CHANGELOG.md

1.1.1 - 2023-07-06

• Fix bug introduced in https://github.com/DataBiosphere/terra-docker/commit/4a5b4c9212aedcafa2f41fbeb2b161089341c578
• Update hail to 0.2.119
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-119 for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.1.1

1.1.0 - 2023-06-23

• Update python 3.7 to 3.10

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.1.0

1.0.26 - 2023-06-07

• Force the regeneration of 1.0.26 that was never published

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.27

1.0.26 - 2023-03-13T17:26:34.162828Z

• Update terra-jupyter-base to 1.0.14
  • Include jupyter lab build step

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.26

1.0.25 - 2023-02-22

• Remove invalid python image dependency

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.25

1.0.24 - 2023-02-08

• Update hail to 0.2.109
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-109) for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.24

1.0.23 - 2023-02-09T14:18:49.030825Z

• Update terra-jupyter-base to 1.0.12
  • Add cloud.google.com gpg key.

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.23

1.0.22 - 2022-12-14

• Update hail to 0.2.107
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-107) for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.22

1.0.21 - 2022-11-01

• Update hail to 0.2.105
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-105) for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.21

1.0.20 - 2022-08-22

• Update hail to 0.2.98
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-98) for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.20

1.0.19 - 2022-06-30

• Update hail to 0.2.96
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-96) for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.19

1.0.18 - 2022-06-23T10:58:12.961300Z

• Update terra-jupyter-base to 1.0.10
  • Fix leo_url variable in workspace_cromwell.py script for AoU projects

1.0.17 - 2022-06-23T10:58:12.961300Z

• reverted, do not use

1.0.16 - 2022-05-25

• Update hail to 0.2.95
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-95 for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.16

1.0.15 - 2022-05-20T18:06:39.466439Z

• Update terra-jupyter-base to 1.0.9
  • Fix adding workspace_cromwell.py script to manage Cromwell App

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.15

1.0.14 - 2022-05-17T17:14:41.258775Z

• Update terra-jupyter-base to 1.0.8
  • Add script that manages Cromwell app

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.14

1.0.13 - 2022-05-10T22:08:25.952927Z

• Update terra-jupyter-base to 1.0.7
  • Install Cromshell 2.0 (https://github.com/broadinstitute/cromshell)

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.13

1.0.12 - 2022-05-02T14:33:23.942987Z

• Update terra-jupyter-base to 1.0.6
  • use new nvidia key

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.12

1.0.11 - 2022-04-17

• Update terra-jupyter-python to 1.0.5
  • Install gcloud alpha storage dependency

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.11

1.0.10 - 2022-03-28

• Update hail to 0.2.93
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-93 for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.10

1.0.9 - 2022-03-18

• Update hail to 0.2.91
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-91 for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.9

1.0.8 - 2022-03-04

• Update hail to 0.2.89
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-89 for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.8

1.0.7 - 2022-02-15

• Update hail to 0.2.85
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-85 for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.7

1.0.6 - 2022-02-07

• Update hail to 0.2.83
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-83 for details

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.6

1.0.5 - 2022-02-02T20:47:42.341058Z

• Update terra-jupyter-base to 1.0.4
  • update notebook_dir to $HOME; install scikit-learn-intelex, xgboost

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.5

1.0.4 - 2022-01-06T18:21:41.170621Z

• Update terra-jupyter-base to 1.0.3
  • Bumping Google Deeplearning image to 2.7, removing gcc-6 and gcc-8 install due to package problems

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.4

1.0.3 - 2021-11-18

• Update hail to 0.2.74
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-74 for details.

1.0.2 - 2021-10-07T14:47:43.375974Z

• Update terra-jupyter-base to 1.0.2
  • Update AsyncMappingKernelManager jupyter/notebook#6164

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.2

1.0.1 - 2021-09-10T15:10:44.093747Z

• Update terra-jupyter-base to 1.0.1
  • Update base image to gcr.io/deeplearning-platform-release/tf2-gpu.2-6 to support TensorFlow 2.6.0
  • Fix multipart Jupyter uploads

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.1

1.0.0 - 2021-06-09T16:18:53.782701Z

• Update terra-jupyter-base to 1.0.0
  • use deep learning images as base

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.0.0

0.1.3 - 2021-06-24T15:47:51.244166Z

• Add gnomad python package to Hail environment

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.1.3

0.1.2 - 2021-05-05T16:19:57.485458Z

• Update terra-jupyter-base to 0.0.20
  • [IA-1644] Install crcmod in base image to support GCS composite objects

