Merge pull request #283 from MannLabs/fix_tests

Fix tests
MannLabs · Jan 21, 2025 · 57e58ab · 57e58ab
2 parents c1efa4b + 3c8fa63
commit 57e58ab
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git 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}

diff --git 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",