Installation through PyPi, Set default --min-kmers to 20

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

MANIFEST.in

@@ -0,0 +1,4 @@
+include README.md
+include LICENSE
+recursive-include bin *
+recursive-exclude 3rd_party *

README.md

@@ -1,11 +1,14 @@
 # <img src="./images/logo.svg" alt="Vclust logo" /> Vclust
 
-![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)
-[![Bioconda downloads](https://img.shields.io/conda/dn/bioconda/vclust.svg?style=flag&label=Bioconda%20downloads)](https://anaconda.org/bioconda/vclust)
+![version](https://img.shields.io/badge/version-1.2.8-blue.svg)
+![PyPI - Version](https://img.shields.io/pypi/v/vclust?label=PyPI%20version&color=blue)
 [![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)
 
+![PyPI - Downloads](https://img.shields.io/pypi/dm/vclust?label=PyPI%20downloads)
+[![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)
+[![Bioconda downloads](https://img.shields.io/conda/dn/bioconda/vclust.svg?style=flag&label=Bioconda%20downloads)](https://anaconda.org/bioconda/vclust)
+
 ![x86-64](https://img.shields.io/static/v1?label=%E2%80%8B&message=x86-64&color=yellow&logo=PCGamingWiki&logoColor=white)
 ![ARM](https://img.shields.io/static/v1?label=%E2%80%8B&message=ARM&color=yellow&logo=Raspberry%20Pi&logoColor=white)
 ![Apple M](https://img.shields.io/static/v1?label=%E2%80%8B&message=Apple%20M&color=yellow&logo=Apple&logoColor=white)
@@ -51,18 +54,17 @@ For datasets containing up to 1000 viral genomes, Vclust is available at [http:/
 ## Quick start
 
 ```bash
-# Clone repository and build Vclust
-git clone --recurse-submodules https://github.com/refresh-bio/vclust
-cd vclust && make -j
+# Install Vclust (requires Python >= 3.7)
+pip install vclust
 
 # Prefilter similar genome sequence pairs before conducting pairwise alignments.
-./vclust.py prefilter -i example/multifasta.fna -o fltr.txt
+vclust prefilter -i example/multifasta.fna -o fltr.txt
 
 # Align similar genome sequence pairs and calculate pairwise ANI measures.
-./vclust.py align -i example/multifasta.fna -o ani.tsv --filter fltr.txt
+vclust align -i example/multifasta.fna -o ani.tsv --filter fltr.txt
 
 # Cluster genome sequences based on given ANI measure and minimum threshold.
-./vclust.py cluster -i ani.tsv -o clusters.tsv --ids ani.ids.tsv --metric ani --ani 0.95
+vclust cluster -i ani.tsv -o clusters.tsv --ids ani.ids.tsv --metric ani --ani 0.95
 ```
 ## Documentation
 

pyproject.toml

@@ -0,0 +1,56 @@
+[build-system]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+py-modules = ["vclust"]
+
+[tool.setuptools.packages.find]
+where = ["./"]
+
+[project]
+name = "vclust-test"
+description = """Fast and accurate tool for calculating \
+Average Nucleotide Identity (ANI) and clustering virus \
+genomes and metagenomic contigs"""
+readme = "README.md"
+license = { file = "LICENSE" }
+authors = [
+  { name = "Andrzej Zielezinski", email = "[email protected]" },
+  { name = "Adam Gudyś", email = "[email protected]" },
+  { name = "Sebastian Deorowicz", email = "[email protected]" },
+]
+requires-python = ">=3.7"
+dynamic = ["version"]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Natural Language :: English",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Operating System :: POSIX :: Linux",
+  "Operating System :: MacOS",
+  "License :: OSI Approved :: GNU Affero General Public License v3",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.7",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12", 
+]
+
+[tool.setuptools.dynamic]
+version = { attr = "vclust.__version__" }
+
+[tool.setuptools.package-data]
+"*" = ["bin/*"]
+
+[project.scripts]
+vclust = "vclust:main"
+
+[project.urls]
+Homepage = "https://github.com/refresh-bio/vclust"
+Documentation = "https://github.com/refresh-bio/vclust/wiki"
+Website = "http://vclust.org"

vclust.py

@@ -9,13 +9,14 @@
 import multiprocessing
 import os
 import pathlib
+import platform
 import shutil
 import subprocess
 import sys
 import typing
 import uuid
 
-__version__ = '1.2.7'
+__version__ = '1.2.8'
 
 DEFAULT_THREAD_COUNT = min(multiprocessing.cpu_count(), 64)
 
@@ -59,7 +60,7 @@ def ranged_float_type(value):
         return f
 
     parser = argparse.ArgumentParser(
-        description=f'%(prog)s v.{__version__}: calculate ANI and cluster '
+        description=f'%(prog)s v{__version__}: calculate ANI and cluster '
         'virus (meta)genome sequences',
         add_help=False,
     )
@@ -117,7 +118,7 @@ def ranged_float_type(value):
         '--min-kmers',
         metavar="<int>",
         type=int,
-        default=10,
+        default=20,
         help='Filter genome pairs based on minimum number of shared k-mers '
              '[%(default)s]'
     )
@@ -531,7 +532,7 @@ def ranged_float_type(value):
         '--bin',
         metavar='<file>',
         type=pathlib.Path,
-        dest="BIN_CLUSTY",
+        dest="bin_clusty",
         default=f'{BIN_CLUSTY}',
         help='Path to the Clusty binary [%(default)s]'
     )
@@ -603,8 +604,8 @@ def get_uuid() -> str:
     return f'vclust-{str(uuid.uuid4().hex)[:10]}'
 
 
-def validate_binary(bin_path: pathlib.Path) -> pathlib.Path:
-    """Validates the existence and executability of a binary file.
+def _validate_binary(bin_path: pathlib.Path) -> pathlib.Path:
+    """Validates the presence and executability of a binary file.
 
