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fixes python version 3.12 (#250)
* fixes #249 * fixes upper boundary for the python version and makes all dependencies open to new versions * fixes github action for testing and configuring poetry * add setuptools as dependencies as this mitigates the missing distutils package in python 3.12 * restricts Jinja2 version to non-vulnarable one * change minimal python version to 3.9 * fixes doctest outputs to be compliant to improved xarray output * small fix to README.rst * make codecov working again
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‎.github/workflows/draft-pdf.yml‎

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@@ -11,7 +11,7 @@ jobs:
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name: Paper Draft
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Build draft PDF
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uses: openjournals/openjournals-draft-action@master
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with:

‎.github/workflows/python-publish.yml‎

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name: Build and upload releases
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name: Build and upload releases (sdist only)
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on:
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release:
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strategy:
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matrix:
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os: [ubuntu-latest]
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python-version: ['3.11']
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python-version: ['3.12']
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# os: [ubuntu-latest, macOS-latest, windows-latest]
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# python-version: ['3.8', '3.9', '3.10', '3.11']
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poetry-version: [1.6]
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poetry-version: ['1.8']
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fail-fast: false
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Run image
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uses: abatilo/actions-poetry@v2.1.3
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uses: abatilo/actions-poetry@v2
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with:
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poetry-version: ${{ matrix.poetry-version }}
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- name: Install package

‎.github/workflows/python-test-publish.yml‎

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@@ -11,19 +11,19 @@ jobs:
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strategy:
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matrix:
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os: [ubuntu-latest, macOS-latest, windows-latest]
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python-version: ['3.8', '3.9', '3.10', '3.11']
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poetry-version: [1.2]
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python-version: ['3.9', '3.10', '3.11', '3.12']
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poetry-version: ['1.8']
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fail-fast: false
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Run image
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uses: abatilo/actions-poetry@v2.1.3
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uses: abatilo/actions-poetry@v2
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with:
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poetry-version: ${{ matrix.poetry-version }}
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- name: Configure test PyPI

‎.github/workflows/python-test.yml‎

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strategy:
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matrix:
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os: [ubuntu-latest, macOS-latest, windows-latest]
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python-version: ['3.8', '3.11']
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poetry-version: [1.1.13]
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python-version: ['3.9', '3.12']
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poetry-version: ["1.8"]
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fail-fast: false
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Get full Python version
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id: full-python-version
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run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
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- name: Display Python version
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run: python -c "import sys; print('-'.join(str(v) for v in sys.version_info))"
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- name: Setup poetry
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uses: abatilo/actions-poetry@v2.1.3
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uses: abatilo/actions-poetry@v2
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with:
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poetry-version: ${{ matrix.poetry-version }}
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- name: Update PATH
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if: ${{ runner.os != 'Windows' }}
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run: echo "$HOME/.local/bin" >> $GITHUB_PATH
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- name: Update Path for Windows
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if: ${{ runner.os == 'Windows' }}
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run: echo "$APPDATA\Python\Scripts" >> $GITHUB_PATH
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- name: Configure poetry
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run: poetry config virtualenvs.in-project true
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- name: Set up cache
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uses: actions/cache@v3
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id: cache
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with:
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path: .venv
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key: venv-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}
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- name: Install dependencies
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- name: Install dependencies and pyndl
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run: poetry install
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- name: Run linux tests
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- name: Run tests on other distributions (skip linux-only tests)
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if: ${{ runner.os != 'Linux' }}
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run: poetry run pytest --no-linux
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run: poetry run pytest --no-linux --cov=pyndl --cov-report=xml --disable-pytest-warnings
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v2
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uses: codecov/codecov-action@v4
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with:
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file: ./coverage.xml
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flags: unittests
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token: ${{ secrets.CODECOV_TOKEN }}
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env_vars: OS,PYTHON

‎README.rst‎

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@@ -8,9 +8,6 @@ Pyndl - Naive Discriminative Learning in Python
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.. image:: https://codecov.io/gh/quantling/pyndl/branch/main/graph/badge.svg?token=2GWUXRA9PD
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:target: https://codecov.io/gh/quantling/pyndl
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.. image:: https://img.shields.io/lgtm/grade/python/g/quantling/pyndl.svg?logo=lgtm&logoWidth=18
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:target: https://lgtm.com/projects/g/quantling/pyndl/context:python
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.. image:: https://img.shields.io/pypi/pyversions/pyndl.svg
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:target: https://pypi.python.org/pypi/pyndl/
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‎docs/source/examples.rst‎

