Auto-versioning changes

When truvari is installed from the repo and if it's a develop version, add the commit hash to the version.
If the repo has unstaged changes, 'uc' is appended to the version as well.
This enables better tracking when results are created off of develop.
setup_logging now optionally shows this version information at the head of logs. This is turned on for
all commands that use setup_logging but will remain off by default for outside tools/scripts that reuse setup_logging

setup.py

@@ -1,6 +1,7 @@
 import codecs
 import os.path
 from setuptools import setup
+import subprocess
 
 def read(rel_path):
     here = os.path.abspath(os.path.dirname(__file__))
@@ -11,17 +12,44 @@ def get_version(rel_path):
     for line in read(rel_path).splitlines():
         if line.startswith('__version__'):
             delim = '"' if '"' in line else "'"
-            return line.split(delim)[1]
+            vers = line.split(delim)[1]
+            if vers.endswith('-dev'):
+                vers += '0+' + _get_repo_hash()
+            return vers
     else:
         raise RuntimeError("Unable to find version string.")
 
+def _get_repo_hash():
+    """
+    Talk to git and find out the tag/hash of our latest commit
+    Add '_uc' to the end if the repo has uncommited changes
+    """
+    try:
+        p = subprocess.Popen("git rev-parse --short HEAD".split(' '),
+                            stdout=subprocess.PIPE)
+    except EnvironmentError:
+        print("Couldn't run git to get a version number for setup.py")
+        return "detached"
+
+    ver = p.communicate()[0].decode().strip()
+    try:
+        p = subprocess.Popen("git diff --exit-code".split(' '),
+                            stdout=subprocess.PIPE)
+        p.communicate()
+        if p.returncode:
+            ver += '_uc'
+    except EnvironmentError:
+        pass
+
+    return ver
+
 
 setup(
     name='Truvari',
     version=get_version('truvari/__init__.py'),
     author="ACEnglish",
     author_email="acenglish@gmail.com",
-    url="https://github.com/spiralgenetics/truvari",
+    url="https://github.com/ACEnglish/truvari",
     packages=['truvari', 'truvari/annotations'],
     license='MIT',
     description="Structural variant comparison tool for VCFs",

truvari/__main__.py

@@ -23,7 +23,8 @@
 
 def version(args):
     """Print the version"""
-    print(f"Truvari v{__version__}")
+    from importlib.metadata import version
+    print(f"Truvari v{version('truvari')}")
 
 
 TOOLS = {'bench': bench_main,

truvari/annotations/bpovl.py

@@ -53,7 +53,7 @@ def parse_args(args):
     else:
         args.anno_psets = [args.sequence, args.begin, args.end,
                            args.one_based, args.comment]
-    truvari.setup_logging()
+    truvari.setup_logging(show_version=True)
     return args
 
 

truvari/annotations/density.py

@@ -30,7 +30,7 @@ def parse_args(args):
     parser.add_argument("-t", "--threshold", type=float, default=3,
                         help="std for identifying 'dense' regions (%(default)s)")
     args = parser.parse_args(args)
-    truvari.setup_logging()
+    truvari.setup_logging(show_version=True)
     return args
 
 def density_main(args):

truvari/annotations/dpcnt.py

@@ -25,7 +25,7 @@ def parse_args(args):
                         help="Only count sites with present (non ./.) genotypes")
     parser.add_argument("-o", "--output", type=str, default="/dev/stdout",
                         help="Output filename (stdout)")
-    truvari.setup_logging()
+    truvari.setup_logging(show_version=True)
     return parser.parse_args(args)
 
 

truvari/annotations/gccontent.py

@@ -21,7 +21,7 @@ def parse_args(args):
                         help="Output filename (stdout)")
     parser.add_argument("-r", "--reference", type=str, required=True,
                         help="Reference fasta")
-    truvari.setup_logging()
+    truvari.setup_logging(show_version=True)
     return parser.parse_args(args)
 
 

truvari/annotations/grm.py

@@ -176,7 +176,7 @@ def parse_args(args):
     parser.add_argument("--debug", action="store_true",
                         help="Verbose logging")
     args = parser.parse_args(args)
-    truvari.setup_logging(args.debug)
+    truvari.setup_logging(args.debug, show_version=True)
     return args
 
 

truvari/annotations/grpaf.py

@@ -30,7 +30,7 @@ def parse_args(args):
     parser.add_argument("--debug", action="store_true",
                         help="Verbose logging")
     args = parser.parse_args(args)
-    truvari.setup_logging(args.debug)
+    truvari.setup_logging(args.debug, show_version=True)
     return args
 
 

truvari/annotations/gtcnt.py

@@ -18,7 +18,7 @@ def parse_args(args):
                         help="VCF to annotate (stdin)")
     parser.add_argument("-o", "--output", type=str, default="/dev/stdout",
                         help="Output filename (stdout)")
-    truvari.setup_logging()
+    truvari.setup_logging(show_version=True)
     return parser.parse_args(args)
 
 

truvari/annotations/hompct.py

@@ -30,7 +30,7 @@ def parse_args(args):
     parser.add_argument("--debug", action="store_true",
                         help="Verbose logging")
     args = parser.parse_args(args)
-    truvari.setup_logging(args.debug)
+    truvari.setup_logging(args.debug, show_version=True)
     return args
 
