From 88f3b8951769c0e12fff8dfb5375b95a2fef5105 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 26 Sep 2023 08:22:09 -0400 Subject: [PATCH 01/16] Updated boto versions. --- poetry.lock | 40 ++++++++++++++++++++-------------------- pyproject.toml | 8 ++++---- 2 files changed, 24 insertions(+), 24 deletions(-) diff --git a/poetry.lock b/poetry.lock index 81cd1d452..d0564a273 100644 --- a/poetry.lock +++ b/poetry.lock @@ -45,17 +45,17 @@ lxml = ["lxml"] [[package]] name = "boto3" -version = "1.28.52" +version = "1.28.54" description = "The AWS SDK for Python" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.28.52-py3-none-any.whl", hash = "sha256:1d36db102517d62c6968b3b0636303241f56859d12dd071def4882fc6e030b20"}, - {file = "boto3-1.28.52.tar.gz", hash = "sha256:a34fc153cb2f6fb2f79a764286c967392e8aae9412381d943bddc576c4f7631a"}, + {file = "boto3-1.28.54-py3-none-any.whl", hash = "sha256:3cb2aee317a1b8686e3b23674e4099b8ff7451bd8acc61b9719acff86fa024d1"}, + {file = "boto3-1.28.54.tar.gz", hash = "sha256:22e37d8c4f2d97b5e5c6ccc1d9edc7760717990b0ba8b8ea17a58cc87e57c5c9"}, ] [package.dependencies] -botocore = ">=1.31.52,<1.32.0" +botocore = ">=1.31.54,<1.32.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.6.0,<0.7.0" @@ -64,13 +64,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.28.52" -description = "Type annotations for boto3 1.28.52 generated with mypy-boto3-builder 7.19.0" +version = "1.28.54" +description = "Type annotations for boto3 1.28.54 generated with mypy-boto3-builder 7.19.0" optional = false python-versions = ">=3.7" files = [ - {file = "boto3-stubs-1.28.52.tar.gz", hash = "sha256:12d7e5865aeec52e1f73b935b1c6a42e61325538fc2cb83a87a83e41e9485241"}, - {file = "boto3_stubs-1.28.52-py3-none-any.whl", hash = "sha256:3ea81a225e062f3bcb205467891086ea031519697ad54622e61251b52609b8d6"}, + {file = "boto3-stubs-1.28.54.tar.gz", hash = "sha256:cb6f6a6cca4826c2b5d61b0a3fcf9cb84d7924c120b7e1c670f08e21cc010425"}, + {file = "boto3_stubs-1.28.54-py3-none-any.whl", hash = "sha256:a58a6ebd0767d7aa1f4ab6f3eec93388b20afff5c5b25c8fe8f866d85eda6f67"}, ] [package.dependencies] @@ -114,7 +114,7 @@ backup-gateway = ["mypy-boto3-backup-gateway (>=1.28.0,<1.29.0)"] backupstorage = ["mypy-boto3-backupstorage (>=1.28.0,<1.29.0)"] batch = ["mypy-boto3-batch (>=1.28.0,<1.29.0)"] billingconductor = ["mypy-boto3-billingconductor (>=1.28.0,<1.29.0)"] -boto3 = ["boto3 (==1.28.52)", "botocore (==1.31.52)"] +boto3 = ["boto3 (==1.28.54)", "botocore (==1.31.54)"] braket = ["mypy-boto3-braket (>=1.28.0,<1.29.0)"] budgets = ["mypy-boto3-budgets (>=1.28.0,<1.29.0)"] ce = ["mypy-boto3-ce (>=1.28.0,<1.29.0)"] @@ -440,13 +440,13 @@ xray = ["mypy-boto3-xray (>=1.28.0,<1.29.0)"] [[package]] name = "botocore" -version = "1.31.52" +version = "1.31.54" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">= 3.7" files = [ - {file = "botocore-1.31.52-py3-none-any.whl", hash = "sha256:46b0a75a38521aa6a75fddccb1542e002930e609d4e13516f40fef170d32e515"}, - {file = "botocore-1.31.52.tar.gz", hash = "sha256:6d09881c5a8be34b497872ca3936f8757d886a6f42f2a8703411928189cfedc0"}, + {file = "botocore-1.31.54-py3-none-any.whl", hash = "sha256:71fdb337ddcdb6bf378e1211cba9ce754c35f12b1524c7d0c0c147b2310356c7"}, + {file = "botocore-1.31.54.tar.gz", hash = "sha256:c98e78a9490c4166b205f87912b46770e156bfe7d53bae54ccbd49c68a336ec6"}, ] [package.dependencies] @@ -459,13 +459,13 @@ crt = ["awscrt (==0.16.26)"] [[package]] name = "botocore-stubs" -version = "1.31.52" +version = "1.31.54" description = "Type annotations