Installing haddock3 on apple-m3 fails (maybe)

[AnnaKravchenko]

I tried to install latest version of haddok3 following instructions from github.
Pip install faild with:

      cc1: error: unknown value 'apple-m3' for ‘-march’
      cc1: note: valid arguments are: armv8-a armv8.1-a armv8.2-a armv8.3-a armv8.4-a armv8.5-a armv8.6-a armv8-r native

I managed to resolve this issue by removing all march=naive from setup.py.

Important!: I do have a copy of mac-arm64-darwin cns, given to me piror to this installation attempt.

I do not know if this issue is due to the existing cns version, thus already covered in the installation troubleshooting, or an actual bug.

Fuller log:

      running build_ext
      Building HADDOCK3 C/C++ binary dependencies…
      moving contact_fcc -> src/haddock/bin/contact_fcc
      copying src/haddock/bin/contact_fcc -> build/lib.macosx-11.0-arm64-cpython-39/haddock/bin
      cc1: error: unknown value 'apple-m3' for ‘-march’
      cc1: note: valid arguments are: armv8-a armv8.1-a armv8.2-a armv8.3-a armv8.4-a armv8.5-a armv8.6-a armv8-r native
      Successfully built and moved contact_fcc
      Error building fast-rmsdmatrix: Command '['gcc', '-Wall', '-O3', '-march=native', '-std=c99', '-o', 'fast-rmsdmatrix', 'src/haddock/deps/fast-rmsdmatrix.c', '-lm']' returned non-zero exit status 1.
      Traceback (most recent call last):
        File "/Users/Kravc006/postdoc/tools/mambaforge/envs/haddock3/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
        File "/Users/Kravc006/postdoc/tools/mambaforge/envs/haddock3/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs”])
        File "/Users/Kravc006/postdoc/tools/mambaforge/envs/haddock3/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
          return _build_backend().build_wheel(
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 435, in build_wheel
          return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 423, in _build
          return self._build_with_temp_dir(
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 404, in _build_with_temp_dir
          self.run_setup()
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 317, in run_setup
          exec(code, locals())
        File "<string>", line 140, in <module>
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 117, in setup
          return distutils.core.setup(**attrs)
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 186, in setup
          return run_commands(dist)
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
          dist.run_commands()
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands
          self.run_command(cmd)
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1104, in run_command
          super().run_command(command)
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
          cmd_obj.run()
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/command/bdist_wheel.py", line 370, in run
          self.run_command(“build”)
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command
          self.distribution.run_command(command)
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1104, in run_command
          super().run_command(command)
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
          cmd_obj.run()
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 135, in run
          self.run_command(cmd_name)
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command
          self.distribution.run_command(command)
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1104, in run_command
          super().run_command(command)
        File "/private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-8yduu_2z/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
          cmd_obj.run()
        File "<string>", line 47, in run
        File "<string>", line 70, in build_executable
        File "/Users/Kravc006/postdoc/tools/mambaforge/envs/haddock3/lib/python3.9/subprocess.py", line 373, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['gcc', '-Wall', '-O3', '-march=native', '-std=c99', '-o', 'fast-rmsdmatrix', 'src/haddock/deps/fast-rmsdmatrix.c', '-lm']' returned non-zero exit status 1.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for haddock3
  DEPRECATION: Building 'freesasa' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'freesasa'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for freesasa (setup.py) … done
  Created wheel for freesasa: filename=freesasa-2.2.1-cp39-cp39-macosx_11_0_arm64.whl size=285687 sha256=de6f26ffdb3f26736fd311682500147f8e411544fa50ac51037183cbdc41ad83
  Stored in directory: /private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-ephem-wheel-cache-5q72lpl4/wheels/cd/f0/b5/1b158a3b1fba5bf481e7af23a8c7479146296531f22f7fee67
Successfully built freesasa
Failed to build haddock3
ERROR: Failed to build installable wheels for some pyproject.toml based projects (haddock3)

[amjjbonvin]

Are you using the c compilers from Apple, coming with the x-code installation?

And which instructions are you following as there are various versions in the documentation?

[amjjbonvin]

Just tested three different installation procedures, all using venv, on my apple-m2 laptop - all working fine

# Installation via python venv via pip
# if needed change to a specific python version 3.9-3.12 supported
python3.9 -m venv haddock3
source haddock3/bin/activate
pip install haddock3

# Installation with a local copy of the haddock3 repo via python venv in user mode
git clone https://github.com/haddocking/haddock3.git
cd haddock3/
# if needed change to a specific python version, 3.9-3.12 supported
python3.9 -m venv .venv
source .venv/bin/activate
pip install .

# Installation with a local copy of the haddock3 repo via venv in devel mode
git clone https://github.com/haddocking/haddock3.git
cd haddock3/
# if needed change to a specific python version, 3.9-3.12 supported
python3.9 -m venv .venv
source .venv/bin/activate
pip install -e '.[dev,doc]'

[AnnaKravchenko]

I used:

git clone https://github.com/haddocking/haddock3.git
cd haddock3
conda create -n haddock3 python=3.9
conda activate haddock3
pip install .

And I still can replicate this apple-m3 error.

Don’t know about the c compilers from Apple, but must be, if it’s default behavior

[AnnaKravchenko]

Tried with venv, following this recipe:

# Installation with a local copy of the haddock3 repo via python venv in user mode
git clone https://github.com/haddocking/haddock3.git
cd haddock3/
# if needed change to a specific python version, 3.9-3.12 supported
python3.9 -m venv .venv
source .venv/bin/activate
pip install .

Same error message

[AnnaKravchenko]

And in addition:

        check.warn(importable)
      /private/var/folders/cv/r0bdb1yd7hg89t1lxw6z90lc0000gn/T/pip-build-env-eqpv3h_8/overlay/lib/python3.12/site-packages/setuptools/command/build_py.py:212: _Warning: Package 'haddock.modules.topology.topoaa.cns' is absent from the `packages` configuration.
      !!

              ********************************************************************************
              ############################
              # Package would be ignored #
              ############################
              Python recognizes 'haddock.modules.topology.topoaa.cns' as an importable package[^1],
              but it is absent from setuptools' `packages` configuration.

              This leads to an ambiguous overall configuration. If you want to distribute this
              package, please make sure that 'haddock.modules.topology.topoaa.cns' is explicitly added
              to the `packages` configuration field.

              Alternatively, you can also rely on setuptools' discovery methods
              (for example by using `find_namespace_packages(...)`/`find_namespace:`
              instead of `find_packages(...)`/`find:`).

              You can read more about "package discovery" on setuptools documentation page:

              - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

              If you don't want 'haddock.modules.topology.topoaa.cns' to be distributed and are
              already explicitly excluding 'haddock.modules.topology.topoaa.cns’ via
              `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
              you can try to use `exclude_package_data`, or `include-package-data=False` in
              combination with a more fine grained `package-data` configuration.

              You can read more about "package data files" on setuptools documentation page:

              - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


              [^1]: For Python, any directory (with suitable naming) can be imported,
                    even if it does not contain any `.py` files.
                    On the other hand, currently there is no concept of package data
                    directory, all directories are treated like packages.
              ********************************************************************************

[amjjbonvin]

Did you install xcode on your mac?

[AnnaKravchenko]

No