StanfordBioinformatics/Hummingbird issues and pull requests

#51 - Bump scikit-learn from 1.1.1 to 1.5.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#50 - Bump azure-identity from 1.5.0 to 1.16.1

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#49 - Bump azure-storage-blob from 12.6.0 to 12.13.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#48 - Bump scipy from 1.8.1 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#47 - Bump future from 0.18.2 to 0.18.3

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#46 - bump python to 3.8 - 3.10

Pull Request - State: closed - Opened by amirstanford over 2 years ago

#45 - bump python to 3.8 - 3.10

Pull Request - State: closed - Opened by amirstanford over 2 years ago

#44 - Bump numpy from 1.19.1 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#43 - enhancements to cleanup aws resource on completion of jobs

Pull Request - State: closed - Opened by amdixit almost 3 years ago

#42 - fix: use xvda for AL2; use unique launch template depending on disk size

Pull Request - State: closed - Opened by a7i about 3 years ago

#41 - fix: use full os path for AWS json template files

Pull Request - State: closed - Opened by a7i about 3 years ago

#40 - Minor update to the documentation

Pull Request - State: closed - Opened by a7i over 3 years ago

#39 - Add pipeline for deploying to PyPi

Pull Request - State: closed - Opened by a7i over 3 years ago

#38 - Add CF Stack + Change Scheduler to use Cloudformation Stack output

Pull Request - State: closed - Opened by a7i over 3 years ago

#37 - Automate AWS Onboarding by using a Cloudformation Stack

Issue - State: closed - Opened by a7i over 3 years ago
Labels: enhancement

#36 - update AWS docs to include steps for compute_environment and job-definition

Pull Request - State: closed - Opened by a7i over 3 years ago

#35 - Extend job waiter to 2 days as long runs (e.g. full-run) can take up to 2 days

Pull Request - State: closed - Opened by a7i over 3 years ago

#34 - Support non-interactive/silent mode

Issue - State: open - Opened by a7i over 3 years ago

#33 - Support for AL2 AMI

Pull Request - State: closed - Opened by a7i over 3 years ago

#32 - Provide support for downsampled files provided manually

Issue - State: open - Opened by amircs over 3 years ago

#31 - Creating separate downsampling input files for every execution cycle (try)

Issue - State: open - Opened by amircs over 3 years ago

#30 - Remove AWS CLI calls and use Boto3 instead

Pull Request - State: closed - Opened by a7i over 3 years ago

#29 - Add support for 64 CPU cores

Pull Request - State: closed - Opened by a7i over 3 years ago

#28 - Use next biggest instance type if one is not available for the given threads/cpu size

Pull Request - State: closed - Opened by a7i over 3 years ago

#27 - Use computeEnvironmentName from the compute_environment.json to allow setting unique compute environment names

Pull Request - State: closed - Opened by a7i over 3 years ago

#26 - Support for AL2

Issue - State: closed - Opened by a7i over 3 years ago

#25 - Fetch supported instance types and pricing

Issue - State: open - Opened by a7i over 3 years ago - 1 comment

#24 - Support additional instance types for AWS

Pull Request - State: closed - Opened by a7i over 3 years ago

#23 - Thread definition and Downsample sizes

Pull Request - State: closed - Opened by a7i over 3 years ago

#22 - Test framework

Issue - State: closed - Opened by a7i over 3 years ago - 1 comment

#21 - Don't use 'import *'

Issue - State: closed - Opened by a7i over 3 years ago - 1 comment

#20 - Use AWS SDK vs. subprocesses on AWS CLI

Issue - State: closed - Opened by a7i over 3 years ago - 1 comment

#19 - Inconsistency in logging and output

Issue - State: closed - Opened by a7i over 3 years ago - 1 comment

#18 - Conf Validation

Pull Request - State: closed - Opened by a7i over 3 years ago

#17 - Support for AWS instance types: [i3, m5, c5, r5]

Pull Request - State: closed - Opened by a7i over 3 years ago

#16 - Restructure code and use relative import

Pull Request - State: closed - Opened by a7i over 3 years ago

#15 - Install time via apt in Dockerfiles

Pull Request - State: closed - Opened by a7i over 3 years ago

#14 - force int for LaunchTemplateData volumesize

Pull Request - State: closed - Opened by a7i over 3 years ago

#13 - Allow override of downsample or profiling images

Pull Request - State: closed - Opened by a7i over 3 years ago

#12 - Use DockerHub images. Fix AWS Batch

Pull Request - State: closed - Opened by a7i over 3 years ago

#11 - Separate gatk and bwa Docker images

Pull Request - State: closed - Opened by a7i over 3 years ago

#10 - Update README for docker images

Pull Request - State: closed - Opened by a7i over 3 years ago

#9 - Support python3.6 subprocess API

Pull Request - State: closed - Opened by a7i over 3 years ago

#8 - Get project ready for community

Pull Request - State: closed - Opened by a7i over 3 years ago

#7 - Update docs to include instructions for ECS/Batch IAM setup

Pull Request - State: closed - Opened by a7i over 3 years ago

#6 - Gracefully handling of aws s3 subprocess call for existence of downsamping file

Pull Request - State: closed - Opened by a7i over 3 years ago

#5 - Do not use relative path for Azure task json so it can be re-used as a library

Pull Request - State: closed - Opened by a7i almost 4 years ago

#4 - Add section 12 to docs

Pull Request - State: closed - Opened by a7i about 4 years ago

#3 - v1.1.0

Pull Request - State: closed - Opened by a7i about 4 years ago

#2 - Filter Azure machines based on threads provided in config json

Pull Request - State: closed - Opened by a7i about 4 years ago

#1 - Azure support

Pull Request - State: closed - Opened by a7i about 4 years ago

GitHub / StanfordBioinformatics/Hummingbird issues and pull requests