Add container message to trackusage

Author: marcelzwiers

Dockerfile

@@ -19,27 +19,38 @@ RUN mkdir -p /opt/miniconda3; \
     . /root/.bashrc; \
     \
 # Create a conda env and install FSL tools needed for (me)deface and slicereport. NB: Keep the version the same as the Docker base image
-    conda create -n fsl python=3.10; \
+    conda create -n fsl python=3.12; \
     conda install -n fsl -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ -c conda-forge fsl-libvis fsl-avwutils fsl-flirt; \
     \
-# Pack the fsl environment into fsl.tar.gz and unpack it in /opt/fsl \
+# Pack the fsl environment into fsl.tar.gz and unpack it in /opt/fsl
     conda install -c conda-forge conda-pack; \
     conda pack -n fsl; \
     mkdir /opt/fsl && tar -xzf fsl.tar.gz -C /opt/fsl; \
-    /opt/fsl/bin/conda-unpack
+    /opt/fsl/bin/conda-unpack; \
+    \
+# Clone bidscoin
+    git clone https://github.com/Donders-Institute/bidscoin.git /opt/bidscoin; \
+    cd /opt/bidscoin; \
+    rm -rf docs tests .git
 
 
 FROM python:3.12-slim
 
 # Install the dcm2niix build. NB: Obsolete with the new `pip install bidscoin[dcm2niix2bids]` extras option
 COPY --from=builder /usr/local/bin/dcm2niix /usr/local/bin/dcm2niix
 COPY --from=builder /opt/fsl /opt/fsl
+# Only needed for pip install from GitHub
+# COPY --from=builder /opt/bidscoin /opt/bidscoin
 
+# Set environment variables
 ENV FSLDIR=/opt/fsl FSLOUTPUTTYPE=NIFTI_GZ \
     PATH=$PATH:/opt/fsl/bin \
-    PIP_NO_CACHE_DIR=off
+    PIP_NO_CACHE_DIR=off \
+    CONTAINER=Docker
 
 # First install pyqt as Debian package to solve dependencies issues occurring when installed with pip
 # Then install the latest stable BIDScoin release (add build-essential for newer python:3-slim base images (pip needs gcc and wayland support is not yet provided for))
 RUN apt update && apt -y --no-install-recommends install pigz curl python3-pyqt6 build-essential libgl1 libxcb-cursor0 dbus qt6-wayland && apt clean; \
     pip install bidscoin[spec2nii2bids,deface]
+    # pip install bidscoin[spec2nii2bids,deface]==VERSION
+    # pip install /opt/bidscoin[spec2nii2bids,deface]   # = GitHub. NB: Also uncomment in xfiles from builder: `/opt/bidscoin /opt/bidscoin`

apptainer.def

@@ -24,7 +24,7 @@ Stage: builder
     . /root/.bashrc
 
     # Create a conda env and install FSL tools needed for (me)deface and slicereport. NB: Keep the version the same as the Docker base image
-    conda create -n fsl python=3.10
+    conda create -n fsl python=3.12
     conda install -n fsl -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ -c conda-forge fsl-libvis fsl-avwutils fsl-flirt
 
     # Pack the fsl environment into fsl.tar.gz and unpack it in /opt/fsl
@@ -63,14 +63,15 @@ Stage: final
         3) The current image does not include the Freesurfer/synthstrip software (needed for `skullstrip`)
 
 %files from builder
-    # /opt/bidscoin /opt/bidscoin     # Only needed for pip install from github
     /usr/local/bin/dcm2niix /usr/local/bin/dcm2niix
     /opt/fsl /opt/fsl
+    # /opt/bidscoin /opt/bidscoin     # Only needed for pip install from GitHub
 
 %environment
     export FSLDIR=/opt/fsl FSLOUTPUTTYPE=NIFTI_GZ
     export PATH=$PATH:/opt/fsl/bin
     export PIP_NO_CACHE_DIR=off
+    export CONTAINER=Apptainer
 
 %post
     # Install curl (sometimes needed by dcm2niix) and pigz (to speed up dcm2niix)
@@ -81,9 +82,9 @@ Stage: final
     apt -y --no-install-recommends install python3-pyqt6 build-essential libgl1 libxcb-cursor0 dbus qt6-wayland && apt clean     # Add build-essential for newer python:3-slim base images (pip needs gcc and wayland support is not yet provided for)
 
     # Install BIDScoin
-    # pip install /opt/bidscoin[spec2nii2bids,deface]   # Also uncomment in xfiles from builder: `/opt/bidscoin /opt/bidscoin`
-    # pip install bidscoin[spec2nii2bids,deface]==VERSION
     pip install bidscoin[spec2nii2bids,deface]
+    # pip install bidscoin[spec2nii2bids,deface]==VERSION
+    # pip install /opt/bidscoin[spec2nii2bids,deface]   # = GitHub. NB: Also uncomment in xfiles from builder: `/opt/bidscoin /opt/bidscoin`
 
     # Uncomment the line below if you get errors like: ImportError: libQt5Core.so.5: cannot open shared object file: No such file or directory
     # strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5

bidscoin/__init__.py

@@ -192,6 +192,8 @@ def trackusage(event: str, message='', dryrun: bool=False) -> dict:
             'hostid':   hashlib.md5(platform.node().encode('utf8')).hexdigest()}
     if message:
         data['message'] = str(message)
+    if container := os.getenv('CONTAINER'):
+        data['container'] = container
 
     # Return if the user disallows tracking, if it is a dry-, pytest-, or a DRMAA-run, or if this is not a stable (#.#.#) version
     if not (os.getenv('BIDSCOIN_TRACKUSAGE') or config['bidscoin'].get('trackusage','yes')).upper() in ('1', 'TRUE', 'Y', 'YES') or dryrun \