tox lint

monarch-initiative · Mar 18, 2024 · 9b524be · 9b524be
1 parent ddc4265
commit 9b524be
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Showing 3 changed files with 39 additions and 32 deletions.
diff --git a/src/pheval_lirical/prepare/prepare_commands.py b/src/pheval_lirical/prepare/prepare_commands.py
@@ -76,12 +76,12 @@ def add_manual_cli_arguments(
             sample_id=self.phenopacket_util.sample_id(),
             output_dir=self.results_dir,
             output_prefix=self.phenopacket_path.stem,
-            exomiser_hg19_data_path=self.exomiser_hg19_data_path
-            if gene_analysis or variant_analysis
-            else None,
-            exomiser_hg38_data_path=self.exomiser_hg38_data_path
-            if gene_analysis or variant_analysis
-            else None,
+            exomiser_hg19_data_path=(
+                self.exomiser_hg19_data_path if gene_analysis or variant_analysis else None
+            ),
+            exomiser_hg38_data_path=(
+                self.exomiser_hg38_data_path if gene_analysis or variant_analysis else None
+            ),
         )
 
     def add_phenopacket_cli_arguments(
@@ -97,12 +97,12 @@ def add_phenopacket_cli_arguments(
             exomiser_data=self.exomiser_data_dir,
             output_dir=self.results_dir,
             output_prefix=self.phenopacket_path.stem,
-            exomiser_hg19_data_path=self.exomiser_hg19_data_path
-            if gene_analysis or variant_analysis
-            else None,
-            exomiser_hg38_data_path=self.exomiser_hg38_data_path
-            if gene_analysis or variant_analysis
-            else None,
+            exomiser_hg19_data_path=(
+                self.exomiser_hg19_data_path if gene_analysis or variant_analysis else None
+            ),
+            exomiser_hg38_data_path=(
+                self.exomiser_hg38_data_path if gene_analysis or variant_analysis else None
+            ),
         )
 
     def add_cli_arguments(
@@ -279,10 +279,10 @@ def write_command(
     ) -> None:
         """Write LIRICAL command."""
         try:
-            self.write_phenopacket_command(
-                command_arguments
-            ) if self.mode.lower() == "phenopacket" else self.write_manual_command(
-                command_arguments
+            (
+                self.write_phenopacket_command(command_arguments)
+                if self.mode.lower() == "phenopacket"
+                else self.write_manual_command(command_arguments)
             )
         except IOError:
             print("Error writing ", self.file)

diff --git a/src/pheval_lirical/run/run.py b/src/pheval_lirical/run/run.py
@@ -23,29 +23,35 @@ def prepare_lirical_commands(
     prepare_commands(
         lirical_jar=input_dir.joinpath(tool_specific_configurations.lirical_jar_executable),
         input_dir=input_dir.joinpath("data"),
-        exomiser_data_dir=input_dir.joinpath(
-            tool_specific_configurations.exomiser_db_configurations.exomiser_database
-        )
-        if tool_specific_configurations.exomiser_db_configurations.exomiser_database is not None
-        else None,
+        exomiser_data_dir=(
+            input_dir.joinpath(
+                tool_specific_configurations.exomiser_db_configurations.exomiser_database
+            )
+            if tool_specific_configurations.exomiser_db_configurations.exomiser_database is not None
+            else None
+        ),
         phenopacket_dir=phenopacket_dir,
         vcf_dir=vcf_dir,
         file_prefix=Path(testdata_dir).name,
         tool_input_commands_dir=tool_input_commands_dir,
         raw_results_dir=raw_results_dir,
         mode=tool_specific_configurations.mode,
         lirical_version=lirical_version,
-        exomiser_hg19_data=input_dir.joinpath(
-            tool_specific_configurations.exomiser_db_configurations.exomiser_hg19_database
-        )
-        if tool_specific_configurations.exomiser_db_configurations.exomiser_hg19_database
-        else None,
-        exomiser_hg38_data=input_dir.joinpath(
-            tool_specific_configurations.exomiser_db_configurations.exomiser_hg38_database
-        )
-        if tool_specific_configurations.exomiser_db_configurations.exomiser_hg38_database
-        is not None
-        else None,
+        exomiser_hg19_data=(
+            input_dir.joinpath(
+                tool_specific_configurations.exomiser_db_configurations.exomiser_hg19_database
+            )
+            if tool_specific_configurations.exomiser_db_configurations.exomiser_hg19_database
+            else None
+        ),
+        exomiser_hg38_data=(
+            input_dir.joinpath(
+                tool_specific_configurations.exomiser_db_configurations.exomiser_hg38_database
+            )
+            if tool_specific_configurations.exomiser_db_configurations.exomiser_hg38_database
+            is not None
+            else None
+        ),
         gene_analysis=gene_analysis,
         variant_analysis=variant_analysis,
     ),

diff --git a/src/pheval_lirical/runner.py b/src/pheval_lirical/runner.py
@@ -1,4 +1,5 @@
 """LIRICAL Runner"""
+
 from dataclasses import dataclass
 from pathlib import Path