Merge pull request #43 from MetaSys-LISBP/master

Get dev uptodate
MetaSys-LISBP · Jan 21, 2025 · 03bc4c6 · 03bc4c6
2 parents b855308 + 6356c13
commit 03bc4c6
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Showing 2 changed files with 26 additions and 9 deletions.
diff --git a/.github/workflows/test_suite.yml b/.github/workflows/test_suite.yml
@@ -15,19 +15,36 @@ jobs:
     runs-on: ${{ matrix.os}}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-latest, windows-latest]
         python-version: [ '3.8', '3.9', '3.10', '3.11']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{matrix.python-version}}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{matrix.python-version}}
           architecture: x64
       - name: Install Dependencies
         run:
-          python -m pip install --upgrade pip
+          python -m pip install --upgrade pip &&
+          pip install tox tox-gh-actions
+      - name: Test with tox
+        run: tox
+# We test macos differently because of new architecture of Apple Silicon processors.
+# Details here: https://github.com/actions/setup-python/issues/948
+  test_macos_latest:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          architecture: x64
+      - name: Install Dependencies
+        run:
+          python -m pip install --upgrade pip &&
           pip install tox tox-gh-actions
       - name: Test with tox
         run: tox
diff --git a/isocor/ui/isocorcli.py b/isocor/ui/isocorcli.py
@@ -2,6 +2,7 @@
 import isocor as hr
 import isocor.ui.isocordb
 import pandas as pd
+import numpy as np
 import io
 import logging
 from pathlib import Path
@@ -148,7 +149,6 @@ def process(args):
             dictMetabolites[label] = None
             errors['labels'] = errors['labels'] + [label]
             logger.error("cannot construct {}: {}".format(label, err))
-            sys.exit(2)
 
     logger.info('------------------------------------------------')
     logger.info('Correcting raw MS data...')
@@ -170,15 +170,15 @@ def process(args):
                     logger.info("{} - {}: processed".format(serie[0], label))
                 except Exception as err:
                     isotopic_inchi = ['']*len(serie[1])
-                    valuesCorrected = ([pd.np.nan]*len(serie[1]), [pd.np.nan]
-                                       * len(serie[1]), [pd.np.nan]*len(serie[1]), pd.np.nan)
+                    valuesCorrected = ([np.nan]*len(serie[1]), [np.nan]
+                                       * len(serie[1]), [np.nan]*len(serie[1]), np.nan)
                     logger.error("{} - {}: {}".format(serie[0], label, err))
                     errors['measurements'] = errors['measurements'] + \
                         ["{} - {}".format(serie[0], label)]
             else:
                 isotopic_inchi = ['']*len(serie[1])
-                valuesCorrected = ([pd.np.nan]*len(serie[1]), [pd.np.nan]
-                                   * len(serie[1]), [pd.np.nan]*len(serie[1]), pd.np.nan)
+                valuesCorrected = ([np.nan]*len(serie[1]), [np.nan]
+                                   * len(serie[1]), [np.nan]*len(serie[1]), np.nan)
                 errors['measurements'] = errors['measurements'] + \
                     ["{} - {}".format(serie[0], label)]
                 logger.error(