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Posted to issues@iceberg.apache.org by GitBox <gi...@apache.org> on 2022/12/09 17:58:48 UTC

[GitHub] [iceberg] RussellSpitzer opened a new issue, #6397: Python Instructions currently do not work for testing

RussellSpitzer opened a new issue, #6397:
URL: https://github.com/apache/iceberg/issues/6397

   ### Apache Iceberg version
   
   main (development)
   
   ### Query engine
   
   Other
   
   ### Please describe the bug 🐞
   
   The instructions listed in the README.md under testing
   
   ```bash
   poetry install -E pyarrow
   poetry run pytest
   ```
   
   Result in an error
   ```
   ImportError while loading conftest '/Users/russellspitzer/Temp/pypypy/iceberg/python/tests/conftest.py'.
   tests/conftest.py:40: in <module>
       import aiobotocore.awsrequest
   E   ModuleNotFoundError: No module named 'aiobotocore'
   ```
   
   This is because pytest triggers all test suites and requires all optional dependencies
   ```
    poetry install --all-extras
    ```
    Fixes this issue but still fails some tests (tests/io/test_fsspec.py) because the S3 Mock doesn't seem to be setup properly
    
    ```
    FAILED tests/io/test_fsspec.py::test_fsspec_write_and_read_file - botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL: "http://localhost:9000/warehouse/18112126-9c9a-40e3-a08a-0fb199dd4f77"
   FAILED tests/io/test_fsspec.py::test_fsspec_getting_length_of_file - botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL: "http://localhost:9000/warehouse/566507b0-e364-464f-9779-17a63329953a"
   FAILED tests/io/test_fsspec.py::test_fsspec_file_tell - botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL: "http://localhost:9000/warehouse/fdc0fd10-132b-4d00-8d04-332dfe20f516"
   FAILED tests/io/test_fsspec.py::test_fsspec_read_specified_bytes_for_file - botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL: "http://localhost:9000/warehouse/f3fc2540-1f7e-43ac-b27a-7a27a3a12216"
   FAILED tests/io/test_fsspec.py::test_fsspec_raise_on_opening_file_not_found - botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL: "http://localhost:9000/warehouse/2ce8b101-bbbc-4242-8cde-6e4e3e83516a"
   FAILED tests/io/test_fsspec.py::test_checking_if_a_file_exists - botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL: "http://localhost:9000/warehouse/does-not-exist.txt"
   FAILED tests/io/test_fsspec.py::test_closing_a_file - botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL: "http://localhost:9000/warehouse/91077182-d448-4f1f-b310-2a60d6799617"
   FAILED tests/io/test_fsspec.py::test_writing_avro_file - botocore.exceptions.EndpointConnectionError: Could not connect to the endpoint URL: "http://localhost:9000/warehouse/c7aeded1-9bc6-4429-923a-d164be4f35e8"
    ```


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[GitHub] [iceberg] Fokko commented on issue #6397: Python Instructions currently do not work for testing

Posted by GitBox <gi...@apache.org>.
Fokko commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1345256690

   @RussellSpitzer Thanks for opening this issue. There are two things going on:
   
   ```
   ImportError while loading conftest '/Users/russellspitzer/Temp/pypypy/iceberg/python/tests/conftest.py'.
   tests/conftest.py:40: in <module>
       import aiobotocore.awsrequest
   E   ModuleNotFoundError: No module named 'aiobotocore'
   ```
   
   Was a bug in 0.2.0 found by @danielcweeks. PyArrow was imported on the file level, while it should have been inlined. So if you didn't have PyArrow installed, this would cause an issue. We did publish the RC because you need PyArrow (currently), if you want to read data. This has been fixed in: https://github.com/apache/iceberg/pull/6362
   
   Running `poetry run pytest` will run all the tests, without looking at the pytest markers. The tests marked with s3 require a minio container to be running. This is part of the Makefile `make run test-s3`: https://github.com/apache/iceberg/blob/master/python/Makefile#L34-L39
   
   @rubenvdg The failing tests are interesting. Do you have more information? Which Python version are you using?
   
   This week I did an overhaul of the documentation, and moved everything to the docs `python/mkdocs`, that is published to https://py.iceberg.apache.org/
   
   > Also, for me it's a bit unclear how the following sections connect:
   > https://github.com/apache/iceberg/blob/master/python/README.md#getting-started
   > https://github.com/apache/iceberg/blob/master/python/README.md#development
   > https://github.com/apache/iceberg/blob/master/python/CONTRIBUTING.md
   
   It seems that I didn't do a very good job on cleaning up the old files. I wanted to remove the `CONTRIBUTING.md`, since it has been ported to the docs: https://py.iceberg.apache.org/contributing/. I think the docs are a good place to centralize everything you need to install pyiceberg, setup your development environment, and everything around releases. I noticed that a lot of people don't find their way to the `CONTRIBUTING.md` and then it doesn't really add value :)
   
   I would suggest:
   
   - Removing `CONTRIBUTING.md`
   - Clean up the `README.md` and point to the docs page
