pip install fails (error: implicit declaration of function 'H5close' is invalid in C99)

[nlaws-camus]

I am on a mac, os 12.2.1, M1 Pro and both pip3 install dsspy and cloning with pip install -e PyDSS give the same error (I tried Python 3.9 and 3.10):

% pip3 install dsspy     
Collecting dsspy
  Using cached dsspy-2.2.3-py3-none-any.whl (252 kB)
Collecting scipy
  Using cached scipy-1.9.2-cp310-cp310-macosx_12_0_arm64.whl (28.5 MB)
Collecting terminaltables
  Using cached terminaltables-3.1.10-py2.py3-none-any.whl (15 kB)
Collecting pymongo
  Downloading pymongo-4.2.0-cp310-cp310-macosx_10_15_universal2.whl (404 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 404.2/404.2 kB 1.4 MB/s eta 0:00:00
Collecting OpenDSSDirect.py>=0.6.0
  Using cached OpenDSSDirect.py-0.7.0-py3-none-any.whl (70 kB)
Collecting toml
  Using cached toml-0.10.2-py2.py3-none-any.whl (16 kB)
Collecting requests
  Using cached requests-2.28.1-py3-none-any.whl (62 kB)
Collecting bokeh
  Using cached bokeh-2.4.3-py3-none-any.whl (18.5 MB)
Collecting networkx
  Using cached networkx-2.8.7-py3-none-any.whl (2.0 MB)
Collecting aiohttp-swagger3==0.4.3
  Using cached aiohttp_swagger3-0.4.3-py3-none-any.whl (1.7 MB)
Collecting tables
  Using cached tables-3.7.0.tar.gz (8.2 MB)
  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
  ╰─> [13 lines of output]
      Error in sitecustomize; set PYTHONVERBOSE for traceback:
      AssertionError:
      /var/folders/lp/z4rnw6755rb4383yr_t2bbbr0000gp/T/H5closekqkx73ks.c:2:5: error: implicit declaration of function 'H5close' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
          H5close();
          ^
      1 error generated.
      cpuinfo failed, assuming no CPU features: No module named 'cpuinfo'
      * Using Python 3.10.6 (main, Aug 11 2022, 13:36:31) [Clang 13.1.6 (clang-1316.0.21.2.5)]
      * USE_PKGCONFIG: True
      .. ERROR:: Could not find a local HDF5 installation.
         You may need to explicitly state where your local HDF5 headers and
         library can be found by setting the ``HDF5_DIR`` environment
         variable or by using the ``--hdf5`` command-line option.
      [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.

[nlaws-camus]

maybe an M1 issue. I just tried on a similar mac with intel chip and pip install dsspy worked with Python 3.9

[daniel-thom]

@nlaws-camus Perhaps you saw this issue: PyTables/PyTables#832. Do workarounds listed their solve your issue?

[nlaws-camus]

Thanks @daniel-thom ! Yes the following worked:

brew install hdf5 c-blosc lzo bzip2

followed by

HDF5_DIR=/opt/homebrew/opt/hdf5 BLOSC_DIR=/opt/homebrew/opt/c-blosc LZO_DIR=/opt/homebrew/opt/lzo BZIP2_DIR=/opt/homebrew/opt/bzip2 pip install -e PyDSS