fixed mrtrix import

Author: tclose

new-docs/source/tutorial/advanced-execution.ipynb

@@ -41,18 +41,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "ename": "ImportError",
-     "evalue": "cannot import name 'MrGrid' from 'pydra.tasks.mrtrix3' (/Users/tclose/.pyenv/versions/3.12.5/envs/wf12/lib/python3.12/site-packages/pydra/tasks/mrtrix3/__init__.py)",
+     "evalue": "cannot import name 'ShellCommandTask' from 'pydra.engine' (/Users/tclose/git/workflows/pydra/pydra/engine/__init__.py)",
      "output_type": "error",
      "traceback": [
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[2], line 5\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfileformats\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmedimage\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Nifti\n\u001b[1;32m      4\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpydra\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mengine\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01msubmitter\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Submitter\n\u001b[0;32m----> 5\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpydra\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mtasks\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmrtrix3\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m MrGrid\n\u001b[1;32m      7\u001b[0m \u001b[38;5;66;03m# Make directory filled with nifti files\u001b[39;00m\n\u001b[1;32m      8\u001b[0m test_dir \u001b[38;5;241m=\u001b[39m Path(tempfile\u001b[38;5;241m.\u001b[39mmkdtemp())\n",
-      "\u001b[0;31mImportError\u001b[0m: cannot import name 'MrGrid' from 'pydra.tasks.mrtrix3' (/Users/tclose/.pyenv/versions/3.12.5/envs/wf12/lib/python3.12/site-packages/pydra/tasks/mrtrix3/__init__.py)"
+      "Cell \u001b[0;32mIn[4], line 5\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfileformats\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmedimage\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Nifti\n\u001b[1;32m      4\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpydra\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mengine\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01msubmitter\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Submitter\n\u001b[0;32m----> 5\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpydra\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mtasks\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmrtrix3\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mv3_0\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m MrGrid\n\u001b[1;32m      7\u001b[0m \u001b[38;5;66;03m# Make directory filled with nifti files\u001b[39;00m\n\u001b[1;32m      8\u001b[0m test_dir \u001b[38;5;241m=\u001b[39m Path(tempfile\u001b[38;5;241m.\u001b[39mmkdtemp())\n",
+      "File \u001b[0;32m~/.pyenv/versions/3.12.5/envs/wf12/lib/python3.12/site-packages/pydra/tasks/mrtrix3/v3_0/__init__.py:3\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;66;03m# Auto-generated, do not edit\u001b[39;00m\n\u001b[0;32m----> 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mfivett2gmwmi_\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Fivett2Gmwmi\n\u001b[1;32m      4\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mfivett2vis_\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Fivett2Vis\n\u001b[1;32m      5\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mfivettcheck_\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m FivettCheck\n",
+      "File \u001b[0;32m~/.pyenv/versions/3.12.5/envs/wf12/lib/python3.12/site-packages/pydra/tasks/mrtrix3/v3_0/fivett2gmwmi_.py:7\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfileformats\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mgeneric\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m File, Directory  \u001b[38;5;66;03m# noqa: F401\u001b[39;00m\n\u001b[1;32m      6\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mfileformats\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmedimage_mrtrix3\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m ImageIn, ImageOut, Tracks  \u001b[38;5;66;03m# noqa: F401\u001b[39;00m\n\u001b[0;32m----> 7\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpydra\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mengine\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m specs, ShellCommandTask\n\u001b[1;32m     10\u001b[0m input_fields \u001b[38;5;241m=\u001b[39m [\n\u001b[1;32m     11\u001b[0m     \u001b[38;5;66;03m# Arguments\u001b[39;00m\n\u001b[1;32m     12\u001b[0m     (\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    104\u001b[0m     ),\n\u001b[1;32m    105\u001b[0m ]\n\u001b[1;32m    107\u001b[0m Fivett2GmwmiInputSpec \u001b[38;5;241m=\u001b[39m specs\u001b[38;5;241m.\u001b[39mSpecInfo(\n\u001b[1;32m    108\u001b[0m     name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFivett2GmwmiInput\u001b[39m\u001b[38;5;124m\"\u001b[39m, fields\u001b[38;5;241m=\u001b[39minput_fields, bases\u001b[38;5;241m=\u001b[39m(specs\u001b[38;5;241m.\u001b[39mShellSpec,)\n\u001b[1;32m    109\u001b[0m )\n",
+      "\u001b[0;31mImportError\u001b[0m: cannot import name 'ShellCommandTask' from 'pydra.engine' (/Users/tclose/git/workflows/pydra/pydra/engine/__init__.py)"
      ]
     }
    ],
@@ -61,7 +63,7 @@
     "import tempfile\n",
     "from fileformats.medimage import Nifti\n",
     "from pydra.engine.submitter import Submitter\n",
-    "from pydra.tasks.mrtrix3 import MrGrid\n",
+    "from pydra.tasks.mrtrix3.v3_0 import MrGrid\n",
     "\n",
     "# Make directory filled with nifti files\n",
     "test_dir = Path(tempfile.mkdtemp())\n",
@@ -209,7 +211,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Provenance\n",
+    "## Provenance and auditing\n",
     "\n",
     "Work in progress..."
    ]

new-docs/source/tutorial/getting-started.ipynb

@@ -146,7 +146,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pydra.tasks.mrtrix3 import MrGrid\n",
+    "from pydra.tasks.mrtrix3.v3_0 import MrGrid\n",
     "\n",
     "# Instantiate the task definition, \"splitting\" over all NIfTI files in the test directory\n",
     "mrgrid = MrGrid(voxel=0.5).split(input=nifti_dir.iterdir())\n",

pyproject.toml

@@ -52,6 +52,7 @@ doc = [
     "pandoc",
     "numpy",
     "scipy",
+    "pydra-mrtrix",
     "sphinx_rtd_theme",
     "sphinx-click",
     "sphinxcontrib-apidoc ~=0.3.0",