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
quantling · Apr 25, 2024 · 60b1d6b · 60b1d6b
1 parent d8b4647
commit 60b1d6b
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Showing 7 changed files with 67 additions and 87 deletions.
diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -11,7 +11,7 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with:

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -1,4 +1,4 @@
-name: Build and upload releases
+name: Build and upload releases (sdist only)
 
 on:
   release:
@@ -10,21 +10,21 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.11']
+        python-version: ['3.12']
 #        os: [ubuntu-latest, macOS-latest, windows-latest]
 #        python-version: ['3.8', '3.9', '3.10', '3.11']
-        poetry-version: [1.6]
+        poetry-version: ['1.8']
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Run image
-        uses: abatilo/actions-poetry@v2.1.3
+        uses: abatilo/actions-poetry@v2
         with:
           poetry-version: ${{ matrix.poetry-version }}
       - name: Install package

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

diff --git a/.github/workflows/python-test.yml b/.github/workflows/python-test.yml
@@ -14,46 +14,27 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macOS-latest, windows-latest]
-        python-version: ['3.8', '3.11']
-        poetry-version: [1.1.13]
+        python-version: ['3.9', '3.12']
+        poetry-version: ["1.8"]
       fail-fast: false
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Get full Python version
-        id: full-python-version
-        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Display Python version
+        run: python -c "import sys; print('-'.join(str(v) for v in sys.version_info))"
 
       - name: Setup poetry
-        uses: abatilo/actions-poetry@v2.1.3
+        uses: abatilo/actions-poetry@v2
         with:
           poetry-version: ${{ matrix.poetry-version }}
 
-      - name: Update PATH
-        if: ${{ runner.os != 'Windows' }}
-        run: echo "$HOME/.local/bin" >> $GITHUB_PATH
-
-      - name: Update Path for Windows
-        if: ${{ runner.os == 'Windows' }}
-        run: echo "$APPDATA\Python\Scripts" >> $GITHUB_PATH
-
-      - name: Configure poetry
-        run: poetry config virtualenvs.in-project true
-
-      - name: Set up cache
-        uses: actions/cache@v3
-        id: cache
-        with:
-          path: .venv
-          key: venv-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}
-
-      - name: Install dependencies
+      - name: Install dependencies and pyndl
         run: poetry install
 
       - name: Run linux tests
@@ -62,11 +43,11 @@ jobs:
 
       - name: Run tests on other distributions (skip linux-only tests)
         if: ${{ runner.os != 'Linux' }}
-        run: poetry run pytest --no-linux
+        run: poetry run pytest --no-linux --cov=pyndl --cov-report=xml --disable-pytest-warnings
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v4
         with:
-          file: ./coverage.xml
           flags: unittests
+          token: ${{ secrets.CODECOV_TOKEN }}
           env_vars: OS,PYTHON
diff --git a/README.rst b/README.rst
@@ -8,9 +8,6 @@ Pyndl - Naive Discriminative Learning in Python
 .. image:: https://codecov.io/gh/quantling/pyndl/branch/main/graph/badge.svg?token=2GWUXRA9PD
     :target: https://codecov.io/gh/quantling/pyndl
 
-.. image:: https://img.shields.io/lgtm/grade/python/g/quantling/pyndl.svg?logo=lgtm&logoWidth=18
-    :target: https://lgtm.com/projects/g/quantling/pyndl/context:python
-
 .. image:: https://img.shields.io/pypi/pyversions/pyndl.svg
     :target: https://pypi.python.org/pypi/pyndl/
 

diff --git a/docs/source/examples.rst b/docs/source/examples.rst
@@ -126,7 +126,7 @@ Let's start:
     >>> weights = ndl.ndl(events='docs/data/lexample.tab.gz', alpha=0.1,
     ...                   betas=(0.1, 0.1), method='threading')
     >>> weights  # doctest: +ELLIPSIS
-    <xarray.DataArray (outcomes: 8, cues: 15)>
+    <xarray.DataArray (outcomes: 8, cues: 15)>...
     ...
 
 ``weights`` is an ``xarray.DataArray`` of dimension ``len(outcomes)``,
@@ -139,21 +139,21 @@ methods
 .. code-block:: python
 
     >>> weights[1, 5]  # doctest: +ELLIPSIS
-    <xarray.DataArray ()>
+    <xarray.DataArray ()>...
     ...
     >>> weights.loc[{'outcomes': 'plural', 'cues': 's#'}]  # doctest: +ELLIPSIS
-    <xarray.DataArray ()>
+    <xarray.DataArray ()>...
     array(0.076988...)
     Coordinates:
-        outcomes  <U6 'plural'
-        cues      <U2 's#'
+        outcomes  <U6 ... 'plural'
+        cues      <U2 ... 's#'
     ...
     >>> weights.loc['plural'].loc['s#']  # doctest: +ELLIPSIS
-    <xarray.DataArray ()>
+    <xarray.DataArray ()>...
     array(0.076988...)
     Coordinates:
-        outcomes  <U6 'plural'
-        cues      <U2 's#'
+        outcomes  <U6 ... 'plural'
+        cues      <U2 ... 's#'
     ...
 
