niwrap-mrtrix3tissue 0.6.2__tar.gz → 0.7.0__tar.gz

niwrap_mrtrix3tissue-0.7.0/PKG-INFO

@@ -0,0 +1,8 @@
+Metadata-Version: 2.4
+Name: niwrap-mrtrix3tissue
+Version: 0.7.0
+Summary: Neuroimaging wrappers.
+Author: CMI DAIR
+License-Expression: MIT
+Requires-Dist: styxdefs>=0.5.0,<0.6.0
+Requires-Python: >=3.10

niwrap_mrtrix3tissue-0.7.0/pyproject.toml

@@ -0,0 +1,17 @@
+[project]
+name = "niwrap_mrtrix3tissue"
+version = "0.7.0"
+description = "Neuroimaging wrappers."
+license = "MIT"
+authors = [{ name = "CMI DAIR" }]
+requires-python = ">=3.10"
+dependencies = [
+    "styxdefs>=0.5.0,<0.6.0"
+]
+
+[tool.uv.build-backend]
+module-name = "niwrap_mrtrix3tissue.mrtrix3tissue"
+
+[build-system]
+requires = ["uv_build>=0.8.13,<0.9.0"]
+build-backend = "uv_build"

niwrap_mrtrix3tissue-0.7.0/src/niwrap_mrtrix3tissue/mrtrix3tissue/__init__.py

@@ -0,0 +1,32 @@
+"""
+MRTrix3Tissue
+
+MRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for
+3-Tissue CSD modelling and analysis to a complete version of the MRtrix3
+software.
+
+Author: MRTrix3Tissue Developers
+
+URL: https://3tissue.github.io/
+"""
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+from .ss3t_csd_beta1 import *
+from styxdefs import Runner as _Runner
+
+
+def execute(
+    params: dict,
+    runner: _Runner | None = None,
+) -> None:
+    """
+    Run a command in this package dynamically from a params object.
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    """
+    return {
+        "mrtrix3tissue/ss3t_csd_beta1": ss3t_csd_beta1_execute,
+    }[params["@type"]](params, runner)

{niwrap_mrtrix3tissue-0.6.2 → niwrap_mrtrix3tissue-0.7.0}/src/niwrap_mrtrix3tissue/mrtrix3tissue/ss3t_csd_beta1.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SS3T_CSD_BETA1_METADATA = Metadata(
-    id="02df08185e6be9ec2c2813ee30e45a9daebade1a.boutiques",
+    id="1232a653007a6a29f9cc9f7f319bd002a791411a.boutiques",
     name="ss3t_csd_beta1",
     package="mrtrix3tissue",
     container_image_tag="brainlife/3tissue:5.2.8",
@@ -14,21 +14,47 @@ SS3T_CSD_BETA1_METADATA = Metadata(
 
 
 Ss3tCsdBeta1ConfigParameters = typing.TypedDict('Ss3tCsdBeta1ConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Ss3tCsdBeta1ConfigParametersTagged = typing.TypedDict('Ss3tCsdBeta1ConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Ss3tCsdBeta1ResponseOdfParameters = typing.TypedDict('Ss3tCsdBeta1ResponseOdfParameters', {
-    "__STYXTYPE__": typing.Literal["response_odf"],
+    "@type": typing.NotRequired[typing.Literal["response_odf"]],
+    "response": InputPathType,
+    "odf": str,
+})
+Ss3tCsdBeta1ResponseOdfParametersTagged = typing.TypedDict('Ss3tCsdBeta1ResponseOdfParametersTagged', {
+    "@type": typing.Literal["response_odf"],
     "response": InputPathType,
     "odf": str,
 })
 
