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Type-hinting elastica#367

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skim0119 merged 175 commits intoupdate-0.3.3GazzolaLab/PyElastica:update-0.3.3from update/mypyGazzolaLab/PyElastica:update/mypyCopy head branch name to clipboardJun 28, 2024

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Commits on Apr 27, 2024

• update: add cli for mypy run and cleanup

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• feat: add mypy checker

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• Update main.yml

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• Update main.yml

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Commits on Apr 28, 2024

• update mypy setup

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• Merge branch 'update/mypy' of https://github.com/GazzolaLab/PyElastica into update/mypy

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• fix python-version string for mypy config

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• rename interface into protocol

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• change interface name to protocol

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• make separate tag module for easy typing

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• add system collection as native subtype

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• Merge branch 'update-0.3.3' into typing/timestepper

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• typehint is_system_a_collection

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• wip: typing symplectic stepper

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• Merge branch 'update-0.3.3' into update/mypy

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Commits on Apr 29, 2024

• wip: timestepper typing

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• add generic system protocol

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• wip explicit stepper typing

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• test: fix rod/rigidbody mocking

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• wip: resolve circular dependencies due to protocol

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• remove protocol from coverage

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• Merge branch 'update/mypy' into typing/timestepper

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Commits on Apr 30, 2024

• Update elastica/timestepper/symplectic_steppers.py

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• formatting: remove any unused imports

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• Create py.typed

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• Merge pull request #372 from skim0119/typing/timestepper

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Commits on May 1, 2024

• refactor: Stateful -> Symplectic

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• update: use string-literal taging instead of class-typing

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Commits on May 3, 2024

• build(deps): bump tqdm from 4.66.2 to 4.66.3

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Commits on May 4, 2024

• redesign integration flow: mypy checked

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• update: save operator sequence without running at each timestep

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• test: remove symple system stepping - no longer support

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• fix: tuple is not supposed to be mutable

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• feat: allow single system integration

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• test: fix broken tests due to changes in steppig method

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• remove: timestepper tag

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• update tutorial with new timestepper syntax

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• feat: add testing for single system integrate overload

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• autoflake8 -> autoflake

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Commits on May 5, 2024

• use isinstance

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• Merge pull request #375 from GazzolaLab/dependabot/pip/tqdm-4.66.3

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Commits on May 6, 2024

• build(deps): bump jinja2 from 3.1.3 to 3.1.4

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Commits on May 7, 2024

• Merge pull request #377 from GazzolaLab/dependabot/pip/jinja2-3.1.4

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• typing: base_system module

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• wip: callback module typing

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• Merge pull request #373 from skim0119/typing/timestepper

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• Merge branch 'update/mypy' into typing/modules

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Commits on May 11, 2024

• Merge branch 'update-0.3.3' into update/mypy

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• Merge branch 'update/mypy' into typing/modules

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Commits on May 13, 2024

• typing: callback module typing

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• test: fix callback module related tests

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• Merge branch 'update-0.3.3' into update/mypy

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• typing: base system with requisite as part of system protocol

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• Merge remote-tracking branch 'origin' into typing/modules

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• Merge branch 'update/mypy' into typing/modules

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• memory block typing for rod, rigid body and rod base

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• fix:typing for rod and rigid body data structures to make consistent

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Commits on May 14, 2024

• Merge branch 'update/mypy' into typing/memory_block

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Commits on May 15, 2024

• Update elastica/memory_block/memory_block_rigid_body.py

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• Update elastica/memory_block/memory_block_rod.py

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• update type hinting in memory block rigid body and rod and add system

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• update elastica typing alias

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• Merge branch 'update/mypy' into typing/modules

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• Merge branch 'update/mypy' into typing/memory_block

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• typing SystemIdxType import added in memory block rigid body and rod

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• fix requisite module type

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Commits on May 16, 2024

• add generic type for operator grouping

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• typing: connections module and necessary changes for protocol

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Commits on May 19, 2024

• Improve typehinting at root directory

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• Improve type hinting in the rod directory

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Commits on May 20, 2024

• KnotTheory remove protocol inherit

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• Merge pull request #341 from ankith26/more-typing

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• Merge branch 'update/mypy' into typing/modules

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• test: fix missing values

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• ignore njit wrapper

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• Merge branch 'update/mypy' into typing/modules

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Commits on Jun 13, 2024

• update: mypy pass for connection module

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• remove unused protocol

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• Merge branch 'update-0.3.3' into update/mypy

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• Merge branch 'update/mypy' into typing/modules

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• typing: edit FreeJoint base indexing type

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• typing: finish constraints hinting

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• typing: finish contact hinting

