Merge branch 'refactor-api' into fixplot

.github/workflows/cd-release.yml

@@ -0,0 +1,36 @@
+# Based on:
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+name: Release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+    - name: Publish distribution 📦 to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/ci-tests.yml

@@ -1,59 +1,80 @@
-# This workflow will install Python dependencies, run tests and lint 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: Tests
+# This workflow will install Python dependencies and run tests with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+name: Test
 
 on:
   push:
-    branches: [ master, refactor-api ]
   pull_request:
-    branches: [ master, refactor-api ]
+  schedule:  # At 00:00 on day-of-month 1
+    - cron: '0 0 1 * *'
 
 jobs:
-  build:
+  test:
+    name: ${{ matrix.os}} / py${{ matrix.python_version }}
+    runs-on: ${{ matrix.os }}-latest
     strategy:
+      fail-fast: false
       matrix:
-        platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7]
-        include:
-          - platform: ubuntu-latest
-            python-version: 3.8
-    runs-on: ${{ matrix.platform }}
+        os: [Ubuntu]
+        python_version: ['3.10', '3.11', '3.12']
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v4
+        name: Install Python ${{ matrix.python_version }}
+        with:
+          python-version: ${{ matrix.python_version }}
+          architecture: x64
+
+      - name: Install (testing) requirements
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install pytest
+      - name: Install psignifit to be tested
+        run: |
+          pip install .
+      - name: Run tests for ${{ matrix.python_version }} through nox
+        run: |
+          pytest -vv
+
+  lint:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install package with dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -e .[tests]
-# Uncomment if sphinx docs are available in the repository
-#        pip install -e .[tests,docs]
-    - name: Lint with flake8
-      run: |
+        python-version: "3.12"
+    - name: flake8 Lint Errors
+      uses: py-actions/flake8@v2
+      with:
+        args: --count --select=E9,F63,F7,F82 --show-source --statistics
         # stop the build if there are Python syntax errors or undefined names
         #    E9: Runtime errors (syntax, indentation, io)
         #    F63: Wrong use of operators and always-true assertion tests
         #    F7: Wrong position of statements (break, continue, return, ...)
         #    F82: Undefined (variable) name
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        #
+    - name: flake8 Lint Warnings
+      uses: py-actions/flake8@v2
+      with:
+        args: --count --exit-zero --statistics --show-source
         # print warnings if other style errors are found.
         #    see .flake8 config file for selected/ignored rules.
-        #    warnings can be found in the action logs https://github.com/wichmann-lab/python-psignifit/actions
-        flake8 . --count --exit-zero --statistics --show-source
-    - name: Test with pytest and measure coverage
-      run: |
-        pytest --cov --cov-report=xml
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+        #    warnings can be found in the action logs
+
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
       with:
-        file: ./coverage.xml
-        flags: unittests
-        env_vars: OS,PYTHON
-# Uncomment if sphinx docs are available in the repository
-#    - name: Build the documentation
-#      run: |
-#        python setup.py build_sphinx
+        python-version: "3.12"
+        cache: pip
+        cache-dependency-path: setup.cfg
+    - name: Install package with docs
+      run: |
+        python3 -m pip install --upgrade pip
+        pip install -e .[docs]
+    - name: Build the documentation
+      run: |
+        cd docs && make html

.readthedocs.yml

@@ -8,11 +8,14 @@ version: 2
 sphinx:
   configuration: docs/conf.py
 
-# Optionally set the version of Python and requirements required to build your docs
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 python:
-  version: 3.7
   install:
     - method: pip
       path: .
       extra_requirements:
-        - docs
+        - docs

COPYRIGHT

@@ -4,7 +4,7 @@ Python toolbox for Bayesian psychometric function estimation.
 
 All the code in this package is distributed under the following conditions:
 
-Copyright (c) 2016-2017, psignifit contributors, www.wichmann-lab.org 
+Copyright (c) 2016-2024, psignifit contributors, www.wichmann-lab.org 
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -18,4 +18,3 @@ GNU General Public License for more details.
 
 You should have received a copy of the GNU General Public License
 along with this program. If not, see <http://www.gnu.org/licenses/>.
-

README.md

@@ -2,8 +2,8 @@
 
 Python toolbox for Bayesian psychometric function estimation.
 [![Tests](https://github.com/wichmann-lab/python-psignifit/actions/workflows/ci-tests.yml/badge.svg)](https://github.com/wichmann-lab/python-psignifit/actions/workflows/ci-tests.yml)
-[![Test Coverage](https://codecov.io/gh/wichmann-lab/python-psignifit/branch/master/graph/badge.svg)](https://codecov.io/gh/wichmann-lab/python-psignifit)
-[![Documentation Status](https://readthedocs.org/projects/psignifit/badge/?version=latest)](https://psignifit.readthedocs.io/en/latest/?badge=latest)
+[![Documentation](https://readthedocs.org/projects/psignifit/badge/?version=latest)](https://psignifit.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://img.shields.io/pypi/v/psignifit.svg)](https://pypi.python.org/pypi/psignifit)
 
