pandas-dev / pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
https://pandas.pydata.org
BSD 3-Clause "New" or "Revised" License
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DOC: Development on Gitpod have problems #59459

Open serl opened 1 month ago

serl commented 1 month ago

Pandas version checks

Location of the documentation

https://pandas.pydata.org/docs/dev/development/contributing_gitpod.html

Documentation problem

Aiming for a quick-start, I wanted to use GitPod to setup my environment.

After a couple of minor hiccups I try to tackle in https://github.com/pandas-dev/pandas/pull/59456, I stepped on a more serious roadblock:

$ python -m pytest pandas

+ /usr/local/bin/ninja
[1/1] Generating write_version_file with a custom command
ImportError while loading conftest '/workspace/pandas/pandas/conftest.py'.
pandas/conftest.py:715: in <module>
    idx = Index(pd.array([f"pandas_{i}" for i in range(10)], dtype="string[pyarrow]"))
pandas/core/construction.py:321: in array
    return cls._from_sequence(data, dtype=dtype, copy=copy)
pandas/core/arrays/string_arrow.py:203: in _from_sequence
    return cls(pa.array(result, type=pa.large_string(), from_pandas=True))
pyarrow/array.pxi:281: in pyarrow.lib.array
    ???
pyarrow/array.pxi:4519: in pyarrow.lib.get_values
    ???
pyarrow/pandas-shim.pxi:228: in pyarrow.lib._PandasAPIShim.is_series
    ???
pyarrow/pandas-shim.pxi:124: in pyarrow.lib._PandasAPIShim._have_pandas_internal
    ???
pyarrow/pandas-shim.pxi:103: in pyarrow.lib._PandasAPIShim._check_import
    ???
pyarrow/pandas-shim.pxi:106: in pyarrow.lib._PandasAPIShim._check_import
    ???
pyarrow/pandas-shim.pxi:74: in pyarrow.lib._PandasAPIShim._import_pandas
    ???
E   UserWarning: pyarrow requires pandas 1.0.0 or above, pandas 0+untagged.1.gd5bbd97 is installed. Therefore, pandas-specific integration is not used.

This comes from a fresh workspace built on main, and it is confirmed by pandas.__version__:

$ python
Python 3.10.8 (main, Dec  6 2022, 14:13:21) [GCC 10.2.1 20210110] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pandas
+ /usr/local/bin/ninja
[1/1] Generating write_version_file with a custom command
>>> pandas.__version__
'0+untagged.1.gd5bbd97'

Note that in the initialization steps, pandas 2.2.0.dev0... got built (output below).

