Open
Description
Describe the bug
Thanks for this great project and for Jupyter Book! Obviously many of the same people work on both projects.
After upgrading to a recent version of this package, I'm getting the error:
Exception occurred:
File "/opt/conda/lib/python3.11/site-packages/jupyter_cache/cache/db.py", line 62, in session_context
raise RuntimeError(
RuntimeError: Unexpected error accessing jupyter cache, it may need to be cleared.
The full traceback has been saved in /tmp/sphinx-err-npmhkzbj.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1969, in _exec_single_context
self.dialect.do_execute(
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/engine/default.py", line 922, in do_execute
cursor.execute(statement, parameters)
sqlite3.OperationalError: no such table: nbproject
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/jupyter_cache/cache/db.py", line 59, in session_context
yield session
File "/opt/conda/lib/python3.11/site-packages/jupyter_cache/cache/db.py", line 212, in create_record
session.commit()
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1969, in commit
trans.commit(_to_root=True)
File "<string>", line 2, in commit
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
ret_value = fn(self, *arg, **kw)
^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1256, in commit
self._prepare_impl()
File "<string>", line 2, in _prepare_impl
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
ret_value = fn(self, *arg, **kw)
^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1231, in _prepare_impl
self.session.flush()
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 4312, in flush
self._flush(objects)
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 4447, in _flush
with util.safe_reraise():
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/util/langhelpers.py", line 146, in __exit__
raise exc_value.with_traceback(exc_tb)
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 4408, in _flush
flush_context.execute()
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/unitofwork.py", line 466, in execute
rec.execute(self)
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/unitofwork.py", line 642, in execute
util.preloaded.orm_persistence.save_obj(
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/persistence.py", line 93, in save_obj
_emit_insert_statements(
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/orm/persistence.py", line 1227, in _emit_insert_statements
result = connection.execute(
^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1416, in execute
return meth(
^^^^^
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/sql/elements.py", line 517, in _execute_on_connection
return connection._execute_clauseelement(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1639, in _execute_clauseelement
ret = self._execute_context(
^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1848, in _execute_context
return self._exec_single_context(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1988, in _exec_single_context
self._handle_dbapi_exception(
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 2344, in _handle_dbapi_exception
raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1969, in _exec_single_context
self.dialect.do_execute(
File "/opt/conda/lib/python3.11/site-packages/sqlalchemy/engine/default.py", line 922, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: nbproject
[SQL: INSERT INTO nbproject (uri, read_data, assets, created, traceback) VALUES (?, ?, ?, ?, ?)]
[parameters: ('/home/jovyan/work/notes/ssc/7-3.md', '{"type": "plugin", "name": "myst_nb_md"}', '[]', '2024-01-25 13:55:36.499957', '')]
(Background on this error at: https://sqlalche.me/e/20/e3q8)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
app.build(force_all, filenames)
File "/opt/conda/lib/python3.11/site-packages/sphinx/application.py", line 329, in build
self.builder.build_update()
File "/opt/conda/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 288, in build_update
self.build(to_build,
File "/opt/conda/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 302, in build
updated_docnames = set(self.read())
^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 409, in read
self._read_serial(docnames)
File "/opt/conda/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 430, in _read_serial
self.read_doc(docname)
File "/opt/conda/lib/python3.11/site-packages/sphinx/builders/__init__.py", line 483, in read_doc
publisher.publish()
File "/opt/conda/lib/python3.11/site-packages/docutils/core.py", line 217, in publish
self.document = self.reader.read(self.source, self.parser,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/sphinx/io.py", line 103, in read
self.parse()
File "/opt/conda/lib/python3.11/site-packages/docutils/readers/__init__.py", line 78, in parse
self.parser.parse(self.input, document)
File "/opt/conda/lib/python3.11/site-packages/myst_nb/sphinx_.py", line 150, in parse
with create_client(
File "/opt/conda/lib/python3.11/site-packages/myst_nb/core/execute/base.py", line 83, in __enter__
self.start_client()
File "/opt/conda/lib/python3.11/site-packages/myst_nb/core/execute/cache.py", line 55, in start_client
stage_record = cache.add_nb_to_project(str(self.path), read_data=read_fmt)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/jupyter_cache/cache/main.py", line 422, in add_nb_to_project
return NbProjectRecord.create_record(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/jupyter_cache/cache/db.py", line 208, in create_record
with session_context(db) as session: # type: Session
File "/opt/conda/lib/python3.11/contextlib.py", line 158, in __exit__
self.gen.throw(typ, value, traceback)
File "/opt/conda/lib/python3.11/site-packages/jupyter_cache/cache/db.py", line 62, in session_context
raise RuntimeError(
RuntimeError: Unexpected error accessing jupyter cache, it may need to be cleared.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/bin/jupyter-book", line 8, in <module>
sys.exit(main())
^^^^^^
File "/opt/conda/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/jupyter_book/cli/main.py", line 317, in build
builder_specific_actions(
File "/opt/conda/lib/python3.11/site-packages/jupyter_book/cli/main.py", line 525, in builder_specific_actions
raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError:
===============================================================================
There was an error in building your book. Look above for the cause.
===============================================================================
Reproduce the bug
It seems likely this is a known issue. See jupyter-cache/CHANGELOG.md and the breaking change mention of nbstage and nbproject.
Unfortunately I've got many notebooks that take hours to execute and use R packages that don't produce completely reliable i.e. reproducible results 🙄 (see e.g. Practice: Chp. 14).
I've not found a way to avoid re-execution and so for now I'm planning to attempt to rebuild the cache over a day or two. I'd just like to confirm there's likely no other way around this problem.
List your environment
$ jupyter-book --version
Jupyter Book : 0.15.1
External ToC : 0.3.1
MyST-Parser : 0.18.1
MyST-NB : 0.17.2
Sphinx Book Theme : 1.0.1
Jupyter-Cache : 0.6.1
NbClient : 0.7.4