 

truvari/annotations/lcr.py

@@ -86,7 +86,7 @@ def parse_args(args):
                         help="VCF to annotate (stdin)")
     parser.add_argument("-o", "--output", type=str, default="/dev/stdout",
                         help="Output filename (stdout)")
-    truvari.setup_logging()
+    truvari.setup_logging(show_version=True)
     return parser.parse_args(args)
 
 def lcr_main(cmdargs):

truvari/annotations/numneigh.py

@@ -38,7 +38,7 @@ def parse_args(args):
     parser.add_argument("--debug", action="store_true", default=False,
                         help="Verbose logging")
     args = parser.parse_args(args)
-    truvari.setup_logging(args.debug)
+    truvari.setup_logging(args.debug, show_version=True)
     return args
 
 

truvari/annotations/remap.py

@@ -162,7 +162,7 @@ def parse_args(args):
     parser.add_argument("--debug", action="store_true",
                         help="Verbose logging")
     args = parser.parse_args(args)
-    truvari.setup_logging(args.debug)
+    truvari.setup_logging(args.debug, show_version=True)
     return args
 
 

truvari/annotations/repmask.py

@@ -195,7 +195,7 @@ def parse_args(args):
     parser.add_argument("--debug", action="store_true",
                         help="Verbose logging")
     args = parser.parse_args(args)
-    truvari.setup_logging(args.debug)
+    truvari.setup_logging(args.debug, show_version=True)
     return args
 
 

truvari/annotations/svinfo.py

@@ -20,7 +20,7 @@ def parse_args(args):
                         help="Output filename (stdout)")
     parser.add_argument("-m", "--minsize", type=truvari.restricted_int, default=50,
                         help="Minimum size of entry to annotate (%(default)s)")
-    truvari.setup_logging()
+    truvari.setup_logging(show_version=True)
     return parser.parse_args(args)
 
 

truvari/annotations/trf.py

@@ -582,7 +582,7 @@ def parse_args(args):
                         help="Verbose logging")
 
     args = parser.parse_args(args)
-    truvari.setup_logging(args.debug)
+    truvari.setup_logging(args.debug, show_version=True)
     return args
 
 def check_params(args):

truvari/bench.py

@@ -438,9 +438,8 @@ def setup_outputs(args):
     """
     os.mkdir(args.output)
     truvari.setup_logging(args.debug, truvari.LogFileStderr(
-        os.path.join(args.output, "log.txt")))
+        os.path.join(args.output, "log.txt")), show_version=True)
     logging.info("Params:\n%s", json.dumps(vars(args), indent=4))
-    logging.info(f"Truvari version: {truvari.__version__}")
 
     outputs = {}
     outputs["vcf_base"] = pysam.VariantFile(args.base)

truvari/collapse.py

@@ -349,7 +349,7 @@ def setup_outputs(args):
     Makes all of the output files
     return a ... to get to each of the
     """
-    truvari.setup_logging(args.debug)
+    truvari.setup_logging(args.debug, show_version=True)
     logging.info("Params:\n%s", json.dumps(vars(args), indent=4))
 
     outputs = {}

truvari/divide.py

@@ -31,7 +31,7 @@ def parse_args(args):
     parser.add_argument("-T", "--threads", type=int, default=1,
                         help="Number of threads for compressing/indexing sub-VCFs (%(default)s)")
     args = parser.parse_args(args)
-    truvari.setup_logging(False)
+    truvari.setup_logging(show_version=True)
     return args
 
 def flush_stack(in_vcf, stack, out_name, compress=True):

truvari/phab.py

@@ -225,7 +225,7 @@ def phab_main(cmdargs):
     Main
     """
     args = parse_args(cmdargs)
-    truvari.setup_logging(args.debug)
+    truvari.setup_logging(args.debug, show_version=True)
     if check_requirements():
         sys.exit(1)
     #if check_params(args):

truvari/segmentation.py

@@ -28,7 +28,7 @@ def parse_args(args):
     # parser.add_argument("--alter", action="store_true",
     # help="Add SEG Format field to all variants (false)")
     args = parser.parse_args(args)
-    truvari.setup_logging()
+    truvari.setup_logging(show_version=True)
     return args
 
 

truvari/utils.py

@@ -124,7 +124,9 @@ def flush(self):
         self.file_handler.flush()
 
 
-def setup_logging(debug=False, stream=sys.stderr, log_format="%(asctime)s [%(levelname)s] %(message)s"):
+def setup_logging(debug=False, stream=sys.stderr,
+                  log_format="%(asctime)s [%(levelname)s] %(message)s",
+                  show_version=False):
     """
     Create default logger
 
@@ -134,10 +136,15 @@ def setup_logging(debug=False, stream=sys.stderr, log_format="%(asctime)s [%(lev
     :type `stream`: file handler, optional
     :param `log_format`: Format of log lines
     :type `log_format`: string, optional
+    :param `show_version`: Start log with truvari version and command line args
+    :type `show_version`: bool, optional
     """
     logLevel = logging.DEBUG if debug else logging.INFO
     logging.basicConfig(stream=stream, level=logLevel, format=log_format)
-    logging.info("Running %s", " ".join(sys.argv))
+    if show_version:
+        from importlib.metadata import version
+        logging.info(f"Truvari v{version('truvari')}")
+        logging.info("Command %s", " ".join(sys.argv))
 
     def sendWarningsToLog(message, category, filename, lineno, *args, **kwargs):  # pylint: disable=unused-argument
         """

truvari/vcf2df.py

@@ -403,7 +403,7 @@ def parse_args(args):
     if args.sample:
         args.sample = args.sample.split(',')
 
-    truvari.setup_logging(args.debug)
+    truvari.setup_logging(args.debug, show_version=True)
     if args.compress not in range(10):
         logging.warning('--compress must be between 0-9. Setting to 3')
         args.compress = 3