Output from the initialization task in .gitpod.yml ``` $ HISTFILE=/workspace/.gitpod/cmd-0 history -r; { > mkdir -p .vscode > cp gitpod/settings.json .vscode/settings.json > git fetch --tags > python -m pip install -ve . --no-build-isolation --config-settings editable-verbose=true > pre-commit install --install-hooks > > } && { > python -m pip install -ve . --no-build-isolation --config-settings editable-verbose=true > echo "✨ Pre-build complete! You can close this terminal ✨ " > > } Using pip 24.2 from /usr/local/lib/python3.10/site-packages/pip (python 3.10) Defaulting to user installation because normal site-packages is not writeable Obtaining file:///workspace/pandas Running command Checking if build backend supports build_editable Checking if build backend supports build_editable ... done Running command Preparing editable metadata (pyproject.toml) + meson setup /workspace/pandas /workspace/pandas/build/cp310 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --vsenv --native-file=/workspace/pandas/build/cp310/meson-python-native-file.ini The Meson build system Version: 1.2.1 Source dir: /workspace/pandas Build dir: /workspace/pandas/build/cp310 Build type: native build Project name: pandas Project version: 0+untagged.1.gd5bbd97 C compiler for the host machine: cc (gcc 10.2.1 "cc (Debian 10.2.1-6) 10.2.1 20210110") C linker for the host machine: cc ld.bfd 2.35.2 C++ compiler for the host machine: c++ (gcc 10.2.1 "c++ (Debian 10.2.1-6) 10.2.1 20210110") C++ linker for the host machine: c++ ld.bfd 2.35.2 Cython compiler for the host machine: cython (cython 3.0.11) Host machine cpu family: x86_64 Host machine cpu: x86_64 Program python found: YES (/usr/local/bin/python) Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency python found: YES 3.10 Build targets in project: 54 pandas 0+untagged.1.gd5bbd97 User defined options Native files: /workspace/pandas/build/cp310/meson-python-native-file.ini buildtype : release vsenv : True b_ndebug : if-release b_vscrt : md Found ninja-1.11.1.git.kitware.jobserver-1 at /usr/local/bin/ninja Visual Studio environment is needed to run Ninja. It is recommended to use Meson wrapper: /usr/local/bin/meson compile -C . + /usr/local/bin/ninja [1/152] Generating pandas/_libs/algos_common_helper_pxi with a custom command [2/152] Generating pandas/_libs/khash_primitive_helper_pxi with a custom command [3/152] Generating pandas/_libs/index_class_helper_pxi with a custom command [4/152] Generating pandas/_libs/algos_take_helper_pxi with a custom command [5/152] Generating pandas/_libs/hashtable_class_helper_pxi with a custom command [6/152] Generating pandas/__init__.py with a custom command [7/152] Generating pandas/_libs/hashtable_func_helper_pxi with a custom command [8/152] Generating pandas/_libs/intervaltree_helper_pxi with a custom command [9/152] Generating pandas/_libs/sparse_op_helper_pxi with a custom command [10/152] Generating write_version_file with a custom command [11/152] Compiling C object pandas/_libs/tslibs/parsing.cpython-310-x86_64-linux-gnu.so.p/.._src_parser_tokenizer.c.o [12/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/base.pyx [13/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/ccalendar.pyx [14/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/dtypes.pyx [15/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/nattype.pyx [16/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/np_datetime.pyx [17/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/vectorized.pyx [18/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/timezones.pyx [19/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/tzconversion.pyx [20/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/fields.pyx [21/152] Compiling C object pandas/_libs/tslibs/base.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_base.pyx.c.o [22/152] Linking target pandas/_libs/tslibs/base.cpython-310-x86_64-linux-gnu.so [23/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/strptime.pyx [24/152] Compiling Cython source /workspace/pandas/pandas/_libs/arrays.pyx [25/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/conversion.pyx [26/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/parsing.pyx [27/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/timestamps.pyx [28/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/timedeltas.pyx [29/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/offsets.pyx [30/152] Compiling Cython source /workspace/pandas/pandas/_libs/tslibs/period.pyx [31/152] Compiling C object pandas/_libs/tslibs/ccalendar.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_ccalendar.pyx.c.o [32/152] Linking target pandas/_libs/tslibs/ccalendar.cpython-310-x86_64-linux-gnu.so [33/152] Compiling Cython source /workspace/pandas/pandas/_libs/hashing.pyx [34/152] Compiling C object pandas/_libs/arrays.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_arrays.pyx.c.o [35/152] Linking target pandas/_libs/arrays.cpython-310-x86_64-linux-gnu.so [36/152] Compiling C object pandas/_libs/tslibs/np_datetime.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_np_datetime.pyx.c.o [37/152] Linking target pandas/_libs/tslibs/np_datetime.cpython-310-x86_64-linux-gnu.so [38/152] Compiling C object pandas/_libs/tslibs/dtypes.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_dtypes.pyx.c.o [39/152] Linking target pandas/_libs/tslibs/dtypes.cpython-310-x86_64-linux-gnu.so [40/152] Compiling C object pandas/_libs/tslibs/vectorized.