From 1872867b3023d484bed4f75b87365c306af16d6a Mon Sep 17 00:00:00 2001
From: MontrealSergiy <sergeboroday@gmail.com>
Date: Mon, 24 Mar 2025 18:52:18 -0400
Subject: [PATCH 1/9] Refactor singularity into apptainer

---
 .../app/controllers/bourreaux_controller.rb   |   2 +-
 .../controllers/tool_configs_controller.rb    |   8 +-
 BrainPortal/app/models/bourreau.rb            |   6 +-
 BrainPortal/app/models/cluster_task.rb        | 142 +++++++++---------
 .../models/sing_bindmount_data_provider.rb    |  52 +++----
 .../app/models/sing_squashfs_data_provider.rb |  79 +++++-----
 BrainPortal/app/models/tool_config.rb         |  50 +++---
 BrainPortal/app/views/bourreaux/show.html.erb |   6 +-
 .../_dp_types_explained.html.erb              |   6 +-
 .../views/tool_configs/_form_fields.html.erb  |  20 +--
 .../app/views/tool_configs/show.html.erb      |   6 +-
 .../singularity_image/singularity_image.rb    |  27 ++--
 .../singularity_image/views/_info.html.erb    |   8 +-
 .../config/console_rc/lib/pretty_view.rb      |   4 +-
 ...8164549_rename_singularity_to_apprainer.rb |   7 +
 BrainPortal/db/schema.rb                      |   6 +-
 BrainPortal/lib/boutiques_ext3_capturer.rb    |   2 +-
 .../schema_task_generator.rb                  |   6 +-
 BrainPortal/spec/models/tool_config_spec.rb   |  11 +-
 19 files changed, 235 insertions(+), 213 deletions(-)
 create mode 100644 BrainPortal/db/migrate/20240408164549_rename_singularity_to_apprainer.rb

diff --git a/BrainPortal/app/controllers/bourreaux_controller.rb b/BrainPortal/app/controllers/bourreaux_controller.rb
index 7219f07f2..362cfbcdc 100644
--- a/BrainPortal/app/controllers/bourreaux_controller.rb
+++ b/BrainPortal/app/controllers/bourreaux_controller.rb
@@ -769,7 +769,7 @@ def bourreau_params #:nodoc:
       :cms_default_queue, :cms_extra_qsub_args, :cms_shared_dir, :workers_instances,
       :workers_chk_time, :workers_log_to, :workers_verbose, :help_url, :rr_timeout, :proxied_host,
       :spaced_dp_ignore_patterns, :support_email, :system_from_email, :external_status_page_url,
-      :docker_executable_name, :docker_present, :singularity_executable_name, :singularity_present,
+      :docker_executable_name, :docker_present, :apptainer_executable_name, :apptainer_present,
       :small_logo, :large_logo, :license_agreements,
       :activity_workers_instances
     )
diff --git a/BrainPortal/app/controllers/tool_configs_controller.rb b/BrainPortal/app/controllers/tool_configs_controller.rb
index b36540403..12ea9f0cd 100644
--- a/BrainPortal/app/controllers/tool_configs_controller.rb
+++ b/BrainPortal/app/controllers/tool_configs_controller.rb
@@ -206,7 +206,7 @@ def update #:nodoc:
            @tool_config.container_image_userfile_id = other_tc.container_image_userfile_id
            @tool_config.container_exec_args         = other_tc.container_exec_args.presence
            @tool_config.container_index_location    = other_tc.container_index_location
-           @tool_config.singularity_overlays_specs  = other_tc.singularity_overlays_specs
+           @tool_config.apptainer_overlays_specs    = other_tc.apptainer_overlays_specs
            @tool_config.extra_qsub_args             = other_tc.extra_qsub_args
            @tool_config.cloud_disk_image            = other_tc.cloud_disk_image
            @tool_config.cloud_vm_user               = other_tc.cloud_vm_user
@@ -243,7 +243,7 @@ def update #:nodoc:
              container_image_userfile_id containerhub_image_name
              container_engine container_index_location container_exec_args
              inputs_readonly
-             singularity_overlays_specs singularity_use_short_workdir
+             apptainer_overlays_specs apptainer_use_short_workdir
              boutiques_descriptor_path
            )
         )
@@ -318,8 +318,8 @@ def tool_config_params #:nodoc:
       :version_name, :description, :tool_id, :bourreau_id, :env_array, :script_prologue, :script_epilogue,
       :group_id, :ncpus, :container_image_userfile_id, :containerhub_image_name, :container_index_location,
       :inputs_readonly,
-      :container_engine, :extra_qsub_args, :singularity_overlays_specs, :container_exec_args,
-      :singularity_use_short_workdir,
+      :container_engine, :extra_qsub_args, :apptainer_overlays_specs, :container_exec_args,
+      :apptainer_use_short_workdir,
       :boutiques_descriptor_path,
       # The configuration of a tool in a VM managed by a
       # ScirCloud Bourreau is defined by the following
diff --git a/BrainPortal/app/models/bourreau.rb b/BrainPortal/app/models/bourreau.rb
index 6e8664fb8..7f0aba9e0 100644
--- a/BrainPortal/app/models/bourreau.rb
+++ b/BrainPortal/app/models/bourreau.rb
@@ -80,11 +80,11 @@ def docker_present? #:nodoc:
   alias docker_present docker_present? #:nodoc:
 
 
-  def singularity_present? #:nodoc:
-    singularity_executable_name.present?
+  def apptainer_present? #:nodoc:
+    apptainer_executable_name.present?
   end
 
-  alias singularity_present singularity_present? #:nodoc:
+  alias apptainer_present apptainer_present? #:nodoc:
 
 
 
diff --git a/BrainPortal/app/models/cluster_task.rb b/BrainPortal/app/models/cluster_task.rb
index 78e02a74c..cf18041c3 100644
--- a/BrainPortal/app/models/cluster_task.rb
+++ b/BrainPortal/app/models/cluster_task.rb
@@ -439,7 +439,7 @@ def make_available(userfile, file_path, userfile_sub_path = nil, start_dir = nil
     userfile = Userfile.find(userfile) unless userfile.is_a?(Userfile)
 
     # Detect if we're trying to access a userfile content that is
-    # containerized in a singularity overlay.
+    # containerized in an Apptainer overlay.
     is_local = nil
     if self.tool_config
            .data_providers_with_overlays
@@ -447,7 +447,7 @@ def make_available(userfile, file_path, userfile_sub_path = nil, start_dir = nil
            .include? userfile.data_provider_id
       userfile_path = Pathname.new(userfile.provider_full_path) # path inside container
       is_local      = true
-      self.addlog("Input file '#{userfile.name}' is on a local Singularity overlay")
+      self.addlog("Input file '#{userfile.name}' is on a local Apptainer overlay")
     else
       userfile.sync_to_cache
       userfile_path  = Pathname.new(userfile.cache_full_path)
@@ -633,10 +633,10 @@ def tool_config_system(command)
 
     # Build script
     script  = ""
-    # flag to guaranty propagation of env variables to the singularity/apptainer
+    # flag to guaranty propagation of env variables to the Apptainer
     # as far I know only needed to reverse effect of --cleanenv option, and otherwise all vars are copied to the container
     # yet potentially more cases may be identified
-    propagate = self.use_singularity?
+    propagate = self.use_apptainer?
     # Add prologues in specialization order
     script += bourreau_glob_config.to_bash_prologue propagate if bourreau_glob_config
     script += tool_glob_config.to_bash_prologue     propagate if tool_glob_config
@@ -1796,14 +1796,14 @@ def submit_cluster_job
     # Joined version of all the lines in the scientific script
     command_script = commands.join("\n")
 
-    # In case of Docker or Singularity, we rewrite the scientific script inside
+    # In case of Docker or Apptainer, we rewrite the scientific script inside
     # yet another wrapper script.
     if self.use_docker?
       command_script = wrap_new_HOME(command_script, self.full_cluster_workdir)
       command_script = self.docker_commands(command_script)
-    elsif self.use_singularity?
-      load_singularity_image
-      command_script = self.singularity_commands(command_script) # note: invokes wrap_new_HOME itself
+    elsif self.use_apptainer?
+      load_apptainer_image
+      command_script = self.apptainer_commands(command_script) # note: invokes wrap_new_HOME itself
     else
       command_script = wrap_new_HOME(command_script, self.full_cluster_workdir)
     end
@@ -1818,9 +1818,9 @@ def submit_cluster_job
 # by ClusterTask
 #   #{ClusterTask.revision_info.to_s}
 
-#{bourreau_glob_config ? bourreau_glob_config.to_bash_prologue(self.use_singularity?) : ""}
-#{tool_glob_config     ? tool_glob_config.to_bash_prologue(self.use_singularity?)     : ""}
-#{tool_config          ? tool_config.to_bash_prologue(self.use_singularity?)          : ""}
+#{bourreau_glob_config ? bourreau_glob_config.to_bash_prologue(self.use_apptainer?) : ""}
+#{tool_glob_config     ? tool_glob_config.to_bash_prologue(self.use_apptainer?)     : ""}
+#{tool_config          ? tool_config.to_bash_prologue(self.use_apptainer?)          : ""}
 #{self.supplemental_cbrain_tool_config_init}
 
 # CbrainTask '#{self.name}' commands section
@@ -1867,9 +1867,9 @@ def submit_cluster_job
 # Record runtime environment
 bash #{Rails.root.to_s.bash_escape}/vendor/cbrain/bin/runtime_info.sh > #{runtime_info_basename}
 
-# With apptainer/singularity jobs, we sometimes get an error booting the container,
+# With Apptainer jobs, we sometimes get an error booting the container,
 # so we try up to five times.
-for singularity_attempts in 1 2 3 4 5 ; do  # note: the number 5 is used a bit below in an 'if'
+for apptainer_attempts in 1 2 3 4 5 ; do  # note: the number 5 is used a bit below in an 'if'
   SECONDS=0 # this is a special bash variable, see the doc
 
   # stdout and stderr captured below will be re-substituted in
@@ -1879,20 +1879,20 @@ def submit_cluster_job
 
   test $status -eq 0 && break # all is good
 
-  # Detect failed boot of singularity container
+  # Detect failed boot of apptainer container
   if ! grep -i 'FATAL.*container.*creation.*failed' #{science_stderr_basename} >/dev/null ; then
     break # move on, for any other error or even non zero successes
   fi
 
   # Detect that final attempt to boot failed
-  if test $singularity_attempts -eq 5 ; then
+  if test $apptainer_attempts -eq 5 ; then
     echo "Apptainer container boot attempts all failed, giving up."
     status=99 # why not
     break
   fi
 
   # Cleanup and try again
-  echo "Apptainer boot attempt number $singularity_attempts failed, trying again."
+  echo "Apptainer boot attempt number $apptainer_attempts failed, trying again."
   grep -v -i 'FATAL.*container.*creation.*failed' < #{science_stderr_basename} > #{science_stderr_basename}.clean
   mv -f #{science_stderr_basename}.clean #{science_stderr_basename}
 done
@@ -2334,34 +2334,34 @@ def load_docker_image_cmd #:nodoc:
 
 
   ##################################################################
-  # Singularity support methods
+  # Apptainer support methods
   ##################################################################
 
-  # Returns true if the task's ToolConfig is configured to point to a singularity image
+  # Returns true if the task's ToolConfig is configured to point to a Apptainer image
   # for the task's processing.
-  def use_singularity?
-    return self.tool_config.use_singularity?
+  def use_apptainer?
+    return self.tool_config.use_apptainer?
   end
 
