adaptivetesting 1.0.0__tar.gz → 1.0.1__tar.gz

adaptivetesting-1.0.1/.github/workflows/publish.yml

@@ -0,0 +1,39 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install uv
+    - name: Build package
+      run: uv build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

adaptivetesting-1.0.1/.github/workflows/python-test.yml

@@ -0,0 +1,63 @@
+# This workflow will install Python dependencies, run tests and lint 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: Package test
+
+on:
+  push:
+    branches: [ "main", "dev"]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+            python -m pip install --upgrade pip
+            python -m pip install uv
+            uv sync
+    - name: Linting
+      run: uv run python -m flake8
+    - name: Type checking
+      run: |
+        uv run mypy
+    - name: Type checking code examples
+      run: |
+        uv run mypy code_examples
+    - name: Test with unittest
+      run: |
+        uv run python -m unittest
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+          python-version: ["3.10", "3.11", "3.12"]
+      
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+              python -m pip install --upgrade pip
+              python -m pip install uv
+              uv sync
+      - name: Build package
+        run: |
+              uv build

adaptivetesting-1.0.1/.gitignore

@@ -0,0 +1,170 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# unignore built documentation
+
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+!docs_generation/build/markdown/
+!docs_generation/build/markdown/*
+docs_generation/build/*
+
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+.DS_Store
+
+

adaptivetesting-1.0.1/.gitlab-ci.yml

@@ -0,0 +1,13 @@
+image: python:latest
+
+deploy:
+  variables:
+    TWINE_USERNAME: gitlab-ci-token
+    TWINE_PASSWORD: $CI_JOB_TOKEN
+  script:
+    - pip install -r requirements.txt
+    - python -m build
+    - python -m twine upload --repository-url ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi dist/*
+  only:
+    refs:
+      - tags

adaptivetesting-1.0.1/.python-version

@@ -0,0 +1 @@
+3.12

adaptivetesting-1.0.1/.vscode/extensions.json

@@ -0,0 +1,8 @@
+{
+    "recommendations": [
+        "ms-python.autopep8",
+        "njpwerner.autodocstring",
+        "ms-python.python",
+        "ms-python.flake8"
+    ]
+}

adaptivetesting-1.0.1/.vscode/settings.json

@@ -0,0 +1,14 @@
+{
+    "python.testing.unittestArgs": [
+        "-v",
+        "-s",
+        "./adaptivetesting/tests",
+        "-p",
+        "test*.py"
+    ],
+    "python.testing.pytestEnabled": false,
+    "python.testing.unittestEnabled": true,
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.autopep8"
+      }
+}

{adaptivetesting-1.0.0 → adaptivetesting-1.0.1}/PKG-INFO

@@ -1,40 +1,22 @@
 Metadata-Version: 2.4
 Name: adaptivetesting
-Version: 1.0.0
+Version: 1.0.1
 Summary: adaptivetesting is a Python package that can be used to simulate and evaluate custom CAT scenarios as well as implement them in real-world testing scenarios from a single codebase
-Home-page: https://github.com/condecon/adaptivetesting
-Author: Jonas Engicht
-Author-email: jonas.engicht@uni-jena.de
-Maintainer: Jonas Engicht
-Maintainer-email: jonas.engicht@uni-jena.de
-License: Mozilla Public License Version 2.0
-Keywords: statistics,psychology,item-response-theory,computerized-adaptive-testing
-Requires-Python: >3.10
-Description-Content-Type: text/markdown
+Author-email: Jonas Engicht <dev@condecon.de>
 License-File: LICENSE
+Keywords: computerized-adaptive-testing,item-response-theory,psychology,statistics
+Requires-Python: >=3.10
 Requires-Dist: jax>=0.5.1
 Requires-Dist: numpy>=1.20.0
-Requires-Dist: scipy>=1.15.0
 Requires-Dist: pandas>=2.2.0
-Dynamic: author
-Dynamic: author-email
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: keywords
-Dynamic: license
-Dynamic: license-file
-Dynamic: maintainer
-Dynamic: maintainer-email
-Dynamic: requires-dist
-Dynamic: requires-python
-Dynamic: summary
+Requires-Dist: scipy>=1.15.0
+Description-Content-Type: text/markdown
 