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• test: update unittest for refactor codes

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• typing: damping module finish

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• typing: finish forcing module hinting

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• typing: make memory block hinting agree to block module

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• remove deprecated functions to avoid unnecessary type hinting

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• Merge branch 'update/mypy' into typing/memory_block

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• Merge pull request #384 from armantekinalp/typing/memory_block

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• Merge branch 'update/mypy' into typing/modules

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• exclude experimental work from type-hinting

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Commits on Jun 14, 2024

• chore: internal _typing.py for typedefs for rebase

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• chore: typing for rigid_body.py

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• refactor: change J_omega to lower case

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• chore: typing for cylinder.py

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• chore: remove commented functions

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• chore: typing for sphere.py

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• refactor: remove unused _bootstrap functions and state classes

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• chore: typing for rigid body data structure

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• fix: fixed repetitive codes in cylinder.py caused by rebase merge

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• refactor: temporarily remove REQUISITE_MODULES

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• typing: rearange protocol for system

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• typing: minor fix that reference RodType

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• typing: rod module and refactor knot theory protocol

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• refactor: remove unused bootstrap code from rigid body data_structure

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• Merge pull request #395 from sy-cui/typing/rigid_body

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Commits on Jun 15, 2024

• Merge branch 'update/mypy' into typing/modules

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• typing: system utility

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• feat: Euler Forward memory

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• Merge branch 'update/mypy' into typing/rods

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• typing: contact related modules

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• remove AllowedContactType union alias to distinguish cases

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• typing: add basic properties for surface_base definition

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• typing: include interaction module

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• Merge pull request #394 from skim0119/typing/systems

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• Merge branch 'update/mypy' into typing/modules

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Commits on Jun 16, 2024

• Merge pull request #382 from skim0119/typing/modules

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• Merge branch 'update/mypy' into typing/rods

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• typing: other minor update for different operators

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• Merge branch 'typing/rods' into typing/contact

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• remove deprecated joint functions

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• refactor: mv memory related methods into separate file

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• Merge pull request #396 from skim0119/typing/rods

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• Merge branch 'update/mypy' into typing/contact

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• resolve circular import

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• test: remove unittest for ExternalContact and SelfContact

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• typing: collision utils

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• wip: typing symplectic stepper

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• fix tests with refactoring symplectic system

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• remove deprecated functions in interaction

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• remove deprecated anisotropic friction msg

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• wip: fixing type disagreements

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• resolve liskov error

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Commits on Jun 17, 2024

• wip: finalizing typing system and system collection relation

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• refactor memory block related utility functions

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• type: finish organizing prototype

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• tests: use tmp_path to save test files

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• fix: formatting

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• fix: directly access number of elements

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• remove indexing feature for connection

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• Merge pull request #397 from skim0119/typing/contact

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• refactor: rigid body numbers typing

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• Merge branch 'update-0.3.3' into update/mypy

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• add static system type

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• Merge branch 'update/mypy' of https://github.com/GazzolaLab/PyElastica into update/mypy

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Commits on Jun 19, 2024

• exclude pyvista untyped import

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Commits on Jun 24, 2024

• docs: add duck-typing structure into documentation

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Commits on Jun 25, 2024

• docs: add duck-typing structure into documentation

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• Merge branch 'update/mypy' of https://github.com/GazzolaLab/PyElastica into update/mypy

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• type: reset functions

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• revert: catenary case

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• type: system factory function np.floating -> float

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• type: feature API np.floating -> float

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• fix CI: minor typo, deprecated functions, and mypy

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• type: remove ignore during timestepper, use type-cast

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• bug: fix issue that boudnary condition was not properly beling applied

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• refactor: rename rod->system for proper inheritance syntax

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• fix: disallow None default value, instead use empty tuple

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• fix: experimental parallel connection to be batch-wise operation

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• check example cases, fix outdated syntax

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• Update elastica/rod/cosserat_rod.py

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• Update elastica/external_forces.py

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• Update elastica/modules/protocol.py

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• Update elastica/typing.py

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Commits on Jun 26, 2024

• remove ambiguity: np.integer -> np.int32, np.floating -> np.float64

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• Merge branch 'update/mypy' of https://github.com/GazzolaLab/PyElastica into update/mypy

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• test: fix few typings that has been ignored

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• add ring-rod typehint check

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• refactor: clarify iterating systems vs block_systems

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• type: remove None-type for connection index for simplicity

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• remove out-dated function

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• fix typo

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Commits on Jun 27, 2024

• change: int_ -> int32

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• Merge branch 'update/mypy' of https://github.com/GazzolaLab/PyElastica into update/mypy

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