-  # Return the 'singularity' command to be used for the task; this is fetched
-  # from the Bourreau's own attribute. Default: "singularity".
-  def singularity_executable_name
-    return self.bourreau.singularity_executable_name.presence || "singularity"
+  # Return the 'apptainer' command to be used for the task; this is fetched
+  # from the Bourreau's own attribute. Default: "apptainer".
+  def apptainer_executable_name
+    return self.bourreau.apptainer_executable_name.presence || "apptainer"
   end
 
   # Returns true if the admin has configured this option in the
   # task's ToolConfig attributes.
-  def use_singularity_short_workdir?
-    self.tool_config.singularity_use_short_workdir
+  def use_apptainer_short_workdir?
+    self.tool_config.apptainer_use_short_workdir
   end
 
   # Returns the command line(s) associated with the task, wrapped in
-  # a Singularity call if a Singularity image has to be used. +command_script+
+  # a Apptainer call if a Apptainer image has to be used. +command_script+
   # is the raw scientific bash script.
-  def singularity_commands(command_script)
+  def apptainer_commands(command_script)
 
-    # Basename of the singularity wrapper script
-    singularity_wrapper_basename = ".singularity.#{self.run_id}.sh"
+    # Basename of the apptainer wrapper script
+    apptainer_wrapper_basename = ".apptainer.#{self.run_id}.sh"
 
     # Values we substitute in our script:
     # Numbers in (paren) correspond to the comment
@@ -2370,9 +2370,9 @@ def singularity_commands(command_script)
     # (7) The path to the task's work directory
     task_workdir   = self.full_cluster_workdir # a string
     short_workdir  = "/T#{self.id}" # only used in short workdir mode
-    effect_workdir = use_singularity_short_workdir? ? short_workdir : task_workdir
+    effect_workdir = use_apptainer_short_workdir? ? short_workdir : task_workdir
 
-    # (1) additional singularity execution command options defined in ToolConfig
+    # (1) additional Apptainer execution command options defined in ToolConfig
     container_exec_args = self.tool_config.container_exec_args.presence
 
     # (2) The root of the DataProvider cache
@@ -2408,7 +2408,7 @@ def singularity_commands(command_script)
     # Some of them might be patterns (e.g. /a/b/data*.squashfs) that need to
     # be resolved locally.
     # This will be a string "--overlay=path:ro --overlay=path:ro" etc.
-    overlay_paths = self.tool_config.singularity_overlays_full_paths.map do |path, knd|
+    overlay_paths = self.tool_config.apptainer_overlays_full_paths.map do |path, knd|
       paths = Dir.glob(path) # assume no glob expression in overlay files
       cb_error "Can't find any local file matching overlay '#{path}'" if paths.blank?
       paths.each do |f|
@@ -2423,8 +2423,8 @@ def singularity_commands(command_script)
     # Wrap new HOME environment
     command_script = wrap_new_HOME(command_script, effect_workdir)
 
-    # Set singularity command
-    singularity_commands = <<-SINGULARITY_COMMANDS
+    # Set apptainer command
+    apptainer_commands = <<-APPTAINER_COMMANDS
 
 # Note to developers:
 # During a standard CBRAIN task, this script is invoked with no arguments
@@ -2434,26 +2434,26 @@ def singularity_commands(command_script)
 
 # These two variables control the mode switching at the end of the script.
 mode="exec"
-sing_basename=./#{singularity_wrapper_basename.bash_escape} # note: the ./ is necessary
+apptainer_basename=./#{apptainer_wrapper_basename.bash_escape} # note: the ./ is necessary
 
 # In 'shell' mode we replace them with other things.
 if test $# -eq 1 -a "X$1" = "Xshell" ; then
   mode="shell"
-  sing_basename=""
+  apptainer_basename=""
 fi
 
-# Build a local wrapper script to run in a singularity container
-cat << \"SINGULARITYJOB\" > #{singularity_wrapper_basename.bash_escape}
+# Build a local wrapper script to run in a apptainer container
+cat << \"APPTAINERJOB\" > #{apptainer_wrapper_basename.bash_escape}
 #!/bin/bash
 
-# Singularity wrapper script created automatically for #{self.class.to_s}
+# Apptainer wrapper script created automatically for #{self.class.to_s}
 #   #{self.class.revision_info.to_s}
 # by ClusterTask
 #   #{ClusterTask.revision_info.to_s}
 
 # CBRAIN internal consistency test 1: must run under proper UID
 if test "$UID" -ne "#{Process.uid}" ; then
-  echo "Singularity internal script running with wrong UID (expected UID=#{Process.uid})"
+  echo "Apptainer internal script running with wrong UID (expected UID=#{Process.uid})"
   echo "Runtime IDs: `id`"
   exit 2
 fi
@@ -2489,7 +2489,7 @@ def singularity_commands(command_script)
 
 # CBRAIN internal consistency test 6: all mounted ext3 filesystems should be
 # on a device different from the task's workdir. Otherwise something went
-# wrong with the mounts. Singularity or Apptainer can sometimes do that
+# wrong with the mounts. Apptainer can sometimes do that
 # if the command is improperly built (order of mounts args etc).
 workdir_devid=$(stat -c %d .)  # dev number of task workdir
 for mount in #{capture_basenames.map(&:bash_escape).join(" ")} ; do
@@ -2507,12 +2507,12 @@ def singularity_commands(command_script)
 # Scientific commands start here
 
 #{command_script}
-SINGULARITYJOB
+APPTAINERJOB
 
 # Make sure it is executable
-chmod 755 #{singularity_wrapper_basename.bash_escape}
+chmod 755 #{apptainer_wrapper_basename.bash_escape}
 
-# Invoke Singularity with our wrapper script above.
+# Invoke Apptainer with our wrapper script above.
 # Tricks used here:
 # 1) we supply (if any) additional options for the exec command
 # 2) we mount the local data provider cache root directory
@@ -2522,8 +2522,8 @@ def singularity_commands(command_script)
 # 4) we mount each (if any) of the root directories for local data providers
 # 5) we mount (if any) other fixed file system overlays
 # 6) we mount (if any) capture ext3 filesystems
-# 7) with -H we set the task's work directory as the singularity $HOME directory
-#{singularity_executable_name}                  \\
+# 7) with -H we set the task's work directory as the apptainer $HOME directory
+#{apptainer_executable_name}                  \\
     $mode                                       \\
     #{container_exec_args}                      \\
     -B #{cache_dir.bash_escape}                 \\
@@ -2535,11 +2535,11 @@ def singularity_commands(command_script)
     #{esc_capture_mounts}                       \\
     -H #{effect_workdir.bash_escape}            \\
     #{container_image_name.bash_escape}         \\
-    $sing_basename
+    $apptainer_basename
 
-    SINGULARITY_COMMANDS
+    APPTAINER_COMMANDS
 
-    return singularity_commands
+    return apptainer_commands
   end
 
 
@@ -2623,7 +2623,7 @@ def install_ext3fs_filesystem(filename,size) #:nodoc:
 
 
   ##################################################################
-  # Singularity load
+  # Apptainer load
   ##################################################################
 
   private
@@ -2635,56 +2635,56 @@ def container_image_name #:nodoc:
     ".container-#{self.id}.img"
   end
 
- # Load the singularity image either from a repository or from a CBRAIN file
-  def load_singularity_image #:nodoc:
+ # Load the Apptainer image either from a repository or from a CBRAIN file
+  def load_apptainer_image #:nodoc:
     if self.tool_config.container_image
-      load_singularity_image_from_userfile
+      load_apptainer_image_from_userfile
     elsif self.tool_config.containerhub_image_name
-      load_singularity_image_from_repo
+      load_apptainer_image_from_repo
     else
-      cb_error "Cannot find source for singularity image..."
+      cb_error "Cannot find source for Apptainer image..."
     end
   end
 
   # Create a link to our image; the image is a registered CBRAIN file
-  def load_singularity_image_from_userfile #:nodoc:
-    singularity_image = self.tool_config.container_image
-    self.addlog("Syncing the singularity image '#{singularity_image.name}'")
+  def load_apptainer_image_from_userfile #:nodoc:
+    apptainer_image = self.tool_config.container_image
+    self.addlog("Syncing the Apptainer image '#{apptainer_image.name}'")
 
     # Sync the userfile content
-    singularity_image.sync_to_cache
+    apptainer_image.sync_to_cache
 
     # Create the symlink to the cached image.
-    cachename = singularity_image.cache_full_path
+    cachename = apptainer_image.cache_full_path
     image_name = container_image_name
     safe_symlink(cachename,image_name)
   end
 
-  # Perform the singularity build; the image will be cached
+  # Perform the Apptainer build; the image will be cached
   # as a special, hidden userfile on the ScratchDataProvider.
-  def load_singularity_image_from_repo #:nodoc:
-    singularity_image_name     = self.tool_config.containerhub_image_name
-    singularity_index_location = self.tool_config.container_index_location.presence || "shub://"
+  def load_apptainer_image_from_repo #:nodoc:
+    apptainer_image_name     = self.tool_config.containerhub_image_name
+    apptainer_index_location = self.tool_config.container_index_location.presence || "shub://"
 
-    self.addlog("Building singularity image '#{singularity_image_name}'")
+    self.addlog("Building Apptainer image '#{apptainer_image_name}'")
 
     # Find or create the userfile holding the image content.
-    scratch_name     = "Singularity-build-" + singularity_image_name.gsub(/[^a-z0-9_\.\-]+/i,"_") # must respect userfile convention.
+    scratch_name     = "Apptainer-build-" + apptainer_image_name.gsub(/[^a-z0-9_\.\-]+/i,"_") # must respect userfile convention.
     scratch_name.sub!(/(\.img)?$/i, ".img")
     scratch_userfile = SingularityImage.find_or_create_as_scratch(:name => scratch_name) do |cache_path|
       # Optimization: if another find_or_create_as_scratch has already beaten us to the punch
       # and dowloaded the file, just skip this block altogether. The way SyncStatus works, several
       # of these blocks can be scheduled to run, but only one will execute at at any given time.
       next if File.exists?(cache_path.to_s) && File.size(cache_path.to_s) > 0
-      # Run singularity build command
-      out, err = tool_config_system("umask 000; #{singularity_executable_name} build #{cache_path.to_s.bash_escape} #{singularity_index_location.bash_escape}#{singularity_image_name.bash_escape}")
+      # Run Apptainer build command
+      out, err = tool_config_system("umask 000; #{apptainer_executable_name} build #{cache_path.to_s.bash_escape} #{apptainer_index_location.bash_escape}#{apptainer_image_name.bash_escape}")
       # Check that all is OK; if not we store the captured outputs for investigation
       if ! File.exists?(cache_path.to_s) || File.size(cache_path.to_s) < 500.kilobytes
-        capfile = "singularity_build_traces-#{self.run_id}.txt"
+        capfile = "apptainer_build_traces-#{self.run_id}.txt"
         File.open(capfile,"w") do |fh|
           fh.write("=== Stdout ===\n#{out}\n=== Stderr ===\n#{err}\n=== ====== ===\n")
         end
-        cb_error "Cannot build singularity image. Captured outputs are in #{capfile}"
+        cb_error "Cannot build apptainer image. Captured outputs are in #{capfile}"
       end
     end
 
diff --git a/BrainPortal/app/models/sing_bindmount_data_provider.rb b/BrainPortal/app/models/sing_bindmount_data_provider.rb
index 5757638e3..5e6822b3d 100644
--- a/BrainPortal/app/models/sing_bindmount_data_provider.rb
+++ b/BrainPortal/app/models/sing_bindmount_data_provider.rb
@@ -22,22 +22,22 @@
 
