Bug#1071123: influxdb-python: FTBFS with pandas 2.2
Control: tags -1 patch https://salsa.debian.org/python-team/packages/influxdb-python/-/merge_requests/2 Not *obviously* known upstream.
Bug#1069792: pandas 2.2
Control: affects 1070359 src:camelot-py Control: affects 1070360 src:glueviz As expected from the version number, this looks easier than the last one: there are only 4 remaining failures and they all look easy to fix. These are: augur (#1071122) camelot-py (tabulate too old #1070359) glueviz (bottleneck too old #1070360) influxdb-python (#1071123) statsmodels 0.14.1 (Ubuntu, due to LP#2064928) fails but 0.14.2 (Debian) doesn't. Build test results: https://launchpad.net/~rebecca-palmer/+archive/ubuntu/pandas2p2/+builds?build_text=_state=failed Autopkgtest results: https://qa.debian.org/excuses.php?experimental=1=pandas Already broken but probably not worse with pandas 2.2: domdf-python-tools python-cooler (dask #1068422) python-workalender (#1060939, package removed from Debian) Not fully tested as already broken: dask.distributed (dask #1068422) igdiscover pychopper pydevd pytorch-geometric qiime Not build-tested as already BD-Uninstallable: python-fastparquet q2-* spopt umap-learn Not build-tested as not in Ubuntu: epigrass intake keras poliastro pymatgen python-cogent python-loompy spaghetti tpot xraylarch
Bug#1069792: pandas 2.2
Control: affects 1070359 src:camelot-py Control: affects 1070360 src:glueviz As expected from the version number, this looks easier than the last one: there are only 4 remaining failures and they all look easy to fix. These are: augur (#1071122) camelot-py (tabulate too old #1070359) glueviz (bottleneck too old #1070360) influxdb-python (#1071123) statsmodels 0.14.1 (Ubuntu, due to LP#2064928) fails but 0.14.2 (Debian) doesn't. Build test results: https://launchpad.net/~rebecca-palmer/+archive/ubuntu/pandas2p2/+builds?build_text=_state=failed Autopkgtest results: https://qa.debian.org/excuses.php?experimental=1=pandas Already broken but probably not worse with pandas 2.2: domdf-python-tools python-cooler (dask #1068422) python-workalender (#1060939, package removed from Debian) Not fully tested as already broken: dask.distributed (dask #1068422) igdiscover pychopper pydevd pytorch-geometric qiime Not build-tested as already BD-Uninstallable: python-fastparquet q2-* spopt umap-learn Not build-tested as not in Ubuntu: epigrass intake keras poliastro pymatgen python-cogent python-loompy spaghetti tpot xraylarch -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1071123: influxdb-python: FTBFS with pandas 2.2
Source: influxdb-python Version: 5.3.1-6 Severity: wishlist Control: block 1069792 by -1 This package's tests fail with pandas 2.2, currently in experimental. https://launchpadlibrarian.net/728496862/buildlog_ubuntu-oracular-amd64.influxdb-python_5.3.1-6_BUILDING.txt.gz == ERROR: Test write points from df w/escaped tag in TestDataFrameClient. -- Traceback (most recent call last): File "/<>/influxdb/tests/dataframe_client_test.py", line 338, in test_write_points_from_dataframe_with_tag_escaped index=pd.period_range(now, freq='H', periods=5), ^ File "/usr/lib/python3/dist-packages/pandas/core/indexes/period.py", line 611, in period_range data, freq = PeriodArray._generate_range(start, end, periods, freq) ^^ File "/usr/lib/python3/dist-packages/pandas/core/arrays/period.py", line 340, in _generate_range freq = Period._maybe_convert_freq(freq) File "pandas/_libs/tslibs/period.pyx", line 1765, in pandas._libs.tslibs.period._Period._maybe_convert_freq File "pandas/_libs/tslibs/offsets.pyx", line 4924, in pandas._libs.tslibs.offsets.to_offset FutureWarning: 'H' is deprecated and will be removed in a future version, please use 'h' instead. --
Bug#1071122: augur: FTBFS with pandas 2.2
Source: augur Version: 24.3.0-1 Severity: wishlist Control: block 1069792 by -1 This package's tests fail with pandas 2.2, currently in experimental. https://ci.debian.net/packages/a/augur/unstable/amd64/46551367/ https://launchpadlibrarian.net/728496766/buildlog_ubuntu-oracular-amd64.augur_24.3.0-1_BUILDING.txt.gz === FAILURES === ___ TestParse.test_fix_dates ___ self = capsys = <_pytest.capture.CaptureFixture object at 0x7fe8582e7ce0> def test_fix_dates(self, capsys): full_date = "4-5-2020" > assert parse.fix_dates(full_date) == "2020-05-04" tests/test_parse.py:14: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ d = '4-5-2020', dayfirst = True def fix_dates(d, dayfirst=True): ''' attempt to parse a date string using pandas date parser. If ambiguous, the argument 'dayfirst' determines whether month or day is assumed to be the first field. Incomplete dates will be padded with XX. On failure to parse the date, the function will return the input. ''' try: > from pandas.core.tools.datetimes import parsing E ImportError: cannot import name 'parsing' from 'pandas.core.tools.datetimes' (/usr/lib/python3/dist-packages/pandas/core/tools/datetimes.py) augur/parse.py:34: ImportError
Bug#1069792: pandas 2.2
I now have a 2.2 package that builds (but installs test_stata.dta somewhere it shouldn't - reminder to self: fix that before uploading to unstable). -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1069792: pandas 2.2
I now have a 2.2 package that builds (but installs test_stata.dta somewhere it shouldn't - reminder to self: fix that before uploading to unstable).
Bug#1070361: blosc: too old for pandas
Package: python3-blosc Version: 1.11.1+ds1-2 Severity: wishlist Control: affects -1 python3-pandas Some pandas functionality is currently unavailable because Debian blosc is too old; it requires >= 1.21.
Bug#1070360: bottleneck: too old for pandas 2.2
Package: python3-bottleneck Version: 1.3.5+ds1-3 Severity: wishlist Control: block 1069792 by -1 (Not actually a hard block as it's not a hard Depends, but I'd prefer not to lose the functionality that does require it.) I would like to upgrade pandas to 2.2.x, but this will only use bottleneck if it is >= 1.3.6. (I don't know whether pandas has an actual reason to care about the micro version, such as a relevant bug fix, or just arbitrarily chose minimum versions that were current as of X time before the pandas release. However, keeping packages reasonably up to date is also more generally a good thing.)
Bug#1068422: can't import dask.dataframe - TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
Control: forwarded -1 https://github.com/dask/dask/pull/11035 Control: tags -1 fixed-upstream patch Thanks and probably yes (but I haven't tested that fix myself), as while it didn't happen in 3.11.8, it *does* happen in 3.11.9: https://ci.debian.net/packages/d/dask/unstable/amd64/46185892/
Bug#1068422: can't import dask.dataframe - TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
Control: forwarded -1 https://github.com/dask/dask/pull/11035 Control: tags -1 fixed-upstream patch Thanks and probably yes (but I haven't tested that fix myself), as while it didn't happen in 3.11.8, it *does* happen in 3.11.9: https://ci.debian.net/packages/d/dask/unstable/amd64/46185892/
Bug#1070359: tabulate: too old for pandas 2.2
Package: python3-tabulate Version: 0.8.10-1 Severity: wishlist Control: block 1069792 by -1 (Not actually a hard block as it's not a hard Depends, but I'd prefer not to lose the functionality that does require it.) I would like to upgrade pandas to 2.2.x, but this will only use tabulate if it is >= 0.9. Caution - I have _not_ checked whether upgrading tabulate would break any other packages that use it.
