coot - pygobject3 error

[huwjenkins]

Coot 1.1.15 emits the following traceback on startup:

(MacCoot:19532): GLib-GIRepository-WARNING **: 13:22:51.096: Failed to load shared library 'libgobject-2.0.0.dylib' referenced by the typelib: dlopen(libgobject-2.0.0.dylib, 0x0009): tried: 'libgobject-2.0.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibgobject-2.0.0.dylib' (no such file), '/usr/lib/libgobject-2.0.0.dylib' (no such file, not in dyld cache), 'libgobject-2.0.0.dylib' (no such file)

(MacCoot:19532): GLib-GIRepository-WARNING **: 13:22:51.098: Failed to load shared library 'libglib-2.0.0.dylib' referenced by the typelib: dlopen(libglib-2.0.0.dylib, 0x0009): tried: 'libglib-2.0.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibglib-2.0.0.dylib' (no such file), '/usr/lib/libglib-2.0.0.dylib' (no such file, not in dyld cache), 'libglib-2.0.0.dylib' (no such file)
Traceback (most recent call last):
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/coot/coot_gui.py", line 39, in <module>
    from gi.repository import Gtk, GObject
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 921, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 813, in module_from_spec
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", line 146, in create_module
    importlib.import_module('gi.repository.' + dep.split("-")[0])
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 921, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 813, in module_from_spec
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", line 146, in create_module
    importlib.import_module('gi.repository.' + dep.split("-")[0])
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 921, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 813, in module_from_spec
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", line 146, in create_module
    importlib.import_module('gi.repository.' + dep.split("-")[0])
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 921, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 813, in module_from_spec
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", line 146, in create_module
    importlib.import_module('gi.repository.' + dep.split("-")[0])
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 921, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 813, in module_from_spec
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/importer.py", line 147, in create_module
    dynamic_module = load_overrides(introspection_module)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/overrides/__init__.py", line 98, in load_overrides
    override_mod = importlib.import_module(override_package_name)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/overrides/GLib.py", line 37, in <module>
    from gi import _option as option
  File "/opt/homebrew/Cellar/python@3.12/3.12.10/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/gi/_option.py", line 41, in <module>
    OPTION_CONTEXT_ERROR_QUARK = GLib.quark_to_string(GLib.option_error_quark())
                                                      ^^^^^^^^^^^^^^^^^^^^^^^^^
gi._error.GError: gi-invoke-error-quark: Could not locate g_option_error_quark: dlopen(libglib-2.0.0.dylib, 0x0009): tried: 'libglib-2.0.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibglib-2.0.0.dylib' (no such file), '/usr/lib/libglib-2.0.0.dylib' (no such file, not in dyld cache), 'libglib-2.0.0.dylib' (no such file) (1)
DEBUG:: in setup_python_with_coot_modules() PyImport_ImportModule() for gui_module: 0x0

This issue suggested GObject>=3.51 was the problem and indeed removing pygobject3 3.52.3 and reverting to pygobject3 3.50.0 removes this traceback. Probably need to version pygobject3@3.50.0 in brewsci/bio?

[YoshitakaMo]

Thanks, @huwjenkins ! I've added pygobject3@3.50.0 formula, but it seems there are still issues to be resolved. I would like to ask one more question: In your use of Coot, has this issue caused any other significant problems?

[huwjenkins]

Thanks! As reported on CootBB - it breaks "Modelling -> Add Other Solvent Molecules..."

To reproduce:

brew uninstall --ignore-dependencies pygobject3@3.50
brew install pygobject3

"Modelling -> Add Other Solvent Molecules..." is broken

brew uninstall --ignore-dependencies pygobject3
brew install pygobject3@3.50

"Modelling -> Add Other Solvent Molecules..." works

Probably this is just masking some other issue as I can't reproduce the traceback with

from gi.repository import Gtk, GObject

outside of Coot.

[YoshitakaMo]

Thank you for your report. As you pointed out, the cause is definitely pygobject3 3.52.3. I've created pygobject3@3.50 formula to fix this issue, but it should be "keg-only" to circumvent the conflict with the latest pygobject3. However, I can't figure out how to pass the test with the current formula (see also this PR). If you have any ideas, please let me know. Otherwise, I can't push the fixed Coot formula...

