Merge pull request #163 from zStupan/main

Switch to uv for dependency management

Author: zStupan

.github/workflows/ci.yml

@@ -0,0 +1,30 @@
+name: NiaARM Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.11', '3.12', '3.13', '3.14']
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+    - uses: actions/checkout@v6
+    - name: Install uv and set up Python
+      uses: astral-sh/setup-uv@v7
+      with:
+        python-version: ${{ matrix.python-version }}
+        enable-cache: true
+    - name: Install the project
+      run: uv sync --locked --all-extras --group test
+    - name: Run tests
+      run: uv run pytest

.github/workflows/publish.yml

@@ -0,0 +1,25 @@
+name: Publish NiaARM to PyPI
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+      - name: Install uv and set up Python
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: "3.13"
+      - name: Build
+        run: uv build
+      - name: Publish
+        run: uv publish

.github/workflows/test.yml

@@ -1,6 +1,6 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
-*.py[cod]
+*.py[codz]
 *$py.class
 
 # C extensions
@@ -27,8 +27,8 @@ share/python-wheels/
 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.
+#   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
 
@@ -46,7 +46,7 @@ htmlcov/
 nosetests.xml
 coverage.xml
 *.cover
-*.py,cover
+*.py.cover
 .hypothesis/
 .pytest_cache/
 cover/
@@ -92,20 +92,64 @@ ipython_config.py
 #   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
+# Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.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
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
 
 # Celery stuff
 celerybeat-schedule
 celerybeat.pid
 
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
 # SageMath parsed files
 *.sage.py
 
 # Environments
 .env
+.envrc
 .venv
 env/
 venv/
@@ -137,9 +181,36 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
-# JOSS artifacts
-paper.pdf
-paper.jats
-
-# Ruff
+# 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/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer,
+#   you could uncomment the following to ignore the entire vscode folder
+.vscode/
+
+# Ruff stuff:
 .ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml

.gitignore

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -15,12 +15,11 @@ repos:
       - id: check-ast
       - id: check-docstring-first
 
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.10.1
-    hooks:
-      - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.3
+    rev: v0.14.8
     hooks:
-      - id: ruff
-        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-check
+        types_or: [ python, pyi ]
+        args: [ --fix ]
+      - id: ruff-format
+        types_or: [ python, pyi ]

.pre-commit-config.yaml

@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: '3.9'
+    python: '3.13'
 
 python:
   install:
@@ -12,3 +12,6 @@ python:
 sphinx:
   configuration: 'docs/conf.py'
   fail_on_warning: true
+
+formats:
+  - pdf

.readthedocs.yml

@@ -7,7 +7,7 @@ This project and everyone participating in it is governed by the [NiaARM Code of
 ## How Can I Contribute?
 
 ### Reporting Bugs
-Before creating bug reports, please check existing issues list as you might find out that you don't need to create one. When you are creating a bug report, please include as many details as possible in the [issue template](.github/templates/ISSUE_TEMPLATE.md).
+Before creating bug reports, please check existing issues list as you might find out that you don't need to create one. When you are creating a bug report, please include as mAll details as possible in the [issue template](.github/templates/ISSUE_TEMPLATE.md).
 
 ### Suggesting Enhancements
 
@@ -21,56 +21,59 @@ Fill in the [pull request template](.github/templates/PULL_REQUEST.md) and make
 
 ### Requirements
 
-* Poetry: [https://python-poetry.org/docs/](https://python-poetry.org/docs/)
+* uv: [https://docs.astral.sh/uv/](https://docs.astral.sh/uv/)
 
-After installing Poetry and cloning the project from GitHub, you should run the following command from the root of the cloned project:
+After installing uv and cloning the project from GitHub, you should
+run the following command from the root of the cloned project:
 
 ```sh
-poetry install
+uv sync --dev
 ```
 
-All the project's dependencies should be installed and the project ready for further development. **Note that Poetry creates a separate virtual environment for your project.**
+All the project's development dependencies should be installed and the project ready for further development.
 
 ### Dependencies
 
-| Package | Version | Platform |
-|---------|:-------:|:--------:|
-| niapy   | ^2.0.5  |   All    |
-| numpy   | ^1.26.1 |   All    |
-| pandas  | ^2.1.1  |   All    |
-| nltk    | ^3.8.1  |   All    |
-| tomli   | ^2.0.1  |   All    |
+| Package      | Version  | Platform |
+|--------------|:--------:|:--------:|
+| niapy        | \>=2.6.1 |   All    |
+| numpy        | \>=2.3.5 |   All    |
+| pandas       | \>=2.3.3 |   All    |
+| nltk         | \>=3.9.2 |   All    |
+| scikit-learn | \>=1.8.0 |   All    |
+| plotly       | \>=6.5.0 |   All    |
 
 #### Development dependencies
 
-| Package          | Version | Platform |
-|------------------|:-------:|:--------:|
-| pytest           | ^7.4.2  |   Any    |
-| pytest-cov       | ^4.1.0  |   Any    |
-| pytest.randomly  | ^3.15.0 |   Any    |
+| Package         |  Version  | Platform |
+|-----------------|:---------:|:--------:|
+| pytest          | \>=9.0.0  |   All    |
+| pytest-cov      | \>=7.0.0  |   All    |
+| pytest.randomly | \>=4.0.1  |   All    |
+| pre-commit      | \>=4.5.0  |   All    |
+| ruff            | \>=0.14.9 |   All    |
 
-#### Extras
+#### Documentation Dependencies
 
-| Package              | Version | Platform |
-|----------------------|:-------:|:--------:|
-| sphinx               | ^7.2.6  |   Any    |
-| sphinx-rtd-theme     | ^1.0.0  |   Any    |
-| sphinxcontrib-bibtex | ^2.4.1  |   Any    |
+| Package              | Version  | Platform |
+|----------------------|:--------:|:--------:|
+| sphinx               | \>=8.2.3 |   All    |
+| sphinx-rtd-theme     | \>=3.0.2 |   All    |
+| sphinxcontrib-bibtex | \>=2.6.5 |   All    |
 
-## Development Tasks
-
-### Testing
+## Testing
 
 Manually run the tests:
 
 ```sh
-$ poetry run pytest
+uv run pytest
 ```
 
-### Documentation
+## Documentation
 
 Build the documentation:
 
 ```sh
-$ poetry run sphinx-build ./docs ./docs/_build
+uv sync --group docs
+uv run sphinx-build ./docs ./docs/_build
 ```

CONTRIBUTING.md

@@ -68,5 +68,4 @@
 html_logo = "_static/logo.png"
 html_theme_options = {
     "logo_only": True,
-    "display_version": False,
 }