Merge branch 'main' into master

.github/workflows/pythonpublish.yml

@@ -16,11 +16,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build setuptools wheel twine
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
         twine upload dist/*

.github/workflows/tests.yml

@@ -1,35 +1,35 @@
 name: Unit tests and coverage
 
-on: [push]
+on: [push, workflow_dispatch, pull_request]
 
 jobs:
   build:
 
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
         os: [ubuntu-latest, macos-latest, windows-latest]
     env:
       OS: ${{ matrix.os }}
       PYHTHON: ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest pytest-cov
-          pip install -r requirements.txt
-          pip install -e .
+          pip install -e .[testing]
       - name: Generate coverage report
         run: |
-          pytest --cov-report=xml
+          pytest --cov=kneed --cov-report=xml:coverage1.xml tests/test_sample.py
+          pip uninstall -y matplotlib
+          pytest --cov=kneed --cov-report=xml:coverage2.xml tests/test_no_matplotlib.py
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         with:
           env_vars: OS,PYTHON
           fail_ci_if_error: true

CONTRIBUTING.md

@@ -6,7 +6,7 @@ I have tried to follow the `Kneedle` algorithm as best as I could interpret from
 but the source code is far from perfect and could benefit from improvements.
 
 - Submit a bug report or feature request on [GitHub Issues](https://github.com/arvkevi/kneed/issues).
-- Contribute a Jupyter notebook to [notebooks](https://github.com/arvkevi/kneed/tree/master/notebooks).
+- Contribute a Jupyter notebook to [notebooks](https://github.com/arvkevi/kneed/tree/main/notebooks).
 - Documenting applications where `kneed` could be useful.
 - Code refactors -- the code was refactored in `0.4.0` to be more human-readable. However I think the code could still be greatly improved
 by breaking the `KneeLocator` class into a collection of methods. This would make the algorithm easier to unittest.
@@ -55,18 +55,11 @@ Once forked, use the following steps to get your development environment set up
 
 3. Install dependencies.
 
-    Kneed's dependencies are in the `requirements.txt` document at the root of the repository. Open this file and uncomment the dependencies that are for development only. Then install the dependencies with `pip`:
+    Kneed's main dependencies are in the `requirements.txt` document at the root of the repository, however you will later also need to install testing dependencies.
+    Install them all with `pip`:
 
     ```
-    $ pip install -r requirements.txt
-    ```
-
-    Note that there are dependencies required for testing, you can simply install them with `pip`. For example to install
-    the additional dependencies for building the documentation or to run the
-    test suite, use the `requirements.txt` files in those directories:
-
-    ```
-    $ pip install -r tests/requirements.txt
+    $ pip install -e .[testing]
     ```
 
 At this point you're ready to get started writing code!

README.md

@@ -1,12 +1,12 @@
 # kneed
  Knee-point detection in Python
 
-[![Downloads](https://pepy.tech/badge/kneed)](https://pepy.tech/project/kneed) [![Downloads](https://pepy.tech/badge/kneed/week)](https://pepy.tech/project/kneed) ![Dependents](https://badgen.net/github/dependents-repo/arvkevi/kneed/?icon=github) [![Open in Streamlit](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://share.streamlit.io/arvkevi/ikneed/main/ikneed.py) [![Build Status](https://travis-ci.com/arvkevi/kneed.svg?branch=master)](https://travis-ci.com/arvkevi/kneed) [![codecov](https://codecov.io/gh/arvkevi/kneed/branch/master/graph/badge.svg)](https://codecov.io/gh/arvkevi/kneed)[![DOI](https://zenodo.org/badge/113799037.svg)](https://zenodo.org/badge/latestdoi/113799037)
+[![Downloads](https://pepy.tech/badge/kneed)](https://pepy.tech/project/kneed) [![Downloads](https://pepy.tech/badge/kneed/week)](https://pepy.tech/project/kneed) ![Dependents](https://badgen.net/github/dependents-repo/arvkevi/kneed/?icon=github) [![Open in Streamlit](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://share.streamlit.io/arvkevi/ikneed/main/ikneed.py) [![codecov](https://codecov.io/gh/arvkevi/kneed/branch/main/graph/badge.svg)](https://codecov.io/gh/arvkevi/kneed)[![DOI](https://zenodo.org/badge/113799037.svg)](https://zenodo.org/badge/latestdoi/113799037)
 
 
 This repository is an attempt to implement the kneedle algorithm, published [here](https://www1.icsi.berkeley.edu/~barath/papers/kneedle-simplex11.pdf). Given a set of `x` and `y` values, `kneed` will return the knee point of the function. The knee point is the point of maximum curvature.
 
-![](https://raw.githubusercontent.com/arvkevi/kneed/master/images/functions_args_summary.png)
+![](https://raw.githubusercontent.com/arvkevi/kneed/main/images/functions_args_summary.png)
 
 ## Table of contents
 - [Installation](#installation)
@@ -20,7 +20,7 @@ This repository is an attempt to implement the kneedle algorithm, published [her
 - [Citation](#citation)
 
 ## Installation  
-`kneed` has been tested with Python 3.5, 3.6, 3.7, 3.8, 3.9, and 3.10.
+`kneed` has been tested with Python 3.7, 3.8, 3.9, and 3.10.
 
