Python3.sif: fix broken ipython magic (#321)

* `Python3.sif`: broken ipython magic, updated Python env to 3.12
Fixes #320

Author: espenhgn

CHANGELOG.md

@@ -37,6 +37,17 @@ Removed features goes here
 
 Miscellaneous goes here
 
+## 1.14.0 - 2025-12-05
+
+### Updated
+
+* Using Miniforge3 installer (was Mambaforge)
+* Updated Python (3.10.6 -> 3.12.12) and installed packages in `python3.sif` container.
+
+### Fixed
+
+* Fixed issue with %matplotlib inline magic with IPython/Jupyter in `python3.sif` container.
+
 ## 1.13.1 - 2025-11-27
 
 ### 

docker/dockerfiles/python3/Dockerfile

@@ -11,74 +11,79 @@ RUN bash apt_get_essential.sh && \
     rm apt_get_essential.sh
 
 WORKDIR /tmp
-COPY /scripts/install_mambaforge.sh .
-RUN bash install_mambaforge.sh && \
-    rm install_mambaforge.sh
+COPY /scripts/install_miniforge.sh .
+RUN bash install_miniforge.sh && \
+    rm install_miniforge.sh
+
+RUN conda install mamba -n base -c conda-forge && \
+    conda clean -a -y
 
 # set up python env.
 # keep the list of packages sorted alphabetically
 # https://www.online-utility.org/text/sort.jsp
-RUN mamba install python=3.10.6 \
-    configparser=7.0.0 \
-    dask=2023.3.0 \
+RUN mamba install python=3.12.12 \
+    configparser=7.2.0 \
+    dask=2025.11.0 \
     fastparquet=2024.11.0 \
-    graphviz=12.2.1 \
-    "h5py=3.7.0=nompi*" \
-    jupyterlab=3.4.8 \
-    lightgbm=4.5.0 \
-    lifelines=0.27.0 \
-    imbalanced-learn=0.12.3 \
+    graphviz=14.0.5 \
+    "h5py=3.15.1=nompi*" \
+    jupyterlab=4.5.0 \
+    lightgbm=4.6.0 \
+    lifelines=0.30.0 \
+    imbalanced-learn=0.14.0 \
     intervaltree=3.1.0 \
-    matplotlib-venn=0.11.5 \
-    matplotlib=3.6.0 \
-    miniwdl=1.12.1 \
-    miniwdl-slurm=0.2.0 \
-    more-itertools=9.0.0 \
-    networkx=3.4 \
-    numdifftools=0.9.39 \
-    numba=0.60.0 \
-    numpy=1.23.3 \
+    matplotlib-venn=1.1.2 \
+    matplotlib=3.10.8 \
+    miniwdl=1.13.1 \
+    miniwdl-slurm=0.4.0 \
+    more-itertools=10.8.0 \
+    networkx=3.6 \
+    numdifftools=0.9.41 \
+    numba=0.62.1 \
+    numpy=2.3.5 \
     openpyxl=3.1.5 \
-    pandas=2.2.3 \
-    pandas-plink=2.2.9 \
+    pandas=2.3.3 \
+    pandas-plink=2.3.2 \
     paramiko=4.0.0 \
-    psutil=5.9.3 \
-    pyarrow=19.0.1 \
-    pydot=3.0.4 \
-    pyreadstat=1.2.7 \
-    pytables=3.7.0 \
-    python-graphviz=0.20.3 \
-    pyyaml=6.0 \
-    scikit-learn=1.5.2 \
-    scikit-survival=0.23.0 \
-    scipy=1.9.1 \
+    psutil=7.1.3 \
+    pyarrow=22.0.0 \
+    pydot=4.0.1 \
+    pyreadstat=1.3.2 \
+    pytables=3.10.2 \
+    python-graphviz=0.21 \
+    pyyaml=6.0.3 \
+    scikit-learn=1.7.2 \
+    scikit-survival=0.25.0 \
+    scipy=1.16.3 \
     seaborn=0.13.2 \
     semantic_version=2.10.0 \
-    shap=0.46.0 \
-    statsmodels=0.13.2 \
-    xgboost=2.1.4 \
-    xlrd=2.0.1 \
-    xmltodict=0.13.0 \
+    shap=0.48.0 \
+    statsmodels=0.14.5 \
+    xgboost=3.1.2 \
+    xlrd=2.0.2 \
+    xmltodict=1.0.2 \
     --yes && \
     mamba clean -a -y
 