Bug#1069792: transition: pandas 2.1 -> 2.2
Package: python3-pandas Version: 2.1.4+dfsg-7 Severity: wishlist Upstream have released pandas 2.2. (Filing this now to have a bug number - I haven't actually uploaded to experimental yet.) Reverse dependencies to be tested: abinit astropy augur azure-kusto-python bmtk bqplot busco camelot-py cfgrib changeo cnvkit dask dask.distributed debian-astro debian-pan debian-science dials dioptas dipy domdf-python-tools drms dxchange dyda edlio emperor epigrass esda extra-data flox folium glueviz guidata harmonypy hdmf hickle igdiscover influxdb-python intake ipython jitterdebugger joypy jsonpickle keras libpysal lmfit-py loki-ecmwf macsyfinder mapclassify matplotlib mcaller mdtraj metaphlan metpy metview-python mirtop mlpack monty nanofilt napari nbsphinx openpyxl optuna orange3 osmnx pairtools parmed partd patsy pdb2pqr pint-xarray plasmidid pointpats poliastro poretools presto psychopy pybel pychopper pycoqc pydevd pyensembl pymatgen pymecavideo pynwb pyodc pyranges pyreadstat pyrle pytest-regressions python-aioinflux python-airr python-altair python-anndata python-apptools python-bioframe python-biom-format python-cgelib python-clevercsv python-cobra python-cogent python-cooler python-datacache python-django-pint python-fastparquet python-feather-format python-fluids python-geopandas python-geotiepoints python-gsd python-gtfparse python-hypothesis python-igraph python-influxdb-client python-iow python-loompy python-lsp-server python-nanoget python-nanomath python-ncls python-numpy-groupies python-pandas-flavor python-parsl python-pauvre python-peakutils python-pomegranate python-pyani python-pybedtools python-pymeasure python-pyomop python-pyproj python-rdata python-skbio python-streamz python-tablib python-throttler python-treetime python-ulmo python-upsetplot python-vega-datasets python-workalendar python-xarray python-xrt pytorch-geometric pyxnat q2-cutadapt q2-demux q2-diversity-lib q2-emperor q2-metadata q2-quality-control q2-quality-filter q2-taxa q2-types q2templates qiime r-bioc-mofa rapidfuzz rdkit recan refnx rickslab-gpu-utils sarsen scikit-learn scikit-rf seaborn sentineldl sherlock skimage sklearn-pandas skorch skyfield slm snakemake sorted-nearest spaghetti spopt spyder spyder-kernels statsmodels stimfit sunpy topplot tpot tqdm traittypes umap-learn umis xarray-safe-s1 xarray-sentinel xpore xraylarch yanagiba
Bug#1069792: transition: pandas 2.1 -> 2.2
Package: python3-pandas Version: 2.1.4+dfsg-7 Severity: wishlist Upstream have released pandas 2.2. (Filing this now to have a bug number - I haven't actually uploaded to experimental yet.) Reverse dependencies to be tested: abinit astropy augur azure-kusto-python bmtk bqplot busco camelot-py cfgrib changeo cnvkit dask dask.distributed debian-astro debian-pan debian-science dials dioptas dipy domdf-python-tools drms dxchange dyda edlio emperor epigrass esda extra-data flox folium glueviz guidata harmonypy hdmf hickle igdiscover influxdb-python intake ipython jitterdebugger joypy jsonpickle keras libpysal lmfit-py loki-ecmwf macsyfinder mapclassify matplotlib mcaller mdtraj metaphlan metpy metview-python mirtop mlpack monty nanofilt napari nbsphinx openpyxl optuna orange3 osmnx pairtools parmed partd patsy pdb2pqr pint-xarray plasmidid pointpats poliastro poretools presto psychopy pybel pychopper pycoqc pydevd pyensembl pymatgen pymecavideo pynwb pyodc pyranges pyreadstat pyrle pytest-regressions python-aioinflux python-airr python-altair python-anndata python-apptools python-bioframe python-biom-format python-cgelib python-clevercsv python-cobra python-cogent python-cooler python-datacache python-django-pint python-fastparquet python-feather-format python-fluids python-geopandas python-geotiepoints python-gsd python-gtfparse python-hypothesis python-igraph python-influxdb-client python-iow python-loompy python-lsp-server python-nanoget python-nanomath python-ncls python-numpy-groupies python-pandas-flavor python-parsl python-pauvre python-peakutils python-pomegranate python-pyani python-pybedtools python-pymeasure python-pyomop python-pyproj python-rdata python-skbio python-streamz python-tablib python-throttler python-treetime python-ulmo python-upsetplot python-vega-datasets python-workalendar python-xarray python-xrt pytorch-geometric pyxnat q2-cutadapt q2-demux q2-diversity-lib q2-emperor q2-metadata q2-quality-control q2-quality-filter q2-taxa q2-types q2templates qiime r-bioc-mofa rapidfuzz rdkit recan refnx rickslab-gpu-utils sarsen scikit-learn scikit-rf seaborn sentineldl sherlock skimage sklearn-pandas skorch skyfield slm snakemake sorted-nearest spaghetti spopt spyder spyder-kernels statsmodels stimfit sunpy topplot tpot tqdm traittypes umap-learn umis xarray-safe-s1 xarray-sentinel xpore xraylarch yanagiba -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1069608: topplot: missing test-depends on python3-all
Source: topplot Version: 0.2.2+repack-1 Tags: patch Severity: serious Justification: blocks testing migration of other packages topplot tries to run its autopkgtest in all versions of Python (which is good), but does not test-depend on all those versions of Python. This previously worked because numpy depended on them. However, this has now been removed (see #945824), causing topplot's autopkgtests to fail. Adding python3-all to the Depends in debian/*tests*/control should fix this bug, but I have not actually tested this.
Bug#1069608: topplot: missing test-depends on python3-all
Source: topplot Version: 0.2.2+repack-1 Tags: patch Severity: serious Justification: blocks testing migration of other packages topplot tries to run its autopkgtest in all versions of Python (which is good), but does not test-depend on all those versions of Python. This previously worked because numpy depended on them. However, this has now been removed (see #945824), causing topplot's autopkgtests to fail. Adding python3-all to the Depends in debian/*tests*/control should fix this bug, but I have not actually tested this.
Bug#1068422: possibly caused by python 3.12.3 Re: Bug#1068422: can't import dask.dataframe - TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
This bug is not *obviously* known to dask upstream, but their CI is failing and I haven't checked why. It happens only in Python 3.12, not 3.11: https://ci.debian.net/packages/d/dask/unstable/amd64/45013666/ and still doesn't happen in testing, but does happen in mostly-testing with src:python3-defaults,src:db5.3,src:keras,src:nodejs,src:openssl,src:python3-stdlib-extensions,src:python3.11,src:python3.12,src:readline,src:udisks2,src:viagee from unstable: https://ci.debian.net/packages/d/dask/testing/amd64/45564690/ This suggests that the trigger may be the upgrade of Python itself (3.12.2-1 in testing -> 3.12.3-1 in unstable). *Possibly* related items from the upstream Python changelog: https://github.com/python/cpython/issues/101293 https://github.com/python/cpython/issues/117110
Bug#1068422: possibly caused by python 3.12.3 Re: Bug#1068422: can't import dask.dataframe - TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
This bug is not *obviously* known to dask upstream, but their CI is failing and I haven't checked why. It happens only in Python 3.12, not 3.11: https://ci.debian.net/packages/d/dask/unstable/amd64/45013666/ and still doesn't happen in testing, but does happen in mostly-testing with src:python3-defaults,src:db5.3,src:keras,src:nodejs,src:openssl,src:python3-stdlib-extensions,src:python3.11,src:python3.12,src:readline,src:udisks2,src:viagee from unstable: https://ci.debian.net/packages/d/dask/testing/amd64/45564690/ This suggests that the trigger may be the upgrade of Python itself (3.12.2-1 in testing -> 3.12.3-1 in unstable). *Possibly* related items from the upstream Python changelog: https://github.com/python/cpython/issues/101293 https://github.com/python/cpython/issues/117110
Bug#1068349: nbsphinx/nbconvert broken by lxml 5.2: lxml.html.clean
Control: unblock 1068104 by -1 Control: unblock 1068104 by 1068422 To avoid being blocked by this bug, the pandas version I just uploaded temporarily disables the documentation. This is also an option for any other affected packages that urgently need to be uploaded. (I don't know whether the other two listed Blocks/Affects are that urgent.)
Bug#1068349: nbsphinx/nbconvert broken by lxml 5.2: lxml.html.clean
Control: unblock 1068104 by -1 Control: unblock 1068104 by 1068422 To avoid being blocked by this bug, the pandas version I just uploaded temporarily disables the documentation. This is also an option for any other affected packages that urgently need to be uploaded. (I don't know whether the other two listed Blocks/Affects are that urgent.)
[med-svn] [Git][med-team/snakemake] Pushed new tag debian/7.32.4-3
Rebecca N. Palmer pushed new tag debian/7.32.4-3 at Debian Med / snakemake -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/debian/7.32.4-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
Bug#1068422: can't import dask.dataframe - TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
Package: python3-dask Version: 2023.12.1+dfsg-2 Severity: serious Control: affects -1 src:pandas Control: block 1068104 by -1 Importing dask.dataframe currently fails with the error TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object amd64 https://salsa.debian.org/science-team/pandas/-/jobs/5543041 https://ci.debian.net/packages/d/dask/unstable/arm64/44706021/ i386 https://salsa.debian.org/science-team/pandas/-/jobs/5543042 This appears to have started recently, as this log from 2024-03-31 doesn't have it, and to occur in unstable but not testing: https://tests.reproducible-builds.org/debian/rb-pkg/unstable/armhf/pandas.html As the version of dask has not changed in this time, the cause is probably a change in some other package; I don't know which one.
Bug#1068422: can't import dask.dataframe - TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object
Package: python3-dask Version: 2023.12.1+dfsg-2 Severity: serious Control: affects -1 src:pandas Control: block 1068104 by -1 Importing dask.dataframe currently fails with the error TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object amd64 https://salsa.debian.org/science-team/pandas/-/jobs/5543041 https://ci.debian.net/packages/d/dask/unstable/arm64/44706021/ i386 https://salsa.debian.org/science-team/pandas/-/jobs/5543042 This appears to have started recently, as this log from 2024-03-31 doesn't have it, and to occur in unstable but not testing: https://tests.reproducible-builds.org/debian/rb-pkg/unstable/armhf/pandas.html As the version of dask has not changed in this time, the cause is probably a change in some other package; I don't know which one.
Bug#1068349: nbsphinx/nbconvert broken by lxml 5.2: lxml.html.clean
Control: tags -1 patch Control: severity -1 serious (probably makes nbconvert/nbsphinx unusable) xml-html-clean is in NEWhttps://ftp-master.debian.org/new/lxml-html-clean_0.1.0-1.html Thanks - that and adding it to the Depends of python3-nbconvert should fix this bug. From codesearch, other packages that may need such a Depends are html-text, extruct, python-html-sanitizer, napari, readability, calibre, python-webob.
Bug#1068349: nbsphinx/nbconvert broken by lxml 5.2: lxml.html.clean
Package: python3-nbconvert,python3-lxml Version: 6.5.3-4,5.2.0-1 Control: affects -1 src:pandas Control: affects -1 python3-nbsphinx Control: block 1068104 by -1 The pandas documentation fails to build in current unstable with: Running Sphinx v7.2.6 nbconvert not installed. Skipping notebooks. Extension error: Could not import extension nbsphinx (exception: lxml.html.clean module is now a separate project lxml_html_clean. Install lxml[html_clean] or lxml_html_clean directly.) Full log: https://salsa.debian.org/science-team/pandas/-/jobs/5538806 This probably makes nbconvert and nbsphinx fail to import at all, and started when lxml was upgraded to 5.2, but I haven't actually tested either of those: https://sources.debian.org/src/nbconvert/6.5.3-4/nbconvert/exporters/templateexporter.py/?hl=25#L25 https://sources.debian.org/src/lxml/5.2.0-1/PKG-INFO/?hl=83#L83 The obvious fix would be to package lxml_html_clean.
Bug#1068104: pandas: FTBFS on 32-bit architectures with -D_TIME_BITS=64
Thanks - I plan to look at this tomorrow.
Bug#1068104: pandas: FTBFS on 32-bit architectures with -D_TIME_BITS=64
Thanks - I plan to look at this tomorrow.
Bug#1068104: pandas: FTBFS on 32-bit architectures with -D_TIME_BITS=64
Thanks - I plan to look at this tomorrow. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1063959: pandas and pytest 8
what's now in Salsa should be. (but please do *not* upload that right now, it is rather likely to have (unrelated) issues) -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1063959: pandas and pytest 8
Control: reopen -1 Control: tags -1 pending Control: tags 1066801 pending Control: tags 1064384 pending Sorry, that wasn't actually a fix, but what's now in Salsa should be. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1063959: pandas and pytest 8
Control: reopen -1 Control: tags -1 pending Control: tags 1066801 pending Control: tags 1064384 pending Sorry, that wasn't actually a fix, but what's now in Salsa should be.
Bug#1066801: pandas: FTBFS: /usr/lib/python3/dist-packages/dateutil/zoneinfo/__init__.py:26: UserWarning: I/O error(2): No such file or directory
Control: retitle -1 pandas: test-failing warning with new xarray This is a warning being treated as an error, but the one in test_to_xarray (probably due to the new version of xarray), not the zoneinfo one. This is a FutureWarning, so it should be OK to *use* the current pandas with the new xarray. The same warning happens in autopkgtest but isn't treated as an error there, so didn't block the new xarray. I intend to try fixing this later. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1066801: pandas: FTBFS: /usr/lib/python3/dist-packages/dateutil/zoneinfo/__init__.py:26: UserWarning: I/O error(2): No such file or directory
Control: retitle -1 pandas: test-failing warning with new xarray This is a warning being treated as an error, but the one in test_to_xarray (probably due to the new version of xarray), not the zoneinfo one. This is a FutureWarning, so it should be OK to *use* the current pandas with the new xarray. The same warning happens in autopkgtest but isn't treated as an error there, so didn't block the new xarray. I intend to try fixing this later.
