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code_checks.sh
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#!/bin/bash
#
# Run checks related to code quality.
#
# This script is intended for both the CI and to check locally that code standards are
# respected. We are currently linting (PEP-8 and similar), looking for patterns of
# common mistakes (sphinx directives with missing blank lines, old style classes,
# unwanted imports...), and we also run doctests here (currently some files only).
# In the future we may want to add the validation of docstrings and other checks here.
#
# Usage:
# $ ./ci/code_checks.sh # run all checks
# $ ./ci/code_checks.sh lint # run linting only
# $ ./ci/code_checks.sh patterns # check for patterns that should not exist
# $ ./ci/code_checks.sh doctests # run doctests
# $ ./ci/code_checks.sh dependencies # check that dependencies are consistent
echo "inside $0"
[[ $LINT ]] || { echo "NOT Linting. To lint use: LINT=true $0 $1"; exit 0; }
[[ -z "$1" || "$1" == "lint" || "$1" == "patterns" || "$1" == "doctests" || "$1" == "dependencies" ]] \
|| { echo "Unknown command $1. Usage: $0 [lint|patterns|doctests|dependencies]"; exit 9999; }
source activate pandas
BASE_DIR="$(dirname $0)/.."
RET=0
CHECK=$1
### LINTING ###
if [[ -z "$CHECK" || "$CHECK" == "lint" ]]; then
# `setup.cfg` contains the list of error codes that are being ignored in flake8
echo "flake8 --version"
flake8 --version
# pandas/_libs/src is C code, so no need to search there.
MSG='Linting .py code' ; echo $MSG
flake8 .
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Linting .pyx code' ; echo $MSG
flake8 pandas --filename=*.pyx --select=E501,E302,E203,E111,E114,E221,E303,E128,E231,E126,E265,E305,E301,E127,E261,E271,E129,W291,E222,E241,E123,F403,C400,C401,C402,C403,C404,C405,C406,C407,C408,C409,C410,C411
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Linting .pxd and .pxi.in' ; echo $MSG
flake8 pandas/_libs --filename=*.pxi.in,*.pxd --select=E501,E302,E203,E111,E114,E221,E303,E231,E126,F403
RET=$(($RET + $?)) ; echo $MSG "DONE"
# Check that cython casting is of the form `<type>obj` as opposed to `<type> obj`;
# it doesn't make a difference, but we want to be internally consistent.
# Note: this grep pattern is (intended to be) equivalent to the python
# regex r'(?<![ ->])> '
MSG='Linting .pyx code for spacing conventions in casting' ; echo $MSG
! grep -r -E --include '*.pyx' --include '*.pxi.in' '[a-zA-Z0-9*]> ' pandas/_libs
RET=$(($RET + $?)) ; echo $MSG "DONE"
