Adding standardized way to define loaders per extension

src/lineagetree/__init__.py

@@ -12,6 +12,7 @@
     read_from_txt_for_celegans,
     read_from_txt_for_celegans_BAO,
     read_from_txt_for_celegans_CAO,
+    LOADERS,
 )
 from .lineage_tree_manager import LineageTreeManager
 
@@ -29,4 +30,5 @@
     "read_from_mastodon",
     "read_from_txt_for_celegans",
     "read_from_txt_for_celegans_CAO",
+    "LOADERS",
 )

src/lineagetree/_io/_loaders.py

@@ -177,7 +177,7 @@ def read_from_bmf(
 
 def read_from_csv(
     file_path: str,
-    z_mult: float,
+    z_mult: float = 1,
     link: int = 1,
     delim: str = ",",
     name: None | str = None,
@@ -1057,3 +1057,33 @@ def read_from_mamut_xml(
         name=name,
         **properties,
     )
+
+
+LOADERS = { # put all formats in smaller case
+    "bmf": {
+        "BMF loader": read_from_bmf
+    },
+    "csv": {
+        "Standard CSV loader": read_from_csv,
+        "Mastodon CSV loader": read_from_mastodon_csv
+    },
+    "binary": {
+        "Binary loader": read_from_binary
+    },
+    "xml": {
+        # "TGMM XML loader": read_from_tgmm_xml, # commented out because it requires a specific file format
+        "MaMuT XML loader": read_from_mamut_xml,
+        "ASTEC XML loader": read_from_ASTEC,
+    },
+    "mastodon": {
+        "Mastodon loader": read_from_mastodon
+    },
+    "pkl": {
+        "ASTEC PKL loader": read_from_ASTEC
+    },
+    "txt": {
+        "C. elegans loader": read_from_txt_for_celegans,
+        "C. elegans CAO loader": read_from_txt_for_celegans_CAO,
+        "C. elegans BAO loader": read_from_txt_for_celegans_BAO,
+    },
+}