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.1.2

0.1.1 - 2021-04-05T17:29:05.415Z

• Update terra-jupyter-python to 0.1.1
  • fix ggplot import bug

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.1.1

0.1.0 - 2021-03-20

• Update terra-jupyter-python to 0.1.0

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.1.0

0.0.31 - 2021-02-05

• Update hail to 0.2.62
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-61 for details.
• Update pandas to 1.1.x

0.0.30 - 2021-01-20T16:00:48.299Z

• Update terra-jupyter-base to 0.0.19
  • [IA-2472] Turn on debug-level logging when JUPYTER_DEBUG_LOGGING env var is true

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.30

0.0.29 - 2020-12-09T18:50:57.298Z

• Update terra-jupyter-python to 0.0.22
  • [IA-2420] Update to a newer version of pymc3

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.29

0.0.28 - 2020-12-03

• Update hail to 0.2.61
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-61 for details.

0.0.27 - 2020-12-02T17:59:36.390Z

• Update terra-jupyter-base to 0.0.18
  • bump terra-notebook-utils version to 0.7.0 and move it to base image

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.27

0.0.26 - 2020-11-16T18:11:40.758876Z

• Update terra-jupyter-base to 0.0.17
  • remove miniconda

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.26

0.0.25 - 2020-11-10T13:26:19.112Z

• Update terra-jupyter-python to 0.0.19
  • Remove Python package enum34. Fixes DataBiosphere#175

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.25

0.0.24 - 2020-10-26T20:13:57.675Z

• Update terra-jupyter-base to 0.0.16
  • add keychain to base image

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.24

0.0.23 - 2020-10-08T18:42:19.690Z

• Update terra-jupyter-base to 0.0.15
  • include pip binary installation location in PATH

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.23

0.0.22 - 2020-09-30

• No changes; version bump due to CI/CD issues

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.22

0.0.21 - 2020-09-17

• Update hail to 0.2.57
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-57 for details.

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.21

0.0.20 - 2020-09-02T15:12:19.860Z

• Update terra-jupyter-base to 0.0.14
  • Terminal now opens to /notebooks directory where PD is mounted

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.20

0.0.19 - 2020-08-18T13:43:26.202Z

• Update terra-jupyter-base to 0.0.13
  • update notebook to 6.1.1, tornado to 5.1.1

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.19

0.0.18 - 07/12/2020

• Upgrade hail to 0.2.54
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-54 for details.

Image URL us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.18

0.0.17 - 07/27/2020

• Update terra-jupyter-python image to 0.0.14

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.17

0.0.16 - 06/27/2020

• Upgrade hail to 0.2.50
  • See https://hail.is/docs/0.2/change_log.html#version-0-2-50 for details.

Image URL us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.16

0.0.15 - 06/15/2020

• Upgrade hail to 0.2.45
• Update terra-jupyter-python image to 0.0.13

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.15

0.0.14 - 06/11/2020

• Upgrade hail to 0.2.44

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.14

0.0.13 - 05/18/2020

• Update terra-jupyter-python image to 0.0.12
  • Adds jupyter notebook extension collapsible headers and code-folding

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.13

0.0.12 - 4/30/2020

• Upgrade hail to 0.2.39

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.12

0.0.11 - 4/28/2020

• Update terra-jupyter-python base image to 0.0.11
  • Add Google Cloud support to pysam

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.11

0.0.10 - 4/22/2020

• Upgrade hail to 0.2.38

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.10

0.0.9 - 02/25/2020

• Update terra-jupyter-python base image to 0.0.10
  • Fixes https://broadworkbench.atlassian.net/browse/IA-1676

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.9

0.0.8 - 02/05/2020

• Update terra-jupyter-python base image to 0.0.9
  • Fixes https://broadworkbench.atlassian.net/browse/IA-1653

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.8

0.0.7 - 01/27/2020

• Specify PYSPARK_PYTHON="python3" in Jupyter kernel to resolve pyspark python mismatch errors
  • See https://broadworkbench.atlassian.net/browse/IA-1637

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.7

0.0.6 - 01/17/2020

• Update terra-jupyter-python version to 0.0.8
• Make docker image locally runnable with:
  • docker run --rm -it -p 8000:8000 <image>

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.6

0.0.5 - 1/2/2020

• Upgrade terra-jupyter-python version
• Upgrade hail to 0.2.30

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.5

0.0.4 - 11/26/2019

• Fix WORKSPACE_BUCKET environment variable

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.4

0.0.3 - 11/16/2019

• Update to use python 0.0.4
• Remove apt-get upgrade for security purposes

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.3

0.0.2 - 10/10/2019

Update to use python 0.0.2

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.2

0.0.1 - 09/03/2019

Image URL: us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:0.0.1