# readability/casting: Warnings about C casting instead of C++ casting
# runtime/int: Warnings about using C number types instead of C++ ones
# build/include_subdir: Warnings about prefacing included header files with directory
# We don't lint all C files because we don't want to lint any that are built
# from Cython files nor do we want to lint C files that we didn't modify for
# this particular codebase (e.g. src/headers, src/klib, src/msgpack). However,
# we can lint all header files since they aren't "generated" like C files are.
MSG='Linting .c and .h' ; echo $MSG
cpplint --quiet --extensions=c,h --headers=h --recursive --filter=-readability/casting,-runtime/int,-build/include_subdir pandas/_libs/src/*.h pandas/_libs/src/parser pandas/_libs/ujson pandas/_libs/tslibs/src/datetime
RET=$(($RET + $?)) ; echo $MSG "DONE"
# Imports - Check formatting using isort see setup.cfg for settings
MSG='Check import format using isort ' ; echo $MSG
isort --recursive --check-only pandas
RET=$(($RET + $?)) ; echo $MSG "DONE"
fi
### PATTERNS ###
if [[ -z "$CHECK" || "$CHECK" == "patterns" ]]; then
# Check for imports from pandas.core.common instead of `import pandas.core.common as com`
MSG='Check for non-standard imports' ; echo $MSG
! grep -R --include="*.py*" -E "from pandas.core.common import " pandas
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Check for pytest warns' ; echo $MSG
! grep -r -E --include '*.py' 'pytest\.warns' pandas/tests/
RET=$(($RET + $?)) ; echo $MSG "DONE"
# Check for the following code in testing: `np.testing` and `np.array_equal`
MSG='Check for invalid testing' ; echo $MSG
! grep -r -E --include '*.py' --exclude testing.py '(numpy|np)(\.testing|\.array_equal)' pandas/tests/
RET=$(($RET + $?)) ; echo $MSG "DONE"
# Check for the following code in the extension array base tests: `tm.assert_frame_equal` and `tm.assert_series_equal`
MSG='Check for invalid EA testing' ; echo $MSG
! grep -r -E --include '*.py' --exclude base.py 'tm.assert_(series|frame)_equal' pandas/tests/extension/base
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Check for deprecated messages without sphinx directive' ; echo $MSG
! grep -R --include="*.py" --include="*.pyx" -E "(DEPRECATED|DEPRECATE|Deprecated)(:|,|\.)" pandas
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Check for old-style classes' ; echo $MSG
! grep -R --include="*.py" -E "class\s\S*[^)]:" pandas scripts
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Check for backticks incorrectly rendering because of missing spaces' ; echo $MSG
! grep -R --include="*.rst" -E "[a-zA-Z0-9]\`\`?[a-zA-Z0-9]" doc/source/
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Check for incorrect sphinx directives' ; echo $MSG
! grep -R --include="*.py" --include="*.pyx" --include="*.rst" -E "\.\. (autosummary|contents|currentmodule|deprecated|function|image|important|include|ipython|literalinclude|math|module|note|raw|seealso|toctree|versionadded|versionchanged|warning):[^:]" ./pandas ./doc/source
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Check for modules that pandas should not import' ; echo $MSG
python -c "
import sys
import pandas
blacklist = {'bs4', 'gcsfs', 'html5lib', 'ipython', 'jinja2' 'hypothesis',
'lxml', 'numexpr', 'openpyxl', 'py', 'pytest', 's3fs', 'scipy',
'tables', 'xlrd', 'xlsxwriter', 'xlwt'}
mods = blacklist & set(m.split('.')[0] for m in sys.modules)
if mods:
sys.stderr.write('pandas should not import: {}\n'.format(', '.join(mods)))
sys.exit(len(mods))
"
RET=$(($RET + $?)) ; echo $MSG "DONE"
fi
### DOCTESTS ###
if [[ -z "$CHECK" || "$CHECK" == "doctests" ]]; then
MSG='Doctests frame.py' ; echo $MSG
pytest -q --doctest-modules pandas/core/frame.py \
-k"-axes -combine -itertuples -join -nunique -pivot_table -quantile -query -reindex -reindex_axis -replace -round -set_index -stack -to_stata"
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Doctests series.py' ; echo $MSG
pytest -q --doctest-modules pandas/core/series.py \
-k"-nonzero -reindex -searchsorted -to_dict"
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Doctests generic.py' ; echo $MSG
pytest -q --doctest-modules pandas/core/generic.py \
-k"-_set_axis_name -_xs -describe -droplevel -groupby -interpolate -pct_change -pipe -reindex -reindex_axis -resample -to_json -transpose -values -xs"
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Doctests top-level reshaping functions' ; echo $MSG
pytest -q --doctest-modules \
pandas/core/reshape/concat.py \
pandas/core/reshape/pivot.py \
pandas/core/reshape/reshape.py \
pandas/core/reshape/tile.py \
-k"-crosstab -pivot_table -cut"
RET=$(($RET + $?)) ; echo $MSG "DONE"
MSG='Doctests interval classes' ; echo $MSG
pytest --doctest-modules -v \
pandas/core/indexes/interval.py \
pandas/core/arrays/interval.py \
-k"-from_arrays -from_breaks -from_intervals -from_tuples -get_loc -set_closed -to_tuples -interval_range"
RET=$(($RET + $?)) ; echo $MSG "DONE"
fi
### DEPENDENCIES ###
if [[ -z "$CHECK" || "$CHECK" == "dependencies" ]]; then
MSG='Check that requirements.txt has been generated from environment.yml' ; echo $MSG
$BASE_DIR/scripts/conda_to_pip.py --compare
RET=$(($RET + $?)) ; echo $MSG "DONE"
fi
exit $RET