PERF: Avoid fragmentation of DataFrame in read_sas #48603
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I know we want to limit network calls, for testing, how about reading OP's URL that points to a CDC .xpt file. Currently, pd.read_sas("https://wwwn.cdc.gov/Nchs/Nhanes/2017-2018/DR1TOT_J.XPT")There is also a pytest decorator check in case link changes to use before test. Given the date and government site, link looks reliable over the years: @pytest.mark.network
@pytest.mark.slow
@tm.network(
url="https://wwwn.cdc.gov/Nchs/Nhanes/2017-2018/DR1TOT_J.XPT",
check_before_test=True,
) |
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This runs forever (25secs), since we don't have slow builds anymore, I don't think this is worth it |
mroeschke
approved these changes
Sep 19, 2022
mroeschke
reviewed
Sep 19, 2022
|
Thanks @phofl |
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* PERF: Avoid fragmentation of DataFrame in read_sas * Add whatsnew * Add warning
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…8662) * BUG: Series.getitem not falling back to positional for bool index * Update pandas/tests/series/indexing/test_getitem.py Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com> * Fix build warning for use of `strdup` in ultrajson (#48369) * WEB: Update versions json to fix version switcher in the docs (#48655) * PERF: join/merge on subset of MultiIndex (#48611) * DOC: Update documentation for date_range(), bdate_range(), and interval_range() to include timedelta as a possible data type for the freq parameter (#48631) * Update documentation for date_range(), bdate_range(), and interval_range() to include timedelta as a possible data type for the freq parameter * Add test case for date_range construction using datetime.timedelta * TYP: tighten Axis (#48612) * TYP: tighten Axis * allow 'rows' * BUG: Fix metadata propagation in df.corr and df.cov, GH28283 (#48616) * Add finalize to df.corr and df.cov * Clean * TST: add test case for PeriodIndex in HDFStore(GH7796) (#48618) * TST: add test case for PeriodIndex in HDFStore * TST: add test case for PeriodIndex in HDFStore * use pytest.mark.parameterize instead * Add OpenSSF Scorecards GitHub Action (#48570) * Create scorecards.yml * Update scorecards.yml * Add OpenSSF Scorecards badge to README.md * Trim whitespace in scorecards.yml * Skip scorecards.yml on forks * Fix whitespace * Pin scorecards.yml dependencies to major versions * ENH: move an exception and add a prehook to check for exception place… (#48088) * ENH: move an exception and add a prehook to check for exception placement * ENH: fix import * ENH: revert moving error * ENH: add docstring and fix import for test * ENH: re-design approach based on feedback * ENH: update whatsnew rst * ENH: apply feedback changes * ENH: refactor to remove exception_warning_list and ignore _version.py * ENH: remove NotThisMethod from tests and all * REGR: TextIOWrapper raising an error in read_csv (#48651) * REGR: TextIOWrapper raising an error in read_csv * pyupgrade * do not try to seek on unseekable buffers * unseekable buffer might also have read ahead * safer alternative: do not mess with internal/private(?) buffer of TextIOWrapper (effectively applies the shortcut only to files pandas opens) * Fix scorecard.yml workflow (#48668) * Set scorecard-action to v2.0.3 scorecard-action does not have a major version tag. Temporarily disabling github.repository check to ensure action now works. * Enable github.repository check * BUG: DatetimeIndex ignoring explicit tz=None (#48659) * BUG: DatetimeIndex ignoring explicit tz=None * GH ref * Corrected pd.merge indicator type hint (#48677) * Corrected pd.merge indicator type hint https://pandas.pydata.org/docs/reference/api/pandas.merge.html It should be "str | bool" instead of just string * Update merge.py fixed type hint in merge.py * Update merge.py Update indicator type hint in _MergeOperation * Update merge.py Added type hint _MergeOperation init * DOC: Document default value for options.display.max_cols when not running in terminal (#48672) DOC: Document default value for options.display.max_cols display.max_cols has a default value of 20 when not running in a terminal such as Jupyter Notebook * ENH: DTA/TDA add datetimelike scalar with mismatched reso (#48669) * ENH: DTA/TDA add datetimelike scalar with mismatched reso * mypy fixup * REF: support reso in remaining tslibs helpers (#48661) * REF: support reso in remaining tslibs helpers * update setup.py * PERF: Avoid fragmentation of DataFrame in read_sas (#48603) * PERF: Avoid fragmentation of DataFrame in read_sas * Add whatsnew * Add warning * DOC: Add deprecation infos to deprecated functions (#48599) * DOC: Add deprecation infos to deprecated functions * Add sections * Fix * BLD: Build wheels using cibuildwheel (#48283) * BLD: Build wheels using cibuildwheel * update from code review Co-Authored-By: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com> * fix 3.11 version * changes from code review * Update test_wheels.py * sync run time with pandas-wheels Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com> * REGR: Performance decrease in factorize (#48620) * TYP: type all arguments with str default values (#48508) * TYP: type all arguments with str default values * na_rep: back to str * na(t)_rep is always a string * add float for some functions * and the same for the few float default arguments * define a few more literal constants * avoid itertools.cycle mypy error * revert mistake * TST: Catch more pyarrow PerformanceWarnings (#48699) * REGR: to_hdf raising AssertionError with boolean index (#48696) * REGR: to_hdf raising AssertionError with boolean index * Add gh ref * REGR: Regression in DataFrame.loc when setting df with all True indexer (#48711) * BUG: pivot_table raising for nullable dtype and margins (#48714) * TST: Address MPL 3.6 deprecation warnings (#48695) * TST: Address MPL 3.6 deprecation warnings * Address min build * missing () Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com> Co-authored-by: Ralf Gommers <ralf.gommers@gmail.com> Co-authored-by: Marc Garcia <garcia.marc@gmail.com> Co-authored-by: Luke Manley <lukemanley@gmail.com> Co-authored-by: Siddhartha Gandhi <siddhartha.a.gandhi@gmail.com> Co-authored-by: Torsten Wörtwein <twoertwein@users.noreply.github.com> Co-authored-by: Xiao Yuan <yuanx749@gmail.com> Co-authored-by: paradox-lab <57354735+paradox-lab@users.noreply.github.com> Co-authored-by: Pedro Nacht <15221358+pnacht@users.noreply.github.com> Co-authored-by: dataxerik <dsshar@gmail.com> Co-authored-by: jbrockmendel <jbrockmendel@gmail.com> Co-authored-by: Pablo <48098178+PabloRuizCuevas@users.noreply.github.com> Co-authored-by: tmoschou <5567550+tmoschou@users.noreply.github.com> Co-authored-by: Thomas Li <47963215+lithomas1@users.noreply.github.com> Co-authored-by: Richard Shadrach <45562402+rhshadrach@users.noreply.github.com>
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* PERF: Avoid fragmentation of DataFrame in read_sas * Add whatsnew * Add warning
noatamir
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…ndas-dev#48662) * BUG: Series.getitem not falling back to positional for bool index * Update pandas/tests/series/indexing/test_getitem.py Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com> * Fix build warning for use of `strdup` in ultrajson (pandas-dev#48369) * WEB: Update versions json to fix version switcher in the docs (pandas-dev#48655) * PERF: join/merge on subset of MultiIndex (pandas-dev#48611) * DOC: Update documentation for date_range(), bdate_range(), and interval_range() to include timedelta as a possible data type for the freq parameter (pandas-dev#48631) * Update documentation for date_range(), bdate_range(), and interval_range() to include timedelta as a possible data type for the freq parameter * Add test case for date_range construction using datetime.timedelta * TYP: tighten Axis (pandas-dev#48612) * TYP: tighten Axis * allow 'rows' * BUG: Fix metadata propagation in df.corr and df.cov, GH28283 (pandas-dev#48616) * Add finalize to df.corr and df.cov * Clean * TST: add test case for PeriodIndex in HDFStore(GH7796) (pandas-dev#48618) * TST: add test case for PeriodIndex in HDFStore * TST: add test case for PeriodIndex in HDFStore * use pytest.mark.parameterize instead * Add OpenSSF Scorecards GitHub Action (pandas-dev#48570) * Create scorecards.yml * Update scorecards.yml * Add OpenSSF Scorecards badge to README.md * Trim whitespace in scorecards.yml * Skip scorecards.yml on forks * Fix whitespace * Pin scorecards.yml dependencies to major versions * ENH: move an exception and add a prehook to check for exception place… (pandas-dev#48088) * ENH: move an exception and add a prehook to check for exception placement * ENH: fix import * ENH: revert moving error * ENH: add docstring and fix import for test * ENH: re-design approach based on feedback * ENH: update whatsnew rst * ENH: apply feedback changes * ENH: refactor to remove