   - Add a section on the pytest markers.
   
   Hope this helps!


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[GitHub] [iceberg] rubenvdg commented on issue #6397: Python Instructions currently do not work for testing

Posted by GitBox <gi...@apache.org>.
rubenvdg commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1346538268

   [@Fokko It seems that it only works on Python >= 3.9.8. There's some stuff on Protocols in the release notes](https://docs.python.org/release/3.9.8/whatsnew/changelog.html) that might ring a bell with you?
   
   To reproduce. This works:
   ```
   FROM python:3.9.8
   WORKDIR /app
   COPY . /app
   RUN pip install --upgrade pip virtualenv
   RUN pip install poetry
   RUN make install
   RUN make test
   ```
   
   But this throws `TypeError: AvroStruct() takes no arguments`.
   
   ```
   FROM python:3.9.8
   WORKDIR /app
   COPY . /app
   RUN pip install --upgrade pip virtualenv
   RUN pip install poetry
   RUN make install
   RUN make test
   ```


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[GitHub] [iceberg] Fokko commented on issue #6397: Python Instructions currently do not work for testing

Posted by GitBox <gi...@apache.org>.
Fokko commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1352734967

   @rubenvdg What do you think of removing the dataclass from the `AvroStruct`. We should be able to create a Struct without including it in the PyIceberg class hierarchy. The `AvroStruct` is currently frozen as well, but that doesn't make much sense since we have a `set` method as well 🤔 😄 


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[GitHub] [iceberg] rubenvdg commented on issue #6397: Python Instructions currently do not work for testing

Posted by GitBox <gi...@apache.org>.
rubenvdg commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1346543174

   Both Docker containers fail btw with:
   
   ```
   #11 21.80 FAILED tests/io/test_pyarrow.py::test_raise_on_opening_a_local_file_no_permission
   #11 21.80 FAILED tests/io/test_pyarrow.py::test_raise_on_checking_if_local_file_exists_no_permission
   #11 21.80 FAILED tests/io/test_pyarrow.py::test_raise_on_creating_a_local_file_no_permission
   #11 21.80 FAILED tests/io/test_pyarrow.py::test_raise_on_delete_file_with_no_permission
   ```
   
   with a.o. 
   
   ```
   FileNotFoundError: [Errno 2] Failed to open local file '/tmp/tmpfj40zq4h/foo.txt'. Detail: [errno 2] No such file or directory
   ```
   
   Is this expected?


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[GitHub] [iceberg] rubenvdg commented on issue #6397: Python Instructions currently do not work for testing

Posted by GitBox <gi...@apache.org>.
rubenvdg commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1345519019

   And so what happens is this:
   
   ```
   (pyiceberg-py3.9) ➜  python git:(master) ✗ python
   Python 3.9.7 (default, Nov 16 2021, 15:21:45) 
   [Clang 13.0.0 (clang-1300.0.29.3)] on darwin
   Type "help", "copyright", "credits" or "license" for more information.
   >>> from pyiceberg.avro.reader import AvroStruct
   >>> AvroStruct([None])
   Traceback (most recent call last):
     File "<stdin>", line 1, in <module>
   TypeError: AvroStruct() takes no arguments
   ```


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[GitHub] [iceberg] github-actions[bot] commented on issue #6397: Python Instructions currently do not work for testing

Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1592149901

   This issue has been automatically marked as stale because it has been open for 180 days with no activity. It will be closed in next 14 days if no further activity occurs. To permanently prevent this issue from being considered stale, add the label 'not-stale', but commenting on the issue is preferred when possible.


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[GitHub] [iceberg] rubenvdg commented on issue #6397: Python Instructions currently do not work for testing

Posted by GitBox <gi...@apache.org>.
rubenvdg commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1355516952

   Yes agreed! It's already part of https://github.com/apache/iceberg/pull/6438, right?


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[GitHub] [iceberg] github-actions[bot] commented on issue #6397: Python Instructions currently do not work for testing

Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1612261931

   This issue has been closed because it has not received any activity in the last 14 days since being marked as 'stale'


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[GitHub] [iceberg] rubenvdg commented on issue #6397: Python Instructions currently do not work for testing

Posted by GitBox <gi...@apache.org>.
rubenvdg commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1345518706

   Maybe it's just my lack of Poetry experience, but this is what I did:
   
   ```
   curl -sSL https://install.python-poetry.org | python3 -  # install poetry
   poetry shell  # shell now shows (pyiceberg-py3.9)
   make install
   make test
   ```
   
   Some info:
   
   ```
   which python
   >>> /Users/rvdgeer/Library/Caches/pypoetry/virtualenvs/pyiceberg-QdNRdoVV-py3.9/bin/python
   
