diff --git a/.github/workflows/blank.yml b/.github/workflows/blank.yml index 08e635491..3b7abd2ea 100644 --- a/.github/workflows/blank.yml +++ b/.github/workflows/blank.yml @@ -65,16 +65,19 @@ jobs: run: yarn build:electron test-server: - defaults: - run: - working-directory: server name: Server Tests - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 strategy: matrix: python-version: [3.8] steps: - - uses: actions/checkout@v2 + - name: Update Package References + run: sudo apt-get update + - name: Install system dependencies + run: apt-fast install --no-install-recommends --yes + libgdal-dev + - name: Checkout repository + uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: @@ -85,3 +88,5 @@ jobs: pip install tox; - name: Run tests run: tox + working-directory: server + diff --git a/server/poetry.lock b/server/poetry.lock index 42684afe7..2bdc3645d 100644 --- a/server/poetry.lock +++ b/server/poetry.lock @@ -803,13 +803,13 @@ numpy = ["numpy (>1.0.0)"] [[package]] name = "girder" -version = "3.1.16" +version = "3.1.22" description = "Web-based data management platform" category = "main" optional = false python-versions = ">=3.6" files = [ - {file = "girder-3.1.16.tar.gz", hash = "sha256:5073c744359beade962c5297769d5eeb68721743caf9abe3d61e11be65d22a9f"}, + {file = "girder-3.1.22.tar.gz", hash = "sha256:3406f5a6b0055b81fa10baa4719686ca4dd4156d8ca7b63c4d0c26b1698363e2"}, ] [package.dependencies] @@ -854,13 +854,13 @@ requests_toolbelt = "*" [[package]] name = "girder-jobs" -version = "3.1.16" +version = "3.1.22" description = "A general purpose plugin for managing offline jobs." category = "main" optional = false python-versions = "*" files = [ - {file = "girder-jobs-3.1.16.tar.gz", hash = "sha256:f9490f0e646ecda8c5380afce51d06dcc1fcc0581561ff100f0a74c4d2b2fd74"}, + {file = "girder-jobs-3.1.22.tar.gz", hash = "sha256:2a84ce4b995c3987cf9971165ee630ef79ca5e4869c9a1522f59e9242e11ea7e"}, ] [package.dependencies] @@ -868,23 +868,23 @@ girder = ">=3" [[package]] name = "girder-large-image" -version = "1.20.6" +version = "1.23.6" description = "A Girder plugin to work with large, multiresolution images." category = "main" optional = false python-versions = ">=3.6" files = [ - {file = "girder-large-image-1.20.6.tar.gz", hash = "sha256:26d223f48c2fc94473cf1787e983c5b30835b208718d45c498572f2f7245fe89"}, - {file = "girder_large_image-1.20.6-py3-none-any.whl", hash = "sha256:62abea29b3aabaabcb312c4a25371fdcf86214adc03d5ed9ebef87ee5181850c"}, + {file = "girder-large-image-1.23.6.tar.gz", hash = "sha256:6d8de95890915d00fd1ed860492164d1bcf830eaa707c95707e524cf687f52c9"}, + {file = "girder_large_image-1.23.6-py3-none-any.whl", hash = "sha256:695cb96847dd93dce05da4447a175d68136efb3886ace825d95c1cd03778d72a"}, ] [package.dependencies] -girder = ">=3.0.4" +girder = ">=3.1.18" girder-jobs = ">=3.0.3" -large-image = ">=1.20.6" +large-image = ">=1.23.6" [package.extras] -tasks = ["girder-worker[girder] (>=0.6.0)", "large-image-tasks[girder] (>=1.20.6)"] +tasks = ["girder-worker[girder] (>=0.6.0)", "large-image-tasks[girder] (>=1.23.6)"] [[package]] name = "girder-worker" @@ -935,25 +935,24 @@ six = "*" urllib3 = ">=1.24.2" [[package]] -name = "Glymur" -version = "0.9.9" -description = "Tools for accessing JPEG2000 files" +name = "glymur" +version = "0.12.8" +description = "" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.8" files = [ - {file = "Glymur-0.9.9-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c884a541b18324ba79f91392d3bb737b447bbd0752e43edcb85eb9751328a848"}, + {file = "Glymur-0.12.8-py3-none-any.whl", hash = "sha256:db7793ebe698576a4626b2c6bfbbaf5f5f075b553596385c9143b25e4f4a6f95"}, + {file = "Glymur-0.12.8.tar.gz", hash = "sha256:20e3a51610c5b2451e6b9afe87ef87bb6d78307f37ce8bebb765eb864045f898"}, ] [package.dependencies] lxml = "*" numpy = "*" packaging = "*" -setuptools = "*" -[package.source] -type = "url" -url = "https://github.com/girder/large_image_wheels/raw/wheelhouse/Glymur-0.9.9-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl" +[package.extras] +test = ["pillow", "pytest"] [[package]] name = "gputil" @@ -1553,19 +1552,16 @@ testing = ["pytest"] [[package]] name = "mapnik" -version = "4.0.0" +version = "0.1" description = "Python bindings for Mapnik" category = "main" optional = false python-versions = "*" files = [ - {file = "mapnik-4.0.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b10bedbfbcd94eae164cda62af6c2db4a9ca5c93b0f0f5f20057a6404b4ec7d3"}, + {file = "mapnik-0.1-cp27-none-any.whl", hash = "sha256:9f612ee05823fa28bea6522bd794b19a8d0c424754dd92e3bc14079fa7f2b848"}, + {file = "mapnik-0.1-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl", hash = "sha256:c2e44960cdbdcfd769f8743e951cf664b1ffad5c3267bd63b965c2844874fc51"}, ] -[package.source] -type = "url" -url = "https://github.com/girder/large_image_wheels/raw/wheelhouse/mapnik-4.0.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl" - [[package]] name = "markupsafe" version = "2.1.3" @@ -1921,21 +1917,30 @@ wcwidth = "*" [[package]] name = "psutil" -version = "5.7.3" +version = "5.9.5" description = "Cross-platform lib for process and system monitoring in Python." category = "main" optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ - {file = "psutil-5.7.3-cp38-cp38-manylinux2010_x86_64.whl", hash = "sha256:89be0d75f520f52737f26a4425fff253d33fb0bb65a2f2396587c8a036aa03ea"}, + {file = "psutil-5.9.5-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:be8929ce4313f9f8146caad4272f6abb8bf99fc6cf59344a3167ecd74f4f203f"}, + {file = "psutil-5.9.5-cp27-cp27m-manylinux2010_i686.whl", hash = "sha256:ab8ed1a1d77c95453db1ae00a3f9c50227ebd955437bcf2a574ba8adbf6a74d5"}, + {file = "psutil-5.9.5-cp27-cp27m-manylinux2010_x86_64.whl", hash = "sha256:4aef137f3345082a3d3232187aeb4ac4ef959ba3d7c10c33dd73763fbc063da4"}, + {file = "psutil-5.9.5-cp27-cp27mu-manylinux2010_i686.whl", hash = "sha256:ea8518d152174e1249c4f2a1c89e3e6065941df2fa13a1ab45327716a23c2b48"}, + {file = "psutil-5.9.5-cp27-cp27mu-manylinux2010_x86_64.whl", hash = "sha256:acf2aef9391710afded549ff602b5887d7a2349831ae4c26be7c807c0a39fac4"}, + {file = "psutil-5.9.5-cp27-none-win32.whl", hash = "sha256:5b9b8cb93f507e8dbaf22af6a2fd0ccbe8244bf30b1baad6b3954e935157ae3f"}, + {file = "psutil-5.9.5-cp27-none-win_amd64.whl", hash = "sha256:8c5f7c5a052d1d567db4ddd231a9d27a74e8e4a9c3f44b1032762bd7b9fdcd42"}, + {file = "psutil-5.9.5-cp36-abi3-macosx_10_9_x86_64.whl", hash = "sha256:3c6f686f4225553615612f6d9bc21f1c0e305f75d7d8454f9b46e901778e7217"}, + {file = "psutil-5.9.5-cp36-abi3-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:7a7dd9997128a0d928ed4fb2c2d57e5102bb6089027939f3b722f3a210f9a8da"}, + {file = "psutil-5.9.5-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:89518112647f1276b03ca97b65cc7f64ca587b1eb0278383017c2a0dcc26cbe4"}, + {file = "psutil-5.9.5-cp36-abi3-win32.whl", hash = "sha256:104a5cc0e31baa2bcf67900be36acde157756b9c44017b86b2c049f11957887d"}, + {file = "psutil-5.9.5-cp36-abi3-win_amd64.whl", hash = "sha256:b258c0c1c9d145a1d5ceffab1134441c4c5113b2417fafff7315a917a026c3c9"}, + {file = "psutil-5.9.5-cp38-abi3-macosx_11_0_arm64.whl", hash = "sha256:c607bb3b57dc779d55e1554846352b4e358c10fff3abf3514a7a6601beebdb30"}, + {file = "psutil-5.9.5.tar.gz", hash = "sha256:5410638e4df39c54d957fc51ce03048acd8e6d60abc0f5107af51e5fb566eb3c"}, ] [package.extras] -test = ["enum34", "ipaddress", "mock", "pywin32", "unittest2", "wmi"] - -[package.source] -type = "url" -url = "https://github.com/girder/large_image_wheels/raw/wheelhouse/psutil-5.7.3-cp38-cp38-manylinux2010_x86_64.whl" +test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] [[package]] name = "py" @@ -2015,21 +2020,20 @@ email = ["email-validator (>=1.0.3)"] [[package]] name = "pylibtiff" -version = "0.5.0" +version = "0.5.1" description = "PyLibTiff: a Python tiff library." category = "main" optional = false -python-versions = "*" +python-versions = ">=3.8" files = [ - {file = "pylibtiff-0.5.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:00f18e0907d309ba7fb2c65bfe709338a6f516d743d46d0488b403c6b17d318e"}, + {file = "pylibtiff-0.5.1.tar.gz", hash = "sha256:52d3e00edbb7aecddabeeb4dff76a6c974b7c90a51a7963ddcefee67453633c4"}, ] [package.dependencies] -numpy = "*" +numpy = ">=1.13.3" -[package.source] -type = "url" -url = "https://github.com/girder/large_image_wheels/raw/wheelhouse/pylibtiff-0.5.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl" +[package.extras] +bitarray = ["bitarray"] [[package]] name = "pymongo" @@ -2271,13 +2275,13 @@ files = [ [[package]] name = "pyvips" -version = "2.2.0" +version = "2.2.1" description = "binding for the libvips image processing library, API mode" category = "main" optional = false python-versions = "*" files = [ - {file = "pyvips-2.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b9fd0aeb0c9df5ad4459bce676948118fad261369295170df175677bec6f9c10"}, + {file = "pyvips-2.2.1.tar.gz", hash = "sha256:b51dbb45b057a282925015d540c5597560993e2986df20a778646a6b37e7cbb5"}, ] [package.dependencies] @@ -2285,13 +2289,9 @@ cffi = ">=1.0.0" pkgconfig = "*" [package.extras] -doc = ["sphinx", "sphinx-rtd-theme"] +doc = ["sphinx", "sphinx_rtd_theme"] test = ["cffi (>=1.0.0)", "pyperf", "pytest", "pytest-flake8", "pytest-runner"] -[package.source] -type = "url" -url = "https://github.com/girder/large_image_wheels/raw/wheelhouse/pyvips-2.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl" - [[package]] name = "pywin32" version = "306" @@ -2871,4 +2871,4 @@ girder-large-image = [] [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.10" -content-hash = "27043de12989ef8f964cb9529675f60be52518b48e6106ee566e3f8d2b3756fe" +content-hash = "61c477c27f80ff084f96c146d70a42d165df1447482f0f461fedbba5e7b1bdc8" diff --git a/server/pyproject.toml b/server/pyproject.toml index 9ba3a1616..ba80dc4fc 100644 --- a/server/pyproject.toml +++ b/server/pyproject.toml @@ -50,8 +50,8 @@ packages = [ python = ">=3.8,<3.10" cheroot = ">=8.4.5" click = "^8.1.3" -girder = "3.1.16" -girder_jobs = "3.1.16" +girder = "3.1.22" +girder_jobs = "3.1.22" girder_worker = "0.9.0" girder_worker_utils = "0.8.7" pydantic = "1.9.0" @@ -60,18 +60,18 @@ typing-extensions = "^4.2.0" GPUtil = "^1.4.0" requests = ">=2.27.1" urllib3 = "<1.27" -girder-large-image = "^1.17.0" -large-image = "^1.17.0" -large-image-source-pil = "^1.17.0" +girder-large-image = "^1.23.6" +large-image = "^1.23.6" +large-image-source-pil = "^1.23.6" simplejpeg = "^1.6.4" -large-image-tasks = "^1.17.0" -large-image-converter = "^1.17.0" +large-image-tasks = "^1.23.6" +large-image-converter = "^1.23.6" bitarray = "^2.5.1" -large-image-source-gdal = "^1.17.0" -large-image-source-tiff = "^1.17.0" -large-image-source-ometiff = "^1.17.0" -large-image-source-openjpeg = "^1.17.0" -large-image-source-mapnik = "^1.17.0" +large-image-source-gdal = "^1.23.6" +large-image-source-tiff = "^1.23.6" +large-image-source-ometiff = "^1.23.6" +large-image-source-openjpeg = "^1.23.6" +large-image-source-mapnik = "^1.23.6" [tool.poetry.group.dev.dependencies] numpy = "^1.21.4" opencv-python = "^4.5.5"