Merge remote-tracking branch 'origin/refactor-api' into fix-warnings

# Conflicts:
#	psignifit/psigniplot.py

.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

@@ -2,7 +2,11 @@
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 name: Test
 
-on: [push, pull_request]
+on:
+  push:
+  pull_request:
+  schedule:  # At 00:00 on day-of-month 1
+    - cron: '0 0 1 * *'
 
 jobs:
   test:
@@ -14,7 +18,7 @@ jobs:
         os: [Ubuntu]
         python_version: ['3.10', '3.11', '3.12']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v4
         name: Install Python ${{ matrix.python_version }}
@@ -31,5 +35,46 @@ jobs:
           pip install .
       - name: Run tests for ${{ matrix.python_version }} through nox
         run: |
-          pytest -vv    
+          pytest -vv
 
+  lint:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+      with:
+        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
+    - 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
+
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+      with:
+        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

psignifit/_configuration.py

@@ -3,8 +3,9 @@
 import re
 import dataclasses
 from typing import Any, Dict, Tuple, Optional, Union
+import warnings
 
-from . import _sigmoids
+from . import sigmoids
 from ._utils import PsignifitException
 from ._typing import ExperimentType, Prior
 
@@ -48,7 +49,7 @@ class Configuration:
     move_bounds: bool = True
     pool_max_blocks: int = 25
     priors: Optional[Dict[str, Prior]] = dataclasses.field(default=None, hash=False)
-    sigmoid: Union[str, _sigmoids.Sigmoid] = 'norm'
+    sigmoid: Union[str, sigmoids.Sigmoid] = 'norm'
     stimulus_range: Optional[Tuple[float, float]] = None
     thresh_PC: float = 0.5
     verbose: bool = True
@@ -93,6 +94,7 @@ def check_foobar(self, value):
                 sanity_check_method = getattr(self, sanity_check_name)
                 attribute_value = getattr(self, attribute.name)
                 sanity_check_method(attribute_value)
+        self.check_experiment_type_matches_fixed_parameters(self.fixed_parameters, self.experiment_type)
 
     def check_bounds(self, value):
         if value is not None:
@@ -120,7 +122,7 @@ def check_bounds(self, value):
     def check_fixed_parameters(self, value):
         if value is not None:
             # fixed parameters is a dict in the form {'parameter_name': value}
-            if type(value) != dict:
+            if isinstance(type(value), dict):
                 raise PsignifitException(
                     f'Option fixed_parameters must be a dictionary ({type(value).__name__} given)!'
                 )
@@ -131,6 +133,14 @@ def check_fixed_parameters(self, value):
                     f'Option fixed_paramters keys must be in {vkeys}. Given {list(value.keys())}!'
                 )
 
+
+    def check_experiment_type_matches_fixed_parameters(self, fixed_params, experiment_type):
+        if experiment_type == ExperimentType.N_AFC.value:
+            if fixed_params is not None and 'gamma' in fixed_params:
+                warnings.warn(
+                    f'The parameter gamma was fixed to {fixed_params["gamma"]}. In {ExperimentType.N_AFC.value} experiments gamma must be fixed to 1/n. Ignoring fixed gamma.')
+
+
     def check_experiment_type(self, value):
         valid_values = [type.value for type in ExperimentType]
         is_valid = value in valid_values
@@ -212,15 +222,15 @@ def check_width_min(self, value):
             except Exception:
                 raise PsignifitException("Option width_min must be a number")
 
-    def make_sigmoid(self) -> _sigmoids.Sigmoid:
+    def make_sigmoid(self) -> sigmoids.Sigmoid:
         """ Construct sigmoid according to this configuration.
 
         Returns:
              Sigmoid object with percentage correct and alpha according to config.
         """
-        if isinstance(self.sigmoid, _sigmoids.Sigmoid):
+        if isinstance(self.sigmoid, sigmoids.Sigmoid):
             self.sigmoid.PC = self.thresh_PC
             self.sigmoid.alpha = self.width_alpha
             return self.sigmoid
         else:
-            return _sigmoids.sigmoid_by_name(self.sigmoid, PC=self.thresh_PC, alpha=self.width_alpha)
+            return sigmoids.sigmoid_by_name(self.sigmoid, PC=self.thresh_PC, alpha=self.width_alpha)

psignifit/_posterior.py

@@ -7,7 +7,7 @@
 
 from ._utils import fp_error_handler, PsignifitException
 from ._typing import Prior, ParameterGrid
-from ._sigmoids import Sigmoid
+from .sigmoids import Sigmoid
 
 
 def integral_weights(grid):
@@ -242,9 +242,13 @@ def objective(x):
 def marginalize_posterior(parameter_grid: ParameterGrid, posterior_mass: np.ndarray) -> Dict[str, np.ndarray]:
     marginals = dict()
     for i, (param, grid) in enumerate(sorted(parameter_grid.items())):
-        if grid is None:
+        if grid is None or len(grid)==1:
             marginals[param] = None
-        axis = tuple(range(0, i)) + tuple(range(i + 1, len(parameter_grid)))
-        marginals[param] = np.squeeze(posterior_mass.sum(axis))
+        else:
+            axis = tuple(range(0, i)) + tuple(range(i + 1, len(parameter_grid)))
+            # we get first the unnormalized marginal, and then we scale it
+            nmarginal = np.squeeze(posterior_mass.sum(axis))
+            integral = np.trapz(nmarginal, x=grid)
+            marginals[param] = nmarginal / integral
 
     return marginals