 ## Getting started
 
@@ -22,4 +22,3 @@ See the [CONTRIBUTORS](https://github.com/wichmann-lab/python-psignifit/blob/mas
 ## License and COPYRIGHT
 
 See the [COPYRIGHT](https://github.com/wichmann-lab/python-psignifit/blob/master/COPYRIGHT) file
-

docs/.gitignore

@@ -0,0 +1 @@
+sg_execution_times.rst

docs/_static/.gitkeep

@@ -0,0 +1 @@
+This is just a file to assure git creates this directory still if empty

docs/conf.py

@@ -21,8 +21,8 @@
 # -- Project information -----------------------------------------------------
 
 project = 'psignifit'
-author = 'Original: Heiko Schütt, Stefan Harmeling, Jakob Macke, and Felix Wichmann; Python implementation: David-Elias Künstle, Tiziano Zito'
-copyright = '2020, ' + author
+author = 'psignifit contributors, www.wichmann-lab.org'
+copyright = '2024, ' + author
 
 
 # -- General configuration ---------------------------------------------------

docs/getting_started.rst

@@ -87,7 +87,7 @@ For example, running
 
 See :ref:`this user guide <plot-functions>` to learn more about the visualizations.
 
-.. figure:: ../images/demo_001_1.png
+.. figure:: ./images/demo_001_1.png
 
 Next steps
 ~~~~~~~~~~

docs/how_to/How-to-Get-Standard-Parameters.rst

@@ -1,4 +1,5 @@
 .. _how-to-get-standard-parameters:
+
 How to: Get Standard Parameters
 ===============================
 

docs/how_to/index.rst

@@ -1,4 +1,5 @@
 .. _how-tos:
+
 How-To
 ======
 

docs/references/index.rst

@@ -8,23 +8,15 @@ This is the class and function reference of psignifit.
 
 :mod:`psignifit` Main Functions
 ===============================
-
-.. autosummary::
-    :toctree: generated/
-
-    psignifit.psignifit
-    psignifit.plot_bias_analysis
-
-:mod:`psignifit` Configration and Result
-========================================
-
 .. currentmodule:: psignifit
 
 .. autosummary::
     :toctree: generated/
 
-    psignifit.configuration.Configuration
-    psignifit.result.Result
+    psignifit
+    pool_blocks
+    Configuration
+    Result
 
 :mod:`psignifit.psigniplot` Plotting
 ====================================
@@ -34,20 +26,24 @@ This is the class and function reference of psignifit.
 .. autosummary::
     :toctree: generated/
 
-    psigniplot.plot2D
-    psigniplot.plotMarginal
-    psigniplot.plotPrior
-    psigniplot.plotPsych
-    psigniplot.plotsModelfit
+    psigniplot.plot_2D_margin
+    psigniplot.plot_marginal
+    psigniplot.plot_prior
+    psigniplot.plot_psychometric_function
+    psigniplot.plot_modelfit
+    psigniplot.plot_stimulus_residuals
+    psigniplot.plot_block_residuals
+    psigniplot.plot_bias_analysis
+
 
 :mod:`psignifit.sigmoids` Sigmoids
 ==================================
 
-.. currentmodule:: psignifit.sigmoids
+.. currentmodule:: psignifit
 
 .. autosummary::
     :toctree: generated/
 
-    psignifit.sigmoids.Sigmoid
-    psignifit.sigmoids.sigmoid_by_name
-    psignifit.sigmoids.ALL_SIGMOID_NAMES
+    sigmoids.Sigmoid
+    sigmoids.sigmoid_by_name
+    sigmoids.ALL_SIGMOID_NAMES

psignifit/__init__.py

@@ -9,39 +9,5 @@
 # import here the main function
 from .psignifit import psignifit
 from ._pooling import pool_blocks
-from . import _sigmoids
-from .psigniplot import plot_bias_analysis
-
-__name__ = 'psignifit'
-__description__ = 'toolbox for Bayesian psychometric function estimation'
-__version__ = '4.0a'
-__url__ = 'https://github.com/wichmann-lab/python-psignifit'
-__author__ = 'psignifit contributors, www.wichmann-lab.org'
-__license__ = 'GPLv3+'
-__revision__ = 'N/A'
-
-# get the git SHA if we are in a git repo (only useful for devs)
-
-# current dir
-CWD = os.path.abspath(os.path.dirname(__file__))
-# try two options for getting the git revision
-# - nice version with tags
-# - plain SHA
-for cmd in ('git describe --tags --dirty=+'), ('git rev-parse HEAD'):
-    try:
-        proc = subprocess.check_output(cmd.split(),
-                                       cwd=CWD,
-                                       stderr=subprocess.PIPE,
-                                       universal_newlines=True)
-        __revision__ = proc.strip()
-    except Exception:
-        # ok, don't bother
-        pass
-
-
-# have a way to test from python
-def test():
-    import pytest
-    pytest.main([
-        CWD,
-    ])
+from ._configuration import Configuration
+from ._result import Result