 **anaconda**
 ```bash
@@ -29,13 +29,14 @@ $ conda install -c conda-forge kneed
 
 **pip**
 ```bash
-$ pip install kneed
+$ pip install kneed # To install only knee-detection algorithm
+$ pip install kneed[plot] # To also install plotting functions for quick visualizations
 ```
 
 **Clone from GitHub**
 ```bash
-$ git clone https://github.com/arvkevi/kneed.git
-$ python setup.py install
+$ git clone https://github.com/arvkevi/kneed.git && cd kneed
+$ pip install -e .
 ```
 
 ## Usage
@@ -85,14 +86,14 @@ The `KneeLocator` class also has two plotting functions for quick visualizations
 kneedle.plot_knee_normalized()
 ```
 
-![](https://raw.githubusercontent.com/arvkevi/kneed/master/images/figure2.knee.png)
+![](https://raw.githubusercontent.com/arvkevi/kneed/main/images/figure2.knee.png)
 
 ```python
 # Raw data and knee.
 kneedle.plot_knee()
 ```
 
-![](https://raw.githubusercontent.com/arvkevi/kneed/master/images/figure2.knee.raw.png)
+![](https://raw.githubusercontent.com/arvkevi/kneed/main/images/figure2.knee.raw.png)
 
 ## Documentation
 Documentation of the parameters and a full API reference can be found [here](https://kneed.readthedocs.io/).
@@ -109,7 +110,7 @@ You can also run your own version -- head over to the [source code for ikneed](h
 
 ## Contributing
 
-Contributions are welcome, please refer to [CONTRIBUTING](https://github.com/arvkevi/kneed/blob/master/CONTRIBUTING.md) 
+Contributions are welcome, please refer to [CONTRIBUTING](https://github.com/arvkevi/kneed/blob/main/CONTRIBUTING.md) 
 to learn more about how to contribute.                            
 
 ## Citation

docs/conf.py

@@ -12,17 +12,22 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
+
+sys.path.insert(0, os.path.abspath(".."))
+
+import kneed
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'kneed'
-copyright = '2020, Kevin Arvai'
-author = 'Kevin Arvai'
+project = "kneed"
+copyright = "2020, Kevin Arvai"
+author = "Kevin Arvai"
 
 # The full version, including alpha/beta/rc tags
-release = '0.6.0'
+release = kneed.__version__
+
+version = kneed.__version__
 
 
 # -- General configuration ---------------------------------------------------
@@ -31,19 +36,22 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.coverage',
-    'sphinx.ext.napoleon',
-    'sphinx_rtd_theme'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.coverage",
+    "sphinx.ext.napoleon",
+    "sphinx_rtd_theme",
 ]
 
+pygments_style = "sphinx"
+
 # 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 -------------------------------------------------
@@ -56,8 +64,8 @@
 # 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 = []
 
-autoclass_content = 'both'
+autoclass_content = "both"
 
-master_doc = 'index'
+master_doc = "index"

docs/index.rst

@@ -8,9 +8,10 @@ Welcome to kneed's documentation!
 
 This is the documentation for the `kneed <https://github.com/arvkevi/kneed>`__ Python package.
 Given `x` and `y` arrays, `kneed` attempts to identify the knee/elbow point of a line fit to the data.
-The knee/elbow is defined as the point of the line with maximum curvature. For more information about how each of
-the parameters affect identification of knee points, check out :ref:`parameters`. For a full reference of the API,
-head over to the :ref:`api`.
+The knee/elbow is defined as the point of the line with maximum curvature.  
+
+For more information about how each of the parameters affect identification of knee points, check out :ref:`parameters`.  
+For a full reference of the API, head over to the :ref:`api`.  
 
 .. toctree::
    parameters

docs/interactive.rst

@@ -4,10 +4,8 @@ Interactive Streamlit App
 =========================
 
 An interactive streamlit app was developed to help users explore the effect of tuning the parameters.
-There are two sites where you can test out kneed by copy-pasting your own data:
 
-1. https://share.streamlit.io/arvkevi/ikneed/main/ikneed.py
-2. https://ikneed.herokuapp.com/
+https://share.streamlit.io/arvkevi/ikneed/main/ikneed.py
 
 You can also run your own version -- head over to the source code for ikneed_.
 

docs/parameters.rst

@@ -110,9 +110,9 @@ Any `S`>200 will result in a knee at 482 (0.48, normalized) in the plot above.
 online
 ------
 
-The knee point can be corrected if the parameter online is `True` (default). This mode will step through each element
+The knee point can be corrected if the parameter online is `True`. This mode will step through each element
 in x.
-In contrast, if online is False, kneed will run in offline mode and return the first knee point identified.
+In contrast, if online is `False` (default), kneed will run in offline mode and return the first knee point identified.
 When `online=False` the first knee point identified is returned regardless of whether it's the local maxima on the
 difference curve or the global maxima.
 So the algorithm stops early. When `online=True`, kneed runs in online mode and "corrects" itself by continuing to

docs/requirements.txt

@@ -0,0 +1,9 @@
+sphinx==6.2.1
+sphinx_rtd_theme==1.2.2
+sphinxcontrib-applehelp==1.0.4
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.1
+sphinxcontrib-jquery==4.1
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5

kneed/__init__.py

@@ -1,5 +1,4 @@
 from .data_generator import DataGenerator
 from .knee_locator import KneeLocator
 from .shape_detector import find_shape
-
-from .version import __version__
+from ._version import __version__

kneed/_version.py

@@ -0,0 +1 @@
+__version__ = "0.8.5"