migrated the package manager and build-backend (#73)

* make package compatible with pip
* update taskfile to use uv
* use uv for package management
* add support automatic versioning from git tags
* make scripts accessible (docs and pyproject.toml update)
* migrate flake-8 config to pyproject.toml

Author: laraibg786

.github/workflows/ci-cd.yml

@@ -33,15 +33,15 @@ jobs:
           sh -c "$(curl --location https://taskfile.dev/install.sh)" -- -d
 
       # Cache dependencies from poetry to speed things up
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v3
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Install and upgrade pip and poetry
-        run: python -m pip install --upgrade pip poetry
+      # - name: Load cached venv
+      #   id: cached-poetry-dependencies
+      #   uses: actions/cache@v3
+      #   with:
+      #     path: .venv
+      #     key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Install and upgrade pip and uv
+        run: python -m pip install --upgrade pip uv
 
       - name: Install Dependencies
         run: ./bin/task setup

Taskfile.yml

@@ -4,24 +4,24 @@ tasks:
   setup:
     desc: Setup the development environment.
     cmds:
-      - poetry install
+      - uv sync
 
   lint:
     desc: Lints the code and reports on issues.
     cmds:
-      - poetry run black --check .
-      - poetry run ruff check .
+      - uv run black --check .
+      - uv run ruff check .
 
   build:
     desc: Builds the python package
     cmds:
-      - poetry build
+      - uv build
 
   test:
     desc: Runs tests on the code
     cmds:
       - >
-        poetry run pytest test
+        uv run pytest test
         --cov=lasso
         --cov-report=html
 
@@ -31,29 +31,29 @@ tasks:
       - test
       - docs:changelog
     cmds:
-      - poetry run mkdocs serve
+      - uv run mkdocs serve
 
   docs:build:
     desc: Build the documentation
     deps:
       - test
       - docs:changelog
     cmds:
-      - poetry run mkdocs build
+      - uv run mkdocs build
 
   docs:deploy:
     desc: Deploys the docs to GitHub (be careful!)
     deps:
       - test
       - docs:changelog
     cmds:
-      - poetry run mkdocs gh-deploy
+      - uv run mkdocs gh-deploy
 
   docs:changelog:
     desc: Generates the changelog
     cmds:
       - >
-        poetry run git-changelog .
+        uv run git-changelog .
         --output CHANGELOG.md
         --style angular
         --template angular

docs/diffcrash/run.md

@@ -18,7 +18,7 @@ easier.
 You can get the run info by performing:
 
 ```console
-$ python -m lasso.diffcrash.run --help
+$ diffcrash --help
 
 ==== D I F F C R A S H ====
 

docs/dimred/command_line_interface.md

@@ -160,7 +160,7 @@ resizeContents()
 You can call the command-line tool as follows:
 
 ```console
-$ python -m lasso.dimred.run --help
+$ dimred --help
 
 usage: run.py [-h] --reference-run REFERENCE_RUN
               [--exclude-runs [EXCLUDE_RUNS [EXCLUDE_RUNS ...]]]

lasso/__init__.py

@@ -0,0 +1,7 @@
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("lasso-python")
+except PackageNotFoundError:
+    # package is not installed
+    pass

lasso/dimred/graph_laplacian.py

@@ -96,7 +96,7 @@ def _laplacian_gauss_idw(
     for i, (j, d, e, k) in enumerate(
         zip(
             *tree.query_radius(points, return_distance=True, r=search_radius),
-            *tree.query(points, return_distance=True, k=1 + min_neighbors)
+            *tree.query(points, return_distance=True, k=1 + min_neighbors),
         )
     ):
         # Always search for k neighbors, this prevents strongly connected local areas

poetry.lock

@@ -1,9 +1,10 @@
-[tool.poetry]
+[project]
 name = "lasso-python"
-version = "2.0.3"
 description = "An open-source CAE and Machine Learning library."
-authors = ["open-lasso-python <[email protected]>"]
-license = "BSD-3"
+license-files = ["LICENSE.md"]
+readme = "README.rst"
+dynamic = ["version"]
+authors = [{ name = "open-lasso-python", email = "[email protected]" }]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Topic :: Scientific/Engineering",
@@ -12,43 +13,52 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
-packages = [
-    { include = "lasso" }
+
+requires-python = ">=3.9"
+dependencies = [
+    "h5py==3.*",
+    "scipy==1.*",
+    "numpy==1.*",
+    "plotly==5.*",
+    # "attrs==23.*"
+    "psutil==5.*",
+    "rich==13.*",
+    "pandas==2.*",
+    "scikit_learn==1.*"
 ]
 
-[tool.poetry.dependencies]
-python = "^3.9"
-h5py = "^3.7.0"
-scipy = "^1.9.1"
-numpy = "^1.23.3"
-plotly = "^5.10.0"
-attrs = "^23.2.0"
-psutil = "^5.9.2"
-rich = "^13.0.0"
-pandas = "^2.2.0"
-scikit-learn = "^1.2.1"
+[project.scripts]
+diffcrash = "lasso.diffcrash.run:main"
+dimred = "lasso.dimred.run:main"
 
-[tool.poetry.group.dev.dependencies]
-pytest = "^8.0.0"
-pytest-cov = "^5.0.0"
-black = "^24.3.0"
-ruff = "^0.3.7"
-mkdocs = "^1.4.2"
-mkdocs-material = "^9.5.0"
-mkdocstrings = {extras = ["python"], version = "^0.24.3"}
-mkdocs-coverage = "^1.0.0"
-git-changelog = "^2.5.0"
-twine = "^5.0.0"
+[dependency-groups]
+dev = [
+    "pytest==8.*",
+    "pytest-cov==5.*",
+    "black==24.*",
+    "ruff==0.3.*",
+    "mkdocs==1.*",
+    "mkdocs-material==9.*",
+    "mkdocstrings[python]==0.*",
+    "mkdocs-coverage==1.*",
+    "git-changelog==2.*",
+    "twine==5.*",
+    "go-task-bin"
+]
 
 [build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ["setuptools>=78", "setuptools-scm>=8"]
+build-backend = "setuptools.build_meta"
 
 [tool.black]
 # We allow longer lines since 80 is quite short
 line-length=100
+
+[tool.flake8]
+exclude = [".git", "*migrations*"]
+max-line-length = 100