[eunos-1128]

Shader compile rotation-centre-cross-hairs-for-ssao.shader validation-failed
DEBUG:: in setup_python_with_coot_modules() pkgpydirectory: /usr/local/Cellar/coot/1.1.16/share/coot/../../lib/python3.13/site-packages/coot
DEBUG:: in setup_python_with_coot_modules()    pydirectory: /usr/local/Cellar/coot/1.1.16/share/coot/../../lib/python3.13/site-packages
DEBUG:: in setup_python_with_coot_modules() appending to sys path: /usr/local/Cellar/coot/1.1.16/share/coot/../../lib/python3.13/site-packages
DEBUG:: in setup_python_with_coot_modules() appending to sys path: /usr/local/Cellar/coot/1.1.16/share/coot/../../lib/python3.13/site-packages/coot
DEBUG:: in setup_python_with_coot_modules() sys imported
DEBUG:: in setup_python_with_coot_modules() PyImport_ImportModule() coot: 0x141a14e50
in PyInit_coot_gui_api() st->error null
Null o
DEBUG:: in setup_python_with_coot_modules() PyImport_ImportModule() coot_utils: 0x0
Traceback (most recent call last):
  File "/usr/local/lib/python3.13/site-packages/coot/coot_gui.py", line 37, in <module>
    import gi
ModuleNotFoundError: No module named 'gi'
DEBUG:: in setup_python_with_coot_modules() PyImport_ImportModule() for gui_module: 0x0

I still get the error even with coot 1.1.16 that comes with pygobject3@3.50.

After running pip3 install PyGObject==3.50 --break the error goes away.

(Intel Mac Sequoia)

[huwjenkins]

Apologies I forgot about this. As @eunos-1128 mentions in pemsley/coot#235 (comment) the problem is because making pygobject3@3.50 "keg-only" means it's not in the PYTHONPATH when Coot starts.

Easy fix would be adding it to the wrapper script $HOMEBREW_PREFIX/bin/coot:

 #!/bin/sh
 export LC_ALL=C
 export LANG=C
+export PYTHONPATH="$(brew --prefix pygobject3@3.50)/lib/python3.13/site-packages:$PYTHONPATH"
 prefix=/opt/homebrew/Cellar/coot/1.1.19_1
 export SYMINFO=$prefix/share/coot/data/syminfo.lib
 exec_prefix=${prefix}

pip3 install PyGObject==3.50 --break sounds bad - doesn't this screw up homebrew's Python?

[eunos-1128]

@huwjenkins

I think brew link pygobject3@3.50 is better than pip3 install PyGObject==3.50 --break if you haven't installed the latest pygobject3 using homebrew.

[huwjenkins]

I think brew link pygobject3@3.50 is better than pip3 install PyGObject==3.50 --break if you haven't installed the latest pygobject3 using homebrew.

yes but doesn't this mean the user's homebrew install is in an "unsupported" state and if they install anything that depends on homebrew-core's PyGObject Coot will unexpectedly be broken again?

If installing PyGObject from PyPI is a workaround then I think it could be done the way we did requests etc in the past.

[eunos-1128]

Easy fix would be adding it to the wrapper script $HOMEBREW_PREFIX/bin/coot

Your script looks the best.

[huwjenkins]

OK. The underlying cause of this is that from version 3.51.0 onwards pygobject uses girepository-2.0 (part of glib) for introspection. In girepository-1.0 the homebrew library path was patched in before it was built:

https://github.com/Homebrew/homebrew-core/blob/2e1d5683d6ac37899052c0a70550404ad4b29619/Formula/g/gobject-introspection.rb#L76-L77

In girepository-2.0 some homebrew specific paths are patched in:

https://github.com/Homebrew/homebrew-core/blob/main/Patches/glib/hardcoded-paths.diff

but not $HOMEBREW_PREFIX/lib. If I add this:

diff --git a/girepository/girepository.c b/girepository/girepository.c
index 1c816d1..44044af 100644
--- a/girepository/girepository.c
+++ b/girepository/girepository.c
@@ -309,6 +309,7 @@ gi_repository_init (GIRepository *repository)
     }

   repository->library_paths = g_ptr_array_new_null_terminated (1, g_free, TRUE);
+  g_ptr_array_add (repository->library_paths, g_strdup ("@@HOMEBREW_PREFIX@@/lib"));

   repository->typelibs
     = g_hash_table_new_full (g_str_hash, g_str_equal,

then build glib from source and install coot all works. This seems to be the same problem as this matplotlib issue so I don't think it's specific to coot.

[huwjenkins]

Probably patching load_one_shared_library() in girepository/gitypelib.c as was done in gobject-introspection is the correct way. I will test this.

[huwjenkins]

I looked at this for quite a bit but gave up as I don't understand how it is supposed to work. As far as I can see nothing in GLib calls gi_repository_prepend_library_path() (https://gitlab.gnome.org/GNOME/glib/-/blob/main/girepository/girepository.c#L434-L458) @pemsley do you have any ideas?