exception_warning_list and ignore _version.py * ENH: remove NotThisMethod from tests and all * REGR: TextIOWrapper raising an error in read_csv (pandas-dev#48651) * REGR: TextIOWrapper raising an error in read_csv * pyupgrade * do not try to seek on unseekable buffers * unseekable buffer might also have read ahead * safer alternative: do not mess with internal/private(?) buffer of TextIOWrapper (effectively applies the shortcut only to files pandas opens) * Fix scorecard.yml workflow (pandas-dev#48668) * Set scorecard-action to v2.0.3 scorecard-action does not have a major version tag. Temporarily disabling github.repository check to ensure action now works. * Enable github.repository check * BUG: DatetimeIndex ignoring explicit tz=None (pandas-dev#48659) * BUG: DatetimeIndex ignoring explicit tz=None * GH ref * Corrected pd.merge indicator type hint (pandas-dev#48677) * Corrected pd.merge indicator type hint https://pandas.pydata.org/docs/reference/api/pandas.merge.html It should be "str | bool" instead of just string * Update merge.py fixed type hint in merge.py * Update merge.py Update indicator type hint in _MergeOperation * Update merge.py Added type hint _MergeOperation init * DOC: Document default value for options.display.max_cols when not running in terminal (pandas-dev#48672) DOC: Document default value for options.display.max_cols display.max_cols has a default value of 20 when not running in a terminal such as Jupyter Notebook * ENH: DTA/TDA add datetimelike scalar with mismatched reso (pandas-dev#48669) * ENH: DTA/TDA add datetimelike scalar with mismatched reso * mypy fixup * REF: support reso in remaining tslibs helpers (pandas-dev#48661) * REF: support reso in remaining tslibs helpers * update setup.py * PERF: Avoid fragmentation of DataFrame in read_sas (pandas-dev#48603) * PERF: Avoid fragmentation of DataFrame in read_sas * Add whatsnew * Add warning * DOC: Add deprecation infos to deprecated functions (pandas-dev#48599) * DOC: Add deprecation infos to deprecated functions * Add sections * Fix * BLD: Build wheels using cibuildwheel (pandas-dev#48283) * BLD: Build wheels using cibuildwheel * update from code review Co-Authored-By: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com> * fix 3.11 version * changes from code review * Update test_wheels.py * sync run time with pandas-wheels Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com> * REGR: Performance decrease in factorize (pandas-dev#48620) * TYP: type all arguments with str default values (pandas-dev#48508) * TYP: type all arguments with str default values * na_rep: back to str * na(t)_rep is always a string * add float for some functions * and the same for the few float default arguments * define a few more literal constants * avoid itertools.cycle mypy error * revert mistake * TST: Catch more pyarrow PerformanceWarnings (pandas-dev#48699) * REGR: to_hdf raising AssertionError with boolean index (pandas-dev#48696) * REGR: to_hdf raising AssertionError with boolean index * Add gh ref * REGR: Regression in DataFrame.loc when setting df with all True indexer (pandas-dev#48711) * BUG: pivot_table raising for nullable dtype and margins (pandas-dev#48714) * TST: Address MPL 3.6 deprecation warnings (pandas-dev#48695) * TST: Address MPL 3.6 deprecation warnings * Address min build * missing () Co-authored-by: Matthew Roeschke <10647082+mroeschke@users.noreply.github.com> Co-authored-by: Ralf Gommers <ralf.gommers@gmail.com> Co-authored-by: Marc Garcia <garcia.marc@gmail.com> Co-authored-by: Luke Manley <lukemanley@gmail.com> Co-authored-by: Siddhartha Gandhi <siddhartha.a.gandhi@gmail.com> Co-authored-by: Torsten Wörtwein <twoertwein@users.noreply.github.com> Co-authored-by: Xiao Yuan <yuanx749@gmail.com> Co-authored-by: paradox-lab <57354735+paradox-lab@users.noreply.github.com> Co-authored-by: Pedro Nacht <15221358+pnacht@users.noreply.github.com> Co-authored-by: dataxerik <dsshar@gmail.com> Co-authored-by: jbrockmendel <jbrockmendel@gmail.com> Co-authored-by: Pablo <48098178+PabloRuizCuevas@users.noreply.github.com> Co-authored-by: tmoschou <5567550+tmoschou@users.noreply.github.com> Co-authored-by: Thomas Li <47963215+lithomas1@users.noreply.github.com> Co-authored-by: Richard Shadrach <45562402+rhshadrach@users.noreply.github.com>
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doc/source/whatsnew/vX.X.X.rstfile if fixing a bug or adding a new feature.Not sure how to test this, the op file is 13mb which is way to large for our repository.