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fix: several issues #349

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merged 1 commit into from
Dec 14, 2023
Merged

fix: several issues #349

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7 changes: 5 additions & 2 deletions .github/workflows/pr.yaml
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,10 @@
name: Checks

"on":
push:
pull_request:

env:
PYTHON_VERSION_DEFAULT: "3.10.8"

jobs:
test:
Expand All @@ -25,7 +28,7 @@ jobs:
uses: actions/cache@v3
with:
path: .venv
key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
key: venv-${{ runner.os }}-${{ env.PYTHON_VERSION_DEFAULT }}-${{ hashFiles('**/poetry.lock') }}
- name: Validate project dependencies
run: poetry check
- name: Install dependencies
Expand Down
50 changes: 9 additions & 41 deletions .github/workflows/release.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,36 +3,6 @@ name: Release
"on":
push:
branches: ["main", "master"]
workflow_dispatch:
inputs:
release_force:
description: |
Force release be one of: [major | minor | patch]
Leave empty for auto-detect based on commit messages.
type: choice
options:
- "" # auto-detect
- major # force major
- minor # force minor
- patch # force patch
default: ""
required: false
prerelease_token:
description: |
'The "prerelease identifier" to use as a prefix for the "prerelease" \
part of a semver. Like the rc in `1.2.0-rc.8`.'
type: choice
options:
- rc
- beta
- alpha
default: rc
required: false
prerelease:
description: "Is a pre-release"
type: boolean
default: false
required: false

concurrency:
group: deploy
Expand Down Expand Up @@ -81,7 +51,7 @@ jobs:

Release:
needs: Test
if: "!contains(github.event.head_commit.message, 'chore(release):')"
if: github.event_name == 'push' && !contains(github.event.head_commit.message, 'chore(release):')
runs-on: ubuntu-latest
permissions:
# NOTE: this enables trusted publishing.
Expand Down Expand Up @@ -121,21 +91,19 @@ jobs:
- name: Install dependencies
if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
run: poetry install --no-interaction --no-root

- name: Python Semantic Release
id: release
# see https://python-semantic-release.readthedocs.io/en/latest/automatic-releases/github-actions.html
# see https://github.com/python-semantic-release/python-semantic-release
uses: python-semantic-release/python-semantic-release@v8.5.0
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
force: ${{ github.event.inputs.release_force }}
prerelease: ${{ github.event.inputs.prerelease }}
prerelease_token: ${{ github.event.inputs.prerelease_token }}
run: |
git config --global user.name "github-actions"
git config --global user.email "action@github.com"
poetry run semantic-release --noop publish -D commit_author="github-actions <action@github.com>"
env:
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# PyPI_TOKEN: ${{secrets.PyPI_TOKEN}}

Documentation:
needs: Release
runs-on: ubuntu-latest
if: github.ref == 'refs/heads/main'
steps:
- uses: actions/checkout@v4
with:
Expand Down
207 changes: 102 additions & 105 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,7 @@ license = "Apache-2.0"
readme = "README.md"
documentation = "https://opentargets.github.io/genetics_etl_python/"
repository = "https://github.com/opentargets/genetics_etl_python"
packages = [
{ include = "otg", from = "src"},
]
packages = [{ include = "otg", from = "src" }]

[tool.poetry.urls]
"Bug Tracker" = "http://github.com/opentargets/issues"
Expand Down Expand Up @@ -80,8 +78,7 @@ yamllint = "^1.33.0"

[tool.semantic_release]
logging_use_named_masks = true
commit_author = "opentargets <opentargets>"
build_command = "pip install poetry && poetry build"
build_command = "poetry build"
assets = []
version_variable = ["src/otg/__init__.py:__version__"]
version_toml = ["pyproject.toml:tool.poetry.version"]
Expand All @@ -92,15 +89,18 @@ upload_to_release = true
match = "(main|master)"
prerelease = false

[tool.semantic_release.branches."0.x.x"]
match = "0.x.x"
prerelease = true
prerelease_token = "rc"

[tool.semantic_release.publish]
dist_glob_patterns = ["dist/*"]
upload_to_vcs_release = true

[tool.semantic_release.changelog]
changelog_file = "CHANGELOG.md"
exclude_commit_patterns = [
"chore\\(release\\):",
]
exclude_commit_patterns = ["chore\\(release\\):"]

[tool.semantic_release.branches."step"]
match = "(build|chore|ci|docs|feat|fix|perf|style|refactor|test)"
Expand All @@ -124,10 +124,7 @@ exclude = ["dist"]