 return the weight of the cue 's#' (the unigram 's' being the word-final) for
@@ -168,13 +168,13 @@ weight matrix by specifying the ``weight`` argument:
     >>> weights2 = ndl.ndl(events='docs/data/lexample.tab.gz', alpha=0.1,
     ...                    betas=(0.1, 0.1), method='threading', weights=weights)
     >>> weights2  # doctest: +ELLIPSIS
-    <xarray.DataArray (outcomes: 8, cues: 15)>
+    <xarray.DataArray (outcomes: 8, cues: 15)>...
     array([[ 0.24...
     ...
     ...]])
     Coordinates:
-      * outcomes  (outcomes) <U6 'hand' 'plural'...
-      * cues      (cues) <U2 '#h' 'ha' 'an' 'nd'...
+      * outcomes  (outcomes) <U6 ... 'hand' 'plural'...
+      * cues      (cues) <U2 ... '#h' 'ha' 'an' 'nd'...
     Attributes:...
         date:...
         event_path:...
@@ -235,7 +235,7 @@ If you prefer to get a ``xarray.DataArray`` returned you can set the flag ``make
     ...                        alphas=alphas_cues, betas=(0.1, 0.1),
     ...                        make_data_array=True)
     >>> weights  # doctest: +ELLIPSIS
-    <xarray.DataArray (outcomes: 8, cues: 15)>
+    <xarray.DataArray (outcomes: 8, cues: 15)>...
     ...
 
 
@@ -449,27 +449,27 @@ gets apparent.
     ...                              'cue_vector_dimensions': ['dim1', 'dim2', 'dim3']}]
     >>> weights_ndl = weights_ndl.loc[{'outcomes': ['A', 'B', 'C', 'D'], 'cues': ['a', 'b', 'c']}]
     >>> print(weights_wh)  # doctest: +ELLIPSIS
-    <xarray.DataArray (outcome_vector_dimensions: 4, cue_vector_dimensions: 3)>
+    <xarray.DataArray (outcome_vector_dimensions: 4, cue_vector_dimensions: 3)>...
     array([[0.06706..., 0.        , 0.        ],
            [0.        , 0.03940..., 0.        ],
            [0.0094... , 0.        , 0.03940...],
            [0.01      , 0.        , 0.        ]])
     Coordinates:
-      * outcome_vector_dimensions  (outcome_vector_dimensions) <U4 'dim1' ... 'dim4'
-      * cue_vector_dimensions      (cue_vector_dimensions) <U4 'dim1' 'dim2' 'dim3'
-        outcomes                   <U1 'A'
-        cues                       <U1 'a'
+      * outcome_vector_dimensions  (outcome_vector_dimensions) <U4 ... 'dim1' ...
+      * cue_vector_dimensions      (cue_vector_dimensions) <U4 ... 'dim1' ...
+        outcomes                   <U1 ... 'A'
+        cues                       <U1 ... 'a'
     Attributes: (12/15)
     ...
     >>> print(weights_ndl)  # doctest: +ELLIPSIS
-    <xarray.DataArray (outcomes: 4, cues: 3)>
+    <xarray.DataArray (outcomes: 4, cues: 3)>...
     array([[0.06706..., 0.        , 0.        ],
            [0.        , 0.03940..., 0.        ],
            [0.0094... , 0.        , 0.03940...],
            [0.01      , 0.        , 0.        ]])
     Coordinates:
-      * outcomes  (outcomes) <U1 'A' 'B' 'C' 'D'
-      * cues      (cues) <U1 'a' 'b' 'c'
+      * outcomes  (outcomes) <U1 ... 'A' 'B' 'C' 'D'
+      * cues      (cues) <U1 ... 'a' 'b' 'c'
     Attributes: (12/17)
     ...
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyndl"
-version = "1.2.2"
+version = "1.2.3"
 description = "Naive discriminative learning implements learning and classification models based on the Rescorla-Wagner equations."
 
 license = "MIT"
@@ -28,29 +28,31 @@ classifiers = ['Development Status :: 5 - Production/Stable',
                'Topic :: Scientific/Engineering :: Information Analysis',]
 
 [tool.poetry.dependencies]
-python = ">=3.8,<3.12"  # Compatible python versions must be declared here
-numpy = "^1.23.1"
-scipy = "^1.9.0"
-pandas = "^1.4.3"
-xarray = "^2022.6.0"
-netCDF4 = "^1.6.0"
-Cython = "^3.0.0"
+python = ">=3.9,<3.13"  # Compatible python versions must be declared here
+numpy = ">=1.24.1"
+scipy = ">=1.13.0"
+pandas = ">=1.4.3"
+xarray = ">=2022.6.0"
+netCDF4 = ">=1.6.0"
+Cython = ">=3.0.0"
+toml = ">=0.10.2"
+setuptools = ">=69.2.0"
 
 [tool.poetry.dev-dependencies]
-pytest = "^7.0"
-pytest-cov = "^2.4"
-pydocstyle = "^6.1.1"
-flake8 = "^4.0.1"
-sphinx = "^1.4"
-sphinx_rtd_theme = "^1.0.0"
-notebook = "^6.4.10"
-seaborn = "^0.12.1"
-numpydoc = "^1.2"
-sphinx-copybutton = "^0.5.1"
-pylint = "^2.0.0"
-nbsphinx = "^0.8.8"
-vulture = "^2.3"
-Jinja2 = "<3.1.0"
+pytest = ">=7.0"
+pytest-cov = ">=2.4"
+pydocstyle = ">=6.1.1"
+flake8 = ">=4.0.1"
+sphinx = ">=1.4"
+sphinx_rtd_theme = ">=1.0.0"
+notebook = ">=6.4.10"
+seaborn = ">=0.12.1"
+numpydoc = ">=1.2"
+sphinx-copybutton = ">=0.5.1"
+pylint = ">=2.0.0"
+nbsphinx = ">=0.8.8"
+vulture = ">=2.3"
+Jinja2 = ">=3.1.3"
 
 [tool.pytest.ini_options]
 addopts = '--doctest-glob "*.rst"'