From 00d46d45625cab39da6b97bfd909ac3bae756e6e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Fri, 29 May 2026 16:54:15 +0200
Subject: [PATCH 1/3] build(environment-dev.yaml): fix env name

---
 environment-dev.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment-dev.yaml b/environment-dev.yaml
index 026c6bf..8656ce9 100644
--- a/environment-dev.yaml
+++ b/environment-dev.yaml
@@ -1,4 +1,4 @@
-name: rpfba
+name: rpscore
 channels:
   - conda-forge
   - nodefaults

From 78efb5f19d8426ba0226c44aa0974d1a740a2d6e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Fri, 29 May 2026 16:55:38 +0200
Subject: [PATCH 2/3] chore(rpscore/__main__.py): rm rptools

---
 rpscore/__main__.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/rpscore/__main__.py b/rpscore/__main__.py
index 38100b2..b38e40d 100644
--- a/rpscore/__main__.py
+++ b/rpscore/__main__.py
@@ -1,7 +1,9 @@
 from os import path as os_path, makedirs as os_makedirs
 from .rpscore import predict_score, ThermoError, FBAError
 from .Args import add_arguments
+from ._version import __version__
 from brs_utils import (
+    init as init_logger,
     build_args_parser,
 )
 from rplibs import rpPathway
@@ -16,9 +18,7 @@ def entry_point():
     )
     args = parser.parse_args()
 
-    from rptools.__main__ import init
-
-    logger = init(parser, args)
+    logger = init_logger(parser, args, __version__)
 
     pathway = rpPathway(infile=args.infile, logger=logger)
 

From 3d45399d8be27abf750b795290a07d279a3a32f3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joan=20H=C3=A9risson?= <joan.herisson@univ-evry.fr>
Date: Fri, 29 May 2026 16:55:48 +0200
Subject: [PATCH 3/3] doc(README.md): rm rptools

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index fb7aac8..d541ecd 100644
--- a/README.md
+++ b/README.md
@@ -104,8 +104,8 @@ subdir: osx-64
 <!-- ### rpScore process -->
 **From Python code**
 ```python
-from rptools.rpscore import predict_score
-from rptools.rplibs import rpPathway
+from rpscore import predict_score
+from rplibs import rpPathway
 
 pathway = rpPathway(
     infile='tests/rpscore/data/pathway.xml'
@@ -115,7 +115,7 @@ global_score = predict_score(pathway)
 ```
 **From CLI**
 ```sh
-python -m rptools.rpscore <input_rpsbml> <output_rpsbml>
+python -m rpscore <input_rpsbml> <output_rpsbml>
 ```
 
 ## Tests