Merge pull request #115 from dnvgl/config-python-versions

Update project configuration and python versions
dnvgl · Dec 5, 2023 · e94c0a5 · e94c0a5
2 parents 1b31108 + f44d5a9
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diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -1,4 +1,7 @@
-# This workflow will upload a Python Package using Twine when a release is created
+# This workflow will upload new releases to PyPi
+# Could write it explicitely ourself but this was neat.
+# Consider moving the docs dependencies to dev to speed up (probably not a problem).
+# reference: https://github.com/marketplace/actions/publish-python-poetry-package
 
 name: Upload Python Package to PyPi
 
@@ -12,20 +15,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
+    - name: Check out repository
+      uses: actions/checkout@v4
+    - name: Build and publish to pypi
+      uses: JRubics/[email protected]
       with:
-        python-version: '3.10'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install wheel twine
-    - name: Build package
-      run: python setup.py sdist bdist_wheel
-    - name: Publish package
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
-      run: |
-        twine upload dist/*
+        python_version: "3.11"
+        plugins: "poetry-dynamic-versioning[plugin]"
+        ignore_dev_requirements: "yes"
+        pypi_token: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,4 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# This workflow will lint, run unit tests, test CLI and build with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: Test Python package
@@ -10,47 +10,98 @@ on:
     branches: [ master ]
 
 jobs:
-  build:
-
-    name: Test with Python ${{ matrix.python-version }} on Ubuntu
+  linting:
+    name: Linting
+    # linting has nothing to do with multiple versions of os and python
+    # (the result will be the same) and therefore separated to save time
     runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - name: Load pip cache if cache exists
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip
+          restore-keys: ${{ runner.os }}-pip
+      - name: Install linters
+        run: python -m pip install black flake8 isort
+      - name: Lint code
+        run: |
+          flake8 ./qats/ --exit-zero --max-complexity=10 --statistics
+          black .
+          isort .
+
+  testing:
+    needs: linting
+    name: Test with Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        os: ["ubuntu-latest"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v2
-      with:
-          fetch-depth: 0
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      # https://stackoverflow.com/questions/75549995/why-do-the-pyside6-qt-modules-cause-tox-to-fail-during-a-github-action
+    - name: Install missing libraries on GitHub agent
+      run: sudo apt update && sudo apt install -y libegl1-mesa-dev
+    - name: Check out repository
+      uses: actions/checkout@v4
+    - name: Set up python ${{ matrix.python-version }}
+      id: setup-python
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Load cached Poetry installation
+      id: cached-poetry
+      uses: actions/cache@v3
+      with:
+        path: ~/.local  # the path depends on the OS
+        key: poetry-0  # increment to reset cache
+    - name: Install and configure Poetry
+      # install if not cached. Create venv in project to simplify caching
+      if: steps.cached-poetry.outputs.cache-hit != 'true'
+      uses: snok/install-poetry@v1
+      with:
+        # Consider specifying version (version: 1.7.1 on Python 3.11)
+        virtualenvs-create: true
+        virtualenvs-in-project: true  #.venv in current directory
+    - name: Load cached venv
+      id: cached-poetry-dependencies
+      uses: actions/cache@v3
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+    - name: Create venv and install project dependencies
+      # install if not cached
+      if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+      run: poetry install --no-interaction --no-root
+    - name: Install project
+      # required to test the CLI, show working directory for debugging
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8
-        # python -m pip install setuptools-scm flake8 wheel pyside2 h5py pymatreader matplotlib npTDMS numpy openpyxl pandas scipy
-        # changed 27.12.2023: install from requirements.txt, so that incompatibilities in requirements lead to failed tests
-        python -m pip install -r requirements.txt
-    - name: Lint with flake8
+        poetry install --no-interaction
+        ls -a
+    - name: Run unit tests
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        #   flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Run tests
+        source .venv/bin/activate
+        pytest test/
+    - name: Test CLI
       env:
-        QT_API: pyside2
+        QT_API: pyside6
       run: |
-        python -m unittest discover
-        python setup.py install
-        # test running qats via entry points
+        source .venv/bin/activate
         qats -h
         qats app -h
         qats config -h
-        # test running qats via __main__ hook
         python -m qats -h
-        # test that building documentation does not fail
+    - name: Test building package
+      run: poetry build
+    - name: Test building documentation
+      run: |
+        source .venv/bin/activate
         sphinx-build -b html docs/source docs/_build
diff --git a/.gitignore b/.gitignore
@@ -108,3 +108,9 @@ code-snippets/
 
