reuse auth decorators without making additional requests Sep 20
[memory] Remove dangling reference to long gone step Sep 19
[deploy] fix reference to GRCH38 image Sep 19
[deploy] Fix deploy script to correctly push 3.11 image and hailtop image Sep 19
[deploy] Fix deploy.sh script Sep 19
[release] 0.2.123 Sep 18
[query] Give test_ld_prune more time on the batch backend Sep 18
[auth] Delete no longer necessary requirements file Sep 18
[batch] Remove batch worker ssh key Sep 18
[gear] Dont cache the db ssl context in a global Sep 18
Some pull requests not shown.

Reviewed 53 pull requests in 1 repository

hail-is/hail 25 pull requests

[ci] Generate PR specific logging queries Sep 28
[batch] Fix missing exact match and partial match search symbols Sep 28
[batch] Sample resource usage more frequently at start Sep 28
[humanizex] Run humanize tests and fix microseconds bug Sep 28
[batch] Ignore client_job attribute in test_callback test Sep 28
[batch] Add client job id to test batch attributes for debugging Sep 27
[qob] include version in batch attributes Sep 27
[batch] Update gcsfuse version to 1.2.0 Sep 27
[batch] Only write logs and resource usage for started containers Sep 27
[batch] Fix GCP fluentd log labels Sep 27
[devbin] Add a script for running a database locally Sep 27
[batch] Use job-only resource usage for running JVM jobs Sep 27
[build.yaml] Give delete_gcp_batch_instances job the proper service account Sep 27
[batch] Turn off sys logs in fluentd Sep 26
[batch] Add SKU to latest_product_versions Sep 26
[website] Make better use of make when building docs locally for the website Sep 26
[Snyk] Security upgrade pillow from 9.5.0 to 10.0.1 Sep 26
[auth] Reuse auth decorators without making additional requests Sep 26
[jvm-fs] simplify use of URLs Sep 26
[pip] update all requirements for new crypto Sep 26
[compiler] Exclude fcc9ffa from git-blame revs Sep 21
[batch] Account for JVM containers when allocating network namespaces Sep 20
[batch] disable bunch submission progress bar when fewer than 100 Sep 19
[qob] back off timeout on test_joins_work_correctly Sep 19
[batch] Remove batch worker ssh key Sep 18
Some pull request reviews not shown.

Created an issue in hail-is/hail that received 3 comments

Sep 20

[batch] Batch does not support nonexistent users or UIDs in the USER image directive

What happened? The following is a valid Dockerfile that does not result in a user entry in /etc/passwd in the image. FROM ubuntu:22.04 USER "1001" T…

3 comments

Opened 5 other issues in 1 repository

hail-is/hail 5 open