From ea85954ffeb6eb77c962fd06f1b311380cdb26e6 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Tue, 1 Oct 2024 13:37:27 -0700
Subject: [PATCH] fixup! Use ISO duration format for clade recency

---
 defaults/parameters.yaml                    |  2 +-
 docs/src/reference/workflow-config-file.rst |  7 ++++---
 workflow/snakemake_rules/common.smk         | 11 ++++++++++-
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/defaults/parameters.yaml b/defaults/parameters.yaml
index bd91600c2..2ff6f2ac0 100644
--- a/defaults/parameters.yaml
+++ b/defaults/parameters.yaml
@@ -135,7 +135,7 @@ ancestral:
   inference: "joint"
 
 colors:
-  # Months back to color clades, if "all" then all clades are colored
+  # Amount of time back to color clades, if "all" then all clades are colored
   # Can be specified per build in builds.yaml
   default:
     clade_recency: "all"
diff --git a/docs/src/reference/workflow-config-file.rst b/docs/src/reference/workflow-config-file.rst
index bfa004f78..ac621b4d4 100644
--- a/docs/src/reference/workflow-config-file.rst
+++ b/docs/src/reference/workflow-config-file.rst
@@ -965,9 +965,10 @@ Each named traits configuration (``default`` or build-named) supports the follow
 clade_recency
 ~~~~~~~~~~~~~
 
--  type: integer
--  description: if integer value is provided, restrict to clades found in tree within X months of present
--  default: ``all``
+-  type: string
+-  format: `ISO 8601 <https://en.wikipedia.org/wiki/ISO_8601#Durations>`__ duration with optional ``P`` prefix (e.g. ``2M``, ``18M``, ``1Y6M``)
+-  description: restrict to clades found in tree within this duration from present
+-  default: ``all`` (no restriction)
 
 traits
 ------
diff --git a/workflow/snakemake_rules/common.smk b/workflow/snakemake_rules/common.smk
index 9a15f2841..91c687e11 100644
--- a/workflow/snakemake_rules/common.smk
+++ b/workflow/snakemake_rules/common.smk
@@ -1,6 +1,7 @@
 """Small, shared functions used to generate inputs and parameters.
 """
 import datetime
+import isodate
 from itertools import product
 from shlex import (
     quote as shquote,       # shquote() is used in this file and also other workflow files
@@ -181,9 +182,17 @@ def _get_clade_recency_for_wildcards(wildcards):
 
 def _get_clade_recency_argument(wildcards):
     clade_recency_setting = _get_clade_recency_for_wildcards(wildcards)
+
+    def is_duration(date):
+        try:
+            isodate.parse_duration(duration)
+            return True
+        except:
+            return False
+
     if clade_recency_setting == "all":
         return ""
-    elif isinstance(clade_recency_setting, int):
+    elif is_duration(clade_recency_setting):
         return "--clade-recency " + shquote(str(clade_recency_setting))
     else:
         return ""