Continuation of #700: Change multiple_sep to ';'

CHANGELOG.md

@@ -2,7 +2,7 @@
 
 ## BREAKING CHANGES
 
-* Change separator for arguments with multiple inputs from `:` to `;` (PR #700). Now, _all_ arguments with `multiple: true` will use `;` as the separator.
+* Change separator for arguments with multiple inputs from `:` to `;` (PR #700 and #707). Now, _all_ arguments with `multiple: true` will use `;` as the separator.
   This change was made to be able to deal with file paths that contain `:`, e.g. `s3://my-bucket/my:file.txt`. Furthermore, the `;` separator will become
   the default separator for all arguments with `multiple: true` in Viash >= 0.9.0.
 

src/annotate/popv/test.py

@@ -19,7 +19,7 @@ def test_simple_execution(run_component):
         "--input", input_file,
         "--reference", reference_file,
         "--output", "output.h5mu",
-        "--methods", "rf:svm"
+        "--methods", "rf;svm"
     ])
 
     # check whether file exists
@@ -43,7 +43,7 @@ def test_popv_with_other_layer(run_component, tmp_path):
         "--input", tmp_path / "input.h5mu",
         "--reference", reference_file,
         "--output", "output.h5mu",
-        "--methods", "rf:svm:knn_on_scanorama"
+        "--methods", "rf;svm;knn_on_scanorama"
     ])
 
 def test_popv_with_non_overlapping_cells(run_component, tmp_path):
@@ -66,7 +66,7 @@ def test_popv_with_non_overlapping_cells(run_component, tmp_path):
         "--input", tmp_path / "input.h5mu",
         "--reference", reference_file,
         "--output", "output.h5mu",
-        "--methods", "rf:svm:knn_on_scanorama"
+        "--methods", "rf;svm;knn_on_scanorama"
     ])
 
 if __name__ == '__main__':

src/cluster/leiden/test.py

@@ -47,7 +47,7 @@ def test_leiden(input_path, run_component, random_h5mu_path, compression, output
     output_path = random_h5mu_path()
     args = [
         "--input", input_path,
-        "--resolution", "1:0.25",
+        "--resolution", "1;0.25",
         "--output", output_path]
     if compression:
         args.extend(["--output_compression", compression])
@@ -67,7 +67,7 @@ def test_leiden_custom_connectivities_key(mudata_custom_connectivities_key, run_
     run_component([
          "--input", mudata_custom_connectivities_key,
         "--obsm_name", "fooleiden",
-        "--resolution", "1:0.25",
+        "--resolution", "1;0.25",
         "--output", output_path,
         "--obsp_connectivities", "custom_connectivities",
         "--output_compression", "gzip"

src/filter/intersect_obs/test.py

@@ -45,7 +45,7 @@ def test_intersect_obs(run_component, sample_mudata, tmp_path):
     # run component
     run_component([
         "--input", sample_mudata,
-        "--modalities", "mod1:mod2",
+        "--modalities", "mod1;mod2",
         "--output", str(output_path),
         "--output_compression", "gzip"
     ])
@@ -69,7 +69,7 @@ def test_intersect_obs_with_real(run_component, tmp_path):
     # run component
     run_component([
         "--input", input_path,
-        "--modalities", "rna:prot",
+        "--modalities", "rna;prot",
         "--output", str(output_path),
         "--output_compression", "gzip"
     ])

src/labels_transfer/knn/test.py

@@ -52,7 +52,7 @@ def test_label_transfer(run_component, test_args):
         "--input_obsm_features", obsm_features,
         "--reference", tempfile_reference_file.name,
         "--reference_obsm_features", obsm_features,
-        "--reference_obs_targets", ",".join(obs_targets),
+        "--reference_obs_targets", ";".join(obs_targets),
         "--output", "output.h5mu",
         "--n_neighbors", "5"
     ]

src/labels_transfer/xgboost/test.py

@@ -56,7 +56,7 @@ def test_label_transfer(run_component, test_args):
         "--input_obsm_features", obsm_features,
         "--reference", str(tempfile_reference_file),
         "--reference_obsm_features", obsm_features,
-        "--reference_obs_targets", ",".join(obs_targets),
+        "--reference_obs_targets", ";".join(obs_targets),
         "--output", "output.h5mu",
         "--model_output", "model_one_class",
         "--use_gpu", "false",
@@ -104,7 +104,7 @@ def test_retraining(run_component, test_args, tmp_path):
     args1 = args + [
         "--input", str(tempfile_input_file),
         "--output", str(output_path),
-        "--reference_obs_targets", ",".join(obs_targets[:2]),
+        "--reference_obs_targets", ";".join(obs_targets[:2]),
         "--max_depth", "6"]
     run_component(args1)
 
@@ -116,7 +116,7 @@ def test_retraining(run_component, test_args, tmp_path):
     args2 = args + [
         "--input", str(output_path),
         "--output", str(output2_path),
-        "--reference_obs_targets", ",".join(obs_targets),
+        "--reference_obs_targets", ";".join(obs_targets),
         "--max_depth", "4"]
     run_component(args2)