Add resource usage

Closes #263

pyproject.toml

@@ -20,6 +20,8 @@ dependencies = [
   "scipy",
   "click",
   "zarr<2.18",
+  "humanize",
+  "resource",
 ]
 dynamic = ["version"]
 

sc2ts/cli.py

@@ -7,6 +7,8 @@
 import contextlib
 import dataclasses
 import datetime
+import time
+import os
 
 import numpy as np
 import tqdm
@@ -15,13 +17,42 @@
 import tsinfer
 import click
 import daiquiri
+import humanize
 import pandas as pd
 
+try:
+    import resource
+except ImportError:
+    resource = None  # resource.getrusage absent on windows, so skip outputting max mem
+
 import sc2ts
 from . import core
+from . import utils
 
 logger = logging.getLogger(__name__)
 
+__before = time.time()
+
+
+def summarise_usage():
+    wall_time = time.time() - __before
+    user_time = os.times().user
+    sys_time = os.times().system
+    if resource is None:
+        # Don't report max memory on Windows. We could do this using the psutil lib, via
+        # psutil.Process(os.getpid()).get_ext_memory_info().peak_wset if demand exists
+        maxmem_str = "?"
+    else:
+        max_mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
+        if sys.platform != "darwin":
+            max_mem *= 1024  # Linux and other OSs (e.g. freeBSD) report maxrss in kb
+        maxmem_str = "; max_memory=" + humanize.naturalsize(max_mem, binary=True)
+    return (
+        f"Done in {humanize.naturaldelta(wall_time)}; "
+        f"elapsed={wall_time:.2f}; user={user_time:.2f}; sys={sys_time:.2f}"
+        + maxmem_str
+    )
+
 
 def get_environment():
     """
@@ -356,6 +387,10 @@ def extend(
             show_progress=progress,
         )
         add_provenance(ts_out, output_ts)
+    resource_usage = f"{date}:{summarise_usage()}"
+    logger.info(resource_usage)
+    if progress:
+        print(resource_usage, file=sys.stderr)
 
 
 @click.command()