Modularity measurements

Generated by nanopnp.validation.modularity.render_measurements from the source tree this site was built from. The modularity report quotes these measurements at a named commit; VER-61 pins the static and string relations.

Import relation

1038 import edges between nanopnp modules, by kind: top 602, deferred 157, typing 160, string 119. Measured by import_edges and subpackage_relation.

Static relation (top, deferred and typing)

Each cell counts the import statements by which the row's subpackage imports the column's.

from \ to	api	charge	cli	core	density	geometry	gui	io	materials	mesh	nanopnp	numerics	physics	pipeline	plot	post	solve	structure	sweep	symmetry	validation
api				8				13	1	1				14	2		1	1	4
charge				19	7	3		14		2		5						3
cli	16	3		13	1	3		22		4				2				1	11		25
core								1
density				9				5										2
geometry				12	1			12		1								2		2
gui	2	8		10	2	7		29		2		2		14		2	2	2		4
io				10					3			1	1
materials				9				2
mesh				16		11		12
nanopnp	4			8				3					5	1				1
numerics				6
physics				13				2	4	1		15
pipeline		1		7	1			14	3	4		2	2		4	1
plot		3		2	3	5		4	2	5						4	1	2		2
post		2		8		2		7		6		4	10				3
solve		2		9				5	2	3		8	7
structure				5				8
sweep				4				10	1	2		1		2		1	1
symmetry				4	4			5
validation	6	2		14	3	6		17	1			1	6	4		2	1

String relation

from \ to	api	charge	cli	core	density	geometry	gui	io	materials	mesh	nanopnp	numerics	physics	pipeline	plot	post	solve	structure	sweep	symmetry	validation
api
charge
cli	3			1				2					1	1				1
core	5	6			4	5	1	10	1	8		2	5	4	12	8	4	5	2	1	14
density
geometry
gui
io
materials
mesh
nanopnp
numerics
physics
pipeline
plot
post
solve
structure
sweep
symmetry
validation

Strongly connected components

Measured by components. Each lists its internal edges, the number of import statements carrying each, lightest first: those are the candidate cuts.

• top: none
• runtime (top and deferred): none
• static:
  • 10 members: core, density, geometry, io, materials, mesh, numerics, physics, structure, symmetry. Lightest edges: core → io (1), geometry → density (1), geometry → mesh (1), io → numerics (1), io → physics (1), physics → mesh (1)
• static and string:
  • 19 members: api, charge, core, density, geometry, gui, io, materials, mesh, numerics, physics, pipeline, plot, post, solve, structure, sweep, symmetry, validation. Lightest edges: api → materials (1), api → mesh (1), api → solve (1), api → structure (1), core → gui (1), core → materials (1)

Module-level cycles among top imports, each package __init__ an import runs included: 0.

Stage conformance

Measured by stage_conformance, against Stage.key(inputs) and Stage.run(inputs, *, progress, cancel).

Stage	Class	key signature	describe	run signature
case	nanopnp.pipeline.case:CaseStage	(inputs)	yes	(inputs, *, progress, cancel)
structure	nanopnp.structure.stage:StructureStage	(inputs)	yes	(inputs, *, progress, cancel)
density	nanopnp.density.stage:DensityStage	(inputs)	yes	(inputs, *, progress, cancel)
symmetry	nanopnp.symmetry.stage:SymmetryStage	(inputs)	yes	(inputs, *, progress, cancel)
contour	nanopnp.geometry.contour:ContourStage	(inputs)	yes	(inputs, *, progress, cancel)
region	nanopnp.geometry.region:RegionStage	(inputs)	yes	(inputs, *, progress, cancel)
mesh	nanopnp.mesh.ingest:MeshStage	(inputs)	yes	(inputs, *, progress, cancel)
protonation	nanopnp.charge.protonation:ProtonationStage	(inputs)	yes	(inputs, *, progress, cancel)
charge	nanopnp.charge.stage:FieldStage	(inputs)	yes	(inputs, *, progress, cancel)
materials	nanopnp.materials.stage:MaterialsStage	(inputs)	yes	(inputs, *, progress, cancel)
solve	nanopnp.solve.stage:SolveStage	(inputs)	yes	(inputs, *, progress, cancel)
qoi	nanopnp.post.stage:QoIStage	(inputs)	yes	(inputs, *, progress, cancel)
report	nanopnp.post.stage:ReportStage	(inputs)	yes	(inputs, *, progress, cancel)

Stage sets written into pipeline/run.py, measured by stage_sets:

• none

Extension points

Measured by extension_points. Spelled in counts the modules outside the home that write a member's name as a string; none is not counted.

Point	Kind	Home	Members	Spelled in
stages	registry	core/stages.py	13	54
corrections	registry	materials/models.py	1	6
physics models	registry	physics/models.py	6	3
stabilisation	registry	physics/stabilisation.py	2	3
charge forms	registry	charge/fields.py	3	0
mesher	registry	mesh/meshers.py	2	7
linear solver	registry	numerics/linear.py	2	2
outputs	branch	io/case.py	6	22
steric models	branch	io/case.py	1	1
correction forms	branch	materials/forms.py	6	0

The backend (QR-13)

38 modules in 11 subpackages import NGSolve or Netgen, measured by backend_imports. Section 5.4.1 names defined: none.

Subpackage	Modules
charge	3
density	1
geometry	3
gui	2
materials	2
mesh	5
numerics	3
physics	9
post	5
solve	2
validation	3

The public surface

PUBLIC has 19 names; its TYPE_CHECKING mirror has 19, differing in none. Outside PUBLIC: with_section, register. Measured by surface.

Size

The ten longest modules and functions, measured by sizes.

Module	Lines
physics/models.py	1926
validation/modularity.py	1667
cli/__init__.py	1572
validation/apbs.py	1446
charge/protonation.py	1384
pipeline/run.py	1205
geometry/region.py	1178
charge/fields.py	1082
charge/stage.py	1029
pipeline/checks.py	979

Function	Lines
cli/__init__.py build_parser	342
solve/continuation.py default_ladder	285
core/stages.py _register_builtins	265
numerics/newton.py damped_newton	204
structure/stage.py align	152
geometry/contour.py measure	149
physics/models.py CoupledModel.residual_form	146
validation/modularity.py render_measurements	143
structure/read.py select	138
charge/stage.py FieldStage._produce	115

Version literals

6 non-docstring strings name a release vX.Y, measured by version_literals; VER-67 refuses one naming a tagged release.

• cli/reference.py:352
• io/case.py:94
• pipeline/checks.py:598
• pipeline/checks.py:604
• validation/case_leaves.py:185
• validation/modularity.py:1282