 
 Ss3tCsdBeta1Parameters = typing.TypedDict('Ss3tCsdBeta1Parameters', {
-    "__STYXTYPE__": typing.Literal["ss3t_csd_beta1"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix3tissue/ss3t_csd_beta1"]],
+    "mask": typing.NotRequired[InputPathType | None],
+    "bzero_pct": typing.NotRequired[float | None],
+    "niter": typing.NotRequired[int | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Ss3tCsdBeta1ConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "dwi": InputPathType,
+    "response_odf": list[Ss3tCsdBeta1ResponseOdfParameters],
+})
+Ss3tCsdBeta1ParametersTagged = typing.TypedDict('Ss3tCsdBeta1ParametersTagged', {
+    "@type": typing.Literal["mrtrix3tissue/ss3t_csd_beta1"],
     "mask": typing.NotRequired[InputPathType | None],
     "bzero_pct": typing.NotRequired[float | None],
     "niter": typing.NotRequired[int | None],
@@ -43,47 +69,12 @@ Ss3tCsdBeta1Parameters = typing.TypedDict('Ss3tCsdBeta1Parameters', {
     "dwi": InputPathType,
     "response_odf": list[Ss3tCsdBeta1ResponseOdfParameters],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "ss3t_csd_beta1": ss3t_csd_beta1_cargs,
-        "config": ss3t_csd_beta1_config_cargs,
-        "response_odf": ss3t_csd_beta1_response_odf_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "ss3t_csd_beta1": ss3t_csd_beta1_outputs,
-        "response_odf": ss3t_csd_beta1_response_odf_outputs,
-    }.get(t)
 
 
 def ss3t_csd_beta1_config_params(
     key: str,
     value: str,
-) -> Ss3tCsdBeta1ConfigParameters:
+) -> Ss3tCsdBeta1ConfigParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +85,7 @@ def ss3t_csd_beta1_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -116,8 +107,8 @@ def ss3t_csd_beta1_config_cargs(
     """
     cargs = []
     cargs.append("-config")
-    cargs.append(params.get("key"))
-    cargs.append(params.get("value"))
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
     return cargs
 
 
@@ -134,7 +125,7 @@ class Ss3tCsdBeta1ResponseOdfOutputs(typing.NamedTuple):
 def ss3t_csd_beta1_response_odf_params(
     response: InputPathType,
     odf: str,
-) -> Ss3tCsdBeta1ResponseOdfParameters:
+) -> Ss3tCsdBeta1ResponseOdfParametersTagged:
     """
     Build parameters.
     
@@ -145,7 +136,7 @@ def ss3t_csd_beta1_response_odf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "response_odf",
+        "@type": "response_odf",
         "response": response,
         "odf": odf,
     }
@@ -166,8 +157,8 @@ def ss3t_csd_beta1_response_odf_cargs(
         Command-line arguments.
     """
     cargs = []
-    cargs.append(execution.input_file(params.get("response")))
-    cargs.append(params.get("odf"))
+    cargs.append(execution.input_file(params.get("response", None)))
+    cargs.append(params.get("odf", None))
     return cargs
 
 
@@ -186,14 +177,14 @@ def ss3t_csd_beta1_response_odf_outputs(
     """
     ret = Ss3tCsdBeta1ResponseOdfOutputs(
         root=execution.output_file("."),
-        odf=execution.output_file(params.get("odf")),
+        odf=execution.output_file(params.get("odf", None)),
     )
     return ret
 
 
 class Ss3tCsdBeta1Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `ss3t_csd_beta1(...)`.
+    Output object returned when calling `Ss3tCsdBeta1Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -216,7 +207,7 @@ def ss3t_csd_beta1_params(
     config: list[Ss3tCsdBeta1ConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Ss3tCsdBeta1Parameters:
+) -> Ss3tCsdBeta1ParametersTagged:
     """
     Build parameters.
     
