Chore/dep update 2411

.github/dependabot.yml

@@ -10,6 +10,11 @@ updates:
     directory: "/" # Location of package manifests
     schedule:
       interval: "monthly"
+      groups:
+        pip-dependencies:
+          applies-to: version-updates
+          patterns:
+            - "*"
 
   # Maintain dependencies for GitHub Actions
   - package-ecosystem: "github-actions"

.github/workflows/CICD.yml

@@ -1,24 +1,21 @@
-
 name: CI Testing
 
 on:
   push:
-    branches: [ main, devel, release ]
+    branches: [main, devel, release]
   pull_request:
-    branches: [ main, devel, release ]
-  schedule:
-  - cron: "4 5 4 1/1 *" # Run monthly.
+    branches: [main, devel, release]
 
 jobs:
   cheap_checks:
-    runs-on: 'ubuntu-latest'
+    runs-on: "ubuntu-latest"
     steps:
       - uses: actions/checkout@v3
 
       # Python setup
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Debug Info
         run: echo ${{ github.ref }} ${{ github.event_name }} ${{ endsWith(github.ref, 'heads/release') && (github.event_name == 'push') }}
@@ -31,7 +28,7 @@ jobs:
       - name: Python Poetry Action
         uses: abatilo/[email protected]
         with:
-          poetry-version: '1.2.2'
+          poetry-version: "1.7.1"
 
       - name: View poetry --version
         run: poetry --version
@@ -49,9 +46,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.10', '3.9']
-        poetry-version: ['1.2.2',]
-        os: ['ubuntu-latest',]
+        python-version: ["3.10", "3.9"]
+        poetry-version: ["1.7.1"]
+        os: ["ubuntu-latest"]
     runs-on: ${{ matrix.os }}
     steps:
       # Initial Setup
@@ -61,8 +58,7 @@ jobs:
       - name: Setup Quarto
         uses: quarto-dev/quarto-actions/setup@v2
       - name: View Quarto version
-        run:
-          quarto --version
+        run: quarto --version
 
       # Python setup
       - uses: actions/setup-python@v4
@@ -81,7 +77,7 @@ jobs:
 
       # Package Setup
       - name: Install deps
-        run: poetry install -n -v --with=plotting,dev,docs 
+        run: poetry install -n -v --with=plotting,dev,docs
 
       # CI checks
       - name: Pytest
@@ -90,10 +86,9 @@ jobs:
       - name: mkdocs
         run: poetry run python -m mkdocs build --strict
 
-
   release:
     # Run when there is a new push on the release branch
-    runs-on: 'ubuntu-latest'
+    runs-on: "ubuntu-latest"
     needs: ci
     if: endsWith(github.ref, 'heads/release') && (github.event_name == 'push')
     steps:
@@ -106,21 +101,20 @@ jobs:
       - name: Setup Quarto
         uses: quarto-dev/quarto-actions/setup@v2
       - name: View Quarto version
-        run:
-          quarto --version
+        run: quarto --version
 
       # Python setup
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: "3.10"
       - name: View Python --version
         run: python --version
 
       # Poetry Setup
       - name: Python Poetry Action
         uses: abatilo/[email protected]
         with:
-          poetry-version: '1.2.2'
+          poetry-version: "1.7.1"
       - name: View poetry --version
         run: poetry --version
 
@@ -147,13 +141,13 @@ jobs:
       - name: Build Docker image
         id: dockerbuild
         run: |
-            docker build -t ghcr.io/jspaezp/elfragmentador:v$(poetry version -s) .
+          docker build -t ghcr.io/jspaezp/elfragmentador:v$(poetry version -s) .
 
       # Publish Docker
       - name: Push the Docker image to the GHCR
         id: ghcr_push
         run: |
-            docker push ghcr.io/jspaezp/elfragmentador:v$(poetry version -s)
+          docker push ghcr.io/jspaezp/elfragmentador:v$(poetry version -s)
 
       # Publishing Docs
       - name: Deploy Docs

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v5.0.0
   hooks:
   - id: check-yaml
     exclude: "mkdocs.yml"
@@ -12,22 +12,22 @@ repos:
   - id: end-of-file-fixer
   - id: detect-private-key
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.146
+  rev: v0.7.4
   hooks:
     - id: ruff
       args: ["--fix"]
 - repo: https://github.com/psf/black
-  rev: 22.10.0
+  rev: 24.10.0
   hooks:
     - id: black
       language_version: python3.9
 - repo: https://github.com/pycqa/isort
-  rev: 5.10.1
+  rev: 5.13.2
   hooks:
     - id: isort
       name: isort (python)
 - repo: https://github.com/python-poetry/poetry
-  rev: 1.3.2  # add version here
+  rev: 1.8.0  # add version here
   hooks:
     - id: poetry-check
     - id: poetry-lock

elfragmentador/data/torch_datasets.py

@@ -19,11 +19,14 @@
 
 class TupleTensorDataset(TensorDataset):
     def __init__(self, tensor_tuple):
-        super().__init__(*tensor_tuple)
+        tmp = list(tensor_tuple)
+        tmp[-1] = tmp[-1].float()
+        super().__init__(*tmp)
         self.builder = type(tensor_tuple)
 
     def __getitem__(self, index):
-        out = self.builder(*super().__getitem__(index))
+        tmp = super().__getitem__(index)
+        out = self.builder(*tmp)
         return out
 
     def as_dataloader(self, batch_size, shuffle, num_workers=0, *args, **kwargs):
@@ -179,7 +182,7 @@ def fast_split(x):
 
 class PeptideDataset(TupleTensorDataset):
     def __init__(self, peptide_list: Iterable[Peptide], nce=None, charge=None):
-        converter = Tensorizer(nce=nce)
-        tmp = [converter(x) for x in peptide_list]
+        converter = Tensorizer()
+        tmp = [converter(x, nce=nce) for x in peptide_list]
         tensor_tuple = concat_batches(tmp)
         super().__init__(tensor_tuple)

elfragmentador/model/__init__.py

@@ -629,7 +629,7 @@ def validation_step(
 
         return step_out["l"]
 
-    def validation_epoch_end(self, outputs: list[Tensor]) -> list[Tensor]:
+    def on_validation_epoch_end(self) -> list[Tensor]:
         """See pytorch lightning documentation."""
         log_dict = {
             "val_irt_l": self.irt_metric.compute(),
@@ -648,7 +648,7 @@ def validation_epoch_end(self, outputs: list[Tensor]) -> list[Tensor]:
         self.spectra_metric.reset()
         self.spectra_metric2.reset()
 
-        return super().validation_epoch_end(outputs)
+        return super().on_validation_epoch_end()
 
     def _evaluation_step(
         self,