[tool.pytest.ini_options]
addopts = "-n auto --doctest-modules --cov=src/ --cov-report=xml"
pythonpath = [
".",
"./src/airflow/dags"
]
pythonpath = [".", "./src/airflow/dags"]

# Semi-strict mode for mypy
[tool.mypy]
Expand All @@ -143,108 +140,108 @@ disallow_untyped_defs = true

[[tool.mypy.overrides]]
module = [
"google.cloud",
"yaml",
"hail",
"pyliftover",
"dbldatagen",
"scipy",
"scipy.stats",
"chardet",
"omegaconf",
"xgboost",
"sklearn",
"google.cloud",
"yaml",
"hail",
"pyliftover",
"dbldatagen",
"scipy",
"scipy.stats",
"chardet",
"omegaconf",
"xgboost",
"sklearn",
]
ignore_missing_imports = true


[tool.ruff]
select = [
"B002", # Python does not support the unary prefix increment
"B007", # Loop control variable {name} not used within loop body
"B014", # Exception handler with duplicate exception
"B023", # Function definition does not bind loop variable {name}
"B026", # Star-arg unpacking after a keyword argument is strongly discouraged
"C", # complexity
"COM818", # Trailing comma on bare tuple prohibited
"D", # docstrings
"DTZ003", # Use datetime.now(tz=) instead of datetime.utcnow()
"DTZ004", # Use datetime.fromtimestamp(ts, tz=) instead of datetime.utcfromtimestamp(ts)
"E", # pycodestyle
"F", # pyflakes/autoflake
"G", # flake8-logging-format
"I", # isort
"ICN001", # import concentions; {name} should be imported as {asname}
"ISC001", # Implicitly concatenated string literals on one line
"N804", # First argument of a class method should be named cls
"N805", # First argument of a method should be named self
"N815", # Variable {name} in class scope should not be mixedCase
"PGH001", # No builtin eval() allowed
"PGH004", # Use specific rule codes when using noqa
"PLC0414", # Useless import alias. Import alias does not rename original package.
"PLC", # pylint
"PLE", # pylint
"PLR", # pylint
"PLW", # pylint
"Q000", # Double quotes found but single quotes preferred
"RUF006", # Store a reference to the return value of asyncio.create_task
"S102", # Use of exec detected
"S103", # bad-file-permissions
"S108", # hardcoded-temp-file
"S306", # suspicious-mktemp-usage
"S307", # suspicious-eval-usage
"S313", # suspicious-xmlc-element-tree-usage
"S314", # suspicious-xml-element-tree-usage
"S315", # suspicious-xml-expat-reader-usage
"S316", # suspicious-xml-expat-builder-usage
"S317", # suspicious-xml-sax-usage
"S318", # suspicious-xml-mini-dom-usage
"S319", # suspicious-xml-pull-dom-usage
"S320", # suspicious-xmle-tree-usage
"S601", # paramiko-call
"S602", # subprocess-popen-with-shell-equals-true
"S604", # call-with-shell-equals-true
"S608", # hardcoded-sql-expression
"S609", # unix-command-wildcard-injection
"SIM105", # Use contextlib.suppress({exception}) instead of try-except-pass
"SIM117", # Merge with-statements that use the same scope
"SIM118", # Use {key} in {dict} instead of {key} in {dict}.keys()
"SIM201", # Use {left} != {right} instead of not {left} == {right}
"SIM208", # Use {expr} instead of not (not {expr})
"SIM212", # Use {a} if {a} else {b} instead of {b} if not {a} else {a}
"SIM300", # Yoda conditions. Use 'age == 42' instead of '42 == age'.
"SIM401", # Use get from dict with default instead of an if block
"T100", # Trace found: {name} used
"T20", # flake8-print
"TID251", # Banned imports
"TRY004", # Prefer TypeError exception for invalid type
"TRY200", # Use raise from to specify exception cause
"TRY302", # Remove exception handler; error is immediately re-raised
"UP", # pyupgrade
"W", # pycodestyle
"B002", # Python does not support the unary prefix increment
"B007", # Loop control variable {name} not used within loop body
"B014", # Exception handler with duplicate exception
"B023", # Function definition does not bind loop variable {name}
"B026", # Star-arg unpacking after a keyword argument is strongly discouraged
"C", # complexity
"COM818", # Trailing comma on bare tuple prohibited
"D", # docstrings
"DTZ003", # Use datetime.now(tz=) instead of datetime.utcnow()
"DTZ004", # Use datetime.fromtimestamp(ts, tz=) instead of datetime.utcfromtimestamp(ts)
"E", # pycodestyle
"F", # pyflakes/autoflake
"G", # flake8-logging-format
"I", # isort
"ICN001", # import concentions; {name} should be imported as {asname}
"ISC001", # Implicitly concatenated string literals on one line
"N804", # First argument of a class method should be named cls
"N805", # First argument of a method should be named self
"N815", # Variable {name} in class scope should not be mixedCase
"PGH001", # No builtin eval() allowed
"PGH004", # Use specific rule codes when using noqa
"PLC0414", # Useless import alias. Import alias does not rename original package.
"PLC", # pylint
"PLE", # pylint
"PLR", # pylint
"PLW", # pylint
"Q000", # Double quotes found but single quotes preferred
"RUF006", # Store a reference to the return value of asyncio.create_task
"S102", # Use of exec detected
"S103", # bad-file-permissions
"S108", # hardcoded-temp-file
"S306", # suspicious-mktemp-usage
"S307", # suspicious-eval-usage
"S313", # suspicious-xmlc-element-tree-usage
"S314", # suspicious-xml-element-tree-usage
"S315", # suspicious-xml-expat-reader-usage
"S316", # suspicious-xml-expat-builder-usage
"S317", # suspicious-xml-sax-usage
"S318", # suspicious-xml-mini-dom-usage
"S319", # suspicious-xml-pull-dom-usage
"S320", # suspicious-xmle-tree-usage
"S601", # paramiko-call
"S602", # subprocess-popen-with-shell-equals-true
"S604", # call-with-shell-equals-true
"S608", # hardcoded-sql-expression
"S609", # unix-command-wildcard-injection
"SIM105", # Use contextlib.suppress({exception}) instead of try-except-pass
"SIM117", # Merge with-statements that use the same scope
"SIM118", # Use {key} in {dict} instead of {key} in {dict}.keys()
"SIM201", # Use {left} != {right} instead of not {left} == {right}
"SIM208", # Use {expr} instead of not (not {expr})
"SIM212", # Use {a} if {a} else {b} instead of {b} if not {a} else {a}
"SIM300", # Yoda conditions. Use 'age == 42' instead of '42 == age'.
"SIM401", # Use get from dict with default instead of an if block
"T100", # Trace found: {name} used
"T20", # flake8-print
"TID251", # Banned imports
"TRY004", # Prefer TypeError exception for invalid type
"TRY200", # Use raise from to specify exception cause
"TRY302", # Remove exception handler; error is immediately re-raised
"UP", # pyupgrade
"W", # pycodestyle
]