 # adaptivetesting
 [![Unittests](https://github.com/condecon/adaptivetesting/actions/workflows/python-test.yml/badge.svg)](https://github.com/condecon/adaptivetesting/actions/workflows/python-test.yml)
 [![Deploy to PyPi](https://github.com/condecon/adaptivetesting/actions/workflows/publish.yml/badge.svg)](https://github.com/condecon/adaptivetesting/actions/workflows/publish.yml)
 
-<img src="/docs/source/_static/logo.svg" style="width: 100%">
+<img src="/docs_generation/source/_static/logo.svg" style="width: 100%">
 </img>
 
 _adaptivetesting_ is a Python package for computerized adaptive 
@@ -104,5 +86,5 @@ For more information, please consult the documentation for the ``AdaptiveTest``
 | tests | Unit test for the entire package |
 
 ## Documentation
-Extensive documentation is available in the source code,
-but it can also be compiled to a webpage using sphinx.
+
+You can find extensiv documentation in the <a href="/docs/">`docs` directory</a>.

{adaptivetesting-1.0.0 → adaptivetesting-1.0.1}/README.md

@@ -2,7 +2,7 @@
 [![Unittests](https://github.com/condecon/adaptivetesting/actions/workflows/python-test.yml/badge.svg)](https://github.com/condecon/adaptivetesting/actions/workflows/python-test.yml)
 [![Deploy to PyPi](https://github.com/condecon/adaptivetesting/actions/workflows/publish.yml/badge.svg)](https://github.com/condecon/adaptivetesting/actions/workflows/publish.yml)
 
-<img src="/docs/source/_static/logo.svg" style="width: 100%">
+<img src="/docs_generation/source/_static/logo.svg" style="width: 100%">
 </img>
 
 _adaptivetesting_ is a Python package for computerized adaptive 
@@ -72,5 +72,5 @@ For more information, please consult the documentation for the ``AdaptiveTest``
 | tests | Unit test for the entire package |
 
 ## Documentation
-Extensive documentation is available in the source code,
-but it can also be compiled to a webpage using sphinx.
+
+You can find extensiv documentation in the <a href="/docs/">`docs` directory</a>.

{adaptivetesting-1.0.0 → adaptivetesting-1.0.1}/adaptivetesting/data/__sqlite_context.py

@@ -1,5 +1,4 @@
 from typing import List
-from ..models.__adaptive_test import AdaptiveTest
 from ..models.__test_result import TestResult
 from ..services.__test_results_interface import ITestResults
 import sqlite3
@@ -26,8 +25,6 @@ class SQLiteContext(ITestResults):
         Args:
             test_results (List[TestResult]): list of test results
         """
-
-
         try:
             con = sqlite3.connect(self.filename)
         except sqlite3.OperationalError:

{adaptivetesting-1.0.0 → adaptivetesting-1.0.1}/adaptivetesting/implementations/__default_implementation.py

@@ -1,4 +1,3 @@
-from typing import List
 from ..models.__adaptive_test import AdaptiveTest
 from ..models.__item_pool import ItemPool
 from ..models.__algorithm_exception import AlgorithmException

{adaptivetesting-1.0.0 → adaptivetesting-1.0.1}/adaptivetesting/implementations/__pre_test.py

@@ -49,7 +49,8 @@ class PreTest:
             TestItem: Selected item.
         """
         # select only items with difficulty in interval
-        items_in_interval: List[TestItem] = [item for item in list(self.items) if lower < item.b <= upper]
+        items_in_interval: List[TestItem] = [item for item in list(self.items)
+                                             if lower < item.b <= upper]
         # draw one item randomly
         if self.seed is not None:
             random.seed(self.seed)
@@ -71,11 +72,10 @@ class PreTest:
         quantiles.extend(list(self.calculate_quantiles()))
         quantiles.extend([difficulties.max()])
 
-        for i in range(len(quantiles)-1):
+        for i in range(len(quantiles) - 1):
             selected_item = self.select_item_in_interval(
-                    lower=float(quantiles[i]),
-                    upper=float(quantiles[i+1])
-            )
+                lower=float(quantiles[i]),
+                upper=float(quantiles[i + 1]))
 
             selected_items.append(selected_item)
 

{adaptivetesting-1.0.0 → adaptivetesting-1.0.1}/adaptivetesting/implementations/__semi_implementation.py

@@ -1,4 +1,3 @@
-from typing import List
 from ..models.__adaptive_test import AdaptiveTest
 from ..models.__item_pool import ItemPool
 from ..models.__algorithm_exception import AlgorithmException

adaptivetesting-1.0.1/adaptivetesting/math/__gen_response_pattern.py

@@ -0,0 +1,35 @@
+from .estimators.__functions.__estimators import probability_y1
+from ..models.__test_item import TestItem
+import numpy as np
+
+
+def generate_response_pattern(ability: float,
+                              items: list[TestItem],
+                              seed: int | None = None) -> list[int]:
+    """Generates a response pattern for a given ability level
+    and item difficulties. Also, a seed can be set.
+
+    Args:
+        ability (float): participants ability
+        items (list[TestItem]): test items
+        seed (int, optional): Seed for the random process.
+
+    Returns:
+        list[int]: response pattern
+    """
+    responses: list[int] = []
+
+    for item in items:
+        probability_of_success = probability_y1(mu=ability,
+                                                a=item.a,
+                                                b=item.b,
+                                                c=item.c,
+                                                d=item.d)
+        
+        # simulate response based on probability of scucess
+        if seed is not None:
+            np.random.seed(seed)
+        response = np.random.binomial(n=1, p=probability_of_success)
+        responses.append(response)
+
+    return responses

{adaptivetesting-1.0.0 → adaptivetesting-1.0.1}/adaptivetesting/math/__init__.py

@@ -1,2 +1,3 @@
 from .__standard_error import standard_error
 from .__test_information import test_information_function
+from .__gen_response_pattern import generate_response_pattern

{adaptivetesting-1.0.0 → adaptivetesting-1.0.1}/adaptivetesting/math/__standard_error.py

@@ -28,10 +28,10 @@ def standard_error(answered_items: List[TestItem],
     Returns:
         float: Standard error
     """
-    a=np.array([item.a for item in answered_items])   
-    b=np.array([item.b for item in answered_items])
-    c=np.array([item.c for item in answered_items])
-    d=np.array([item.d for item in answered_items])
+    a = np.array([item.a for item in answered_items])
+    b = np.array([item.b for item in answered_items])
+    c = np.array([item.c for item in answered_items])
+    d = np.array([item.d for item in answered_items])
 
     if estimator == "ML":
         error = 1 / math.sqrt(test_information_function(mu=np.array(estimated_ability_level),
@@ -45,10 +45,11 @@ def standard_error(answered_items: List[TestItem],
     
     if estimator == "BM":
         information = test_information_function(mu=np.array(estimated_ability_level),
-                                                        a=a,
-                                                        b=b,
-                                                        c=c,
-                                                        d=d)
+                                                a=a,
+                                                b=b,
+                                                c=c,
+                                                d=d)
+
         if sd is None:
             raise ValueError("sd cannot be None if BM is used as estimator.")
         

