Merge pull request #13 from ArtesiaWater/dev

Release v0.5.0

.github/workflows/ci.yml

@@ -11,31 +11,60 @@ on:
       - master
 
 jobs:
-  build:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
+          cache: "pip"
+          cache-dependency-path: pyproject.toml
+
+      - name: Install Python dependencies
+        run: |
+          pip install .
+
+      - name: ruff-lint
+        uses: chartboost/ruff-action@v1
+
+      - name: ruff-format
+        uses: chartboost/ruff-action@v1
+        with:
+          args: "format --check"
+
+  test:
+    needs: lint
+    name: Test
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9, "3.10", "3.11"]
+        python-version: [3.9, "3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: "pip"
+          cache-dependency-path: pyproject.toml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install -e .[ci]
-      - 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.
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=80 --statistics
+
+
       - name: Run pytest
         run: |
           pytest
+
       - name: Run codacy-coverage-reporter
         uses: codacy/codacy-coverage-reporter-action@master
         with:

.readthedocs.yml

@@ -8,15 +8,12 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# Optionally build your docs in additional formats such as PDF and ePub
-formats: all
-
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:

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 traval import __version__
 
-
 # -- Project information -----------------------------------------------------
 
-project = 'traval'
-copyright = '2021, Artesia'
-author = 'Artesia'
+project = "traval"
+copyright = "2024, Artesia"
+author = "Artesia"
 
 # 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/ArtesiaWater/traval",
 }
 
 # 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"]

docs/examples.rst

@@ -3,8 +3,12 @@ Examples
 
 The following notebooks contain examples showcasing traval.
 
-The first example shows how to apply the tools contained in traval to detect errors in a single timeseries. 
-The second example shows how the same can be done for a full dataset with lots of timeseries. 
+- The first example shows how to apply the tools contained in traval to detect errors in
+  a single time series. 
+- The second example shows how the same can be done for a full
+  dataset with lots of time series.
+- The third notebook contains small examples for each of the error detection rules 
+  contained in traval.
 
 .. toctree::
   :maxdepth: 1

docs/examples/ex03_rules.nblink

@@ -0,0 +1,3 @@
+{
+    "path": "../../examples/notebooks/ex03_testing_rules.ipynb"
+}

docs/getting_started.rst

@@ -5,11 +5,8 @@ Getting Started
 Installation
 ------------
 
-To install traval, 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 3.7 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. 
+To install traval, a working version of Python 3.9 or higher has to be installed on 
+your computer.
 
 To install traval, use:
 
@@ -71,18 +68,18 @@ Take a look at the ruleset by just typing `ruleset`:
           1: rule1                  0
 
 
-Next define a Detector object. This object is designed to store a timeseries 
+Next define a Detector object. This object is designed to store a time series 
 and the intermediate and final results after applying an error detection 
-algorithm. Initialize the Detector object with some timeseries. In this example 
-we assume there is a timeseries called `raw_series`:
+algorithm. Initialize the Detector object with some time series. In this example 
+we assume there is a time series called `raw_series`:
 
 
 .. code:: python
     
     detect = traval.Detector(raw_series)
 
 
-Apply our first algorithm to the timeseries.
+Apply our first algorithm to the time series.
 
 .. code:: python
 

docs/index.rst

@@ -6,20 +6,20 @@
 Welcome to traval's documentation!
 ==================================
 
-Python package for applying automatic error detection algorithms to timeseries.
+Python package for applying automatic error detection algorithms to time series.
 
 This module is set up to provide tools for applying any error detection 
-algorithm to any timeseries. The module consists of three main components:
+algorithm to any time series. The module consists of three main components:
 
--   `Detector`: a data management object for storing timeseries and error detection results.
+-   `Detector`: a data management object for storing time series and error detection results.
 -   `RuleSet`: the RuleSet object is a highly flexible object for defining error detection algorithms based on (user-defined) functions.
--   `SeriesComparison*`: objects for comparing timeseries. These objects include plots for visualizing the comparisons.
+-   `SeriesComparison*`: objects for comparing time series. These objects include plots for visualizing the comparisons.
 
 The general workflow consists of the following steps:
 
 1.  Define error detection algorithm(s).
-2.  Load data, i.e. raw timeseries data and optionally timeseries representing the "truth" to see how well the algorithms perform.
-3.  Initialize Detector objects and apply algorithms to timeseries.
+2.  Load data, i.e. raw time series data and optionally time series representing the "truth" to see how well the algorithms perform.
+3.  Initialize Detector objects and apply algorithms to time series.
 4.  Store and analyze the results.
 
 For more detailed information and examples, please refer to the notebooks in 

docs/modules.rst

@@ -25,15 +25,15 @@ Rule Library
     :members:
 
 
-Timeseries Comparison
----------------------
+Time Series Comparison
+----------------------
 
 .. automodule:: traval.ts_comparison
     :members:
 
 
-Timeseries Utilities
---------------------
+Time series Utilities
+---------------------
 
 .. automodule:: traval.ts_utils
     :members: