mnt: nodes context settings are no longer a regular input

[pfebrer]

Closes #538

Previously, settings that controlled the behavior of nodes where passed as function arguments, which was confusing:

from sisl.nodes import Node

@Node.from_func
def sum_node(a, b):
    return a + b

my_node = sum_node(1, 2, automatic_recalc=True)

Now it is instead controlled with contexts. A node's behavior is defined by its context, which is a chainmap from sisl's main context (sisl.nodes.context.MAIN_CONTEXT), the node class context (Node.context), the instance context and a global temporal context.

Therefore, the same behavior can be obtained in different ways, which act at different levels:

from sisl.nodes import Node, temporal_context

@Node.from_func
def sum_node(a, b):
    return a + b

my_node = sum_node(1, 2)

# Option 1: Modify the global sisl context, which affects all nodes
sisl.nodes.MAIN_CONTEXT.update(lazy=False)

# Option 2: Set the laziness for all instances of a Node
Node.context.update(lazy=False)

# Option 3: Set the laziness for all instances of a sum_node
sum_node.context.update(lazy=False)

# Option 4: Set the laziness only for this instance
my_node.context.update(lazy=False)

# Option 5: Set a temporal context, which overrides all contexts.
with temporal_context(lazy=False):
    ... do whatever

I also changed what lazy means. Before this PR it defined what was returned when calling a node class. If lazy, a node instance was returned and if not, the result was directly returned. Since it is now very easy to go from function to node and viceversa I thought that calling a node class should always return a node instance to avoid confusion. Now lazy means just whether the node should be recomputed on change of inputs, which was the old automatic_recalc, now removed.

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CodeQL found more than 10 potential problems in the proposed changes. Check the Files changed tab for more details.

[codecov]

Codecov Report

Merging #547 (6667362) into main (d7fd5af) will decrease coverage by 0.02%.
The diff coverage is 1.08%.

❗ Current head 6667362 differs from pull request most recent head 66576b1. Consider uploading reports for the commit 66576b1 to get more accurate results

@@            Coverage Diff             @@
##             main     #547      +/-   ##
==========================================
- Coverage   86.25%   86.24%   -0.02%     
==========================================
  Files         366      367       +1     
  Lines       46500    46465      -35     
==========================================
- Hits        40107    40072      -35     
  Misses       6393     6393              

Impacted Files	Coverage Δ
sisl/nodes/__init__.py	0.00% <0.00%> (ø)
sisl/nodes/context.py	0.00% <0.00%> (ø)
sisl/nodes/node.py	0.00% <0.00%> (ø)
sisl/nodes/workflow.py	0.00% <0.00%> (ø)
sisl/geometry.py	86.09% <100.00%> (-0.36%)	⬇️
sisl/io/sile.py	86.32% <0.00%> (-0.40%)	⬇️
sisl/io/xyz.py	97.10% <0.00%> (-0.16%)	⬇️
sisl/io/tests/test_xyz.py	100.00% <0.00%> (ø)
sisl/io/siesta/__init__.py	100.00% <0.00%> (ø)
... and 6 more

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[zerothi]

Great!!!

I'll just merge!