Bug#1066801: pandas: FTBFS: /usr/lib/python3/dist-packages/dateutil/zoneinfo/__init__.py:26: UserWarning: I/O error(2): No such file or directory
Control: retitle -1 pandas: test-failing warning with new xarray This is a warning being treated as an error, but the one in test_to_xarray (probably due to the new version of xarray), not the zoneinfo one. This is a FutureWarning, so it should be OK to *use* the current pandas with the new xarray. The same warning happens in autopkgtest but isn't treated as an error there, so didn't block the new xarray. I intend to try fixing this later.
Bug#1064368: python-xarray: intermittent segfault in test_open_mfdataset_manyfiles[netcdf4-20-True-*-5]
Control: forwarded -1 https://github.com/pydata/xarray/issues/7079 (actually found independently) The above upstream report suggests that this is because netcdf-python is no longer thread-safe. The 3 random-autopkgtest-fail bugs (this, #1064326 and #1064370) together seem to be more common in pandas 2. It's possible that some of them are actually the same underlying bug. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1064368: python-xarray: intermittent segfault in test_open_mfdataset_manyfiles[netcdf4-20-True-*-5]
Control: forwarded -1 https://github.com/pydata/xarray/issues/7079 (actually found independently) The above upstream report suggests that this is because netcdf-python is no longer thread-safe. The 3 random-autopkgtest-fail bugs (this, #1064326 and #1064370) together seem to be more common in pandas 2. It's possible that some of them are actually the same underlying bug.
Bug#1043240: transition: pandas 1.5 -> 2.1
Remaining blockers for testing migration: - python-ulmo #1044057: has a patch, please upload - pydevd #1063274: unclear whether my patch breaks something else, please leave alone for now Status unclear: - python-xarray: autopkgtest has failed 3 times, but all 3 are (different) failures that have occurred without pandas 2, apparently at random - q2-*: autopkgtest fails in "fixed" versions, but possibly because they're not all being tested together -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1043240: transition: pandas 1.5 -> 2.1
Remaining blockers for testing migration: - python-ulmo #1044057: has a patch, please upload - pydevd #1063274: unclear whether my patch breaks something else, please leave alone for now Status unclear: - python-xarray: autopkgtest has failed 3 times, but all 3 are (different) failures that have occurred without pandas 2, apparently at random - q2-*: autopkgtest fails in "fixed" versions, but possibly because they're not all being tested together
Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1
Is that a yes to>> Does just the patch (not the new upstream) also break debugpy?or have you not tried specifically that? (I'm looking for a quick fix for the autopkgtest fail to unblock the pandas 2.x transition. I agree that upgrading to a new upstream is a good idea in the long run.) the bytecode version in pydevd is behind that in Debian, This is currently true (Debian has python3-bytecode 0.15.1, upstream pydevd 2.10.0 vendors 0.13.0.dev), but if it were a problem I'd expect it to mean that pydevd/debugpy were *already* buggy, not that my patch makes them worse.
Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1
Is that a yes to>> Does just the patch (not the new upstream) also break debugpy?or have you not tried specifically that? (I'm looking for a quick fix for the autopkgtest fail to unblock the pandas 2.x transition. I agree that upgrading to a new upstream is a good idea in the long run.) the bytecode version in pydevd is behind that in Debian, This is currently true (Debian has python3-bytecode 0.15.1, upstream pydevd 2.10.0 vendors 0.13.0.dev), but if it were a problem I'd expect it to mean that pydevd/debugpy were *already* buggy, not that my patch makes them worse.
Bug#1064370: python-xarray: intermittent fail in TestOpenMFDatasetWithDataVarsAndCoordsKw
Package: python3-xarray Version: 2023.12.0-3 The xarray autopkgtest sometimes (~20% of the time) fails with RuntimeError: NetCDF: Not a valid ID in tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw Unlike the other random failures, this seems to be amd64-specific. Exactly which test case fails varies: test_open_mfdataset_does_same_as_concat[left-different-by_coords-None] https://ci.debian.net/packages/p/python-xarray/testing/amd64/43085145/ test_open_mfdataset_dataset_combine_attrs[drop] https://ci.debian.net/packages/p/python-xarray/testing/amd64/42861417/ test_open_mfdataset_does_same_as_concat[right-minimal-nested-t] + test_open_mfdataset_does_same_as_concat[right-minimal-by_coords-None] https://ci.debian.net/packages/p/python-xarray/testing/amd64/42753466/ test_open_mfdataset_does_same_as_concat[outer-minimal-by_coords-None] https://ci.debian.net/packages/p/python-xarray/testing/amd64/43021198/ -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1064370: python-xarray: intermittent fail in TestOpenMFDatasetWithDataVarsAndCoordsKw
Package: python3-xarray Version: 2023.12.0-3 The xarray autopkgtest sometimes (~20% of the time) fails with RuntimeError: NetCDF: Not a valid ID in tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw Unlike the other random failures, this seems to be amd64-specific. Exactly which test case fails varies: test_open_mfdataset_does_same_as_concat[left-different-by_coords-None] https://ci.debian.net/packages/p/python-xarray/testing/amd64/43085145/ test_open_mfdataset_dataset_combine_attrs[drop] https://ci.debian.net/packages/p/python-xarray/testing/amd64/42861417/ test_open_mfdataset_does_same_as_concat[right-minimal-nested-t] + test_open_mfdataset_does_same_as_concat[right-minimal-by_coords-None] https://ci.debian.net/packages/p/python-xarray/testing/amd64/42753466/ test_open_mfdataset_does_same_as_concat[outer-minimal-by_coords-None] https://ci.debian.net/packages/p/python-xarray/testing/amd64/43021198/
Bug#1064368: python-xarray: intermittent segfault in test_open_mfdataset_manyfiles[netcdf4-20-True-*-5]
Package: python3-xarray Version: 2023.12.0-3 xarray sometimes (~10% of the time) segfaults in tests/test_backends.py::test_open_mfdataset_manyfiles, usually [netcdf4-20-True-None-5] but sometimes [netcdf4-20-True-5-5]. This has happened in both Python 3.11 and 3.12, and on various architectures: https://ci.debian.net/packages/p/python-xarray/testing/amd64/43068287/ https://ci.debian.net/packages/p/python-xarray/testing/armhf/42545225/ https://ci.debian.net/packages/p/python-xarray/testing/s390x/43076980/ https://ci.debian.net/packages/p/python-xarray/testing/ppc64el/42673240/ -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1064368: python-xarray: intermittent segfault in test_open_mfdataset_manyfiles[netcdf4-20-True-*-5]
Package: python3-xarray Version: 2023.12.0-3 xarray sometimes (~10% of the time) segfaults in tests/test_backends.py::test_open_mfdataset_manyfiles, usually [netcdf4-20-True-None-5] but sometimes [netcdf4-20-True-5-5]. This has happened in both Python 3.11 and 3.12, and on various architectures: https://ci.debian.net/packages/p/python-xarray/testing/amd64/43068287/ https://ci.debian.net/packages/p/python-xarray/testing/armhf/42545225/ https://ci.debian.net/packages/p/python-xarray/testing/s390x/43076980/ https://ci.debian.net/packages/p/python-xarray/testing/ppc64el/42673240/
Bug#1064326: python-xarray: intermittent hang in test_roundtrip_coordinates
Package: python3-xarray Version: 2023.12.0-3 The xarray autopkgtest sometimes (~10% of the time) hangs in test_roundtrip_coordinates, and hence fails with a timeout. Example failure log (but this is _not_ specific to pandas 2.x): https://ci.debian.net/packages/p/python-xarray/testing/amd64/43065828/ -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1064326: python-xarray: intermittent hang in test_roundtrip_coordinates
Package: python3-xarray Version: 2023.12.0-3 The xarray autopkgtest sometimes (~10% of the time) hangs in test_roundtrip_coordinates, and hence fails with a timeout. Example failure log (but this is _not_ specific to pandas 2.x): https://ci.debian.net/packages/p/python-xarray/testing/amd64/43065828/
Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1
Thank you for caring about not breaking other packages, and yes, that's a good reason to not upload that new upstream for now. Does just the patch (not the new upstream) also break debugpy? (It shouldn't be able to, since it only touches test code.)
Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1
Thank you for caring about not breaking other packages, and yes, that's a good reason to not upload that new upstream for now. Does just the patch (not the new upstream) also break debugpy? (It shouldn't be able to, since it only touches test code.)
Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1
This has been merged but not uploaded - is there a reason it shouldn't be, or have you just not had time?
Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1
This has been merged but not uploaded - is there a reason it shouldn't be, or have you just not had time?
Bug#1044057: python-ulmo and pandas 2
Control: tags -1 patch
This should fix this (and as the filename suggests, also re-adds spme
older fixes that seem to have been dropped by mistake between -1.1 and
-2), but has not been tested: the relevant tests aren't run by default
and there vaguely might be legal issues around ulmo's tests.Description: Don't fail on malformed or changed test data
CDEC has malformed lines that pandas 1.4+ errors out on
(I'm not sure why earlier pandas didn't do the same);
GHCN has simply changed at the source.
Author: Rebecca N. Palmer (but upstream independently came up with the on_bad_lines part)
Bug-Debian: https://bugs.debian.org/1017573 https://bugs.debian.org/1044057
Forwarded: partly no, partly not-needed, partly https://github.com/ulmo-dev/ulmo/pull/214
--- a/test/cdec_historical_test.py
+++ b/test/cdec_historical_test.py
@@ -9,7 +9,7 @@ def test_get_stations():
stations_file = 'cdec/historical/all_stations.csv'
with test_util.mocked_urls(stations_file):
stations = ulmo.cdec.historical.get_stations()
-assert 2000 < len(stations)
+assert 1900 < len(stations)
assert u'PRA' in stations.index
--- a/test/ghcn_daily_test.py
+++ b/test/ghcn_daily_test.py
@@ -10,12 +10,12 @@ import test_util
test_stations = [
{
'country': 'US',
-'elevation': 286.5,
+'elevation': 325.8,
'gsn_flag': 'GSN',
'hcn_flag': 'HCN',
'id': 'USW3870',
-'latitude': 34.8831,
-'longitude': -82.2203,
+'latitude': 34.8833,
+'longitude': -82.2197,
'name': 'GREER',
'network': 'W',
'network_id': '3870',
--- a/ulmo/cdec/historical/core.py
+++ b/ulmo/cdec/historical/core.py
@@ -74,9 +74,9 @@ def get_stations():
# I haven't found a better list of stations, seems pretty janky
# to just have them in a file, and not sure if/when it is updated.
url = 'http://cdec.water.ca.gov/misc/all_stations.csv'
-# the csv is malformed, so some rows think there are 7 fields
-col_names = ['id','meta_url','name','num','lat','lon','junk']
-df = pd.read_csv(url, names=col_names, header=None, quotechar="'",index_col=0)
+# the csv is malformed, so some rows think there are 7-8 fields
+col_names = ['id','meta_url','name','num','lat','lon']
+df = pd.read_csv(url, names=col_names, header=None, quotechar="'",index_col=0,on_bad_lines='skip')
return df
@@ -170,7 +170,7 @@ def get_station_sensors(station_ids=None, sensor_ids=None, resolutions=None):
sensor_list.columns = ['sensor_id', 'variable', 'resolution','timerange']
except:
sensor_list.columns = ['variable', 'sensor_id', 'resolution', 'varcode', 'method', 'timerange']
-sensor_list[['variable', 'units']] = sensor_list.variable.str.split(',', 1, expand=True)
+sensor_list[['variable', 'units']] = sensor_list.variable.str.split(',', n=1, expand=True)
sensor_list.resolution = sensor_list.resolution.str.strip('()')
station_sensors[station_id] = _limit_sensor_list(sensor_list, sensor_ids, resolutions)
--
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Bug#1044057: python-ulmo and pandas 2
Control: tags -1 patch
This should fix this (and as the filename suggests, also re-adds spme
older fixes that seem to have been dropped by mistake between -1.1 and
-2), but has not been tested: the relevant tests aren't run by default
and there vaguely might be legal issues around ulmo's tests.Description: Don't fail on malformed or changed test data
CDEC has malformed lines that pandas 1.4+ errors out on
(I'm not sure why earlier pandas didn't do the same);
GHCN has simply changed at the source.
Author: Rebecca N. Palmer (but upstream independently came up with the on_bad_lines part)
Bug-Debian: https://bugs.debian.org/1017573 https://bugs.debian.org/1044057
Forwarded: partly no, partly not-needed, partly https://github.com/ulmo-dev/ulmo/pull/214
--- a/test/cdec_historical_test.py
+++ b/test/cdec_historical_test.py
@@ -9,7 +9,7 @@ def test_get_stations():
stations_file = 'cdec/historical/all_stations.csv'
with test_util.mocked_urls(stations_file):
stations = ulmo.cdec.historical.get_stations()
-assert 2000 < len(stations)
+assert 1900 < len(stations)
assert u'PRA' in stations.index
--- a/test/ghcn_daily_test.py
+++ b/test/ghcn_daily_test.py
@@ -10,12 +10,12 @@ import test_util
test_stations = [
{
'country': 'US',
-'elevation': 286.5,
+'elevation': 325.8,
'gsn_flag': 'GSN',
'hcn_flag': 'HCN',
'id': 'USW3870',
-'latitude': 34.8831,
-'longitude': -82.2203,
+'latitude': 34.8833,
+'longitude': -82.2197,
'name': 'GREER',
'network': 'W',
'network_id': '3870',
--- a/ulmo/cdec/historical/core.py
+++ b/ulmo/cdec/historical/core.py
@@ -74,9 +74,9 @@ def get_stations():
# I haven't found a better list of stations, seems pretty janky
# to just have them in a file, and not sure if/when it is updated.
url = 'http://cdec.water.ca.gov/misc/all_stations.csv'
-# the csv is malformed, so some rows think there are 7 fields
-col_names = ['id','meta_url','name','num','lat','lon','junk']
-df = pd.read_csv(url, names=col_names, header=None, quotechar="'",index_col=0)
+# the csv is malformed, so some rows think there are 7-8 fields
+col_names = ['id','meta_url','name','num','lat','lon']
+df = pd.read_csv(url, names=col_names, header=None, quotechar="'",index_col=0,on_bad_lines='skip')
return df
@@ -170,7 +170,7 @@ def get_station_sensors(station_ids=None, sensor_ids=None, resolutions=None):
sensor_list.columns = ['sensor_id', 'variable', 'resolution','timerange']
except:
sensor_list.columns = ['variable', 'sensor_id', 'resolution', 'varcode', 'method', 'timerange']
-sensor_list[['variable', 'units']] = sensor_list.variable.str.split(',', 1, expand=True)
+sensor_list[['variable', 'units']] = sensor_list.variable.str.split(',', n=1, expand=True)
sensor_list.resolution = sensor_list.resolution.str.strip('()')
station_sensors[station_id] = _limit_sensor_list(sensor_list, sensor_ids, resolutions)
Bug#1044057: python-ulmo and pandas 2
Control: tags -1 patch
This should fix this (and as the filename suggests, also re-adds spme
older fixes that seem to have been dropped by mistake between -1.1 and
-2), but has not been tested: the relevant tests aren't run by default
and there vaguely might be legal issues around ulmo's tests.Description: Don't fail on malformed or changed test data
CDEC has malformed lines that pandas 1.4+ errors out on
(I'm not sure why earlier pandas didn't do the same);
GHCN has simply changed at the source.
