Merge pull request #26 from saeyslab/aggregate_flowframes_testing + specify higher version of pyflowsom for testing

Update aggregate_flowframes to work with list of flowframes and pin pyflowsom >=0.1.5 to avoid build error in CI

Author: robbefonteyn

pyproject.toml

@@ -4,13 +4,14 @@ requires = [ "hatchling" ]
 
 [project]
 name = "flowsom"
-version = "0.2.2"
+version = "0.2.3"
 description = "The complete FlowSOM package known from R, now available in Python!"
 readme = "README.md"
 license = { file = "LICENSE" }
 maintainers = [
   { name = "Artuur Couckuyt", email = "[email protected]" },
   { name = "Benjamin Rombaut", email = "[email protected]" },
+  { name = "Robbe Fonteyn", email = "[email protected]" },
   { name = "Yvan Saeys", email = "[email protected]" },
   { name = "Sofie Van Gassen", email = "[email protected]" },
 ]
@@ -66,7 +67,7 @@ optional-dependencies.doc = [
   "sphinxcontrib-bibtex>=1",
   "sphinxext-opengraph",
 ]
-optional-dependencies.test = [ "coverage", "pyflowsom", "pytest" ]
+optional-dependencies.test = [ "coverage", "pyflowsom>=0.1.5", "pytest" ]
 urls.Documentation = "https://flowsom.readthedocs.io/en/latest/"
 urls.Home-page = "https://github.com/saeyslab/FlowSOM_Python"
 urls.Source = "https://github.com/saeyslab/FlowSOM_Python"

src/flowsom/pp/fcs_functions.py

@@ -9,11 +9,11 @@
 from flowsom.tl import get_markers
 
 
-def aggregate_flowframes(filenames, c_total, channels=None, keep_order=False):
+def aggregate_flowframes(files, c_total, channels=None, keep_order=False):
     """Aggregate multiple FCS files together.
 
-    :param filenames: An array containing full paths to the FCS files
-    :type filenames: np.array
+    :param files: An array/list containing full paths to the FCS files or fcs files as anndata objects
+    :type files: np.array
     :param c_total: Total number of cells to write to the output file
     :type c_total: int
     :param channels: Channels/markers to keep in the aggregate. Default None
@@ -26,12 +26,14 @@ def aggregate_flowframes(filenames, c_total, channels=None, keep_order=False):
     new file. Default = False.
     :type silent: boolean.
     """
-    nFiles = len(filenames)
+    nFiles = len(files)
     cFile = int(np.ceil(c_total / nFiles))
 
     flow_frame = []
-    for i, file_path in enumerate(filenames):
-        f = read_FCS(file_path)
+    for i, f in enumerate(files):
+        if not isinstance(f, ad.AnnData):
+            f = read_FCS(f)
+
         if channels is not None:
             f = f[:, list(get_markers(f, channels).keys())]
         cPerFile = min([f.X.shape[0], cFile])