ignore = [
"E501", # line too long
"E731", # do not assign a lambda expression, use a def

# Ignore ignored, as the rule is now back in preview/nursery, which cannot
# be ignored anymore without warnings.
# https://github.com/astral-sh/ruff/issues/7491
# "PLC1901", # Lots of false positives

# False positives https://github.com/astral-sh/ruff/issues/5386
"PLC0208", # Use a sequence type instead of a `set` when iterating over values
"PLR0911", # Too many return statements ({returns} > {max_returns})
"PLR0912", # Too many branches ({branches} > {max_branches})
"PLR0913", # Too many arguments to function call ({c_args} > {max_args})
"PLR0915", # Too many statements ({statements} > {max_statements})
"PLR2004", # Magic value used in comparison, consider replacing {value} with a constant variable
"PLW2901", # Outer {outer_kind} variable {name} overwritten by inner {inner_kind} target
"UP006", # keep type annotation style as is
"UP007", # keep type annotation style as is
# Ignored due to performance: https://github.com/charliermarsh/ruff/issues/2923
"UP038", # Use `X | Y` in `isinstance` call instead of `(X, Y)`
"E501", # line too long
"E731", # do not assign a lambda expression, use a def

# Ignore ignored, as the rule is now back in preview/nursery, which cannot
# be ignored anymore without warnings.
# https://github.com/astral-sh/ruff/issues/7491
# "PLC1901", # Lots of false positives

# False positives https://github.com/astral-sh/ruff/issues/5386
"PLC0208", # Use a sequence type instead of a `set` when iterating over values
"PLR0911", # Too many return statements ({returns} > {max_returns})
"PLR0912", # Too many branches ({branches} > {max_branches})
"PLR0913", # Too many arguments to function call ({c_args} > {max_args})
"PLR0915", # Too many statements ({statements} > {max_statements})
"PLR2004", # Magic value used in comparison, consider replacing {value} with a constant variable
"PLW2901", # Outer {outer_kind} variable {name} overwritten by inner {inner_kind} target
"UP006", # keep type annotation style as is
"UP007", # keep type annotation style as is
# Ignored due to performance: https://github.com/charliermarsh/ruff/issues/2923
"UP038", # Use `X | Y` in `isinstance` call instead of `(X, Y)`

]

Expand Down