 # local test folders
 tmp*/*
+
+# version file written by poetry dynamic versioning
+*/_version.py
+
+# Poetry
+poetry.lock
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -8,22 +8,20 @@ version: 2
 # Set the version of Python and other tools you might need
 build:
   os: ubuntu-20.04
-  tools:
-    # minimum supported Python version
-    python: "3.7"
+  tools: {python: "3.11"}
+  # A solution to build docs with Poetry and avoid an additional (out of sync) requirements.txt
+  # https://github.com/Robpol86/sphinx-multi-theme/blob/28aac0ac3bd54387bd51bfb9c673c2208394c729/.readthedocs.yaml
+  jobs:
+    pre_create_environment:
+      - asdf plugin add poetry
+      - asdf install poetry latest
+      - asdf global poetry latest
+      - poetry config virtualenvs.create false
+    post_install:
+      - poetry install
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   builder: html
   configuration: docs/source/conf.py
   fail_on_warning: true
-
-# Optionally declare the Python requirements required to build your docs
-python:
-  # install qats first, then requirements 
-  # (because RTD uses `--upgrade-strategy eager` to install the package, 
-  # which installs the latest possible version of all dependencies)
-  install:
-    - method: pip
-      path: .
-    - requirements: requirements.txt
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,9 @@
 # Changelog
+
+> **Note:**
+> After version 4.12.1 this changelog is deprecated. Releases will in future be documented in [Github's releases page](https://github.com/dnvgl/qats/releases). 
+
+
 All notable changes to the project will be documented in this file, with format based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 We apply the *"major.minor.micro"* versioning scheme defined in [PEP 440](https://www.python.org/dev/peps/pep-0440).

diff --git a/README.md b/README.md
@@ -33,10 +33,6 @@ perfect for inspecting, comparing and reporting:
 
 ![QATS GUI](https://raw.githubusercontent.com/dnvgl/qats/master/docs/source/demo.gif)
 
-## Python version support
-
-QATS supports Python 3.7, 3.8, 3.9 and 3.10.
-
 ## Getting started
 
 ### Installation
@@ -56,21 +52,20 @@ python -m pip install --upgrade qats
 You may now import qats in your own scripts:
 
 ```python
-from qats import TsDB, TimeSeries
+>>> from qats import TsDB, TimeSeries
 ```
 
-... or use the GUI to inspect time series. Note that as of version 4.2.0 you are quite free to choose which 
-[Qt](https://www.qt.io) binding you would like to use for the GUI: [PyQt5](https://pypi.org/project/PyQt5/) or 
-[PySide2](https://pypi.org/project/PySide2/), or even [PyQt4](https://pypi.org/project/PyQt4/) / 
-[PySide](https://pypi.org/project/PySide/).
+... or use the GUI to inspect time series. 
 
-Install the chosen binding (here PyQt5 as an example):
+_New in version 5.0.0._ 
+The [Qt](https://www.qt.io) binding [PySide6](https://pypi.org/project/PySide6/) is installed with `qats`. 
+If you would rather like to use [PyQt6](https://pypi.org/project/PyQt6/), run
 
 ```console
-python -m pip install pyqt5
+python -m pip install pyqt6
 ```
 
-If multiple Qt bindinds are installed, the one to use may be controlled by setting the environmental variable `QT_API` to the desired package. Accepted values include `pyqt5` (to use PyQt5) and `pyside2` (PySide2). For more details, see [README file for qtpy](https://github.com/spyder-ide/qtpy/blob/master/README.md).
+If multiple Qt bindinds are installed, the one to use may be controlled by setting the environmental variable `QT_API` to the desired package. Accepted values include `pyqt6` (to use PyQt6) and `pyside6` (PySide6). For more details, see [README file for qtpy](https://github.com/spyder-ide/qtpy/blob/master/README.md).
 
 The GUI may now be launched by:
 
@@ -97,7 +92,7 @@ python -m qats config --link-app
 
 * [**Source**](https://github.com/dnvgl/qats)
 * [**Issues**](https://github.com/dnvgl/qats/issues)
-* [**Changelog**](https://github.com/dnvgl/qats/blob/master/CHANGELOG.md)
+* [**Changelog**](https://github.com/dnvgl/qats/releases)
 * [**Documentation**](https://qats.readthedocs.io)
 * [**Download**](https://pypi.org/project/qats/)
 
@@ -108,7 +103,13 @@ purposes. See deployment for notes on how to deploy the project on a live system
 
 ### Prerequisites
 
-Install Python version 3.7 or later from either https://www.python.org or https://www.anaconda.com.
+Install Python version 3.8 or later from either https://www.python.org or https://www.anaconda.com.
+
+Install Poetry with [the official installer](https://python-poetry.org/docs/#installing-with-the-official-installer).
+
+Install the [poetry-dynamic-versioning](https://pypi.org/project/poetry-dynamic-versioning/) plugin:
+
+```poetry self add "poetry-dynamic-versioning[plugin]"```
 
 ### Clone the source code repository
 
@@ -118,35 +119,22 @@ At the desired location, run:
 
 ### Installing
 
-To get the development environment running:
-
-... create an isolated Python environment and activate it,
-
-```console
-python -m venv /path/to/new/virtual/environment
-
-/path/to/new/virtual/environment/Scripts/activate
-```
-
-... install the dev dependencies in [requirements.txt](requirements.txt),
-
-```console
-python -m pip install -r requirements.txt
-```
-
-.. and install the package in development ("editable") mode.
+To get the development environment running...
 
 ```console
-python -m pip install -e .
+poetry install
 ```
 
-_Note: This is similar to the "legacy" development installation command ``python setup.py develop``, see the [setuptools page on development mode](https://setuptools.pypa.io/en/latest/userguide/development_mode.html)._
+This will
+- create an isolated environment
+- install all dependencies including those required for development, testing and building documentation
+- and install the package in development ("editable") mode
 
 You should now be able to import the package in the Python console,
 
 ```python
-import qats
-help(qats)
+>>> import qats
+>>> help(qats)
 ```
 
 ... and use the command line interface (CLI).
@@ -171,13 +159,13 @@ python -m unittest discover
 
 ### Building the package
 
-Build tarball and wheel distributions by:
+Build tarball and wheel distributions by
 
 ```console
-python setup.py sdist bdist_wheel
+poetry build
 ```
 
-The distribution file names adhere to the [PEP 0427](https://www.python.org/dev/peps/pep-0427/#file-name-convention) 
+The builds appear in the `.dist` folder. The distributions adhere to the [PEP 0427](https://www.python.org/dev/peps/pep-0427/#file-name-convention) 
 convention `{distribution}-{version}(-{build tag})?-{python tag}-{abi tag}-{platform tag}.whl`.
 
