add development instructions

[rvhonorato]

This PR adds instructions on how to develop haddock3 and also updates the setup.py to include a CustomDevelop instruction class

[rvhonorato]

After irl discussion it was decided we need to also add a "Developing HADDOCK3 in a HPC environment" section

[rvhonorato]

This will change after #1013 - best to solve that one first

[amjjbonvin]

I can’t reproduce this error. May-be linked to the installed compilers and such? Do you have xcode installed on your mac? If not try installing it first. If this solves the problem we should make a note of it

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On 24 Sep 2024, at 09:33, Victor Reys ***@***.***> wrote: building 'haddock.bin.fast_rmsdmatrix' extension clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -iwithsysroot/System/Library/Frameworks/System.framework/PrivateHeaders -iwithsysroot/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.9/Headers -arch arm64 -arch x86_64 -Werror=implicit-function-declaration -Wno-error=unreachable-code -I/Users/vreys/Desktop/HADDOCK3/.venv/include -I/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/include/python3.9 -c src/haddock/deps/fast-rmsdmatrix.c -o build/temp.macosx-10.9-universal2-3.9/src/haddock/deps/fast-rmsdmatrix.o -Wall -O3 -march=native -std=c99 error: unknown target CPU 'apple-m1' note: valid target CPU values are: nocona, core2, penryn, bonnell, atom, silvermont, slm, goldmont, goldmont-plus, tremont, nehalem, corei7, westmere, sandybridge, corei7-avx, ivybridge, core-avx-i, haswell, core-avx2, broadwell, skylake, skylake-avx512, skx, cascadelake, cooperlake, cannonlake, icelake-client, rocketlake, icelake-server, tigerlake, sapphirerapids, alderlake, knl, knm, k8, athlon64, athlon-fx, opteron, k8-sse3, athlon64-sse3, opteron-sse3, amdfam10, barcelona, btver1, btver2, bdver1, bdver2, bdver3, bdver4, znver1, znver2, znver3, x86-64, x86-64-v2, x86-64-v3, x86-64-v4 error: command '/usr/bin/clang' failed with exit code 1

[amjjbonvin]

Getting errors in the tests: FAILED tests/test_cli_restraints.py::test_restrain_bodies - AssertionError: assert 'assign (segi...1.582 0.0 0.0' == 'assign (segi...6.542 0.0 0.0' FAILED tests/test_cli_restraints.py::test_restrain_bodies_exclude - AssertionError: assert 'assign (segi...7.660 0.0 0.0' == 'assign (segi...5.187 0.0 0

As the residues are randomly selected, could this be the problem? E.g. a different pair is selected because of different random numbers or related?

[amjjbonvin]

And another issue with the instructions is that we are missing a step about CNS - without the executable the tests will fail.

[VGPReys]

Also missing instructions for the softlink to CNS ?

ln -s /path/to/cns-os-cpu.exe src/haddock/bin/cns

[rvhonorato]

Getting errors in the tests: FAILED tests/test_cli_restraints.py::test_restrain_bodies - AssertionError: assert 'assign (segi...1.582 0.0 0.0' == 'assign (segi...6.542 0.0 0.0' FAILED tests/test_cli_restraints.py::test_restrain_bodies_exclude - AssertionError: assert 'assign (segi...7.660 0.0 0.0' == 'assign (segi...5.187 0.0 0

As the residues are randomly selected, could this be the problem? E.g. a different pair is selected because of different random numbers or related?

Unclear to me how the different installations would fail this test.

[rvhonorato]

Also missing instructions for the softlink to CNS ?

ln -s /path/to/cns-os-cpu.exe src/haddock/bin/cns

Why have a link and not use the pre-compiled ones?

[rvhonorato]

@haddocking/haddock-developers I have updated the instructions, please try again - make sure all your system dependencies are installed.

[amjjbonvin]

Now working as a charm!