diff --git a/pyproject.toml b/pyproject.toml index ffae2aa..d1ca395 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,22 +5,32 @@ 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 = "artuur.couckuyt@ugent.be" }] -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 = "Artuur.Couckuyt@ugent.be" }, + { name = "Benjamin Rombaut", email = "Benjamin.Rombaut@ugent.be" }, + { name = "Yvan Saeys", email = "Yvan.Saeys@UGent.be" }, + { name = "Sofie Van Gassen", email = "Sofie.VanGassen@UGent.be" }, +] +maintainers = [ + { name = "Artuur Couckuyt", email = "Artuur.Couckuyt@ugent.be" }, + { name = "Benjamin Rombaut", email = "Benjamin.Rombaut@ugent.be" }, + { name = "Yvan Saeys", email = "Yvan.Saeys@UGent.be" }, + { name = "Sofie Van Gassen", email = "Sofie.VanGassen@UGent.be" }, +] +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", @@ -28,9 +38,7 @@ dependencies = [ "numba", "scanpy", "seaborn", - "readfcs", "anndata", - "dask[dataframe]", "loguru", ] diff --git a/src/flowsom/io/read_fcs.py b/src/flowsom/io/read_fcs.py index 2132a10..67a6323 100644 --- a/src/flowsom/io/read_fcs.py +++ b/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()