Merge pull request #86 from VegeWaterDynamics/fix_dependecies

Fix dependecies

.github/workflows/build.yml

@@ -1,37 +1,28 @@
-name: Build
+name: Build and test Python package
 
 on: [push, pull_request]
 
 jobs:
 
   build:
-    name: Build for ${{ matrix.python-version }}
-    runs-on: 'ubuntu-latest'
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10']
+        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        python-version: ['3.10', '3.11']
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Python info
-        shell: bash -l {0}
-        run: |
-          which python
-          python --version
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
-      - name: Build
-        shell: bash -l {0}
-        run: |
-          python setup.py build
-      - name: Test
-        shell: bash -l {0}
-        run: |
-          pip install pytest pytest-cov pycodestyle
-          pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
+          python -m pip install build
+          python -m pip install .[dev]
+      - name: Build the package
+        run: python -m build
+      - name: Run tests
+        run: pytest tests/

pyproject.toml

@@ -0,0 +1,105 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "motrainer"
+version = "0.1.0"
+requires-python = ">=3.10, <3.12"
+dependencies = [
+    "dask[complete]",
+    "ipykernel",
+    "numpy<1.24.0",
+    "pandas==2.0.3",
+    "scikit-learn",
+    "scikit-optimize",
+    "scipy",
+    "tensorflow",
+    "xarray",
+    "zarr",
+]
+description = "Machine Learning module to train a surrogate module using Land-surface model output"
+readme = "README.rst"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Ou Ku", email = "[email protected]"},
+    {name = "Fakhereh Sarah Alidoost"},
+    {name = "Pranav Chandramouli"},
+    {name = "Francesco Nattino"},
+    {name = "Meiert Willem Grootes"},
+    {name = "Xu Shan"},
+    {name = "Sonja Georgievska"},
+    {name = "Susan Steele-Dunne"},
+]
+keywords = ["machine learning", "earth observation", "data assimilations", "training", "sensor"]
+classifiers=[
+    'Development Status :: 3 - Alpha',
+    'Intended Audience :: Developers',
+    'License :: OSI Approved :: Apache Software License',
+    'Natural Language :: English',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+]
+
+[project.urls]
+repository = "https://github.com/VegeWaterDynamics/motrainer"
+doi = "https://zenodo.org/doi/10.5281/zenodo.7540442"
+documentation = "https://VegeWaterDynamics.github.io/motrainer/"
+changelog = "https://VegeWaterDynamics.github.io/motrainer/CHANGELOG/"
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytest-cov",
+    "pycodestyle",
+    "ruff",
+]
+docs = [
+    "mkdocs",
+    "mkdocs-material",
+    "mkdocs-jupyter",
+    "mkdocstrings[python]",
+    "mkdocs-gen-files",
+]
+demo = [
+    "jupyterlab",
+    "matplotlib",
+]
+
+[tool.setuptools]
+packages = ["motrainer"]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "--cov --cov-report term"
+testpaths = [
+    "tests",
+]
+
+[tool.coverage.run]
+branch = true
+source = ["motrainer"]
+
+[tool.ruff]
+select = [
+  "E",  # pycodestyle
+  "F",  # pyflakes
+  "B",  # flake8-bugbear
+  "D",  # pydocstyle
+  "I",  # isort
+  "N",  # PEP8-naming
+  "UP",  # pyupgrade (upgrade syntax to current syntax)
+  "PLE",  # Pylint error https://github.com/charliermarsh/ruff#error-ple
+]
+ignore = [
+"D100", "D101", "D104", "D105", "D106", "D107", "D203", "D213"
+] # docstring style
+
+line-length = 88
+exclude = ["docs", "build"]
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+target-version = "py310"
+
+[tool.ruff.per-file-ignores]
+"tests/**" = ["D"]

setup.py

@@ -1,50 +1,5 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-from setuptools import setup
-
-# To update the package version number, edit CITATION.cff
-with open('CITATION.cff', 'r') as cff:
-    for line in cff:
-        if 'version:' in line:
-            version = line.replace('version:', '').strip().strip('"')
+"""The setup script."""
 
-with open('README.rst') as readme_file:
-    readme = readme_file.read()
-
-with open('requirements.txt') as requirements_file:
-    requirements = requirements_file.read().split()
+from setuptools import setup
 
-setup(
-    name='motrainer',
-    version=version,
-    description="Machine Learning module to train a surrogate module using Land-surface model dtput",
-    long_description=readme + '\n\n',
-    author="Netherlands eScience Center, TUDelft",
-    author_email='[email protected]',
-    url='https://github.com/VegeWaterDynamics/motrainer',
-    packages=[
-        'motrainer',
-    ],
-    include_package_data=True,
-    license="Apache Software License 2.0",
-    zip_safe=False,
-    keywords='motrainer',
-    classifiers=[
-        'Development Status :: 2 - Pre-Alpha',
-        'Intended Audience :: Developers',
-        'License :: OSI Approved :: Apache Software License',
-        'Natural Language :: English',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-    ],
-    test_suite='tests',
-    install_requires=requirements,  
-    tests_require=[
-        'pytest',
-        'pytest-cov',
-        'pycodestyle',
-    ],
-    data_files=[('citation/motrainer', ['CITATION.cff'])]
-)
+setup()