From d873d0be9e5b5cf1cad4228b27f16b2765ac4dcd Mon Sep 17 00:00:00 2001
From: BenoitMorel <morelbt@hitssv543.villa-bosch.de>
Date: Sat, 24 Feb 2024 16:38:13 +0100
Subject: [PATCH] Add an error message for deprecated --per-species-rates and
 --per-family-rates

---
 src/ale/AleArguments.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/ale/AleArguments.cpp b/src/ale/AleArguments.cpp
index 1b0bc1a..52999d0 100644
--- a/src/ale/AleArguments.cpp
+++ b/src/ale/AleArguments.cpp
@@ -103,8 +103,6 @@ AleArguments::AleArguments(int iargc, char * iargv[]):
       ccpRooting = ArgumentsHelper::strToCCPRooting(std::string(argv[++i]));
     } else if (arg == "--fraction-missing-file") {
       fractionMissingFile = argv[++i];
-    } else if (arg == "--param-opt-classes") {
-      optimizationClassFile = argv[++i];
     } else if (arg == "--gene-tree-samples") {
       geneTreeSamples = atoi(argv[++i]);
     } else if (arg == "--model-parametrization") {
@@ -131,6 +129,9 @@ AleArguments::AleArguments(int iargc, char * iargv[]):
       randomSpeciesRoot = true;
     } else if (arg == "--verbose-opt-rates") {
       verboseOptRates = true;
+    } else if (arg == "--per-family-rates" || arg == "--per-species-rates") {
+      Logger::error << "Error: --per-family-rates and --per-species-rates are deprecated and have been replaced with --model-parametrization PER-FAMILY or --model-paramtetrization PER-SPECIES"<< std::endl;
+      ParallelContext::abort(10);
     } else {
       std::cerr << "Unknown argument " << arg << std::endl;
       ParallelContext::abort(10);