   poetry show
   aiobotocore        2.4.1     Async client for aws services using botocore and aiohttp
   aiohttp            3.8.3     Async http client/server framework (asyncio)
   aioitertools       0.11.0    itertools and builtins for AsyncIO and mixed iterables
   aiosignal          1.3.1     aiosignal: a list of registered asynchronous callbacks
   async-timeout      4.0.2     Timeout context manager for asyncio programs
   attrs              22.1.0    Classes Without Boilerplate
   boto3              1.24.59   The AWS SDK for Python
   botocore           1.27.59   Low-level, data-driven core of boto 3.
   build              0.9.0     A simple, correct PEP 517 build frontend
   certifi            2022.12.7 Python package for providing Mozilla's CA Bundle.
   cffi               1.15.1    Foreign Function Interface for Python calling C code.
   cfgv               3.3.1     Validate configuration and produce human readable error messages.
   charset-normalizer 2.1.1     The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet.
   click              8.1.3     Composable command line interface toolkit
   commonmark         0.9.1     Python parser for the CommonMark Markdown spec
   coverage           6.5.0     Code coverage measurement for Python
   cryptography       38.0.4    cryptography is a package which provides cryptographic recipes and primitives to Python developers.
   distlib            0.3.6     Distribution utilities
   docutils           0.19      Docutils -- Python Documentation Utilities
   duckdb             0.6.0     DuckDB embedded database
   exceptiongroup     1.0.4     Backport of PEP 654 (exception groups)
   fastavro           1.7.0     Fast read/write of AVRO files
   filelock           3.8.0     A platform independent file lock.
   frozenlist         1.3.3     A list-like structure which implements collections.abc.MutableSequence
   fsspec             2022.10.0 File-system specification
   identify           2.5.9     File identification library for Python
   idna               3.4       Internationalized Domain Names in Applications (IDNA)
   importlib-metadata 5.1.0     Read metadata from Python packages
   iniconfig          1.1.1     iniconfig: brain-dead simple config-ini parsing
   jinja2             3.1.2     A very fast and expressive template engine.
   jmespath           1.0.1     JSON Matching Expressions
   markupsafe         2.1.1     Safely add untrusted strings to HTML/XML markup.
   mmhash3            3.0.1     Python wrapper for MurmurHash (MurmurHash3), a set of fast and robust hash functions.
   moto               4.0.11    A library that allows your python tests to easily mock out the boto library
   multidict          6.0.2     multidict implementation
   nodeenv            1.7.0     Node.js virtual environment builder
   numpy              1.23.5    NumPy is the fundamental package for array computing with Python.
   packaging          21.3      Core utilities for Python packages
   pep517             0.13.0    Wrappers to build Python packages using PEP 517 hooks
   platformdirs       2.5.4     A small Python package for determining appropriate platform-specific dirs, e.g. a "user data dir".
   pluggy             1.0.0     plugin and hook calling mechanisms for python
   pre-commit         2.20.0    A framework for managing and maintaining multi-language pre-commit hooks.
   pyarrow            10.0.1    Python library for Apache Arrow
   pycparser          2.21      C parser in Python
   pydantic           1.10.2    Data validation and settings management using python type hints
   pygments           2.13.0    Pygments is a syntax highlighting package written in Python.
   pyparsing          3.0.9     pyparsing module - Classes and methods to define and execute parsing grammars
   pytest             7.2.0     pytest: simple powerful testing with Python
   pytest-checkdocs   2.9.0     check the README when running tests
   python-dateutil    2.8.2     Extensions to the standard Python datetime module
   python-snappy      0.6.1     Python library for the snappy compression library from Google
   pytz               2022.6    World timezone definitions, modern and historical
   pyyaml             6.0       YAML parser and emitter for Python
   requests           2.28.1    Python HTTP for Humans.
   requests-mock      1.10.0    Mock out responses from the requests package
   responses          0.22.0    A utility library for mocking out the `requests` Python library.
   rich               12.6.0    Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal
   s3fs               2022.10.0 Convenient Filesystem interface over S3
   s3transfer         0.6.0     An Amazon S3 Transfer Manager
   setuptools         65.6.3    Easily download, build, install, upgrade, and uninstall Python packages
   six                1.16.0    Python 2 and 3 compatibility utilities
   thrift             0.16.0    Python bindings for the Apache Thrift RPC system
   toml               0.10.2    Python Library for Tom's Obvious, Minimal Language
   tomli              2.0.1     A lil' TOML parser
   types-toml         0.10.8.1  Typing stubs for toml
   typing-extensions  4.4.0     Backported and Experimental Type Hints for Python 3.7+
   urllib3            1.26.13   HTTP library with thread-safe connection pooling, file post, and more.
   virtualenv         20.17.0   Virtual Python Environment builder
   werkzeug           2.2.2     The comprehensive WSGI web application library.
   wrapt              1.14.1    Module for decorators, wrappers and monkey patching.
   xmltodict          0.13.0    Makes working with XML feel like you are working with JSON
   yarl               1.8.1     Yet another URL library
   zipp               3.11.0    Backport of pathlib-compatible object wrapper for zip files
   zstandard          0.19.0    Zstandard bindings for Python
   
   pip freeze
   aiobotocore==2.4.1
   aiohttp==3.8.3
   aioitertools==0.11.0
   aiosignal==1.3.1
   async-timeout==4.0.2
   attrs==22.1.0
   boto3==1.24.59
   botocore==1.27.59
   build==0.9.0
   CacheControl==0.12.11
   certifi==2022.12.7
   cffi==1.15.1
   cfgv==3.3.1
   charset-normalizer==2.1.1
   cleo==2.0.1
   click==8.1.3
   commonmark==0.9.1
   coverage==6.5.0
   crashtest==0.4.1
   cryptography==38.0.4
   distlib==0.3.6
   docutils==0.19
   dulwich==0.20.50
   exceptiongroup==1.0.4
   fastavro==1.7.0
   filelock==3.8.0
   frozenlist==1.3.3
   fsspec==2022.10.0
   html5lib==1.1
   identify==2.5.9
   idna==3.4
   importlib-metadata==5.1.0
   iniconfig==1.1.1
   jaraco.classes==3.2.3
   Jinja2==3.1.2
   jmespath==1.0.1
   jsonschema==4.17.3
   keyring==23.11.0
   lockfile==0.12.2
   MarkupSafe==2.1.1
   mmhash3==3.0.1
   more-itertools==9.0.0
   moto==4.0.11
   msgpack==1.0.4
   multidict==6.0.2
   nodeenv==1.7.0
   numpy==1.23.5
   packaging==21.3
   pep517==0.13.0
   pexpect==4.8.0
   pkginfo==1.9.2
   platformdirs==2.5.4
   pluggy==1.0.0
   poetry==1.3.0
   poetry-core==1.4.0
   poetry-plugin-export==1.2.0
   pre-commit==2.20.0
   ptyprocess==0.7.0
   pyarrow==10.0.1
   pycparser==2.21
   pydantic==1.10.2
   Pygments==2.13.0
   -e git+ssh://git@github.com/rubenvdg/iceberg.git@3b6c74d5a434ccab2116bf1984be9012198ff4bf#egg=pyiceberg&subdirectory=python
   pyparsing==3.0.9
   pyrsistent==0.19.2
   pytest==7.2.0
   pytest-checkdocs==2.9.0
   python-dateutil==2.8.2
   pytz==2022.6
   PyYAML==6.0
   rapidfuzz==2.13.5
   requests==2.28.1
   requests-mock==1.10.0
   requests-toolbelt==0.10.1
   responses==0.22.0
   rich==12.6.0
   s3fs==2022.10.0
   s3transfer==0.6.0
   shellingham==1.5.0
   six==1.16.0
   thrift==0.16.0
   toml==0.10.2
   tomli==2.0.1
   tomlkit==0.11.6
   trove-classifiers==2022.12.1
   types-toml==0.10.8.1
   typing_extensions==4.4.0
   urllib3==1.26.13
   virtualenv==20.17.0
   webencodings==0.5.1
   Werkzeug==2.2.2
   wrapt==1.14.1
   xattr==0.10.1
   xmltodict==0.13.0
   yarl==1.8.1
   zipp==3.11.0
   zstandard==0.19.0
   ```


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[GitHub] [iceberg] Fokko commented on issue #6397: Python Instructions currently do not work for testing

Posted by GitBox <gi...@apache.org>.
Fokko commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1346447504

   @rubenvdg `poetry shell` is not required, since the [Makefile](https://github.com/apache/iceberg/blob/master/python/Makefile#L28-L32) already executes the tests `poetry run`. I'm still puzzled by the error because the `dataclass` should generate an init for us.


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[GitHub] [iceberg] Fokko commented on issue #6397: Python Instructions currently do not work for testing

Posted by GitBox <gi...@apache.org>.
Fokko commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1346548075

   > It seems that it only works on Python >= 3.9.8. There's some bugfix on Protocols in the [release notes](https://docs.python.org/release/3.9.8/whatsnew/changelog.html) that might ring a bell with you?
   
   Great catch! I wasn't aware of this! 
   
   The failed tests on Docker are because there is a single user in Docker. In the test, we create a file and then change the permissions in such a way that we don't have read permissions. However, if you run it in Docker, you're root, so the test doesn't work. We can either introduce another user in Docker, or mock the call to the filesystem. 


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[GitHub] [iceberg] Fokko commented on issue #6397: Python Instructions currently do not work for testing

Posted by GitBox <gi...@apache.org>.
Fokko commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1355517950

   @rubenvdg Yes, I was doing some refactoring yesterday, and also included it in there 👍🏻  Feel free to review the PR :)


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[GitHub] [iceberg] rubenvdg commented on issue #6397: Python Instructions currently do not work for testing

Posted by GitBox <gi...@apache.org>.
rubenvdg commented on issue #6397:
URL: https://github.com/apache/iceberg/issues/6397#issuecomment-1345240557

   I was trying to set up the development environment this week and was running into similar issues. When running `make tests` I get:
   
   ```
   FAILED tests/avro/test_reader.py::test_read_header - TypeError: AvroStruct() takes no arguments
   FAILED tests/avro/test_reader.py::test_read_manifest_entry_file - TypeError: AvroStruct() takes no arguments
   FAILED tests/avro/test_reader.py::test_read_manifest_file_file - TypeError: AvroStruct() takes no arguments
   FAILED tests/avro/test_reader.py::test_null_list_convert_pos_to_dict - TypeError: AvroStruct() takes no arguments
   FAILED tests/avro/test_reader.py::test_null_dict_convert_pos_to_dict - TypeError: AvroStruct() takes no arguments
   FAILED tests/avro/test_reader.py::test_null_struct_convert_pos_to_dict - TypeError: AvroStruct() takes no arguments
   FAILED tests/table/test_snapshots.py::test_fetch_manifest_list - TypeError: AvroStruct() takes no arguments
   FAILED tests/utils/test_manifest.py::test_read_manifest_entry - TypeError: AvroStruct() takes no arguments
   FAILED tests/utils/test_manifest.py::test_read_manifest_list - TypeError: AvroStruct() takes no arguments
   FAILED tests/utils/test_manifest.py::test_read_manifest - TypeError: AvroStruct() takes no arguments
   ```
   
   Also, for me it's a bit unclear how the following sections connect:
   
   - https://github.com/apache/iceberg/blob/master/python/README.md#getting-started
   - https://github.com/apache/iceberg/blob/master/python/README.md#development
   - https://github.com/apache/iceberg/blob/master/python/CONTRIBUTING.md
   
   it would maybe be nice if there's a single source of truth for how to set up the dev environment.


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[GitHub] [iceberg] github-actions[bot] closed issue #6397: Python Instructions currently do not work for testing

Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] closed issue #6397: Python Instructions currently do not work for testing
URL: https://github.com/apache/iceberg/issues/6397


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