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} 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",