much nicer printing

harpy/_launch.py

@@ -21,6 +21,24 @@ def iserror(text):
     """logical check for erroring trigger words in snakemake output"""
     return "Exception" in text or "Error" in text or "MissingOutputException" in text
 
+def highlight_params(text):
+    """make important snakemake attributes like 'input:' highlighted in the error output"""
+    if text.startswith("    jobid:"):
+        return text.replace("jobid:", "[bold default]jobid:[/bold default]").rstrip()
+    if text.startswith("    input:"):
+        return text.replace("input:", "[bold default]input:[/bold default]").rstrip()
+    if text.startswith("    output:"):
+        return text.replace("output:", "[bold default]output:[/bold default]").rstrip()
+    if text.startswith("    log:"):
+        return text.replace("log:", "[bold default]log:[/bold default]").rstrip()
+    if text.startswith("    conda-env:"):
+        return text.replace("conda-env:", "[bold default]conda-env:[/bold default]").rstrip()
+    if text.startswith("    container:"):
+        return text.replace("container:", "[bold default]container:[/bold default]").rstrip()
+    if text.startswith("    shell:"): 
+        return text.replace("shell:", "[bold default]shell:[/bold default]").rstrip()
+    return text.rstrip()
+
 def purge_empty_logs(target_dir):
     """scan target_dir and remove empty files, then scan it again and remove empty directories"""
     for logfile in glob.glob(f"{target_dir}/logs/**/*", recursive = True):
@@ -166,17 +184,18 @@ def launch_snakemake(sm_args, workflow, starttext, outdir, sm_logfile, quiet, su
             elif exitcode == 3:
                 print_onerror(sm_logfile)
             while output and not output.endswith("]") and not output.startswith("Shutting down"):                   
+                console = Console(stderr = True, tab_size = 4, highlight=False)
                 if "Exception" in output or "Error" in output:
-                    rprint("[yellow bold]" + output.rstrip(), file = sys.stderr)
+                    console.print("[yellow bold]" + output.rstrip(), overflow = "ignore", crop = False)
                     output = process.stderr.readline()
                     continue
-                if output.startswith("Logfile"):
-                    rprint("[yellow]" + output.rstrip(), file = sys.stderr)
+                if output.startswith("Logfile") or output.startswith("======"):
+                    console.print("[yellow bold]" + output.rstrip(), overflow = "ignore", crop = False)
                     output = process.stderr.readline()
                     continue
                 if output:
                     if not output.startswith("Complete log"):
-                        rprint("[red]" + output.replace("\t","    ").rstrip(), file = sys.stderr)
+                        console.print("[red]" + highlight_params(output), overflow = "ignore", crop = False)
                     if output.startswith("Removing output files of failed job"):
                         break
                 output = process.stderr.readline()

harpy/_printing.py

@@ -7,7 +7,7 @@
 from rich.table import Table
 from rich.panel import Panel
 
-console = Console()
+console = Console(stderr=True)
 
 def print_error(errortitle, errortext):
     """Print a yellow panel with error text"""
@@ -98,5 +98,5 @@ def print_onsuccess(outdir, summary = None, time = None):
 def print_onerror(logfile):
     """Print a red panel with error text. To be used in place of onerror: inside a snakefile. Expects the erroring rule printed after it."""
     console.rule("[bold]Workflow Error", style = "red")
-    console.print(f"The workflow terminated from an error. See the full log for more info:\n[bold]{logfile}[/bold]")
+    console.print(f"The workflow stopped because of an error. Full workflow log:\n[bold]{logfile}[/bold]")
     console.rule("[bold]Where Error Occurred", style = "red")

harpy/snakefiles/qc.smk

@@ -59,19 +59,19 @@ if not deconvolve:
         log:
             serr = outdir + "/logs/fastp/{sample}.log"
         params:
+            static = "--trim_poly_g --cut_right",
             minlen = f"--length_required {min_len}",
             maxlen = f"--max_len1 {max_len}",
             trim_adapters = trim_arg,
             dedup = "-D" if dedup else "",
+            title = lambda wc: f"-R \"{wc.sample} QC Report\"",
             extra = extra
         threads:
             workflow.cores
         conda:
             f"{envdir}/qc.yaml"
         shell: 
-            """
-            fastp --trim_poly_g --cut_right {params} --thread {threads} -i {input.fw} -I {input.rv} -o {output.fw} -O {output.rv} -h {output.html} -j {output.json} -R "{wildcards.sample} QC Report" 2> {log.serr}
-            """
+            "fastp {params} --thread {threads} -i {input.fw} -I {input.rv} -o {output.fw} -O {output.rv} -h {output.html} -j {output.json} 2> {log.serr}"
 else:
     rule fastp:
         priority: 100
@@ -85,19 +85,19 @@ else:
         log:
             serr = outdir + "/logs/fastp/{sample}.log"
         params:
+            static = "--trim_poly_g --cut_right",
             minlen = f"--length_required {min_len}",
             maxlen = f"--max_len1 {max_len}",
             trim_adapters = trim_arg,
             dedup = "-D" if dedup else "",
+            title = lambda wc: f"-R \"{wc.sample} QC Report\"",
             extra = extra
         threads:
             workflow.cores
         conda:
             f"{envdir}/qc.yaml"
         shell: 
-            """
-            fastp --trim_poly_g --cut_right {params} --thread {threads} -i {input.fw} -I {input.rv} --stdout -h {output.html} -j {output.json} -R "{wildcards.sample} QC Report" 2> {log.serr} > {output.fq}
-            """
+            "fastp {params} --thread {threads} -i {input.fw} -I {input.rv} --stdout -h {output.html} -j {output.json} 2> {log.serr} > {output.fq}"
 
     rule deconvolve:
         input: