From b355f7828b04f25ac4b2cc090ca7458fb017c4b5 Mon Sep 17 00:00:00 2001
From: Eudes Barbosa <eudes.barbosa@bihealth.de>
Date: Tue, 22 Jun 2021 11:10:04 +0200
Subject: [PATCH] Partially removed PendingDeprecationWarning warnings.

---
 snappy_pipeline/workflows/abstract/__init__.py         |  3 ++-
 .../workflows/test_workflows_abstract.py               | 10 +++++-----
 .../test_workflows_gene_expression_quantification.py   | 10 +++++-----
 .../workflows/test_workflows_hla_typing.py             | 10 +++++-----
 .../workflows/test_workflows_ngs_mapping.py            | 10 +++++-----
 .../workflows/test_workflows_roh_calling.py            | 10 +++++-----
 .../workflows/test_workflows_somatic_msi_calling.py    | 10 +++++-----
 .../test_workflows_somatic_targeted_seq_cnv_calling.py | 10 +++++-----
 .../test_workflows_somatic_variant_calling.py          | 10 +++++-----
 .../test_workflows_somatic_wgs_cnv_calling.py          | 10 +++++-----
 .../test_workflows_targeted_seq_cnv_calling.py         | 10 +++++-----
 .../workflows/test_workflows_variant_annotation.py     | 10 +++++-----
 .../workflows/test_workflows_variant_calling.py        | 10 +++++-----
 ...ariant_denovo_filtration_from_variant_annotation.py | 10 +++++-----
 ...s_variant_denovo_filtration_from_variant_calling.py | 10 +++++-----
 ...s_variant_denovo_filtration_from_variant_phasing.py | 10 +++++-----
 .../workflows/test_workflows_variant_phasing.py        | 10 +++++-----
 .../workflows/test_workflows_wgs_cnv_calling.py        | 10 +++++-----
 .../workflows/test_workflows_wgs_mei_calling.py        | 10 +++++-----
 .../workflows/test_workflows_wgs_sv_calling.py         | 10 +++++-----
 20 files changed, 97 insertions(+), 96 deletions(-)

diff --git a/snappy_pipeline/workflows/abstract/__init__.py b/snappy_pipeline/workflows/abstract/__init__.py
index c1868e48..94465b9e 100644
--- 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
index fefbecf4..85ed93ab 100644
--- 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
index 68bc8a5e..1337f9c0 100644
--- 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
index d628d56a..3a4b7111 100644
--- 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
index de50f8b0..4a04e60a 100644
--- 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
index 66e09997..73ff2b2d 100644
--- 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
index 795b5475..44e319d2 100644
--- 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
index d20d406a..9eb31f40 100644
--- 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
index dd5dacba..c3634dc8 100644
--- 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
index e1155b0d..eb6d5ba8 100644
--- 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
index 4e18731b..793b2d9c 100644
--- 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
index 982e06e8..ec7c0a73 100644
--- 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
index 08fccd39..9bf9d4f3 100644
--- 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/tests/snappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_annotation.py b/tests/snappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_annotation.py
index 9b409435..02ee00ff 100644
--- a/tests/snappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_annotation.py
+++ b/tests/snappy_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/tests/snappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_calling.py b/tests/snappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_calling.py
index b6525450..f304a0b9 100644
--- a/tests/snappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_calling.py
+++ b/tests/snappy_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/tests/snappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_phasing.py b/tests/snappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_phasing.py
index 914c326c..33724cb8 100644
--- a/tests/snappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_phasing.py
+++ b/tests/snappy_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
index b93e96f0..7563478a 100644
--- 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
diff --git a/tests/snappy_pipeline/workflows/test_workflows_wgs_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_wgs_cnv_calling.py
index d70d9150..dcbbf979 100644
--- a/tests/snappy_pipeline/workflows/test_workflows_wgs_cnv_calling.py
+++ b/tests/snappy_pipeline/workflows/test_workflows_wgs_cnv_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
@@ -54,8 +53,9 @@ 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_wgs_mei_calling.py b/tests/snappy_pipeline/workflows/test_workflows_wgs_mei_calling.py
index bf234ba6..d6e791dc 100644
--- a/tests/snappy_pipeline/workflows/test_workflows_wgs_mei_calling.py
+++ b/tests/snappy_pipeline/workflows/test_workflows_wgs_mei_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
@@ -53,8 +52,9 @@ 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_wgs_sv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_wgs_sv_calling.py
index 93b769fa..3443eff5 100644
--- a/tests/snappy_pipeline/workflows/test_workflows_wgs_sv_calling.py
+++ b/tests/snappy_pipeline/workflows/test_workflows_wgs_sv_calling.py
@@ -18,9 +18,8 @@
 @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
@@ -53,8 +52,9 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
-    )
+    ).lstrip()
+    yaml_ = yaml.YAML()
+    return yaml_.load(config_str)
 
 
 @pytest.fixture