Merge branch 'update-0.3.3' into master

.flake8

@@ -1,5 +1,5 @@
 [flake8]
-ignore = E203, E266, E501, W503, F403, F401, W191
+ignore = E203, E266, E501, W503, F403, F401, W191, E704
 max-line-length = 88
 max-complexity = 18
 select = B,C,E,F,W,T4,B9

.github/dependabot.yml

@@ -10,5 +10,5 @@ updates:
     schedule:
       interval: "daily"
     open-pull-requests-limit: 99
-    target-branch: "update-0.3.1"
+    target-branch: "update-0.3.3"
     versioning-strategy: lockfile-only

.github/workflows/main.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-latest, macos-latest] #, windows-latest] # Run macos tests if really required, since they charge 10 times more for macos
         include:
           - os: ubuntu-latest
@@ -66,11 +66,15 @@ jobs:
       - name: Run tests
         run: |
           make test
-  report-coverage:  # Report coverage from python 3.8 and mac-os. May change later
+      - name: Typechecking
+        if: ${{ startsWith(runner.os, 'macOS') }}
+        run: |
+          make mypy
+  report-coverage:  # Report coverage from python 3.10 and mac-os. May change later
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8"]
+        python-version: ["3.10"]
         os: [macos-latest]
         include:
           - os: macos-latest

.gitignore

@@ -6,6 +6,8 @@ __pycache__/
 # C extensions
 *.so
 
+*.swp
+
 # Distribution / packaging
 .Python
 build/

.readthedocs.yaml

@@ -10,7 +10,7 @@ build:
       - pip install poetry
       - poetry config virtualenvs.create false
     post_install:
-      - poetry install --all-extras
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --all-extras
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

CONTRIBUTING.md

@@ -44,12 +44,12 @@ First **create the fork repository and clone** to your local machine.
 
 2. Virtual python workspace: `conda`, `pyenv`, or `venv`.
 
-We recommend using python version above 3.8.0.
+We recommend using python version above 3.10.0.
 
 ```bash
 conda create --name pyelastica-dev
 conda activate pyelastica-dev
-conda install python==3.8
+conda install python==3.10
 ```
 
 3. Setup [`poetry`](https://python-poetry.org) and `dependencies`!
@@ -61,7 +61,7 @@ make pre-commit-install
 ```
 
 If you are planning to contribute to the examples,
-extra dependencies can be installed using `poetry install -E examples`.
+extra dependencies can be installed using `make install_examples_dependencies`.
 
 If you are planning to contribute on documentation, extra dependencies can be installed
 using `poetry install -E docs`.

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019-2023 GazzolaLab
+Copyright (c) 2019-2024 GazzolaLab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Makefile

@@ -1,7 +1,7 @@
 #* Variables
 PYTHON := python3
 PYTHONPATH := `pwd`
-AUTOFLAKE8_ARGS := -r --exclude '__init__.py' --keep-pass-after-docstring
+AUTOFLAKE_ARGS := -r
 #* Poetry
 .PHONY: poetry-download
 poetry-download:
@@ -35,7 +35,7 @@ pre-commit-install:
 .PHONY: black
 black:
 	poetry run black --version
-	poetry run black --config pyproject.toml --required-version 21.12b0 elastica tests examples
+	poetry run black --config pyproject.toml --required-version 24.3.0 elastica tests examples
 
 .PHONY: black-check
 black-check:
@@ -47,19 +47,22 @@ flake8:
 	poetry run flake8 --version
 	poetry run flake8 elastica tests
 
-.PHONY: autoflake8-check
-autoflake8-check:
-	poetry run autoflake8 --version
-	poetry run autoflake8 $(AUTOFLAKE8_ARGS) elastica tests examples
-	poetry run autoflake8 --check $(AUTOFLAKE8_ARGS) elastica tests examples
+.PHONY: autoflake-check
+autoflake-check:
+	poetry run autoflake --version
+	poetry run autoflake --check $(AUTOFLAKE_ARGS) elastica tests examples
 
-.PHONY: autoflake8-format
-autoflake8-format:
-	poetry run autoflake8 --version
-	poetry run autoflake8 --in-place $(AUTOFLAKE8_ARGS) elastica tests examples
+.PHONY: autoflake-format
+autoflake-format:
+	poetry run autoflake --version
+	poetry run autoflake --in-place $(AUTOFLAKE_ARGS) elastica tests examples
 
 .PHONY: format-codestyle
-format-codestyle: black flake8
+format-codestyle: black autoflake-format
+
+.PHONY: mypy
+mypy:
+	poetry run mypy --config-file pyproject.toml elastica
 
 .PHONY: test
 test:
@@ -74,14 +77,14 @@ test_coverage_xml:
 	NUMBA_DISABLE_JIT=1 poetry run pytest --cov=elastica --cov-report=xml
 
 .PHONY: check-codestyle
-check-codestyle: black-check flake8 autoflake8-check
+check-codestyle: black-check flake8 autoflake-check
 
 .PHONY: formatting
 formatting: format-codestyle
 
 .PHONY: update-dev-deps
 update-dev-deps:
-	poetry add -D pytest@latest coverage@latest pytest-html@latest pytest-cov@latest black@latest
+	poetry add -D mypy@latest pytest@latest coverage@latest pytest-html@latest pytest-cov@latest black@latest
 
 #* Cleaning
 .PHONY: pycache-remove
@@ -92,6 +95,10 @@ pycache-remove:
 dsstore-remove:
 	find . | grep -E ".DS_Store" | xargs rm -rf
 
+.PHONY: mypycache-remove
+mypycache-remove:
+	find . | grep -E ".mypy_cache" | xargs rm -rf
+
 .PHONY: ipynbcheckpoints-remove
 ipynbcheckpoints-remove:
 	find . | grep -E ".ipynb_checkpoints" | xargs rm -rf
@@ -105,7 +112,7 @@ build-remove:
 	rm -rf build/
 
 .PHONY: cleanup
-cleanup: pycache-remove dsstore-remove ipynbcheckpoints-remove pytestcache-remove
+cleanup: pycache-remove dsstore-remove ipynbcheckpoints-remove pytestcache-remove mypycache-remove
 
 all: format-codestyle cleanup test
 

README.md

@@ -8,12 +8,12 @@ PyElastica is the python implementation of **Elastica**: an *open-source* projec
 
 [![gallery][link-readme-gallary]][link-project-website]
 
-Visit [cosseratrods.org][link-project-website] for more information and learn about Elastica and Cosserat rod theory.
+Visit [www.cosseratrods.org][link-project-website] for more information and learn about Elastica and Cosserat rod theory.
 
 ## How to Start
 [![PyPI version][badge-pypi]][link-pypi] [![Documentation Status][badge-docs-status]][link-docs-status]
 
-PyElastica is compatible with Python 3.8 - 3.10.
+PyElastica is compatible with Python 3.10 - 3.11.
 