 # This class implements a Data Provider which fetches
 # files out of a single filesystem file. The
-# implementation requires Singularity 3.2 or better to
-# be installed on the host, as well as a singularity
+# implementation requires Apptainer 1.1 or  better
+# be installed on the host, as well as an Apptainer
 # container image that contains the basic Linux
 # commands and the 'rsync' command too.
 #
 # For the moment the DP is read-only. Allowing
 # write access would require a mechanism in CBRAIN
-# to prevent more than one singularity process to
+# to prevent more than one Apptainer process to
 # be accessing the mounted file at any one time.
 #
 # Bind mounts are performed using a command such as:
 #
-#   singularity shell -B filesystem.img:/my/mount/point:image-src=/inside/dir,ro sing_squashfs.simg
+#   apptainer shell -B filesystem.img:/my/mount/point:image-src=/inside/dir,ro sing_squashfs.simg
 #
 # where:
-# 1- sing_squashfs.simg is a singularity image file,
+# 1- sing_squashfs.simg is an Apptainer image file,
 # 2- filesystem.img is either a ext3 or squashfs filesystem,
 # 3- /inside/dir is a path inside that filesystem,
 # 4- /my/mount/point is a path where the data will be mounted under
@@ -51,7 +51,7 @@
 #
 # The attribute 'remote_dir' must be a full path to the location of
 # the filesystem image 'filesystem.img' (even though it is not a 'dir').
-# The singularity image file will be expected to be called 'sing_squashfs.simg'
+# The Apptainer image file will be expected to be called 'sing_squashfs.simg'
 # and be located in the same subdirectory as 'filesystem.img'.
 class SingBindmountDataProvider < SshDataProvider
 
@@ -64,14 +64,14 @@ class SingBindmountDataProvider < SshDataProvider
   # TODO: Change this is the DP is ever made writable!
   BROWSE_CACHE_EXPIRATION = 2.months #:nodoc:
 
-  # This is the basename of the singularity image
+  # This is the basename of the Apptainer image
   # we use to access the remote filesystem; we
   # expect this image to be installed in the same
   # directory that contains it. Its minimum
   # requirements are that 1) basic UNIX commands
   # exist on it 2) the rsync command is installed
   # in it too.
-  SINGULARITY_IMAGE_BASENAME = 'sing_squashfs.simg'
+  APPTAINER_IMAGE_BASENAME = 'sing_squashfs.simg'
 
   # We use this to point to the directory INSIDE the container
   # were the root of the data is stored.
@@ -96,7 +96,7 @@ def read_only=(val) #:nodoc:
 
   # This returns the category of the data provider
   def self.pretty_category_name #:nodoc:
-    "Singularity Bind Mount"
+    "Apptainer Bind Mount"
   end
 
   # This uses the new CBRAIN capability of registering
@@ -114,20 +114,20 @@ def impl_is_alive? #:nodoc:
   # Raise an exception with a message indicating what is wrong with the config.
   # This method is not part of the official method API
   def check_remote_config! #:nodoc:
-    # Check we have one singularity image file
-    remote_cmd  = "cd #{self.real_remote_dir.to_s.bash_escape} && test -f #{SINGULARITY_IMAGE_BASENAME} && echo OK-Exists"
+    # Check we have one Apptainer image file
+    remote_cmd  = "cd #{self.real_remote_dir.to_s.bash_escape} && test -f #{APPTAINER_IMAGE_BASENAME} && echo OK-Exists"
     text        = self.remote_bash_this(remote_cmd)
     # The following check will also make sure the remote shell is clean!
-    cb_error "No installed singularity image #{SINGULARITY_IMAGE_BASENAME}, or remote shell is unclean" unless text =~ /\AOK-Exists\s*\z/
+    cb_error "No installed apptainer image #{APPTAINER_IMAGE_BASENAME}, or remote shell is unclean" unless text =~ /\AOK-Exists\s*\z/
 
     # Check we have the remote filesystem file
     remote_cmd  = "test -f #{self.remote_dir.to_s.bash_escape} && echo OK-Exists"
     cb_error "Filesystem file '#{self.remote_dir}' not found" unless text =~ /\AOK-Exists\s*\z/
 
-    # Check we have singularity version 3.7 or better
+    # Check we have Apptainer 1.1 or better
     remote_cmd = "(singularity --version 2>/dev/null || apptainer --version 2>/dev/null)"
     text       = self.remote_bash_this(remote_cmd)
-    cb_error "Can't find singularity version number on remote host" unless text =~ /^((singularity|apptainer) version )?(\d+)\.(\d+)/
+    cb_error "Can't find apptainer version number on remote host" unless text =~ /^((singularity|apptainer) version )?(\d+)\.(\d+)/
     _, _, tool, major, minor = Regexp.last_match.to_a
     major = major.to_i
     minor = minor.to_i
@@ -139,7 +139,7 @@ def check_remote_config! #:nodoc:
 
     # Check that inside the container, the containerized path exists
     checkdir     = "test -d #{self.containerized_path.bash_escape} && echo OK-Exists"
-    text         = remote_in_sing_bash_this(checkdir)
+    text         = remote_in_apptainer_bash_this(checkdir)
     cb_error "No path '#{self.containerized_path}' inside container" unless text =~ /\AOK-Exists\s*\z/
 
     # Well, we passed all the tests
@@ -184,7 +184,7 @@ def impl_provider_list_all(user=nil, browse_path=nil) #:nodoc:
 
     file_infos = Rails.cache.fetch(cache_key, :expires_in => BROWSE_CACHE_EXPIRATION) do
       dir  = Pathname.new(self.containerized_path) + browse_path.to_s
-      text = remote_in_sing_stat_all(dir,".",true)
+      text = remote_in_apptainer_stat_all(dir,".",true)
       stat_reports_to_fileinfos(text)
     end
 
@@ -216,7 +216,7 @@ def impl_provider_collection_index(userfile, directory = :all, allowed_types = :
     type_opt   = allowed_types == [ :regular   ] ? "f" :
                  allowed_types == [ :directory ] ? "d" :
                  nil # we can still filter for other combinations on Ruby side
-    text       = remote_in_sing_stat_all(basedir, subdir, one_level, type_opt)
+    text       = remote_in_apptainer_stat_all(basedir, subdir, one_level, type_opt)
     file_infos = stat_reports_to_fileinfos(text)
 
     # Apply more complex filters if necessary
@@ -272,8 +272,8 @@ def impl_provider_rename(userfile,newname) #:nodoc:
 
   # Returns true if we have to use 'ssh' to
   # connect to the remote server. Returns false
-  # when we can optimize requests by running
-  # singularity locally. The local situation is
+  # when we can optimize requests by running the
+  # Apptainer locally. The local situation is
   # detected pretty much like in the Smart DP
   # module: if the hostname is the same as *remote_host*
   # or *alternate_host*, and if the *remote_dir* exists
@@ -299,8 +299,8 @@ def provider_is_remote #:nodoc:
     @provider_is_remote
   end
 
-  def singularity_exec_prefix #:nodoc:
-    "cd #{self.real_remote_dir.to_s.bash_escape} && singularity -s exec #{self.local_bind_opt} #{SINGULARITY_IMAGE_BASENAME}"
+  def apptainer_exec_prefix #:nodoc:
+    "cd #{self.real_remote_dir.to_s.bash_escape} && singularity -s exec #{self.local_bind_opt} #{APPTAINER_IMAGE_BASENAME}"
   end
 
   def local_bind_opt #:nodoc:
@@ -308,7 +308,7 @@ def local_bind_opt #:nodoc:
   end
 
   def remote_rsync_command #:nodoc:
-    "#{singularity_exec_prefix} rsync"
+    "#{apptainer_exec_prefix} rsync"
   end
 
   def real_remote_dir #:nodoc:
@@ -338,12 +338,12 @@ def rsync_over_ssh_prefix
     rsync
   end
 
-  def remote_in_sing_bash_this(com) #:nodoc:
-    newcom = "#{singularity_exec_prefix} bash -c #{com.bash_escape}"
+  def remote_in_apptainer_bash_this(com) #:nodoc:
+    newcom = "#{apptainer_exec_prefix} bash -c #{com.bash_escape}"
     remote_bash_this(newcom)
   end
 
-  def remote_in_sing_stat_all(basedir, subdir, one_level = true, find_type = nil) #:nodoc:
+  def remote_in_apptainer_stat_all(basedir, subdir, one_level = true, find_type = nil) #:nodoc:
     max_depth   = one_level ? "-maxdepth 1"        : ""
     type_opt    = find_type ? "-type #{find_type}" : ""
     # Linux 'stat' command formats:
@@ -359,7 +359,7 @@ def remote_in_sing_stat_all(basedir, subdir, one_level = true, find_type = nil)
     # Linux 'find' command format:
     find_format = "E=%y,%m,%s,%U,%u,%G,%g,%A@,%T@,%C@,%p\\n"
     com = "cd #{basedir.to_s.bash_escape} && find #{subdir.to_s.bash_escape} #{max_depth} #{type_opt} -printf \"#{find_format}\""
-    remote_in_sing_bash_this(com)
+    remote_in_apptainer_bash_this(com)
   end
 
   # Given a text file report such as this:
diff --git a/BrainPortal/app/models/sing_squashfs_data_provider.rb b/BrainPortal/app/models/sing_squashfs_data_provider.rb
index 2ebeb411a..adf1ec2d2 100644
--- a/BrainPortal/app/models/sing_squashfs_data_provider.rb
+++ b/BrainPortal/app/models/sing_squashfs_data_provider.rb
@@ -22,8 +22,8 @@
 
 # This class implements a Data Provider which fetches
 # files out of one or several SquashFS files. The
-# implementation requires Singularity 3.2 or better to
-# be installed on the host, as well as a singularity
+# implementation requires Apptainer 1.1 or better to
+# be installed on the host, as well as an Apptainer
 # container image that contains the basic Linux
 # commands and the 'rsync' command too.
 class SingSquashfsDataProvider < SshDataProvider
@@ -35,14 +35,14 @@ class SingSquashfsDataProvider < SshDataProvider
   # be forever, really.
   BROWSE_CACHE_EXPIRATION = 6.months #:nodoc:
 
-  # This is the basename of the singularity image
+  # This is the basename of the Apptainer image
   # we use to access the squashfs filesystems; we
   # expect this image to be installed in the same
   # directory that contain them. Its minimum
   # requirements are that 1) basic UNIX commands
   # exist on it 2) the rsync command is installed
   # in it too.
-  SINGULARITY_IMAGE_BASENAME = 'sing_squashfs.simg'
+  APPTAINER_IMAGE_BASENAME = 'sing_squashfs.simg'
 
   # We use this to point to the directory INSIDE the container
   # were the root of the data is stored
@@ -77,37 +77,48 @@ def impl_is_alive? #:nodoc:
     false
   end
 