 ### Building the documentation
@@ -194,16 +182,19 @@ To force a build to read/write all files (always read all files and don't use a
 sphinx-build -a -E -b html docs\source docs\_build
 ```
 
-### Deployment
-Packaging, unit testing and deployment to [PyPi](https://pypi.org/project/qats/) is automated using [GitHub Actions](https://docs.github.com/en/actions).
-
 ### Versioning
 
 We apply the "major.minor.micro" versioning scheme defined in [PEP 440](https://www.python.org/dev/peps/pep-0440/). See also [Scheme choices](https://packaging.python.org/en/latest/guides/distributing-packages-using-setuptools/#scheme-choices) on https://packaging.python.org/.
 
-We cut a new version by applying a Git tag like `3.0.1` at the desired commit and then 
-[setuptools_scm](https://github.com/pypa/setuptools_scm/#setup-py-usage) takes care of the rest. For the versions 
-available, see the [tags on this repository](https://github.com/dnvgl/qats/tags). 
+Versions are tagged with Git tags like `v3.0.1`. See the [tags on this repository](https://github.com/dnvgl/qats/tags). 
+
+### Release and deployment
+
+We use the [release cycle in GitHub](https://github.com/dnvgl/qats/releases) to cut new releases.
+
+Once a new release is published, [GitHub Actions](https://docs.github.com/en/actions) takes care of the packaging, unit testing and deployment to [PyPi](https://pypi.org/project/qats/).
+
+The workflows for continuous integration and deployment are found in [.github/workflows](.github/workflows/).
 
 ## Authors
 

diff --git a/data/model_test_data.dat b/data/model_test_data.dat
@@ -1,3 +1,5 @@
+# test comment
+# another comment
          time[s]        WaveC[m]       Wave-F[m]       Wave-S[m]        Surge[m]         Sway[m]        Heave[m]       Roll[deg]      Pitch[deg]        Yaw[deg]    Acc-X[m/s^2]    Acc-Y[m/s^3]    Acc-Z[m/s^4]    Ten-S-FP[kN]    Ten-S-FS[kN]    Ten-S-AS[kN]    Ten-S-AP[kN]          RW1[m]          RW3[m]          RW5[m]          RW7[m]         RW13[m]         RW14[m]          RW2[m]          RW4[m]          RW6[m]          RW8[m]          RW9[m]         RW10[m]         RW11[m]         RW12[m]         RW15[m]         RW16[m]         RW17[m]         RW18[m]         RW19[m]    Ten-P-FP[kN]    Ten-P-FS[kN]    Ten-P-AS[kN]    Ten-P-AP[kN]
    0.0000000e+00   1.1468169e+00  -6.2024932e+00   1.5963418e+00  -1.2440454e+01   1.8175390e+00   5.8588385e-01   3.3933087e-01   1.6214460e+00   4.1363153e-01   1.1196024e-01  -2.3473288e-02   1.5040265e-01   3.6432728e+03   3.7840381e+03   2.5385340e+03   2.3443660e+03  -9.3945101e-01  -1.5887219e+00  -2.6872322e+00  -2.7754727e+00   9.6520604e-01   2.1473762e+00  -1.4565005e+00  -2.1295738e+00  -2.5923946e+00  -1.2597798e+00  -2.6924590e+00  -7.5948454e-01   1.4100411e+00   1.4251543e+00  -1.1114424e+00  -1.2456250e+00   1.1438377e+00   3.4769380e-01  -5.0987183e-01   3.6178672e+03   3.6655819e+03   2.5026818e+03   2.3855970e+03
    7.0710678e-02   1.3147447e+00  -6.1294752e+00   1.5299688e+00  -1.2476236e+01   1.8165961e+00   6.0005881e-01   3.3398525e-01   1.6583331e+00   4.2669511e-01   1.1747680e-01  -2.1960561e-02   1.7126258e-01   3.6428042e+03   3.7912919e+03   2.5447336e+03   2.3366768e+03  -9.1152887e-01  -1.5730936e+00  -2.6601386e+00  -2.7932502e+00   1.1041916e+00   2.1576044e+00  -1.4025477e+00  -2.1228321e+00  -2.6254164e+00  -1.2523734e+00  -2.7433894e+00  -7.6519707e-01   1.4704902e+00   1.4266390e+00  -1.0990665e+00  -1.2547405e+00   1.1563448e+00   4.1997923e-01  -3.6905164e-01   3.6210090e+03   3.6738023e+03   2.5028865e+03   2.3816678e+03