Merge pull request #14 from RasmussenLab/slim_default_installation

🎨 ➖ remove umap-learn. also remove lifelines dependency for default pkg

.github/workflows/packaging.yml

@@ -43,14 +43,14 @@ jobs:
     strategy:
       matrix:
         python:
+          - version: "3.12"
+            toxenv: "py312"
           - version: "3.11"
             toxenv: "py311"
           - version: "3.10"
             toxenv: "py310"
           - version: "3.9"
             toxenv: "py39"
-          - version: "3.8"
-            toxenv: "py38"
     steps:
       - uses: actions/checkout@v4
 
@@ -139,4 +139,4 @@ jobs:
           - uses: pypa/gh-action-pypi-publish@release/v1
             with:
               user: __token__
-              password: ${{ secrets.PYPI_API_TOKEN }}
+              password: ${{ secrets.PYPI_API_TOKEN }}

.readthedocs.yaml

@@ -32,3 +32,4 @@ python:
       path: .
       extra_requirements:
         - docs
+        - all

docs/tutorial/explorative_analysis.ipynb

@@ -22,7 +22,7 @@
    },
    "outputs": [],
    "source": [
-    "%pip install njab openpyxl"
+    "%pip install 'njab[all]' openpyxl"
    ]
   },
   {

docs/tutorial/explorative_analysis.py

@@ -20,7 +20,7 @@
 # First install the dependencies:
 
 # %% tags=["hide-output"]
-# %pip install njab openpyxl
+# %pip install 'njab[all]' openpyxl
 
 # %% tags=["hide-cell"]
 from functools import partial

docs/tutorial/log_reg.ipynb

@@ -27,7 +27,7 @@
    "source": [
     "# Setup colab installation\n",
     "# You need to restart the runtime after running this cell\n",
-    "%pip install njab heatmapz openpyxl plotly"
+    "%pip install njab heatmapz openpyxl plotly umap-learn"
    ]
   },
   {

docs/tutorial/log_reg.py

@@ -25,7 +25,7 @@
 # %% tags=["hide-output"]
 # Setup colab installation
 # You need to restart the runtime after running this cell
-# %pip install njab heatmapz openpyxl plotly
+# %pip install njab heatmapz openpyxl plotly umap-learn
 
 # %% tags=["hide-input"]
 import itertools

pyproject.toml

@@ -3,7 +3,7 @@ name = "njab"
 authors = [{ name = "Henry Webel", email = "[email protected]" }]
 description = "not Just Another Biomarker"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 keywords = ["bioinformatics", "biomarker"]
 license = { file = "LICENSE" }
 classifiers = [
@@ -15,12 +15,10 @@ classifiers = [
 ]
 dependencies = [
   "omegaconf",
-  "lifelines",
   "numpy",
   "pandas",
   "scikit-learn",
   "statsmodels",
-  "umap-learn",
   "matplotlib",
   "mrmr_selection",
   "pingouin",
@@ -29,6 +27,9 @@ dependencies = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
+all = [
+  "lifelines",
+]
 docs = [
   "sphinx",
   "sphinx-book-theme",

setup.cfg

@@ -6,7 +6,7 @@ based_on_style = pep8
 ######################
 
 [mypy]
-python_version = 3.8
+python_version = 3.10
 warn_unused_configs = True
 show_error_context = True
 pretty = True
@@ -39,7 +39,7 @@ source =
 #########################
 
 [tox:tox]
-envlist = py38,py39,py310,py311
+envlist = py39,py310,py311,py312
 isolated_build = True
 
 [testenv]

src/njab/io/__init__.py

@@ -1,4 +1,3 @@
-from __future__ import annotations
 import pathlib
 
 

src/njab/plotting/__init__.py

@@ -1,17 +1,17 @@
 """Matplotlib functionality for custom plots."""
 
-import numpy as np
-import pandas as pd
-import matplotlib
 import logging
 import pathlib
 from typing import Iterable
+
+import matplotlib
 import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
 
 from njab.plotting.lifelines import plot_lifelines
-from njab.plotting.km import compare_km_curves
 
-__all__ = ['plot_lifelines', 'compare_km_curves']
+__all__ = ['plot_lifelines']
 
 plt.rcParams['figure.figsize'] = [4.0, 3.0]
 plt.rcParams['pdf.fonttype'] = 42

src/njab/plotting/km.py

@@ -1,8 +1,15 @@
-from __future__ import annotations
-from matplotlib.axes import Axes
-import lifelines.statistics
-from lifelines import KaplanMeierFitter
+try:
+    import lifelines.statistics
+    from lifelines import KaplanMeierFitter
+except ModuleNotFoundError as e:
+    msg = (
+        "lifelines not available. Please install all njab dependencies typing:"
+        "\n\tpip install 'njab[all]'"
+        "\nor separately typing:\n\tpip install lifelines")
+    e.args = (msg, *e.args[1:])
+    raise ModuleNotFoundError(*e.args) from e
 import pandas as pd
+from matplotlib.axes import Axes
 
 
 def compare_km_curves(
@@ -56,13 +63,16 @@ def compare_km_curves(
     mask = pred
     kmf_1 = KaplanMeierFitter()
     kmf_1.fit(time.loc[mask], event_observed=y.loc[mask])
-    ax = kmf_1.plot(xlim=xlim,
-                    ylim=ylim,
-                    xlabel=xlabel,
-                    ylabel=ylabel,
-                    legend=False)
+    ax = kmf_1.plot(
+        xlim=xlim,
+        ylim=ylim,
+        xlabel=xlabel,
+        ylabel=ylabel,
+        legend=False,
+    )
     if add_risk_counts:
         from lifelines.plotting import add_at_risk_counts
+
         add_at_risk_counts(kmf_0, kmf_1, ax=ax)
     return ax, kmf_0, kmf_1
 

src/njab/sklearn/pca.py

@@ -1,5 +1,5 @@
-from __future__ import annotations
 from typing import Optional
+
 import matplotlib
 import pandas as pd
 import sklearn.decomposition

src/njab/stats/ancova.py

@@ -1,6 +1,5 @@
 """Analysis of covariance using pingouin and statsmodels."""
 from __future__ import annotations
-
 import numpy as np
 import pandas as pd
 import pingouin as pg

src/njab/stats/groups_comparision.py

@@ -1,5 +1,4 @@
 """Bionomial test and t-test for groups comparision."""
-from __future__ import annotations
 import logging
 import pandas as pd
 import pingouin as pg