tox lint

src/pheval_exomiser/post_process/post_process_results_format.py

@@ -265,15 +265,21 @@ def post_process_exomiser_results(
     disease_analysis: bool,
 ):
     """Post-process Exomiser json results into PhEval gene and variant outputs."""
-    output_dir.joinpath("pheval_gene_results").mkdir(
-        parents=True, exist_ok=True
-    ) if gene_analysis else None
-    output_dir.joinpath("pheval_variant_results").mkdir(
-        parents=True, exist_ok=True
-    ) if variant_analysis else None
-    output_dir.joinpath("pheval_disease_results").mkdir(
-        parents=True, exist_ok=True
-    ) if disease_analysis else None
+    (
+        output_dir.joinpath("pheval_gene_results").mkdir(parents=True, exist_ok=True)
+        if gene_analysis
+        else None
+    )
+    (
+        output_dir.joinpath("pheval_variant_results").mkdir(parents=True, exist_ok=True)
+        if variant_analysis
+        else None
+    )
+    (
+        output_dir.joinpath("pheval_disease_results").mkdir(parents=True, exist_ok=True)
+        if disease_analysis
+        else None
+    )
     create_standardised_results(
         results_dir,
         output_dir,

src/pheval_exomiser/prepare/create_batch_commands.py

@@ -78,9 +78,11 @@ def add_phenotype_only_arguments(self) -> ExomiserCommandLineArguments:
             return ExomiserCommandLineArguments(
                 sample=f"{PHENOPACKET_TARGET_DIRECTORY_DOCKER}{Path(self.phenopacket_path.name)}",
                 variant_analysis=self.variant_analysis,
-                output_options_file=f"{OUTPUT_OPTIONS_TARGET_DIRECTORY_DOCKER}{Path(output_options_file).name}"
-                if output_options_file is not None
-                else None,
+                output_options_file=(
+                    f"{OUTPUT_OPTIONS_TARGET_DIRECTORY_DOCKER}{Path(output_options_file).name}"
+                    if output_options_file is not None
+                    else None
+                ),
                 raw_results_dir=RAW_RESULTS_TARGET_DIRECTORY_DOCKER,
             )
         elif self.environment == "local":
@@ -111,9 +113,11 @@ def add_variant_analysis_arguments(self, vcf_dir: Path) -> ExomiserCommandLineAr
                 sample=f"{PHENOPACKET_TARGET_DIRECTORY_DOCKER}{Path(self.phenopacket_path.name)}",
                 vcf_file=f"{VCF_TARGET_DIRECTORY_DOCKER}{Path(vcf_file_data.uri).name}",
                 vcf_assembly=vcf_file_data.file_attributes["genomeAssembly"],
-                output_options_file=f"{OUTPUT_OPTIONS_TARGET_DIRECTORY_DOCKER}{Path(output_options_file).name}"
-                if output_options_file is not None
-                else None,
+                output_options_file=(
+                    f"{OUTPUT_OPTIONS_TARGET_DIRECTORY_DOCKER}{Path(output_options_file).name}"
+                    if output_options_file is not None
+                    else None
+                ),
                 variant_analysis=self.variant_analysis,
                 raw_results_dir=RAW_RESULTS_TARGET_DIRECTORY_DOCKER,
                 analysis_yaml=f"{EXOMISER_YAML_TARGET_DIRECTORY_DOCKER}{Path(self.analysis_yaml).name}",
@@ -185,18 +189,22 @@ def write_basic_analysis_command(self, command_arguments: ExomiserCommandLineArg
     def write_results_dir(self, command_arguments: ExomiserCommandLineArguments) -> None:
         """Write results directory for exomiser ≥13.2.0 to run."""
         try:
-            self.file.write(
-                " --output-directory " + str(command_arguments.raw_results_dir)
-            ) if command_arguments.raw_results_dir is not None else None
+            (
+                self.file.write(" --output-directory " + str(command_arguments.raw_results_dir))
+                if command_arguments.raw_results_dir is not None
+                else None
+            )
         except IOError:
             print("Error writing ", self.file)
 
     def write_output_options(self, command_arguments: ExomiserCommandLineArguments) -> None:
         """Write a command out for exomiser ≤13.1.0 to run - including output option file specified."""
         try:
-            self.file.write(
-                " --output " + str(command_arguments.output_options_file)
-            ) if command_arguments.output_options_file is not None else None
+            (
+                self.file.write(" --output " + str(command_arguments.output_options_file))
+                if command_arguments.output_options_file is not None
+                else None
+            )
         except IOError:
             print("Error writing ", self.file)
 
@@ -230,9 +238,11 @@ def write_phenotype_only_command(self, command_arguments: ExomiserCommandLineArg
         self.file.write("\n")
 
     def write_local_commands(self, command_arguments: ExomiserCommandLineArguments):
-        self.write_analysis_command(
-            command_arguments
-        ) if self.variant_analysis else self.write_phenotype_only_command(command_arguments)
+        (
+            self.write_analysis_command(command_arguments)
+            if self.variant_analysis
+            else self.write_phenotype_only_command(command_arguments)
+        )
 
     def close(self) -> None:
         """Close file."""
@@ -324,18 +334,20 @@ def create_batch_file(
         output_options_file,
         analysis,
     )
-    BatchFileWriter(
-        command_arguments,
-        variant_analysis,
-        output_dir,
-        batch_prefix,
-    ).write_all_commands() if max_jobs == 0 else BatchFileWriter(
-        command_arguments,
-        variant_analysis,
-        output_dir,
-        batch_prefix,
-    ).create_split_batch_files(
-        max_jobs
+    (
+        BatchFileWriter(
+            command_arguments,
+            variant_analysis,
+            output_dir,
+            batch_prefix,
+        ).write_all_commands()
+        if max_jobs == 0
+        else BatchFileWriter(
+            command_arguments,
+            variant_analysis,
+            output_dir,
+            batch_prefix,
+        ).create_split_batch_files(max_jobs)
     )
 
 

src/pheval_exomiser/run/run.py

@@ -195,13 +195,17 @@ def run_exomiser(
     variant_analysis: bool,
 ):
     """Run Exomiser with specified environment."""
-    run_exomiser_local(
-        input_dir, testdata_dir, config, output_dir, tool_input_commands_dir, exomiser_version
-    ) if config.environment == "local" else run_exomiser_docker(
-        input_dir,
-        testdata_dir,
-        tool_input_commands_dir,
-        raw_results_dir,
-        exomiser_version,
-        variant_analysis,
+    (
+        run_exomiser_local(
+            input_dir, testdata_dir, config, output_dir, tool_input_commands_dir, exomiser_version
+        )
+        if config.environment == "local"
+        else run_exomiser_docker(
+            input_dir,
+            testdata_dir,
+            tool_input_commands_dir,
+            raw_results_dir,
+            exomiser_version,
+            variant_analysis,
+        )
     )

src/pheval_exomiser/runner.py

@@ -1,4 +1,5 @@
 """Exomiser Runner"""
+
 from dataclasses import dataclass
 from pathlib import Path