From 165c139c8f32e8f72b4ebed82ccfeaac01632c5f Mon Sep 17 00:00:00 2001 From: Michael Byrnes Date: Wed, 7 Dec 2022 16:20:19 -0600 Subject: [PATCH 1/2] DEV-1583: Switch to poetry and test py36-11. --- .secrets.baseline | 10 +- .travis.yml | 37 ++- dev-requirements.in | 5 - dev-requirements.txt | 93 ------- poetry.lock | 631 +++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 33 +++ setup.py | 23 -- tests/schema_test.py | 4 +- tox.ini | 23 +- 9 files changed, 719 insertions(+), 140 deletions(-) delete mode 100644 dev-requirements.in delete mode 100644 dev-requirements.txt create mode 100644 poetry.lock create mode 100644 pyproject.toml delete mode 100644 setup.py diff --git a/.secrets.baseline b/.secrets.baseline index 84125eb1f..7098b60f9 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -3,7 +3,7 @@ "files": "^.secrets.baseline$", "lines": null }, - "generated_at": "2020-11-19T20:50:10Z", + "generated_at": "2022-07-01T18:34:48Z", "plugins_used": [ { "name": "AWSKeyDetector" @@ -358,6 +358,14 @@ "line_number": 7, "type": "Hex High Entropy String" } + ], + "poetry.lock": [ + { + "hashed_secret": "cd0f8c41d6567393ba59db5dca0bf2ab2ce167dc", + "is_verified": false, + "line_number": 346, + "type": "Hex High Entropy String" + } ] }, "version": "0.13.0", diff --git a/.travis.yml b/.travis.yml index 76e6700d9..8f7874063 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,8 +1,35 @@ +os: linux +dist: jammy language: python python: - - "2.7" - - "3.5" - - "3.6" + - "3.7" + - "3.8" + - "3.9" + - "3.10" + - "3.11" +env: + TOX_PYTHON=python +addons: + apt: + packages: + - "python3-pip" + - "python3-venv" +before_install: + - /usr/bin/python -m pip install pipx --user +install: + - pipx install --python=$TOX_PYTHON tox + - pipx inject --pip-args='--upgrade' tox setuptools + - pipx install poetry + - pipx inject poetry poetry-dynamic-versioning +script: + - export TOXENV=$(python -V | sed -E 's/Python ([2-3]).([0-9]+?).[0-9]+/py\1\2/g') + - tox -install: pip install tox-travis -script: tox +jobs: + include: + - dist: focal + python: "3.6" + env: + TOX_PYTHON=/usr/bin/python3.8 + before_install: + - /usr/bin/python3.8 -m pip install pipx --user diff --git a/dev-requirements.in b/dev-requirements.in deleted file mode 100644 index 26c382259..000000000 --- a/dev-requirements.in +++ /dev/null @@ -1,5 +0,0 @@ -pytest~=4.6.3 -more-itertools<6 -pytest-cov>=2.7.1,<2.12 -pre-commit~=1.21.0 -cfgv~=2.0.1; python_version == '2.7' diff --git a/dev-requirements.txt b/dev-requirements.txt deleted file mode 100644 index 5f1ce2c0a..000000000 --- a/dev-requirements.txt +++ /dev/null @@ -1,93 +0,0 @@ -# -# This file is autogenerated by pip-compile -# To update, run: -# -# pip-compile --output-file=dev-requirements.txt dev-requirements.in setup.py -# -appdirs==1.4.4 - # via virtualenv -aspy.yaml==1.3.0 - # via pre-commit -atomicwrites==1.4.0 - # via pytest -attrs==20.3.0 - # via - # jsonschema - # pytest -cfgv==2.0.1 - # via pre-commit -coverage==5.5 - # via pytest-cov -distlib==0.3.1 - # via virtualenv -filelock==3.0.12 - # via virtualenv -identify==1.6.2 - # via pre-commit -importlib-metadata==2.1.1 - # via - # jsonschema - # pluggy - # pre-commit - # pytest - # virtualenv -importlib-resources==3.2.1 - # via - # pre-commit - # virtualenv -jsonschema==3.2.0 - # via gdcdictionary (setup.py) -more-itertools==5.0.0 - # via - # -r dev-requirements.in - # pytest -nodeenv==1.5.0 - # via pre-commit -packaging==20.9 - # via pytest -pathlib2==2.3.5 - # via pytest -pluggy==0.13.1 - # via pytest -pre-commit==1.21.0 - # via -r dev-requirements.in -py==1.10.0 - # via pytest -pyparsing==2.4.7 - # via packaging -pyrsistent==0.16.1 - # via jsonschema -pytest-cov==2.11.1 - # via -r dev-requirements.in -pytest==4.6.11 - # via - # -r dev-requirements.in - # pytest-cov -pyyaml==5.3.1 - # via - # aspy.yaml - # gdcdictionary (setup.py) - # pre-commit -six==1.15.0 - # via - # cfgv - # jsonschema - # more-itertools - # pathlib2 - # pre-commit - # pyrsistent - # pytest - # virtualenv -toml==0.10.2 - # via pre-commit -virtualenv==20.4.3 - # via pre-commit -wcwidth==0.2.5 - # via pytest -zipp==1.2.0 - # via - # importlib-metadata - # importlib-resources - -# The following packages are considered to be unsafe in a requirements file: -# setuptools diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 000000000..57cf1be8c --- /dev/null +++ b/poetry.lock @@ -0,0 +1,631 @@ +[[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.