Merge pull request #287 from MuellerSeb/refactor_setup

Refactor setup and modernize package structure as well as CI

.github/workflows/main.yml

@@ -0,0 +1,115 @@
+name: Continuous Integration
+
+on:
+  push:
+    branches:
+      - "master"
+    tags:
+      - "*"
+  pull_request:
+    branches:
+      - "master"
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+env:
+  # needed by coveralls
+  GITHUB_TOKEN: ${{ secrets.COVERALLS_TOKEN }}
+
+jobs:
+  source_check:
+    name: source check
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black 'isort[colors]<6'
+          pip install --editable .
+
+      - name: black check
+        run: |
+          python -m black --check --diff --color .
+
+      - name: isort check
+        run: |
+          python -m isort --check --diff --color .
+
+  build_sdist:
+    name: sdist on ${{ matrix.os }} with py ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.7', '3.8', '3.9', '3.10']
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: '0'
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build coveralls>=3.0.0
+          pip install --editable .[test]
+
+      - name: Run tests
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          python -m pytest --cov spotpy --cov-report term-missing -v tests/
+          python -m coveralls --service=github
+
+      - name: Build sdist
+        run: |
+          python -m build
+
+      - uses: actions/upload-artifact@v2
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'
+        with:
+          path: dist
+
+  upload_to_pypi:
+    needs: [build_sdist]
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: artifact
+          path: dist
+
+      - name: Publish to Test PyPI
+        # only if working on master
+        if: github.ref == 'refs/heads/master'
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TEST_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+          skip_existing: true
+
+      - name: Publish to PyPI
+        # only if tagged
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

.gitignore

@@ -9,7 +9,8 @@ __pycache__/
 #other files
 *.out
 *.png
-*.csv
+test_DDS.csv
+./*.csv
 site/*
 #mkdocs.yml
 
@@ -32,6 +33,9 @@ wheels/
 .installed.cfg
 *.egg
 
+# generated version file
+src/spotpy/_version.py
+
 # Python Unittest tool `py.test`
 .pytest_cache/*
 
@@ -98,6 +102,8 @@ ENV/
 .spyderproject
 # PyCharm
 .idea/
+# VSCode
+.vscode/
 
 # Rope project settings
 .ropeproject
@@ -108,12 +114,12 @@ ENV/
 .settings/
 
 # hymod example
-spotpy/examples/hymod/*
+src/spotpy/examples/hymod/*
 
 # Test Cases
-spotpy/hymod/testHymod/*
-spotpy/hymod/RunsWithNewHymod/*
-spotpy/hymod/likelihood_test/*
+src/spotpy/hymod/testHymod/*
+src/spotpy/hymod/RunsWithNewHymod/*
+src/spotpy/hymod/likelihood_test/*
 
 # a doc folder for some notices
 _doc

CONTRIBUTING.md

@@ -6,7 +6,7 @@ There are 4 main ways of contributing to the SPOTPY project (in descending order
 
 * Adding new or improved functionality to the existing codebase
 * Fixing outstanding issues (bugs) with the existing codebase. They range from low-level software bugs to higher-level design problems.
-* Contributing or improving the documentation (`docs`) or examples (`spotpy/examples`)
+* Contributing or improving the documentation (`docs`) or examples (`src/spotpy/examples`)
 * Submitting issues related to bugs or desired enhancements
 
 # Opening issues
@@ -76,7 +76,7 @@ We recommended that your contribution complies with the following guidelines bef
 
 *  Please prefix the title of incomplete contributions with `[WIP]` (to indicate a work in progress). WIPs may be useful to (1) indicate you are working on something to avoid duplicated work, (2) request broad review of functionality or API, or (3) seek collaborators.
 
-*  When adding additional functionality, you may want to provide at least one example script in the ``spotpy/examples/`` folder. Have a look at other examples for reference. Examples should demonstrate why the new functionality is useful in practice and, if possible, compare it to other methods available in SPOTPY.
+*  When adding additional functionality, you may want to provide at least one example script in the ``src/spotpy/examples/`` folder. Have a look at other examples for reference. Examples should demonstrate why the new functionality is useful in practice and, if possible, compare it to other methods available in SPOTPY.
 
 You can also check for common programming errors with the following
 tools:
@@ -111,7 +111,7 @@ tools:
 
 ## Style guide
 
-Follow [TensorFlow's style guide](https://www.tensorflow.org/versions/master/how_tos/style_guide.html) or the [Google style guide](https://google.github.io/styleguide/pyguide.html) for writing code, which more or less follows PEP 8.
+Try to make sure to follow the [Black style guide](https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html) and [isort](https://pypi.org/project/isort/) for code submissions.
 
 
-#### This guide was derived from the [scikit-learn guide to contributing](https://github.com/scikit-learn/scikit-learn/blob/master/CONTRIBUTING.md)
+#### This guide was derived from the [scikit-learn guide to contributing](https://github.com/scikit-learn/scikit-learn/blob/master/CONTRIBUTING.md) and adopted to SPOTPY.

MANIFEST.in

@@ -1,9 +1,6 @@
-include README.md
-include MANIFEST.in
-include setup.py
-include setup.cfg
-recursive-include spotpy/examples/cmf_data *
-recursive-include spotpy/examples/hymod_exe *
-recursive-include spotpy/examples/hymod_unix *
-recursive-include spotpy/examples/hymod_python *
-include LICENSE
+prune **
+graft src/spotpy
+graft tests
+graft tutorials
+include LICENSE README.md pyproject.toml setup.py
+global-exclude __pycache__ *.py[co]