Merge pull request #139 from Roestlab/dependabot

Feature: Add Dependabot for automatic software updates

.github/dependabot.yml

@@ -0,0 +1,9 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"  # Location of your pyproject.toml or requirements.txt
+    schedule:
+      interval: "weekly"  # Checks for updates every week
+    commit-message:
+      prefix: "deps"  # Prefix for pull request titles
+    open-pull-requests-limit: 5  # Limit the number of open PRs at a time

.github/workflows/ci.yml

@@ -22,14 +22,11 @@ jobs:
       if: runner.os == 'macOS'
       run: |
         brew install hdf5
-        pip install -r requirements-dev.txt
-
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install --index-url https://pypi.cs.uni-tuebingen.de/simple/ pyopenms
         pip install .[testing,conformer]
-        #pip install -r requirements.txt -r requirements-dev.txt -r requirements-optional.txt
 
     - name: Test
       run: |

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
@@ -25,9 +25,6 @@ formats:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
   install:
-    - requirements: docs/requirements.txt
     - requirements: requirements.txt
-    - requirements: requirements-dev.txt
-    - requirements: requirements-optional.txt
     - method: pip
       path: .

pyproject.toml

@@ -38,11 +38,11 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-testing = ["pytest", "syrupy", "tables" ]
-docs = [ 'nbsphinx', 'sphinx-copybutton', 'sphinx-rtd-theme', 'sphinx==5.3.0' ]
-gui = [ 'streamlit>=1.30.0', 'streamlit-javascript', 'tk', 'pyautogui' ] 
-conformer= [ 'onnxruntime' ]
 
+conformer= [ 'onnxruntime' ]
+docs = [ 'nbsphinx', 'sphinx-copybutton', 'sphinx-rtd-theme', 'sphinx==5.3.0', 'ipykernel' ]
+gui = [ 'streamlit>=1.30.0', 'streamlit-javascript', 'tk', 'pyautogui' ] 
+testing = ["pytest", "syrupy", "tables" ]
 
 [project.scripts]
 massdash = 'massdash.main:cli'