Adjusted versions for new pre-release 2.0.0a1 #121

draeger-lab · Sep 1, 2024 · 25e6990 · 25e6990
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Showing 4 changed files with 3 additions and 10 deletions.
diff --git a/dev/tutorial.ipynb b/dev/tutorial.ipynb
@@ -9,7 +9,7 @@
     "You need Python to use refineGEMs. It runs with versions 3.10+.\n",
     "\n",
     "Install refineGEMs' latest pre-release in an environment with:\n",
-    "`pip install refineGEMs==2.0.0a0`\n",
+    "`pip install refineGEMs==2.0.0a1`\n",
     "\n",
     "refineGEMs also requires the tools MassChargeCuration and BOFdat. Please install these in the same environment with:\n",
     "\n",

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -28,7 +28,7 @@
 author = 'Famke Bäuerle, Gwendolyn O. Döbel and Carolin Brune'
 
 # The full version, including alpha/beta/rc tags
-release = '2.0.0-alpha.0'
+release = '2.0.0-alpha.1'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -2,13 +2,6 @@ Welcome to refineGEMs!
 ======================================
 ``refineGEMs`` is a Python-based toolbox for the curation and analysis of genome-scale metabolic models (GEMS).
 
-.. warning:: 
-    | *Will be deprecated from version 2.0.0 onwards.*
-    | Due to massive restructuring and extension, all functions have been moved into new modules.
-    | If you used any functions from refineGEMs until now and want to use version 2.0.0 in the future, make sure to check your code after the version change.
-    | For the main pipeline in main.py see `SPECIMEN <https://github.com/draeger-lab/SPECIMEN>`__ as it will be deprecated from version 2.0.0 onwards.
-    | Beware that SPECIMEN only runs with refineGEMs 2.0.0 (starting with developmental versions).
-
 Overview
 --------
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "refineGEMs"
-version = "2.0.0-alpha.0"  
+version = "2.0.0-alpha.1"  
 requires-python = ">=3.10, <3.12"
 authors = [
     {name = "Famke Baeuerle", email = "[email protected]"},