Merge pull request #25 from pastas/dev

Release 0.3.0

.github/workflows/ci.yml

@@ -1,49 +1,93 @@
 name: metran
 
 on:
-  # Trigger the workflow on push or pull request on master,
-  # and only on pull-requests on dev branch
-  push:
-    branches:
-      - main
-  pull_request:
-    branches:
-      - main
+  - push
+  - pull_request
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
+  test:
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        include:
+          - name: Test suite with py38-ubuntu
+            python: "3.8"
+            os: ubuntu-latest
+            toxenv: py38
+            experimental: false
+          - name: Test suite with py39-ubuntu
+            python: "3.9"
+            os: ubuntu-latest
+            toxenv: py39
+            experimental: false
+          - name: Test suite with py310-ubuntu
+            python: "3.10"
+            os: ubuntu-latest
+            toxenv: py310
+            experimental: false
+          - name: Test suite with py311-ubuntu
+            python: "3.11"
+            os: ubuntu-latest
+            toxenv: py311
+            experimental: false
+          - name: Test suite with py312-ubuntu
+            python: "3.12-dev"
+            os: ubuntu-latest
+            toxenv: py312
+            experimental: true
+          - name: Formatting with black + isort
+            python: "3.9"
+            os: ubuntu-latest
+            toxenv: format
+            experimental: false
+          - name: Linting with flake8
+            python: "3.9"
+            os: ubuntu-latest
+            toxenv: lint
+            experimental: false
+          - name: Codacy Coverage Report
+            python: "3.9"
+            os: ubuntu-latest
+            toxenv: coverage
+            experimental: false
 
+    name: ${{ matrix.name }}
+    env:
+      # Color Output
+      # Rich (pip)
+      FORCE_COLOR: 1
+      # Tox
+      PY_COLORS: 1
+      # MyPy
+      TERM: xterm-color
+      MYPY_FORCE_COLOR: 1
+      MYPY_FORCE_TERMINAL_WIDTH: 200
+      # Pytest
+      PYTEST_ADDOPTS: "--color=yes"
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.python }}
+          check-latest: true
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install flake8 pytest
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-          pip install codecov
-          pip install pytest-cov
-          pip install pytest-dependency
-          pip install codacy-coverage
-          pip install -e .
-      - name: Lint with flake8
-        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=80 --statistics
-      - name: Run pytest
-        run: |
-          pytest
+          pip install tox
+
+      - name: Setup tox environment
+        run: tox -e ${{ matrix.toxenv }} --notest
+
+      - name: Test
+        run: tox -e ${{ matrix.toxenv }} --skip-pkg-install
+
       - name: Run codacy-coverage-reporter
+        if: ${{ matrix.toxenv == 'coverage' && github.repository == 'pastas/metran' && success() }}
         uses: codacy/codacy-coverage-reporter-action@master
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}

.github/workflows/python-publish.yml

@@ -13,19 +13,19 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install wheel twine build
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        python3 -m build
+        python3 -m twine upload --repository pypi dist/*

.readthedocs.yml

@@ -14,9 +14,8 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: "3.8"
   install:
-    - requirements: docs/requirements.txt
     - method: pip
       path: .
 

README.md

@@ -6,59 +6,52 @@
 
 # Metran
 
-Metran is a package for performing multivariate timeseries analysis using a 
-technique called dynamic factor modelling. It can be used to describe the 
-variation among many variables in terms of a few underlying but unobserved 
+Metran is a package for performing multivariate timeseries analysis using a
+technique called dynamic factor modelling. It can be used to describe the
+variation among many variables in terms of a few underlying but unobserved
 variables called factors.
 
-## Installation
+## Documentation
 
-To install Metran, a working version of Python 3.7 or 3.8 has to be installed on your computer. 
-We recommend using the Anaconda Distribution with Python 3.8 as it includes most 
-of the python package dependencies and the Jupyter Notebook software to run the 
-notebooks. However, you are free to install any Python distribution you want.
+The documention can be found on [metran.readthedocs.io](https://metran.readthedocs.io/)
 
-To install `metran`, type the following command
+### Examples
 
-`pip install metran`
+For a brief introduction of the theory behind Metran on multivariate timeseries analysis with
+dynamic factor modeling see the notebook:
 
-To install in development mode, clone the repository and type the following from the module root directory:
+- [The Dynamic Factor Model](https://github.com/pastas/metran/blob/main/examples/dynamic_factor_model.ipynb)
 
-`pip install -e .`
+A practical real-world example, as published in Stromingen (Van Geer, 2015), is given in the following notebook:
 
-## Documentation
+- [Metran practical example](https://github.com/pastas/metran/blob/main/examples/metran_practical_example.ipynb)
 
