sbi cannot be installed in python version 3.7

[michaeldeistler]

Installing sbi (from source) fails in python version 3.7. It works in version 3.6, 3.8, and 3.9 (and probably also 3.10 and higher, but I did not check).

This also leads to failing tests.

[michaeldeistler]

Getting requirements to build wheel ... error
  ERROR: Command errored out with exit status 1:
   command: /Users/deismic/anaconda3/envs/sbi_test_36/bin/python /Users/deismic/anaconda3/envs/sbi_test_36/lib/python3.6/site-packages/pip/_vendor/pep517/in_process/_in_process.py get_requires_for_build_wheel /var/folders/j9/w7ftvg_16t1f9bgp1cy4bt1r0000gn/T/tmp9rb7qkio
       cwd: /private/var/folders/j9/w7ftvg_16t1f9bgp1cy4bt1r0000gn/T/pip-install-tyzx6lgk/netcdf4_0ce9b5aaec844fccab9aa9f82e9c6072
  Complete output (39 lines):
  reading from setup.cfg...
  
      HDF5_DIR environment variable not set, checking some standard locations ..
  checking /Users/deismic/anaconda3/envs/sbi_test_36/include ...
  hdf5 headers not found in /Users/deismic/anaconda3/envs/sbi_test_36/include
  checking /Users/deismic/anaconda3/envs/sbi_test_36/Library/include ...
  hdf5 headers not found in /Users/deismic/anaconda3/envs/sbi_test_36/Library/include
  checking /Users/deismic/include ...
  hdf5 headers not found in /Users/deismic/include
  checking /usr/local/include ...
  hdf5 headers not found in /usr/local/include
  checking /sw/include ...
  hdf5 headers not found in /sw/include
  checking /opt/include ...
  hdf5 headers not found in /opt/include
  checking /opt/local/include ...
  hdf5 headers not found in /opt/local/include
  checking /opt/homebrew/include ...
  hdf5 headers not found in /opt/homebrew/include
  checking /usr/include ...
  hdf5 headers not found in /usr/include
  Traceback (most recent call last):
    File "/Users/deismic/anaconda3/envs/sbi_test_36/lib/python3.6/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 349, in <module>
      main()
    File "/Users/deismic/anaconda3/envs/sbi_test_36/lib/python3.6/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 331, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/Users/deismic/anaconda3/envs/sbi_test_36/lib/python3.6/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 117, in get_requires_for_build_wheel
      return hook(config_settings)
    File "/private/var/folders/j9/w7ftvg_16t1f9bgp1cy4bt1r0000gn/T/pip-build-env-ss2qqkey/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 163, in get_requires_for_build_wheel
      config_settings, requirements=['wheel'])
    File "/private/var/folders/j9/w7ftvg_16t1f9bgp1cy4bt1r0000gn/T/pip-build-env-ss2qqkey/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 143, in _get_build_requires
      self.run_setup()
    File "/private/var/folders/j9/w7ftvg_16t1f9bgp1cy4bt1r0000gn/T/pip-build-env-ss2qqkey/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 158, in run_setup
      exec(compile(code, __file__, 'exec'), locals())
    File "setup.py", line 449, in <module>
      _populate_hdf5_info(dirstosearch, inc_dirs, libs, lib_dirs)
    File "setup.py", line 390, in _populate_hdf5_info
      raise ValueError('did not find HDF5 headers')
  ValueError: did not find HDF5 headers
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/a6/f9/12f43c2e31d1c7aae0827820ae747fa4c7cc382b38dab11e8c11575d3af6/netCDF4-1.6.2.tar.gz#sha256=0382b02ff6a288419f6ffec85dec40f451f41b8755547154c575ddd9f0f4ae53 (from https://pypi.org/simple/netcdf4/) (requires-python:>=3.6). Command errored out with exit status 1: /Users/deismic/anaconda3/envs/sbi_test_36/bin/python /Users/deismic/anaconda3/envs/sbi_test_36/lib/python3.6/site-packages/pip/_vendor/pep517/in_process/_in_process.py get_requires_for_build_wheel /var/folders/j9/w7ftvg_16t1f9bgp1cy4bt1r0000gn/T/tmp9rb7qkio Check the logs for full command output.```

[bnicenboim]

Hi, I solved that problem by installing libnetcdf-dev in linux

[etouron1]

Hello, I had a similar error due with Python 3.7 when installing sbi.
I work on Ubuntu 22.04.3 LTS.
I tried to install sbi in a new conda environment following the section Installation from the README of the sbi github.
When doing pip install sbi in this environment, I get the following error :

(...)

Collecting netcdf4
  Using cached netCDF4-1.6.5.tar.gz (764 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [37 lines of output]
      reading from setup.cfg...
      
          HDF5_DIR environment variable not set, checking some standard locations ..
      checking /home/sbi/miniconda3/envs/try_env/include ...
      hdf5 headers not found in /home/sbi/miniconda3/envs/try_env/include
      checking /home/sbi/miniconda3/envs/try_env/Library/include ...
      hdf5 headers not found in /home/sbi/miniconda3/envs/try_env/Library/include
      checking /home/sbi/include ...
      hdf5 headers not found in /home/sbi/include
      checking /usr/local/include ...
      hdf5 headers not found in /usr/local/include
      checking /sw/include ...
      hdf5 headers not found in /sw/include
      checking /opt/include ...
      hdf5 headers not found in /opt/include
      checking /opt/local/include ...
      hdf5 headers not found in /opt/local/include
      checking /opt/homebrew/include ...
      hdf5 headers not found in /opt/homebrew/include
      checking /usr/include ...
      hdf5 headers not found in /usr/include
      Traceback (most recent call last):
        File "/home/sbi/miniconda3/envs/try_env/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
          main()
        File "/home/sbi/miniconda3/envs/try_env/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/home/sbi/miniconda3/envs/try_env/lib/python3.7/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
        File "/tmp/pip-build-env-o3frre5j/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=['wheel'])
        File "/tmp/pip-build-env-o3frre5j/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires
          self.run_setup()
        File "/tmp/pip-build-env-o3frre5j/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 338, in run_setup
          exec(code, locals())
        File "<string>", line 457, in <module>
        File "<string>", line 398, in _populate_hdf5_info
      ValueError: did not find HDF5 headers
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

To solve it, I install the package netcdf4 via the command conda install -c conda-forge netCDF4 and then re-do pip install sbi.
It works.

I don't know where the error comes from but trying to install sbi with a higher version of Python (>3.7) does not throw any error.

[michaeldeistler]

Related to #928

[janfb]

I can confirm @etouron1's fix: On Ubuntu 20.04.2 the following works:

conda create -n sbi_env python==3.7
conda activate sbi_env
conda install -c conda-forge netCDF4
pip install sbi

Installing sbi with python 3.6 or 3.8, 3.9, 3.10, 3.11 works fine.