*" + +[[package]] +name = "attrs" +version = "22.1.0" +description = "Classes Without Boilerplate" +category = "main" +optional = false +python-versions = ">=3.5" + +[package.extras] +dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", 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generated by the GDC." +include = ["schemas/**/*.yaml"] +license = "Apache-2.0" +name = "gdcdictionary" +version = "0.0.0" + +[tool.poetry.dependencies] +PyYAML = "^6.0" +jsonschema = "^3.2.0" +python = "^3.6" + +[tool.poetry.group.test.dependencies] +coverage = [ + {version = "^6.2.0", python = "^3.6"}, + {version = "^6.4.0", python = "^3.7"}, +] +more-itertools = "^8.13.0" +pytest = "^7.0.0" + +[tool.poetry.group.dev.dependencies] +pre-commit = "^2.0.0" + +[tool.poetry-dynamic-versioning] +dirty = true +enable = true +metadata = true +pattern = "default-unprefixed" + +[build-system] +build-backend = "poetry.core.masonry.api" +requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"] diff --git a/setup.py b/setup.py deleted file mode 100644 index d5ed3ec4f..000000000 --- a/setup.py +++ /dev/null @@ -1,23 +0,0 @@ -from setuptools import setup, find_packages - -setup( - name='gdcdictionary', - packages=find_packages(), - use_scm_version={ - 'local_scheme': 'dirty-tag', - 'write_to': 'gdcdictionary/_version.py', - }, - setup_requires=['setuptools_scm<6'], - install_requires=[ - 'PyYAML>=5.1.2,<5.5', - 'jsonschema>=3.0.2,<3.3', - 'pyrsistent~=0.16.1; python_version=="2.7"', - ], - package_data={ - "gdcdictionary": [ - "schemas/*.yaml", - "schemas/projects/*.yaml", - "schemas/projects/*/*.yaml", - ] - }, -) diff --git a/tests/schema_test.py b/tests/schema_test.py index 0c099f4e8..c638cd22f 100644 --- a/tests/schema_test.py +++ b/tests/schema_test.py @@ -90,7 +90,7 @@ def test_acyclicalty_without_ignored_types(self): If the acyclicality check passes like this, either the algorithm is missing something or we're ignoring types that we shouldn't. """ - with self.assertRaisesRegexp(AssertionError, 'cycle detected'): + with self.assertRaisesRegex(AssertionError, 'cycle detected'): check_for_cycles(self.dictionary.schema) def test_check_for_cycles_positive(self): @@ -188,7 +188,7 @@ def test_check_for_cycles_negative(self): 'tissue_source_site': {'links': []}, } - with self.assertRaisesRegexp(AssertionError, 'cycle detected'): + with self.assertRaisesRegex(AssertionError, 'cycle detected'): check_for_cycles(schemata) def test_links_to_annotation(self): diff --git a/tox.ini b/tox.ini index 91be14f0a..460b45a9d 100644 --- a/tox.ini +++ b/tox.ini @@ -1,15 +1,16 @@ [tox] -envlist = py27, py36 +envlist = py3{6,7,8,9,10,11} +isolated_build = True +skip_missing_interpreters = True [testenv] -deps = - -rdev-requirements.txt +skip_install = True +allowlist_externals = + poetry +commands_pre = + poetry install --with=test commands = - pytest -lvv --cov=gdcdictionary --cov-report xml --cov-report html --junit-xml test-reports/results.xml {posargs} - -[testenv:py27] -deps = - setuptools==44.1.1 - -rdev-requirements.txt -commands = - pytest -lvv --cov=gdcdictionary --cov-report xml --cov-report html --junit-xml test-reports/results.xml {posargs} + coverage run --source gdcdictionary -m pytest -lvv --junit-xml test-reports/results.xml {posargs} + coverage report + coverage xml + coverage html From fa78156622d11f370b1514de4b7136a260f6ed70 Mon Sep 17 00:00:00 2001 From: Michael Byrnes Date: Wed, 7 Dec 2022 16:26:44 -0600 Subject: [PATCH 2/2] DEV-1583: Revert test and tox.ini. --- tests/schema_test.py | 4 ++-- tox.ini | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/tests/schema_test.py b/tests/schema_test.py index c638cd22f..0c099f4e8 100644 --- a/tests/schema_test.py +++ b/tests/schema_test.py @@ -90,7 +90,7 @@ def test_acyclicalty_without_ignored_types(self): If the acyclicality check passes like this, either the algorithm is missing something or we're ignoring types that we shouldn't. """ - with self.assertRaisesRegex(AssertionError, 'cycle detected'): + with self.assertRaisesRegexp(AssertionError, 'cycle detected'): check_for_cycles(self.dictionary.schema) def test_check_for_cycles_positive(self): @@ -188,7 +188,7 @@ def test_check_for_cycles_negative(self): 'tissue_source_site': {'links': []}, } - with self.assertRaisesRegex(AssertionError, 'cycle detected'): + with self.assertRaisesRegexp(AssertionError, 'cycle detected'): check_for_cycles(schemata) def test_links_to_annotation(self): diff --git a/tox.ini b/tox.ini index 460b45a9d..4428ef8c1 100644 --- a/tox.ini +++ b/tox.ini @@ -1,7 +1,6 @@ [tox] envlist = py3{6,7,8,9,10,11} isolated_build = True -skip_missing_interpreters = True [testenv] skip_install = True