moducomp 0.7.12__tar.gz → 0.7.14__tar.gz

{moducomp-0.7.12 → moducomp-0.7.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: moducomp
-Version: 0.7.12
+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>
@@ -60,16 +60,22 @@ 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
 ```
 
-If `EGGNOG_DATA_DIR` is not set, `moducomp download-eggnog-data` defaults to `${XDG_DATA_HOME:-~/.local/share}/moducomp/eggnog`.
+By default, the data are stored in `${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 "$EGGNOG_DATA_DIR"
+# equivalent:
+# moducomp download-eggnog-data --eggnog-data-dir "$EGGNOG_DATA_DIR"
+```
 
 ### Quick test
 
@@ -260,7 +266,7 @@ 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-0.7.12 → moducomp-0.7.14}/README.md

@@ -35,16 +35,22 @@ 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
 ```
 
-If `EGGNOG_DATA_DIR` is not set, `moducomp download-eggnog-data` defaults to `${XDG_DATA_HOME:-~/.local/share}/moducomp/eggnog`.
+By default, the data are stored in `${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 "$EGGNOG_DATA_DIR"
+# equivalent:
+# moducomp download-eggnog-data --eggnog-data-dir "$EGGNOG_DATA_DIR"
+```
 
 ### Quick test
 
@@ -235,7 +241,7 @@ 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-0.7.12 → moducomp-0.7.14}/moducomp/__init__.py

@@ -2,7 +2,7 @@
 moducomp: metabolic module completeness and complementarity for microbiomes.
 """
 
-__version__ = "0.7.12"
+__version__ = "0.7.14"
 __author__ = "Juan C. Villada"
 __email__ = "jvillada@lbl.gov"
 __title__ = "moducomp"

{moducomp-0.7.12 → moducomp-0.7.14}/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():
@@ -3762,7 +3770,19 @@ 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 +3903,10 @@ 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 → moducomp-0.7.14}/pyproject.toml

@@ -29,6 +29,7 @@ dynamic = ["version", "description"]
 [project.scripts]
 moducomp = "moducomp.moducomp:app"
 download-eggnog-data = "moducomp.moducomp:download_eggnog_data_cli"
+"download_eggnog_data.py" = "moducomp.moducomp:download_eggnog_data_cli"
 
 [project.urls]
 Homepage = "https://github.com/NeLLi-team/moducomp"

{moducomp-0.7.12 → moducomp-0.7.14}/recipe.yaml

@@ -1,5 +1,5 @@
 context:
-  version: 0.7.12
+  version: 0.7.14
 
 package:
   name: moducomp
@@ -7,7 +7,7 @@ package:
 
 source:
 - url: https://pypi.org/packages/source/m/moducomp/moducomp-${{ version }}.tar.gz
-  sha256: bf876d320c88ae31dabe4f43086fbb3b2d0d10a153fa2effb09f2a6be394d2f1
+  sha256: bfa45b0d4383ce954e89dceb9b54f4502e02b6ebe995f6a07395ce6a6ede7360
 
 build:
   script:
@@ -15,6 +15,8 @@ build:
   python:
     entry_points:
     - moducomp = moducomp.moducomp:app
+    - download-eggnog-data = moducomp.moducomp:download_eggnog_data_cli
+    - download_eggnog_data.py = moducomp.moducomp:download_eggnog_data_cli
   noarch: python
 
 requirements: