From 2039f371b9402ee056615d6e65e48ae392619bff Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Tue, 21 Jan 2025 11:10:19 +0100
Subject: [PATCH 1/2] add missing imports

---
 nbs_tests/peptide/fragment.ipynb | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/nbs_tests/peptide/fragment.ipynb b/nbs_tests/peptide/fragment.ipynb
index a6cfe076..2030c753 100644
--- a/nbs_tests/peptide/fragment.ipynb
+++ b/nbs_tests/peptide/fragment.ipynb
@@ -33,7 +33,8 @@
     "from alphabase.peptide.fragment import get_charged_frag_types, parse_charged_frag_type, \\\n",
     "    create_fragment_mz_dataframe_by_sort_precursor, get_sliced_fragment_dataframe, update_sliced_fragment_dataframe, \\\n",
     "    create_fragment_mz_dataframe, flatten_fragments, remove_unused_fragments, join_left, calc_fragment_cardinality\n",
-    "from alphabase.peptide.precursor import update_precursor_mz "
+    "from alphabase.peptide.precursor import update_precursor_mz\n",
+    "from alphabase.peptide.fragment import FRAGMENT_TYPES, FragmentType, sort_charged_frag_types"
    ]
   },
   {
@@ -88,9 +89,7 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "assert sort_charged_frag_types(['b_modloss_z1','a_z1','b_z1','b_z2','b_modloss_z2','a_z2']) == ['a_z1','a_z2','b_z1','b_z2','b_modloss_z1','b_modloss_z2']"
-   ]
+   "source": "assert sort_charged_frag_types(['b_modloss_z1','a_z1','b_z1','b_z2','b_modloss_z2','a_z2']) == ['a_z1','a_z2','b_z1','b_z2','b_modloss_z1','b_modloss_z2']"
   },
   {
    "cell_type": "code",

From 3c8fa63a68e9ffed2a39aa8a21010d4d7b976817 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Tue, 21 Jan 2025 11:10:37 +0100
Subject: [PATCH 2/2] use requirements in CI

---
 .github/workflows/_run_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/_run_tests.yml b/.github/workflows/_run_tests.yml
index 6b313d63..2961ebb1 100644
--- a/.github/workflows/_run_tests.yml
+++ b/.github/workflows/_run_tests.yml
@@ -35,7 +35,7 @@ jobs:
       shell: bash -le {0}
       run: |
         conda activate alphabase
-        pip install pytest nbmake==1.5.3
+        pip install -r requirements/requirements_tests.txt
         conda deactivate
     - name: Run tests
       shell: bash -le {0}