Move from requirements.txt to pyproject.toml to conform to PEP 621

.gitignore

@@ -1,4 +1,162 @@
 /out
-/venv
-*.DS_Store
-**/__pycache__/
+!/src/dtpo/lib
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# setuptools_scm
+src/*/_version.py
+
+
+# ruff
+.ruff_cache/
+
+# OS specific stuff
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Common editor files
+*~
+*.swp
+
+# Hatch-vcs version file
+_version.py
+
+# VSCode
+.vscode/

docs/index.md

@@ -0,0 +1,3 @@
+# dtpo
+::: dtpo
+    show_root: true(base)

mkdocs.yml

@@ -0,0 +1,15 @@
+site_name: Documentation
+
+nav:
+  - Home: index.md
+
+theme: material
+
+plugins:
+  - autorefs:
+      resolve_closest: true
+  - mkdocstrings:
+      handlers:
+        python:
+          options:
+            show_submodules: true

pyproject.toml

@@ -0,0 +1,186 @@
+[project]
+name = "dtpo"
+version = "0.1.0"
+authors = [
+  { name = "Daniel Vos", email = "d.a.vos@tudelft.nl" },
+]
+description = "Interpretable reinforcement learning using policy gradients to optimize decision trees"
+readme = "README.md"
+requires-python = ">=3.11"
+dependencies = [
+    "absl-py==2.1.0",
+    "black==23.12.1",
+    "chex==0.1.85",
+    "click==8.1.7",
+    "cloudpickle==3.0.0",
+    "contourpy==1.2.0",
+    "cycler==0.12.1",
+    "decorator==5.1.1",
+    "distrax==0.1.5",
+    "dm-env==1.6",
+    "dm-tree==0.1.8",
+    "etils==1.5.2",
+    "farama-notifications==0.0.4",
+    "filelock==3.13.1",
+    "flax==0.7.5",
+    "fonttools==4.47.2",
+    "fsspec==2023.12.2",
+    "gast==0.5.4",
+    "gym==0.26.2",
+    "gym-notices==0.0.8",
+    "gymnasium==0.29.1",
+    "gymnax==0.0.6",
+    "importlib-metadata==7.0.1",
+    "importlib-resources==6.1.1",
+    "jax==0.4.23",
+    "jaxlib==0.4.23",
+    "jinja2==3.1.3",
+    "joblib==1.3.2",
+    "kiwisolver==1.4.5",
+    "markdown-it-py==3.0.0",
+    "markupsafe==2.1.4",
+    "matplotlib==3.8.2",
+    "mdurl==0.1.2",
+    "ml-dtypes==0.3.2",
+    "mpmath==1.3.0",
+    "msgpack==1.0.7",
+    "mypy-extensions==1.0.0",
+    "nest-asyncio==1.6.0",
+    "networkx==3.2.1",
+    "numpy==1.26.3",
+    "opt-einsum==3.3.0",
+    "optax==0.1.8",
+    "orbax-checkpoint==0.5.0",
+    "packaging==23.2",
+    "pandas==2.2.0",
+    "pathspec==0.12.1",
+    "pillow==10.2.0",
+    "platformdirs==4.1.0",
+    "protobuf==4.25.2",
+    "pydot==2.0.0",
+    "pygments==2.17.2",
+    "pyparsing==3.1.1",
+    "python-dateutil==2.8.2",
+    "pytz==2023.3.post1",
+    "pyyaml==6.0.1",
+    "rich==13.7.0",
+    "rlax==0.1.6",
+    "scikit-learn==1.2.2",
+    "scipy==1.12.0",
+    "seaborn==0.13.1",
+    "six==1.16.0",
+    "stable-baselines3==2.2.1",
+    "sympy==1.12",
+    "tensorflow-probability==0.23.0",
+    "tensorstore==0.1.52",
+    "threadpoolctl==3.2.0",
+    "tomli==2.0.1",
+    "toolz==0.12.0",
+    "torch==2.1.2",
+    "tqdm==4.66.1",
+    "typing-extensions==4.9.0",
+    "tzdata==2023.4",
+    "zipp==3.17.0",
+]
+
+[dependency-groups]
+dev = [
+  "hatch>=1.13.0,<2",
+  "pre-commit>=3.8.0,<4",
+  "pytest>=8.3.3,<9",
+  "pytest-cov>=5.0.0,<6",
+  "mkdocstrings[python]>=0.26.1,<1",
+  "mkdocs-material>=9.5.39,<10",
+  "setuptools-scm>=8.1.0,<9",
+  "pyinstaller>=6.16.0",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/dtpo"]
+
+[project.urls]
+Homepage = "https://github.com/tudelft-cda-lab/DTPO"
+
+[project.scripts]
+dtpo = "dtpo.run_dtpo:main"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+xfail_strict = true
+filterwarnings = [
+  "error",
+]
+log_cli_level = "INFO"
+testpaths = [
+  "tests",
+]
+
+[tool.coverage]
+run.source = ["boswachter"]
+port.exclude_lines = [
+  'pragma: no cover',
+  '\.\.\.',
+  'if typing.TYPE_CHECKING:',
+]
+
+[tool.ruff]
+src = ["src"]
+exclude = []
+line-length = 120  # how long you want lines to be
+
+[tool.ruff.format]
+docstring-code-format = true  # code snippets in docstrings will be formatted
+
+[tool.ruff.lint]
+# For more strict linting and code simplifications, replace this with
+# https://github.com/NLeSC/python-template/blob/main/template/pyproject.toml.jinja#L121-L136
+select = [
+  "E", "F", "W", # flake8
+  "B",           # flake8-bugbear
+  "I",           # isort
+  "ARG",         # flake8-unused-arguments
+  "C4",          # flake8-comprehensions
+  "EM",          # flake8-errmsg
+  "ICN",         # flake8-import-conventions
+  "ISC",         # flake8-implicit-str-concat
+  "G",           # flake8-logging-format
+  "PGH",         # pygrep-hooks
+  "PIE",         # flake8-pie
+  "PL",          # pylint
+  "PT",          # flake8-pytest-style
+  "RET",         # flake8-return
+  "RUF",         # Ruff-specific
+  "SIM",         # flake8-simplify
+  "UP",          # pyupgrade
+  "YTT",         # flake8-2020
+  "EXE",         # flake8-executable
+  # "D",           # pydocstyle, uncomment to have the docstrings linted
+  # "ANN",         # flake8-annotations, uncomment to have type hint annotations linted
+]
+ignore = [
+  "PLR",    # Design related pylint codes
+  "ISC001", # Conflicts with formatter
+  "SIM108", # Ternary operator is rarely nicer
+]
+pydocstyle.convention = "google"
+
+[tool.ruff.lint.per-file-ignores]
+# Tests can ignore a few extra rules
+"tests/**.py" = [
+    "ANN201", # Missing return type annotation for public function
+    "D103",   # Missing docstring
+    "S101",   # Use of assert is detected
+    "INP001", # Missing __init__.py file
+]
+
+[tool.yamlfix]
+line_length = 120
+sequence_style = "keep_style"
+explicit_start = false
+whitelines = 1
+section_whitelines = 1