Add set_execution_mode param and UDOCKER_SET_EXECUTION_MODE to for udocker run

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## udocker (1.3.18) - 2025-08-22
+
+* New environment variable `UDOCKER_SET_EXECUTION_MODE` and configuration parameter
+  `set_execution_mode` to automatically set execution mode when running containers
+  from images. When set, this automatically creates a container and sets the
+  execution mode before running, equivalent to running `create`, `setup --execmode`,
+  and `run` commands in sequence.
+
 ## udocker (1.3.17) - 2024-08-28
 
 * Update docker tools url location

codemeta.json

@@ -6,7 +6,7 @@
     "@type": "SoftwareSourceCode",
     "identifier": "udocker",
     "name": "udocker",
-    "version": "1.3.17",
+    "version": "1.3.18",
     "description": "A basic user tool to execute simple docker containers in batch or interactive systems without root privileges",
     "license": "Apache Software License 2.0, OSI Approved :: Apache Software License",
     "author": [

docs/installation_manual.md

@@ -201,6 +201,7 @@ The configuration files allow overriding of the udocker `Config` class
 dockerio_registry_url = "https://myregistry.mydomain:5000"
 http_insecure = True
 verbose_level = 5
+set_execution_mode = "F3"
 ```
 
 udocker loads the following configuration files if they are present:
@@ -269,6 +270,11 @@ from the host or from the udocker installation.
   in udocker under `$HOME/.udocker/lib`.
 * `UDOCKER_DEFAULT_EXECUTION_MODE`: default execution mode can be P1, P2, F1,
   S1, R1, R2 or R3.
+* `UDOCKER_SET_EXECUTION_MODE`: automatically set execution mode when running
+  containers from images. When set, this automatically creates a container and
+  sets the execution mode before running, equivalent to running `create`,
+  `setup --execmode`, and `run` commands in sequence. Can also be set via
+  configuration file as `set_execution_mode`.
 
 Several executables and libraries are shipped with udocker. For instance
 the executable for the Rn modes can be selected to be either `runc` or
@@ -283,6 +289,16 @@ export UDOCKER_DEFAULT_EXECUTION_MODE=R1
 udocker run <mycontainerid>
 ```
 
+```
+# Automatically set execution mode when running from images
+export UDOCKER_SET_EXECUTION_MODE=F3
+udocker run quay.io/pacbio/hiphase:1.5.0_build1 hiphase --help
+# This is equivalent to:
+# udocker create --name=hiphase quay.io/pacbio/hiphase:1.5.0_build1
+# udocker setup --execmode=F3 hiphase
+# udocker run hiphase hiphase --help
+```
+
 ## 6. External tools and libraries
 
 ### 6.1. Source code repositories

docs/reference_card.md

@@ -22,6 +22,7 @@ The configuration files allow overriding of the udocker `Config` class
 dockerio_registry_url = https://myregistry.mydomain:5000
 http_insecure = True
 verbose_level = 5
+set_execution_mode = F3
 ```
 
 udocker loads the following configuration files if they are present:
@@ -45,6 +46,8 @@ udocker loads the following configuration files if they are present:
 * `UDOCKER_REGISTRY`: override default registry default is Docker Hub.
 * `UDOCKER_INDEX`: override default index default is Docker Hub.
 * `UDOCKER_DEFAULT_EXECUTION_MODE`: change default execution mode
+* `UDOCKER_SET_EXECUTION_MODE`: automatically set execution mode when running
+  containers from images (can also be set via configuration file as `set_execution_mode`)
 * `UDOCKER_USE_CURL_EXECUTABLE`: pathname for curl executable
 * `UDOCKER_USE_PROOT_EXECUTABLE`: change pathname for proot executable
 * `UDOCKER_USE_RUNC_EXECUTABLE`: change pathname for runc executable
@@ -53,7 +56,26 @@ udocker loads the following configuration files if they are present:
 * `UDOCKER_FAKECHROOT_EXPAND_SYMLINKS`: translate symbolic links in Fn modes
 * `UDOCKER_NOSYSCONF`: prevent loading of udocker system wide configuration
 
-## 4. Verbosity
+## 4. Automatic Execution Mode Setting
+
+The `UDOCKER_SET_EXECUTION_MODE` environment variable allows automatic setting
+of execution mode when running containers from images. When set, udocker will
+automatically create a container and set the execution mode before running,
+equivalent to running `create`, `setup --execmode`, and `run` commands in sequence.
+
+```bash
+export UDOCKER_SET_EXECUTION_MODE=F3
+udocker run quay.io/pacbio/hiphase:1.5.0_build1 hiphase --help
+```
+
+This is equivalent to:
+```bash
+udocker create --name=hiphase quay.io/pacbio/hiphase:1.5.0_build1
+udocker setup --execmode=F3 hiphase
+udocker run hiphase hiphase --help
+```
+
+## 5. Verbosity
 
 The verbosity level of udocker can be enforced. Removing banners and most
 messages can be achieved by executing with `UDOCKER_LOGLEVEL=2`:
@@ -66,7 +88,7 @@ Optionally invoke udocker with `--quiet` or `-q` to decrease verbosity.
 udocker --quiet run <container>
 ```
 
-## 5. Security
+## 6. Security
 
 udocker does not require any type of privileges nor the deployment of
 services by system administrators. It can be downloaded and executed
@@ -77,15 +99,15 @@ Most udocker execution modes do not provide process isolation features
 such as docker. Due to the lack of isolation udocker must not be run
 by privileged users.
 
-## 6. Troubleshooting
+## 7. Troubleshooting
 
 Invoke udocker with `-D` for debugging.
 
 ```bash
 udocker -D run <container>
 ```
 
-## 7. Documentation
+## 8. Documentation
 
 For Python 3:
 

docs/user_manual.md

@@ -619,6 +619,11 @@ within a container. Execution modes can be changed using the command
 `udocker setup --execmode=<mode> <container-id>` for more information
 on available modes and their characteristics see section 3.27.
 
+When running containers from images (using `udocker run REPO/IMAGE:TAG`),
+the execution mode can be automatically set using the environment variable
+`UDOCKER_SET_EXECUTION_MODE` or the configuration parameter `set_execution_mode`.
+This automatically creates a container and sets the execution mode before running.
+
 Options:
 
 * `--rm` delete the container after execution
@@ -677,6 +682,11 @@ udocker run fedora:29 cat /etc/redhat-release
 # calls to run only create a single container that is then reused.
 udocker run --name=F29 --pull=reuse fedora:29 cat /etc/redhat-release
 
+# Automatically set execution mode when running from images
+export UDOCKER_SET_EXECUTION_MODE=F3
+udocker run quay.io/pacbio/hiphase:1.5.0_build1 hiphase --help
+# This automatically creates a container and sets F3 execution mode
+
 # In this example the host /tmp is mapped to the container /tmp
 udocker run --volume=/tmp  myfed  /bin/bash
 
@@ -986,10 +996,25 @@ default modes:
 **P1**, **P2**, **F1**, **S1**, and **R1**. Changing the default execution
 mode can be useful if the default does not work as expected.
 
-Example:
+Additionally, udocker provides an automatic execution mode setting feature
+through the environment variable **UDOCKER_SET_EXECUTION_MODE** or the
+configuration parameter **set_execution_mode**. When set, this automatically
+creates a container and sets the execution mode before running when using
+`udocker run` with an image name, equivalent to running `create`,
+`setup --execmode`, and `run` commands in sequence.
+
+Examples:
 
 ```bash
 UDOCKER_DEFAULT_EXECUTION_MODE=P2 ./udocker run mycontainer /bin/ls
+
+# Automatically set execution mode when running from images
+export UDOCKER_SET_EXECUTION_MODE=F3
+udocker run quay.io/pacbio/hiphase:1.5.0_build1 hiphase --help
+# This is equivalent to:
+# udocker create --name=hiphase quay.io/pacbio/hiphase:1.5.0_build1
+# udocker setup --execmode=F3 hiphase
+# udocker run hiphase hiphase --help
 ```
 
 ### 3.28. tag

udocker/__init__.py

@@ -32,5 +32,5 @@
     "Singularity http://singularity.lbl.gov"
     ]
 __license__ = "Licensed under the Apache License, Version 2.0"
-__version__ = "1.3.17"
-__date__ = "2024"
+__version__ = "1.3.18"
+__date__ = "2025"

udocker/cli.py

@@ -810,6 +810,11 @@ def do_run(self, cmdp):
                     if not container_id:
                         Msg().err("Error: image or container not available")
                         return self.STATUS_ERROR
+                if Config.conf['set_execution_mode']:
+                    Msg().out("setting execmode: %s" % (Config.conf['set_execution_mode']))
+                    exec_mode = ExecutionMode(self.localrepo, container_id)
+                    if not exec_mode.set_mode(Config.conf['set_execution_mode'].upper(), False):
+                        return self.STATUS_ERROR
             if name and container_id:
                 if not self.localrepo.set_container_name(container_id, name):
                     if pull != "reuse":

udocker/config.py

@@ -75,6 +75,8 @@ class Config(object):
                                        'arm64': "P1", 'arm': "P2",
                                        'ppc64le': "R1", 'DEFAULT': "R1"}
 
+    conf['set_execution_mode'] = ""
+
     # PRoot override seccomp
     # conf['proot_noseccomp'] = True
     conf['proot_noseccomp'] = None
@@ -255,6 +257,9 @@ def _env_override(self):
         Config.conf['override_default_execution_mode'] = \
             os.getenv("UDOCKER_DEFAULT_EXECUTION_MODE",
                       Config.conf['override_default_execution_mode'])
+        Config.conf['set_execution_mode'] = \
+            os.getenv("UDOCKER_SET_EXECUTION_MODE",
+                      Config.conf['set_execution_mode'])
         Config.conf['fakechroot_so'] = \
             os.getenv("UDOCKER_FAKECHROOT_SO", Config.conf['fakechroot_so'])
         Config.conf['fakechroot_libc'] = \