fix version output

Author: rpetit3

CHANGELOG.md

@@ -1,6 +1,12 @@
 
 # Changelog
 
+## v0.2.2 rpetit3/camlhmp "Even a few baby birds" 2024/07/22
+
+### `Fixed`
+
+- `--version` flag now works as expected
+
 ## v0.2.1 rpetit3/camlhmp "And a bunch of birds" 2024/07/22
 
 ### `Added`

camlhmp/cli/blast.py

@@ -57,21 +57,24 @@
 
 @click.command()
 @click.option(
-    "--input", "-i", required=True, help="Input file in FASTA format to classify"
+    "--input",
+    "-i",
+    required=False if "--version" in sys.argv else True,
+    help="Input file in FASTA format to classify",
 )
 @click.option(
     "--yaml",
     "-y",
     required=True,
-    default=os.environ.get("CAML_YAML", ""),
+    default=os.environ.get("CAML_YAML", None),
     show_default=True,
     help="YAML file documenting the targets and types",
 )
 @click.option(
     "--targets",
     "-t",
-    required=True,
-    default=os.environ.get("CAML_TARGETS", ""),
+    required=False if "--version" in sys.argv else True,
+    default=os.environ.get("CAML_TARGETS", None),
     show_default=True,
     help="Query targets in FASTA format",
 )
@@ -106,7 +109,7 @@
 @click.option("--force", is_flag=True, help="Overwrite existing reports")
 @click.option("--verbose", is_flag=True, help="Increase the verbosity of output")
 @click.option("--silent", is_flag=True, help="Only critical errors will be printed")
-@click.option("--version", "-V", is_flag=True, help="Print schema and camlhmp version")
+@click.option("--version", is_flag=True, help="Print schema and camlhmp version")
 def camlhmp_blast(
     input,
     yaml,
@@ -133,10 +136,6 @@ def camlhmp_blast(
         logging.ERROR if silent else logging.DEBUG if verbose else logging.INFO
     )
 
-    # Create the output directory
-    logging.debug(f"Creating output directory: {outdir}")
-    Path(outdir).mkdir(parents=True, exist_ok=True)
-
     # Verify input files are available
     yaml_path = validate_file(yaml)
 
@@ -152,6 +151,10 @@ def camlhmp_blast(
     targets_path = validate_file(targets)
     logging.debug(f"Processing {targets}")
 
+    # Create the output directory
+    logging.debug(f"Creating output directory: {outdir}")
+    Path(outdir).mkdir(parents=True, exist_ok=True)
+
     # Output files
     result_tsv = f"{outdir}/{prefix}.tsv".replace("//", "/")
     blast_tsv = f"{outdir}/{prefix}.{framework['engine']['tool']}.tsv".replace(

camlhmp/cli/blast_region.py

@@ -57,21 +57,24 @@
 
 @click.command()
 @click.option(
-    "--input", "-i", required=True, help="Input file in FASTA format to classify"
+    "--input",
+    "-i",
+    required=False if "--version" in sys.argv else True,
+    help="Input file in FASTA format to classify"
 )
 @click.option(
     "--yaml",
     "-y",
     required=True,
-    default=os.environ.get("CAML_YAML", ""),
+    default=os.environ.get("CAML_YAML", None),
     show_default=True,
     help="YAML file documenting the targets and types",
 )
 @click.option(
     "--targets",
     "-t",
-    required=True,
-    default=os.environ.get("CAML_TARGETS", ""),
+    required=False if "--version" in sys.argv else True,
+    default=os.environ.get("CAML_TARGETS", None),
     show_default=True,
     help="Query targets in FASTA format",
 )
@@ -106,7 +109,7 @@
 @click.option("--force", is_flag=True, help="Overwrite existing reports")
 @click.option("--verbose", is_flag=True, help="Increase the verbosity of output")
 @click.option("--silent", is_flag=True, help="Only critical errors will be printed")
-@click.option("--version", "-V", is_flag=True, help="Print schema and camlhmp version")
+@click.option("--version", is_flag=True, help="Print schema and camlhmp version")
 def camlhmp_blast_region(
     input,
     yaml,
@@ -133,9 +136,7 @@ def camlhmp_blast_region(
         logging.ERROR if silent else logging.DEBUG if verbose else logging.INFO
     )
 
-    # Create the output directory
-    logging.debug(f"Creating output directory: {outdir}")
-    Path(outdir).mkdir(parents=True, exist_ok=True)
+    print(f"yaml {yaml}")
 
     # Verify input files are available
     yaml_path = validate_file(yaml)
@@ -152,6 +153,10 @@ def camlhmp_blast_region(
     targets_path = validate_file(targets)
     logging.debug(f"Processing {targets}")
 
+    # Create the output directory
+    logging.debug(f"Creating output directory: {outdir}")
+    Path(outdir).mkdir(parents=True, exist_ok=True)
+
     # Output files
     result_tsv = f"{outdir}/{prefix}.tsv".replace("//", "/")
     blast_tsv = f"{outdir}/{prefix}.{framework['engine']['tool']}.tsv".replace(

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "camlhmp"
-version = "0.2.1"
+version = "0.2.2"
 description = "Classification through yAML Heuristic Mapping Protocol"
 authors = [
     "Robert A. Petit III <robbie.petit@gmail.com>",