Report Augur versions on error without --use-conda

Snakefile

@@ -8,6 +8,7 @@ from getpass import getuser
 from snakemake.logging import logger
 from snakemake.utils import validate
 from collections import OrderedDict
+import textwrap
 import time
 
 # Store the user's configuration prior to loading defaults, so we can check for
@@ -132,3 +133,21 @@ if "localrules" in config:
 if "custom_rules" in config:
     for rule_file in config["custom_rules"]:
         include: rule_file
+
+onerror:
+    # If the workflow failed and the user isn't using the workflow's Conda
+    # environment, report the required and installed Augur versions and a
+    # recommendation to use the `--use-conda` flag.
+    if not workflow.use_conda:
+        min_augur_version, actual_augur_version = report_augur_versions(config["conda_environment"])
+
+        print(f"Required Augur version: {min_augur_version}", file=sys.stderr)
+        print(f"Installed Augur version: {actual_augur_version}", file=sys.stderr)
+        print(
+            textwrap.fill(
+                "Run this workflow with Snakemake's `--use-conda` flag " +
+                "or update your Docker image " +
+                "to ensure you're using the latest versions of the required software."
+            ),
+            file=sys.stderr
+        )

workflow/snakemake_rules/common.smk

@@ -2,6 +2,50 @@
 """
 import datetime
 from urllib.parse import urlsplit
+import yaml
+
+
+def report_augur_versions(conda_env_file):
+    """Check the globally available version of Augur against the version required in
+    the Conda environment file.
+
+    """
+    with open(conda_env_file, "r") as fh:
+        env = yaml.load(fh, yaml.FullLoader)
+
+    # Check for Conda installation of Augur first.
+    augur_package = [
+        package
+        for package in env["dependencies"]
+        if not isinstance(package, dict) and package.startswith("augur")
+    ] or None
+
+    if augur_package is None:
+        # Check for pip installation of Augur.
+        pip_packages = [
+            package["pip"]
+            for package in env["dependencies"]
+            if isinstance(package, dict) and "pip" in package
+        ] or None
+
+        if pip_packages is not None:
+            augur_package = [
+                package
+                for package in pip_packages[0]
+                if package.startswith("nextstrain-augur")
+            ] or None
+
+    min_augur_version = "unknown"
+    if augur_package is not None and "=" in augur_package[0]:
+        min_augur_version = augur_package[0].split("=")[-1]
+
+    try:
+        from augur.__version__ import __version__ as augur_version
+    except ModuleNotFoundError:
+        augur_version = "not installed"
+
+    return min_augur_version, augur_version
+
 
 def numeric_date(dt=None):
     """