Author: Rebecca N. Palmer (but upstream independently came up with the on_bad_lines part)
Bug-Debian: https://bugs.debian.org/1017573 https://bugs.debian.org/1044057
Forwarded: partly no, partly not-needed, partly https://github.com/ulmo-dev/ulmo/pull/214
--- a/test/cdec_historical_test.py
+++ b/test/cdec_historical_test.py
@@ -9,7 +9,7 @@ def test_get_stations():
stations_file = 'cdec/historical/all_stations.csv'
with test_util.mocked_urls(stations_file):
stations = ulmo.cdec.historical.get_stations()
-assert 2000 < len(stations)
+assert 1900 < len(stations)
assert u'PRA' in stations.index
--- a/test/ghcn_daily_test.py
+++ b/test/ghcn_daily_test.py
@@ -10,12 +10,12 @@ import test_util
test_stations = [
{
'country': 'US',
-'elevation': 286.5,
+'elevation': 325.8,
'gsn_flag': 'GSN',
'hcn_flag': 'HCN',
'id': 'USW3870',
-'latitude': 34.8831,
-'longitude': -82.2203,
+'latitude': 34.8833,
+'longitude': -82.2197,
'name': 'GREER',
'network': 'W',
'network_id': '3870',
--- a/ulmo/cdec/historical/core.py
+++ b/ulmo/cdec/historical/core.py
@@ -74,9 +74,9 @@ def get_stations():
# I haven't found a better list of stations, seems pretty janky
# to just have them in a file, and not sure if/when it is updated.
url = 'http://cdec.water.ca.gov/misc/all_stations.csv'
-# the csv is malformed, so some rows think there are 7 fields
-col_names = ['id','meta_url','name','num','lat','lon','junk']
-df = pd.read_csv(url, names=col_names, header=None, quotechar="'",index_col=0)
+# the csv is malformed, so some rows think there are 7-8 fields
+col_names = ['id','meta_url','name','num','lat','lon']
+df = pd.read_csv(url, names=col_names, header=None, quotechar="'",index_col=0,on_bad_lines='skip')
return df
@@ -170,7 +170,7 @@ def get_station_sensors(station_ids=None, sensor_ids=None, resolutions=None):
sensor_list.columns = ['sensor_id', 'variable', 'resolution','timerange']
except:
sensor_list.columns = ['variable', 'sensor_id', 'resolution', 'varcode', 'method', 'timerange']
-sensor_list[['variable', 'units']] = sensor_list.variable.str.split(',', 1, expand=True)
+sensor_list[['variable', 'units']] = sensor_list.variable.str.split(',', n=1, expand=True)
sensor_list.resolution = sensor_list.resolution.str.strip('()')
station_sensors[station_id] = _limit_sensor_list(sensor_list, sensor_ids, resolutions)
[med-svn] [Git][med-team/snakemake] Pushed new tag debian/7.32.4-2
Rebecca N. Palmer pushed new tag debian/7.32.4-2 at Debian Med / snakemake -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/debian/7.32.4-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/snakemake] Pushed new tag upstream/8.2.3
Rebecca N. Palmer pushed new tag upstream/8.2.3 at Debian Med / snakemake -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/upstream/8.2.3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/snakemake][pristine-tar] pristine-tar data for snakemake_8.2.3.orig.tar.gz
Rebecca N. Palmer pushed to branch pristine-tar at Debian Med / snakemake Commits: 66a8a8a6 by Rebecca N. Palmer at 2024-01-20T10:42:57+00:00 pristine-tar data for snakemake_8.2.3.orig.tar.gz - - - - - 2 changed files: - + snakemake_8.2.3.orig.tar.gz.delta - + snakemake_8.2.3.orig.tar.gz.id Changes: = snakemake_8.2.3.orig.tar.gz.delta = Binary files /dev/null and b/snakemake_8.2.3.orig.tar.gz.delta differ = snakemake_8.2.3.orig.tar.gz.id = @@ -0,0 +1 @@ +cb0f818f4aa59c6d522cd3313cf2686813983c32 View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/66a8a8a6d47f963ed3f623b2334fae0c37758912 -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/66a8a8a6d47f963ed3f623b2334fae0c37758912 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/snakemake][upstream] New upstream version 8.2.3
Rebecca N. Palmer pushed to branch upstream at Debian Med / snakemake Commits: cc1b5000 by Rebecca N. Palmer at 2024-01-20T10:42:31+00:00 New upstream version 8.2.3 - - - - - 30 changed files: - .github/workflows/docker-publish.yml - .github/workflows/main.yml - .github/workflows/release-please.yml - − .github/workflows/test-flux.yaml - .gitignore - .readthedocs.yml - .sonarcloud.properties - + .test_durations - CHANGELOG.md - CODE_OF_CONDUCT.md - Dockerfile - LICENSE.md - README.md - + apidocs/.readthedocs.yaml - + apidocs/Makefile - + apidocs/_templates/module_template.rst - + apidocs/api_reference/internal/modules.rst - + apidocs/api_reference/snakemake_api.rst - docs/apidocs/api_reference/snakemake_utils.rst → apidocs/api_reference/snakemake_utils.rst - docs/apidocs/conf.py → apidocs/conf.py - docs/apidocs/index.rst → apidocs/index.rst - + apidocs/requirements.txt - + docs/_static/custom.css - + docs/_static/logo-snake.svg - − docs/_static/theme.css - − docs/apidocs/api_reference/internal/modules.rst - − docs/apidocs/api_reference/internal/snakemake.remote.rst - − docs/apidocs/api_reference/internal/snakemake.report.rst - − docs/apidocs/api_reference/internal/snakemake.rst - − docs/apidocs/api_reference/snakemake.rst The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/cc1b501289ef4cd0ac0f1ae903e864b45d22 -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/cc1b501289ef4cd0ac0f1ae903e864b45d22 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/snakemake][debian-v7] work around patch not adding empty files
Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake
Commits:
26e21c8f by Rebecca N. Palmer at 2024-02-09T19:11:31+00:00
work around patch not adding empty files
- - - - -
2 changed files:
- debian/changelog
- debian/patches/fstring.patch
Changes:
=
debian/changelog
=
@@ -4,7 +4,7 @@ snakemake (7.32.4-2) unstable; urgency=medium
* Adapt to f-strings being tokenized in Python 3.12.
