From 023b686aeb8985166c0a3dde1ae60662541840bb Mon Sep 17 00:00:00 2001
From: gp201 <praneethg2001@gmail.com>
Date: Thu, 12 Jun 2025 22:24:30 -0700
Subject: [PATCH 1/4] feat: add new command line options for tree format, usher
 arguments, threads, matutils overlap, prefix, and plot chunk size

---
 barcodeforge/cli.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/barcodeforge/cli.py b/barcodeforge/cli.py
index 4ff7d12..75ea685 100644
--- a/barcodeforge/cli.py
+++ b/barcodeforge/cli.py
@@ -34,17 +34,20 @@ def cli(ctx, debug):
 @click.argument("tree", type=click.Path(exists=True, readable=True))
 @click.argument("lineages", type=click.Path(exists=True, readable=True))
 @click.option(
+    "-t",
     "--tree_format",
     type=click.Choice(["newick", "nexus"], case_sensitive=False),
     help="Specify the format of the tree file (newick or nexus)",
 )
 @click.option(
+    "-u",
     "--usher-args",
     type=str,
     default="",
     help="Additional arguments to pass to usher (e.g., '-U -l'). Quote multiple arguments.",
 )
 @click.option(
+    "-T",
     "--threads",
     type=int,
     default=8,
@@ -52,6 +55,7 @@ def cli(ctx, debug):
     help="Number of CPUs/threads to use.",
 )
 @click.option(
+    "-m",
     "--matutils-overlap",
     type=float,
     metavar="FLOAT",
@@ -60,6 +64,7 @@ def cli(ctx, debug):
     help="Value for --set-overlap in matUtils annotate.",
 )
 @click.option(
+    "-p",
     "--prefix",
     type=str,
     default="",
@@ -67,6 +72,7 @@ def cli(ctx, debug):
     help="Prefix to add to lineage names in the barcode file.",
 )
 @click.option(
+    "-c",
     "--plot-chunk-size",
     type=int,
     default=100,

From 059138f83441b10eac5ff636cc9b9599074ceb11 Mon Sep 17 00:00:00 2001
From: gp201 <praneethg2001@gmail.com>
Date: Thu, 12 Jun 2025 22:36:05 -0700
Subject: [PATCH 2/4] fix: update option types for threads and matutils overlap
 in CLI to enforce input constraints

---
 barcodeforge/cli.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/barcodeforge/cli.py b/barcodeforge/cli.py
index 75ea685..c9f829d 100644
--- a/barcodeforge/cli.py
+++ b/barcodeforge/cli.py
@@ -49,7 +49,7 @@ def cli(ctx, debug):
 @click.option(
     "-T",
     "--threads",
-    type=int,
+    type=click.IntRange(min=1),
     default=8,
     show_default=True,
     help="Number of CPUs/threads to use.",
@@ -57,7 +57,7 @@ def cli(ctx, debug):
 @click.option(
     "-m",
     "--matutils-overlap",
-    type=float,
+    type=click.FloatRange(min=0.0, max=1.0),
     metavar="FLOAT",
     default="0",
     show_default=True,

From 3175a689436287f7fbf4cd7e8b2ea1823d4cf4a0 Mon Sep 17 00:00:00 2001
From: gp201 <praneethg2001@gmail.com>
Date: Thu, 12 Jun 2025 22:40:23 -0700
Subject: [PATCH 3/4] refactor: standardize option names and types in CLI for
 consistency

---
 barcodeforge/cli.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/barcodeforge/cli.py b/barcodeforge/cli.py
index c9f829d..b04e2ff 100644
--- a/barcodeforge/cli.py
+++ b/barcodeforge/cli.py
@@ -35,7 +35,7 @@ def cli(ctx, debug):
 @click.argument("lineages", type=click.Path(exists=True, readable=True))
 @click.option(
     "-t",
-    "--tree_format",
+    "--tree-format",
     type=click.Choice(["newick", "nexus"], case_sensitive=False),
     help="Specify the format of the tree file (newick or nexus)",
 )
@@ -50,6 +50,7 @@ def cli(ctx, debug):
     "-T",
     "--threads",
     type=click.IntRange(min=1),
+    metavar="INT",
     default=8,
     show_default=True,
     help="Number of CPUs/threads to use.",
@@ -59,7 +60,7 @@ def cli(ctx, debug):
     "--matutils-overlap",
     type=click.FloatRange(min=0.0, max=1.0),
     metavar="FLOAT",
-    default="0",
+    default=0,
     show_default=True,
     help="Value for --set-overlap in matUtils annotate.",
 )

From 466e983e3a595ef7cbb5f109dc3697886d305353 Mon Sep 17 00:00:00 2001
From: gp201 <praneethg2001@gmail.com>
Date: Thu, 12 Jun 2025 22:48:06 -0700
Subject: [PATCH 4/4] fix: standardize CLI option name for tree format to
 improve consistency

---
 barcodeforge/utils.py | 2 +-
 tests/test_cli.py     | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/barcodeforge/utils.py b/barcodeforge/utils.py
index 5639529..31305ca 100644
--- a/barcodeforge/utils.py
+++ b/barcodeforge/utils.py
@@ -43,7 +43,7 @@ def resolve_tree_format(
                     f"[{STYLES['error']}]Error: Unknown tree format for file '{tree_path}'. Extension '{ext}' is not recognized.[/{STYLES['error']}]"
                 )
                 console.print(
-                    f"[{STYLES['error']}]Please specify the format using --tree_format ('newick' or 'nexus').[/]"
+                    f"[{STYLES['error']}]Please specify the format using --tree-format ('newick' or 'nexus').[/]"
                 )
             raise click.Abort()
 
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 51b09d6..c738802 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -389,7 +389,7 @@ def test_barcode_command_nexus_tree(runner, temp_files, mocker):
         temp_files["alignment"],
         temp_files["tree"],
         temp_files["lineages"],
-        "--tree_format",
+        "--tree-format",
         "nexus",
     ]
     result = runner.invoke(cli, args, catch_exceptions=False)
@@ -446,7 +446,7 @@ def test_barcode_command_newick_tree_reformat(runner, temp_files, mocker):
         temp_files["alignment"],
         temp_files["tree"],
         temp_files["lineages"],
-        "--tree_format",
+        "--tree-format",
         "newick",
     ]
     result = runner.invoke(cli, args, catch_exceptions=False)