immucellai2 2.1.17__tar.gz → 2.1.19__tar.gz

{immucellai2-2.1.17 → immucellai2-2.1.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: immucellai2
-Version: 2.1.17
+Version: 2.1.19
 Summary: A tool for immune cell type deconvolution
 Home-page: https://github.com/VyvyanYjm/ImmuCellAI2.0
 Author: YangJingmin

{immucellai2-2.1.17 → immucellai2-2.1.19}/immucellai2/myfunction2.py

@@ -3,6 +3,7 @@ from .myclasses import CLASS_FOR_RUN
 from .myfunction3 import ObtainCellTypeCateogry
 import pandas
 import os
+import importlib.util
 import re
 import sys
 import multiprocessing as mp
@@ -11,93 +12,30 @@ def Obtainmyconfigpath():
    script_dir = os.path.dirname(os.path.abspath(sys.argv[0]))
    return os.path.join(script_dir, "immucellai2", "myconfig", "")
 
+def get_package_dir(package_name):
+    spec = importlib.util.find_spec(package_name)
+    if spec is None:
+        raise ModuleNotFoundError(f"Package '{package_name}' not found")
+    path = spec.origin or spec.submodule_search_locations[0]
+    return os.path.dirname(path) 
+
 def SelectGeneForDeconvolution(DFReferenceProfile, FileCoveredGenes="", Method="UsedMarker"):
     print("Select the gene for the following deconvolution...")
     GeneUsedForDeconvolution = []
     DFReferenceProfileGenes = DFReferenceProfile.index.values
-    print(f"[DEBUG] reference genes: {len(DFReferenceProfileGenes)}")
-    print(f"[DEBUG] head: {DFReferenceProfileGenes[:5]}")
-
     if Method == "UsedMarker":
         if FileCoveredGenes == "":
-            # ===== ͨ�û�·�����������ȼ��Ӹߵ��� =====
-            FileCoveredGenes = None
-            
-            # ���ȼ�1����̬����immucellai2���ڵ�myconfigĿ¼�����ģ�
             try:
-                # ��ʽ1��ͨ��ģ�鵼���ȡ����·�������ȶ����������а�װ��ʽ��
-                import immucellai2.myconfig
-                pkg_config_dir = os.path.dirname(immucellai2.myconfig.__file__)
-                pkg_marker_path = os.path.join(pkg_config_dir, "MarkerUsedDeconvolution.txt")
+                pkg_marker_path = os.path.join(get_package_dir("immucellai2"), "myconfig/MarkerUsedDeconvolution.txt")
                 if os.path.exists(pkg_marker_path):
                     FileCoveredGenes = pkg_marker_path
                     print(f"[INFO] Found marker file in immucellai2 package: {FileCoveredGenes}")
-            except ImportError:
-                # ��ʽ2��ͨ��importlib.resources.files����������Դ�����ã�
-                try:
-                    marker_resource = files("immucellai2.myconfig").joinpath("MarkerUsedDeconvolution.txt")
-                    with as_file(marker_resource) as marker_path:
-                        if marker_path.exists():
-                            FileCoveredGenes = str(marker_path)
-                            print(f"[INFO] Found marker file in immucellai2 package (resources API): {FileCoveredGenes}")
-                except Exception as e:
-                    pass  # ����������һ������
-            
-            # ���ȼ�2���û��Զ��廷������������Դ������/�DZ�׼��װ��
-            if FileCoveredGenes is None:
-                config_dir = os.getenv("IMMUCELLAI_CONFIG_DIR")
-                if config_dir:
-                    env_marker_path = os.path.join(config_dir, "MarkerUsedDeconvolution.txt")
-                    if os.path.exists(env_marker_path):
-                        FileCoveredGenes = env_marker_path
-                        print(f"[WARNING] Use marker file from env IMMUCELLAI_CONFIG_DIR: {FileCoveredGenes}")
-            
