`tools.costs` requires `plotnine` dependency

[glatterf42]

As discovered in #322, when installing message-ix-models in a fresh virtual environment from PyPI and trying to run

from message_ix_models.tools.costs.config import Config

I receive a ModuleNotFoundError: No module named 'plotnine'.

Full traceback

>>> from message_ix_models.tools.costs.config import Config
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/fridolin/.virtualenvs/fix-git-lfs-pointers/lib/python3.12/site-packages/message_ix_models/__init__.py", line 30, in <module>
    Context()
  File "/home/fridolin/.virtualenvs/fix-git-lfs-pointers/lib/python3.12/site-packages/message_ix_models/util/context.py", line 118, in __init__
    kwargs[key] = cls(**values)
                  ^^^^^^^^^^^^^
  File "<string>", line 3, in __init__
  File "/home/fridolin/.virtualenvs/fix-git-lfs-pointers/lib/python3.12/site-packages/message_ix_models/report/config.py", line 26, in _default_callbacks
    from message_ix_models.report import plot
  File "/home/fridolin/.virtualenvs/fix-git-lfs-pointers/lib/python3.12/site-packages/message_ix_models/report/plot.py", line 15, in <module>
    import plotnine as p9
ModuleNotFoundError: No module named 'plotnine'

For installation, I simply ran pip install message-ix-models because there is no dependency section for tools.costs, indicating that no special dependencies are required.

Manually installing plotnine fixes the issue. Note, though, that this is only testing a part of tools.costs, so other parts of the module may required additional dependencies that I haven't discovered so far.

So to resolve this issue, I suggest to add a tools.costs (or maybe tools-costs or just costs) section to pyproject.toml and list plotnine in there.

To completely resolve the issue of any additional dependencies, I suggest running the full demo file and noting what else comes up as missing. Running the test suite is not really an option, I think, since that requires the tests section, which already brings in report and transport, including plotnine, so with that, we would even miss the dependency responsible for this issue.

[khaeru]

So to resolve this issue, I suggest to add a tools.costs (or maybe tools-costs or just costs) section to pyproject.toml and list plotnine in there.

Rather than doing this directly, we should follow the same pattern as:

message-ix-models/pyproject.toml

Lines 78 to 83 in ae96255

	transport = [
	"message-ix-models[iea-web,report]",
	"requests-cache",
	"transport-energy",
	"xarray",
	]

That is:

• if message_ix_models.x imports message_ix_models.y, and we have an optional dependency group already for y including the particular packages it needs, then add (or extend) the optional dependency group x to include "message-ix-models[y]".
• if OTOH there is a direct dependency on some package from message_ix_models.x or a submodule, then add that package to directly to the optional dependency group x.

This way the relationships in pyproject.toml mirror those in the code, and we don't have to scratch our heads about whether to update, add, remove the same package name appearing in multiple places.

[khaeru]

Also, if we add a dependencies group, the respective documentation page must include a mention of that group and remind users that those are necessary for using the module in question.