Add a debugging mode controlled by AUGUR_DEBUG

At the moment, this only enables printing of stack traces and the full
exception chain for handled (i.e. anticipated) errors, which otherwise
were not printed.  In the future, this mode can also control the output
of verbose debugging/troubleshooting logging for more commands.

Commit contents and message based on similar commits I made to
Nextstrain CLI.¹

Resolves <#1308>.

¹ <nextstrain/cli@229f2e8>
  <nextstrain/cli@b6d9290>
  <nextstrain/cli#208>

CHANGES.md

@@ -6,6 +6,7 @@
 
 * A new command, `augur merge`, now allows for generalized merging of two or more metadata tables. [#1563][] (@tsibley)
 * Two new commands, `augur read-file` and `augur write-file`, now allow external programs to do i/o like Augur by piping from/to these new commands.  They provide handling of compression formats and newlines consistent with the rest of Augur. [#1562][] (@tsibley)
+* A new debugging mode can be enabled by setting the `AUGUR_DEBUG` environment variable to `1` (or another truthy value).  Currently the only effect is to print more information about handled (i.e. anticipated) errors.  For example, stack traces and parent exceptions in an exception chain are normally omitted for handled errors, but setting this env var includes them.  Future debugging and troubleshooting features, like verbose operation logging, will likely also condition on this new debugging mode. [#1563][] (@tsibley)
 
 ### Bug Fixes
 

augur/__init__.py

@@ -11,6 +11,7 @@
 from types import SimpleNamespace
 from treetime import TreeTimeError, TreeTimeUnknownError
 
+from .debug import DEBUGGING
 from .errors import AugurError
 from .io.print import print_err
 from .argparse_ import add_command_subparsers, add_default_command
@@ -68,21 +69,35 @@ def run(argv):
     try:
         return args.__command__.run(args)
     except AugurError as e:
+        if DEBUGGING:
+            traceback.print_exc(file=sys.stderr)
         print_err(f"ERROR: {e}")
         sys.exit(2)
     except RecursionError:
+        if DEBUGGING:
+            traceback.print_exc(file=sys.stderr)
         print_err("FATAL: Maximum recursion depth reached. You can set the env variable AUGUR_RECURSION_LIMIT to adjust this (current limit: {})".format(sys.getrecursionlimit()))
         sys.exit(2)
     except FileNotFoundError as e:
+        if DEBUGGING:
+            traceback.print_exc(file=sys.stderr)
         print_err(f"ERROR: {e.strerror}: '{e.filename}'")
         sys.exit(2)
     except TreeTimeUnknownError as e:
+        # TreeTime already prints the traceback (and some other verbiage) in
+        # TreeTime.run()¹, so don't duplicate it.  This is also why the "(see
+        # above)" in our message below makes sense.
+        #   -trs, 14 Aug 2024
+        #
+        # ¹ <https://github.com/neherlab/treetime/blob/531f776bcad3b8b11fd470a403a9c06c78b07e36/treetime/treetime.py#L54-L73>
         print_err(dedent("""\
             ERROR from TreeTime: An error occurred in TreeTime (see above). This may be due to an issue with TreeTime or Augur.
             Please report you are calling TreeTime via Augur.
             """))
         sys.exit(2)
     except TreeTimeError as e:
+        if DEBUGGING:
+            traceback.print_exc(file=sys.stderr)
         print_err(f"ERROR: {e}")
         print_err("\n")
         print_err(dedent("""\

augur/debug.py

@@ -0,0 +1,12 @@
+"""
+Debug flags and utilities.
+
+.. envvar:: AUGUR_DEBUG
+
+    Set to a truthy value (e.g. 1) to print more information about (handled)
+    errors.  For example, when this is not set or falsey, stack traces and
+    parent exceptions in an exception chain are omitted from handled errors.
+"""
+from os import environ
+
+DEBUGGING = bool(environ.get("AUGUR_DEBUG"))