From 5967586214b23d70dad11abd9cd27f78d3b8aa75 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Wed, 7 Aug 2024 06:09:09 +1000
Subject: [PATCH] fixed up imports

---
 tests/test_bet.py                     |  8 ++--
 tests/test_zip.py                     |  8 ++--
 tutorial/ais-pipelines-tutorial.ipynb | 58 ++++++++++++++++++++++++---
 3 files changed, 60 insertions(+), 14 deletions(-)

diff --git a/tests/test_bet.py b/tests/test_bet.py
index 9970f39..9309148 100644
--- a/tests/test_bet.py
+++ b/tests/test_bet.py
@@ -1,13 +1,13 @@
 from pathlib import Path
 import tempfile
-from arcana.common import Clinical
+from frametree.common import Clinical
 from fileformats.medimage import NiftiGz
-from arcana.common import DirTree
+from frametree.common import DirTree
 from arcana.testing.data.blueprint import (
     TestDatasetBlueprint,
     FileSetEntryBlueprint as FileBP,
 )
-from arcana.core.deploy.command import ContainerCommand
+from pydra2app.core.command import ContainerCommand
 from medimages4tests.mri.neuro.t1w import get_image
 
 
@@ -33,7 +33,7 @@
 saved_dataset = bp.make_dataset(DirTree(), dataset_id, name="", source_data=source_dir)
 
 command_spec = ContainerCommand(
-    task="arcana.common:shell",
+    task="common:shell",
     row_frequency=Clinical.session,
     inputs=[
         {
diff --git a/tests/test_zip.py b/tests/test_zip.py
index 329389b..56e48b4 100644
--- a/tests/test_zip.py
+++ b/tests/test_zip.py
@@ -4,13 +4,13 @@
 import functools
 from fileformats.generic import Directory
 from fileformats.application import Zip
-from arcana.common import DirTree
-from arcana.testing import TestDataSpace
-from arcana.testing.data.blueprint import (
+from frametree.common import DirTree
+from frametree.testing import TestDataSpace
+from frametree.testing.blueprint import (
     TestDatasetBlueprint,
     FileSetEntryBlueprint as FileBP,
 )
-from arcana.core.deploy.command import ContainerCommand
+from pydra2app.core.command import ContainerCommand
 
 
 bp = TestDatasetBlueprint(
diff --git a/tutorial/ais-pipelines-tutorial.ipynb b/tutorial/ais-pipelines-tutorial.ipynb
index 57643f4..834af7f 100644
--- a/tutorial/ais-pipelines-tutorial.ipynb
+++ b/tutorial/ais-pipelines-tutorial.ipynb
@@ -1244,7 +1244,35 @@
    "id": "779803ec-756d-4369-b763-3e1a90045fbc",
    "metadata": {},
    "source": [
-    "##"
+    "### Create a test pull-request on GitHub"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2ecf3933-1360-42a4-acf1-eacefea46502",
+   "metadata": {},
+   "source": [
+    "Commit and your changes"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 44,
+   "id": "686d7741-a77e-43da-b175-237f3ba9bef5",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[detached HEAD e6aff42] added specification for Freesurfer's mri_convert\n",
+      " 1 file changed, 32 insertions(+), 7 deletions(-)\n"
+     ]
+    }
+   ],
+   "source": [
+    "git commit -am\"added specification for Freesurfer's mri_convert\"\n",
+    "git push"
    ]
   },
   {
@@ -1252,12 +1280,12 @@
    "id": "dba5c217",
    "metadata": {},
    "source": [
-    "### Create a test pull-request on GitHub\n",
+    "Create the pull-request on GitHub\n",
     "\n",
     "1. Navigate to your fork of the AIS community pipelines repo, https://github.com/your-github-username/pipelines-community\n",
     "1. Select \"Pull requests\" in the top ribbon\n",
     "1. Click the \"New pull request\" button\n",
-    "1. Select \"base:main\" <- \"your-fork:my-mri-synthstrip\" from the drop-down lists\n",
+    "1. Select \"base:main\" <- \"your-fork:my-mri-convert\" from the drop-down lists\n",
     "1. Click \"Create pull request\"\n",
     "\n",
     "This will then start the process for the pipeline to be accepted and deployed\n",
@@ -1276,8 +1304,26 @@
    "metadata": {},
    "source": [
     "## Design your own pipeline\n",
-    "1. Create a new Git branch (`git checkout main; git checkout -b my-own-pipeline`)\n",
-    "1. Bootstrap your new specification\n",
+    "1. Create and switch to a new Git branch (you will notice that your mri-convert changes will disappear)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3fea2b35-755c-4bef-94b0-4434b40e5abb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "git checkout main\n",
+    "git checkout -b my-own-pipeline"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "030a88e8-dd59-4de3-8411-58b042135109",
+   "metadata": {},
+   "source": [
+    "2. Bootstrap your new specification\n",
     "1. Build your specifcation\n",
     "1. Test your specification\n",
     "1. Create a pull-request on GitHub to add your pipeline to the central repository, https://github.com/Australian-Imaging-Service/pipelines-community"
@@ -1286,7 +1332,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "dba95bec",
+   "id": "8672c17e-186a-409f-846f-220844c7eeb3",
    "metadata": {},
    "outputs": [],
    "source": []