feat: Added triangle accuracy tests. Moved some types out of System a…

.github/workflows/tests.yml

@@ -17,26 +17,18 @@ permissions:
   contents: read
 
 jobs:
-  pre-commit:
+  fmt:
     runs-on: ubuntu-latest
     steps:
-      - name: Setup | Checkout
-        uses: actions/checkout@v4
-      - name: Setup | Rust
-        uses: actions-rust-lang/setup-rust-toolchain@v1
-        with:
-          toolchain: stable
-          components: |
-            clippy
-            rustfmt
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+      - uses: earthly/actions-setup@v1
         with:
-          python-version: '3.9'
-      - uses: pre-commit/[email protected]
+          version: v0.8.4
+      - name: Fmt
+        run: earthly +fmt
 
   test:
-    needs: pre-commit
-    name: Tests
+    needs: fmt
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

.gitignore

@@ -2,18 +2,17 @@
 # Local files and folders #
 ###########################
 .DS_Store
-/.vscode/settings.json
-.idea/
-.venv
 logs
 .hermit
 *.so
 .coverage
 .tmp-earthly-out
+.vscode/settings.json
+.ruff_cache
 
-############################
-# Rust. Generated by Cargo #
-############################
+################################################################################
+# Rust. Generated by Cargo                                                     #
+################################################################################
 
 # Generated by Cargo, will have compiled files and executables
 /target/
@@ -25,3 +24,170 @@ poetry.lock
 
 # These are backup files generated by rustfmt
 **/*.rs.bk
+
+################################################################################
+# Python.                                                                      #
+################################################################################
+
+# 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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/

.pre-commit-config.yaml

@@ -32,10 +32,11 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.3.1
+    rev: v0.5.1
     hooks:
       # Run the linter.
       - id: ruff
+        args: ["--fix"]
       # Run the formatter.
       - id: ruff-format
 

Cargo.toml

@@ -2,13 +2,33 @@
 members = [
     "crates/abd-clam",
     "crates/distances",
-    "crates/SyMaGen",
-    "crates/pancakes-results",
+    "crates/symagen",
+    "crates/results/pancakes",
+    "crates/results/chaoda",
+    "crates/results/vis",
     "pypi/distances",
-    # "py-clam",  # TODO: re-enable when we have python bindings
 ]
 resolver = "2"
 
+[workspace.dependencies]
+abd-clam = { version = "0.30.0", path = "crates/abd-clam" }
+distances = { version = "1.7.0", path = "crates/distances" }
+symagen = { version = "0.4.0", path = "crates/symagen" }
+
+rayon = "1.8"
+rand = "0.8"
+serde = { version = "1.0", features = ["derive"] }
+mt_logger = "3.0"
+libm = "0.2"
+ndarray = { version = "0.15.6", features = ["rayon"] }
+ndarray-npy = "0.8.0"
+ordered-float = "4.2"
+
+# Python wrapper dependencies
+numpy = "0.20.0"
+pyo3 = { version = "0.20", features = ["extension-module", "abi3-py39"] }
+pyo3-ffi = { version = "0.20", features = ["extension-module", "abi3-py39"] }
+
 [profile.test]
 opt-level = 3
 debug = true

Earthfile

@@ -36,10 +36,10 @@ chef-prepare:
 chef-cook:
     COPY +chef-prepare/recipe.json ./
     RUN cargo chef cook --release
-    COPY Cargo.toml pyproject.toml requirements.lock requirements-dev.lock ruff.toml .
+    COPY Cargo.toml pyproject.toml requirements.lock requirements-dev.lock ruff.toml rustfmt.toml .
     # TODO: Replace with recursive globbing, blocked on https://github.com/earthly/earthly/issues/1230
-    COPY --dir pypi .
     COPY --dir crates .
+    COPY --dir pypi .
     RUN rye sync --no-lock
 
 # This target builds the project using the cached dependencies.
@@ -72,7 +72,7 @@ fix:
 
 # This target runs the tests.
 test:
-    FROM +fmt
+    FROM +chef-cook
     RUN cargo test --release --lib --bins --examples --tests --all-features
     # TODO: switch to --all, blocked on https://github.com/astral-sh/rye/issues/853
     RUN rye test --package abd-distances