+  # Check we have Apptainer 1.1 or better
+  def apptainer_executable_name
+    return @_tool if @_tool # cached name of executable
+
+    remote_cmd = "( apptainer --version 2>/dev/null || singularity --version 2>/dev/null )"
+    # Apptainer is preferable so it comes first in the command
+    # also works if an old Singularity and uptodate Apptainer
+    # todo loop over list of several candidate executables
+    text       = self.remote_bash_this(remote_cmd)
+    cb_error "Can't find apptainer version number on remote host" unless text =~ /^((singularity|apptainer) version )?(\d+)\.(\d+)/
+    _, _, @_tool, major, minor = Regexp.last_match.to_a
+    major = major.to_i
+    minor = minor.to_i
+    if @_tool == 'singularity'
+      cb_error "Singularity version number on remote host is less than 3.7" if major  < 3 || (major == 3 && minor < 7)
+    else # tool == 'apptainer'
+      cb_error "Apptainer version number on remote host is less than 1.1"   if major  < 1 || (major == 1 && minor < 1)
+    end
+
+    return @_tool
+
+  end
+
+
+
   # Raise an exception with a message indicating what is wrong with the config.
   # This method is not part of the official method API
   def check_remote_config! #:nodoc:
-    # Check we have one singularity image file
-    remote_cmd  = "cd #{self.remote_dir.bash_escape};test -f #{SINGULARITY_IMAGE_BASENAME} && echo OK-Exists"
+    # Check we have one Apptainer image file
+    remote_cmd  = "cd #{self.remote_dir.bash_escape};test -f #{APPTAINER_IMAGE_BASENAME} && echo OK-Exists"
     text        = self.remote_bash_this(remote_cmd)
     # The following check will also make sure the remote shell is clean!
-    cb_error "No installed singularity image #{SINGULARITY_IMAGE_BASENAME}, or remote shell is unclean" unless text =~ /\AOK-Exists\s*\z/
+    cb_error "No installed Apptainer image #{APPTAINER_IMAGE_BASENAME}, or remote shell is unclean" unless text =~ /\AOK-Exists\s*\z/
 
     # Check we have at least one .squashfs file in the remote_dir
     sq_files = get_squashfs_basenames
     cb_error "No .squashfs files found" unless sq_files.present?
-
-    # Check we have singularity version 3.2 or better
-    remote_cmd = "(singularity --version 2>/dev/null || apptainer --version 2>/dev/null)"
-    text       = self.remote_bash_this(remote_cmd)
-    cb_error "Can't find singularity version number on remote host" unless text =~ /^((singularity|apptainer) version )?(\d+)\.(\d+)/
-    _, _, tool, major, minor = Regexp.last_match.to_a
-    major = major.to_i
-    minor = minor.to_i
-    if tool == 'singularity'
-      cb_error "singularity version number on remote host is less than 3.7" if major  < 3 || (major == 3 && minor < 7)
-    else # tool == 'apptainer'
-      cb_error "apptainer version number on remote host is less than 1.1"   if major  < 1 || (major == 1 && minor < 1)
-    end
-
     # Check that inside the container
     all_sq_files = @sq_files
     @sq_files    = [ @sq_files.first ] # To speed up check, use only the first squashfs file
     checkdir     = "test -d #{self.containerized_path.bash_escape} && echo OK-Exists"
-    text         = remote_in_sing_bash_this(checkdir)
+    text         = remote_in_apptainer_bash_this(checkdir)
     @sq_files    = all_sq_files # return it to proper full list
     cb_error "No path '#{self.containerized_path}' inside container" unless text =~ /\AOK-Exists\s*\z/
 
@@ -158,7 +169,7 @@ def impl_provider_list_all(user=nil,browse_path=nil) #:nodoc:
     file_infos = Rails.cache.fetch(cache_key, :expires_in => BROWSE_CACHE_EXPIRATION) do
       sourcedir  = Pathname.new(self.containerized_path)
       sourcedir += browse_path if browse_path.present?
-      text = remote_in_sing_stat_all(sourcedir.to_s, "." ,true)
+      text = remote_in_apptainer_stat_all(sourcedir.to_s, "." ,true)
       stat_reports_to_fileinfos(text)
     end
 
@@ -190,7 +201,7 @@ def impl_provider_collection_index(userfile, directory = :all, allowed_types = :
     type_opt   = allowed_types == [ :regular   ] ? "f" :
                  allowed_types == [ :directory ] ? "d" :
                  nil # we can still filter for other combinations on Ruby side
-    text       = remote_in_sing_stat_all(basedir, subdir, one_level, type_opt)
+    text       = remote_in_apptainer_stat_all(basedir, subdir, one_level, type_opt)
     file_infos = stat_reports_to_fileinfos(text)
 
     # Apply more complex filters if necessary
@@ -245,7 +256,7 @@ def impl_provider_rename(userfile,newname) #:nodoc:
   public
 
   # Returns the full paths to the overlays
-  def singularity_overlays_full_paths #:nodoc:
+  def apptainer_overlays_full_paths #:nodoc:
     self.get_squashfs_basenames.map do |basename|
       Pathname.new(self.remote_dir) + basename
     end.map(&:to_s)
@@ -256,7 +267,7 @@ def singularity_overlays_full_paths #:nodoc:
   # Returns true if we have to use 'ssh' to
   # connect to the remote server. Returns false
   # when we can optimize requests by running
-  # singularity locally. The local situation is
+  # Apptainer locally. The local situation is
   # detected pretty much like in the Smart DP
   # module: if the hostname is the same as *remote_host*
   # or *alternate_host*, and if the *remote_dir* exists
@@ -271,7 +282,7 @@ def provider_is_remote #:nodoc:
                     .map(&:presence)
                     .compact
 
-    # Or test is biased so that we try local only if we have a local dir
+    # Our test is biased so that we try local only if we have a local dir
     # and the hostname match.
     if dp_hostnames.include?(Socket.gethostname) && File.directory?(self.remote_dir)
       @provider_is_remote = false
@@ -296,14 +307,14 @@ def get_squashfs_basenames(force = false) #:nodoc:
     @sq_files
   end
 
-  def singularity_exec_prefix #:nodoc:
+  def apptainer_exec_prefix #:nodoc:
     sq_files     = get_squashfs_basenames
     overlay_opts = sq_files.map { |f| "--overlay=#{f.bash_escape}:ro" }.join(" ")
-    "cd #{self.remote_dir.bash_escape} && singularity -s exec #{overlay_opts} #{SINGULARITY_IMAGE_BASENAME}"
+    "cd #{self.remote_dir.bash_escape} && #{apptainer_executable_name} -s exec #{overlay_opts} #{APPTAINER_IMAGE_BASENAME}"
   end
 
   def remote_rsync_command #:nodoc:
-    "#{singularity_exec_prefix} rsync"
+    "#{apptainer_exec_prefix} rsync"
   end
 
   # Builds a prefix for a +rsync+ command, such as
@@ -325,12 +336,12 @@ def rsync_over_ssh_prefix
     rsync
   end
 
-  def remote_in_sing_bash_this(com) #:nodoc:
-    newcom = "#{singularity_exec_prefix} bash -c #{com.bash_escape}"
+  def remote_in_apptainer_bash_this(com) #:nodoc:
+    newcom = "#{apptainer_exec_prefix} bash -c #{com.bash_escape}"
     remote_bash_this(newcom)
   end
 
-  def remote_in_sing_stat_all(basedir, subdir, one_level = true, find_type = nil) #:nodoc:
+  def remote_in_apptainer_stat_all(basedir, subdir, one_level = true, find_type = nil) #:nodoc:
     max_depth   = one_level ? "-maxdepth 1"        : ""
     type_opt    = find_type ? "-type #{find_type}" : ""
     # Linux 'stat' command formats:
@@ -346,7 +357,7 @@ def remote_in_sing_stat_all(basedir, subdir, one_level = true, find_type = nil)
     # Linux 'find' command format:
     find_format = "E=%y,%m,%s,%U,%u,%G,%g,%A@,%T@,%C@,%p\\n"
     com = "cd #{basedir.to_s.bash_escape} && find #{subdir.to_s.bash_escape} #{max_depth} #{type_opt} -printf \"#{find_format}\""
-    remote_in_sing_bash_this(com)
+    remote_in_apptainer_bash_this(com)
   end
 
   # Given a text file report such as this:
diff --git a/BrainPortal/app/models/tool_config.rb b/BrainPortal/app/models/tool_config.rb
index b6c5ba068..6de420c37 100644
--- a/BrainPortal/app/models/tool_config.rb
+++ b/BrainPortal/app/models/tool_config.rb
@@ -195,10 +195,10 @@ def extended_environment
 
   # Generates a partial BASH script that initializes environment
   # variables and is followed a the script prologue stored in the
-  # object. For singularity prologues, special prefixes are added to
+  # object. For Apptainer prologues, special prefixes are added to
   # variable names to ensure they will be propagated to the container
   # even in presence of --cleanenv parameteres and such
-  def to_bash_prologue(singularity=false)
+  def to_bash_prologue(apptainer=false)
     tool     = self.tool
     bourreau = self.bourreau
     group    = self.group
@@ -239,15 +239,14 @@ def to_bash_prologue(singularity=false)
     ENV_HEADER
     script += vars_to_export_script
 
-    if singularity
+    if apptainer
       script += <<-ENV_HEADER
 #---------------------------------------------------
 # Ensuring that environment variables are propagated:#{env.size == 0 ? " (NONE DEFINED)" : ""}
 #---------------------------------------------------
 
       ENV_HEADER
-      script += vars_to_export_script("SINGULARITYENV_")
-      script += vars_to_export_script("APPTAINERENV_")  #  SINGULARITYENV is to be depricated
+      script += vars_to_export_script("APPTAINERENV_")
 
     end
     script += "\n" if env.size > 0
@@ -341,9 +340,10 @@ def is_at_least_version(version)
      end
   end
 
-  # true if singularity image is defined
-  def use_singularity?
-    return self.container_engine == "Singularity" &&
+  # true if Apptainer image is defined
+  def use_apptainer?
+    return (self.container_engine == "Singularity" ||     # Currently Boutiques keeps singularity only
+            self.container_engine == "Apptainer") &&    # Singularity will be probably deprecated by Boutiques soon
         ( self.containerhub_image_name.present? ||
             self.container_image_userfile_id.present? )
   end
@@ -381,7 +381,7 @@ def cbrain_task_class
     self.tool.cbrain_task_class
   end
 
-  # Returns a hash of full paths to the Singularity overlay files that
+  # Returns a hash of full paths to the Apptainer overlay files that
   # need to be mounted along with explanation of their origin.
   # Some of paths might
   # be patterns and will need to be resolved at run time. The dsl is
@@ -393,7 +393,7 @@ def cbrain_task_class
   #         userfile:1234
   #      # A ext3 capture filesystem, will NOT be returned here as an overlay
   #         ext3capture:basename=12G
-  def singularity_overlays_full_paths
+  def apptainer_overlays_full_paths
     specs = parsed_overlay_specs
     specs.map do |knd, id_or_name|
 
@@ -401,7 +401,7 @@ def singularity_overlays_full_paths
       when 'dp'
         dp = DataProvider.where_id_or_name(id_or_name).first
         cb_error "Can't find DataProvider #{id_or_name} for fetching overlays" if ! dp
-        dp_ovs = dp.singularity_overlays_full_paths rescue nil
+        dp_ovs = dp.apptainer_overlays_full_paths rescue nil
         cb_error "DataProvider #{id_or_name} does not have any overlays configured." if dp_ovs.blank?
         dp_ovs.map do |dp_path|
           { dp_path => "Data Provider" }
@@ -424,7 +424,7 @@ def singularity_overlays_full_paths
   end
 
