Quit after command-line parses env var

.gitignore

@@ -56,3 +56,6 @@ testing/src/project_version.h
 .__tmp.log
 .check_syntax.tmp
 .check_syntax2.tmp
+*.venv
+__pycache__
+.DS_Store

core/command.h

@@ -24,6 +24,7 @@
 
 #include "app.h"
 #include "exec_version.h"
+#include "mrtrix.h"
 #ifdef MRTRIX_PROJECT
 namespace MR {
   namespace App {
@@ -98,6 +99,18 @@ int main (int cmdline_argc, char** cmdline_argv)
     ::MR::GUI::App app (cmdline_argc, cmdline_argv);
 #endif
     ::MR::App::parse ();
+
+    //ENVVAR name: MRTRIX_CLI_PARSE_ONLY
+    //ENVVAR Set the command to parse the provided inputs and then quit
+    //ENVVAR if it is 1. This can be used in the CI of wrapping code,
+    //ENVVAR such as the automatically generated Pydra interfaces
+    char* parse_only = std::getenv("MRTRIX_CLI_PARSE_ONLY");
+    if (parse_only && ::MR::to<int>(parse_only)) {
+      WARN(
+        "Quitting after parsing command-line arguments successfully because environment variable 'MRTRIX_CLI_PARSE_ONLY' is set to '1'"
+      );
+      return 0;
+    }
     run ();
   }
   catch (::MR::Exception& E) {

core/exception.h

@@ -68,11 +68,11 @@ namespace MR
    * debugging information; anything else: none. */
   extern void (*report_to_user_func) (const std::string& msg, int type);
 
-#define CONSOLE(msg) if (MR::App::log_level >= 1) report_to_user_func (msg, -1)
-#define FAIL(msg) if (MR::App::log_level >= 0) report_to_user_func (msg, 0)
-#define WARN(msg) if (MR::App::log_level >= 1) report_to_user_func (msg, 1)
-#define INFO(msg) if (MR::App::log_level >= 2) report_to_user_func (msg, 2)
-#define DEBUG(msg) if (MR::App::log_level >= 3) report_to_user_func (msg, 3)
+#define CONSOLE(msg) if (MR::App::log_level >= 1) MR::report_to_user_func (msg, -1)
+#define FAIL(msg) if (MR::App::log_level >= 0) MR::report_to_user_func (msg, 0)
+#define WARN(msg) if (MR::App::log_level >= 1) MR::report_to_user_func (msg, 1)
+#define INFO(msg) if (MR::App::log_level >= 2) MR::report_to_user_func (msg, 2)
+#define DEBUG(msg) if (MR::App::log_level >= 3) MR::report_to_user_func (msg, 3)
 
 
 

docs/reference/environment_variables.rst

@@ -24,6 +24,12 @@ List of MRtrix3 environment variables
      when reading DICOM data, match the StudyName entry against
      the string provided
 
+.. envvar:: MRTRIX_CLI_PARSE_ONLY
+
+     Set the command to parse the provided inputs and then quit
+     if it is 1. This can be used in the CI of wrapping code,
+     such as the automatically generated Pydra interfaces
+
 .. envvar:: MRTRIX_CONFIGFILE
 
      This can be used to set the location of the system-wide

lib/mrtrix3/app.py

@@ -192,6 +192,15 @@ def _execute(module): #pylint: disable=unused-variable
   CMDLINE.print_citation_warning()
 
   return_code = 0
+
+  cli_parse_only = os.getenv("MRTRIX_CLI_PARSE_ONLY")
+  if cli_parse_only == "1":
+    warn(
+      "Quitting after parsing command-line arguments successfully because "
+      "environment variable 'MRTRIX_CLI_PARSE_ONLY' is set to '1'"
+    )
+    sys.exit(return_code)
+
   try:
     module.execute()
   except (run.MRtrixCmdError, run.MRtrixFnError) as exception:

pydra/fileformats-mrtrix3/fileformats/mrtrix3/_version.py

@@ -0,0 +1,4 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+__version__ = version = '3.0.5.dev628+g49e520c06.d20230822'
+__version_tuple__ = version_tuple = (3, 0, 5, 'dev628', 'g49e520c06.d20230822')

pydra/src/pydra/tasks/mrtrix3/_version.py

@@ -0,0 +1,4 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+__version__ = version = '3.0.5.dev589+g9e2806609.d20230817'
+__version_tuple__ = version_tuple = (3, 0, 5, 'dev589', 'g9e2806609.d20230817')

