From ec64d40410a2e07fa712eccfa9c6c5a8a750d3f8 Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Tue, 2 Jan 2024 11:56:43 -0600 Subject: [PATCH 1/3] chore(deps): cleanup dependencies, update to newer versions & remove unnecessary ones --- poetry.lock | 305 ++++++++++++++++++++----------------------------- pyproject.toml | 16 ++- 2 files changed, 132 insertions(+), 189 deletions(-) diff --git a/poetry.lock b/poetry.lock index 6f76abf..a681f73 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,40 +1,28 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. - -[[package]] -name = "atomicwrites" -version = "1.4.1" -description = "Atomic file writes." -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -files = [ - {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"}, -] +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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"pytest-5.4.3-py3-none-any.whl", hash = "sha256:5c0db86b698e8f170ba4582a492248919255fcd4c79b1ee64ace34301fb589a1"}, - {file = "pytest-5.4.3.tar.gz", hash = "sha256:7979331bfcba207414f5e1263b5a0f8f521d0f457318836a7355531ed1a4c7d8"}, + {file = "pytest-7.4.4-py3-none-any.whl", hash = "sha256:b090cdf5ed60bf4c45261be03239c2c1c22df034fbffe691abe93cd80cea01d8"}, + {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"}, ] [package.dependencies] -atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""} -attrs = ">=17.4.0" colorama = {version = "*", markers = "sys_platform == \"win32\""} -more-itertools = ">=4.0.0" +exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} +iniconfig = "*" packaging = "*" -pluggy = ">=0.12,<1.0" -py = ">=1.5.0" -wcwidth = "*" +pluggy = ">=0.12,<2.0" +tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] -checkqa-mypy = ["mypy (==v0.761)"] -testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"] +testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] [[package]] name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" -category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -872,7 +828,6 @@ six = ">=1.5" name = "pytz" version = "2023.3.post1" description = "World timezone definitions, modern and historical" -category = "dev" optional = false python-versions = "*" files = [ @@ -884,7 +839,6 @@ files = [ name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -944,7 +898,6 @@ files = [ name = "requests" version = "2.31.0" description = "Python HTTP for Humans." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -966,7 +919,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "rstr" version = "2.2.6" description = "Generate random strings in Python" -category = "dev" optional = false python-versions = "*" files = [ @@ -976,14 +928,13 @@ files = [ [[package]] name = "setuptools" -version = "69.0.2" +version = "69.0.3" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "setuptools-69.0.2-py3-none-any.whl", hash = "sha256:1e8fdff6797d3865f37397be788a4e3cba233608e9b509382a2777d25ebde7f2"}, - {file = "setuptools-69.0.2.tar.gz", hash = "sha256:735896e78a4742605974de002ac60562d286fa8051a7e2299445e8e8fbb01aa6"}, + {file = "setuptools-69.0.3-py3-none-any.whl", hash = "sha256:385eb4edd9c9d5c17540511303e39a147ce2fc04bc55289c322b9e5904fe2c05"}, + {file = "setuptools-69.0.3.tar.gz", hash = "sha256:be1af57fc409f93647f2e8e4573a142ed38724b8cdd389706a867bb4efcf1e78"}, ] [package.extras] @@ -995,7 +946,6 @@ testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jar name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1007,7 +957,6 @@ files = [ name = "sqlalchemy" version = "1.4.50" description = "Database Abstraction Library" -category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -1039,7 +988,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and platform_machine == \"aarch64\" or python_version >= \"3\" and platform_machine == \"ppc64le\" or python_version >= \"3\" and platform_machine == \"x86_64\" or python_version >= \"3\" and platform_machine == \"amd64\" or python_version >= \"3\" and platform_machine == \"AMD64\" or python_version >= \"3\" and platform_machine == \"win32\" or python_version >= \"3\" and platform_machine == \"WIN32\""} +greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (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\")"} [package.extras] aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"] @@ -1062,11 +1011,21 @@ postgresql-psycopg2cffi = ["psycopg2cffi"] pymysql = ["pymysql", "pymysql (<1)"] sqlcipher = ["sqlcipher3-binary"] +[[package]] +name = "tomli" +version = "2.0.1" +description = "A lil' TOML parser" +optional = false +python-versions = ">=3.7" +files = [ + {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"}, + {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"}, +] + [[package]] 