From b82ed080066ca9876938cc47b68c2e68431d4458 Mon Sep 17 00:00:00 2001
From: ammarcsj <70114795+ammarcsj@users.noreply.github.com>
Date: Wed, 16 Oct 2024 16:06:15 +0200
Subject: [PATCH] change path finding

---
 .../run_pipeline_w_different_input_formats.ipynb   | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/tests/quicktests/run_pipeline_w_different_input_formats.ipynb b/tests/quicktests/run_pipeline_w_different_input_formats.ipynb
index 9def785..881b2df 100644
--- a/tests/quicktests/run_pipeline_w_different_input_formats.ipynb
+++ b/tests/quicktests/run_pipeline_w_different_input_formats.ipynb
@@ -8,18 +8,20 @@
    "source": [
     "import os\n",
     "import alphabase.test_data_downloader\n",
+    "from IPython import get_ipython\n",
     "\n",
-    "# Use the current working directory as a starting point\n",
-    "current_dir = os.getcwd()\n",
+    "# Get the directory of the current notebook\n",
+    "notebook_path = get_ipython().kernel.path\n",
+    "notebook_dir = os.path.dirname(notebook_path)\n",
     "\n",
-    "# Navigate up two levels to reach the project root\n",
-    "project_root = os.path.abspath(os.path.join(current_dir, '..', '..','..'))\n",
+    "# Navigate up three levels to reach the project root\n",
+    "project_root = os.path.abspath(os.path.join(notebook_dir, '..', '..'))\n",
     "\n",
     "output_dir = os.path.join(project_root, 'test_data', 'system_tests')\n",
     "\n",
     "os.makedirs(output_dir, exist_ok=True)\n",
     "# Now use the absolute path in the DataShareDownloader call\n",
-    "alphabase.test_data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/VJm70w0p2P86tE1\", output_dir=output_dir).download()"
+    "alphabase.test_data_downloader.DataShareDownloader(url=\"https://datashare.biochem.mpg.de/s/VJm70w0p2P86tE1\", output_dir=output_dir).download()\n"
    ]
   },
   {
@@ -28,7 +30,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "quicktest_folder_mq_peptides = \"../../test_data/system_tests/quicktests/mq_peptides\"\n",
+    "quicktest_folder_mq_peptides = f\"../../test_data/system_tests/quicktests/mq_peptides\"\n",
     "\n",
     "quicktest_folder_mq_evidence = \"../../test_data/system_tests/quicktests/mq_evidence\"\n",
     "\n",