Use "Apptainer" instead of "Singularity"

docs/contributors.rst

@@ -33,24 +33,24 @@ For example, ::
         pennbbl/qsiprep:latest /data /out/out participant \
         -w /out/work/
 
-In order to work directly in the container, use ``--entrypoint=bash`` 
+In order to work directly in the container, use ``--entrypoint=bash``
 arguments in a ``docker`` command::
 
     $ docker run --rm -v $HOME/fullds005:/data:ro -v $HOME/dockerout:/out \
         -v $HOME/projects/qsiprep/qsiprep:/usr/local/miniconda/lib/python3.10/site-packages/qsiprep:ro --entrypoint=bash \
         pennbbl/qsiprep:latest
 
-Patching containers can be achieved in Singularity analogous to ``docker``
+Patching containers can be achieved in Apptainer analogous to ``docker``
 using the ``--bind`` (``-B``) option: ::
 
-    $ singularity run \
+    $ apptainer run \
         -B $HOME/projects/qsiprep/qsiprep:/usr/local/miniconda/lib/python3.10/site-packages/qsiprep \
         qsiprep.img \
         /scratch/dataset /scratch/out participant -w /out/work/
 
-Or you can patch Singularity containers using the PYTHONPATH variable: ::
+Or you can patch Apptainer containers using the PYTHONPATH variable: ::
 
-   $ PYTHONPATH="$HOME/projects/qsiprep" singularity run qsiprep.img \
+   $ PYTHONPATH="$HOME/projects/qsiprep" apptainer run qsiprep.img \
         /scratch/dataset /scratch/out participant -w /out/work/
 
 

docs/installation.rst

@@ -64,19 +64,19 @@ and how it's built.
 
 
 
-Singularity Container
+Apptainer Container
 =====================
 
-The easiest way to get a Sigularity image is to run::
+The easiest way to get an Apptainer (formerly Singularity) image is to run::
 
-    $ singularity build qsiprep-<version>.sif docker://pennbbl/qsiprep:<version>
+    $ apptainer build qsiprep-<version>.sif docker://pennbbl/qsiprep:<version>
 
 Where ``<version>`` should be replaced with the desired version of qsiprep that you want to download.
 Do not use ``latest`` or ``unstable`` unless you are performing limited testing.
 
-As with Docker, you will need to bind the Freesurfer license.txt when running Singularity ::
+As with Docker, you will need to bind the Freesurfer license.txt when running Apptainer ::
 
-    $ singularity run --containall --writable-tmpfs \
+    $ apptainer run --containall --writable-tmpfs \
         -B $HOME/fullds005,$HOME/dockerout,${FREESURFER_HOME}/license.txt:/opt/freesurfer/license.txt \
         qsiprep-<version>.sif \
         $HOME/fullds005 $HOME/dockerout participant \

docs/usage.rst

@@ -60,8 +60,8 @@ Note on using CUDA
 The CUDA runtime version 9.1 is included in the QSIPrep docker image.
 The CUDA version of eddy is dramatically faster than the openmp version.
 Information on running Docker with CUDA enabled can be found on
-`dockerhub <https://github.com/NVIDIA/nvidia-docker/wiki/CUDA>`_. If running with singularity,
-the call to singularity should include ``--nv``. To enable CUDA, see :ref:`configure_eddy`.
+`dockerhub <https://github.com/NVIDIA/nvidia-docker/wiki/CUDA>`_. If running with Apptainer,
+the call to Apptainer should include ``--nv``. To enable CUDA, see :ref:`configure_eddy`.
 
 Debugging
 =========
@@ -77,4 +77,4 @@ CUDA Support
 
 As of version 0.6.7 CUDA version 9.1 is supported in the QSIPrep container! To run locally
 using docker you will need the nvidia container runtime installed for Docker version 19.0.3
-or higher. Singularity images will run with CUDA 9.1 with the ``-nv`` flag.
+or higher. Apptainer images will run with CUDA 9.1 with the ``-nv`` flag.

qsiprep/cli/run.py

@@ -155,6 +155,7 @@ def main():
         boiler_file = output_dir / "logs" / "CITATION.md"
         if boiler_file.exists():
             if config.environment.exec_env in (
+                "apptainer",
                 "singularity",
                 "docker",
             ):

qsiprep/config.py

@@ -162,7 +162,7 @@
 _docker_ver = None
 # special variable set in the container
 if os.getenv("IS_DOCKER_8395080871"):
-    _exec_env = "singularity"
+    _exec_env = "apptainer"
     _cgroup = Path("/proc/1/cgroup")
     if _cgroup.exists() and "docker" in _cgroup.read_text():
         _exec_env = "docker"

qsiprep/utils/bids.py

@@ -260,6 +260,13 @@ def write_derivative_description(bids_dir, deriv_dir):
             desc["SingularityContainerMD5"] = _get_shub_version(singularity_url)
         except ValueError:
             pass
+    if "QSIPREP_APPTAINER_URL" in os.environ:
+        apptainer_url = os.environ["QSIPREP_APPTAINER_URL"]
+        desc["ApptainerContainerURL"] = apptainer_url
+        try:
+            desc["ApptainerContainerMD5"] = _get_ahub_version(apptainer_url)
+        except ValueError:
+            pass
 
     # Keys deriving from source dataset
     fname = os.path.join(bids_dir, "dataset_description.json")
@@ -366,6 +373,14 @@ def validate_input_dir(exec_env, bids_dir, participant_label):
                     "all paths are mapped properly (see https://www.sylabs.io/"
                     "guides/3.0/user-guide/bind_paths_and_mounts.html)"
                 )
+            if exec_env == "apptainer":
+                error_msg += (
+                    " This error can be caused by the input data not being "
+                    "accessible inside the Apptainer container. Please make sure "
+                    "all paths are mapped properly (see https://apptainer.org/",
+                    "docs/user/main/bind_paths_and_mounts.html)",
+                )
+
             raise RuntimeError(error_msg % ",".join(bad_labels))
 
         ignored_subs = all_subs.difference(selected_subs)
@@ -385,6 +400,10 @@ def _get_shub_version(singularity_url):
     raise ValueError("Not yet implemented")
 
 
+def _get_ahub_version(apptainer_url):
+    raise ValueError("Not yet implemented")
+
+
 def update_metadata_from_nifti_header(metadata, nifti_file):
     """Update a BIDS metadata dictionary with info from a NIfTI header.