Fix: Only use --pre for latest, remove pyopenms from requirements.txt to avoid reinstall

Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>

Author: Copilot

docs/README.md

@@ -23,6 +23,7 @@ Once the environment is active, you can install all required python packages usi
 
     cd <pyOpenMS_dir>/docs
     pip install -r requirements.txt
+    python install_pyopenms.py
 
 
 To build the docs run the line below (works on all operating systems), but make sure that your working dir is `<pyOpenMS_dir>/docs` (see above):

docs/install_pyopenms.py

@@ -56,12 +56,12 @@ def install_pyopenms(version):
     # Build pip install command
     cmd = [
         sys.executable, "-m", "pip", "install",
-        "--extra-index-url", "https://pypi.cs.uni-tuebingen.de/simple/",
-        "--pre"  # Allow pre-release versions
+        "--extra-index-url", "https://pypi.cs.uni-tuebingen.de/simple/"
     ]
 
     if version == 'latest':
-        print("Installing latest version of pyopenms")
+        print("Installing latest version of pyopenms (including pre-releases)")
+        cmd.append("--pre")  # Allow pre-release versions only for latest
         cmd.append("pyopenms")
     else:
         print(f"Installing pyopenms=={version}")

docs/requirements.txt

@@ -9,4 +9,5 @@ ipython
 pygments-lexer-pseudocode
 
 # Note: pyopenms is installed via docs/install_pyopenms.py script
-# which reads the version from READTHEDOCS_VERSION_NAME environment variable
+# On ReadTheDocs: uses READTHEDOCS_VERSION_NAME to install the correct version (--pre only for "latest")
+# For local builds: run "python docs/install_pyopenms.py" manually after installing requirements