[BUG] Missing dependency: sphinx python package

[acardona]

When attempting to import skeletons via pymaid, we get this error:

{
  "error": "Could not import 'custom_rest_swagger_googledoc.get_googledocstring' for API setting 'VIEW_DESCRIPTION_FUNCTION'. ModuleNotFoundError: No module named 'sphinx'.",
  "detail": "Traceback (most recent call last):\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/rest_framework/settings.py\", line 179, in import_from_string\n    return import_string(val)\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/django/utils/module_loading.py\", line 30, in import_string\n    return cached_import(module_path, class_name)\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/django/utils/module_loading.py\", line 15, in cached_import\n    module = import_module(module_path)\n  File \"/usr/lib/python3.10/importlib/__init__.py\", line 126, in import_module\n    return _bootstrap._gcd_import(name[level:], package, level)\n  File \"\u003Cfrozen importlib._bootstrap\u003E\", line 1050, in _gcd_import\n  File \"\u003Cfrozen importlib._bootstrap\u003E\", line 1027, in _find_and_load\n  File \"\u003Cfrozen importlib._bootstrap\u003E\", line 1006, in _find_and_load_unlocked\n  File \"\u003Cfrozen importlib._bootstrap\u003E\", line 688, in _load_unlocked\n  File \"\u003Cfrozen importlib._bootstrap_external\u003E\", line 883, in exec_module\n  File \"\u003Cfrozen importlib._bootstrap\u003E\", line 241, in _call_with_frames_removed\n  File \"/opt/catmaid/fibsem/django/lib/custom_rest_swagger_googledoc.py\", line 8, in \u003Cmodule\u003E\n    from sphinx.ext.napoleon import Config\nModuleNotFoundError: No module named 'sphinx'\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/django/core/handlers/base.py\", line 220, in _get_response\n    response = response.render()\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/django/template/response.py\", line 114, in render\n    self.content = self.rendered_content\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/rest_framework/response.py\", line 74, in rendered_content\n    ret = renderer.render(self.data, accepted_media_type, context)\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/rest_framework/renderers.py\", line 727, in render\n    context = self.get_context(data, accepted_media_type, renderer_context)\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/rest_framework/renderers.py\", line 689, in get_context\n    'description': self.get_description(view, response.status_code),\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/rest_framework/renderers.py\", line 604, in get_description\n    return view.get_view_description(html=True)\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/rest_framework/views.py\", line 244, in get_view_description\n    func = self.settings.VIEW_DESCRIPTION_FUNCTION\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/rest_framework/settings.py\", line 227, in __getattr__\n    val = perform_import(val, attr)\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/rest_framework/settings.py\", line 168, in perform_import\n    return import_from_string(val, setting_name)\n  File \"/opt/catmaid/fibsem/django/env/lib/python3.10/site-packages/rest_framework/settings.py\", line 182, in import_from_string\n    raise ImportError(msg)\nImportError: Could not import 'custom_rest_swagger_googledoc.get_googledocstring' for API setting 'VIEW_DESCRIPTION_FUNCTION'. ModuleNotFoundError: No module named 'sphinx'.\n",
  "type": "ImportError",
  "meta": null
}

Likely the 'sphinx' python package is missing from the requirements text files for building the python virtual environment.

[acardona]

Turns out it's the sphinx package and not sphynx that is missing.

[tomka]

sphinx is usually only needed for building the documentation and is part of the requirements-doc.txt requirements file. It looks like pymaid tries to access an endpoint that returns the documentation HTML rather than the requested content (maybe because the Content-Type header wasn't set to application/json?).

Accessing the HTML version of some endpoints for documentation purposes seems useful generally and I think it would make sense to move the "doc" requirement into the main requirements.txt file.

[tomka]

This is updated in dev now.