catch import errors

.github/workflows/test.yaml

@@ -52,7 +52,7 @@ jobs:
           python -m pip install --upgrade pip wheel
       - name: Install dependencies
         run: |
-          pip install ${{ matrix.pip-flags }} ".[dev,test,rpack,dandelion,diversity]"
+          pip install ${{ matrix.pip-flags }} ".[dev,test,rpack,dandelion,diversity,parasail]"
       - name: Test
         env:
           MPLBACKEND: agg

CHANGELOG.md

@@ -19,7 +19,8 @@ and this project adheres to [Semantic Versioning][].
 ### Other changes
 
 -   Make `parasail` an optional dependency since it is hard to install it on ARM CPUs. `TCRdist` is now the
-    recommended default distance metric which is much faster than parasail-based pairwise sequence alignments.
+    recommended default distance metric which is much faster than parasail-based pairwise sequence alignments while
+    providing very similar results ([#547](https://github.com/scverse/scirpy/pull/547)).
 
 ## v0.17.2
 

src/scirpy/ir_dist/metrics.py

@@ -1039,7 +1039,13 @@ def __init__(
         self.gap_extend = gap_extend
 
     def _compute_block(self, seqs1, seqs2, origin):
-        import parasail
+        try:
+            import parasail
+        except ImportError:
+            raise ImportError(
+                "Using the alignment distance requires the installation of `parasail`. "
+                "You can install it with `pip install parasail`."
+            ) from None
 
         subst_mat = parasail.Matrix(self.subst_mat)
         origin_row, origin_col = origin
@@ -1071,7 +1077,13 @@ def _self_alignment_scores(self, seqs: Sequence) -> dict:
         """Calculate self-alignments. We need them as reference values
         to turn scores into dists
         """
-        import parasail
+        try:
+            import parasail
+        except ImportError:
+            raise ImportError(
+                "Using the alignment distance requires the installation of `parasail`. "
+                "You can install it with `pip install parasail`."
+            ) from None
 
         return np.fromiter(
             (
@@ -1218,7 +1230,13 @@ def __init__(
         self.estimated_penalty = estimated_penalty if estimated_penalty is not None else penalty_dict[subst_mat]
 
     def _compute_block(self, seqs1, seqs2, origin):
-        import parasail
+        try:
+            import parasail
+        except ImportError:
+            raise ImportError(
+                "Using the alignment distance requires the installation of `parasail`. "
+                "You can install it with `pip install parasail`."
+            ) from None
 
         subst_mat = parasail.Matrix(self.subst_mat)
         origin_row, origin_col = origin
@@ -1267,7 +1285,13 @@ def _self_alignment_scores(self, seqs: Sequence) -> dict:
         """Calculate self-alignments. We need them as reference values
         to turn scores into dists
         """
-        import parasail
+        try:
+            import parasail
+        except ImportError:
+            raise ImportError(
+                "Using the alignment distance requires the installation of `parasail`. "
+                "You can install it with `pip install parasail`."
+            ) from None
 
         return np.fromiter(
             (