check if osqp is there

.github/workflows/pythonpackage.yml

@@ -30,7 +30,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip cryptography
         pip install wheel numpy Cython
-        pip install biom-format
+        pip install biom-format highspy
     - name: Install MICOM
       run: pip install -e .
     - name: install CPLEX

micom/taxonomy.py

@@ -101,7 +101,9 @@ def rank_prefixes(manifest: pd.DataFrame) -> pd.Series:
         The detected prefix for each taxonomic rank in the manifest.
     """
     ranks = [c for c in manifest.columns if c.lower() in RANKS]
-    prefixes = pd.Series({r: manifest[r].str.extract(r"^([a-z]__)").iloc[0, 0] for r in ranks})
+    prefixes = pd.Series(
+        {r: manifest[r].str.extract(r"^([a-z]__)").iloc[0, 0] for r in ranks}
+    )
 
     return prefixes
 
@@ -131,9 +133,7 @@ def unify_rank_prefixes(taxonomy: pd.DataFrame, manifest: pd.DataFrame) -> pd.Da
     ranks = [c for c in taxonomy.columns if c.lower() in RANKS]
     if db_prefixes.isna().all():
         for r in ranks:
-            taxonomy[r] = taxonomy[r].str.replace(
-                r"^[a-z]__", "", regex=True
-            )
+            taxonomy[r] = taxonomy[r].str.replace(r"^[a-z]__", "", regex=True)
     else:
         for r in ranks:
             taxonomy[r] = db_prefixes[r] + taxonomy[r]

tests/test_osqp.py

@@ -4,6 +4,7 @@
 """
 
 from .fixtures import community
+import cobra.util.solver as su
 import micom.data as md
 from micom.workflows import (
     build,
@@ -17,6 +18,8 @@
 import pytest
 from pytest import approx
 
+pytestmark = pytest.mark.skipif("osqp" not in su.solvers)
+
 medium = load_qiime_medium(md.test_medium)
 db = md.test_db