Fixes issue 232: Pyani throws an error when it fails to find 3rd-party tool versions (but they are installed)

.circleci/config.yml

@@ -47,7 +47,8 @@ jobs:
       - run:
           name: update apt-get
           command: |
-            sudo apt-get update
+            sudo apt-get update --allow-releaseinfo-change
+            sudo apt-get upgrade
       - run:
           name: install third-party tools
           command: |

pyani/anib.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # (c) The James Hutton Institute 2016-2019
-# (c) University of Strathclyde 2019-2020
+# (c) University of Strathclyde 2019-2021
 # Author: Leighton Pritchard
 #
 # Contact: leighton.pritchard@strath.ac.uk
@@ -16,7 +16,7 @@
 # The MIT License
 #
 # Copyright (c) 2016-2019 The James Hutton Institute
-# Copyright (c) 2019-2020 University of Strathclyde
+# Copyright (c) 2019-2021 University of Strathclyde
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -81,6 +81,7 @@
 aligned sequence identity used to calculate ANI.
 """
 
+import os
 import platform
 import re
 import shutil
@@ -114,7 +115,24 @@ def get_version(blast_exe: Path = pyani_config.BLASTN_DEFAULT) -> str:
         Package: blast 2.9.0, build Jun 10 2019 09:40:53
 
     This is concatenated with the OS name.
+
+    The following circumstances are explicitly reported as strings
+
+    - no executable at passed path
+    - non-executable file at passed path
+    - no version info returned
     """
+    blastn_path = Path(shutil.which(blast_exe))  # type:ignore
+
+    if blastn_path is None:
+        return f"{blast_exe} is not found in $PATH"
+
+    if not blastn_path.is_file():  # no executable
+        return f"No blastn executable at {blastn_path}"
+
+    if not os.access(blastn_path, os.X_OK):  # file exists but not executable
+        return f"blastn exists at {blastn_path} but not executable"
+
     cmdline = [blast_exe, "-version"]
     result = subprocess.run(
         cmdline,  # type: ignore
@@ -126,7 +144,11 @@ def get_version(blast_exe: Path = pyani_config.BLASTN_DEFAULT) -> str:
     version = re.search(  # type: ignore
         r"(?<=blastn:\s)[0-9\.]*\+", str(result.stdout, "utf-8")
     ).group()
-    return f"{platform.system()}_{version}"
+
+    if 0 == len(version.strip()):
+        return f"blastn exists at {blastn_path} but could not retrieve version"
+
+    return f"{platform.system()}_{version} ({blastn_path})"
 
 
 # Divide input FASTA sequences into fragments

pyani/aniblastall.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# (c) University of Strathclyde 2020
+# (c) University of Strathclyde 2021
 # Author: Leighton Pritchard
 #
 # Contact: leighton.pritchard@strath.ac.uk
@@ -14,7 +14,7 @@
 #
 # The MIT License
 #
-# Copyright (c) 2020 University of Strathclyde
+# Copyright (c) 2021 University of Strathclyde
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -35,11 +35,13 @@
 # THE SOFTWARE.
 """Code to implement the ANIblastall average nucleotide identity method."""
 
+import logging
+import os
 import platform
 import re
+import shutil
 import subprocess
 
-
 from pathlib import Path
 
 from . import pyani_config
@@ -59,16 +61,48 @@ def get_version(blast_exe: Path = pyani_config.BLASTALL_DEFAULT) -> str:
         one-line descriptions for (V) [ersion] is bad or out of range [? to ?]
 
     This is concatenated with the OS name.
+
+    The following circumstances are explicitly reported as strings
+
+    - no executable at passed path
+    - non-executable file at passed path
+    - no version info returned
+    - executable cannot be run on this OS
     """
-    cmdline = [blast_exe, "-version"]
-    result = subprocess.run(
-        cmdline,  # type: ignore
-        shell=False,
-        stdout=subprocess.PIPE,  # type: ignore
-        stderr=subprocess.PIPE,
-        check=False,  # blastall doesn't return 0
-    )
-    version = re.search(  # type: ignore
-        r"(?<=blastall\s)[0-9\.]*", str(result.stderr, "utf-8")
-    ).group()
-    return f"{platform.system()}_{version}"
+    logger = logging.getLogger(__name__)
+
+    blastall_path = Path(shutil.which(blast_exe))  # type:ignore
+
+    if blastall_path is None:
+        return f"{blast_exe} is not found in $PATH"
+
+    if not blastall_path.is_file():  # no executable
+        return f"No blastall at {blastall_path}"
+
+    if not os.access(blastall_path, os.X_OK):  # file exists but not executable
+        return f"blastall exists at {blastall_path} but not executable"
+
+    if platform.system() == "Darwin":
+        cmdline = [blast_exe, "-version"]
+    else:
+        cmdline = [blast_exe]
+
+    try:
+        result = subprocess.run(
+            cmdline,  # type: ignore
+            shell=False,
+            stdout=subprocess.PIPE,  # type: ignore
+            stderr=subprocess.PIPE,
+            check=False,  # blastall doesn't return 0
+        )
+        version = re.search(  # type: ignore
+            r"(?<=blastall\s)[0-9\.]*", str(result.stderr, "utf-8")
+        ).group()
+    except OSError:
+        logger.warning("blastall executable will not run", exc_info=True)
+        return f"blastall exists at {blastall_path} but could not be executed"
+
+    if 0 == len(version.strip()):
+        return f"blastall exists at {blastall_path} but could not retrieve version"
+
+    return f"{platform.system()}_{version} ({blastall_path})"