and code completion for botocore" optional = false python-versions = ">=3.7,<4.0" files = [ - {file = "botocore_stubs-1.31.52-py3-none-any.whl", hash = "sha256:11431ac0faa35cad6deed6e87002f312f8ea6358d8106a241b60bcead2f84279"}, - {file = "botocore_stubs-1.31.52.tar.gz", hash = "sha256:2fa9b78c7a335a94d918079773dc3198786de741586187d847a8710b9c337009"}, + {file = "botocore_stubs-1.31.54-py3-none-any.whl", hash = "sha256:6e3e015ba4d2172c6a9bd5ff5131c39c995991559a567dce6c8534884f83ded1"}, + {file = "botocore_stubs-1.31.54.tar.gz", hash = "sha256:96223fdf87a68037dd1ed366ffe28b5b744aca495a365f4535e2179c9a88455c"}, ] [package.dependencies] @@ -865,20 +865,20 @@ smmap = ">=3.0.1,<6" [[package]] name = "gitpython" -version = "3.1.36" +version = "3.1.37" description = "GitPython is a Python library used to interact with Git repositories" optional = false python-versions = ">=3.7" files = [ - {file = "GitPython-3.1.36-py3-none-any.whl", hash = "sha256:8d22b5cfefd17c79914226982bb7851d6ade47545b1735a9d010a2a4c26d8388"}, - {file = "GitPython-3.1.36.tar.gz", hash = "sha256:4bb0c2a6995e85064140d31a33289aa5dce80133a23d36fcd372d716c54d3ebf"}, + {file = "GitPython-3.1.37-py3-none-any.whl", hash = "sha256:5f4c4187de49616d710a77e98ddf17b4782060a1788df441846bddefbb89ab33"}, + {file = "GitPython-3.1.37.tar.gz", hash = "sha256:f9b9ddc0761c125d5780eab2d64be4873fc6817c2899cbcb34b02344bdc7bc54"}, ] [package.dependencies] gitdb = ">=4.0.1,<5" [package.extras] -test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-sugar", "virtualenv"] +test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-sugar"] [[package]] name = "idna" @@ -1606,4 +1606,4 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.12" -content-hash = "fb29c53ae0f29eab1185dee384d1cd3b7dd039ca2cef7a5a38915de0e939a6a1" +content-hash = "6cdcf4e9fab04bbcaa83c3054b61356b4830b55c67e2a362dd1af635ae75a688" diff --git a/pyproject.toml b/pyproject.toml index ac8a71e1e..288228385 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,8 +36,8 @@ classifiers = [ [tool.poetry.dependencies] python = ">=3.8,<3.12" -boto3 = "^1.28.51" -botocore = "^1.31.51" +boto3 = "^1.28.54" +botocore = "^1.31.54" # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version. # This value is intentionally pinned and must not be changed casually. elasticsearch = "7.13.4" @@ -61,8 +61,8 @@ tqdm = "^4.65.0" [tool.poetry.dev-dependencies] -botocore-stubs = "^1.31.51" -boto3-stubs = "^1.28.51" +boto3-stubs = "^1.28.54" +botocore-stubs = "^1.31.54" coverage = ">=7.2.3" # Loaded manually in GA workflow for coverage because a dependency on 2to3 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023 From 3e5cf5f4be1f2a9d0af835e521690af93c345e2c Mon Sep 17 00:00:00 2001 From: David Michaels Date: Tue, 26 Sep 2023 08:22:22 -0400 Subject: [PATCH 02/16] Updated boto versions. --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 288228385..ccc85023e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicutils" -version = "7.12.0.1b5" # TODO: To become 8.0.0 +version = "7.12.0.1b6" # TODO: To become 8.0.0 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" authors = ["4DN-DCIC Team "] license = "MIT" From e24b3e04fa36d695f84c76c431f4d89a27a5b93c Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 07:03:24 -0400 Subject: [PATCH 03/16] Added Python 3.10, 3.11 to pyproject Python list --- pyproject.toml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ccc85023e..6ea1bef40 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicutils" -version = "7.12.0.1b6" # TODO: To become 8.0.0 +version = "7.12.0.1b7" # TODO: To become 8.0.0 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" authors = ["4DN-DCIC Team "] license = "MIT" @@ -31,6 +31,8 @@ classifiers = [ 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9', + 'Programming Language :: Python :: 3.10', + 'Programming Language :: Python :: 3.11' ] From c760707150588d65eb8085fb39eb0bf957910404 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 10:14:58 -0400 Subject: [PATCH 04/16] Update Ubuntu to 22.04 for GA --- .github/workflows/main.yml | 2 +- pyproject.toml | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d9d6dd741..5ec18cdda 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -20,7 +20,7 @@ jobs: name: Test dcicutils with Python ${{ matrix.python_version }} # The type of runner that the job will run on - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 strategy: matrix: python_version: [3.8, 3.9, 3.11] diff --git a/pyproject.toml b/pyproject.toml index 6ea1bef40..4597cbdb7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicutils" -version = "7.12.0.1b7" # TODO: To become 8.0.0 +version = "7.12.0.1b8" # TODO: To become 8.0.0 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" authors = ["4DN-DCIC Team "] license = "MIT" @@ -38,8 +38,8 @@ classifiers = [ [tool.poetry.dependencies] python = ">=3.8,<3.12" -boto3 = "^1.28.54" -botocore = "^1.31.54" +boto3 = "^1.28.56" +botocore = "^1.31.56" # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version. # This value is intentionally pinned and must not be changed casually. elasticsearch = "7.13.4" @@ -63,8 +63,8 @@ tqdm = "^4.65.0" [tool.poetry.dev-dependencies] -boto3-stubs = "^1.28.54" -botocore-stubs = "^1.31.54" +boto3-stubs = "^1.28.56" +botocore-stubs = "^1.31.56" coverage = ">=7.2.3" # Loaded manually in GA workflow for coverage because a dependency on 2to3 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023 From 7b3daafb46785295258dbed1f40252b9b519db40 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 10:17:15 -0400 Subject: [PATCH 05/16] Update Ubuntu to 22.04 for GA and poetry update --- poetry.lock | 46 +++++++++++++++++++++++----------------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/poetry.lock b/poetry.lock index d0564a273..d7a42df51 100644 --- a/poetry.lock +++ b/poetry.lock @@ -45,32 +45,32 @@ lxml = ["lxml"] [[package]] name = "boto3" -version = "1.28.54" +version = "1.28.56" description = "The AWS SDK for Python" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.28.54-py3-none-any.whl", hash = "sha256:3cb2aee317a1b8686e3b23674e4099b8ff7451bd8acc61b9719acff86fa024d1"}, - {file = "boto3-1.28.54.tar.gz", hash = "sha256:22e37d8c4f2d97b5e5c6ccc1d9edc7760717990b0ba8b8ea17a58cc87e57c5c9"}, + {file = "boto3-1.28.56-py3-none-any.whl", hash = "sha256:f5fcb27cdbd08ca38d699f2d2e32d96d1d9fab3368c15c6bc326256612d2cfd7"}, + {file = "boto3-1.28.56.tar.gz", hash = "sha256:b927a7ed335d543c33c15fa63f1076f3fa8422959771c2187da74bc4395ab6e3"}, ] [package.dependencies] -botocore = ">=1.31.54,<1.32.0" +botocore = ">=1.31.56,<1.32.0" jmespath = ">=0.7.1,<2.0.0" -s3transfer = ">=0.6.0,<0.7.0" +s3transfer = ">=0.7.0,<0.8.0" [package.extras] crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.28.54" -description = "Type annotations for boto3 1.28.54 generated with mypy-boto3-builder 7.19.0" +version = "1.28.56" +description = "Type annotations for boto3 1.28.56 generated with mypy-boto3-builder 7.19.0" optional = false python-versions = ">=3.7" files = [ - {file = "boto3-stubs-1.28.54.tar.gz", hash = "sha256:cb6f6a6cca4826c2b5d61b0a3fcf9cb84d7924c120b7e1c670f08e21cc010425"}, - {file = "boto3_stubs-1.28.54-py3-none-any.whl", hash = "sha256:a58a6ebd0767d7aa1f4ab6f3eec93388b20afff5c5b25c8fe8f866d85eda6f67"}, + {file = "boto3-stubs-1.28.56.tar.gz", hash = "sha256:2b77d4b9e944ffa4308822dc0327269f47cc4527a97903a3c5d14b9abed4eaad"}, + {file = "boto3_stubs-1.28.56-py3-none-any.whl", hash = "sha256:e9c1f32463cf8e6ba56588f7c0f5cae52190b87eb19744ad1067a717be1c80b3"}, ] [package.dependencies] @@ -114,7 +114,7 @@ backup-gateway = ["mypy-boto3-backup-gateway (>=1.28.0,<1.29.0)"] backupstorage = ["mypy-boto3-backupstorage (>=1.28.0,<1.29.0)"] batch = ["mypy-boto3-batch (>=1.28.0,<1.29.0)"] billingconductor = ["mypy-boto3-billingconductor (>=1.28.0,<1.29.0)"] -boto3 = ["boto3 (==1.28.54)", "botocore (==1.31.54)"] +boto3 = ["boto3 (==1.28.56)", "botocore (==1.31.56)"] braket = ["mypy-boto3-braket (>=1.28.0,<1.29.0)"] budgets = ["mypy-boto3-budgets (>=1.28.0,<1.29.0)"] ce = ["mypy-boto3-ce (>=1.28.0,<1.29.0)"] @@ -440,13 +440,13 @@ xray = ["mypy-boto3-xray (>=1.28.0,<1.29.0)"] [[package]] name = "botocore" -version = "1.31.54" +version = "1.31.56" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">= 3.7" files = [ - {file = "botocore-1.31.54-py3-none-any.whl", hash = "sha256:71fdb337ddcdb6bf378e1211cba9ce754c35f12b1524c7d0c0c147b2310356c7"}, - {file = "botocore-1.31.54.tar.gz", hash = "sha256:c98e78a9490c4166b205f87912b46770e156bfe7d53bae54ccbd49c68a336ec6"}, + {file = "botocore-1.31.56-py3-none-any.whl", hash = "sha256:66c686e4eda7051ffcc9357d9075390c8ab2f95a2977669039618ee186fb533b"}, + {file = "botocore-1.31.56.tar.gz", hash = "sha256:70252cd8abc2fe9b791328e187620f5a3911545e2520486b01ecfad31f41b9cb"}, ] [package.dependencies] @@ -459,13 +459,13 @@ crt = ["awscrt (==0.16.26)"] [[package]] name = "botocore-stubs" -version = "1.31.54" +version = "1.31.56" description = "Type annotations and code completion for botocore" optional = false python-versions = ">=3.7,<4.0" files = [ - {file = "botocore_stubs-1.31.54-py3-none-any.whl", hash = "sha256:6e3e015ba4d2172c6a9bd5ff5131c39c995991559a567dce6c8534884f83ded1"}, - {file = "botocore_stubs-1.31.54.tar.gz", hash = "sha256:96223fdf87a68037dd1ed366ffe28b5b744aca495a365f4535e2179c9a88455c"}, + {file = "botocore_stubs-1.31.56-py3-none-any.whl", hash = "sha256:e8f7273f57c09ef47f8bdc89765b151f43a46b3c29c52fb58e9982115ed14d84"}, + {file = "botocore_stubs-1.31.56.tar.gz", hash = "sha256:e1510bd361acf755ecace42ee984281adfea6f96695ed22a08a4ceeabfe66f5f"}, ] [package.dependencies] @@ -1366,13 +1366,13 @@ idna2008 = ["idna"] [[package]] name = "s3transfer" -version = "0.6.2" +version = "0.7.0" description = "An Amazon S3 Transfer Manager" optional = false python-versions = ">= 3.7" files = [ - {file = "s3transfer-0.6.2-py3-none-any.whl", hash = "sha256:b014be3a8a2aab98cfe1abc7229cc5a9a0cf05eb9c1f2b86b230fd8df3f78084"}, - {file = "s3transfer-0.6.2.tar.gz", hash = "sha256:cab66d3380cca3e70939ef2255d01cd8aece6a4907a9528740f668c4b0611861"}, + {file = "s3transfer-0.7.0-py3-none-any.whl", hash = "sha256:10d6923c6359175f264811ef4bf6161a3156ce8e350e705396a7557d6293c33a"}, + {file = "s3transfer-0.7.0.tar.gz", hash = "sha256:fd3889a66f5fe17299fe75b82eae6cf722554edca744ca5d5fe308b104883d2e"}, ] [package.dependencies] @@ -1489,13 +1489,13 @@ files = [ [[package]] name = "types-s3transfer" -version = "0.6.2" +version = "0.7.0" description = "Type annotations and code completion for s3transfer" optional = false python-versions = ">=3.7,<4.0" files = [ - {file = "types_s3transfer-0.6.2-py3-none-any.whl", hash = "sha256:1068877b6e59be5226fa3006ae64371ac9d5bc590dfdbd9c66fd0a075d3254ac"}, - {file = "types_s3transfer-0.6.2.tar.gz", hash = "sha256:4ba9b483796fdcd026aa162ee03bdcedd2bf7d08e9387c820dcdd158b0102057"}, + {file = "types_s3transfer-0.7.0-py3-none-any.whl", hash = "sha256:ae9ed9273465d9f43da8b96307383da410c6b59c3b2464c88d20b578768e97c6"}, + {file = "types_s3transfer-0.7.0.tar.gz", hash = "sha256:aca0f2486d0a3a5037cd5b8f3e20a4522a29579a8dd183281ff0aa1c4e2c8aa7"}, ] [[package]] @@ -1606,4 +1606,4 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.12" -content-hash = "6cdcf4e9fab04bbcaa83c3054b61356b4830b55c67e2a362dd1af635ae75a688" +content-hash = "cf533f908fb4f451ada1932dfa17d6c47beb8052126bf286ee82a4fa3eb1cc65" From 099a32e7869a630c58625179053945ded1ae88aa Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 10:34:21 -0400 Subject: [PATCH 06/16] back out ubuntu to 22.04 for now to test - ga failing all of a sudden --- .github/workflows/main.yml | 2 +- poetry.lock | 2 +- pyproject.toml | 8 ++++---- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 5ec18cdda..d9d6dd741 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -20,7 +20,7 @@ jobs: name: Test dcicutils with Python ${{ matrix.python_version }} # The type of runner that the job will run on - runs-on: ubuntu-22.04 + runs-on: ubuntu-20.04 strategy: matrix: python_version: [3.8, 3.9, 3.11] diff --git a/poetry.lock b/poetry.lock index d7a42df51..ea0071db0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1606,4 +1606,4 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.12" -content-hash = "cf533f908fb4f451ada1932dfa17d6c47beb8052126bf286ee82a4fa3eb1cc65" +content-hash = "6cdcf4e9fab04bbcaa83c3054b61356b4830b55c67e2a362dd1af635ae75a688" diff --git a/pyproject.toml b/pyproject.toml index 4597cbdb7..56c666321 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,8 +38,8 @@ classifiers = [ [tool.poetry.dependencies] python = ">=3.8,<3.12" -boto3 = "^1.28.56" -botocore = "^1.31.56" +boto3 = "^1.28.54" +botocore = "^1.31.54" # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version. # This value is intentionally pinned and must not be changed casually. elasticsearch = "7.13.4" @@ -63,8 +63,8 @@ tqdm = "^4.65.0" [tool.poetry.dev-dependencies] -boto3-stubs = "^1.28.56" -botocore-stubs = "^1.31.56" +boto3-stubs = "^1.28.54" +botocore-stubs = "^1.31.54" coverage = ">=7.2.3" # Loaded manually in GA workflow for coverage because a dependency on 2to3 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023 From 25a4b5829ee6a935b324d741f8b3ae647812ce3c Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 10:38:57 -0400 Subject: [PATCH 07/16] put back update to ubuntu 20.04 -> 22.04 for ga and see if ga fails now --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d9d6dd741..5ec18cdda 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -20,7 +20,7 @@ jobs: name: Test dcicutils with Python ${{ matrix.python_version }} # The type of runner that the job will run on - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 strategy: matrix: python_version: [3.8, 3.9, 3.11] From 96cc528c1e620bb0a8b1b49a44f2f3f7075346bf Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 10:44:08 -0400 Subject: [PATCH 08/16] ga failed with ubuntu 22.04 for python 3.11 - put back 20.04 to make sure it passes again --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 5ec18cdda..d9d6dd741 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -20,7 +20,7 @@ jobs: name: Test dcicutils with Python ${{ matrix.python_version }} # The type of runner that the job will run on - runs-on: ubuntu-22.04 + runs-on: ubuntu-20.04 strategy: matrix: python_version: [3.8, 3.9, 3.11] From 97f1173700a3da101951f13b7678df12e19896fd Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 11:07:10 -0400 Subject: [PATCH 09/16] put ubuntu 22.04 back for ga and add testing hack in qa_utils.py --- .github/workflows/main.yml | 2 +- dcicutils/qa_utils.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d9d6dd741..5ec18cdda 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -20,7 +20,7 @@ jobs: name: Test dcicutils with Python ${{ matrix.python_version }} # The type of runner that the job will run on - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 strategy: matrix: python_version: [3.8, 3.9, 3.11] diff --git a/dcicutils/qa_utils.py b/dcicutils/qa_utils.py index 8b440c413..c55a8b812 100644 --- a/dcicutils/qa_utils.py +++ b/dcicutils/qa_utils.py @@ -2308,6 +2308,7 @@ def get_object(self, Bucket, Key, **kwargs): # noqa - Uppercase argument names "application/json": [".json"], "text/plain": [".txt", ".text"], "binary/octet-stream": [".fo"], + "application/vnd.software602.filler.form+xml": [".json"], # xyzzy: temporary hack to see if fixes with ubuntu 22.04 2023-09-28 } def put_object(self, *, Bucket, Key, Body, ContentType=None, **kwargs): # noqa - Uppercase argument names are chosen by AWS From b226d61379d6f785d1f5a540b0069a20ade731fa Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 11:08:55 -0400 Subject: [PATCH 10/16] flake8 error --- dcicutils/qa_utils.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/dcicutils/qa_utils.py b/dcicutils/qa_utils.py index c55a8b812..41f85aa7a 100644 --- a/dcicutils/qa_utils.py +++ b/dcicutils/qa_utils.py @@ -2308,7 +2308,8 @@ def get_object(self, Bucket, Key, **kwargs): # noqa - Uppercase argument names "application/json": [".json"], "text/plain": [".txt", ".text"], "binary/octet-stream": [".fo"], - "application/vnd.software602.filler.form+xml": [".json"], # xyzzy: temporary hack to see if fixes with ubuntu 22.04 2023-09-28 + # xyzzy: temporary hack to see if fixes with ubuntu 22.04 2023-09-28 ... + "application/vnd.software602.filler.form+xml": [".json"], } def put_object(self, *, Bucket, Key, Body, ContentType=None, **kwargs): # noqa - Uppercase argument names are chosen by AWS From 45064b2f60487ec008cfaddd8c35a97b3ee79636 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 11:13:45 -0400 Subject: [PATCH 11/16] more hacking of qa_utils for troubleshooting ga failure with ubuntu 22.04 --- dcicutils/qa_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dcicutils/qa_utils.py b/dcicutils/qa_utils.py index 41f85aa7a..42271fd54 100644 --- a/dcicutils/qa_utils.py +++ b/dcicutils/qa_utils.py @@ -2309,7 +2309,7 @@ def get_object(self, Bucket, Key, **kwargs): # noqa - Uppercase argument names "text/plain": [".txt", ".text"], "binary/octet-stream": [".fo"], # xyzzy: temporary hack to see if fixes with ubuntu 22.04 2023-09-28 ... - "application/vnd.software602.filler.form+xml": [".json"], + "application/vnd.software602.filler.form+xml": [".fo"], } def put_object(self, *, Bucket, Key, Body, ContentType=None, **kwargs): # noqa - Uppercase argument names are chosen by AWS From bd6a79748df638e8ce1f558b3b2362630ec043ed Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 12:02:10 -0400 Subject: [PATCH 12/16] Updated comments --- dcicutils/qa_utils.