     This function checks if the provided path points to an existing binary file
     and if it is executable. It also attempts to run the binary to ensure it
@@ -618,16 +619,16 @@ def validate_binary(bin_path: pathlib.Path) -> pathlib.Path:
         pathlib.Path: The resolved path to the binary file.
 
     Raises:
-        SystemExit: If the binary file does not exist, is not executable, or 
-                    if running the binary encounters an error.
+        RuntimeError: If the binary file does not exist, is not executable, 
+                      or if running the binary encounters an error.
     """
     bin_path = bin_path.resolve()
 
     if not bin_path.exists():
-        exit(f'error: Executable not found: {bin_path}')
+        raise RuntimeError(f'File not found: {bin_path}')
 
     if not bin_path.is_file() or not os.access(bin_path, os.X_OK):
-        exit(f'error: Binary file not executable: {bin_path}')
+        raise RuntimeError(f'Binary file not executable: {bin_path}')
 
     try:
         subprocess.run(
@@ -638,14 +639,21 @@ def validate_binary(bin_path: pathlib.Path) -> pathlib.Path:
             check=True
         )
     except subprocess.CalledProcessError as e:
-        exit(f'error: Running {bin_path} failed with message: {e.stderr}')
+        raise RuntimeError(f'Running {bin_path} failed with message: {e.stderr}')
     except OSError as e:
-        exit(f'error: OSError in {bin_path} - {e}')
+        raise RuntimeError(f'OSError in {bin_path} - {e}')
     except Exception as e:
-        exit(f'error: Unexpected error in binary {bin_path} - {e}')
+        raise RuntimeError(f'Unexpected error in binary {bin_path} - {e}')
     return bin_path
 
 
+def validate_binary(bin_path: pathlib.Path) -> pathlib.Path:
+    try:
+        return _validate_binary(bin_path)
+    except RuntimeError as e:
+        sys.exit(f'error: {e}')
+
+
 def validate_args_fasta_input(args, parser) -> argparse.Namespace:
     """Validates the arguments for FASTA input."""
     args.is_multifasta = True
@@ -732,13 +740,13 @@ def run(
         )
     except subprocess.CalledProcessError as e:
         logger.error(f'Process {" ".join(cmd)} failed with message: {e.stderr}')
-        exit(1)
+        sys.exit(1)
     except OSError as e:
         logger.error(f'OSError: {" ".join(cmd)} failed with message: {e}')
-        exit(1)
+        sys.exit(1)
     except Exception as e:
         logger.error(f'Unexpected: {" ".join(cmd)} failed with message: {e}')
-        exit(1)  
+        sys.exit(1)  
     logger.info(f'Done')
     return process
 
@@ -1145,11 +1153,75 @@ 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')
+def vclust_info() -> None:
+    """    
+    Displays the Vclust version, installation paths, and binary dependencies. 
+    Checks for the presence and executable status of required binaries.
+
+    Exits with a non-zero status if any dependencies are missing or 
+    not executable.
+
+    Returns:
+        None
+    
+    Raises:
+        SystemExit: If any binary dependencies are missing or not executable.
+    
+    """
+    # ANSI color codes for terminal output.
+    GREEN = '\033[92m'
+    RED = '\033[91m'
+    RESET = '\033[0m'
+
+    binaries = {
+        'Kmer-db': BIN_KMERDB,
+        'LZ-ANI': BIN_LZANI,
+        'Clusty': BIN_CLUSTY,
+        'multi-fasta-split': BIN_FASTASPLIT,
+    }
+
+    output_lines = [
+        f'Vclust version {__version__} (Python {platform.python_version()})',
+        '',
+        'Installed at:',
+        f'   {pathlib.Path(__file__).resolve()}',
+        f'   {BIN_DIR.resolve()}',
+        '',
+        'Binary dependencies:',
+    ]
+
+    errors = []  # List to collect any errors encountered during binary checks.
+
+    # Check each binary's presence and version.
+    for name, path in binaries.items():
+        try:
+            _validate_binary(path)
+            version = subprocess.run(
+                [str(path), '-version' if name == 'Kmer-db' else '--version'],
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,
+                text=True,
+                check=True
+            ).stderr.strip()
+            output_lines.append(f'   {name:<20} v{version:<10}')
+        except Exception as e:
+            output_lines.append(f'   {name:<20} [error]')
+            errors.append((name, e))
+
+    # Append the status summary based on any encountered errors.
+    output_lines.append('')
+
+    if errors:
+        output_lines.append(f'{RED}Status: error{RESET}')
+        output_lines.extend(f"   - {name}: {error}" for name, error in errors)
+    else:
+        output_lines.append(f'{GREEN}Status: ok{RESET}')
+
+    # Output the complete information.
+    print('\n'.join(output_lines))
+
+    if errors:
+        sys.exit(1)
 
 
 class CustomHelpFormatter(argparse.HelpFormatter):
@@ -1324,7 +1396,7 @@ def main():
 
     # Cluster
     elif args.command == 'cluster':
-        args.BIN_CLUSTY = validate_binary(args.BIN_CLUSTY)
+        args.bin_clusty = validate_binary(args.bin_clusty)
         args = validate_args_cluster(args, parser)
 
         cmd = cmd_clusty(
@@ -1344,7 +1416,7 @@ def main():
             leiden_resolution=args.leiden_resolution,
             leiden_beta=args.leiden_beta,
             leiden_iterations=args.leiden_iterations,
-            bin_path=args.BIN_CLUSTY,
+            bin_path=args.bin_clusty,
         )
         p = run(cmd, args.verbose, logger)