From 8935b265a0ace853f9f03891315e043951415a35 Mon Sep 17 00:00:00 2001
From: Zach Bjornson <zbbjornson@gmail.com>
Date: Thu, 18 Jul 2024 18:20:00 -0700
Subject: [PATCH] deps(flowio): v1.1

Moves from our fork to v1.1. Our fork ignored nan reagent values when writing files, but we should instead filter them out before calling flowio.
---
 cellengine/resources/fcs_file.py | 4 +++-
 setup.py                         | 3 +--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/cellengine/resources/fcs_file.py b/cellengine/resources/fcs_file.py
index 517db5e3..dd43d345 100644
--- a/cellengine/resources/fcs_file.py
+++ b/cellengine/resources/fcs_file.py
@@ -262,7 +262,7 @@ def create_from_dataframe(
         experiment_id: str,
         filename: str,
         df: DataFrame,
-        reagents: Optional[List[str]] = None,
+        reagents: Optional[List[Union[str, None]]] = None,
         headers: Dict[str, str] = {},
     ) -> FcsFile:
         """Creates an FCS file from a DataFrame and uploads it CellEngine.
@@ -361,6 +361,8 @@ def create_from_dataframe(
             channels = df.columns.get_level_values(0).tolist()
             if reagents is None:
                 reagents = df.columns.get_level_values(1).tolist()
+                # Filter out nan values. An Index will cast None to float (nan).
+                reagents = [r if r == r else None for r in reagents]
         else:
             channels = df.columns
 
diff --git a/setup.py b/setup.py
index 90acf7a8..d6519cb9 100644
--- a/setup.py
+++ b/setup.py
@@ -40,8 +40,7 @@
     ],
     platforms="Posix; MacOS X; Windows",
     install_requires=[
-        "flowio~=1.0",
-        "flowio @ git+https://github.com/cellengine/FlowIO.git@next",
+        "flowio~=1.1",
         "numpy~=1.17",
         "pandas~=1.1",
         "requests~=2.22",