moducomp 0.7.12__py3-none-any.whl → 0.7.13__py3-none-any.whl

moducomp/__init__.py

@@ -2,7 +2,7 @@
 moducomp: metabolic module completeness and complementarity for microbiomes.
 """
 
-__version__ = "0.7.12"
+__version__ = "0.7.13"
 __author__ = "Juan C. Villada"
 __email__ = "jvillada@lbl.gov"
 __title__ = "moducomp"

moducomp/moducomp.py

@@ -3762,7 +3762,19 @@ def download_eggnog_data(
     data_dir.mkdir(parents=True, exist_ok=True)
     logger.info("Downloading eggNOG data into %s", data_dir)
 
-    downloader = shutil.which("download_eggnog_data.py")
+    downloader = None
+    for path_entry in os.environ.get("PATH", "").split(os.pathsep):
+        candidate = Path(path_entry) / "download_eggnog_data.py"
+        if not candidate.is_file() or not os.access(candidate, os.X_OK):
+            continue
+        try:
+            wrapper_text = candidate.read_text(encoding="utf-8", errors="ignore")
+        except OSError:
+            wrapper_text = ""
+        if "moducomp.moducomp" in wrapper_text and "download_eggnog_data_cli" in wrapper_text:
+            continue
+        downloader = str(candidate)
+        break
     if downloader is None:
         message = (
             "download_eggnog_data.py not found in PATH. "
@@ -3883,9 +3895,10 @@ def download_eggnog_data(
 
 
 def download_eggnog_data_cli() -> None:
-    """Entry point for the download-eggnog-data script."""
+    """Entry point for download-eggnog-data/download_eggnog_data.py scripts."""
+    prog = Path(sys.argv[0]).name if sys.argv else "download-eggnog-data"
     app(
-        prog_name="download-eggnog-data",
+        prog_name=prog,
         args=["download-eggnog-data", *sys.argv[1:]],
     )
 

{moducomp-0.7.12.dist-info → moducomp-0.7.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moducomp
-Version: 0.7.12
+Version: 0.7.13
 Summary: moducomp: metabolic module completeness and complementarity for microbiomes.
 Keywords: bioinformatics,microbiome,metabolic,kegg,genomics
 Author-email: "Juan C. Villada" <jvillada@lbl.gov>
@@ -60,16 +60,16 @@ pixi global install \
 
 ## Setup data (required)
 
-`moducomp` needs the eggNOG-mapper database to run. Download it once:
+`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
 export EGGNOG_DATA_DIR="/path/to/eggnog-data"
-moducomp download-eggnog-data --eggnog-data-dir "$EGGNOG_DATA_DIR"
-# or the standalone script:
-# download_eggnog_data.py
+download_eggnog_data.py --eggnog-data-dir "$EGGNOG_DATA_DIR"
+# equivalent:
+# moducomp download-eggnog-data --eggnog-data-dir "$EGGNOG_DATA_DIR"
 ```
 
-If `EGGNOG_DATA_DIR` is not set, `moducomp download-eggnog-data` defaults to `${XDG_DATA_HOME:-~/.local/share}/moducomp/eggnog`.
+If `EGGNOG_DATA_DIR` is not set, the downloader defaults to `${XDG_DATA_HOME:-~/.local/share}/moducomp/eggnog`.
 
 ### Quick test
 
@@ -260,7 +260,7 @@ moducomp validate /path/to/output --strict
 You can override the bundled data location with `MODUCOMP_DATA_DIR`.
 When working from source, the bundled test genomes live at `moducomp/data/test_genomes`.
 
-`download_eggnog_data.py` is provided by eggnog-mapper and is available in the Pixi environment (or via `pixi global` installs).
+`download_eggnog_data.py` is exposed by `moducomp` as a convenience wrapper for the eggnog-mapper downloader and is available in the Pixi environment (including `pixi global` installs).
 
 Pixi task (supports passing a custom location):
 

moducomp-0.7.13.dist-info/RECORD

@@ -0,0 +1,11 @@
+moducomp/__init__.py,sha256=4JZhb_CRk2p0sYjkmp2gH__rAKsrR1CdZshT9XGbXEg,659
+moducomp/__main__.py,sha256=1O2pv6IGjUgqnbqsiMLtVqjxWQpRtZUjp8LDljZ1bsI,185
+moducomp/moducomp.py,sha256=ntC6RHC1yb5Pa3WFFEASfkvG6z_fSc0q12PDbjGxsLQ,178488
+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-0.7.12.dist-info → moducomp-0.7.13.dist-info}/entry_points.txt

@@ -1,4 +1,5 @@
 [console_scripts]
 download-eggnog-data=moducomp.moducomp:download_eggnog_data_cli
+download_eggnog_data.py=moducomp.moducomp:download_eggnog_data_cli
 moducomp=moducomp.moducomp:app
 

moducomp-0.7.12.dist-info/RECORD

@@ -1,11 +0,0 @@
-moducomp/__init__.py,sha256=P0sHK6IWgEersAkHlDWWFlWULUH_C-ytp5vStZDJqiY,659
-moducomp/__main__.py,sha256=1O2pv6IGjUgqnbqsiMLtVqjxWQpRtZUjp8LDljZ1bsI,185
-moducomp/moducomp.py,sha256=9eLxngLe0zRcevy6x9a-80-MGUjIEOYLTCQr6crnYRM,177904
-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-0.7.12.dist-info/entry_points.txt,sha256=dwt0_w7Ex9p1vhfp2fl4WXJLBh50u9fXTRNlAOJkAd4,114
-moducomp-0.7.12.dist-info/licenses/LICENSE.txt,sha256=pt0cfIq9Wop21KDZYyQgP0M1YWYvKG0PomA5cUDC4TI,1536
-moducomp-0.7.12.dist-info/WHEEL,sha256=_2ozNFCLWc93bK4WKHCO-eDUENDlo-dgc9cU3qokYO4,82
-moducomp-0.7.12.dist-info/METADATA,sha256=L7JsOoEk8dYNWZcCWmmQXy1ZPow3iRb_d7XrSsanOAg,21146
-moducomp-0.7.12.dist-info/RECORD,,