   # Returns an array of the data providers that are
-  # specified in the attribute singularity_overlays_specs,
+  # specified in the attribute apptainer_overlays_specs,
   # ignoring all other overlay specs for normal files.
   def data_providers_with_overlays
     return @_data_providers_with_overlays_ if @_data_providers_with_overlays_
@@ -452,7 +452,7 @@ def ext3capture_basenames
   # Validate some rules for container_engine, container_image_userfile_id, containerhub_image_name
   def validate_container_rules #:nodoc:
     # Should only have one container_engine of particular type
-    available_engine = ["Singularity","Docker"]
+    available_engine = ["Apptainer","Singularity","Docker"]
     if self.container_engine.present? && available_engine.exclude?(self.container_engine)
       errors[:container_engine] = "is not valid"
     end
@@ -470,9 +470,9 @@ def validate_container_rules #:nodoc:
       errors[:container_engine] = "a container hub image name or a container image userfile ID should be set when the container engine is set"
     end
 
-    if self.container_engine.present? && self.container_engine == "Singularity"
+    if self.container_engine.present? && (self.container_engine == "Apptainer" ||  self.container_engine == "Singularity")
       if self.container_index_location.present? && self.container_index_location !~ /\A[a-z0-9]+\:\/\/\z/i
-        errors[:container_index_location] = "is invalid for container engine Singularity. Should end in '://'."
+        errors[:container_index_location] = "is invalid for container engine Apptainer. Should end in '://'."
       end
     elsif self.container_engine.present? && self.container_engine == "Docker"
       if self.container_index_location.present? && self.container_index_location !~ /\A[a-z0-9]+([\-\.]{1}[a-z0-9]+)*\.[a-z]{2,6}\z/i
@@ -484,7 +484,7 @@ def validate_container_rules #:nodoc:
 
   # breaks down overlay spec onto a list of overlays
   def parsed_overlay_specs
-    specs = self.singularity_overlays_specs
+    specs = self.apptainer_overlays_specs
     return [] if specs.blank?
     lines = specs.split(/^#.*|\s+#.*|\n/) # split on lines and drop comments
     lines.map(&:presence).compact.map do |spec|
@@ -513,24 +513,24 @@ def validate_overlays_specs #:nodoc:
       case kind # different validations rules for file, userfile and dp specs
       when 'file' # full path specification for a local file, e.g. "file:/myfiles/c.sqs"
         if id_or_name !~ /^\/\S+\.(sqs|sqfs|squashfs)$/
-          self.errors.add(:singularity_overlays_specs,
+          self.errors.add(:apptainer_overlays_specs,
             " contains invalid #{kind} named '#{id_or_name}'. It should be a full path that ends in .squashfs, .sqs or .sqfs")
         end
 
       when 'userfile' # db-registered file spec, e.g. "userfile:42"
         if id_or_name !~ /\A\d+\z/
-          self.errors.add(:singularity_overlays_specs,
+          self.errors.add(:apptainer_overlays_specs,
             %{" contains invalid userfile id '#{id_or_name}'. The userfile id should be an integer number."}
           )
         else
           userfile = SingleFile.where(:id => id_or_name).first
         end
         if ! userfile
-          self.errors.add(:singularity_overlays_specs,
+          self.errors.add(:apptainer_overlays_specs,
             %{" contains invalid userfile id '#{id_or_name}'. The file with id '#{id_or_name}' is not found."}
           )
         elsif userfile.name.to_s !~ /\.(sqs|sqfs|squashfs)$/
-          self.errors.add(:singularity_overlays_specs,
+          self.errors.add(:apptainer_overlays_specs,
           " contains invalid userfile with id '#{id_or_name}' and name '#{userfile.name}'. File name should end in .squashfs, .sqs or .sqfs")
           # todo maybe or/and check file type?
         end
@@ -538,20 +538,20 @@ def validate_overlays_specs #:nodoc:
       when 'dp' # DataProvider specs: "dp:name" or "dp:ID"
         dp = DataProvider.where_id_or_name(id_or_name).first
         if !dp
-          self.errors.add(:singularity_overlays_specs, "contains invalid DP '#{id_or_name}' (no such DP)")
+          self.errors.add(:apptainer_overlays_specs, "contains invalid DP '#{id_or_name}' (no such DP)")
         elsif ! dp.is_a?(SingSquashfsDataProvider)
-          self.errors.add(:singularity_overlays_specs, "DataProvider '#{id_or_name}' is not a SingSquashfsDataProvider")
+          self.errors.add(:apptainer_overlays_specs, "DataProvider '#{id_or_name}' is not a SingSquashfsDataProvider")
         end
 
       when 'ext3capture' # ext3 filesystem as a basename with an initial size
         # The basename is limited to letters, digits, numbers and dashes; the =SIZE suffix must end with G or M
         if id_or_name !~ /\A\w[\w\.-]+=([1-9]\d*)[mg]\z/i
-          self.errors.add(:singularity_overlays_specs, "contains invalid ext3capture specification (must be like ext3capture:basename=1g or 2m etc)")
+          self.errors.add(:apptainer_overlays_specs, "contains invalid ext3capture specification (must be like ext3capture:basename=1g or 2m etc)")
         end
 
       else
         # Other errors
-        self.errors.add(:singularity_overlays_specs, "contains invalid specification '#{kind}:#{id_or_name}'")
+        self.errors.add(:apptainer_overlays_specs, "contains invalid specification '#{kind}:#{id_or_name}'")
       end
     end
 
@@ -662,7 +662,7 @@ def self.create_from_descriptor(bourreau, tool, descriptor, record_path=false)
     container_engine = container_info['type'].presence.try(:capitalize)
     container_engine = "Singularity" if (container_engine == "Docker" &&
                                          !bourreau.docker_present?    &&
-                                          bourreau.singularity_present?
+                                          bourreau.apptainer_present?
                                         )
     container_index  = container_info['index'].presence
     container_index  = 'docker://' if container_index == 'index.docker.io' # old convention
diff --git a/BrainPortal/app/views/bourreaux/show.html.erb b/BrainPortal/app/views/bourreaux/show.html.erb
index 73f2dec0b..43c24208d 100644
--- a/BrainPortal/app/views/bourreaux/show.html.erb
+++ b/BrainPortal/app/views/bourreaux/show.html.erb
@@ -475,9 +475,9 @@
            <div class="field_explanation">Name of the Docker executable available on the machines where tasks will run. It should always be set if Docker is present.</div>
         <% end %>
         <!-- Singularity -->
-        <% t.edit_cell :singularity_executable_name, :header => "Singularity executable" do |f| %>
-          <%= f.text_field :singularity_executable_name, :size => 60 %><br/>
-           <div class="field_explanation">Name of the Singularity executable available on the machines where tasks will run. It should always be set if Singularity is present.</div>
+        <% t.edit_cell :apptainer_executable_name, :header => "Apptainer executable" do |f| %>
+          <%= f.text_field :apptainer_executable_name, :size => 60 %><br/>
+           <div class="field_explanation">Name of the Apptainer or Singularity executable available on the machines where tasks will run. It should always be set if Singularity is present.</div>
         <% end %>
       <% end %>
     <% end %>
diff --git a/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb b/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb
index 951970e11..73070cfb8 100644
--- a/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb
+++ b/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb
@@ -114,12 +114,12 @@ acts like a FlatDataProvider.
 
 <p>
 
-<strong>SingSquashfsDataProvider</strong> This class connects to a set of
+<strong>ApptainerSquashfsDataProvider</strong> This class connects to a set of
 one or several squashfs files (all named with <em>.squashfs</em> extensions) through
-a Singularity container handler. The requirements are:<br>
+a Apptainer container handler. The requirements are:<br>
 <ul>
   <li>that all the squashfs files are in the <em>Physical Data Location</em>,
-  <li>the Singularity image is also there and named <em><%= SingSquashfsDataProvider::SINGULARITY_IMAGE_BASENAME %></em>,
+  <li>the Apptainer image is also there and named <em><%= ApptainerSquashfsDataProvider::APPTAINER_IMAGE_BASENAME %></em>,
   <li>that this image contains a basic Linux system with at least <em>rsync</em> installed in it,
   <li>and that the path to the data root inside the container must be provided in the <em>Containerized Data Path</em> under the <em>Containerized Storage Configuration</em> section.
 </ul>
diff --git a/BrainPortal/app/views/tool_configs/_form_fields.html.erb b/BrainPortal/app/views/tool_configs/_form_fields.html.erb
index fb166cb6a..aac81f17f 100644
--- a/BrainPortal/app/views/tool_configs/_form_fields.html.erb
+++ b/BrainPortal/app/views/tool_configs/_form_fields.html.erb
@@ -194,10 +194,10 @@
     <% t.edit_cell(:container_index_location, :header => "Index of the container image") do |f| %>
       <%= f.text_field :container_index_location %>
       <div class="field_explanation">
-        The index (url) of the container image in which the docker or singularity container is
+        The index (url) of the container image in which the docker or Apptainer/Singularity container is
         accessible through.
         Examples for Docker are: quay.io, index.docker.io (default).
-        Examples for Singularity are: docker:&sol;&sol;, shub:&sol;&sol; (default).
+        Examples for Apptainer are: docker://, shub:// (default).
       </div>
     <% end %>
 
@@ -219,11 +219,11 @@
       </div>
     <% end %>
 
-    <% t.edit_cell(:singularity_overlays_specs, :header => "Singularity Overlays", :show_width => 2, :content => full_description(@tool_config.singularity_overlays_specs)) do |f| %>
-      <%= f.text_area :singularity_overlays_specs, :rows => 6, :cols => 120 %>
+    <% t.edit_cell(:apptainer_overlays_specs, :header => "Apptainer/Singularity Overlays", :show_width => 2, :content => full_description(@tool_config.apptainer_overlays_specs)) do |f| %>
+      <%= f.text_area :apptainer_overlays_specs, :rows => 6, :cols => 120 %>
         <div class="wide_field_explanation">
         This field can contain one or several specifications for data overlays
-        to be included when the task is started with Singularity.
+        to be included when the task is started with Apptainer (formerly known as Singularity).
         A specification can be either
         a full path (e.g. <em>file:/a/b/data.squashfs</em>),
         a path with a pattern (e.g. <em>file:/a/b/data*.squashfs</em>),
@@ -237,18 +237,18 @@
         </div>
     <% end %>
 
-    <% t.edit_cell(:container_exec_args, :header => "Misc Singularity Options", :show_width => 2) do |f| %>
+    <% t.edit_cell(:container_exec_args, :header => "Misc Apptainter Options", :show_width => 2) do |f| %>
       <%= f.text_field :container_exec_args, :size => 60 %>
       <div class="field_explanation">
-        This field can contain singularity exec command options. Please use appropriate quotation or escaping
+        This field can contain apptainer/singularity exec command options. Please use appropriate quotation or escaping
         For example, <em>--cleanenv --env MYPATH='/My Documents'</em>.
       </div>
     <% end %>
 
-    <% t.boolean_edit_cell('tool_config[singularity_use_short_workdir]',
-         (@tool_config.singularity_use_short_workdir ? "1" : "0"),
+    <% t.boolean_edit_cell('tool_config[apptainer_use_short_workdir]',
+         (@tool_config.apptainer_overlays_specs ? "1" : "0"),
          "1", "0",
-         :header => "Use short workdirs inside Singularity")
+         :header => "Use short workdirs inside Apptainer")
     %>
 