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_vectorized.pyx.c.o [41/152] Linking target pandas/_libs/tslibs/vectorized.cpython-310-x86_64-linux-gnu.so [42/152] Compiling C object pandas/_libs/tslibs/nattype.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_nattype.pyx.c.o [43/152] Linking target pandas/_libs/tslibs/nattype.cpython-310-x86_64-linux-gnu.so [44/152] Compiling Cython source /workspace/pandas/pandas/_libs/indexing.pyx [45/152] Compiling C object pandas/_libs/tslibs/timezones.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_timezones.pyx.c.o [46/152] Linking target pandas/_libs/tslibs/timezones.cpython-310-x86_64-linux-gnu.so [47/152] Compiling Cython source /workspace/pandas/pandas/_libs/algos.pyx [48/152] Compiling C object pandas/_libs/indexing.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_indexing.pyx.c.o [49/152] Linking target pandas/_libs/indexing.cpython-310-x86_64-linux-gnu.so [50/152] Compiling C object pandas/_libs/tslibs/conversion.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_conversion.pyx.c.o [51/152] Linking target pandas/_libs/tslibs/conversion.cpython-310-x86_64-linux-gnu.so [52/152] Compiling Cython source /workspace/pandas/pandas/_libs/index.pyx [53/152] Compiling Cython source /workspace/pandas/pandas/_libs/internals.pyx [54/152] Compiling C object pandas/_libs/hashing.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_hashing.pyx.c.o [55/152] Linking target pandas/_libs/hashing.cpython-310-x86_64-linux-gnu.so [56/152] Compiling C object pandas/_libs/tslibs/fields.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_fields.pyx.c.o [57/152] Linking target pandas/_libs/tslibs/fields.cpython-310-x86_64-linux-gnu.so [58/152] Compiling C object pandas/_libs/lib.cpython-310-x86_64-linux-gnu.so.p/src_parser_tokenizer.c.o [59/152] Compiling C object pandas/_libs/tslibs/tzconversion.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_tzconversion.pyx.c.o [60/152] Linking target pandas/_libs/tslibs/tzconversion.cpython-310-x86_64-linux-gnu.so [61/152] Compiling C object pandas/_libs/pandas_datetime.cpython-310-x86_64-linux-gnu.so.p/src_vendored_numpy_datetime_np_datetime.c.o [62/152] Compiling C object pandas/_libs/pandas_datetime.cpython-310-x86_64-linux-gnu.so.p/src_datetime_date_conversions.c.o [63/152] Compiling C object pandas/_libs/pandas_datetime.cpython-310-x86_64-linux-gnu.so.p/src_datetime_pd_datetime.c.o [64/152] Compiling C object pandas/_libs/pandas_datetime.cpython-310-x86_64-linux-gnu.so.p/src_vendored_numpy_datetime_np_datetime_strings.c.o [65/152] Compiling Cython source /workspace/pandas/pandas/_libs/groupby.pyx [66/152] Compiling C object pandas/_libs/pandas_parser.cpython-310-x86_64-linux-gnu.so.p/src_parser_io.c.o [67/152] Linking target pandas/_libs/pandas_datetime.cpython-310-x86_64-linux-gnu.so [68/152] Compiling C object pandas/_libs/pandas_parser.cpython-310-x86_64-linux-gnu.so.p/src_parser_pd_parser.c.o [69/152] Compiling C object 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pandas/_libs/json.cpython-310-x86_64-linux-gnu.so.p/src_vendored_ujson_lib_ultrajsondec.c.o [79/152] Linking target pandas/_libs/json.cpython-310-x86_64-linux-gnu.so [80/152] Compiling Cython source /workspace/pandas/pandas/_libs/interval.pyx [81/152] Compiling Cython source /workspace/pandas/pandas/_libs/lib.pyx [82/152] Compiling C object pandas/_libs/tslibs/strptime.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_strptime.pyx.c.o [83/152] Linking target pandas/_libs/tslibs/strptime.cpython-310-x86_64-linux-gnu.so [84/152] Compiling Cython source /workspace/pandas/pandas/_libs/parsers.pyx [85/152] Compiling Cython source /workspace/pandas/pandas/_libs/hashtable.pyx [86/152] Compiling Cython source /workspace/pandas/pandas/_libs/ops_dispatch.pyx [87/152] Compiling C object pandas/_libs/tslibs/parsing.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_parsing.pyx.c.o [88/152] Linking target 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pandas/_libs/testing.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_testing.pyx.c.o [119/152] Linking target pandas/_libs/testing.cpython-310-x86_64-linux-gnu.so [120/152] Compiling Cython source /workspace/pandas/pandas/_libs/window/aggregations.pyx [121/152] Compiling C object pandas/_libs/reshape.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_reshape.pyx.c.o [122/152] Linking target pandas/_libs/reshape.cpython-310-x86_64-linux-gnu.so [123/152] Compiling C object pandas/_libs/sas.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_sas.pyx.c.o [124/152] Linking target pandas/_libs/sas.cpython-310-x86_64-linux-gnu.so [125/152] Compiling C object pandas/_libs/window/indexers.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_window_indexers.pyx.c.o [126/152] Linking target pandas/_libs/window/indexers.cpython-310-x86_64-linux-gnu.so [127/152] Compiling C object 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pandas/_libs/join.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_join.pyx.c.o [146/152] Linking target pandas/_libs/join.cpython-310-x86_64-linux-gnu.so [147/152] Compiling C object pandas/_libs/algos.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_algos.pyx.c.o [148/152] Linking target pandas/_libs/algos.cpython-310-x86_64-linux-gnu.so [149/152] Compiling C object pandas/_libs/groupby.