remove unneeded imports

pyproject.toml

@@ -5,32 +5,40 @@ requires = ["hatchling"]
 [project]
 name = "flowsom"
 version = "0.0.1"
-description = "The complete FlowSOM package known from R, now available in Python"
+description = "The complete FlowSOM package known from R, now available in Python!"
 readme = "README.md"
 requires-python = ">=3.9"
 license = { file = "LICENSE" }
-authors = [{ name = "Artuur Couckuyt" }]
-maintainers = [{ name = "Artuur Couckuyt", email = "[email protected]" }]
-urls.Documentation = "https://FlowSOM.readthedocs.io/"
-urls.Source = "https://github.com/artuurC/FlowSOM"
-urls.Home-page = "https://github.com/artuurC/FlowSOM"
+authors = [
+ { name = "Artuur Couckuyt", email = "[email protected]" },
+ { name = "Benjamin Rombaut", email = "[email protected]" },
+ { name = "Yvan Saeys", email = "[email protected]" },
+ { name = "Sofie Van Gassen", email = "[email protected]" },
+]
+maintainers = [
+ { name = "Artuur Couckuyt", email = "[email protected]" },
+ { name = "Benjamin Rombaut", email = "[email protected]" },
+ { name = "Yvan Saeys", email = "[email protected]" },
+ { name = "Sofie Van Gassen", email = "[email protected]" },
+]
+urls.Documentation = "https://flowsom.readthedocs.io/en/latest/"
+urls.Source = "https://github.com/saeyslab/FlowSOM_Python"
+urls.Home-page = "https://github.com/saeyslab/FlowSOM_Python"
 dependencies = [
  "mudata",
  "numpy",
  "matplotlib",
  "pandas",
  "scipy",
- "pytometry",
+ "readfcs",
  "scikit-learn",
  "python-igraph",
  "pytest",
  "session-info",
  "numba",
  "scanpy",
  "seaborn",
- "readfcs",
  "anndata",
- "dask[dataframe]",
  "loguru",
 ]
 

src/flowsom/io/read_fcs.py

@@ -4,6 +4,7 @@
 
 import anndata as ad
 import pandas as pd
+import readfcs
 
 
 def read_FCS(filepath):
@@ -12,16 +13,14 @@ def read_FCS(filepath):
  :param filepath: An array containing a full path to the FCS file
  :type filepath: str
  """
- import pytometry as pm
-
  try:
- f = pm.io.read_fcs(filepath)
+ f = readfcs.read(filepath, reindex=True)
  f.var.n = f.var.n.astype(int)
  f.var = f.var.sort_values(by="n")
  f.uns["meta"]["channels"].index = f.uns["meta"]["channels"].index.astype(int)
  f.uns["meta"]["channels"] = f.uns["meta"]["channels"].sort_index()
  except ValueError:
- f = pm.io.read_fcs(filepath, reindex=False)
+ f = readfcs.read(filepath, reindex=False)
  markers = {
  str(re.sub("S$", "", re.sub("^P", "", string))): f.uns["meta"][string]
  for string in f.uns["meta"].keys()