From 050a88e80419acd747704c82d1a431601c1aaafe Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Thu, 17 Jul 2025 19:20:09 +0100
Subject: Turn arguments of the encrypt subcommand into options.

Prefixed options are easier to follow than the order of positional
arguments.

* pyhegp/pyhegp.py (encrypt): Turn summary, key and ciphertext
arguments into options.
---
 pyhegp/pyhegp.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/pyhegp/pyhegp.py b/pyhegp/pyhegp.py
index 0c0d237..2f0bdb4 100644
--- a/pyhegp/pyhegp.py
+++ b/pyhegp/pyhegp.py
@@ -90,9 +90,15 @@ def pool(pooled_summary_file, summary_files):
 
 @main.command()
 @click.argument("genotype-file", type=click.File("r"))
-@click.argument("summary-file", type=click.File("rb"))
-@click.argument("key-path", type=click.Path())
-@click.argument("ciphertext-path", type=click.Path())
+@click.option("--summary", "-s", "summary_file", type=click.File("rb"),
+              help="Summary statistics file",
+              required=True)
+@click.option("--key", "-k", "key_path", type=click.Path(),
+              help="Output key",
+              required=True)
+@click.option("--output", "-o", "ciphertext_path", type=click.Path(),
+              default="-",
+              help="Output ciphertext")
 def encrypt(genotype_file, summary_file, key_path, ciphertext_path):
     genotype = read_genotype(genotype_file)
     summary = read_summary(summary_file)
-- 
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