From fdbdd9e0047f4e4811b8c4ddd40c59c7e5a29d0a Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 8 Apr 2024 12:11:21 -0700 Subject: [PATCH 1/3] fix failing tests via upstream biolink changes --- .github/workflows/check-dependencies.yaml | 44 +++++++++++++++++++ .../{run_tests.yml => run-tests.yml} | 0 2 files changed, 44 insertions(+) create mode 100644 .github/workflows/check-dependencies.yaml rename .github/workflows/{run_tests.yml => run-tests.yml} (100%) diff --git a/.github/workflows/check-dependencies.yaml b/.github/workflows/check-dependencies.yaml new file mode 100644 index 00000000..4104ba30 --- /dev/null +++ b/.github/workflows/check-dependencies.yaml @@ -0,0 +1,44 @@ +--- +name: Check Dependencies in Pyproject.toml + +# Controls when the action will run. +on: + pull_request: + types: [opened, synchronize, reopened] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + types: trigger-run-check-dependencies + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + # This workflow contains a single job called "build" + build: + # The type of runner that the job will run on + runs-on: ubuntu-latest + strategy: + matrix: + python: [ "3.9", "3.10" ] + + # Steps represent a sequence of tasks that will be executed as part of the job + steps: + # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it + - uses: actions/checkout@v2 + + - uses: actions/setup-python@v2 + name: setup python environment + with: + python-version: ${{ matrix.python }} + + # this step we remove and rebuild the poetry.lock file to ensure that the tests that follow can be run + # with the latest dependencies + - name: Install dependencies + run: | + pip install --upgrade pip + pip install poetry + rm -rf poetry.lock + poetry install + + - name: Run tests + run: | + poetry run make test \ No newline at end of file diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run-tests.yml similarity index 100% rename from .github/workflows/run_tests.yml rename to .github/workflows/run-tests.yml From 01c100f7f873e39ec38ed165b5517695e13c6700 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 8 Apr 2024 13:17:59 -0700 Subject: [PATCH 2/3] refresh dependencies so that KGX test will work inside of bmt GH action --- kgx/validator.py | 4 +- poetry.lock | 243 ++++++++++++++++++++++++++-------------- pyproject.toml | 6 +- tests/resources/test.db | Bin 20480 -> 20480 bytes 4 files changed, 166 insertions(+), 87 deletions(-) diff --git a/kgx/validator.py b/kgx/validator.py index 90e2b412..6982ce68 100644 --- a/kgx/validator.py +++ b/kgx/validator.py @@ -66,7 +66,7 @@ def get_the_validator( Creates and manages a default singleton Validator in the module, when called """ if not cls._the_validator: - cls.set_biolink_model("v3.1.2") + cls.set_biolink_model("v4.1.6") cls._the_validator = Validator( verbose=verbose, progress_monitor=progress_monitor, @@ -232,7 +232,7 @@ def get_required_node_properties(toolkit: Optional[Toolkit] = None) -> list: toolkit = Validator.get_toolkit() node_properties = toolkit.get_all_node_properties() # TODO: remove this append statement when Biolink 3.1.3 is released - need to add domain:entity to id slot. - node_properties.append("id") + # node_properties.append("id") required_properties = [] for p in node_properties: element = toolkit.get_element(p) diff --git a/poetry.lock b/poetry.lock index fe56e7b5..febaf849 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -15,6 +16,7 @@ files = [ name = "annotated-types" version = "0.6.0" description = "Reusable constraint types to use with typing.Annotated" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -26,6 +28,7 @@ files = [ name = "antlr4-python3-runtime" version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" +category = "main" optional = false python-versions = "*" files = [ @@ -36,6 +39,7 @@ files = [ name = "arrow" version = "1.3.0" description = "Better dates & times for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -49,12 +53,13 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] +test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] [[package]] name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -73,6 +78,7 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "babel" version = "2.13.1" description = "Internationalization utilities" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -88,24 +94,26 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "bmt" -version = "1.1.2" +version = "1.2.1" description = "Biolink Model Toolkit: A Python API for working with the Biolink Model" +category = "main" optional = false python-versions = ">=3.9,<4.0" files = [ - {file = "bmt-1.1.2-py3-none-any.whl", hash = "sha256:16c2a1b5dafe585d93540189e97b0687a1c41ad936856033818ab174749ef30d"}, - {file = "bmt-1.1.2.tar.gz", hash = "sha256:51a80ab5035cf8ebe11ab130cff6171e2d745c6a6a4752de633be76b5f12aad6"}, + {file = "bmt-1.2.1-py3-none-any.whl", hash = "sha256:5dda82c872ca4ee615e22a2dcd3b647491149ad8f92aaa3f04a69e5832542771"}, + {file = "bmt-1.2.1.tar.gz", hash = "sha256:9a0100458bc9d8045a9f268ee919819a254c84c36820f82703c92738cd294ae8"}, ] [package.dependencies] deprecation = ">=2.1.0,<3.0.0" -linkml-runtime = ">=1.5.0,<2.0.0" +linkml-runtime = ">=1.6.3,<2.0.0" stringcase = ">=1.2.0,<2.0.0" [[package]] name = "cachetools" version = "5.3.2" description = "Extensible memoizing collections and decorators" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -117,6 +125,7 @@ files = [ name = "certifi" version = "2023.11.17" description = "Python package for providing Mozilla's CA Bundle." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -128,6 +137,7 @@ files = [ name = "cfgraph" version = "0.2.1" description = "rdflib collections flattening graph" +category = "main" optional = false python-versions = "*" files = [ @@ -141,6 +151,7 @@ rdflib = ">=0.4.2" name = "chardet" version = "5.2.0" description = "Universal encoding detector for Python 3" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -152,6 +163,7 @@ files = [ name = "charset-normalizer" version = "3.3.2" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." +category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -251,6 +263,7 @@ files = [ name = "click" version = "8.1.7" description = "Composable command line interface toolkit" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -265,6 +278,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -276,6 +290,7 @@ files = [ name = "commonmark" version = "0.9.1" description = "Python parser for the CommonMark Markdown spec" +category = "main" optional = false python-versions = "*" files = [ @@ -290,6 +305,7 @@ test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"] name = "curies" version = "0.7.4" description = "Idiomatic conversion between URIs and compact URIs (CURIEs)." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -314,6 +330,7 @@ tests = ["coverage", "pytest"] name = "decorator" version = "5.1.1" description = "Decorators for Humans" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -325,6 +342,7 @@ files = [ name = "deprecated" version = "1.2.14" description = "Python @deprecated decorator to deprecate old python classes, functions or methods." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -342,6 +360,7 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"] name = "deprecation" version = "2.1.0" description = "A library to handle automated deprecations" +category = "main" optional = false python-versions = "*" files = [ @@ -356,6 +375,7 @@ packaging = "*" name = "distlib" version = "0.3.7" description = "Distribution utilities" +category = "main" optional = false python-versions = "*" 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file lock." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -440,6 +465,7 @@ typing = ["typing-extensions (>=4.8)"] name = "fqdn" version = "1.5.1" description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers" +category = "main" optional = false python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" files = [ @@ -451,6 +477,7 @@ files = [ name = "graphviz" version = "0.20.1" description = "Simple Python interface for Graphviz" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -467,6 +494,7 @@ test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>= name = "greenlet" version = "3.0.1" description = "Lightweight in-process concurrent programming" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -537,6 +565,7 @@ test = ["objgraph", "psutil"] name = "hbreader" version = "0.9.1" description = "Honey Badger reader - a generic 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clear AST for metaprogramming." +category = "main" optional = false python-versions = "*" files = [ @@ -836,6 +869,7 @@ ply = "*" name = "jsonpointer" version = "2.4" description = "Identify specific nodes in a JSON document (RFC 6901)" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -847,6 +881,7 @@ files = [ name = "jsonschema" version = "4.20.0" description = "An implementation of JSON Schema validation for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -876,6 +911,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jsonschema-specifications" version = "2023.11.