improve file list

Author: pdimens

harpy/commands/view.py

@@ -5,6 +5,7 @@
 import glob
 import gzip
 import curses
+from datetime import datetime
 from pygments import highlight
 from pygments.lexers import get_lexer_by_name
 from pygments.formatters import get_formatter_by_name
@@ -13,7 +14,6 @@
 from rich.console import Console
 from rich.panel import Panel
 from rich.prompt import Prompt
-from rich.table import Table
 from rich import print as rprint
 from harpy.common.printing import harpy_table, print_error
 from harpy.common.file_ops import is_gzip
@@ -43,7 +43,7 @@ def check_terminal_colors():
 
 def parse_file(infile: str):
     '''
-    take an input file name, get the most recent by modificiation time, and print it via pygmentized less
+    take a list of input file name, get the most recent by modificiation time, and print it via pygmentized less
     returns a string of the file that was viewed
     '''
     if not os.access(infile, os.R_OK):
@@ -69,7 +69,8 @@ def _read_file(x: str):
     echo_via_pager(_read_file(infile), color = n_colors > 0)
     return infile
 
-@click.group(options_metavar='', context_settings={"help_option_names" : ["-h", "--help"]})
+@click.group(options_metavar='')
+@click.help_option('--help', panel = "Workflow Options", hidden = True)
 def view():
     """
     View a workflow's components
@@ -81,6 +82,7 @@ def view():
 @click.command(no_args_is_help = True, context_settings={"allow_interspersed_args" : False})
 @click.option("-e", "--edit", is_flag=True, default=False, help = "Open the config file in you system's default editor")
 @click.argument('directory', required=True, type=click.Path(exists=True, file_okay=False), nargs=1)
+@click.help_option('--help', panel = "Workflow Options", hidden = True)
 def config(directory, edit):
     """
     View/edit a workflow's config file
@@ -118,6 +120,7 @@ def config(directory, edit):
     )
 
 @click.command()
+@click.help_option('--help', panel = "Workflow Options", hidden = True)
 @click.argument('program', required=False, type=str, nargs=1)
 def environments(program):
     """
@@ -156,23 +159,27 @@ def environments(program):
             console.print()
             console.rule(i.removesuffix('.yaml'), style = "blue")
             for d in deps.split():
-                if program and program.lower() in d:
-                    console.print(f"→ {d}", style = "bold green")
+                if program:
+                    if program.lower() in d:
+                        console.print(f"→ {d}", style = "bold blue", highlight = False)
+                    else:
+                        console.print(f"- {d}", style = "dim", highlight=False)
                 else:
                     console.print(f"- {d}", style = "default", highlight=False)
             console.print()
     return
 
 @click.command(no_args_is_help = True, context_settings={"allow_interspersed_args" : False})
-@click.option("-c", "--choose", is_flag=True, default=False, help = "From one from all the logs")
+@click.option("-c", "--choose", is_flag=True, default=False, help = "List logs for user choice")
 @click.argument('directory', required=True, type=click.Path(exists=True, file_okay=False), nargs=1)
 def log(directory, choose):
     """
-    View a workflow's last log file
+    View a workflow's Snakemake log file
     
     The log file contains everything Snakemake printed during runtime.
-    The only required input is the output folder previously created by Harpy where you can find
-    `.snakemake/log`. Navigate with the typical `less` keyboard bindings, e.g.:
+    The only required input is an output folder created by Harpy where you can find
+    `.snakemake/log`. Use `--choose` to pick from a list of all Snakemake logfiles in
+    the `directory`. Navigate with the typical `less` keyboard bindings, e.g.:
     
     | key                     | function                   |
     | :---------------------- | :------------------------- |
@@ -196,19 +203,23 @@ def log(directory, choose):
         )
 
     files = sorted(files, key = os.path.getmtime, reverse = True)
-    if choose:
+    if choose and len(files) > 1:
         console = Console()
         console.print()
-        console.rule('Snakemake Log Files', style = "green")
+        #console.rule('Snakemake Log Files', style = "green")
         _tb = harpy_table()
-        _tb.add_column("Number", justify="left", style="bold green", no_wrap=True)
-        _tb.add_column("File", justify="left")
+        _tb.show_header=True
+        _tb.add_column("[bold green]#", style="bold green", min_width=2)
+        _tb.add_column("[dim yellow]Last Modification",style = "dim yellow")
+        _tb.add_column("Log File", justify="right", no_wrap=True)
         for i,j in enumerate(files,1):
-            _tb.add_row(str(i), os.path.basename(j))
+            filename = os.path.basename(j).removesuffix(".snakemake.log") + "[dim].snakemake.log[/]"
+            modtime = datetime.fromtimestamp(os.path.getmtime(j)).strftime('%Y-%m-%d %H:%M')
+            _tb.add_row(str(i), modtime , filename)
         console.print(_tb)
-        console.rule('[dim]sorted newest (top) to oldest (bottom)[/]', style = 'dim')
+        #console.rule('[dim]second column shows last modification time[/]', style = 'dim')
         selection = Prompt.ask(
-            "\n[bold blue]Select a log file by number[/]",
+            "\n[bold blue]Select a log file by number ([bold green]#[/])[/]",
             choices=list(str(i) for i in range(1,len(files) + 1)),
             show_choices=False
         )
@@ -232,10 +243,11 @@ def log(directory, choose):
 
 @click.command(no_args_is_help = True, context_settings={"allow_interspersed_args" : False})
 @click.option("-e", "--edit", is_flag=True, default=False, help = "Open the config file in you system's default editor")
+@click.help_option('--help', panel = "Workflow Options", hidden = True)
 @click.argument('directory', required=True, type=click.Path(exists=True, file_okay=False), nargs=1)
 def snakefile(directory, edit):
     """
-    View/edit a workflow's snakefile
+    View/edit a workflow's Snakefile
     
     The snakefile contains all the instructions for a workflow. The only required input is the output folder
     previously created by Harpy where you can find `workflow/workflow.smk`.
@@ -270,10 +282,11 @@ def snakefile(directory, edit):
 
 @click.command(no_args_is_help = True, context_settings={"allow_interspersed_args" : False})
 @click.option("-e", "--edit", is_flag=True, default=False, help = "Open the config file in you system's default editor")
+@click.help_option('--help', panel = "Workflow Options", hidden = True)
 @click.argument('directory', required=True, type=click.Path(exists=True, file_okay=False), nargs=1)
 def snakeparams(directory, edit):
     """
-    View/edit a workflow's snakemake configurations
+    View/edit a workflow's Snakemake configurations
     
     The snakemake configuration file has the runtime parameters snakemake was invoked with (i.e.,
     computational specifics that don't impact your results). The only required input is the output folder