Fix script to create requirements.txt

export requirements.txt and requirements.cpu.txt from respective docker images

env/export_pip-r.sh

@@ -48,21 +48,23 @@ echo "Exporting versions from $2..."
   echo "#"
 } > $1
 
-pip_cmd="python --version && pip list --format=freeze --no-color --all --disable-pip-version-check --no-input"
+pip_cmd="python --version && pip list --format=freeze --no-color --disable-pip-version-check --no-input"
 if [ "${2/#.sif}" != "$2" ]
 then
   # singularity
-  cmd="singularity exec $2 /bin/bash -c '$pip_cmd'"
+  cmd=("singularity" "exec" "$2" "/bin/bash" -c "$pip_cmd")
+  clean_cmd="singularity exec $2 /bin/bash -c '$pip_cmd'"
 else
   # docker
-  cmd="docker run --entrypoint /bin/bash $2 -c '$pip_cmd'"
+  clean_cmd="docker run --rm -u <user_id>:<group_id> --entrypoint /bin/bash $2 -c '$pip_cmd'"
+  cmd=("docker" "run" --rm -u "$(id -u):$(id -g)" --entrypoint /bin/bash "$2" -c "$pip_cmd")
 fi
 {
   echo "# Which ran the following command:"
-  echo "#    $cmd"
+  echo "#    $clean_cmd"
   echo "#"
 } >> $1
-out=$($cmd)
+out=$("${cmd[@]}")
 hardware=$(echo "$out" | grep "torch==" | cut -d"+" -f2)
 pyversion=$(echo "$out" | head -n 1 | cut -d" " -f2)
 {

requirements.cpu.txt

@@ -0,0 +1,104 @@
+#
+# This file is autogenerated by kueglerd from deepmi/fastsurfer:cpu-v2.3.0
+# by the following command from FastSurfer:
+#
+#    ./requirements.cpu.txt deepmi/fastsurfer:cpu-v2.3.0
+#
+# Which ran the following command:
+#    docker run --rm -u <user_id>:<group_id> --entrypoint /bin/bash deepmi/fastsurfer:cpu-v2.3.0 -c 'python --version && pip list --format=freeze --no-color --disable-pip-version-check --no-input'
+#
+#
+# Image was configured for cpu using python version 3.10.14
+#
+--extra-index-url https://download.pytorch.org/whl/cpu
+
+# Python 3.10.14
+absl-py==2.1.0
+Brotli==1.1.0
+cached-property==1.5.2
+certifi==2024.7.4
+cffi==1.17.0
+charset-normalizer==3.3.2
+click==8.1.7
+colorama==0.4.6
+contourpy==1.2.1
+cycler==0.12.1
+Deprecated==1.2.14
+filelock==3.15.4
+fonttools==4.53.1
+fsspec==2024.6.1
+grpcio==1.62.2
+h2==4.1.0
+h5py==3.11.0
+hpack==4.0.0
+humanize==4.10.0
+hyperframe==6.0.1
+idna==3.8
+imagecodecs==2024.6.1
+imageio==2.35.1
+importlib_metadata==8.4.0
+importlib_resources==6.4.4
+Jinja2==3.1.4
+joblib==1.4.2
+kiwisolver==1.4.5
+lapy==1.1.0
+lazy_loader==0.4
+Markdown==3.6
+markdown-it-py==3.0.0
+MarkupSafe==2.1.5
+matplotlib==3.9.2
+mdurl==0.1.2
+mpmath==1.3.0
+munkres==1.1.4
+networkx==3.3
+nibabel==5.2.1
+numpy==1.26.4
+packaging==24.1
+pandas==2.2.2
+pillow==10.4.0
+pip==24.2
+plotly==5.23.0
+protobuf==4.25.3
+psutil==6.0.0
+pycparser==2.22
+Pygments==2.18.0
+pyparsing==3.1.4
+PySide6==6.7.2
+PySocks==1.7.1
+python-dateutil==2.9.0
+pytz==2024.1
+PyWavelets==1.7.0
+PyYAML==6.0.2
+requests==2.32.3
+rich==13.8.0
+scikit-image==0.24.0
+scikit-learn==1.5.1
+scikit-sparse==0.4.14
+scipy==1.14.1
+setuptools==72.2.0
+shellingham==1.5.4
+shiboken6==6.7.2
+SimpleITK==2.4.0
+six==1.16.0
+sympy==1.13.2
+tenacity==9.0.0
+tensorboard==2.17.1
+tensorboard-data-server==0.7.0
+threadpoolctl==3.5.0
+tifffile==2024.8.24
+torch==2.4.0+cpu
+torchio==0.19.9
+torchvision==0.19.0+cpu
+tornado==6.4.1
+tqdm==4.66.5
+typer==0.12.5
+typing_extensions==4.12.2
+tzdata==2024.1
+unicodedata2==15.1.0
+urllib3==2.2.2
+Werkzeug==3.0.4
+wheel==0.44.0
+wrapt==1.16.0
+yacs==0.1.8
+zipp==3.20.0
+zstandard==0.23.0