From db1271bf4739324ea2ba1946176956233b27fad4 Mon Sep 17 00:00:00 2001 From: jules-vanaret Date: Wed, 24 Sep 2025 01:06:27 +0200 Subject: [PATCH 1/4] added loaders dict --- src/lineagetree/__init__.py | 2 ++ src/lineagetree/_io/_loaders.py | 15 +++++++++++++++ 2 files changed, 17 insertions(+) diff --git a/src/lineagetree/__init__.py b/src/lineagetree/__init__.py index 92063a7..b63388d 100644 --- a/src/lineagetree/__init__.py +++ b/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", ) \ No newline at end of file diff --git a/src/lineagetree/_io/_loaders.py b/src/lineagetree/_io/_loaders.py index c91c897..aaf3147 100644 --- a/src/lineagetree/_io/_loaders.py +++ b/src/lineagetree/_io/_loaders.py @@ -1057,3 +1057,18 @@ def read_from_mamut_xml( name=name, **properties, ) + + +LOADERS = { + "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, "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, + }, +} \ No newline at end of file From 86dbfb77abb766d80adc66abdcba1726bb5780f2 Mon Sep 17 00:00:00 2001 From: jules-vanaret Date: Wed, 24 Sep 2025 01:23:28 +0200 Subject: [PATCH 2/4] commented specific function --- src/lineagetree/_io/_loaders.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/lineagetree/_io/_loaders.py b/src/lineagetree/_io/_loaders.py index aaf3147..4fd630d 100644 --- a/src/lineagetree/_io/_loaders.py +++ b/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, @@ -1063,7 +1063,11 @@ def read_from_mamut_xml( "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, "MaMuT XML loader": read_from_mamut_xml, "ASTEC XML loader": read_from_ASTEC}, + "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": { From c6bcf60649ff5fa922038adae5a18725b72c2113 Mon Sep 17 00:00:00 2001 From: jules-vanaret Date: Wed, 24 Sep 2025 01:25:50 +0200 Subject: [PATCH 3/4] added comment on case --- src/lineagetree/_io/_loaders.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/lineagetree/_io/_loaders.py b/src/lineagetree/_io/_loaders.py index 4fd630d..3423748 100644 --- a/src/lineagetree/_io/_loaders.py +++ b/src/lineagetree/_io/_loaders.py @@ -1059,7 +1059,7 @@ def read_from_mamut_xml( ) -LOADERS = { +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}, From c320aea1674cefbca1baa9e8cbf5ed5fa31fa3d0 Mon Sep 17 00:00:00 2001 From: jules-vanaret Date: Wed, 24 Sep 2025 12:03:59 +0200 Subject: [PATCH 4/4] changed layout --- src/lineagetree/_io/_loaders.py | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/src/lineagetree/_io/_loaders.py b/src/lineagetree/_io/_loaders.py index 3423748..fe69fd1 100644 --- a/src/lineagetree/_io/_loaders.py +++ b/src/lineagetree/_io/_loaders.py @@ -1060,16 +1060,27 @@ def read_from_mamut_xml( 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}, + "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}, + "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,