   <% end %>
diff --git a/BrainPortal/app/views/tool_configs/show.html.erb b/BrainPortal/app/views/tool_configs/show.html.erb
index 6b570a903..ff02fd003 100644
--- a/BrainPortal/app/views/tool_configs/show.html.erb
+++ b/BrainPortal/app/views/tool_configs/show.html.erb
@@ -69,9 +69,9 @@
 
     <pre class="script_preview">
 
-<%= @bourreau_glob_config.to_bash_prologue @tool_local_config&.use_singularity? if @bourreau_glob_config %>
-<%= @tool_glob_config.to_bash_prologue     @tool_local_config&.use_singularity? if @tool_glob_config     %>
-<%= @tool_local_config.to_bash_prologue    @tool_local_config&.use_singularity? if @tool_local_config    %>
+<%= @bourreau_glob_config.to_bash_prologue @tool_local_config&.use_apptainer? if @bourreau_glob_config %>
+<%= @tool_glob_config.to_bash_prologue     @tool_local_config&.use_apptainer? if @tool_glob_config     %>
+<%= @tool_local_config.to_bash_prologue    @tool_local_config&.use_apptainer? if @tool_local_config    %>
 ##########################################
 #### [Wrapped commands would be here] ####
 ##########################################
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
index 8953c769e..1f155744e 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
@@ -32,28 +32,33 @@ def self.file_name_pattern #:nodoc:
   end
 
   def is_viewable? #:nodoc:
-    if ! self.has_singularity_support?
-      return [ "The local portal doesn't support inspecting Singularity images." ]
+    if ! self.has_apptainer_support?
+      return [ "The local portal doesn't support inspecting Apptainer (aka Singularity) images." ]
     elsif ! self.is_locally_synced?
-      return [ "Singularity image file not yet synchronized" ]
+      return [ "Apptainer (aka Singularity) image file not yet synchronized" ]
     else
       true
     end
   end
 
-  def has_singularity_support? #:nodoc:
-    self.class.has_singularity_support?
+  def has_apptainer_support? #:nodoc:
+    self.class.has_apptainer_support?
   end
 
-  # Detects if the system has the 'singularity' command.
+  # caches apptainer_executable_name (which does not change that often)
+  def self.apptainer_executable  #:nodoc:
+    @_executable ||= RemoteResource.current_resource.apptainer_executable_name.presence || "apptainer"
+  end
+
+  # Detects if the system has the Apptainer command.
+  # Singularity command is still supported on best effort basis
   # Caches the result in the class so it won't need to
   # be detected again after the first time, for the life
   # of the current process.
-  def self.has_singularity_support? #:nodoc:
-    return @_has_singularity_support if ! @_has_singularity_support.nil?
-    out = IO.popen("bash -c 'type -p singularity'","r") { |f| f.read }
-    @_has_singularity_support = out.present?
+  def self.has_apptainer_support? #:nodoc:
+    return @_has_apptainer_support if ! @_has_apptainer_support.nil?
+    out = IO.popen("bash -c 'type -p #{apptainer_executable}'","r") { |f| f.read }
+    @_has_apptainer_support = out.present?
   end
 
 end
-
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/views/_info.html.erb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/views/_info.html.erb
index 1f45c8ff0..0c49d8934 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/views/_info.html.erb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/views/_info.html.erb
@@ -27,21 +27,21 @@
 
 <h5>Image Inspect</h5>
 
-<pre><%= cat.("singularity inspect #{path}") %></pre>
+<pre><%= cat.("#{SingularityImage.apptainer_executable} inspect #{path}") %></pre>
 
 <h5>SIF Header</h5>
 
-<pre><%= cat.("singularity sif header #{path}") %></pre>
+<pre><%= cat.("#{SingularityImage.apptainer_executable} sif header #{path}") %></pre>
 
 <h5>SIF List</h5>
 
-<pre><%= text = cat.("singularity sif list #{path}") %></pre>
+<pre><%= text = cat.("#{SingularityImage.apptainer_executable} sif list #{path}") %></pre>
 
 <h5>SIF Items</h5>
 
 <% text.split(/\n/).map { |line| line[/^(\d+)/] }.compact.each do |id| %>
 
-  <pre><%= cat.("singularity sif info #{id} #{path}") %></pre><p>
+  <pre><%= cat.("#{SingularityImage.apptainer_executable} sif info #{id} #{path}") %></pre><p>
 
 <% end %>
 
diff --git a/BrainPortal/config/console_rc/lib/pretty_view.rb b/BrainPortal/config/console_rc/lib/pretty_view.rb
index 77fa24e99..8945f1d0b 100644
--- a/BrainPortal/config/console_rc/lib/pretty_view.rb
+++ b/BrainPortal/config/console_rc/lib/pretty_view.rb
@@ -234,7 +234,7 @@ def pretview
   Created:  %s
   Updated:  %s
   Docker:   %s
-  Singularity: %s
+  Apptainer: %s
   Flags:    %s %s %s
     VIEW
     sprintf report,
@@ -266,7 +266,7 @@ def pretview
       ConsoleCtx.send(:pretty_past_date,created_at),
       ConsoleCtx.send(:pretty_past_date,updated_at),
       docker_executable_name.presence || "",
-      singularity_executable_name.presence || "",
+      apptainer_executable_name.presence || "",
       (online? ? "Online" : "Offline"),
       (read_only? ? "ReadOnly" : "R/W"),
       (portal_locked? ? "LOCKED" : "")
diff --git a/BrainPortal/db/migrate/20240408164549_rename_singularity_to_apprainer.rb b/BrainPortal/db/migrate/20240408164549_rename_singularity_to_apprainer.rb
new file mode 100644
index 000000000..ee000e29d
--- /dev/null
+++ b/BrainPortal/db/migrate/20240408164549_rename_singularity_to_apprainer.rb
@@ -0,0 +1,7 @@
+class RenameSingularityToApprainer < ActiveRecord::Migration[5.0]
+  def change
+    rename_column :tool_configs, :singularity_overlays_specs, :apptainer_overlays_specs
+    rename_column :tool_configs, :singularity_use_short_workdir, :apptainer_use_short_workdir
+    rename_column :remote_resources, :singularity_executable_name, :apptainer_executable_name
+  end
+end
diff --git a/BrainPortal/db/schema.rb b/BrainPortal/db/schema.rb
index f8e0f11f7..5f7ca44c9 100644
--- a/BrainPortal/db/schema.rb
+++ b/BrainPortal/db/schema.rb
@@ -315,7 +315,7 @@
     t.string   "nh_system_from_email"
     t.string   "external_status_page_url"
     t.string   "docker_executable_name"
-    t.string   "singularity_executable_name"
+    t.string   "apptainer_executable_name"
     t.string   "small_logo"
     t.string   "large_logo"
     t.index ["type"], name: "index_remote_resources_on_type", using: :btree
@@ -485,8 +485,8 @@
     t.string   "containerhub_image_name"
     t.string   "container_engine"
     t.string   "container_index_location"
-    t.text     "singularity_overlays_specs",    limit: 65535
-    t.boolean  "singularity_use_short_workdir",               default: false, null: false
+    t.text     "apptainer_overlays_specs",      limit: 65535
+    t.boolean  "apptainer_use_short_workdir",                 default: false, null: false
     t.string   "container_exec_args"
     t.boolean  "inputs_readonly",                             default: false
     t.string   "boutiques_descriptor_path"
diff --git a/BrainPortal/lib/boutiques_ext3_capturer.rb b/BrainPortal/lib/boutiques_ext3_capturer.rb
index 1345eb6e2..239b0ea86 100644
--- a/BrainPortal/lib/boutiques_ext3_capturer.rb
+++ b/BrainPortal/lib/boutiques_ext3_capturer.rb
@@ -22,7 +22,7 @@
 
 # This module adds automatic setting up of mounted
 # ext3 filesystem as subdirectories of a task, provided
-# the tool works in Singularity/Apptainer.
+# the tool works in Apptainer.
 # It is the exact equivalent of adding an ext3 overlay
 # configuration entry in the task's tool config.
 #
diff --git a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
index 48edeed38..42cb0ecd2 100644
--- a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
+++ b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
@@ -259,10 +259,10 @@ def register(task)
       return if container_engine.blank?  # Singularity or Docker
       return if container_image.blank?   # Container name or url
                 container_engine.capitalize!
-      return if container_engine == "Singularity" && !resource.singularity_present?
-      return if container_engine == "Docker"      && (!resource.docker_present? && !resource.singularity_present?)
+      return if container_engine == ("Singularity" || "Apptainer") && !resource.apptainer_present?
+      return if container_engine == "Docker"      && (!resource.docker_present? && !resource.apptainer_present?)
 
-      # If Docker engine isn't present use Singularity
+      # If Docker engine isn't present use Apptainer
       container_engine = "Singularity" if (container_engine == "Docker" && !resource.docker_present?)
       container_index  = 'docker://'   if container_index == 'index.docker.io' # old convention
 
diff --git a/BrainPortal/spec/models/tool_config_spec.rb b/BrainPortal/spec/models/tool_config_spec.rb
index 731851f1f..9e788da6d 100644
--- a/BrainPortal/spec/models/tool_config_spec.rb
+++ b/BrainPortal/spec/models/tool_config_spec.rb
@@ -159,13 +159,13 @@
    context "fill HEADER" do
       it "should print 'Configuration: tool_config.id'" do
         expect(tool_config.to_bash_prologue).to                    match(/Configuration\s?:\s+#\s+#{tool_config.id}/)
-        expect(tool_config.to_bash_prologue(singularity: true)).to match(/Configuration\s?:\s+#\s+#{tool_config.id}/)
+        expect(tool_config.to_bash_prologue(true)).to match(/Configuration\s?:\s+#\s+#{tool_config.id}/)
       end
 
       it "should print 'Tool: ALL' if specific tool is not defined"  do
         tool_config.tool = nil
         expect(tool_config.to_bash_prologue).to                    match(/Tool\s?:\s+ALL/)
-        expect(tool_config.to_bash_prologue(singularity: true)).to match(/Tool\s?:\s+ALL/)
+        expect(tool_config.to_bash_prologue(apptainer: true)).to match(/Tool\s?:\s+ALL/)
       end
 
       it "should print 'Tool: tool_config.tool.name' if specific tool is defined"  do
@@ -225,16 +225,16 @@
 
         expect(tool_config.to_bash_prologue).to match(/Environment variables\s?:\n\#\-+\n\n#{script}/)
       end
-      it "should not print 'Environment variables: export SINGULARITYENV_name1=\"value1\".... if config has no singularity" do
+      it "should not print 'Environment variables: export APPTAINERENV_name1=\"value1\".... if config has no singularity" do
         tool_config.env_array = [["name1", "value1"],["name2","value2"]]
         expect(tool_config.to_bash_prologue).not_to match(/(SINGULARITYENV|APPTAINERENV)/)
       end
-      it "should print 'export SINGULARITYENV_name1=\"value1\".... if env is not empty and config uses singularity" do
+      it "should print 'export APPTAINERENV_name1=\"value1\".... if env is not empty and config uses singularity" do
         tool_config.env_array = [["name1", "value1"],["name2","value2"]]
 
         script = ""
         tool_config.env_array.each do |name_val|
-          name = "SINGULARITYENV_" + name_val[0].strip
+          name = "APPTAINERENV_" + name_val[0].strip
           val  = name_val[1]
           script += "export #{name}=\\\"#{val}\\\"\\n"
         end
@@ -279,4 +279,3 @@
   end
 
 end
-

From 3ed1da8747d6747b2b55fe17c27d375f73a3d28e Mon Sep 17 00:00:00 2001
From: MontrealSergiy <sergeboroday@gmail.com>
Date: Mon, 24 Mar 2025 19:05:14 -0400
Subject: [PATCH 2/9] Refactor singularity into apptainer - update migration
 timestamp

