From a3a79a3ecef68dd12cab6edf1b922becdcf1d593 Mon Sep 17 00:00:00 2001 From: Julia Klugherz Date: Thu, 29 Feb 2024 11:53:47 -0500 Subject: [PATCH 1/5] bump hail to 0.2.128 --- .github/workflows/hail-search-unit-tests.yaml | 2 +- hail_search/deploy/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/hail-search-unit-tests.yaml b/.github/workflows/hail-search-unit-tests.yaml index da9b6cd60c..ab1c716b24 100644 --- a/.github/workflows/hail-search-unit-tests.yaml +++ b/.github/workflows/hail-search-unit-tests.yaml @@ -17,7 +17,7 @@ on: jobs: hail_search: runs-on: ubuntu-latest - container: hailgenetics/hail:0.2.126 + container: hailgenetics/hail:0.2.128 steps: - uses: actions/checkout@v2 diff --git a/hail_search/deploy/Dockerfile b/hail_search/deploy/Dockerfile index ef7408bbf5..4a41eb0e7f 100644 --- a/hail_search/deploy/Dockerfile +++ b/hail_search/deploy/Dockerfile @@ -1,4 +1,4 @@ -FROM hailgenetics/hail:0.2.126 +FROM hailgenetics/hail:0.2.128 LABEL maintainer="Broad TGG" From af3d3ae40fe3431dd22ae90bd88fc221a90b724d Mon Sep 17 00:00:00 2001 From: Julia Klugherz Date: Thu, 29 Feb 2024 12:12:42 -0500 Subject: [PATCH 2/5] google cloud storage --- hail_search/requirements-test.in | 1 + hail_search/requirements-test.txt | 53 +++++++++++++++++++++++++++++-- 2 files changed, 51 insertions(+), 3 deletions(-) diff --git a/hail_search/requirements-test.in b/hail_search/requirements-test.in index 245d0d3637..fb3b9831d4 100644 --- a/hail_search/requirements-test.in +++ b/hail_search/requirements-test.in @@ -1,2 +1,3 @@ coverage<5.2 pytest-aiohttp +google-cloud-storage>=2.14.0 diff --git a/hail_search/requirements-test.txt b/hail_search/requirements-test.txt index 22a794b31a..e9b1f2f074 100644 --- a/hail_search/requirements-test.txt +++ b/hail_search/requirements-test.txt @@ -1,8 +1,8 @@ # # This file is autogenerated by pip-compile with Python 3.9 -# To update, run: +# by the following command: # -# pip-compile hail_search/requirements-test.in +# pip-compile requirements-test.in # aiohttp==3.9.2 # via pytest-aiohttp @@ -12,6 +12,12 @@ async-timeout==4.0.2 # via aiohttp attrs==23.1.0 # via aiohttp +cachetools==5.3.3 + # via google-auth +certifi==2024.2.2 + # via requests +charset-normalizer==3.3.2 + # via requests coverage==5.1 # via -r requirements-test.in exceptiongroup==1.1.3 @@ -20,8 +26,31 @@ frozenlist==1.3.3 # via # aiohttp # aiosignal +google-api-core==2.17.1 + # via + # google-cloud-core + # google-cloud-storage +google-auth==2.28.1 + # via + # google-api-core + # google-cloud-core + # google-cloud-storage +google-cloud-core==2.4.1 + # via google-cloud-storage +google-cloud-storage==2.14.0 + # via -r requirements-test.in +google-crc32c==1.5.0 + # via + # google-cloud-storage + # google-resumable-media +google-resumable-media==2.7.0 + # via google-cloud-storage +googleapis-common-protos==1.62.0 + # via google-api-core idna==3.4 - # via yarl + # via + # requests + # yarl iniconfig==2.0.0 # via pytest multidict==6.0.4 @@ -32,6 +61,16 @@ packaging==23.1 # via pytest pluggy==1.2.0 # via pytest +protobuf==4.25.3 + # via + # google-api-core + # googleapis-common-protos +pyasn1==0.5.1 + # via + # pyasn1-modules + # rsa +pyasn1-modules==0.3.0 + # via google-auth pytest==7.4.0 # via # pytest-aiohttp @@ -40,7 +79,15 @@ pytest-aiohttp==1.0.4 # via -r requirements-test.in pytest-asyncio==0.21.0 # via pytest-aiohttp +requests==2.31.0 + # via + # google-api-core + # google-cloud-storage +rsa==4.9 + # via google-auth tomli==2.0.1 # via pytest +urllib3==2.2.1 + # via requests yarl==1.9.2 # via aiohttp From 886e2ead2d9a3b784d38779eb0c065d94ba6d6a7 Mon Sep 17 00:00:00 2001 From: Julia Klugherz Date: Thu, 29 Feb 2024 12:31:47 -0500 Subject: [PATCH 3/5] Revert "bump hail to 0.2.128" This reverts commit a3a79a3ecef68dd12cab6edf1b922becdcf1d593. --- .github/workflows/hail-search-unit-tests.yaml | 2 +- hail_search/deploy/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/hail-search-unit-tests.yaml b/.github/workflows/hail-search-unit-tests.yaml index ab1c716b24..da9b6cd60c 100644 --- a/.github/workflows/hail-search-unit-tests.yaml +++ b/.github/workflows/hail-search-unit-tests.yaml @@ -17,7 +17,7 @@ on: jobs: hail_search: runs-on: ubuntu-latest - container: hailgenetics/hail:0.2.128 + container: hailgenetics/hail:0.2.126 steps: - uses: actions/checkout@v2 diff --git a/hail_search/deploy/Dockerfile b/hail_search/deploy/Dockerfile index 4a41eb0e7f..ef7408bbf5 100644 --- a/hail_search/deploy/Dockerfile +++ b/hail_search/deploy/Dockerfile @@ -1,4 +1,4 @@ -FROM hailgenetics/hail:0.2.128 +FROM hailgenetics/hail:0.2.126 LABEL maintainer="Broad TGG" From 34674a96bde8ec05d33b156377b1b075f7e02ed8 Mon Sep 17 00:00:00 2001 From: Julia Klugherz Date: Thu, 29 Feb 2024 11:53:47 -0500 Subject: [PATCH 4/5] bump hail to 0.2.128 --- .github/workflows/hail-search-unit-tests.yaml | 2 +- hail_search/deploy/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/hail-search-unit-tests.yaml b/.github/workflows/hail-search-unit-tests.yaml index da9b6cd60c..ab1c716b24 100644 --- a/.github/workflows/hail-search-unit-tests.yaml +++ b/.github/workflows/hail-search-unit-tests.yaml @@ -17,7 +17,7 @@ on: jobs: hail_search: runs-on: ubuntu-latest - container: hailgenetics/hail:0.2.126 + container: hailgenetics/hail:0.2.128 steps: - uses: actions/checkout@v2 diff --git a/hail_search/deploy/Dockerfile b/hail_search/deploy/Dockerfile index ef7408bbf5..4a41eb0e7f 100644 --- a/hail_search/deploy/Dockerfile +++ b/hail_search/deploy/Dockerfile @@ -1,4 +1,4 @@ -FROM hailgenetics/hail:0.2.126 +FROM hailgenetics/hail:0.2.128 LABEL maintainer="Broad TGG" From 9bebaee3abaa3d1b7a1aae41a67fdd1c59cd25cd Mon Sep 17 00:00:00 2001 From: Julia Klugherz Date: Thu, 29 Feb 2024 12:32:57 -0500 Subject: [PATCH 5/5] Revert "google cloud storage" This reverts commit af3d3ae40fe3431dd22ae90bd88fc221a90b724d. --- hail_search/requirements-test.in | 1 - hail_search/requirements-test.txt | 53 ++----------------------------- 2 files changed, 3 insertions(+), 51 deletions(-) diff --git a/hail_search/requirements-test.in b/hail_search/requirements-test.in index fb3b9831d4..245d0d3637 100644 --- a/hail_search/requirements-test.in +++ b/hail_search/requirements-test.in @@ -1,3 +1,2 @@ coverage<5.2 pytest-aiohttp -google-cloud-storage>=2.14.0 diff --git a/hail_search/requirements-test.txt b/hail_search/requirements-test.txt index e9b1f2f074..22a794b31a 100644 --- a/hail_search/requirements-test.txt +++ b/hail_search/requirements-test.txt @@ -1,8 +1,8 @@ # # This file is autogenerated by pip-compile with Python 3.9 -# by the following command: +# To update, run: # -# pip-compile requirements-test.in +# pip-compile hail_search/requirements-test.in # aiohttp==3.9.2 # via pytest-aiohttp @@ -12,12 +12,6 @@ async-timeout==4.0.2 # via aiohttp attrs==23.1.0 # via aiohttp -cachetools==5.3.3 - # via google-auth -certifi==2024.2.2 - # via requests -charset-normalizer==3.3.2 - # via requests coverage==5.1 # via -r requirements-test.in exceptiongroup==1.1.3 @@ -26,31 +20,8 @@ frozenlist==1.3.3 # via # aiohttp # aiosignal -google-api-core==2.17.1 - # via - # google-cloud-core - # google-cloud-storage -google-auth==2.28.1 - # via - # google-api-core - # google-cloud-core - # google-cloud-storage -google-cloud-core==2.4.1 - # via google-cloud-storage -google-cloud-storage==2.14.0 - # via -r requirements-test.in -google-crc32c==1.5.0 - # via - # google-cloud-storage - # google-resumable-media -google-resumable-media==2.7.0 - # via google-cloud-storage -googleapis-common-protos==1.62.0 - # via google-api-core idna==3.4 - # via - # requests - # yarl + # via yarl iniconfig==2.0.0 # via pytest multidict==6.0.4 @@ -61,16 +32,6 @@ packaging==23.1 # via pytest pluggy==1.2.0 # via pytest -protobuf==4.25.3 - # via - # google-api-core - # googleapis-common-protos -pyasn1==0.5.1 - # via - # pyasn1-modules - # rsa -pyasn1-modules==0.3.0 - # via google-auth pytest==7.4.0 # via # pytest-aiohttp @@ -79,15 +40,7 @@ pytest-aiohttp==1.0.4 # via -r requirements-test.in pytest-asyncio==0.21.0 # via pytest-aiohttp -requests==2.31.0 - # via - # google-api-core - # google-cloud-storage -rsa==4.9 - # via google-auth tomli==2.0.1 # via pytest -urllib3==2.2.1 - # via requests yarl==1.9.2 # via aiohttp