-The docs can be viewed [here](https://metran.readthedocs.io/).
+A notebook on how to use [Pastas](https://github.com/pastas/pastas) models output with Metran:
 
-## Examples
+- [Pastas Metran example](https://github.com/pastas/metran/blob/main/examples/pastas_metran_example.ipynb)
 
-For a brief introduction of the theory behind Metran on multivariate timeseries analysis with
-dynamic factor modeling see the notebook:
+## Installation
 
--   [The Dynamic Factor Model](https://github.com/pastas/metran/blob/main/examples/dynamic_factor_model.ipynb)
+To install Metran, a working version of Python 3.8 or higher has to be installed on your computer.
+We recommend using the [Anaconda distribution](https://www.anaconda.com/) as it includes most
+of the python package dependencies and the Jupyter Notebook software to run the
+notebooks. However, you are free to install any Python distribution you want.
 
-A practical real-world example, as published in Stromingen (Van Geer, 2015), is given in the following notebook:
+To install `metran`, type the following command
 
--   [Metran practical example](https://github.com/pastas/metran/blob/main/examples/metran_practical_example.ipynb)
+`pip install metran`
 
-A notebook on how to use [Pastas](https://github.com/pastas/pastas) models output with Metran:
+To install in development mode, clone the repository and type the following from the module root directory:
 
--   [Pastas Metran example](https://github.com/pastas/metran/blob/main/examples/pastas_metran_example.ipynb)
+`pip install -e .`
 
-## Dependencies
+### Dependencies
 
 Metran has the following dependencies which are automatically installed if
-not already available:
-
--   numpy>=1.16.5
--   pandas>=1.0
--   scipy>=1.1
--   matplotlib>=3.0
--   pastas>=0.16.0
--   numba
+not already available: `numpy`, `scipy`, `pandas`, `matplotlib`, `numba` and `pastas`
 
 ## References
 
--   Berendrecht, W.L. (2004). State space modeling of groundwater fluctuations. 
--   Berendrecht, W.L., F.C. van Geer (2016). A dynamic factor modeling framework for analyzing multiple groundwater head series simultaneously, Journal of Hydrology, 536, pp. 50-60, doi:<http://dx.doi.org/10.1016/j.jhydrol.2016.02.028>.
--   Van Geer, F.C. en W.L. Berendrecht (2015) Meervoudige tijdreeksmodellen en de samenhang in stijghoogtereeksen. Stromingen 23 nummer 3, pp. 25-36.
+- Berendrecht, W.L. (2004). [State space modeling of groundwater fluctuations](https://repository.tudelft.nl/islandora/object/uuid:f12775fc-a804-4d4a-8872-664e5a61cbf5/datastream/OBJ). Doctoral Thesis, Delft University of Technology.
+- Berendrecht, W.L., F.C. van Geer (2016). [A dynamic factor modeling framework for analyzing multiple groundwater head series simultaneously](http://dx.doi.org/10.1016/j.jhydrol.2016.02.028). Journal of Hydrology, 536, pp. 50-60.
+- Van Geer, F.C. en W.L. Berendrecht (2015) [Meervoudige tijdreeksmodellen en de samenhang in stijghoogtereeksen](https://edepot.wur.nl/378871). Stromingen 23 nummer 3, pp. 25-36.

docs/conf.py

@@ -13,15 +13,14 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath("."))
 from metran import __version__
 
-
 # -- Project information -----------------------------------------------------
 
-project = 'metran'
-copyright = '2021, W.L. Berendrecht'
-author = 'W.L. Berendrecht'
+project = "metran"
+copyright = "2021, W.L. Berendrecht"
+author = "W.L. Berendrecht"
 
 # The short X.Y version
 version = __version__
@@ -34,54 +33,54 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'IPython.sphinxext.ipython_console_highlighting',  # lowercase didn't work
-    'sphinx.ext.autosectionlabel',
-    'nbsphinx',
-    'nbsphinx_link'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "IPython.sphinxext.ipython_console_highlighting",  # lowercase didn't work
+    "sphinx.ext.autosectionlabel",
+    "nbsphinx",
+    "nbsphinx_link",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 html_theme_options = {
-    'display_version': True,
-    'prev_next_buttons_location': 'bottom',
+    "display_version": True,
+    "prev_next_buttons_location": "bottom",
     # 'style_external_links': False,
     # 'vcs_pageview_mode': '',
     # 'style_nav_header_background': 'white',
     # Toc options
-    'collapse_navigation': False,
-    'sticky_navigation': False,
-    'navigation_depth': 4,
-    'includehidden': True,
-    'titles_only': False,
+    "collapse_navigation": False,
+    "sticky_navigation": False,
+    "navigation_depth": 4,
+    "includehidden": True,
+    "titles_only": False,
     "github_url": "https://github.com/pastas/metran",
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]