@@ -246,7 +237,7 @@ def ss3t_csd_beta1_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ss3t_csd_beta1",
+        "@type": "mrtrix3tissue/ss3t_csd_beta1",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -284,42 +275,42 @@ def ss3t_csd_beta1_cargs(
     """
     cargs = []
     cargs.append("ss3t_csd_beta1")
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("bzero_pct") is not None:
+    if params.get("bzero_pct", None) is not None:
         cargs.extend([
             "-bzero_pct",
-            str(params.get("bzero_pct"))
+            str(params.get("bzero_pct", None))
         ])
-    if params.get("niter") is not None:
+    if params.get("niter", None) is not None:
         cargs.extend([
             "-niter",
-            str(params.get("niter"))
+            str(params.get("niter", None))
         ])
-    if params.get("info"):
+    if params.get("info", False):
         cargs.append("-info")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("nthreads") is not None:
+    if params.get("nthreads", None) is not None:
         cargs.extend([
             "-nthreads",
-            str(params.get("nthreads"))
+            str(params.get("nthreads", None))
         ])
-    if params.get("config") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
-    if params.get("help"):
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [ss3t_csd_beta1_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    cargs.append(execution.input_file(params.get("dwi")))
-    cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("response_odf")] for a in c])
+    cargs.append(execution.input_file(params.get("dwi", None)))
+    cargs.extend([a for c in [ss3t_csd_beta1_response_odf_cargs(s, execution) for s in params.get("response_odf", None)] for a in c])
     return cargs
 
 
@@ -338,16 +329,18 @@ def ss3t_csd_beta1_outputs(
     """
     ret = Ss3tCsdBeta1Outputs(
         root=execution.output_file("."),
-        response_odf=[dyn_outputs(i["__STYXTYPE__"])(i, execution) if dyn_outputs(i["__STYXTYPE__"]) else None for i in params.get("response_odf")],
+        response_odf=[ss3t_csd_beta1_response_odf_outputs(i, execution) if ss3t_csd_beta1_response_odf_outputs else None for i in params.get("response_odf")],
     )
     return ret
 
 
 def ss3t_csd_beta1_execute(
     params: Ss3tCsdBeta1Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Ss3tCsdBeta1Outputs:
     """
+    ss3t_csd_beta1
+    
     SS3T-CSD: beta 1 implementation
     
     * Dhollander, T. & Connelly, A. A novel iterative approach to reap the
@@ -360,10 +353,12 @@ def ss3t_csd_beta1_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Ss3tCsdBeta1Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SS3T_CSD_BETA1_METADATA)
     params = execution.params(params)
     cargs = ss3t_csd_beta1_cargs(params, execution)
     ret = ss3t_csd_beta1_outputs(params, execution)
@@ -388,6 +383,8 @@ def ss3t_csd_beta1(
     runner: Runner | None = None,
 ) -> Ss3tCsdBeta1Outputs:
     """
+    ss3t_csd_beta1
+    
     SS3T-CSD: beta 1 implementation
     
     * Dhollander, T. & Connelly, A. A novel iterative approach to reap the
@@ -424,8 +421,6 @@ def ss3t_csd_beta1(
     Returns:
         NamedTuple of outputs (described in `Ss3tCsdBeta1Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SS3T_CSD_BETA1_METADATA)
     params = ss3t_csd_beta1_params(
         mask=mask,
         bzero_pct=bzero_pct,
@@ -441,18 +436,16 @@ def ss3t_csd_beta1(
         dwi=dwi,
         response_odf=response_odf,
     )
-    return ss3t_csd_beta1_execute(params, execution)
+    return ss3t_csd_beta1_execute(params, runner)
 
 
 __all__ = [
     "SS3T_CSD_BETA1_METADATA",
-    "Ss3tCsdBeta1ConfigParameters",
     "Ss3tCsdBeta1Outputs",
-    "Ss3tCsdBeta1Parameters",
     "Ss3tCsdBeta1ResponseOdfOutputs",
-    "Ss3tCsdBeta1ResponseOdfParameters",
     "ss3t_csd_beta1",
     "ss3t_csd_beta1_config_params",
+    "ss3t_csd_beta1_execute",
     "ss3t_csd_beta1_params",
     "ss3t_csd_beta1_response_odf_params",
 ]

