fmt

Author: johanneskoester

workflow/Snakefile

@@ -1,14 +1,14 @@
 configfile: "config/config.yaml"
 
+
 include: "rules/common.smk"
 include: "rules/processing.smk"
 include: "rules/plotting.smk"
 include: "rules/datavzrd.smk"
 include: "rules/testing.smk"
 
 
-report:
-    "report/workflow.rst"
+report: "report/workflow.rst"
 
 
 rule all:
@@ -27,4 +27,4 @@ rule all:
         collect(
             "results/datavzrd/{dataset}",
             dataset=config["datasets"],
-        )
+        ),

workflow/rules/common.smk

@@ -6,7 +6,9 @@ def get_value_column(wildcards):
         data_path = lookup(f"datasets/{dataset}/data", within=config)
         with open(data_path) as f:
             header = f.readline().strip().split("\t")
-            col_idx = lookup(f"datasets/{dataset}/value_column_index", within=config, default=None)
+            col_idx = lookup(
+                f"datasets/{dataset}/value_column_index", within=config, default=None
+            )
             if col_idx is not None:
                 return header[col_idx]
             elif len(header) == n_vars + 1:
@@ -18,4 +20,4 @@ def get_value_column(wildcards):
                     "file contains exactly #variables + 1 columns."
                 )
     else:
-        return definition
+        return definition

workflow/rules/datavzrd.smk

@@ -2,9 +2,9 @@ rule parquet_to_tsv:
     input:
         "{prefix}.parquet",
     output:
-        "{prefix}.tsv"
+        "{prefix}.tsv",
     log:
-        "logs/parquet_to_tsv/{prefix}.log"
+        "logs/parquet_to_tsv/{prefix}.log",
     conda:
         "../envs/pystats.yaml"
     script:
@@ -25,9 +25,9 @@ rule datavzrd_report:
                 "dataset": "{dataset}",
             },
             caption="../report/datavzrd.rst",
-        )
+        ),
     log:
-        "logs/datavzrd_report/{dataset}.log"
+        "logs/datavzrd_report/{dataset}.log",
     params:
         value_column=get_value_column,
         variables=lookup("datasets/{dataset}/variables", within=config),

workflow/rules/plotting.smk

@@ -24,7 +24,9 @@ rule plot_dists_and_effects:
     input:
         cis="results/bootstrap/confidence_intervals/{dataset}.parquet",
         data="results/data/{dataset}.sorted.parquet",
-        comparisons=local(lookup("datasets/{dataset}/comparisons", within=config, default=[])),
+        comparisons=local(
+            lookup("datasets/{dataset}/comparisons", within=config, default=[])
+        ),
     output:
         report(
             "results/plots/{dataset}/distributions_{mode,all|selected}_legend_{legend,yes|no}_effects.html",

workflow/rules/testing.smk

@@ -14,7 +14,8 @@ for test_name, test in tests.items():
 
 rule all_tests:
     input:
-        "results/tests.tsv"
+        "results/tests.tsv",
+
 
 rule simulate_data:
     output:
@@ -45,4 +46,4 @@ rule validate_results:
     conda:
         "../envs/simulation.yaml"
     script:
-        "../scripts/validate_results.py"
+        "../scripts/validate_results.py"