{adaptivetesting-1.0.0 → adaptivetesting-1.0.1}/adaptivetesting/math/__test_information.py

@@ -1,16 +1,14 @@
 import jax.numpy as np
-from .estimators.__functions.__estimators import probability_y1, probability_y0
-from jax import jit, grad
+from .estimators.__functions.__estimators import probability_y1
 from scipy.differentiate import derivative
 
 
-
 def test_information_function(
-            mu: np.ndarray,
-               a: np.ndarray, 
-               b: np.ndarray, 
-               c: np.ndarray, 
-               d: np.ndarray, 
+        mu: np.ndarray,
+        a: np.ndarray,
+        b: np.ndarray,
+        c: np.ndarray,
+        d: np.ndarray,
 ) -> float:
     """
     Calculates test information.
@@ -28,16 +26,12 @@ def test_information_function(
     """
     p_y1 = probability_y1(mu, a, b, c, d)
     
-    p_y1_grad = derivative(probability_y1, 
+    p_y1_grad = derivative(probability_y1,
                            mu,
                            args=(a, b, c, d))
-    
-    
 
     product = (p_y1_grad.df ** 2) / (p_y1 * (1 - p_y1))
     information_tensor = np.cumsum(product)
-    # print(f"Information tensor: {information_tensor}")
     information = information_tensor[len(information_tensor) - 1]
     # convert information to float and return
     return float(information)
-

adaptivetesting-1.0.1/adaptivetesting/math/estimators/__bayes_modal_estimation.py

@@ -0,0 +1,45 @@
+from typing import List, Tuple
+import jax.numpy as np
+from ...services.__estimator_interface import IEstimator
+from ...models.__test_item import TestItem
+from .__functions.__bayes import maximize_posterior
+from .__prior import Prior
+
+
+class BayesModal(IEstimator):
+    def __init__(self,
+                 response_pattern: List[int] | np.ndarray,
+                 items: List[TestItem],
+                 prior: Prior,
+                 optimization_interval: Tuple[float, float] = (-10, 10)):
+        """This class can be used to estimate the current ability level
+            of a respondent given the response pattern and the corresponding
+            item difficulties.
+            The estimation is based on maximum likelihood estimation and the
+            Rasch model.
+
+            Args:
+                response_pattern (List[int]): list of response patterns (0: wrong, 1:right)
+
+                items (List[TestItem]): list of answered items
+            
+                prior (Prior): prior distribution
+            """
+        super().__init__(response_pattern, items, optimization_interval)
+
+        self.prior = prior
+
+    def get_estimation(self) -> float:
+        """Estimate the current ability level using Bayes Modal.
+        
+        Returns:
+            float: ability estimation
+        """
+        return maximize_posterior(
+            self.a,
+            self.b,
+            self.c,
+            self.d,
+            self.response_pattern,
+            self.prior
+        )

adaptivetesting-1.0.1/adaptivetesting/math/estimators/__functions/__bayes.py

@@ -0,0 +1,45 @@
+import jax.numpy as np
+from scipy.optimize import minimize_scalar, OptimizeResult # type: ignore
+from .__estimators import likelihood
+from ..__prior import Prior
+from ....models.__algorithm_exception import AlgorithmException
+
+
+def maximize_posterior(
+    a: np.ndarray,
+    b: np.ndarray,
+    c: np.ndarray,
+    d: np.ndarray,
+    response_pattern: np.ndarray,
+    prior: Prior
+) -> float:
+    """_summary_
+
+    Args:
+        a (np.ndarray): _description_
+        
+        b (np.ndarray): _description_
+        
+        c (np.ndarray): _description_
+        
+        d (np.ndarray): _description_
+        
+        response_pattern (np.ndarray): _description_
+        
+        prior (Prior): _description_
+
+    Returns:
+        float: Bayes Modal estimator for the given parameters
+    """
+    def posterior(mu) -> np.ndarray:
+        return likelihood(mu, a, b, c, d, response_pattern) * prior.pdf(mu)
+    
+    result: OptimizeResult = minimize_scalar(lambda mu: posterior(mu),
+                                             bounds=(-10, 10),
+                                             method="bounded") # type: ignore
+    
+    if not result.success:
+        raise AlgorithmException(f"Optimization failed: {result.message}")
+    
+    else:
+        return float(result.x)