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -890,6 +926,7 @@ referencing = ">=0.31.0" name = "jsonstreams" version = "0.6.0" description = "A JSON streaming writer" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -906,13 +943,14 @@ test = ["tox"] [[package]] name = "linkml" -version = "1.6.3" +version = "1.7.8" description = "Linked Open Data Modeling Language" +category = "main" optional = false -python-versions = ">=3.8.1,<4.0.0" +python-versions = "<4.0.0,>=3.8.1" files = [ - {file = "linkml-1.6.3-py3-none-any.whl", hash = "sha256:2bcfa9e35b3e0d868f396fa48ede1b9e3c6016df956dd5ca92d70ff621ffc77e"}, - {file = "linkml-1.6.3.tar.gz", hash = "sha256:2692243c9fb1c262ea83b725c70d6f537844ae7a9405101c94bccf65def6d952"}, + {file = "linkml-1.7.8-py3-none-any.whl", hash = "sha256:4b8ebe33b422517b08ca01802dc2899ac133c502a71d811c58fa6f4263130709"}, + {file = "linkml-1.7.8.tar.gz", hash = "sha256:af48ee1ad6751c8d20de2832dbeefe225da9be5f39a7f8ea7821a691cf7c0148"}, ] [package.dependencies] @@ -925,11 +963,11 @@ jinja2 = ">=3.1.0" jsonasobj2 = ">=1.0.3,<2.0.0" 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= "main" optional = false python-versions = "*" files = [ @@ -2162,6 +2211,7 @@ files = [ name = "sortedcontainers" version = "2.4.0" description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" +category = "main" optional = false python-versions = "*" files = [ @@ -2173,6 +2223,7 @@ files = [ name = "sparqlslurper" version = "0.5.1" description = "SPARQL Slurper for rdflib" +category = "main" optional = false python-versions = ">=3.7.4" files = [ @@ -2189,6 +2240,7 @@ sparqlwrapper = ">=1.8.2" name = "sparqlwrapper" version = "2.0.0" description = "SPARQL Endpoint interface to Python" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2209,6 +2261,7 @@ pandas = ["pandas (>=1.3.5)"] name = "sphinx" version = "7.2.6" description = "Python documentation generator" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2244,6 +2297,7 @@ test = ["cython (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools name = "sphinx-click" version = "5.1.0" description = "Sphinx extension that automatically documents click applications" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2260,6 +2314,7 @@ sphinx = ">=2.0" name = "sphinx-rtd-theme" version = "2.0.0" description = "Read the Docs theme for Sphinx" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -2279,6 +2334,7 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"] name = "sphinxcontrib-applehelp" version = "1.0.7" description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2297,6 +2353,7 @@ test = ["pytest"] name = "sphinxcontrib-devhelp" version = "1.0.5" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2315,6 +2372,7 @@ test = ["pytest"] name = "sphinxcontrib-htmlhelp" version = "2.0.4" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2333,6 +2391,7 @@ test = ["html5lib", "pytest"] name = "sphinxcontrib-jquery" version = "4.1" description = "Extension to include jQuery on newer Sphinx releases" +category = "dev" optional = false python-versions = ">=2.7" files = [ @@ -2347,6 +2406,7 @@ Sphinx = ">=1.8" name = "sphinxcontrib-jsmath" version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -2361,6 +2421,7 @@ test = ["flake8", "mypy", "pytest"] name = "sphinxcontrib-qthelp" version = "1.0.6" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2379,6 +2440,7 @@ test = ["pytest"] name = "sphinxcontrib-serializinghtml" version = "1.1.9" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2397,6 +2459,7 @@ test = ["pytest"] name = "sqlalchemy" version = "2.0.23" description = "Database Abstraction Library" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2452,7 +2515,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "platform_machine == \"win32\" or platform_machine == \"WIN32\" or platform_machine == \"AMD64\" or platform_machine == \"amd64\" or platform_machine == \"x86_64\" or platform_machine == \"ppc64le\" or platform_machine == \"aarch64\""} +greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""} typing-extensions = ">=4.2.0" [package.extras] @@ -2484,6 +2547,7 @@ sqlcipher = ["sqlcipher3-binary"] name = "stringcase" version = "1.2.0" description = "String case converter." +category = "main" optional = false python-versions = "*" files = [ @@ -2494,6 +2558,7 @@ files = [ name = "terminaltables" version = "3.1.10" description = "Generate simple tables in terminals from a nested list of strings." +category = "main" optional = false python-versions = ">=2.6" files = [ @@ -2505,6 +2570,7 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2516,6 +2582,7 @@ files = [ name = "tox" version = "4.13.0" description = "tox is a generic virtualenv management and test command line tool" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2543,6 +2610,7 @@ testing = ["build[virtualenv] (>=1.0.3)", "covdefaults (>=2.3)", "detect-test-po name = "types-python-dateutil" version = "2.8.19.14" description = "Typing stubs for python-dateutil" +category = "main" optional = false python-versions = "*" files = [ @@ -2554,6 +2622,7 @@ files = [ name = "typing-extensions" version = "4.8.0" description = "Backported and Experimental Type Hints for Python 3.8+" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2565,6 +2634,7 @@ files = [ name = "tzdata" version = "2023.3" description = "Provider of IANA time zone data" +category = "main" optional = false python-versions = ">=2" files = [ @@ -2576,6 +2646,7 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2590,6 +2661,7 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "urllib3" version = "2.1.0" description = "HTTP library with thread-safe connection pooling, file post, and more." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2606,6 +2678,7 @@ zstd = ["zstandard (>=0.18.0)"] name = "validators" version = "0.20.0" description = "Python Data Validation for Humans™." +category = "main" optional = false python-versions = ">=3.4" files = [ @@ -2622,6 +2695,7 @@ test = ["flake8 (>=2.4.0)", "isort (>=4.2.2)", "pytest (>=2.2.3)"] name = "virtualenv" version = "20.25.1" description = "Virtual Python Environment builder" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2642,6 +2716,7 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess name = "watchdog" version = "3.0.0" description = "Filesystem events monitoring" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2681,6 +2756,7 @@ watchmedo = ["PyYAML (>=3.10)"] name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2696,6 +2772,7 @@ tests = ["pytest", "pytest-cov"] name = "websocket-client" version = "1.6.4" description = "WebSocket client for Python with low level API options" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2712,6 +2789,7 @@ test = ["websockets"] name = "wrapt" version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2791,6 +2869,7 @@ files = [ name = "zipp" version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2805,4 +2884,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "8a2b7d320e83750238961d5bbd76e685061702a18cb04eee65b48e4170221f6a" +content-hash = "06fea4730596c448e54905987cdf6bf53d4b7b686901511e5800fa9dbd1bd9be" diff --git a/pyproject.toml b/pyproject.toml index e852993c..5f5e361e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,7 +22,7 @@ python = "^3.9" Click = "*" SPARQLWrapper = ">=1.8.2" Sphinx = "*" -bmt = "^1.1.0" +bmt = "^1.2.1" cachetools = "^5.0.0" deprecation = "^2.1.0" docker = "^6.0.0" @@ -31,8 +31,8 @@ ijson = "^3.1.3" inflection = "^0.5.1" jsonlines = "^4.0.0" jsonstreams = "^0.6.0" -linkml = "^1.5.0" -linkml-runtime = "^1.5.0" +linkml = "^1.7.7" +linkml-runtime = "^1.7.5" mypy = "*" neo4j = "^4.4.10" networkx = "*" diff --git a/tests/resources/test.db b/tests/resources/test.db index ad15ff4818e2f7f92140b0ff3f8d1a8f0afae5a7..34dd59b301e0510a7419ad74ab739169b669cfb2 100644 GIT binary patch delta 354 zcmZozz}T>Wae_1>*F+g-RxSp;aF2~C3-|@tc(*X{uj04id&XD6r^LHuW8(r|rX04( zcJjH5tdrNshcM-^fH}+{&SV?;6I{%E*BSWd@>}s;-z+F_lFvMmnIqj;TalNSx3nnF zsQs4$;rt{x+bYWae_1>+e8^>RyGE`v{xHb7VvX0@!K%)uj04atY~1sKiNk91REp&Tn7HR xKz=s=#0eUc=jx{e72RUsf60FfDwsUE$DVKU3ws%$+H(y2=b*xolh64Z0RT~6AtL|) From f007f3eec639c70c58715e4892ffccd2168b09d2 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 8 Apr 2024 13:22:47 -0700 Subject: [PATCH 3/3] add docker spin up to testing of dependencies --- .github/workflows/check-dependencies.yaml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/check-dependencies.yaml b/.github/workflows/check-dependencies.yaml index 4104ba30..d028e6de 100644 --- a/.github/workflows/check-dependencies.yaml +++ b/.github/workflows/check-dependencies.yaml @@ -38,6 +38,14 @@ jobs: pip install poetry rm -rf poetry.lock poetry install + docker run --detach --name kgx-neo4j-unit-test -p 8484:7474 -p 8888:7687 --env NEO4J_AUTH=neo4j/test neo4j:4.3.0 + docker run --detach --name kgx-neo4j-integration-test -p 7474:7474 -p 7687:7687 --env NEO4J_AUTH=neo4j/test neo4j:4.3.0 + docker ps -a + + - name: Wait + uses: jakejarvis/wait-action@master + with: + time: '45s' - name: Run tests run: |