niwrap_mrtrix3tissue-0.6.2/.gitignore

@@ -1,301 +0,0 @@
-# NODE #
-
-# Logs
-logs
-*.log
-npm-debug.log*
-yarn-debug.log*
-yarn-error.log*
-lerna-debug.log*
-.pnpm-debug.log*
-
-# Diagnostic reports (https://nodejs.org/api/report.html)
-report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
-
-# Runtime data
-pids
-*.pid
-*.seed
-*.pid.lock
-
-# Directory for instrumented libs generated by jscoverage/JSCover
-lib-cov
-
-# Coverage directory used by tools like istanbul
-coverage
-*.lcov
-
-# nyc test coverage
-.nyc_output
-
-# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
-.grunt
-
-# Bower dependency directory (https://bower.io/)
-bower_components
-
-# node-waf configuration
-.lock-wscript
-
-# Compiled binary addons (https://nodejs.org/api/addons.html)
-build/Release
-
-# Dependency directories
-node_modules/
-jspm_packages/
-
-# Snowpack dependency directory (https://snowpack.dev/)
-web_modules/
-
-# TypeScript cache
-*.tsbuildinfo
-
-# Optional npm cache directory
-.npm
-
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-.eslintcache
-
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-.stylelintcache
-
-# Microbundle cache
-.rpt2_cache/
-.rts2_cache_cjs/
-.rts2_cache_es/
-.rts2_cache_umd/
-
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-.node_repl_history
-
-# Output of 'npm pack'
-*.tgz
-
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-.yarn-integrity
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-# https://nextjs.org/blog/next-9-1#public-directory-support
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-.temp
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-
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-.fusebox/
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-.dynamodb/
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-.tern-port
-
-# Stores VSCode versions used for testing VSCode extensions
-.vscode-test
-
-# yarn v2
-.yarn/cache
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-
-# PYTHON #
-
-# Byte-compiled / optimized / DLL files
-__pycache__/
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-
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-*.so
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-MANIFEST
-
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-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
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-#   For a library or package, you might want to ignore these files since the code is
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-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
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-#   in version control.
-#   https://pdm.fming.dev/#use-with-ide
-.pdm.toml
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
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-
-# SageMath parsed files
-*.sage.py
-
-# Environments
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-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
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-
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-/local_scripts
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niwrap_mrtrix3tissue-0.6.2/PKG-INFO

@@ -1,8 +0,0 @@
-Metadata-Version: 2.4
-Name: niwrap_mrtrix3tissue
-Version: 0.6.2
-Summary: NiWrap wrappers for MRTrix3Tissue.
-Author-email: CMI DAIR <dair@childmind.org>
-License-Expression: LGPL-2.1
-Requires-Python: >=3.10
-Requires-Dist: styxdefs~=0.5.0

niwrap_mrtrix3tissue-0.6.2/README.md

@@ -1,7 +0,0 @@
-# NiWrap wrappers for [MRTrix3Tissue](https://3tissue.github.io/)
-
-MRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for 3-Tissue CSD modelling and analysis to a complete version of the MRtrix3 software.
-
-MRTrix3Tissue is made by MRTrix3Tissue Developers.
-
-This package contains wrappers only and has no affiliation with the original authors.

niwrap_mrtrix3tissue-0.6.2/pyproject.toml

@@ -1,17 +0,0 @@
-[project]
-name = "niwrap_mrtrix3tissue"
-version = "0.6.2"
-description = "NiWrap wrappers for MRTrix3Tissue."
-license = "LGPL-2.1"
-authors = [{ name = "CMI DAIR", email = "dair@childmind.org" }]
-requires-python = ">=3.10"
-dependencies = [
-    "styxdefs~=0.5.0"
-]
-
-[tool.hatch.build.targets.wheel]
-packages = ["src/niwrap_mrtrix3tissue"]
-
-[build-system]
-requires = ["hatchling"]
-build-backend = "hatchling.build"

niwrap_mrtrix3tissue-0.6.2/src/niwrap_mrtrix3tissue/mrtrix3tissue/__init__.py

@@ -1,13 +0,0 @@
-"""
-MRTrix3Tissue
-
-MRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for
-3-Tissue CSD modelling and analysis to a complete version of the MRtrix3
-software.
-
-URL: https://3tissue.github.io/
-"""
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-from .ss3t_csd_beta1 import *