-            # ���ȼ�3����ǰ����Ŀ¼�µ�myconfig�������ֶ�����
-            if FileCoveredGenes is None:
-                cwd_config_dir = os.path.join(os.getcwd(), "myconfig")
-                cwd_marker_path = os.path.join(cwd_config_dir, "MarkerUsedDeconvolution.txt")
-                if os.path.exists(cwd_marker_path):
-                    FileCoveredGenes = cwd_marker_path
-                    print(f"[WARNING] Use marker file from current directory: {FileCoveredGenes}")
-            
-            # �������ȼ���ʧ�ܣ���ʾ�û�
-            if FileCoveredGenes is None:
-                print("[ERROR] Marker file 'MarkerUsedDeconvolution.txt' not found!")
-                print("Solutions for users:")
-                print("  1. Install immucellai2 correctly: pip install --upgrade immucellai2")
-                print("  2. Set environment variable: export IMMUCELLAI_CONFIG_DIR='/path/to/your/myconfig/'")
-                print("  3. Put MarkerUsedDeconvolution.txt in ./myconfig/ (current working directory)")
-                return []
-
-        # ===== ͨ�û��ļ���ȡ�����ݸ�ʽ+³���� =====
-        try:
-            print(f"[DEBUG] getwd: {FileCoveredGenes}")
-            # �޸�iloc[1] �� iloc[:,0]����ȡ��һ�������У����䵥�б���ļ���
-            # ����error_bad_lines=False��������ʽ�������
-            df_marker = pd.read_table(
-                FileCoveredGenes, 
-                sep="\t", 
-                header=None, 
-                error_bad_lines=False,
-                warn_bad_lines=True
-            )
-            # ��ȡ��һ�У�ȥ��+ȥ��+ת��д�����ݻ�������Сд��
-            GeneUsedForDeconvolution0 = df_marker.iloc[:, 0].astype(str).str.strip()
-            GeneUsedForDeconvolution0 = [gene.upper() for gene in GeneUsedForDeconvolution0 if gene and not gene.isdigit()]
-            GeneUsedForDeconvolution0 = list(set(GeneUsedForDeconvolution0))  # ȥ��
-
-            # �ο��׻�����Ҳת��д��ȷ������ƥ��
-            DFReferenceProfileGenes_upper = [gene.upper() for gene in DFReferenceProfileGenes]
-            # ȡ����
-            GeneUsedForDeconvolution = list(set(GeneUsedForDeconvolution0) & set(DFReferenceProfileGenes_upper))
-
-            print(f"[DEBUG] marker genes head: {GeneUsedForDeconvolution0[:5]}")
-            print(f"Successfully loaded {len(GeneUsedForDeconvolution)} valid marker genes (total: {len(GeneUsedForDeconvolution0)})")
+            GeneUsedForDeconvolution0 = (pandas.read_table(FileCoveredGenes, sep= "\t")).iloc[0].to_list()
+            GeneUsedForDeconvolution = list(set(GeneUsedForDeconvolution0).intersection(set(DFReferenceProfileGenes)))
         except Exception as e:
             print(f"[ERROR] Failed to read marker file: {str(e)}")
             print("Tips for users: Check if MarkerUsedDeconvolution.txt is in 'single-column, no header' format")
             return []
-
     return GeneUsedForDeconvolution
 
 def CelltypeCategoryCheck(FileCellTypeCategory = "", celltypelist = [] ):

{immucellai2-2.1.17 → immucellai2-2.1.19}/immucellai2.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: immucellai2
-Version: 2.1.17
+Version: 2.1.19
 Summary: A tool for immune cell type deconvolution
 Home-page: https://github.com/VyvyanYjm/ImmuCellAI2.0
 Author: YangJingmin

{immucellai2-2.1.17 → immucellai2-2.1.19}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = immucellai2
-version = 2.1.17
+version = 2.1.19
 author = YangJingmin
 author_email = yangjingmin2021@163.com
 description = A tool for immune cell type deconvolution