moducomp 0.7.13__py3-none-any.whl → 0.7.14__py3-none-any.whl

moducomp/__init__.py

@@ -2,7 +2,7 @@
 moducomp: metabolic module completeness and complementarity for microbiomes.
 """
 
-__version__ = "0.7.13"
+__version__ = "0.7.14"
 __author__ = "Juan C. Villada"
 __email__ = "jvillada@lbl.gov"
 __title__ = "moducomp"

moducomp/moducomp.py

@@ -145,15 +145,23 @@ def require_eggnog_data_dir(eggnog_data_dir: Optional[str], logger: Optional[log
     if eggnog_data_dir:
         os.environ["EGGNOG_DATA_DIR"] = eggnog_data_dir
 
-    env_value = os.environ.get("EGGNOG_DATA_DIR", "")
-    if not env_value.strip():
-        message = (
-            "EGGNOG_DATA_DIR is required to run eggNOG-mapper. "
-            "Set the EGGNOG_DATA_DIR environment variable or pass --eggnog-data-dir. "
-            "Download the data with: download_eggnog_data.py or moducomp download-eggnog-data"
-        )
-        emit_error(message, logger)
-        raise typer.Exit(1)
+    env_value = os.environ.get("EGGNOG_DATA_DIR", "").strip()
+    if not env_value:
+        default_dir = default_eggnog_data_dir()
+        if default_dir.exists() and default_dir.is_dir() and any(default_dir.iterdir()):
+            os.environ["EGGNOG_DATA_DIR"] = str(default_dir)
+            env_value = str(default_dir)
+            if logger:
+                logger.info("EGGNOG_DATA_DIR not set; using default %s", env_value)
+        else:
+            message = (
+                "EGGNOG_DATA_DIR is required to run eggNOG-mapper. "
+                "Set the EGGNOG_DATA_DIR environment variable or pass --eggnog-data-dir. "
+                f"Default location is {default_dir}. "
+                "Download the data with: download_eggnog_data.py or moducomp download-eggnog-data"
+            )
+            emit_error(message, logger)
+            raise typer.Exit(1)
 
     data_dir = Path(env_value).expanduser().resolve()
     if not data_dir.exists() or not data_dir.is_dir():

{moducomp-0.7.13.dist-info → moducomp-0.7.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moducomp
-Version: 0.7.13
+Version: 0.7.14
 Summary: moducomp: metabolic module completeness and complementarity for microbiomes.
 Keywords: bioinformatics,microbiome,metabolic,kegg,genomics
 Author-email: "Juan C. Villada" <jvillada@lbl.gov>
@@ -62,6 +62,14 @@ pixi global install \
 
 `moducomp` needs the eggNOG-mapper database to run. The primary (recommended) way to download it is using the `download_eggnog_data.py` wrapper, which mirrors the upstream downloader behavior. For upstream details, see the eggNOG-mapper setup guide: [eggNOG-mapper database setup](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.13#user-content-Setup).
 
+```bash
+download_eggnog_data.py
+```
+
+By default, the data are stored in `${XDG_DATA_HOME:-~/.local/share}/moducomp/eggnog`, and `moducomp` will auto-detect that location without needing `EGGNOG_DATA_DIR`.
+
+To use a custom location:
+
 ```bash
 export EGGNOG_DATA_DIR="/path/to/eggnog-data"
 download_eggnog_data.py --eggnog-data-dir "$EGGNOG_DATA_DIR"
@@ -69,8 +77,6 @@ download_eggnog_data.py --eggnog-data-dir "$EGGNOG_DATA_DIR"
 # moducomp download-eggnog-data --eggnog-data-dir "$EGGNOG_DATA_DIR"
 ```
 
-If `EGGNOG_DATA_DIR` is not set, the downloader defaults to `${XDG_DATA_HOME:-~/.local/share}/moducomp/eggnog`.
-
 ### Quick test
 
 Small test data sets ship with `moducomp`. After installation you can confirm the pipeline by running:

{moducomp-0.7.13.dist-info → moducomp-0.7.14.dist-info}/RECORD

@@ -1,11 +1,11 @@
-moducomp/__init__.py,sha256=4JZhb_CRk2p0sYjkmp2gH__rAKsrR1CdZshT9XGbXEg,659
+moducomp/__init__.py,sha256=X6clbSkbbep0QQrY0sh9zG3HV2dI9AErsPMaQ5342hM,659
 moducomp/__main__.py,sha256=1O2pv6IGjUgqnbqsiMLtVqjxWQpRtZUjp8LDljZ1bsI,185
-moducomp/moducomp.py,sha256=ntC6RHC1yb5Pa3WFFEASfkvG6z_fSc0q12PDbjGxsLQ,178488
+moducomp/moducomp.py,sha256=Xdtjsx-BAmhZ3LXZgfuGUTzF46Q4bHSjMfvYTrkjLOY,178931
 moducomp/data/test_genomes/IMG2562617132.faa,sha256=gZPh-08pMRdAWJRr3__TbnU1F68CdkDb3gxtpaCLTTc,356863
 moducomp/data/test_genomes/IMG2568526683.faa,sha256=PxFJwe-68UGw7il1hGlNhZt4-2WzzxXxGE1GTskDnow,343109
 moducomp/data/test_genomes/IMG2740892217.faa,sha256=WsId4sIPxENbqF6tYFouAgDCy6T0SXNY6TywxBNe-3E,548954
-moducomp-0.7.13.dist-info/entry_points.txt,sha256=oIUiacp53fiOCWDXpc2rpq5hS4wDdpasx24EXit3daE,181
-moducomp-0.7.13.dist-info/licenses/LICENSE.txt,sha256=pt0cfIq9Wop21KDZYyQgP0M1YWYvKG0PomA5cUDC4TI,1536
-moducomp-0.7.13.dist-info/WHEEL,sha256=_2ozNFCLWc93bK4WKHCO-eDUENDlo-dgc9cU3qokYO4,82
-moducomp-0.7.13.dist-info/METADATA,sha256=Aj9sjpYv4eFd1dbRJsyot2NKp_-RMi3x1K2SlXy9wYg,21520
-moducomp-0.7.13.dist-info/RECORD,,
+moducomp-0.7.14.dist-info/entry_points.txt,sha256=oIUiacp53fiOCWDXpc2rpq5hS4wDdpasx24EXit3daE,181
+moducomp-0.7.14.dist-info/licenses/LICENSE.txt,sha256=pt0cfIq9Wop21KDZYyQgP0M1YWYvKG0PomA5cUDC4TI,1536
+moducomp-0.7.14.dist-info/WHEEL,sha256=_2ozNFCLWc93bK4WKHCO-eDUENDlo-dgc9cU3qokYO4,82
+moducomp-0.7.14.dist-info/METADATA,sha256=rvBZ2J1n1NDC05UMDB4NE6jq4IG3QRqMqk5plIsfm-4,21640
+moducomp-0.7.14.dist-info/RECORD,,