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 = [ @@ -1079,23 +1038,10 @@ brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] -[[package]] -name = "wcwidth" -version = "0.2.12" -description = "Measures the displayed width of unicode strings in a terminal" -category = "dev" -optional = false -python-versions = "*" -files = [ - {file = "wcwidth-0.2.12-py2.py3-none-any.whl", hash = "sha256:f26ec43d96c8cbfed76a5075dac87680124fa84e0855195a6184da9c187f133c"}, - {file = "wcwidth-0.2.12.tar.gz", hash = "sha256:f01c104efdf57971bcb756f054dd58ddec5204dd15fa31d6503ea57947d97c02"}, -] - [[package]] name = "xlocal" version = "0.5" description = "execution locals: killing global state (including thread locals)" -category = "dev" optional = false python-versions = "*" files = [ @@ -1106,7 +1052,6 @@ files = [ name = "xmltodict" version = "0.13.0" description = "Makes working with XML feel like you are working with JSON" -category = "dev" optional = false python-versions = ">=3.4" files = [ @@ -1117,4 +1062,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = ">=3.9, <4" -content-hash = "807ed8da9c1fe8f9a148749ca49c13cd22e7121235926de46d9b59e1d6c54758" +content-hash = "f3c5492087aa78a398df286cdb8f6a4818e61535bf4645c9818c65188b360e88" diff --git a/pyproject.toml b/pyproject.toml index 06786ce..75b5f54 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dictionaryutils" -version = "3.4.10" +version = "3.5.0" description = "Python wrapper and metaschema for datadictionary." authors = ["CTDS UChicago "] license = "Apache-2.0" @@ -10,16 +10,14 @@ repository = "https://github.com/uc-cdis/dictionaryutils" [tool.poetry.dependencies] python = ">=3.9, <4" PyYAML = "*" -jsonschema = ">=2.5,<4" -cdislogging = "^1.0.0" -requests = "~=2.18" +jsonschema = "*" +cdislogging = "*" +requests = "*" [tool.poetry.dev-dependencies] -cdislogging = "^1.0.0" -pytest = "^5.4.3" -gen3datamodel = "3.0.2" +pytest = "*" data-simulator = {git = "https://github.com/uc-cdis/data-simulator.git", rev = "1.5.1"} [build-system] -requires = ["poetry>=0.12"] -build-backend = "poetry.masonry.api" +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" From 33487e9f60f61ed480fbe259bd1cc6faa3388336 Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Tue, 2 Jan 2024 12:08:25 -0600 Subject: [PATCH 2/3] chore(tests): use GH Actions for testing --- .github/workflows/ci.yaml | 20 ++++++++++++++++++++ .github/workflows/lint.yaml | 17 +++++++++++++++++ .travis.yml | 2 +- 3 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/ci.yaml create mode 100644 .github/workflows/lint.yaml diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml new file mode 100644 index 0000000..abbc826 --- /dev/null +++ b/.github/workflows/ci.yaml @@ -0,0 +1,20 @@ +name: CI + +on: + # run on pushed commits to master and on new commits on pull requests + push: + pull_request: + types: [opened, synchronize] + +jobs: + Security: + name: Security Pipeline + uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master + with: + python-poetry: 'false' + secrets: inherit # pragma: allowlist secret + UnitTest: + name: Python Unit Test + uses: uc-cdis/.github/.github/workflows/python_unit_test.yaml@master + with: + python-version: '3.9' \ No newline at end of file diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml new file mode 100644 index 0000000..8cc8100 --- /dev/null +++ b/.github/workflows/lint.yaml @@ -0,0 +1,17 @@ +on: + pull_request: + types: [opened, synchronize] + issue_comment: + types: [created, edited] + +name: Wool + +jobs: + runWool: + name: Run black + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@master + - uses: uc-cdis/wool@master + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file diff --git a/.travis.yml b/.travis.yml index b1a79de..6e4be32 100644 --- a/.travis.yml +++ b/.travis.yml @@ -11,7 +11,7 @@ install: before_script: - git clone https://github.com/uc-cdis/datadictionary && (cd datadictionary && yes | poetry install) script: -- "./run_tests.sh" +- echo Unit testing is now done in GH Actions, this just pushing to pypi as necessary before_deploy: - poetry config pypi-token.pypi $PYPI_API_TOKEN - poetry build -f sdist From 1cc7bc06e4fb2e2189eefcc00f116032732b4d07 Mon Sep 17 00:00:00 2001 From: Alex VanTol Date: Tue, 2 Jan 2024 14:27:09 -0600 Subject: [PATCH 3/3] chore(ci): remove unnecessary command from release (require GH release creation by user) --- .travis.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 6e4be32..91befe7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -25,4 +25,3 @@ deploy: tags: true after_deploy: - pip install gen3git -- gen3git release