Make jupyter a dev-only dependency

[valentinsulzer]

There are some issues with dependencies on arm64 (qtconsole)

[valentinsulzer]

Further, with the exception of numpy, all of our dependencies could be "optional" (i.e. some features don't work if you don't have them installed). For most dependencies this is easy (e.g. anytree, imageio), for others this will require some refactoring (casadi).

The goal eventually is to have a pybamm-lite package that only installs numpy and pybamm, and a pybamm that installs all the optional dependencies

[ayeankit]

hey @tinosulzer, I want to work in this issue. Can you please assign me?

[deepeshaburse]

Hi @tinosulzer, can I work on this issue?

[deepeshaburse]

@tinosulzer I was looking through some solutions. I was thinking we could make a separate dev-requirements.txt and add jupyter to it (and remove it from requirements.txt). I could also make the required changes in the README. Would that be the right approach to solve this issue? There are other solutions like Poetry and pyenv, but it will only add more dependencies to the project.

[deepeshaburse]

@Saransh-cpp should I go ahead with this?

[Saransh-cpp]

This would require removing jupyter completely from requirements.txt and moving it from a required dependency to a dev dependency in setup.py.

From here -

PyBaMM/setup.py

Lines 191 to 209 in f45f4a5

	install_requires=[
	"numpy>=1.16",
	"scipy>=1.3",
	"pandas>=0.24",
	"anytree>=2.4.3",
	"autograd>=1.2",
	"scikit-fem>=0.2.0",
	"casadi>=3.5.0",
	"imageio>=2.9.0",
	"jupyter", # For example notebooks
	"pybtex>=0.24.0",
	"sympy>=1.8",
	"bpx",
	# Note: Matplotlib is loaded for debug plots, but to ensure pybamm runs
	# on systems without an attached display, it should never be imported
	# outside of plot() methods.
	# Should not be imported
	"matplotlib>=2.0",
	],

to here -

PyBaMM/setup.py

Lines 218 to 221 in f45f4a5

	"dev": [
	"pre-commit", # For code style checking
	"black", # For code style auto-formatting
	],

I remember there was some discussion about creating more optional dependency groups (for instance notebooks and plot, just like dev), but I think the message vanished in slack. You might have to wait till there is a consensus on this 🙂

[deepeshaburse]

This would require removing jupyter completely from requirements.txt and moving it from a required dependency to a dev dependency in setup.py.

From here -

PyBaMM/setup.py

Lines 191 to 209 in f45f4a5

	install_requires=[
	"numpy>=1.16",
	"scipy>=1.3",
	"pandas>=0.24",
	"anytree>=2.4.3",
	"autograd>=1.2",
	"scikit-fem>=0.2.0",
	"casadi>=3.5.0",
	"imageio>=2.9.0",
	"jupyter", # For example notebooks
	"pybtex>=0.24.0",
	"sympy>=1.8",
	"bpx",
	# Note: Matplotlib is loaded for debug plots, but to ensure pybamm runs
	# on systems without an attached display, it should never be imported
	# outside of plot() methods.
	# Should not be imported
	"matplotlib>=2.0",
	],

to here -

PyBaMM/setup.py

Lines 218 to 221 in f45f4a5

	"dev": [
	"pre-commit", # For code style checking
	"black", # For code style auto-formatting
	],

I remember there was some discussion about creating more optional dependency groups (for instance notebooks and plot, just like dev), but I think the message vanished in slack. You might have to wait till there is a consensus on this 🙂

Sure, thanks for letting me know ☺️

[valentinsulzer]

Happy to proceed with just moving jupyter to the dev for now. This the largest and most optional dependency so it makes sense to just do that one first

[valentinsulzer]

Here's an example of how pandas does it: https://pandas.pydata.org/docs/dev/whatsnew/v2.0.0.html#installing-optional-dependencies-with-pip-extras

[arjxn-py]

If no one is working on this issue, may I look into this and try to do it? @tinosulzer @Saransh-cpp

[Saransh-cpp]

Let's wait for @deepeshaburse's response for a couple of days. If there is no activity then you can take this up.

[arjxn-py]

@Saransh-cpp I believe she's not responding

[arjxn-py]

@Saransh-cpp I have opened this PR trying to solve this issue but I am getting some failing tests, I would be glad if any lead could be provided.