Merge pull request #414 from sunbeam-labs/413-get-rid-of-warningerror…

…-summary

Remove annoyances

.github/PULL_REQUEST_TEMPLATE.md

@@ -5,5 +5,6 @@
 
 If this is for a release:
 * [ ] I have updated documentation
+* [ ] I have updated all conda pin files (`snakedeploy update-conda-envs workflow/envs/*.yml`)
 * [ ] I have updated the hardcoded version at the top of `install.sh` to match what this release's version will be
 * [ ] I have created a release archive that will be attached to this release

sunbeamlib/post.py

@@ -3,39 +3,6 @@
 import os
 
 
-WARN_STR = ["warn", "warning"]
-ERR_STR = ["err", "error", "exception"]
-
-
-def parse_err_and_warn(log_fp: str) -> tuple:
-    """Go through output log and return a list of warnings and a list of errors"""
-    warns = list()
-    errs = list()
-
-    with open(log_fp) as f:
-        for n, l in enumerate(f, 1):
-            if [1 for w in WARN_STR if w in l.lower()]:
-                warns.append(n)
-            if [1 for e in ERR_STR if e in l.lower()]:
-                errs.append(n)
-
-    return warns, errs
-
-
-def parse_rule_logs(log_fp: str) -> list:
-    """Go through each per-rule log and report any warnings or errors"""
-    log_fps = os.listdir(log_fp)
-    alerts = []
-    for fp in log_fps:
-        warns, errs = parse_err_and_warn(os.path.join(log_fp, fp))
-        if warns or errs:
-            alerts.append(
-                f"{fp}:\nWarnings: ({len(warns)}) {warns}\nErrors: ({len(errs)}) {errs}"
-            )
-
-    return alerts
-
-
 def compile_benchmarks(benchmark_fp: str, stats_fp: str):
     """Aggregate all the benchmark files into one and put it in stats_fp"""
     benchmarks = []

workflow/Snakefile

@@ -156,10 +156,4 @@ onsuccess:
 
 onerror:
     print("Sunbeam failed with error.")
-    warnings, errors = parse_err_and_warn(log)
-    print(f"Warnings: ({len(warnings)}) {warnings}")
-    print(f"Errors: ({len(errors)}) {errors}")
-    alerts = parse_rule_logs(LOG_FP)
-    for a in alerts:
-        print(a)
     compile_benchmarks(BENCHMARK_FP, Cfg["all"]["root"] / "stats")

workflow/scripts/remove_low_complexity.py

@@ -4,6 +4,6 @@
     ids = []
     with open(snakemake.input.ids) as f:
         ids = [remove_pair_id(id, log) for id in f.readlines()]
-    log.write(f"Komplexity IDs to be filtered: {str(ids)}\n")
+    log.write(f"Num Komplexity IDs to be filtered: {len(ids)}\n")
 
     filter_ids(snakemake.input.reads, snakemake.output[0], ids, log)