Merge branch 'main' into intersphinx

.github/workflows/colab.yml

@@ -0,0 +1,25 @@
+name: Test that tutorial runs on latest colab image
+
+on:
+  push:
+  schedule:
+    - cron: '0 2 * * 3'
+
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest-4core # increase disk space  
+    # https://console.cloud.google.com/artifacts/docker/colab-images/europe/public/runtime
+    container:
+      image: europe-docker.pkg.dev/colab-images/public/runtime:latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Test tutorials
+        run: | 
+          python3 -m pip install papermill ipykernel njab
+          cd docs/tutorial
+          papermill explorative_analysis.ipynb --help-notebook
+          papermill log_reg.ipynb --help-notebook
+          papermill explorative_analysis.ipynb explorative_analysis_tested.ipynb
+          pip install njab heatmapz openpyxl "matplotlib<3.7" plotly
+          papermill log_reg.ipynb log_reg_tested.ipynb

.github/workflows/packaging.yml

@@ -10,9 +10,9 @@ jobs:
     name: Check formatting
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4.0.0
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
@@ -26,9 +26,9 @@ jobs:
     name: Lint
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4.0.0
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
@@ -52,9 +52,9 @@ jobs:
           - version: "3.8"
             toxenv: "py38"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4.0.0
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python.version }}
 
@@ -72,3 +72,71 @@ jobs:
           papermill log_reg.ipynb --help-notebook
           papermill explorative_analysis.ipynb explorative_analysis_tested.ipynb
           papermill log_reg.ipynb log_reg_tested.ipynb
+  
+  build_source_dist:
+    name: Build source distribution
+    if: startsWith(github.ref, 'refs/heads/main') || startsWith(github.ref, 'refs/tags')
+    runs-on: ubuntu-latest
+    steps:
+        - uses: actions/checkout@v4
+
+        - uses: actions/setup-python@v5
+          with:
+            python-version: "3.10"
+
+        - name: Install build
+          run: python -m pip install build
+
+        - name: Run build
+          run: python -m build --sdist
+
+        - uses: actions/upload-artifact@v4
+          with:
+            path: ./dist/*.tar.gz
+
+  # build_wheels:
+  #   name: Build wheels on ${{ matrix.os }}
+  #   if: startsWith(github.ref, 'refs/heads/main') || startsWith(github.ref, 'refs/tags')
+  #   runs-on: ${{ matrix.os }}
+  #   strategy:
+  #       matrix:
+  #         os: [ubuntu-20.04, windows-2019, macOS-10.15]
+
+  #   steps:
+  #       - uses: actions/checkout@v4
+
+  #       - uses: actions/setup-python@v5
+  #         with:
+  #           python-version: "3.10"
+
+  #       - name: Install cibuildwheel
+  #         run: python -m pip install cibuildwheel==2.3.1
+
+  #       - name: Build wheels
+  #         run: python -m cibuildwheel --output-dir wheels
+
+  #       - uses: actions/upload-artifact@v4
+  #         with:
+  #           path: ./wheels/*.whl
+
+  publish:
+      name: Publish package
+      if: startsWith(github.ref, 'refs/tags')
+      needs:
+          - format
+          - lint
+          - test
+          - build_source_dist
+          # - build_wheels
+      runs-on: ubuntu-latest
+
+      steps:
+          - uses: actions/download-artifact@v4
+            with:
+              name: artifact
+              path: ./dist
+
+          - uses: pypa/gh-action-pypi-publish@release/v1
+            with:
+              user: __token__
+              password: ${{ secrets.PYPI_API_TOKEN }}

CHANGELOG.md

@@ -1,3 +1,8 @@
+## Version 0.0.4
+
+- [x] Add `pandas` styling compability with pandas v2.2 (PR #4)
+- [x] moved `get_lr_multiplicative_decomposition` function to package [78b0c2](https://github.com/RasmussenLab/njab/commit/78b0c27c3ab11489fb81ca320e03485cdc0b1344)
+
 ## Version 0.0.3
 
 - [x] Add pandas styling 

docs/index.rst

@@ -9,7 +9,7 @@ functionality used two papers.
 .. include:: ../README.md
    :parser: myst_parser.sphinx_
    :start-line: 1
-   :end-line: 54
+   :end-line: 69
 
 
 

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = njab
-version = 0.0.3
+version = 0.0.4
 description = not Just Another Biomarker
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -40,7 +40,7 @@ docs =
     sphinx-book-theme
     myst-nb
     ipywidgets
-    sphinx-new-tab-link
+    sphinx-new-tab-link!=0.2.2
 
 [options.packages.find]
 where = src
@@ -88,7 +88,7 @@ source =
 #########################
 
 [tox:tox]
-envlist = py38
+envlist = py38,py39,py310,py311
 isolated_build = True
 
 [testenv]

src/njab/pandas/__init__.py

@@ -15,15 +15,28 @@ def set_pandas_options() -> None:
     pd.options.display.max_rows = 30
     pd.options.display.min_rows = 20
     pd.options.display.float_format = '{:,.3f}'.format
+    # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.describe_option.html#pandas.describe_option
+    pd.options.styler.format.thousands = ','
+    # # https://github.com/pandas-dev/pandas/blob/main/pandas/io/formats/format.py#L1475
+    # Originally found: https://stackoverflow.com/a/29663750/9684872
 
-    class IntArrayFormatter(pf.GenericArrayFormatter):
+    try:
+        base_class = pf.GenericArrayFormatter
+    except AttributeError:
+        base_class = pf._GenericArrayFormatter
+
+    class IntArrayFormatter(base_class):
 
         def _format_strings(self):
             formatter = self.formatter or '{:,d}'.format
             fmt_values = [formatter(x) for x in self.values]
             return fmt_values
 
-    pf.IntArrayFormatter = IntArrayFormatter
+    try:
+        pf.IntArrayFormatter
+        pf.IntArrayFormatter = IntArrayFormatter
+    except AttributeError:
+        pf._IntArrayFormatter = IntArrayFormatter
 
 
 def replace_with(string_key: str,

test/test_pandas.py

@@ -0,0 +1,8 @@
+import pandas as pd
+import njab
+
+
+def test_thousands_display():
+    njab.pandas.set_pandas_options()
+    s = pd.Series([1_000_000])
+    assert str(s)[4:13] == '1,000,000'