 # pip install stuff in env.
-RUN pip install --no-cache-dir --no-deps cbgen==1.0.2 \
-    bgen-reader==4.0.8 \
-    bed-reader==0.2.24 \
-    dxpy==0.383.1 \
-    fastlmm==0.6.3 \
+RUN pip install --no-cache-dir --no-deps \
+    bed-reader==1.0.6 \
+    bgen-reader==4.0.9 \
+    cbgen==1.0.6 \
+    crc32c==2.8 \
+    dxpy==0.400.1 \
+    fastlmm==0.6.12 \
     hdf5storage==0.2.2 \
     LDpred==1.0.11 \
     Pgenlib==0.93.0 \
     plinkio==0.9.8 \
     plinkliftover==0.5.2 \
     poetry==2.2.1 \
     pooch==1.8.2 \
-    pycap==2.1.0 \
+    pycap==2.7.0 \
     pyliftover==0.4.1 \
-    pysnptools==0.5.7 && \
-    pip cache purge 
+    pysnptools==0.5.14 && \
+    pip cache purge
 
 # Plink (as python_convert depends on plink)
 WORKDIR /tmp/plink
@@ -112,4 +117,4 @@ WORKDIR /tools
 
 # https://github.com/comorment/containers/issues/267:
 ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
- 
+

docker/scripts/install_mambaforge.sh docker/scripts/install_miniforge.shdocker/scripts/install_mambaforge.sh renamed to docker/scripts/install_miniforge.sh

@@ -1,10 +1,10 @@
 #!/bin/sh
 set -euo pipefail
 
-version=25.3.1-0
-curl -sSL https://github.com/conda-forge/miniforge/releases/download/$version/Miniforge3-$version-$(uname)-$(uname -m).sh -o /tmp/mambaforge.sh \
-  && mkdir /root/.conda \
-  && bash /tmp/mambaforge.sh -bfp /usr/local \
-  && rm -rf /tmp/mambaforge.sh
+version=25.11.0-1
+curl -sSL https://github.com/conda-forge/miniforge/releases/download/$version/Miniforge3-$version-$(uname)-$(uname -m).sh -o /tmp/miniforge.sh
+mkdir /root/.conda
+bash /tmp/miniforge.sh -bfp /usr/local
+rm -rf /tmp/miniforge.sh
 
 export PATH=$PATH:/opt/conda/bin

tests/test_python3.py

@@ -21,6 +21,7 @@
     subprocess.run('apptainer', check=False)
     PREFIX = f'apptainer run {pth}'
     PREFIX_MOUNT = f'apptainer run --home={cwd}:/home/ {pth}'
+    IPYTHON = f'{PREFIX} ipython'
     PYTHON = f'{PREFIX} python'
     PYTHON_MOUNT = f'{PREFIX_MOUNT} python'
     PLINK = f'{PREFIX} plink'
@@ -37,6 +38,7 @@
             f'--mount type=bind,source={cwd},target={cwd} ' +
             '--platform linux/amd64 ' +
             'ghcr.io/comorment/python3')
+        IPYTHON = f'{PREFIX} ipython'
         PYTHON = f'{PREFIX} python'
         PYTHON_MOUNT = f'{PREFIX_MOUNT} python'
         PLINK = f'{PREFIX} plink'
@@ -46,6 +48,7 @@
     except FileNotFoundError:
         # neither apptainer nor docker found, fall back to plain python
         # presumably because we are running on the client
+        IPYTHON = 'ipython'
         PYTHON = 'python'
         PYTHON_MOUNT = 'python'
         PLINK = 'plink'
@@ -104,6 +107,7 @@ def test_python3_miniwdl():
 def test_python3_packages():
     packages = [
         'configparser',
+        'crc32c',
         'dask',
         'fastparquet',
         'dxpy',
@@ -151,3 +155,8 @@ def test_python3_import_pandas_scipy_stats():
     call = f'{PYTHON_MOUNT} -c "import pandas as pd; from scipy import *"'
     out = subprocess.run(call, shell=True, check=False)
     assert out.returncode == 0
+
+def test_python3_ipython_magic():
+    call = f'{IPYTHON} -c "get_ipython().run_line_magic(\'matplotlib\', \'inline\')"'
+    out = subprocess.run(call, shell=True, check=False)
+    assert out.returncode == 0

version/version.py

@@ -1,8 +1,8 @@
 _MAJOR = "1"
-_MINOR = "13"
+_MINOR = "14"
 # On main and in a nightly release the patch should be one ahead of the last
 # released build.
-_PATCH = "1"
+_PATCH = "0"
 # This is mainly for nightly builds which have the suffix ".dev$DATE". See
 # https://semver.org/#is-v123-a-semantic-version for the semantics.
 _SUFFIX = ""