Dev

CONTRIBUTING.md

@@ -43,6 +43,7 @@ Older versions of models should stay available to enable users to reproduce past
 3. **Make Your Changes**: Follow the project's coding standards and conventions.  
 4. **Test Your Changes**: Ensure your changes work as expected and don't introduce new issues.  
 5. **Submit a Pull Request (PR)**:  
+   - Open your PR for the dev branch.
    - Provide a clear and concise description of your changes.  
    - Reference related issues (e.g., “Closes #123”).  
    - Be responsive to feedback during the review process.  

clients/python/koinapy/grpc.py

@@ -96,7 +96,7 @@ def _is_server_ready(self):
                 if self.ssl:
                     raise InferenceServerException(
                         "The public koina network seems to be inaccessible at the moment. "
-                        "Please notify ludwig.lautenbacher@tum.de."
+                        "Please notify j.angelis@tum.de."
                     ) from e
                 else:
                     raise InferenceServerException(

models/3dmolms/3dmolms_orbitrap_core/1/.zenodo

@@ -1,3 +1,3 @@
-https://zenodo.org/records/13928958/files/model_orbitrap.zip?download=1
 md5:0b3beb45d6ca6e7c82271bf3be9e3eee 
-https://ndownloader.figshare.com/files/61421536
+https://ndownloader.figshare.com/files/61421536
+https://zenodo.org/records/13928958/files/model_orbitrap.zip?download=1

models/3dmolms/3dmolms_qtof_core/1/.zenodo

@@ -1,3 +1,3 @@
-https://zenodo.org/records/13928958/files/model_qtof.zip?download=1
 md5:8ac637326f9378c6c3d2535183ae439a
-https://ndownloader.figshare.com/files/61458817
+https://ndownloader.figshare.com/files/61458817
+https://zenodo.org/records/13928958/files/model_qtof.zip?download=1

models/Altimeter/Altimeter_2024_core/1/.zenodo

@@ -1,3 +1,3 @@
-https://zenodo.org/records/14894501/files/model.pt.zip?download=1
 md5:714e2cd897171e42e61cce94bba28f8e
-https://ndownloader.figshare.com/files/61459279
+https://ndownloader.figshare.com/files/61459279
+https://zenodo.org/records/14894501/files/model.pt.zip?download=1

models/Altimeter/Altimeter_2024_eval_splines/1/.zenodo

@@ -1,2 +1,3 @@
-https://zenodo.org/records/14896508/files/model.onnx.zip?download=1
-md5:98d179ccb6f46d8eee540044e18203b1
+md5:98d179ccb6f46d8eee540044e18203b1
+https://ndownloader.figshare.com/files/62589634
+https://zenodo.org/records/14896508/files/model.onnx.zip?download=1

models/Prosit/Prosit_2025_irt_22PTM_core/1/.zenodo

@@ -1,3 +1,3 @@
-https://zenodo.org/record/17798879/files/model.savedmodel.zip?download=1
 md5:0f9196ee4b4cf381de476afccb38c61e
-https://ndownloader.figshare.com/files/61465183
+https://ndownloader.figshare.com/files/61465183
+https://zenodo.org/record/17798879/files/model.savedmodel.zip?download=1

models/Prosit/Prosit_2025_irt_40PTM_core/1/.zenodo

@@ -1,3 +1,3 @@
-https://zenodo.org/record/17798825/files/model.savedmodel.zip?download=1
-md5:bfdb1b153911388793f11b240455d076
-https://ndownloader.figshare.com/files/61465183
+md5:412556912991b4b190b3215b825858e1
+https://ndownloader.figshare.com/files/62592103
+https://zenodo.org/record/18935907/files/model.savedmodel.zip?download=1

models/ms2pip/model_20210316_Immuno_HCD_B/1/.zenodo

@@ -1,3 +1,3 @@
-https://zenodo.org/records/12903888/files/model_20210316_Immuno_HCD_B.json.zip?download=1
 md5:b3a644da2b026deed832730f8ec53b02
-https://ndownloader.figshare.com/files/61461328
+https://ndownloader.figshare.com/files/61461328
+https://zenodo.org/records/12903888/files/model_20210316_Immuno_HCD_B.json.zip?download=1

models/ms2pip/model_20210316_Immuno_HCD_Y/1/.zenodo

@@ -1,3 +1,3 @@
-https://zenodo.org/records/12903888/files/model_20210316_Immuno_HCD_Y.json.zip?download=1
 md5:379bd15fa12cbec627d172a949b26aed
-https://ndownloader.figshare.com/files/61461364
+https://ndownloader.figshare.com/files/61461364
+https://zenodo.org/records/12903888/files/model_20210316_Immuno_HCD_Y.json.zip?download=1

models/ms2pip/model_20210416_HCD2021_Y/1/.zenodo

@@ -1,3 +1,3 @@
-https://zenodo.org/record/7576711/files/xgboost.json.zip?download=1
 md5:8fc9a3a075a90fee10ec22942dceb123
-https://ndownloader.figshare.com/files/61461475
+https://ndownloader.figshare.com/files/61461475
+https://zenodo.org/record/7576711/files/xgboost.json.zip?download=1

models/start.py

@@ -98,12 +98,16 @@ def find_and_download():
         path_zen = Path(path_zen)
         target_zip = Path(f"{path_zen.parent}/zenodo.zip")
         with open(path_zen) as f:
-            url_zip = f.readline()
             content = [line.strip() for line in f.readlines()]
             checksum_matches = False
+            checksum = ''
             for line in content:
                 if line[:3] == "md5":
                     checksum_algorithm, checksum = line.split(":")
+                    break
+            for line in content:
+                if line[:3] == "md5":
+                    continue
                 else:
                     url_zip = line