---
 ...ainer.rb => 20250324164549_rename_singularity_to_apprainer.rb} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename BrainPortal/db/migrate/{20240408164549_rename_singularity_to_apprainer.rb => 20250324164549_rename_singularity_to_apprainer.rb} (100%)

diff --git a/BrainPortal/db/migrate/20240408164549_rename_singularity_to_apprainer.rb b/BrainPortal/db/migrate/20250324164549_rename_singularity_to_apprainer.rb
similarity index 100%
rename from BrainPortal/db/migrate/20240408164549_rename_singularity_to_apprainer.rb
rename to BrainPortal/db/migrate/20250324164549_rename_singularity_to_apprainer.rb

From 7930f636c82a2904fda41e503907c4d0deed86da Mon Sep 17 00:00:00 2001
From: MontrealSergiy <sergeboroday@gmail.com>
Date: Mon, 24 Mar 2025 19:06:18 -0400
Subject: [PATCH 3/9] Refactor singularity into apptainer - update migration
 timestamp

---
 BrainPortal/db/schema.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BrainPortal/db/schema.rb b/BrainPortal/db/schema.rb
index 5f7ca44c9..c42097873 100644
--- a/BrainPortal/db/schema.rb
+++ b/BrainPortal/db/schema.rb
@@ -11,7 +11,7 @@
 # It's strongly recommended that you check this file into your version control system.
 
 
-ActiveRecord::Schema.define(version: 20250417170914) do
+ActiveRecord::Schema.define(version: 20250513170914) do
 
   create_table "access_profiles", force: :cascade, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci" do |t|
     t.string   "name",        null: false

From 8c58a750ed88fd5497a9ec59513eb2d74479969e Mon Sep 17 00:00:00 2001
From: MontrealSergiy <sergeboroday@gmail.com>
Date: Wed, 2 Apr 2025 17:42:20 -0400
Subject: [PATCH 4/9] bugfix

---
 BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
index 42cb0ecd2..9e6e596e4 100644
--- a/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
+++ b/BrainPortal/lib/cbrain_task_generators/schema_task_generator.rb
@@ -259,7 +259,7 @@ def register(task)
       return if container_engine.blank?  # Singularity or Docker
       return if container_image.blank?   # Container name or url
                 container_engine.capitalize!
-      return if container_engine == ("Singularity" || "Apptainer") && !resource.apptainer_present?
+      return if ( container_engine == "Singularity" || container_engine == "Apptainer") && !resource.apptainer_present?
       return if container_engine == "Docker"      && (!resource.docker_present? && !resource.apptainer_present?)
 
       # If Docker engine isn't present use Apptainer

From a70f3b028e1dcb9bd601a9f757a4390db918bc2b Mon Sep 17 00:00:00 2001
From: MontrealSergiy <sergeboroday@gmail.com>
Date: Thu, 3 Apr 2025 17:15:24 -0400
Subject: [PATCH 5/9] drop a comment

---
 .../userfiles/singularity_image/singularity_image.rb             | 1 -
 1 file changed, 1 deletion(-)

diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
index 1f155744e..ceda43bb9 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
@@ -45,7 +45,6 @@ def has_apptainer_support? #:nodoc:
     self.class.has_apptainer_support?
   end
 
-  # caches apptainer_executable_name (which does not change that often)
   def self.apptainer_executable  #:nodoc:
     @_executable ||= RemoteResource.current_resource.apptainer_executable_name.presence || "apptainer"
   end

From 41890ec68272ca5ee34813bf6d09e7d062a264d7 Mon Sep 17 00:00:00 2001
From: MontrealSergiy <sergeboroday@gmail.com>
Date: Mon, 7 Apr 2025 10:44:33 -0400
Subject: [PATCH 6/9] shorten verbiage

---
 .../userfiles/singularity_image/singularity_image.rb            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
index ceda43bb9..ec51e74ae 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
@@ -35,7 +35,7 @@ def is_viewable? #:nodoc:
     if ! self.has_apptainer_support?
       return [ "The local portal doesn't support inspecting Apptainer (aka Singularity) images." ]
     elsif ! self.is_locally_synced?
-      return [ "Apptainer (aka Singularity) image file not yet synchronized" ]
+      return [ "Apptainer (Singularity) image file not yet synchronized" ]
     else
       true
     end

From e60ac8a74ae09b5cd82bcf2efcacdb993d2f18b1 Mon Sep 17 00:00:00 2001
From: MontrealSergiy <sergeboroday@gmail.com>
Date: Mon, 7 Apr 2025 10:50:20 -0400
Subject: [PATCH 7/9] roll back a change

---
 .../app/views/data_providers/_dp_types_explained.html.erb   | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb b/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb
index 73070cfb8..34a15cdf1 100644
--- a/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb
+++ b/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb
@@ -114,12 +114,12 @@ acts like a FlatDataProvider.
 
 <p>
 
-<strong>ApptainerSquashfsDataProvider</strong> This class connects to a set of
+<strong>SingSquashfsDataProvider</strong> This class connects to a set of
 one or several squashfs files (all named with <em>.squashfs</em> extensions) through
-a Apptainer container handler. The requirements are:<br>
+a Apptainer (Sigularity container handler. The requirements are:<br>
 <ul>
   <li>that all the squashfs files are in the <em>Physical Data Location</em>,
-  <li>the Apptainer image is also there and named <em><%= ApptainerSquashfsDataProvider::APPTAINER_IMAGE_BASENAME %></em>,
+  <li>the Apptainer image is also there and named <em><%= SingSquashfsDataProvider::APPTAINER_IMAGE_BASENAME %></em>,
   <li>that this image contains a basic Linux system with at least <em>rsync</em> installed in it,
   <li>and that the path to the data root inside the container must be provided in the <em>Containerized Data Path</em> under the <em>Containerized Storage Configuration</em> section.
 </ul>

From 1da44b00c9591b3c6b820700192f889fb71b96dd Mon Sep 17 00:00:00 2001
From: MontrealSergiy <sergeboroday@gmail.com>
Date: Mon, 7 Apr 2025 11:43:43 -0400
Subject: [PATCH 8/9] Verbiage: more of Uppercase Apptainer in comments and
 messages, less aka

---
 BrainPortal/app/models/cluster_task.rb               | 12 ++++++------
 .../app/models/sing_bindmount_data_provider.rb       |  6 +++---
 .../app/models/sing_squashfs_data_provider.rb        |  2 +-
 .../data_providers/_dp_types_explained.html.erb      |  2 +-
 .../userfiles/singularity_image/singularity_image.rb |  2 +-
 5 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/BrainPortal/app/models/cluster_task.rb b/BrainPortal/app/models/cluster_task.rb
index cf18041c3..6b9011922 100644
--- a/BrainPortal/app/models/cluster_task.rb
+++ b/BrainPortal/app/models/cluster_task.rb
@@ -1879,7 +1879,7 @@ def submit_cluster_job
 
   test $status -eq 0 && break # all is good
 
-  # Detect failed boot of apptainer container
+  # Detect failed boot of Apptainer container
   if ! grep -i 'FATAL.*container.*creation.*failed' #{science_stderr_basename} >/dev/null ; then
     break # move on, for any other error or even non zero successes
   fi
@@ -2360,7 +2360,7 @@ def use_apptainer_short_workdir?
   # is the raw scientific bash script.
   def apptainer_commands(command_script)
 
-    # Basename of the apptainer wrapper script
+    # Basename of the Apptainer wrapper script
     apptainer_wrapper_basename = ".apptainer.#{self.run_id}.sh"
 
     # Values we substitute in our script:
@@ -2423,7 +2423,7 @@ def apptainer_commands(command_script)
     # Wrap new HOME environment
     command_script = wrap_new_HOME(command_script, effect_workdir)
 
-    # Set apptainer command
+    # Set Apptainer command
     apptainer_commands = <<-APPTAINER_COMMANDS
 
 # Note to developers:
@@ -2442,7 +2442,7 @@ def apptainer_commands(command_script)
   apptainer_basename=""
 fi
 
-# Build a local wrapper script to run in a apptainer container
+# Build a local wrapper script to run in an Apptainer container
 cat << \"APPTAINERJOB\" > #{apptainer_wrapper_basename.bash_escape}
 #!/bin/bash
 
@@ -2522,7 +2522,7 @@ def apptainer_commands(command_script)
 # 4) we mount each (if any) of the root directories for local data providers
 # 5) we mount (if any) other fixed file system overlays
 # 6) we mount (if any) capture ext3 filesystems
-# 7) with -H we set the task's work directory as the apptainer $HOME directory
+# 7) with -H we set the task's work directory as the Apptainer $HOME directory
 #{apptainer_executable_name}                  \\
     $mode                                       \\
     #{container_exec_args}                      \\
@@ -2684,7 +2684,7 @@ def load_apptainer_image_from_repo #:nodoc:
         File.open(capfile,"w") do |fh|
           fh.write("=== Stdout ===\n#{out}\n=== Stderr ===\n#{err}\n=== ====== ===\n")
         end
-        cb_error "Cannot build apptainer image. Captured outputs are in #{capfile}"
+        cb_error "Cannot build Apptainer image. Captured outputs are in #{capfile}"
       end
     end
 
diff --git a/BrainPortal/app/models/sing_bindmount_data_provider.rb b/BrainPortal/app/models/sing_bindmount_data_provider.rb
index 5e6822b3d..aeb5b0542 100644
--- a/BrainPortal/app/models/sing_bindmount_data_provider.rb
+++ b/BrainPortal/app/models/sing_bindmount_data_provider.rb
@@ -118,7 +118,7 @@ def check_remote_config! #:nodoc:
     remote_cmd  = "cd #{self.real_remote_dir.to_s.bash_escape} && test -f #{APPTAINER_IMAGE_BASENAME} && echo OK-Exists"
     text        = self.remote_bash_this(remote_cmd)
     # The following check will also make sure the remote shell is clean!
-    cb_error "No installed apptainer image #{APPTAINER_IMAGE_BASENAME}, or remote shell is unclean" unless text =~ /\AOK-Exists\s*\z/
+    cb_error "No installed Apptainer image #{APPTAINER_IMAGE_BASENAME}, or remote shell is unclean" unless text =~ /\AOK-Exists\s*\z/
 
     # Check we have the remote filesystem file
     remote_cmd  = "test -f #{self.remote_dir.to_s.bash_escape} && echo OK-Exists"
@@ -127,14 +127,14 @@ def check_remote_config! #:nodoc:
     # Check we have Apptainer 1.1 or better
     remote_cmd = "(singularity --version 2>/dev/null || apptainer --version 2>/dev/null)"
     text       = self.remote_bash_this(remote_cmd)
-    cb_error "Can't find apptainer version number on remote host" unless text =~ /^((singularity|apptainer) version )?(\d+)\.(\d+)/
+    cb_error "Can't find Apptainer version number on remote host" unless text =~ /^((singularity|apptainer) version )?(\d+)\.(\d+)/
     _, _, tool, major, minor = Regexp.last_match.to_a
     major = major.to_i
     minor = minor.to_i
     if tool == 'singularity'
       cb_error "singularity version number on remote host is less than 3.7" if major  < 3 || (major == 3 && minor < 7)
     else # tool == 'apptainer'
-      cb_error "apptainer version number on remote host is less than 1.1"   if major  < 1 || (major == 1 && minor < 1)
+      cb_error "Apptainer version number on remote host is less than 1.1"   if major  < 1 || (major == 1 && minor < 1)
     end
 
