Merge branch 'update-v1' of https://github.com/GazzolaLab/PyElastica into update-v1

Author: skim0119

.github/workflows/elasticapp.yml

@@ -0,0 +1,61 @@
+name: elasticapp (Elastica++ based backend) tests
+
+# trigger run only on changes to the backend folder.
+on:
+  push:
+    paths:
+      - backend/**
+  pull_request:
+    paths:
+      - backend/**
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.11"] #, "3.12"]
+        os: [ubuntu-latest] # , macos-latest]
+        include:
+          - os: ubuntu-latest
+            path: ~/.cache/pip
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          uv-version: latest
+      - name: Compile OpenMP
+        env:
+          OMP_NUM_THREADS: 2
+        run: |
+          sudo apt-get update; sudo apt-get install -y libomp5 libomp-dev
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Set up cache
+        uses: actions/cache@v5
+        with:
+          path: ${{ matrix.path }}
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('uv.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('uv.lock') }}
+            ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
+
+      - name: Install PyElastica and dependencies
+        run: |
+          make install-dev-deps PYTHON_VERSION=${{ matrix.python-version }}
+          uv cache prune --ci
+
+      - name: Run elasticapp tests
+        run: |
+          source .venv/bin/activate
+          cd backend
+          make clean-build
+          make test
+          # pytest backend/tests/py

.github/workflows/main.yml

@@ -44,7 +44,7 @@ jobs:
         run: python -c "import sys; print(sys.version)"
       # Set up cache
       - name: Set up cache
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: ${{ matrix.path }}
           key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}-${{ hashFiles('uv.lock') }}

.gitignore

@@ -219,6 +219,7 @@ sample_prog.py
 
 # txt files
 *.txt
+!CMakelists.txt
 
 # movie or video file formats
 *.mp4
@@ -241,3 +242,6 @@ outcmaes/*
 
 # csv files
 *.csv
+
+# ./backend dependencies
+deps

Makefile

@@ -34,7 +34,7 @@ pre-commit-install:
 .PHONY: black
 black:
 	uv run black --version
-	uv run black --config pyproject.toml elastica tests examples
+	uv run black --config pyproject.toml elastica tests examples backend
 
 .PHONY: black-check
 black-check:
@@ -54,7 +54,7 @@ autoflake-check:
 .PHONY: autoflake-format
 autoflake-format:
 	uv run autoflake --version
-	uv run autoflake --in-place $(AUTOFLAKE_ARGS) elastica tests examples
+	uv run autoflake --in-place $(AUTOFLAKE_ARGS) elastica tests examples backend
 
 .PHONY: format-codestyle
 format-codestyle: black autoflake-format
@@ -71,15 +71,15 @@ mypy:
 
 .PHONY: test
 test:
-	uv run pytest -c pyproject.toml
+	uv run pytest -c pyproject.toml tests
 
 .PHONY: test_coverage
 test_coverage:
-	NUMBA_DISABLE_JIT=1 uv run pytest --cov=elastica -c pyproject.toml
+	NUMBA_DISABLE_JIT=1 uv run pytest --cov=elastica -c pyproject.toml tests
 
 .PHONY: test_coverage_xml
 test_coverage_xml:
-	NUMBA_DISABLE_JIT=1 uv run pytest --cov=elastica --cov-report=xml -c pyproject.toml
+	NUMBA_DISABLE_JIT=1 uv run pytest --cov=elastica --cov-report=xml -c pyproject.toml tests
 
 .PHONY: check-codestyle
 check-codestyle: black-check flake8 autoflake-check

backend/.clang-format

@@ -0,0 +1,17 @@
+---
+# We'll use defaults from the Google style.
+# See http://clang.llvm.org/docs/ClangFormat.html for help.
+Language: Cpp
+BasedOnStyle: Google
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+PointerAlignment: Left
+DerivePointerAlignment: false
+FixNamespaceComments: true
+IncludeCategories:
+  - Regex: "^<.*"
+    Priority: 1
+  - Regex: ".*"
+    Priority: 2
+NamespaceIndentation: All
+SortIncludes: false

backend/.gitignore

@@ -0,0 +1,12 @@
+CMakeLists.txt.user
+CMakeCache.txt
+CMakeFiles
+CMakeScripts
+Testing
+Makefile
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps
+