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dcicutils/qa_utils.py b/dcicutils/qa_utils.py index 42271fd54..0c9b019ed 100644 --- a/dcicutils/qa_utils.py +++ b/dcicutils/qa_utils.py @@ -2308,7 +2308,9 @@ def get_object(self, Bucket, Key, **kwargs): # noqa - Uppercase argument names "application/json": [".json"], "text/plain": [".txt", ".text"], "binary/octet-stream": [".fo"], - # xyzzy: temporary hack to see if fixes with ubuntu 22.04 2023-09-28 ... + # The below is because on Ubuntu 22.04 (docker), as opposed to 20.04, the mimetypes.guess_type + # function returns this strange value for an argument ending in ".fo"; this manifested as a test + # failure (put_object assert below) in test_s3_utils.test_unzip_s3_to_s3_unit. dmichaels/2023-09-28. "application/vnd.software602.filler.form+xml": [".fo"], } From 96a10cb6189884221cc9fe218e836f3b765c50f4 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 28 Sep 2023 12:54:07 -0400 Subject: [PATCH 13/16] Fix to qa_utils for application/vnd.software602.filler.form+xml mime type return from mimetypes.guess_type on Ubuntu 22.04. --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 56c666321..f87568801 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicutils" -version = "7.12.0.1b8" # TODO: To become 8.0.0 +version = "7.12.0.1b9" # TODO: To become 8.0.0 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" authors = ["4DN-DCIC Team "] license = "MIT" From f7c05b5d1aeaed68b8f747833b558a17e4d42954 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Fri, 29 Sep 2023 13:44:49 -0400 Subject: [PATCH 14/16] poetry update --- poetry.lock | 163 +++++++++++++++++++++++-------------------------- pyproject.toml | 8 +-- 2 files changed, 80 insertions(+), 91 deletions(-) diff --git a/poetry.lock b/poetry.lock index 471323aa3..ba5a1bb74 100644 --- a/poetry.lock +++ b/poetry.lock @@ -45,17 +45,17 @@ lxml = ["lxml"] [[package]] name = "boto3" -version = "1.28.56" +version = "1.28.57" description = "The AWS SDK for Python" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.28.56-py3-none-any.whl", hash = "sha256:f5fcb27cdbd08ca38d699f2d2e32d96d1d9fab3368c15c6bc326256612d2cfd7"}, - {file = "boto3-1.28.56.tar.gz", hash = "sha256:b927a7ed335d543c33c15fa63f1076f3fa8422959771c2187da74bc4395ab6e3"}, + {file = "boto3-1.28.57-py3-none-any.whl", hash = "sha256:5ddf24cf52c7fb6aaa332eaa08ae8c2afc8f2d1e8860680728533dd573904e32"}, + {file = "boto3-1.28.57.tar.gz", hash = "sha256:e2d2824ba6459b330d097e94039a9c4f96ae3f4bcdc731d620589ad79dcd16d3"}, ] [package.dependencies] -botocore = ">=1.31.56,<1.32.0" +botocore = ">=1.31.57,<1.32.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.7.0,<0.8.0" @@ -64,13 +64,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "boto3-stubs" -version = "1.28.56" -description = "Type annotations for boto3 1.28.56 generated with mypy-boto3-builder 7.19.0" +version = "1.28.57" +description = "Type annotations for boto3 1.28.57 generated with mypy-boto3-builder 7.19.0" optional = false python-versions = ">=3.7" files = [ - {file = "boto3-stubs-1.28.56.tar.gz", hash = "sha256:2b77d4b9e944ffa4308822dc0327269f47cc4527a97903a3c5d14b9abed4eaad"}, - {file = "boto3_stubs-1.28.56-py3-none-any.whl", hash = "sha256:e9c1f32463cf8e6ba56588f7c0f5cae52190b87eb19744ad1067a717be1c80b3"}, + {file = "boto3-stubs-1.28.57.tar.gz", hash = "sha256:61cd792792c2a16d70801d187ebed705c39962a70e90b5dc0f33d04001fb39ae"}, + {file = "boto3_stubs-1.28.57-py3-none-any.whl", hash = "sha256:b389a693e33d75ed19d38b4a2ba99d25f4f2045a3136f816d7fec4d27a71ddb4"}, ] [package.dependencies] @@ -84,7 +84,7 @@ account = ["mypy-boto3-account (>=1.28.0,<1.29.0)"] acm = ["mypy-boto3-acm (>=1.28.0,<1.29.0)"] acm-pca = ["mypy-boto3-acm-pca (>=1.28.0,<1.29.0)"] alexaforbusiness = ["mypy-boto3-alexaforbusiness (>=1.28.0,<1.29.0)"] -all = ["mypy-boto3-accessanalyzer (>=1.28.0,<1.29.0)", "mypy-boto3-account (>=1.28.0,<1.29.0)", "mypy-boto3-acm (>=1.28.0,<1.29.0)", "mypy-boto3-acm-pca (>=1.28.0,<1.29.0)", "mypy-boto3-alexaforbusiness (>=1.28.0,<1.29.0)", "mypy-boto3-amp (>=1.28.0,<1.29.0)", "mypy-boto3-amplify (>=1.28.0,<1.29.0)", "mypy-boto3-amplifybackend (>=1.28.0,<1.29.0)", "mypy-boto3-amplifyuibuilder (>=1.28.0,<1.29.0)", "mypy-boto3-apigateway (>=1.28.0,<1.29.0)", "mypy-boto3-apigatewaymanagementapi (>=1.28.0,<1.29.0)", "mypy-boto3-apigatewayv2 (>=1.28.0,<1.29.0)", "mypy-boto3-appconfig (>=1.28.0,<1.29.0)", "mypy-boto3-appconfigdata (>=1.28.0,<1.29.0)", "mypy-boto3-appfabric (>=1.28.0,<1.29.0)", "mypy-boto3-appflow (>=1.28.0,<1.29.0)", "mypy-boto3-appintegrations (>=1.28.0,<1.29.0)", "mypy-boto3-application-autoscaling (>=1.28.0,<1.29.0)", "mypy-boto3-application-insights (>=1.28.0,<1.29.0)", "mypy-boto3-applicationcostprofiler (>=1.28.0,<1.29.0)", "mypy-boto3-appmesh (>=1.28.0,<1.29.0)", "mypy-boto3-apprunner (>=1.28.0,<1.29.0)", "mypy-boto3-appstream (>=1.28.0,<1.29.0)", "mypy-boto3-appsync (>=1.28.0,<1.29.0)", "mypy-boto3-arc-zonal-shift (>=1.28.0,<1.29.0)", "mypy-boto3-athena (>=1.28.0,<1.29.0)", "mypy-boto3-auditmanager (>=1.28.0,<1.29.0)", "mypy-boto3-autoscaling (>=1.28.0,<1.29.0)", "mypy-boto3-autoscaling-plans (>=1.28.0,<1.29.0)", "mypy-boto3-backup (>=1.28.0,<1.29.0)", "mypy-boto3-backup-gateway (>=1.28.0,<1.29.0)", "mypy-boto3-backupstorage (>=1.28.0,<1.29.0)", "mypy-boto3-batch (>=1.28.0,<1.29.0)", "mypy-boto3-billingconductor (>=1.28.0,<1.29.0)", "mypy-boto3-braket (>=1.28.0,<1.29.0)", "mypy-boto3-budgets (>=1.28.0,<1.29.0)", "mypy-boto3-ce (>=1.28.0,<1.29.0)", "mypy-boto3-chime (>=1.28.0,<1.29.0)", "mypy-boto3-chime-sdk-identity (>=1.28.0,<1.29.0)", 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casually. elasticsearch = "7.13.4" @@ -64,8 +64,8 @@ tqdm = "^4.65.0" [tool.poetry.dev-dependencies] -boto3-stubs = "^1.28.54" -botocore-stubs = "^1.31.54" +boto3-stubs = "^1.28.57" +botocore-stubs = "^1.31.57" coverage = ">=7.2.3" # Loaded manually in GA workflow for coverage because a dependency on 2to3 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023 From 27e11b6a08750036ec0c905a0ef3d5d5618e41ae Mon Sep 17 00:00:00 2001 From: David Michaels Date: Fri, 29 Sep 2023 13:59:41 -0400 Subject: [PATCH 15/16] Bumped to Python 3.11 in static-checks.yml --- .github/workflows/static-checks.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/static-checks.yml b/.github/workflows/static-checks.yml index 0d914f264..aa2a095b6 100644 --- a/.github/workflows/static-checks.yml +++ b/.github/workflows/static-checks.yml @@ -27,7 +27,7 @@ jobs: - uses: actions/checkout@v3 - uses: actions/setup-python@v2 with: - python-version: 3.9 + python-version: 3.11 - name: Python Package Setup run: | make configure From 2699a4da5a203b49abf88187a9eb8901297dd91e Mon Sep 17 00:00:00 2001 From: David Michaels Date: Thu, 5 Oct 2023 12:25:26 -0400 Subject: [PATCH 16/16] Update version to 8.0.0; ready to merge to master. --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 290713fe3..804de6f74 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dcicutils" -version = "7.12.0.1b10" # TODO: To become 8.0.0 +version = "8.0.0" description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" authors = ["4DN-DCIC Team "] license = "MIT"