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@@ -126,7 +126,7 @@ Let's start:
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>>> weights = ndl.ndl(events='docs/data/lexample.tab.gz', alpha=0.1,
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... betas=(0.1, 0.1), method='threading')
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>>> weights # doctest: +ELLIPSIS
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<xarray.DataArray (outcomes: 8, cues: 15)>
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<xarray.DataArray (outcomes: 8, cues: 15)>...
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...
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``weights`` is an ``xarray.DataArray`` of dimension ``len(outcomes)``,
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.. code-block:: python
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>>> weights[1, 5] # doctest: +ELLIPSIS
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<xarray.DataArray ()>
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<xarray.DataArray ()>...
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...
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>>> weights.loc[{'outcomes': 'plural', 'cues': 's#'}] # doctest: +ELLIPSIS
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<xarray.DataArray ()>
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<xarray.DataArray ()>...
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array(0.076988...)
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Coordinates:
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outcomes <U6 'plural'
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cues <U2 's#'
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outcomes <U6 ... 'plural'
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cues <U2 ... 's#'
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...
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>>> weights.loc['plural'].loc['s#'] # doctest: +ELLIPSIS
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<xarray.DataArray ()>
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<xarray.DataArray ()>...
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array(0.076988...)
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outcomes <U6 'plural'
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cues <U2 's#'
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outcomes <U6 ... 'plural'
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cues <U2 ... 's#'
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...
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return the weight of the cue 's#' (the unigram 's' being the word-final) for
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>>> weights2 = ndl.ndl(events='docs/data/lexample.tab.gz', alpha=0.1,
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... betas=(0.1, 0.1), method='threading', weights=weights)
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>>> weights2 # doctest: +ELLIPSIS
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<xarray.DataArray (outcomes: 8, cues: 15)>
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<xarray.DataArray (outcomes: 8, cues: 15)>...
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array([[ 0.24...
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...
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...]])
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Coordinates:
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* outcomes (outcomes) <U6 'hand' 'plural'...
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* cues (cues) <U2 '#h' 'ha' 'an' 'nd'...
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* outcomes (outcomes) <U6 ... 'hand' 'plural'...
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* cues (cues) <U2 ... '#h' 'ha' 'an' 'nd'...
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Attributes:...
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date:...
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event_path:...
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... alphas=alphas_cues, betas=(0.1, 0.1),
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... make_data_array=True)
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>>> weights # doctest: +ELLIPSIS
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<xarray.DataArray (outcomes: 8, cues: 15)>
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<xarray.DataArray (outcomes: 8, cues: 15)>...
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...
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... 'cue_vector_dimensions': ['dim1', 'dim2', 'dim3']}]
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>>> weights_ndl = weights_ndl.loc[{'outcomes': ['A', 'B', 'C', 'D'], 'cues': ['a', 'b', 'c']}]
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>>> print(weights_wh) # doctest: +ELLIPSIS
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<xarray.DataArray (outcome_vector_dimensions: 4, cue_vector_dimensions: 3)>
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<xarray.DataArray (outcome_vector_dimensions: 4, cue_vector_dimensions: 3)>...
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array([[0.06706..., 0. , 0. ],
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[0. , 0.03940..., 0. ],
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[0.0094... , 0. , 0.03940...],
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[0.01 , 0. , 0. ]])
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Coordinates:
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* outcome_vector_dimensions (outcome_vector_dimensions) <U4 'dim1' ... 'dim4'
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* cue_vector_dimensions (cue_vector_dimensions) <U4 'dim1' 'dim2' 'dim3'
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outcomes <U1 'A'
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cues <U1 'a'
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* outcome_vector_dimensions (outcome_vector_dimensions) <U4 ... 'dim1' ...
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* cue_vector_dimensions (cue_vector_dimensions) <U4 ... 'dim1' ...
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outcomes <U1 ... 'A'
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cues <U1 ... 'a'
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Attributes: (12/15)
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...
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>>> print(weights_ndl) # doctest: +ELLIPSIS
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<xarray.DataArray (outcomes: 4, cues: 3)>
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<xarray.DataArray (outcomes: 4, cues: 3)>...
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array([[0.06706..., 0. , 0. ],
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[0. , 0.03940..., 0. ],
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[0.0094... , 0. , 0.03940...],
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[0.01 , 0. , 0. ]])
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Coordinates:
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* outcomes (outcomes) <U1 'A' 'B' 'C' 'D'
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* cues (cues) <U1 'a' 'b' 'c'
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* outcomes (outcomes) <U1 ... 'A' 'B' 'C' 'D'
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* cues (cues) <U1 ... 'a' 'b' 'c'
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...
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‎pyproject.toml‎

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[tool.poetry]
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name = "pyndl"
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version = "1.2.2"
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version = "1.2.3"
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description = "Naive discriminative learning implements learning and classification models based on the Rescorla-Wagner equations."
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license = "MIT"
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'Topic :: Scientific/Engineering :: Information Analysis',]
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[tool.poetry.dependencies]
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python = ">=3.8,<3.12" # Compatible python versions must be declared here
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numpy = "^1.23.1"
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scipy = "^1.9.0"
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pandas = "^1.4.3"
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xarray = "^2022.6.0"
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netCDF4 = "^1.6.0"
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Cython = "^3.0.0"
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python = ">=3.9,<3.13" # Compatible python versions must be declared here
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numpy = ">=1.24.1"
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scipy = ">=1.13.0"
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pandas = ">=1.4.3"
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xarray = ">=2022.6.0"
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netCDF4 = ">=1.6.0"
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Cython = ">=3.0.0"
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toml = ">=0.10.2"
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setuptools = ">=69.2.0"
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[tool.poetry.dev-dependencies]
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pytest = "^7.0"
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pytest-cov = "^2.4"
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pydocstyle = "^6.1.1"
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flake8 = "^4.0.1"
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sphinx = "^1.4"
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sphinx_rtd_theme = "^1.0.0"
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notebook = "^6.4.10"
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seaborn = "^0.12.1"
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numpydoc = "^1.2"
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sphinx-copybutton = "^0.5.1"
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pylint = "^2.0.0"
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nbsphinx = "^0.8.8"
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vulture = "^2.3"
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Jinja2 = "<3.1.0"
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pytest = ">=7.0"
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pytest-cov = ">=2.4"
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pydocstyle = ">=6.1.1"
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flake8 = ">=4.0.1"
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sphinx = ">=1.4"
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sphinx_rtd_theme = ">=1.0.0"
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notebook = ">=6.4.10"
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seaborn = ">=0.12.1"
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numpydoc = ">=1.2"
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sphinx-copybutton = ">=0.5.1"
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pylint = ">=2.0.0"
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nbsphinx = ">=0.8.8"
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vulture = ">=2.3"
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Jinja2 = ">=3.1.3"
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[tool.pytest.ini_options]
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addopts = '--doctest-glob "*.rst"'

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