GRASS-MIL 1.1.0: one default path, niche analysis as primary results, validity fixes

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,22 +1,9 @@
-## What does this PR do?
+## What does this change?
 
-<!--
-Please include a summary of the change and which issue is fixed.
-Please also include relevant motivation and context.
-List any dependencies that are required for this change.
-List all the breaking changes introduced by this pull request.
--->
+<!-- A summary of the change, the issue it fixes, and any breaking change. -->
 
-Fixes #\<issue_number>
+## Checklist
 
-## Before submitting
-
-- [ ] Did you make sure **title is self-explanatory** and **the description concisely explains the PR**?
-- [ ] Did you make sure your **PR does only one thing**, instead of bundling different changes together?
-- [ ] Did you list all the **breaking changes** introduced by this pull request?
-- [ ] Did you **test your PR locally** with `pytest` command?
-- [ ] Did you **run pre-commit hooks** with `pre-commit run -a` command?
-
-## Did you have fun?
-
-Make sure you had fun coding 🙃
+- [ ] `pytest` passes locally
+- [ ] `pre-commit run -a` passes
+- [ ] Documentation and `CHANGELOG.md` updated where behaviour changed

.github/codecov.yml

@@ -1,15 +1,8 @@
 coverage:
   status:
-    # measures overall project coverage
     project:
       default:
-        threshold: 100% # how much decrease in coverage is needed to not consider success
-
-    # measures PR or single commit coverage
+        threshold: 2% # allowed drop in total coverage
     patch:
       default:
-        threshold: 100% # how much decrease in coverage is needed to not consider success
-
-
-    # project: off
-    # patch: off
+        target: 70%

.github/dependabot.yml

@@ -1,16 +1,13 @@
-# To get started with Dependabot version updates, you'll need to specify which
-# package ecosystems to update and where the package manifests are located.
-# Please see the documentation for all configuration options:
-# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
-
 version: 2
 updates:
-  - package-ecosystem: "pip" # See documentation for possible values
-    directory: "/" # Location of package manifests
+  - package-ecosystem: "pip"
+    directory: "/"
     schedule:
-      interval: "daily"
+      interval: "weekly"
     ignore:
-      - dependency-name: "pytorch-lightning"
-        update-types: ["version-update:semver-patch"]
-      - dependency-name: "torchmetrics"
+      - dependency-name: "lightning"
         update-types: ["version-update:semver-patch"]
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/code-quality.yml

@@ -0,0 +1,18 @@
+name: Code quality
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - run: python -m pip install --upgrade pip pre-commit
+      - run: pre-commit run --all-files --show-diff-on-failure