Dependencies: update `Sphinx` and `jinja2` for compability

[sphuber]

Jinja2 recently removed some resources that were still being used by Sphinx 3. Upgrading both solves the issue. myst-nb also needed to be upgraded to get compatibility with latest Sphinx.

[chrisjsewell]

upgraded to get compatibility with latest Sphinx.

Note sphinx v5 is actually the latest, but sphinx-book-theme is still pinned to v4 (myst-nb is compatible)

[chrisjsewell]

So change jupyter_execute_notebooks to nb_execution_mode, and maybe just delete the nb_render_priority variable, since that has changed completely in format and may no longer be necessary.

Plus, at the top of https://github.com/aiidateam/aiida-tutorials/blob/tutorial-2022-intro/docs/sections/running_processes/workflows.md, change

---
substitutions:
  seekpath: "[SeeK-path](https://www.materialscloud.org/work/tools/seekpath)"
---

to

---
myst:
  substitutions:
    seekpath: "[SeeK-path](https://www.materialscloud.org/work/tools/seekpath)"
---

[sphuber]

@chrisjsewell addressed the warnings for newer myst-nb but the build is still failing as mentioned in the slack thread. You know how to fix it?

[chrisjsewell]

for the pre-commit, just change https://github.com/aiidateam/aiida-tutorials/blob/485a9dd366fff418a1a4c2be7c19cf86060e2f8b/.pre-commit-config.yaml#L21-L26, so that rev points towards v6.1.0 (latest on https://github.com/rstcheck/rstcheck), and I guess also update the sphinx version dependency

[sphuber]

for the pre-commit, just change

https://github.com/aiidateam/aiida-tutorials/blob/485a9dd366fff418a1a4c2be7c19cf86060e2f8b/.pre-commit-config.yaml#L21-L26 , so that rev points towards v6.1.0 (latest on https://github.com/rstcheck/rstcheck), and I guess also update the sphinx version dependency

Yeah, just did that. Ah, missed the sphinx reference though. Will update that now

[chrisjsewell]

and yeh the linking is due to https://github.com/aiidateam/aiida-core/issues/5518, I'll have a look/think today, if there is a decent fix

[chrisjsewell]

For the two issues with intersphinx:

/home/runner/work/aiida-tutorials/aiida-tutorials/docs/sections/writing_workflows/errors.md:34: WARNING: py:meth reference target not found: aiida.orm.nodes.process.ProcessNode.is_failed
/home/runner/work/aiida-tutorials/aiida-tutorials/docs/sections/writing_workflows/errors.md:427: WARNING: py:meth reference target not found: aiida.orm.nodes.process.process.ProcessNode.exit_status

I downloaded https://aiida.readthedocs.io/projects/aiida-core/en/latest/objects.inv, then used https://github.com/bskinn/sphobjinv to inspect.

Its actually the case that now both are not py:meth but py:property:

:py:property:`aiida.orm.nodes.process.process.ProcessNode.is_failed`, :py:property:`aiida.orm.nodes.process.process.ProcessNode.exit_status`

[chrisjsewell]

oh and one more, change git://github.com/pre-commit/pre-commit-hooks in the pre-commit config to https://github.com/pre-commit/pre-commit-hooks