consistenly use bactopia-path across subcommands

bactopia · Apr 25, 2023 · 90c83c4 · 90c83c4
1 parent b2494a0
commit 90c83c4
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Showing 4 changed files with 17 additions and 15 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,7 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## 1.0.2
 
-Added `bactopia-datasets` to download optional datasets outside of Nextflow
+- Added `bactopia-datasets` to download optional datasets outside of Nextflow
+- consistently use `--bactopia-path` across sub-commands
 
 ## 1.0.1
 

diff --git a/README.md b/README.md
@@ -28,11 +28,12 @@ Below is the `--help` output for each subcommand.
  Print out tools and citations used throughout Bactopia
 
 ╭─ Options ────────────────────────────────────────────────────────────────────────────╮
-│    --version     -V        Show the version and exit.                                │
-│ *  --bactopia    -b  TEXT  Directory where Bactopia repository is stored [required]  │
-│    --name        -n  TEXT  Only print citation matching a given name                 │
-│    --plain-text  -p        Disable rich formatting                                   │
-│    --help                  Show this message and exit.                               │
+│    --version        -V        Show the version and exit.                             │
+│ *  --bactopia-path  -b  TEXT  Directory where Bactopia repository is stored          │
+│                               [required]                                             │
+│    --name           -n  TEXT  Only print citation matching a given name              │
+│    --plain-text     -p        Disable rich formatting                                │
+│    --help                     Show this message and exit.                            │
 ╰──────────────────────────────────────────────────────────────────────────────────────╯
 ```
 
@@ -216,7 +217,7 @@ Below is the `--help` output for each subcommand.
  Generate a summary table from the Bactopia results.
 
 ╭─ Required Options ───────────────────────────────────────────────────────────────────╮
-│ *  --bactopia  -b  TEXT  Directory where Bactopia results are stored [required]      │
+│ *  --bactopia-path  -b  TEXT  Directory where Bactopia results are stored [required] │
 ╰──────────────────────────────────────────────────────────────────────────────────────╯
 ╭─ Gold Cutoffs ───────────────────────────────────────────────────────────────────────╮
 │ --gold-coverage     -gcov      INTEGER  Minimum amount of coverage required for Gold │

diff --git a/bactopia/cli/citations.py b/bactopia/cli/citations.py
@@ -39,17 +39,17 @@ def parse_citations(yml: str) -> list:
 @click.command()
 @click.version_option(bactopia.__version__, "--version", "-V")
 @click.option(
-    "--bactopia",
+    "--bactopia-path",
     "-b",
     required=True,
     help="Directory where Bactopia repository is stored",
 )
 @click.option("--name", "-n", help="Only print citation matching a given name")
 @click.option("--plain-text", "-p", is_flag=True, help="Disable rich formatting")
-def citations(bactopia: str, name: str, plain_text: bool) -> None:
+def citations(bactopia_path: str, name: str, plain_text: bool) -> None:
     """Print out tools and citations used throughout Bactopia"""
 
-    citations_yml = validate_file(f"{bactopia}/citations.yml")
+    citations_yml = validate_file(f"{bactopia_path}/citations.yml")
     citations, module_citations = parse_citations(citations_yml)
 
     markdown = []

diff --git a/bactopia/cli/summary.py b/bactopia/cli/summary.py
@@ -25,7 +25,7 @@
 click.rich_click.USE_RICH_MARKUP = True
 click.rich_click.OPTION_GROUPS = {
     "bactopia-summary": [
-        {"name": "Required Options", "options": ["--bactopia"]},
+        {"name": "Required Options", "options": ["--bactopia-path"]},
         {
             "name": "Gold Cutoffs",
             "options": [
@@ -144,7 +144,7 @@ def process_sample(df: pd.DataFrame, rank_cutoff: dict) -> list:
 @click.command()
 @click.version_option(bactopia.__version__, "--version", "-V")
 @click.option(
-    "--bactopia",
+    "--bactopia-path",
     "-b",
     required=True,
     help="Directory where Bactopia results are stored",
@@ -274,7 +274,7 @@ def process_sample(df: pd.DataFrame, rank_cutoff: dict) -> list:
 @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")
 def summary(
-    bactopia,
+    bactopia_path,
     gold_coverage,
     gold_quality,
     gold_read_length,
@@ -347,8 +347,8 @@ def summary(
     processed_samples = {}
     versions = []
     dfs = []
-    samples = parse_bactopia_directory(bactopia)
-    logging.info(f"Found {len(samples)} samples in {bactopia} to process")
+    samples = parse_bactopia_directory(bactopia_path)
+    logging.info(f"Found {len(samples)} samples in {bactopia_path} to process")
     if samples:
         for sample in samples:
             if sample["is_bactopia"]: