nlm-ingestor installation is failing due to lxml, pandas, xxhash

[kcmuthyala]

Hi,
nlm-ingestor seems promising one but i couldn't able to move forward with the installation issue.
I got the "ERROR: Failed to build installable wheels for some pyproject.toml based projects (lxml, pandas, xxhash)" when i try to install using the command "pip install nlm-ingestor".

I thought it may be due to dependencies lower versions issue and tried installation using constraints.txt by specifying latest versions (lxml>=5.2.1, pandas>=2.2.2) with the command "pip install -c constraints.txt nlm-ingestor". This also failed saying "nlm-ingestor 0.1.5 depends on pandas==1.2.4"

Please advise on this issue. Thanks in Advance !!

[diganta037]

Getting the same issue. Actually I even tried to break it down step by step and even had it installed but now it asks for OPENAI_API_KEY as env variable while running the ingestion daemon. Seems like these packages are configured for python3.10 and not for the latest 3.12+

[KOG-Nisse]

Same issue, any updates?

I am running on windows 11

Reproduction:
conda create -n sherpa python=3.11
conda activate sherpa
java -jar <path_to_nlm_ingestor>/jars/tika-server-standard-nlm-modified-2.9.2_v1.jar
pip install nlm-ingestor

Error output:
...
building 'pandas._libs.algos' extension
creating build\temp.win-amd64-cpython-311
creating build\temp.win-amd64-cpython-311\Release
creating build\temp.win-amd64-cpython-311\Release\pandas
creating build\temp.win-amd64-cpython-311\Release\pandas_libs
cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -DNPY_NO_DEPRECATED_API=0 -I.\pandas_libs -Ipandas/_libs/src/klib -IC:\Users\username\AppData\Local\Temp\pip-build-env-qknhqgkg\overlay\Lib\site-packages\numpy_core\include -IC:\Users\username\miniconda3\envs\sherpa\include -IC:\Users\username\miniconda3\envs\sherpa\Include -I\targets\x64 /Tcpandas_libs/algos.c /Fobuild\temp.win-amd64-cpython-311\Release\pandas_libs/algos.obj
error: command 'cl.exe' failed: None
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pandas
Building wheel for xxhash (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [16 lines of output]
running bdist_wheel
creating build
creating build\lib.win-amd64-cpython-311
creating build\lib.win-amd64-cpython-311\xxhash
copying xxhash_init_.py -> build\lib.win-amd64-cpython-311\xxhash
running build_ext
building '_xxhash' extension
creating build\temp.win-amd64-cpython-311
creating build\temp.win-amd64-cpython-311\Release
creating build\temp.win-amd64-cpython-311\Release\deps
creating build\temp.win-amd64-cpython-311\Release\deps\xxhash
creating build\temp.win-amd64-cpython-311\Release\src
cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Ideps/xxhash -IC:\Users\username\miniconda3\envs\sherpa\include -IC:\Users\username\miniconda3\envs\sherpa\Include -I\targets\x64 /Tcdeps/xxhash/xxhash.c /Fobuild\temp.win-amd64-cpython-311\Release\deps/xxhash/xxhash.obj
error: command 'cl.exe' failed: None
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for xxhash
Running setup.py clean for xxhash
Failed to build lxml pandas xxhash
ERROR: Could not build wheels for lxml, pandas, xxhash, which is required to install pyproject.toml-based projects

[KOG-Nisse]

this fixed the issue for me:

conda create -n sherpa39 python=3.9
conda activate sherpa39

pip install nlm-ingestor
pip uninstall python-magic
pip install python-magic-bin==0.4.14

[kcmuthyala]

Thank you KOG-Nisse. Its worked for me also with your suggestion.
Now i am getting SSLCertVerificationError when i ran the nlm_ingestor.ingestion_daemon. I've opened new issue for this.
#81
Please respond if you encounter this ?

[kcmuthyala]

Getting the same issue. Actually I even tried to break it down step by step and even had it installed but now it asks for OPENAI_API_KEY as env variable while running the ingestion daemon. Seems like these packages are configured for python3.10 and not for the latest 3.12+

Thanks for your input. Its configured for lower python version. Now i am getting SSLCertVerificationError when i ran the nlm_ingestor.ingestion_daemon. I've opened new issue for this.
#81
Please respond if you encounter this ?