Bump actions/checkout from 3 to 4

.flake8

@@ -0,0 +1,16 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+	env,
+	venv,
+    build,
+    dist
+docstring-convention = numpy
+max-line-length = 100
+max_complexity = 15
+max_function_length = 100
+ignore = D100, D102, D103, D104, W503
+# for compatibility with black
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#flake8
+extend-ignore = E203

.github/dependabot.yml

@@ -0,0 +1,14 @@
+---
+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+- package-ecosystem: github-actions
+  directory: /
+  schedule:
+    interval: weekly
+
+- package-ecosystem: gitsubmodule
+  directory: /
+  schedule:
+    interval: weekly

.github/workflows/system_test.yml

@@ -0,0 +1,33 @@
+---
+name: system test
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: ['*']
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.11']
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dev
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[dev]

.github/workflows/test.yml

@@ -0,0 +1,42 @@
+---
+name: test
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: ['*']
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[tests]
+    - name: Run tests and coverage
+      run: make coverage
+    - name: Code coverage
+      uses: codecov/codecov-action@v3
+      with:
+        file: coverage.xml
+        flags: ${{ matrix.os }}-${{ matrix.python-version }}
+        name: codecov
+        fail_ci_if_error: false

.gitignore

@@ -0,0 +1,2 @@
+*.pt
+archive

.pre-commit-config.yaml

@@ -0,0 +1,72 @@
+---
+repos:
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-added-large-files
+
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: v1.10.0
+  hooks:
+  - id: rst-backticks     # Detect common mistake of using single backticks when writing rst
+  - id: rst-inline-touching-normal     # Detect mistake of inline code touching normal text in rst
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.9.0
+  hooks:
+  - id: pyupgrade
+    args: [--py38-plus]
+
+- repo: https://github.com/ikamensh/flynt/
+  rev: 1.0.0
+  hooks:
+  - id: flynt
+
+- repo: https://github.com/asottile/reorder-python-imports
+  rev: v3.10.0
+  hooks:
+  - id: reorder-python-imports
+    args: [--py38-plus, --add-import, from __future__ import annotations]
+
+# - repo: https://github.com/pre-commit/mirrors-mypy
+#   rev: v1.3.0
+#   hooks:
+#   - id: mypy
+#     additional_dependencies: [types-all]
+#     files: bidspm
+#     args: [--config-file, setup.cfg]
+
+- repo: https://github.com/MarcoGorelli/auto-walrus
+  rev: v0.2.2
+  hooks:
+  - id: auto-walrus
+
+- repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+  rev: 0.2.3
+  hooks:
+  - id: yamlfmt
+    args: [--mapping, '2', --sequence, '2', --offset, '0']
+
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.5
+  hooks:
+  - id: codespell
+    args: [--toml, pyproject.toml]
+    additional_dependencies: [tomli]
+
+- repo: https://github.com/psf/black
+  rev: 23.7.0
+  hooks:
+  - id: black
+    args: [--config, pyproject.toml]
+
+- repo: https://github.com/pycqa/flake8
+  rev: 6.0.0
+  hooks:
+  - id: flake8
+    args: [--config, .flake8]
+    additional_dependencies: [flake8-docstrings]

Makefile

@@ -0,0 +1,6 @@
+coverage:
+	coverage erase
+	coverage run -m pytest
+	coverage report
+	coverage html
+	coverage xml

EquationTokenizer.py → NumGI/EquationTokenizer.py

@@ -220,4 +220,4 @@ def defaultTokenizer():
 
     dict_size = len(tokenize_dict)
 
-    return tokenize_dict, decode_dict, tokenize, decode
+    return tokenize_dict, decode_dict, tokenize, decode

pyproject.toml

@@ -0,0 +1,48 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "NumGI"
+description = "Differential equation solver."
+readme = "README.md"
+requires-python = ">=3.8"
+license = { file = "LICENSE.txt" }
+authors = [{ name = "Arnaud Bergeron", email = "[email protected]" }]
+dynamic = ["version"]
+dependencies = ["sympy", "torch", "NumGI", "Numba"]
+
+[project.optional-dependencies]
+doc = [
+  "sphinx",
+  "sphinx-argparse",
+  "sphinx-copybutton",
+  "sphinx_rtd_theme",
+  "myst-parser",
+  "rstcheck",
+]
+
+
+
+[tool.hatch.build.targets.wheel]
+packages = ["NumGI"]
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "NumGI/_version.py"
+
+[tool.pytest.ini_options]
+addopts = "-ra -vv"
+
+[tool.coverage.run]
+branch = true
+source = ["NumGI/"]
+
+
+[tool.codespell]
+skip = "./.git,.mypy_cache,env,venv,tests,*bval,*bvec"
+
+[tool.black]
+line-length = 100