Added mode info for veryfying availability of submodules binaries.

Co-authored-by: aziele <[email protected]>

Author: agudys

.github/workflows/deploy.yml

@@ -72,6 +72,8 @@ jobs:
     steps:
     - name: help
       run: python3 vclust.py
+    - name: print info
+      run: python3 vclust.py info
 
 ########################################################################################
   upload:

.github/workflows/self-hosted.yml

@@ -51,11 +51,35 @@ jobs:
     steps:
     - name: make
       run: make -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} PLATFORM=${{ matrix.platform }} LEIDEN=true
+    - name: print info
+      run: python3 vclust.py info 
+
+########################################################################################
+  print-info:
+    name: Print info
+    needs: make
+    strategy:
+      fail-fast: false
+      matrix:
+        machine: [x64_linux]
+        platform: [avx2]
+        compiler: [14]
+        include:
+        - {machine: arm64_linux, platform: arm8, compiler: 12}
+        - {machine: x64_mac, platform: avx2, compiler: 12}
+        - {machine: arm64_mac, platform: m1, compiler: 12}
+        
+    runs-on: [self-hosted, vclust, '${{ matrix.machine }}'] 
+
+    steps:
+    - name: print info
+      run: python3 vclust.py info 
+
 
 ########################################################################################
   pipeline-linux:
     name: Pipeline (linux)
-    needs: make
+    needs: print-info
     strategy:
       fail-fast: false
       matrix:
@@ -70,7 +94,7 @@ jobs:
   ########################################################################################
   pipeline-macos:
     name: Pipeline (macOS)
-    needs: make
+    needs: print-info
     strategy:
       fail-fast: false
       matrix:

README.md

@@ -1,6 +1,6 @@
 # <img src="./images/logo.svg" alt="Vclust logo" /> Vclust
 
-![version](https://img.shields.io/badge/version-1.2.6-blue.svg)
+![version](https://img.shields.io/badge/version-1.2.7-blue.svg)
 [![GitHub downloads](https://img.shields.io/github/downloads/refresh-bio/vclust/total.svg?style=flag&label=GitHub%20downloads)](https://github.com/refresh-bio/vclust/releases)
 [![Build and tests](../../workflows/Build%20and%20tests/badge.svg)](../../actions/workflows/main.yml)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)

test.py

@@ -33,7 +33,7 @@ def test_dir():
 
 
 @pytest.mark.parametrize('subcommand',[
-    'prefilter', 'align', 'cluster',
+    'prefilter', 'align', 'cluster', 'info',
 ])
 def test_subcommands(subcommand):
     cmd = [

vclust.py

@@ -15,7 +15,7 @@
 import typing
 import uuid
 
-__version__ = '1.2.6'
+__version__ = '1.2.7'
 
 DEFAULT_THREAD_COUNT = min(multiprocessing.cpu_count(), 64)
 
@@ -33,7 +33,7 @@
     'qidx', 'ridx', 'query', 'reference',  'tani', 'gani', 'ani', 'qcov',
     'rcov', 'num_alns', 'len_ratio', 'qlen', 'rlen',  'nt_match', 'nt_mismatch', 
 ]
-# vclust align output formats
+# Vclust align output formats
 ALIGN_OUTFMT = {
     'lite': ALIGN_FIELDS[:2] + ALIGN_FIELDS[4:11],
     'standard': ALIGN_FIELDS[:11],
@@ -546,6 +546,14 @@ def ranged_float_type(value):
         help='Show this help message and exit'
     )
 
+    # Info parser
+    info_parser = subparsers.add_parser(
+        'info',
+        help='Show information about the tool and its dependencies',
+        formatter_class=fmt,
+        add_help=False,
+    )
+
     # Show help message if the script is run without any arguments.
     if len(sys.argv[1:]) == 0:
         parser.print_help()
@@ -1137,6 +1145,13 @@ def cmd_clusty(
     return cmd
 
 
+def vclust_info():
+    print(f'Vclust               {__version__}')
+    for bin_path in [BIN_KMERDB, BIN_FASTASPLIT, BIN_LZANI, BIN_CLUSTY]:
+        validate_binary(bin_path)
+        print(f'{bin_path.name:<20} ok')
+
+
 class CustomHelpFormatter(argparse.HelpFormatter):
     """Custom help message formatter for argparse."""
 
@@ -1166,11 +1181,16 @@ def main():
     # Initialize logger
     logger = create_logger(
         name='vclust',
-        log_level=logging.INFO if args.verbose else logging.ERROR,
+        log_level=(logging.INFO 
+                   if (hasattr(args, 'verbose') and args.verbose) 
+                   else logging.ERROR),
     )
 
+    # Info
+    if args.command == 'info':
+        vclust_info()
     # Prefilter
-    if args.command == 'prefilter':
+    elif args.command == 'prefilter':
         args.bin_kmerdb = validate_binary(args.bin_kmerdb)
         args = validate_args_prefilter(args, parser)
         args = validate_args_fasta_input(args, parser)