 ~~~bash
 $ pip install pyelastica
@@ -31,6 +31,11 @@ Options can be combined e.g.
 $ pip install "pyelastica[examples,docs]"
 ```
 
+For plotting videos, ffmpeg has to be installed:
+```bash
+$ conda install -c conda-forge ffmpeg
+```
+
 Documentation of PyElastica is available [here][link-docs-website].
 
 If you want to simulate magnetic Cosserat rods interacting with external magnetic environments you can install the derived package using
@@ -46,25 +51,26 @@ Details can be found [here](https://github.com/armantekinalp/MagnetoPyElastica).
 We ask that any publications which use Elastica cite as following:
 
 ```
-@software{arman_tekinalp_2023_7931429,
+@software{arman_tekinalp_2024_10883271,
   author       = {Arman Tekinalp and
                   Seung Hyun Kim and
                   Yashraj Bhosale and
                   Tejaswin Parthasarathy and
                   Noel Naughton and
-                  Ilia Nasiriziba and
+                  Ali Albazroun and
+                  Rahul Joon and
                   Songyuan Cui and
+                  Ilia Nasiriziba and
                   Maximilian Stölzle and
                   Chia-Hsien (Cathy) Shih and
-                  Mattia Gazzola
-                  },
-  title        = {GazzolaLab/PyElastica: v0.3.1},
-  month        = may,
-  year         = 2023,
+                  Mattia Gazzola},
+  title        = {GazzolaLab/PyElastica: v0.3.2},
+  month        = mar,
+  year         = 2024,
   publisher    = {Zenodo},
-  version      = {v0.3.1},
-  doi          = {10.5281/zenodo.7931429},
-  url          = {https://doi.org/10.5281/zenodo.7931429}
+  version      = {v0.3.2},
+  doi          = {10.5281/zenodo.10883271},
+  url          = {https://doi.org/10.5281/zenodo.10883271}
 }
 ```
 
@@ -77,8 +83,11 @@ We ask that any publications which use Elastica cite as following:
 </details>
 
 ## List of publications and submissions
+- [Soft, slender and active structures in fluids: embedding Cosserat rods in vortex methods](https://doi.org/10.48550/arXiv.2401.09506) (UIUC 2024)
+- [Neural models and algorithms for sensorimotor control of an octopus arm](https://doi.org/10.48550/arXiv.2402.01074)(UIUC 2024)
+- [On the mechanical origins of waving, coiling and skewing in Arabidopsis thaliana roots](https://www.pnas.org/doi/10.1073/pnas.2312761121) (Tel Aviv University, UIUC 2024) (PNAS)
 - [Topology, dynamics, and control of an octopus-analog muscular hydrostat](https://arxiv.org/abs/2304.08413) (UIUC, 2023)
-- [Hierarchical control and learning of a foraging CyberOctopus](https://arxiv.org/abs/2302.05811) (UIUC, 2023)
+- [Hierarchical control and learning of a foraging CyberOctopus](https://onlinelibrary.wiley.com/doi/full/10.1002/aisy.202300088) (UIUC, 2023) (Advanced Intelligent Systems)
 - [Energy-shaping control of a muscular octopus arm moving in three dimensions](https://royalsocietypublishing.org/doi/full/10.1098/rspa.2022.0593) (UIUC, 2023) (Proceedings of the Royal Society A 2023)
 - [A sensory feedback control law for octopus arm movements](https://ieeexplore.ieee.org/abstract/document/9993021/) (UIUC, 2022) (IEEE CDC 2022)
 - [Control-oriented modeling of bend propagation in an octopus arm](https://ieeexplore.ieee.org/abstract/document/9867689/) (UIUC, 2021) (IEEE ACC 2022)
@@ -93,16 +102,17 @@ We ask that any publications which use Elastica cite as following:
 
 We have created several Jupyter notebooks and Python scripts to help users get started with PyElastica. The Jupyter notebooks are available on Binder, allowing you to try out some of the tutorials without having to install PyElastica.
 
-We have also included an example script for visualizing PyElastica simulations using POVray. This script is located in the examples folder ([`examples/visualization`](examples/visualization)).
+We have also included an example script for visualizing PyElastica simulations using POVray. This script is located in the examples folder ([`examples/Visualization`](examples/Visualization)).
 
 ## Contribution
 
 If you would like to participate, please read our [contribution guideline](CONTRIBUTING.md)
 
-PyElastica is developed by the [Gazzola Lab][link-lab-website] at the University of Illinois at Urbana-Champaign.
+PyElastica is developed by the [Gazzola Lab][link-lab-website] at the University of Illinois Urbana-Champaign.
 
 ## Senior Developers ✨
 _Names arranged alphabetically_
+- Ali Albazroun
 - Arman Tekinalp
 - Chia-Hsien Shih (Cathy)
 - Fan Kiat Chan
@@ -111,6 +121,7 @@ _Names arranged alphabetically_
 - [Seung Hyun Kim](https://github.com/skim0119)
 - Songyuan Cui
 - Tejaswin Parthasarathy (Teja)
+- Xiaotian Zhang
 - [Yashraj Bhosale](https://github.com/bhosale2)
 
 [//]: # (Collection of URLs.)

RELEASE.md

@@ -1,3 +1,38 @@
+# Release 0.3.2
+
+## New Features
+
+* Rod sphere contact by @Rahul-JOON in https://github.com/GazzolaLab/PyElastica/pull/298 and @Ali-7800 in https://github.com/GazzolaLab/PyElastica/pull/301
+* Importing mesh capability is implemented @Rahul-JOON in https://github.com/GazzolaLab/PyElastica/pull/275, https://github.com/GazzolaLab/PyElastica/pull/277, https://github.com/GazzolaLab/PyElastica/pull/283
+
+## What's Changed
+
+* Contact unit tests were implemented @Rahul-JOON in https://github.com/GazzolaLab/PyElastica/pull/257, https://github.com/GazzolaLab/PyElastica/pull/258, https://github.com/GazzolaLab/PyElastica/pull/260, https://github.com/GazzolaLab/PyElastica/pull/261, https://github.com/GazzolaLab/PyElastica/pull/262, https://github.com/GazzolaLab/PyElastica/pull/267, https://github.com/GazzolaLab/PyElastica/pull/269, https://github.com/GazzolaLab/PyElastica/pull/274
+* Contact functions refactored and moved to a standalone contact module @Ali-7800 in https://github.com/GazzolaLab/PyElastica/pull/281, https://github.com/GazzolaLab/PyElastica/pull/291, https://github.com/GazzolaLab/PyElastica/pull/293, https://github.com/GazzolaLab/PyElastica/pull/314, https://github.com/GazzolaLab/PyElastica/pull/316, https://github.com/GazzolaLab/PyElastica/pull/317, https://github.com/GazzolaLab/PyElastica/pull/328
+* Memory block refactor by @sy-cui in https://github.com/GazzolaLab/PyElastica/pull/296
+* New example Continuum Snake With Lifting Wave added by @Ali-7800 in https://github.com/GazzolaLab/PyElastica/pull/317
+* Catenary curve validation  by @Ali-7800 in https://github.com/GazzolaLab/PyElastica/pull/335
+
+## Minor Fixes
+
+* Fix links in README.md by @tokoro10g in https://github.com/GazzolaLab/PyElastica/pull/256
+* Fix knot theory functionalities import by @Ali-7800 in https://github.com/GazzolaLab/PyElastica/pull/268
+* Binder snake example bug fix by @Ali-7800 in https://github.com/GazzolaLab/PyElastica/pull/330
+* Binder environment setup fix  by @Ali-7800 in https://github.com/GazzolaLab/PyElastica/pull/340
+
+## Repository Update
+
+* Python 3.11 support by @bhosale2 in https://github.com/GazzolaLab/PyElastica/pull/307
+
+
+## New Contributors
+
+* @tokoro10g made their first contribution in https://github.com/GazzolaLab/PyElastica/pull/256
+* @Ali-7800 made their first contribution in https://github.com/GazzolaLab/PyElastica/pull/268
+
+**Full Changelog**: https://github.com/GazzolaLab/PyElastica/compare/v0.3.1...v0.3.2
+
+
 # Release 0.3.1
 
 ## New Features