From 28bfa7345afe8f69b3a146eb36f18995c5af778d Mon Sep 17 00:00:00 2001
From: Yang Chen <60239063+yangchen2@users.noreply.github.com>
Date: Sun, 5 Nov 2023 18:14:04 -0800
Subject: [PATCH] Confounders not accepted as string, issue #51

---
 qadabra/workflow/rules/common.smk | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/qadabra/workflow/rules/common.smk b/qadabra/workflow/rules/common.smk
index 46643b9..40a6d8f 100644
--- a/qadabra/workflow/rules/common.smk
+++ b/qadabra/workflow/rules/common.smk
@@ -8,7 +8,7 @@ names = datasets.index
 def get_dataset_cfg(wildcards, keys):
     d = datasets.loc[wildcards.dataset, keys].to_dict()
     if "confounders" in keys:
-        if not np.isnan(d["confounders"]):
+        if not np.isnull(d["confounders"]):
             d["confounders"] = d["confounders"].split(";")
         else:
             d["confounders"] = []
@@ -20,7 +20,7 @@ def get_songbird_formula(wildcards):
     covariate = d["factor_name"]
     reference = d["reference_level"]
     formula = f"C({covariate}, Treatment('{reference}'))"
-    if not np.isnan(d["confounders"]):
+    if not np.isnull(d["confounders"]):
         confounders = d["confounders"].split(";")
         formula = f"{formula} + {' + '.join(confounders)}"
     return formula
@@ -126,4 +126,4 @@ for dataset in datasets.iterrows():
             dataset=names,
             out=["empress"]
             )
-        all_input = all_input + empress_output
\ No newline at end of file
+        all_input = all_input + empress_output