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_groupby.pyx.c.o [150/152] Linking target pandas/_libs/groupby.cpython-310-x86_64-linux-gnu.so [151/152] Compiling C object pandas/_libs/hashtable.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_hashtable.pyx.c.o [152/152] Linking target pandas/_libs/hashtable.cpython-310-x86_64-linux-gnu.so Preparing editable metadata (pyproject.toml) ... done Requirement already satisfied: numpy>=1.23.5 in /usr/local/lib/python3.10/site-packages (from pandas==0+untagged.1.gd5bbd97) (1.26.4) Requirement already satisfied: python-dateutil>=2.8.2 in /usr/local/lib/python3.10/site-packages (from pandas==0+untagged.1.gd5bbd97) (2.9.0.post0) Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/site-packages (from pandas==0+untagged.1.gd5bbd97) (2024.1) Requirement already satisfied: tzdata>=2022.7 in /usr/local/lib/python3.10/site-packages (from pandas==0+untagged.1.gd5bbd97) (2024.1) Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas==0+untagged.1.gd5bbd97) (1.16.0) Building wheels for collected packages: pandas Running command Building editable for pandas (pyproject.toml) Building editable for pandas (pyproject.toml) ... done Created wheel for pandas: filename=pandas-0+untagged.1.gd5bbd97-cp310-cp310-linux_x86_64.whl size=33543 sha256=79eb7f15ae85d6c0e578a26bf5b074cb095a89e3875b24dfebe9d646c9483d49 Stored in directory: /tmp/pip-ephem-wheel-cache-8vso3s_8/wheels/39/77/57/1c321003879eca324f847754963bcb179286b0b84b53b1dde9 Successfully built pandas Installing collected packages: pandas ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. fastparquet 2024.5.0 requires pandas>=1.5.0, but you have pandas 0+untagged.1.gd5bbd97 which is incompatible. pyreadstat 1.2.7 requires pandas>=1.2.0, but you have pandas 0+untagged.1.gd5bbd97 which is incompatible. seaborn 0.13.2 requires pandas>=1.2, but you have pandas 0+untagged.1.gd5bbd97 which is incompatible. xarray 2024.7.0 requires pandas>=2.0, but you have pandas 0+untagged.1.gd5bbd97 which is incompatible. Successfully installed pandas-0+untagged.1.gd5bbd97 pre-commit installed at .git/hooks/pre-commit Using pip 24.2 from /usr/local/lib/python3.10/site-packages/pip (python 3.10) Defaulting to user installation because normal site-packages is not writeable Obtaining file:///workspace/pandas Running command Checking if build backend supports build_editable Checking if build backend supports build_editable ... done Running command Preparing editable metadata (pyproject.toml) + meson setup --reconfigure /workspace/pandas /workspace/pandas/build/cp310 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --vsenv --native-file=/workspace/pandas/build/cp310/meson-python-native-file.ini Cleaning... 0 files. The Meson build system Version: 1.2.1 Source dir: /workspace/pandas Build dir: /workspace/pandas/build/cp310 Build type: native build Project name: pandas Project version: 2.2.0.dev0+2274.gd5bbd97345 C compiler for the host machine: cc (gcc 10.2.1 "cc (Debian 10.2.1-6) 10.2.1 20210110") C linker for the host machine: cc ld.bfd 2.35.2 C++ compiler for the host machine: c++ (gcc 10.2.1 "c++ (Debian 10.2.1-6) 10.2.1 20210110") C++ linker for the host machine: c++ ld.bfd 2.35.2 Cython compiler for the host machine: cython (cython 3.0.11) Host machine cpu family: x86_64 Host machine cpu: x86_64 Program python found: YES (/usr/local/bin/python) Build targets in project: 54 pandas 2.2.0.dev0+2274.gd5bbd97345 User defined options Native files: /workspace/pandas/build/cp310/meson-python-native-file.ini buildtype : release vsenv : True b_ndebug : if-release b_vscrt : md Found ninja-1.11.1.git.kitware.jobserver-1 at /usr/local/bin/ninja Visual Studio environment is needed to run Ninja. It is recommended to use Meson wrapper: /usr/local/bin/meson compile -C . + /usr/local/bin/ninja [1/1] Generating write_version_file with a custom command Preparing editable metadata (pyproject.toml) ... done Requirement already satisfied: numpy>=1.23.5 in /usr/local/lib/python3.10/site-packages (from pandas==2.2.0.dev0+2274.gd5bbd97345) (1.26.4) Requirement already satisfied: python-dateutil>=2.8.2 in /usr/local/lib/python3.10/site-packages (from pandas==2.2.0.dev0+2274.gd5bbd97345) (2.9.0.post0) Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/site-packages (from pandas==2.2.0.dev0+2274.gd5bbd97345) (2024.1) Requirement already satisfied: tzdata>=2022.7 in /usr/local/lib/python3.10/site-packages (from pandas==2.2.0.dev0+2274.gd5bbd97345) (2024.1) Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas==2.2.0.dev0+2274.gd5bbd97345) (1.16.0) Building wheels for collected packages: pandas Running command Building editable for pandas (pyproject.toml) Building editable for pandas (pyproject.toml) ... done Created wheel for pandas: filename=pandas-2.2.0.dev0+2274.gd5bbd97345-cp310-cp310-linux_x86_64.whl size=33657 sha256=daf4cb77e643e000d8a22b50e7d228127e739772ec5c687040f2a9fee9b0b81b Stored in directory: /tmp/pip-ephem-wheel-cache-va_pbd3a/wheels/39/77/57/1c321003879eca324f847754963bcb179286b0b84b53b1dde9 Successfully built pandas Installing collected packages: pandas Attempting uninstall: pandas Found existing installation: pandas 0+untagged.1.gd5bbd97 Uninstalling pandas-0+untagged.1.gd5bbd97: Removing file or directory /home/gitpod/.local/lib/python3.10/site-packages/ Successfully uninstalled pandas-0+untagged.1.gd5bbd97 Successfully installed pandas-2.2.0.dev0+2274.gd5bbd97345 ✨ Pre-build complete! You can close this terminal ✨ ```

Reading around, seems like it could be a shallow clone/missing tags problem, but git fetch --unshallow happily reports that the repo is indeed not shallow, and git tag reports a lot of tags:

$ git fetch --unshallow 
fatal: --unshallow on a complete repository does not make sense

$ git tag | wc -l
157

Suggested fix for documentation

By digging a bit, I feel that the Gitpod files has been touched after the documentation has been written, and the screenshots/information are not really up-to-date. Also, after https://github.com/pandas-dev/pandas/pull/54046 I think that most of the gitpod directory is now unused and might be deleted(?)

I'm willing to help with the housekeeping if you have any advices... And if you have ideas on how to make pytest run, I'm interested!

serl commented 1 month ago

Related to #55214 (but not really a duplicate as I've different problems here)

serl commented 3 weeks ago

Still investigating on this thing. Something that seems to help is to delete the file build/cp310/_version_meson.py.

That's because if that file exist it is taken as-is: https://github.com/pandas-dev/pandas/blob/3ba3cd00e143e283019649d839c9e2eaac287353/generate_version.py#L17-L24

Given how unusable is anything with version starting with 0+ (I mean we cannot even run a single test), what about discarding the cache and always call versioneer if it's the case? We could probably throw some more explicit error, it should be easy to have something clearer than "pyarrow requires pandas 1.0.0 or above" 😁

(That said, I'd really like to understand how 0+blabla ends there sometimes in gitpod)