     # Check that inside the container, the containerized path exists
diff --git a/BrainPortal/app/models/sing_squashfs_data_provider.rb b/BrainPortal/app/models/sing_squashfs_data_provider.rb
index adf1ec2d2..7763c06c4 100644
--- a/BrainPortal/app/models/sing_squashfs_data_provider.rb
+++ b/BrainPortal/app/models/sing_squashfs_data_provider.rb
@@ -86,7 +86,7 @@ def apptainer_executable_name
     # also works if an old Singularity and uptodate Apptainer
     # todo loop over list of several candidate executables
     text       = self.remote_bash_this(remote_cmd)
-    cb_error "Can't find apptainer version number on remote host" unless text =~ /^((singularity|apptainer) version )?(\d+)\.(\d+)/
+    cb_error "Can't find Apptainer version number on remote host" unless text =~ /^((singularity|apptainer) version )?(\d+)\.(\d+)/
     _, _, @_tool, major, minor = Regexp.last_match.to_a
     major = major.to_i
     minor = minor.to_i
diff --git a/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb b/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb
index 34a15cdf1..79ce60137 100644
--- a/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb
+++ b/BrainPortal/app/views/data_providers/_dp_types_explained.html.erb
@@ -116,7 +116,7 @@ acts like a FlatDataProvider.
 
 <strong>SingSquashfsDataProvider</strong> This class connects to a set of
 one or several squashfs files (all named with <em>.squashfs</em> extensions) through
-a Apptainer (Sigularity container handler. The requirements are:<br>
+a Apptainer (Singularity) container handler. The requirements are:<br>
 <ul>
   <li>that all the squashfs files are in the <em>Physical Data Location</em>,
   <li>the Apptainer image is also there and named <em><%= SingSquashfsDataProvider::APPTAINER_IMAGE_BASENAME %></em>,
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
index ec51e74ae..157dab731 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/singularity_image/singularity_image.rb
@@ -33,7 +33,7 @@ def self.file_name_pattern #:nodoc:
 
   def is_viewable? #:nodoc:
     if ! self.has_apptainer_support?
-      return [ "The local portal doesn't support inspecting Apptainer (aka Singularity) images." ]
+      return [ "The local portal doesn't support inspecting Apptainer (Singularity) images." ]
     elsif ! self.is_locally_synced?
       return [ "Apptainer (Singularity) image file not yet synchronized" ]
     else

From d9668abd03581d958f31694157c3156b5258fd26 Mon Sep 17 00:00:00 2001
From: MontrealSergiy <sergeboroday@gmail.com>
Date: Tue, 13 May 2025 18:17:32 -0400
Subject: [PATCH 9/9] rebase, apply refactoring to new tool

---
 .../app/models/sing_squashfs_data_provider.rb |  2 +-
 BrainPortal/app/models/tool_config.rb         |  2 +-
 .../boutiques_tool_configurator_handler.rb    | 20 +++++++++----------
 ...170914_rename_singularity_to_apptainer.rb} |  2 +-
 BrainPortal/db/schema.rb                      |  6 +++---
 5 files changed, 16 insertions(+), 16 deletions(-)
 rename BrainPortal/db/migrate/{20250324164549_rename_singularity_to_apprainer.rb => 20250513170914_rename_singularity_to_apptainer.rb} (82%)

diff --git a/BrainPortal/app/models/sing_squashfs_data_provider.rb b/BrainPortal/app/models/sing_squashfs_data_provider.rb
index 7763c06c4..365d0b584 100644
--- a/BrainPortal/app/models/sing_squashfs_data_provider.rb
+++ b/BrainPortal/app/models/sing_squashfs_data_provider.rb
@@ -83,7 +83,7 @@ def apptainer_executable_name
 
     remote_cmd = "( apptainer --version 2>/dev/null || singularity --version 2>/dev/null )"
     # Apptainer is preferable so it comes first in the command
-    # also works if an old Singularity and uptodate Apptainer
+    # also works if an old Singularity
     # todo loop over list of several candidate executables
     text       = self.remote_bash_this(remote_cmd)
     cb_error "Can't find Apptainer version number on remote host" unless text =~ /^((singularity|apptainer) version )?(\d+)\.(\d+)/
diff --git a/BrainPortal/app/models/tool_config.rb b/BrainPortal/app/models/tool_config.rb
index 6de420c37..8bedbb314 100644
--- a/BrainPortal/app/models/tool_config.rb
+++ b/BrainPortal/app/models/tool_config.rb
@@ -470,7 +470,7 @@ def validate_container_rules #:nodoc:
       errors[:container_engine] = "a container hub image name or a container image userfile ID should be set when the container engine is set"
     end
 
-    if self.container_engine.present? && (self.container_engine == "Apptainer" ||  self.container_engine == "Singularity")
+    if self.container_engine.present? && (self.container_engine == "Apptainer" || self.container_engine == "Singularity")
       if self.container_index_location.present? && self.container_index_location !~ /\A[a-z0-9]+\:\/\/\z/i
         errors[:container_index_location] = "is invalid for container engine Apptainer. Should end in '://'."
       end
diff --git a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_tool_configurator_handler/portal/boutiques_tool_configurator_handler.rb b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_tool_configurator_handler/portal/boutiques_tool_configurator_handler.rb
index 22bb3c3d3..a1be658f5 100644
--- a/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_tool_configurator_handler/portal/boutiques_tool_configurator_handler.rb
+++ b/BrainPortal/cbrain_plugins/cbrain-plugins-base/cbrain_task/boutiques_tool_configurator_handler/portal/boutiques_tool_configurator_handler.rb
@@ -75,9 +75,9 @@ def refresh_form
       change.(:copy_env,      old_tc.env_array.present?,            "the flag to copy the environment variables")
       change.(:copy_bash,     (old_tc.script_prologue.present? || old_tc.script_epilogue.present?),  "the flag to copy the bash prologue and epilogue")
       change.(:copy_overlays,
-         (old_tc.singularity_overlays_specs.present? ||
+         (old_tc.apptainer_overlays_specs.present? ||
           old_tc.container_exec_args.present? ||
-          (old_tc.singularity_use_short_workdir? != new_tc.singularity_use_short_workdir?)
+          (old_tc.apptainer_use_short_workdir? != new_tc.apptainer_use_short_workdir?)
          ),
          "the flag to copy miscellaneous Apptainer options")
     end
@@ -209,8 +209,8 @@ def copy_attributes
       new_tc.script_epilogue = old_tc.script_epilogue
     end
     if bool.(invoke_params[:copy_overlays])
-      new_tc.singularity_overlays_specs    = old_tc.singularity_overlays_specs
-      new_tc.singularity_use_short_workdir = old_tc.singularity_use_short_workdir
+      new_tc.apptainer_overlays_specs    = old_tc.apptainer_overlays_specs
+      new_tc.apptainer_use_short_workdir = old_tc.apptainer_use_short_workdir
       new_tc.container_exec_args           = old_tc.container_exec_args
     end
 
@@ -231,8 +231,8 @@ def copy_attributes
           env_array
             script_prologue
             script_epilogue
-          singularity_overlays_specs
-          singularity_use_short_workdir
+          apptainer_overlays_specs
+          apptainer_use_short_workdir
           container_exec_args
             container_image_userfile_id
             containerhub_image_name
@@ -337,11 +337,11 @@ def add_all_input_notes(descriptor) #:nodoc:
 
     cp_ovrl = descriptor.input_by_id('copy_overlays')
     cp_ovrl.cbrain_input_notes = []
-    cp_ovrl.cbrain_input_notes << "OLD ToolConfig has overlays" if old_tc&.singularity_overlays_specs.present?
-    cp_ovrl.cbrain_input_notes << "OLD ToolConfig uses short workdirs" if old_tc&.singularity_use_short_workdir?
+    cp_ovrl.cbrain_input_notes << "OLD ToolConfig has overlays" if old_tc&.apptainer_overlays_specs.present?
+    cp_ovrl.cbrain_input_notes << "OLD ToolConfig uses short workdirs" if old_tc&.apptainer_use_short_workdir?
     cp_ovrl.cbrain_input_notes << "OLD ToolConfig uses special container options" if old_tc&.container_exec_args.present?
-    cp_ovrl.cbrain_input_notes << "NEW ToolConfig has overlays" if new_tc&.singularity_overlays_specs.present?
-    cp_ovrl.cbrain_input_notes << "NEW ToolConfig uses short workdirs" if new_tc&.singularity_use_short_workdir?
+    cp_ovrl.cbrain_input_notes << "NEW ToolConfig has overlays" if new_tc&.apptainer_overlays_specs.present?
+    cp_ovrl.cbrain_input_notes << "NEW ToolConfig uses short workdirs" if new_tc&.apptainer_use_short_workdir?
     cp_ovrl.cbrain_input_notes << "NEW ToolConfig uses special container options" if new_tc&.container_exec_args.present?
 
   end
diff --git a/BrainPortal/db/migrate/20250324164549_rename_singularity_to_apprainer.rb b/BrainPortal/db/migrate/20250513170914_rename_singularity_to_apptainer.rb
similarity index 82%
rename from BrainPortal/db/migrate/20250324164549_rename_singularity_to_apprainer.rb
rename to BrainPortal/db/migrate/20250513170914_rename_singularity_to_apptainer.rb
index ee000e29d..14c80b36b 100644
--- a/BrainPortal/db/migrate/20250324164549_rename_singularity_to_apprainer.rb
+++ b/BrainPortal/db/migrate/20250513170914_rename_singularity_to_apptainer.rb
@@ -1,4 +1,4 @@
-class RenameSingularityToApprainer < ActiveRecord::Migration[5.0]
+class RenameSingularityToApptainer < ActiveRecord::Migration[5.0]
   def change
     rename_column :tool_configs, :singularity_overlays_specs, :apptainer_overlays_specs
     rename_column :tool_configs, :singularity_use_short_workdir, :apptainer_use_short_workdir
diff --git a/BrainPortal/db/schema.rb b/BrainPortal/db/schema.rb
index c42097873..f8ee642cd 100644
--- a/BrainPortal/db/schema.rb
+++ b/BrainPortal/db/schema.rb
@@ -11,7 +11,7 @@
 # It's strongly recommended that you check this file into your version control system.
 
 
-ActiveRecord::Schema.define(version: 20250513170914) do
+ActiveRecord::Schema.define(version: 20250417170914) do
 
   create_table "access_profiles", force: :cascade, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci" do |t|
     t.string   "name",        null: false
@@ -485,8 +485,8 @@
     t.string   "containerhub_image_name"
     t.string   "container_engine"
     t.string   "container_index_location"
-    t.text     "apptainer_overlays_specs",      limit: 65535
-    t.boolean  "apptainer_use_short_workdir",                 default: false, null: false
+    t.text     "apptainer_overlays_specs",    limit: 65535
+    t.boolean  "apptainer_use_short_workdir"
     t.string   "container_exec_args"
     t.boolean  "inputs_readonly",                             default: false
     t.string   "boutiques_descriptor_path"