Merge branch 'develop' into mock_pubmed_557

ISA-tools · Aug 27, 2024 · fc63569 · fc63569
2 parents a0adc99 + 00c2f63
commit fc63569
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diff --git a/.github/workflows/buildandtestpython.yml b/.github/workflows/buildandtestpython.yml
@@ -10,12 +10,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: [3.9, '3.10', '3.11', '3.12']
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Download Test Data

diff --git a/.github/workflows/pythonpublish.yml b/.github/workflows/pythonpublish.yml
@@ -8,9 +8,9 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

diff --git a/isa-cookbook/content/notebooks/ISA-json to ISA-Tab and back to ISA-json - roundtrip.ipynb b/isa-cookbook/content/notebooks/ISA-json to ISA-Tab and back to ISA-json - roundtrip.ipynb
diff --git a/...nt/notebooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_negative_hilic_metabolite_profiling.txt b/...nt/notebooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_negative_hilic_metabolite_profiling.txt
diff --git a/...ooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_negative_reverse-phase_metabolite_profiling.txt b/...ooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_negative_reverse-phase_metabolite_profiling.txt
diff --git a/...nt/notebooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_positive_hilic_metabolite_profiling.txt b/...nt/notebooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_positive_hilic_metabolite_profiling.txt
diff --git a/...ooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_positive_reverse-phase_metabolite_profiling.txt b/...ooks/MTBLS2746-QuickFix/a_MTBLS2746_LC-MS_positive_reverse-phase_metabolite_profiling.txt
diff --git a/isa-cookbook/content/notebooks/MTBLS2746-QuickFix/i_Investigation.txt b/isa-cookbook/content/notebooks/MTBLS2746-QuickFix/i_Investigation.txt
diff --git a/...books/MTBLS2746-QuickFix/m_MTBLS2746_LC-MS_negative_hilic_metabolite_profiling_v2_maf.tsv b/...books/MTBLS2746-QuickFix/m_MTBLS2746_LC-MS_negative_hilic_metabolite_profiling_v2_maf.tsv
@@ -0,0 +1,2 @@
+database_identifier	chemical_formula	smiles	inchi	metabolite_identification	mass_to_charge	fragmentation	modifications	charge	retention_time	taxid	species	database	database_version	reliability	uri	search_engine	search_engine_score	smallmolecule_abundance_sub	smallmolecule_abundance_stdev_sub	smallmolecule_abundance_std_error_sub
+0																				
diff --git a/...BLS2746-QuickFix/m_MTBLS2746_LC-MS_negative_reverse-phase_metabolite_profiling_v2_maf.tsv b/...BLS2746-QuickFix/m_MTBLS2746_LC-MS_negative_reverse-phase_metabolite_profiling_v2_maf.tsv
@@ -0,0 +1,2 @@
+database_identifier	chemical_formula	smiles	inchi	metabolite_identification	mass_to_charge	fragmentation	modifications	charge	retention_time	taxid	species	database	database_version	reliability	uri	search_engine	search_engine_score	smallmolecule_abundance_sub	smallmolecule_abundance_stdev_sub	smallmolecule_abundance_std_error_sub
+0																				
diff --git a/...books/MTBLS2746-QuickFix/m_MTBLS2746_LC-MS_positive_hilic_metabolite_profiling_v2_maf.tsv b/...books/MTBLS2746-QuickFix/m_MTBLS2746_LC-MS_positive_hilic_metabolite_profiling_v2_maf.tsv
@@ -0,0 +1,2 @@
+database_identifier	chemical_formula	smiles	inchi	metabolite_identification	mass_to_charge	fragmentation	modifications	charge	retention_time	taxid	species	database	database_version	reliability	uri	search_engine	search_engine_score	smallmolecule_abundance_sub	smallmolecule_abundance_stdev_sub	smallmolecule_abundance_std_error_sub
+0																				
diff --git a/...BLS2746-QuickFix/m_MTBLS2746_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsv b/...BLS2746-QuickFix/m_MTBLS2746_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsv
@@ -0,0 +1,2 @@
+database_identifier	chemical_formula	smiles	inchi	metabolite_identification	mass_to_charge	fragmentation	modifications	charge	retention_time	taxid	species	database	database_version	reliability	uri	search_engine	search_engine_score	smallmolecule_abundance_sub	smallmolecule_abundance_stdev_sub	smallmolecule_abundance_std_error_sub
+0																				
diff --git a/isa-cookbook/content/notebooks/MTBLS2746-QuickFix/s_MTBLS2746.txt b/isa-cookbook/content/notebooks/MTBLS2746-QuickFix/s_MTBLS2746.txt
diff --git a/...estigation-from-datascriptor-config-observational-variables-and-ontology-annotation.ipynb b/...estigation-from-datascriptor-config-observational-variables-and-ontology-annotation.ipynb
@@ -364,7 +364,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -378,7 +378,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.1"
+   "version": "3.9.0"
   }
  },
  "nbformat": 4,