Merge branch 'download' of github.com:maxibor/AMDirT into download

maxibor · maxibor · commit 1470cc44e1de · 2024-04-08T11:28:05.000+02:00
diff --git a/AMDirT/core/__init__.py b/AMDirT/core/__init__.py
@@ -67,7 +67,7 @@ def get_amdir_tags():
         ]
     else:
         logger.warning(
-            "Could not fetch tags from AncientMetagenomeDir. Defaulting to master"
+            "Could not fetch tags from AncientMetagenomeDir. Defaulting to master. Metadata may not yet be officially released."
         )
         return ["master"]
 
diff --git a/AMDirT/download/__init__.py b/AMDirT/download/__init__.py
@@ -14,7 +14,7 @@ def download(table: str, table_type: str, release: str, output: str = ".") -> st
     Parameters
     ----------
     table : str
-        The table to download.
+        The AncientMetagenomeDir table to download.
     table_type : str
         The type of table to download. Allowed values are ['samples', 'libraries'].
     release : str
diff --git a/docs/source/how_to/download.md b/docs/source/how_to/download.md
@@ -18,4 +18,4 @@ AMDirT download --table ancientsinglegenome-hostassociated --table_type samples
 
 ## Output
 
-This command will download the `ancientsinglegenome-hostassociated` `sample` table from the `v23.12.0` AncientMetagenomeDir release, and save it locally to `ancientmetagenome-hostassociated_samples_v23.12.0.tsv`
+This example command above will download the `ancientsinglegenome-hostassociated` `sample` table from the `v23.12.0` AncientMetagenomeDir release, and save it locally to `ancientmetagenome-hostassociated_samples_v23.12.0.tsv`

Original file line number	Diff line number	Diff line change
`@@ -67,7 +67,7 @@ def get_amdir_tags():`
`67`	`67`	`]`
`68`	`68`	`else:`
`69`	`69`	`logger.warning(`
`70`		`- "Could not fetch tags from AncientMetagenomeDir. Defaulting to master"`
	`70`	`+ "Could not fetch tags from AncientMetagenomeDir. Defaulting to master. Metadata may not yet be officially released."`
`71`	`71`	`)`
`72`	`72`	`return ["master"]`
`73`	`73`
Original file line number	Diff line number	Diff line change
`@@ -18,4 +18,4 @@ AMDirT download --table ancientsinglegenome-hostassociated --table_type samples`
`18`	`18`
`19`	`19`	`## Output`
`20`	`20`
`21`		-This command will download the `ancientsinglegenome-hostassociated` `sample` table from the `v23.12.0` AncientMetagenomeDir release, and save it locally to `ancientmetagenome-hostassociated_samples_v23.12.0.tsv`
	`21`	+This example command above will download the `ancientsinglegenome-hostassociated` `sample` table from the `v23.12.0` AncientMetagenomeDir release, and save it locally to `ancientmetagenome-hostassociated_samples_v23.12.0.tsv`