(together, Closes: #1061761)
- -- Rebecca N. Palmer Fri, 09 Feb 2024 07:51:55
+
+ -- Rebecca N. Palmer Fri, 09 Feb 2024 19:11:23
+
snakemake (7.32.4-1) unstable; urgency=medium
=
debian/patches/fstring.patch
=
@@ -143,6 +143,10 @@ Author: Hocnonsense, Rebecca N. Palmer
+linemap[last + 1] = linemap[last]
+return join_compilation, linemap, snakefile.rulecount
--- /dev/null
b/tests/test_fstring/expected-results/SID23454678.txt
+@@ -0,0 +1,1 @@
++rrr
+--- /dev/null
+++ b/tests/test_fstring/Snakefile
@@ -0,0 +1,51 @@
+shell.executable("bash")
@@ -154,7 +158,7 @@ Author: Hocnonsense, Rebecca N. Palmer
+output:
+f"{PREFIX}{mid}xt",
+shell:
-+"echo '>'{output}'<'; touch {output}; sleep 1"
++"echo '>'{output}'<'; echo 'rrr' > {output}; sleep 1"
+
+
+rule unit2:
View it on GitLab:
https://salsa.debian.org/med-team/snakemake/-/commit/26e21c8f0a0f420597689816e697159757defeff
--
View it on GitLab:
https://salsa.debian.org/med-team/snakemake/-/commit/26e21c8f0a0f420597689816e697159757defeff
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[med-svn] [Git][med-team/snakemake][debian-v7] revert accidental interface change
Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake Commits: a0c4af75 by Rebecca N. Palmer at 2024-02-09T07:52:23+00:00 revert accidental interface change - - - - - 2 changed files: - debian/changelog - debian/patches/fstring.patch Changes: = debian/changelog = @@ -4,7 +4,7 @@ snakemake (7.32.4-2) unstable; urgency=medium * Adapt to f-strings being tokenized in Python 3.12. (together, Closes: #1061761) - -- Rebecca N. Palmer Thu, 08 Feb 2024 22:16:41 + + -- Rebecca N. Palmer Fri, 09 Feb 2024 07:51:55 + snakemake (7.32.4-1) unstable; urgency=medium = debian/patches/fstring.patch = @@ -141,7 +141,7 @@ Author: Hocnonsense, Rebecca N. Palmer +if linemap: +last = max(linemap) +linemap[last + 1] = linemap[last] -+return join_compilation, snakefile.rulecount ++return join_compilation, linemap, snakefile.rulecount --- /dev/null +++ b/tests/test_fstring/Snakefile @@ -0,0 +1,51 @@ View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/a0c4af759db2ee0e0a3ec6672b966ba8ad6b7cfb -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/a0c4af759db2ee0e0a3ec6672b966ba8ad6b7cfb You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
Bug#1044071: feather and pandas 2.0
Control: tags -1 patch It does sometimes happen that fixing "can't import the tests" reveals "the tests fail". Fixed in the Salsa merge request.
Bug#1044071: feather and pandas 2.0
Control: tags -1 patch It does sometimes happen that fixing "can't import the tests" reveals "the tests fail". Fixed in the Salsa merge request.
Bug#1063435: pandas 2.x fixes
Control: tags -1 patch See the Salsa merge request. ___ Pkg-grass-devel mailing list Pkg-grass-devel@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/pkg-grass-devel
Bug#1063274: pandas 2.x fixes
Control: tags -1 patch See the Salsa merge request.
Bug#1063274: pandas 2.x fixes
Control: tags -1 patch See the Salsa merge request.
Bug#1061761: marked as pending in snakemake
Control: tag -1 pending Hello, Bug #1061761 in snakemake reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/snakemake/-/commit/607bd710a51b77502c641443cf68a2dae025c695 Adapt to f-strings being tokenized in Python 3.12. (Closes: #1061761) (this message was generated automatically) -- Greetings https://bugs.debian.org/1061761
Bug#1063273: seaborn: autopkgtest fail on i386 - probable rounding error
Control: tags -1 pending This appears to be fixed in Salsa (before I reported it) - is there any reason not to upload this now? -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1063273: seaborn: autopkgtest fail on i386 - probable rounding error
Control: tags -1 pending This appears to be fixed in Salsa (before I reported it) - is there any reason not to upload this now?
Bug#1063273: seaborn: autopkgtest fail on i386 - probable rounding error
Control: tags -1 pending This appears to be fixed in Salsa (before I reported it) - is there any reason not to upload this now?
Bug#1063435: geopandas: test fail with pandas 2.x on 32 bit - int32 vs int64 mismatch
Package: python3-geopandas Version: 0.14.3-1 Severity: serious Control: block 1043240 by -1 In pandas 2.x (now in unstable), there are a few places where geopandas uses native-size int but the plain pandas objects used as test references are always int64, failing the test: https://ci.debian.net/packages/p/python-geopandas/testing/armhf/42777226/ Probably a reasonable response is to ignore this (check_index_type=False/check_dtype=False) but I haven't looked carefully. ___ Pkg-grass-devel mailing list Pkg-grass-devel@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/pkg-grass-devel
Bug#1063435: geopandas: test fail with pandas 2.x on 32 bit - int32 vs int64 mismatch
Package: python3-geopandas Version: 0.14.3-1 Severity: serious Control: block 1043240 by -1 In pandas 2.x (now in unstable), there are a few places where geopandas uses native-size int but the plain pandas objects used as test references are always int64, failing the test: https://ci.debian.net/packages/p/python-geopandas/testing/armhf/42777226/ Probably a reasonable response is to ignore this (check_index_type=False/check_dtype=False) but I haven't looked carefully.
Bug#1063435: geopandas: test fail with pandas 2.x on 32 bit - int32 vs int64 mismatch
Package: python3-geopandas Version: 0.14.3-1 Severity: serious Control: block 1043240 by -1 In pandas 2.x (now in unstable), there are a few places where geopandas uses native-size int but the plain pandas objects used as test references are always int64, failing the test: https://ci.debian.net/packages/p/python-geopandas/testing/armhf/42777226/ Probably a reasonable response is to ignore this (check_index_type=False/check_dtype=False) but I haven't looked carefully.
Bug#1063325: mdanalysis: random autopkgtest hangs
Package: python3-mdanalysis Version: 2.5.0+dfsg1-2 The autopkgtest sometimes hangs at the 85% point, causing it to time out and fail. (This is probably a hang and not just slowness, because when it doesn't fail, this test doesn't take anywhere near that long.) https://ci.debian.net/packages/m/mdanalysis/testing/i386/42756824/ https://ci.debian.net/packages/m/mdanalysis/testing/armel/42726120/ https://ci.debian.net/packages/m/mdanalysis/testing/amd64/42461650/
Bug#1043240: transition: pandas 1.5 -> 2.1
Control: block -1 by 1063274 Thank you for uploading those fixes. Note to self: pandas will need another upload, to remove the numba B-D and skip those tests (because numba is not in testing), and do something about 'ignoredtests' being slow enough to time out in i386 and arm64.
Bug#1043240: transition: pandas 1.5 -> 2.1
Control: block -1 by 1063274 Thank you for uploading those fixes. Note to self: pandas will need another upload, to remove the numba B-D and skip those tests (because numba is not in testing), and do something about 'ignoredtests' being slow enough to time out in i386 and arm64. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1
Source: pydevd Severity: serious Tags: patch A pydevd test uses DataFrame.applymap(), and fails because this now raises a FutureWarning. Replacing it with DataFrame.map() as this message suggests would probably fix it.
Bug#1063274: pydevd: autopkgtest-failing warning with pandas 2.1
Source: pydevd Severity: serious Tags: patch A pydevd test uses DataFrame.applymap(), and fails because this now raises a FutureWarning. Replacing it with DataFrame.map() as this message suggests would probably fix it.
Bug#1063273: seaborn: autopkgtest fail on i386 - probable rounding error
Package: python3-seaborn Version: 0.13.2-1 Severity: serious seaborn's autopkgtest failed on i386, with differences small enough that they are plausibly rounding error (i.e. should be ignored, by using *almost_equal instead of exact comparisons), but I haven't looked carefully.
Bug#1063273: seaborn: autopkgtest fail on i386 - probable rounding error
Package: python3-seaborn Version: 0.13.2-1 Severity: serious seaborn's autopkgtest failed on i386, with differences small enough that they are plausibly rounding error (i.e. should be ignored, by using *almost_equal instead of exact comparisons), but I haven't looked carefully.
Bug#1063273: seaborn: autopkgtest fail on i386 - probable rounding error
Package: python3-seaborn Version: 0.13.2-1 Severity: serious seaborn's autopkgtest failed on i386, with differences small enough that they are plausibly rounding error (i.e. should be ignored, by using *almost_equal instead of exact comparisons), but I haven't looked carefully. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1044073: Sorry Re: python-altair and pandas 2.0
On 03/02/2024 22:01, Andreas Tille wrote: The point I was making in my mail was that I had trouble running the tests in **latest** upstream version (5.2.0). Sorry - I'd misread your previous message as you having tried 5.x, found that it didn't work due to the missing dependency, and decided to try 4.x with tests skipped instead. I think we should strive for latest upstream in general Agreed, assuming that doing so doesn't break things.
Bug#1044073: Sorry Re: python-altair and pandas 2.0
On 03/02/2024 22:01, Andreas Tille wrote: The point I was making in my mail was that I had trouble running the tests in **latest** upstream version (5.2.0). Sorry - I'd misread your previous message as you having tried 5.x, found that it didn't work due to the missing dependency, and decided to try 4.x with tests skipped instead. I think we should strive for latest upstream in general Agreed, assuming that doing so doesn't break things.
Bug#1061761: snakemake issues with Python 3.12
It looks like this is at least two issues: - Tests mix tabs and spaces, which is no longer allowed = upstream 2459 - Assumes f-strings are not tokenized, which they now are = upstream 2485/2588/2649 Fix in progress on the debian-v7 branch. (The main branch has 8.x, which doesn't work due to missing dependencies.)
Bug#1061761: snakemake issues with Python 3.12
It looks like this is at least two issues: - Tests mix tabs and spaces, which is no longer allowed = upstream 2459 - Assumes f-strings are not tokenized, which they now are = upstream 2485/2588/2649 Fix in progress on the debian-v7 branch. (The main branch has 8.x, which doesn't work due to missing dependencies.)
[med-svn] [Git][med-team/snakemake] Pushed new branch debian-v7
Rebecca N. Palmer pushed new branch debian-v7 at Debian Med / snakemake -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/tree/debian-v7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
Bug#1044073: python-altair and pandas 2.0
Please don't skip/xfail tests - my suggestion above is an actual fix: https://salsa.debian.org/rnpalmer-guest/python-altair/-/tree/fix1044073?ref_type=heads (In a fork because, despite its description, this is not actually a debian-science package. The Salsa CI "fail" is because the *old* version is uninstallable due to Breaks: in pandas and the piuparts upgrade test counts this as a fail.)
Bug#1044073: python-altair and pandas 2.0
Please don't skip/xfail tests - my suggestion above is an actual fix: https://salsa.debian.org/rnpalmer-guest/python-altair/-/tree/fix1044073?ref_type=heads (In a fork because, despite its description, this is not actually a debian-science package. The Salsa CI "fail" is because the *old* version is uninstallable due to Breaks: in pandas and the piuparts upgrade test counts this as a fail.)
Bug#1044076: influxdb-python and pandas 2.1
My fixes are pushed to Salsa, but they're in a fork because this isn't a debian-science package: https://salsa.debian.org/rnpalmer-guest/influxdb-python
Bug#1043240: transition: pandas 1.5 -> 2.1 - please upload fixes
seaborn has now been fixed. I intend to look at python-altair later. -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1044076: influxdb-python and pandas 2.1
My fixes are pushed to Salsa, but they're in a fork because this isn't a debian-science package: https://salsa.debian.org/rnpalmer-guest/influxdb-python
Bug#1043240: transition: pandas 1.5 -> 2.1 - please upload fixes
seaborn has now been fixed. I intend to look at python-altair later.
Re: Bug#1043240: transition: pandas 1.5 -> 2.1 - please upload fixes
I intend to upload pandas 2.x to unstable soon. These packages have a patch in their bug - please upload them (I'm a DM, I can't do that), or if you think this patch won't work or isn't a good idea, tell me why: dials influxdb-python python-altair python-feather-format seaborn tqdm In particular, I'd like the seaborn fix uploaded before pandas, so I can set Breaks for it. (The pandas documentation build-depends on seaborn.)
Bug#1044076: influxdb-python and pandas 2.1
Note that this uncertainty is only around whether this is a complete fix - even in the case where it's not, it *wouldn't* be actively worse than doing nothing, though it would be hiding the problem.
Bug#1044076: influxdb-python and pandas 2.1
Note that this uncertainty is only around whether this is a complete fix - even in the case where it's not, it *wouldn't* be actively worse than doing nothing, though it would be hiding the problem.
Bug#1043240: transition: pandas 1.5 -> 2.1 - please upload fixes
I intend to upload pandas 2.x to unstable soon. These packages have a patch in their bug - please upload them (I'm a DM, I can't do that), or if you think this patch won't work or isn't a good idea, tell me why: dials influxdb-python python-altair python-feather-format seaborn tqdm In particular, I'd like the seaborn fix uploaded before pandas, so I can set Breaks for it. (The pandas documentation build-depends on seaborn.)
Bug#1043240: transition: pandas 1.5 -> 2.1 - please upload fixes
I intend to upload pandas 2.x to unstable soon. These packages have a patch in their bug - please upload them (I'm a DM, I can't do that), or if you think this patch won't work or isn't a good idea, tell me why: dials influxdb-python python-altair python-feather-format seaborn tqdm In particular, I'd like the seaborn fix uploaded before pandas, so I can set Breaks for it. (The pandas documentation build-depends on seaborn.) -- debian-science-maintainers mailing list debian-science-maintainers@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
Bug#1044076: influxdb-python and pandas 2.1
Some looking through the code suggests that the precision is user-set and hence constant within a single query, and hence that this fix is OK, but I'm not entirely certain of that. There are ways to make pandas 2.x accept mixed time format, but I think they're 2.x _only_ and/or slow.
Bug#1044076: influxdb-python and pandas 2.1
Some looking through the code suggests that the precision is user-set and hence constant within a single query, and hence that this fix is OK, but I'm not entirely certain of that. There are ways to make pandas 2.x accept mixed time format, but I think they're 2.x _only_ and/or slow.
Bug#1053946: tqdm and pandas 2.1 / python 3.12
That turned out to be easier than it looked - fixing the easy one also made the others go away. Please upload this: https://salsa.debian.org/rnpalmer-guest/tqdm
Bug#1053946: tqdm and pandas 2.1 / python 3.12
That turned out to be easier than it looked - fixing the easy one also made the others go away. Please upload this: https://salsa.debian.org/rnpalmer-guest/tqdm
Bug#1058160: tqdm and pandas 2.1 / python 3.12
Control: retitle 1058160 tqdm: tests failing/hanging in Python 3.12 That works for #1053946 (pandas 2.x), but #1058160 (python 3.12) is more than a single hanging test, and it's not immediately obvious what should be done. Attempted fix (caution, currently just skips the hanging test) and failure logs: https://salsa.debian.org/rnpalmer-guest/tqdm
