python3: add missing packages (#274)

* `python3`: add missing packages
Fixes #273

* pip install pysurvival, add tests

* drop pysurvival

* pin versions

CHANGELOG.md

@@ -21,6 +21,7 @@ If MD5 sum is not listed for a certain release then it means that the container
 
 ### Added
 
+* Add Python packages `imbalanced-learn, lightgbm, openpyxl` + PRSice_linux binary to `python3.sif` container
 * Add Conda environment file for project dependencies
 * Add Python packages `scikit-survival, pandas-plink, numba, xmltodict, pyliftover, configparser, intervaltree` to `python3.sif` container
 * Add `Haplin`, `WSpiller/MVMR`, `noahlorinczcomi/MRBEE` R packages to `r.sif` container

docker/dockerfiles/python3/Dockerfile

@@ -22,14 +22,17 @@ RUN mamba install python=3.10.6 \
     configparser=7.0.0 \
     "h5py=3.7.0=nompi*" \
     jupyterlab=3.4.8 \
+    lightgbm=4.5.0 \
     lifelines=0.27.0 \
+    imbalanced-learn=0.12.3 \
     intervaltree=3.1.0 \
     matplotlib-venn=0.11.5 \
     matplotlib=3.6.0 \
     more-itertools=9.0.0 \
     numdifftools=0.9.39 \
     numba=0.60.0 \
     numpy=1.23.3 \
+    openpyxl=3.1.5 \
     pandas=1.5.0 \
     pandas-plink=2.2.9 \
     psutil=5.9.3 \
@@ -46,7 +49,6 @@ RUN mamba install python=3.10.6 \
     --yes && \
     mamba clean -a -y
 
-
 # pip install stuff in env.
 RUN pip install --no-cache-dir cbgen==1.0.2 && \
     pip install --no-cache-dir bgen-reader==4.0.8 && \
@@ -75,6 +77,12 @@ WORKDIR /tools/ukb
 RUN git clone https://github.com/precimed/ukb.git . && \
     git reset --hard dc57e0d8380cd9b2eca479dc6f181d76ca5a429a
 
+# PRSice_linux binary (useful)
+WORKDIR /tmp/prsice
+COPY /scripts/install_prsice.sh /tmp/prsice/
+RUN bash /tmp/prsice/install_prsice.sh && \
+    rm -rf /tmp/prsice
+
 WORKDIR /tools
 
 # https://github.com/comorment/containers/issues/267:

tests/test_python3.py

@@ -15,6 +15,10 @@ def test_python3_plink():
     out = subprocess.run(call.split(' '))
     assert out.returncode == 0
 
+def test_python3_prsice():
+    call = f'singularity run {pth} PRSice_linux --version'
+    out = subprocess.run(call.split(' '))
+    assert out.returncode == 0
 
 def test_python3_python():
     call = f'singularity run {pth} python --version'
@@ -51,14 +55,17 @@ def test_python3_packages():
     packages = [
         'configparser',
         'h5py',
+        'imblearn',
         'intervaltree',
         'ldpred',
         'lifelines',
+        'lightgbm',
         'matplotlib',
         'matplotlib_venn',
         'numba',
         'numdifftools',
         'numpy',
+        'openpyxl',
         'pandas',
         'pandas_plink',
         'plinkio',