pydra/src/pydra/tasks/mrtrix3/v3_0/fivetissuetype2gmwmi.py

@@ -0,0 +1,161 @@
+import typing as ty
+from pathlib import Path  # noqa: F401
+from fileformats.generic import File, Directory  # noqa: F401
+from fileformats.mrtrix3 import TrackFile  # noqa: F401
+from pydra import ShellCommandTask
+from pydra.engine import specs
+from pydra.tasks.mrtrix3.fileformats import ImageIn, ImageOut  # noqa: F401
+
+
+input_fields = [
+    # Arguments
+    (
+        "in_5tt",
+        ImageIn,
+        {
+            "argstr": "",
+            "position": 0,
+            "help_string": """the input 5TT segmented anatomical image""",
+            "mandatory": True,
+        },
+    ),
+    (
+        "mask_out",
+        Path,
+        {
+            "argstr": "",
+            "position": 1,
+            "output_file_template": "mask_out.mif",
+            "help_string": """the output mask image""",
+        },
+    ),
+    (
+        "mask_in",
+        ImageIn,
+        {
+            "argstr": "-mask_in",
+            "help_string": """Filter an input mask image according to those voxels that lie upon the grey matter - white matter boundary. If no input mask is provided, the output will be a whole-brain mask image calculated using the anatomical image only.""",
+        },
+    ),
+    # Standard options
+    (
+        "info",
+        bool,
+        {
+            "argstr": "-info",
+            "help_string": """display information messages.""",
+        },
+    ),
+    (
+        "quiet",
+        bool,
+        {
+            "argstr": "-quiet",
+            "help_string": """do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.""",
+        },
+    ),
+    (
+        "debug",
+        bool,
+        {
+            "argstr": "-debug",
+            "help_string": """display debugging messages.""",
+        },
+    ),
+    (
+        "force",
+        bool,
+        {
+            "argstr": "-force",
+            "help_string": """force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).""",
+        },
+    ),
+    (
+        "nthreads",
+        int,
+        {
+            "argstr": "-nthreads",
+            "help_string": """use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).""",
+        },
+    ),
+    (
+        "config",
+        specs.MultiInputObj[ty.Tuple[str, str]],
+        {
+            "argstr": "-config",
+            "help_string": """temporarily set the value of an MRtrix config file entry.""",
+        },
+    ),
+    (
+        "help",
+        bool,
+        {
+            "argstr": "-help",
+            "help_string": """display this information page and exit.""",
+        },
+    ),
+    (
+        "version",
+        bool,
+        {
+            "argstr": "-version",
+            "help_string": """display version information and exit.""",
+        },
+    ),
+]
+
+fivetissuetype2gmwmi_input_spec = specs.SpecInfo(
+    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
+)
+
+
+output_fields = [
+    (
+        "mask_out",
+        ImageOut,
+        {
+            "help_string": """the output mask image""",
+        },
+    ),
+]
+fivetissuetype2gmwmi_output_spec = specs.SpecInfo(
+    name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
+)
+
+
+class fivetissuetype2gmwmi(ShellCommandTask):
+    """
+        References
+        ----------
+
+            Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. Anatomically-constrained tractography:Improved diffusion MRI streamlines tractography through effective use of anatomical information. NeuroImage, 2012, 62, 1924-1938
+
+            Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137
+
+
+        MRtrix
+        ------
+
+            Version:3.0.4-624-g4fb87551-dirty, built Aug 21 2023
+
+            Author: Robert E. Smith ([email protected])
+
+            Copyright: Copyright (c) 2008-2023 the MRtrix3 contributors.
+
+    This Source Code Form is subject to the terms of the Mozilla Public
+    License, v. 2.0. If a copy of the MPL was not distributed with this
+    file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+    Covered Software is provided under this License on an "as is"
+    basis, without warranty of any kind, either expressed, implied, or
+    statutory, including, without limitation, warranties that the
+    Covered Software is free of defects, merchantable, fit for a
+    particular purpose or non-infringing.
+    See the Mozilla Public License v. 2.0 for more details.
+
+    For more details, see http://www.mrtrix.org/.
+    """
+
+    executable = "fivetissuetype2gmwmi"
+    input_spec = fivetissuetype2gmwmi_input_spec
+    output_spec = fivetissuetype2gmwmi_output_spec