Merge branch 'main' of https://github.com/compomics/ms2rescore into f…

…eature/direct-flashlfq-output

.github/workflows/test.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
     steps:
       - uses: actions/checkout@v4
 

README.md

@@ -47,8 +47,7 @@ timsTOF fragmentation and IM2Deep for ion mobility separation. Bruker .d and min
 files are directly supported through the [timsrust](https://github.com/MannLabs/timsrust) library.
 
 Checkout our [preprint](https://doi.org/10.1101/2024.05.29.596400) for more information and the
-[TIMS²Rescore documentation](https://ms2rescore.readthedocs.io/en/stable/userguide/tims2rescore)
-to get started.
+[TIMS²Rescore documentation][tims2rescore] to get started.
 
 ## Citing
 
@@ -99,15 +98,16 @@ make a [pull request][pr]!
 [issues]: https://github.com/compomics/ms2rescore/issues/
 [discussions]: https://github.com/compomics/ms2rescore/discussions/
 [pr]: https://github.com/compomics/ms2rescore/pulls/
-[desktop]: https://ms2rescore.readthedocs.io/gui.html
+[desktop]: https://ms2rescore.readthedocs.io/en/stable/gui/
 [desktop-installer]: https://github.com/compomics/ms2rescore/releases/latest
-[cli]: https://ms2rescore.readthedocs.io/cli/cli.html
-[python-package]: https://ms2rescore.readthedocs.io/api/ms2rescore.html
-[docker]: https://ms2rescore.readthedocs.io/installation.html#docker-container
+[cli]: https://ms2rescore.readthedocs.io/en/stable/cli/
+[python-package]: https://ms2rescore.readthedocs.io/en/stable/api/ms2rescore/
+[docker]: https://ms2rescore.readthedocs.io/en/stable/installation#docker-container
 [publication-branch]: https://github.com/compomics/ms2rescore/tree/pub
 [ms2pip]: https://github.com/compomics/ms2pip
 [deeplc]: https://github.com/compomics/deeplc
 [percolator]: https://github.com/percolator/percolator/
 [mokapot]: https://mokapot.readthedocs.io/
 [psm_utils]: https://github.com/compomics/psm_utils
 [file-formats]: https://psm-utils.readthedocs.io/en/stable/#supported-file-formats
+[tims2rescore]: https://ms2rescore.readthedocs.io/en/stable/userguide/tims2Rescore

ms2rescore/__init__.py

@@ -1,6 +1,6 @@
 """MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and RTs."""
 
-__version__ = "3.1.1"
+__version__ = "3.1.2"
 
 from warnings import filterwarnings
 

ms2rescore/feature_generators/deeplc.py

@@ -139,7 +139,7 @@ def add_features(self, psm_list: PSMList) -> None:
 
                 # Disable wild logging to stdout by Tensorflow, unless in debug mode
                 with contextlib.redirect_stdout(
-                    open(os.devnull, "w")
+                    open(os.devnull, "w", encoding="utf-8")
                 ) if not self._verbose else contextlib.nullcontext():
                     # Make new PSM list for this run (chain PSMs per spectrum to flat list)
                     psm_list_run = PSMList(psm_list=list(chain.from_iterable(psms.values())))

pyproject.toml

@@ -30,21 +30,21 @@ classifiers = [
     "Development Status :: 5 - Production/Stable",
 ]
 dynamic = ["version"]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies = [
     "cascade-config>=0.4.0",
     "click>=7",
     "customtkinter>=5,<6",
-    "deeplc>=2.2",
-    "deeplcretrainer>=0.2",
+    "deeplc>=3.1",
+    "deeplcretrainer",
     "im2deep>=0.1.3",
     "jinja2>=3",
     "lxml>=4.5",
-    "mokapot>=0.9",
+    "mokapot>=0.10",
     "ms2pip>=4.0.0",
     "ms2rescore_rs>=0.3.0",
-    "numpy>=1.16.0",
-    "pandas>=1.0",
+    "numpy>=1.25",
+    "pandas>=1",
     "plotly>=5",
     "psm_utils>=1.1",
     "pyteomics>=4.7.2",