pyani/anim.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 # (c) The James Hutton Institute 2016-2019
-# (c) University of Strathclyde 2019
+# (c) University of Strathclyde 2019-2021
 # Author: Leighton Pritchard
 #
 # Contact:
@@ -17,7 +17,7 @@
 # The MIT License
 #
 # Copyright (c) 2016-2019 The James Hutton Institute
-# Copyright (c) 2019 University of Strathclyde
+# Copyright (c) 2019-2021 University of Strathclyde
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -53,8 +53,10 @@
 """
 
 import logging
+import os
 import platform
 import re
+import shutil
 import subprocess
 import sys
 
@@ -101,14 +103,35 @@ def get_version(nucmer_exe: Path = pyani_config.NUCMER_DEFAULT) -> str:
         NUCmer (NUCleotide MUMmer) version 3.1
 
     we concatenate this with the OS name.
+
+    The following circumstances are explicitly reported as strings
+
+    - no executable at passed path
+    - non-executable file at passed path
+    - no version info returned
     """
+    nucmer_path = Path(shutil.which(nucmer_exe))  # type:ignore
+
+    if nucmer_path is None:
+        return f"{nucmer_exe} is not found in $PATH"
+
+    if not nucmer_path.is_file():  # no executable
+        return f"No nucmer at {nucmer_path}"
+
+    if not os.access(nucmer_path, os.X_OK):  # file exists but not executable
+        return f"nucmer exists at {nucmer_path} but not executable"
+
     cmdline = [nucmer_exe, "-V"]  # type: List
     result = subprocess.run(
         cmdline, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True
     )
     match = re.search(r"(?<=version\s)[0-9\.]*", str(result.stderr, "utf-8"))
     version = match.group()  # type: ignore
-    return f"{platform.system()}_{version}"
+
+    if 0 == len(version.strip()):
+        return f"nucmer exists at {nucmer_path} but could not retrieve version"
+
+    return f"{platform.system()}_{version} ({nucmer_path})"
 
 
 # Generate list of Job objects, one per NUCmer run

pyani/scripts/pyani_script.py

@@ -56,8 +56,7 @@
 
 CITATION_INFO = [
     termcolor(
-        "If you use pyani in your work, please cite the following publication:",
-        "green",
+        "If you use pyani in your work, please cite the following publication:", "green"
     ),
     termcolor(
         "\tPritchard, L., Glover, R. H., Humphris, S., Elphinstone, J. G.,", "yellow",
@@ -69,8 +68,7 @@
         "\tfood security: soft-rotting enterobacterial plant pathogens.'", "yellow"
     ),
     termcolor(
-        "\tAnalytical Methods, 8(1), 12–24. http://doi.org/10.1039/C5AY02550H",
-        "yellow",
+        "\tAnalytical Methods, 8(1), 12–24. http://doi.org/10.1039/C5AY02550H", "yellow"
     ),
 ]
 
@@ -81,14 +79,25 @@ def run_main(argv: Optional[List[str]] = None) -> int:
 
     :param argv:
     """
+    # We need to catch the case with no arguments here, otherwise
+    # argparse will infer -h as an implied argument
+    if len(sys.argv) == 1 and argv is None:
+        sys.stderr.write(f"{VERSION_INFO}\n")
+        return 0
+
     # If we need to (i.e. a namespace isn't passed), parse the command-line
     if argv is None:
         args = parse_cmdline()
     else:
         args = parse_cmdline(argv)
 
-    # Catch execution with no arguments
-    if len(sys.argv) == 1 and argv is None:
+    # Catch requests for citation and version information.
+    # This should stop any subcommands from running, also.
+    if args.citation:
+        sys.stderr.write(f"{VERSION_INFO}\n")
+        sys.stderr.write("\n".join(CITATION_INFO) + "\n")
+        return 0
+    if args.version:
         sys.stderr.write(f"{VERSION_INFO}\n")
         return 0