Partially removed PendingDeprecationWarning warnings.

bihealth · Jun 22, 2021 · b355f78 · b355f78
1 parent 9e64d82
commit b355f78
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Showing 20 changed files with 97 additions and 96 deletions.
diff --git a/snappy_pipeline/workflows/abstract/__init__.py b/snappy_pipeline/workflows/abstract/__init__.py
@@ -276,7 +276,8 @@ def _cached_read_generic_tsv_sheet(path_abs, path_rel, naming_scheme):
 @lru_cache()
 def _cached_yaml_round_trip_load_str(str_value):
     """Cached reading of YAML ``str`` objects."""
-    return yaml.round_trip_load(StringIO(str_value))
+    yaml_ = yaml.YAML()
+    return yaml_.load(str_value)
 
 
 class DataSetInfo:

diff --git a/tests/snappy_pipeline/workflows/test_workflows_abstract.py b/tests/snappy_pipeline/workflows/test_workflows_abstract.py
@@ -127,9 +127,8 @@ def test_link_in_path_generator(germline_sheet_fake_fs, config_lookup_paths, wor
 @pytest.fixture
 def dummy_config():
     """Return dummy configuration OrderedDicts"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         step_config: {}
         static_data_config: {}
         data_sets:
@@ -142,8 +141,9 @@ def dummy_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_gene_expression_quantification.py b/tests/snappy_pipeline/workflows/test_workflows_gene_expression_quantification.py
@@ -19,9 +19,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -42,8 +41,9 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_hla_typing.py b/tests/snappy_pipeline/workflows/test_workflows_hla_typing.py
@@ -17,9 +17,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -33,8 +32,9 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py
@@ -22,9 +22,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -52,8 +51,9 @@ def minimal_config():
             naming_scheme: only_secondary_id
             pedigree_field: pedigree_field
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_roh_calling.py b/tests/snappy_pipeline/workflows/test_workflows_roh_calling.py
@@ -18,9 +18,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -51,8 +50,9 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_msi_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_msi_calling.py
@@ -17,9 +17,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -44,8 +43,9 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py
@@ -22,9 +22,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (somatic) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -55,8 +54,9 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_calling.py
@@ -18,9 +18,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -54,8 +53,9 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_wgs_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_wgs_cnv_calling.py
@@ -19,9 +19,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (somatic) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -60,8 +59,9 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_targeted_seq_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_targeted_seq_cnv_calling.py
@@ -78,9 +78,8 @@ def get_expected_gcnv_log_file(step_name):
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (somatic) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -121,8 +120,9 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_variant_annotation.py b/tests/snappy_pipeline/workflows/test_workflows_variant_annotation.py
@@ -17,9 +17,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -48,8 +47,9 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_variant_calling.py b/tests/snappy_pipeline/workflows/test_workflows_variant_calling.py
@@ -19,9 +19,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -55,8 +54,9 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/...py_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_annotation.py b/...py_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_annotation.py
@@ -19,9 +19,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -52,8 +51,9 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/...nappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_calling.py b/...nappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_calling.py
@@ -19,9 +19,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -52,8 +51,9 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/...nappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_phasing.py b/...nappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_phasing.py
@@ -19,9 +19,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -52,8 +51,9 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture

diff --git a/tests/snappy_pipeline/workflows/test_workflows_variant_phasing.py b/tests/snappy_pipeline/workflows/test_workflows_variant_phasing.py
@@ -19,9 +19,8 @@
 @pytest.fixture(scope="module")  # otherwise: performance issues
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
-    return yaml.round_trip_load(
-        textwrap.dedent(
-            r"""
+    config_str = textwrap.dedent(
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -59,8 +58,9 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture