Merge branch 'main' into pixi

Author: VeckoTheGecko

.github/dependabot.yml

@@ -4,7 +4,7 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "weekly"
+      interval: "quarterly"
     groups:
       actions:
         patterns:

.github/workflows/cd.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -43,13 +43,13 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v7
         with:
           name: Packages
           path: dist
 
       - name: Generate artifact attestation for sdist and wheel
-        uses: actions/attest-build-provenance@v2.2.3
+        uses: actions/attest-build-provenance@v3.2.0
         with:
           subject-path: "dist/*"
 

.github/workflows/ci.yml

@@ -48,7 +48,7 @@ jobs:
         pixi-environment: ["test-py310", "test-py312"]
         runs-on: [ubuntu-latest, windows-latest, macos-14]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - uses: Parcels-code/pixi-lock/restore@9a2866f8258b87a3c616d5ad7d51c6cd853df78b
@@ -66,31 +66,31 @@ jobs:
           --durations=20
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v5.4.0
+        uses: codecov/codecov-action@v5.5.2
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-  typechecking:
-    name: "TypeChecking: pixi run typing"
-    runs-on: ubuntu-latest
-    if: false
-    needs: cache-pixi-lock
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-      - uses: Parcels-code/pixi-lock/restore@9a2866f8258b87a3c616d5ad7d51c6cd853df78b
-        with:
-          cache-key: ${{ needs.cache-pixi-lock.outputs.cache-key }}
-      - uses: prefix-dev/setup-pixi@v0.9.4
-        with:
-          cache: true
-          pixi-version: ${{ needs.cache-pixi-lock.outputs.pixi-version }}
-          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
-      - name: Typechecking
-        run: pixi run typing --non-interactive --html-report mypy-report
-      - name: Upload test results
-        if: ${{ always() }} # Upload even on mypy error
-        uses: actions/upload-artifact@v4
-        with:
-          name: Mypy report
-          path: mypy-report
+#   typechecking:
+#     name: "TypeChecking: pixi run typing"
+#     runs-on: ubuntu-latest
+#     if: false
+#     needs: cache-pixi-lock
+#     steps:
+#       - uses: actions/checkout@v4
+#         with:
+#           fetch-depth: 0
+#       - uses: Parcels-code/pixi-lock/restore@9a2866f8258b87a3c616d5ad7d51c6cd853df78b
+#         with:
+#           cache-key: ${{ needs.cache-pixi-lock.outputs.cache-key }}
+#       - uses: prefix-dev/setup-pixi@v0.9.4
+#         with:
+#           cache: true
+#           pixi-version: ${{ needs.cache-pixi-lock.outputs.pixi-version }}
+#           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
+#       - name: Typechecking
+#         run: pixi run typing --non-interactive --html-report mypy-report
+#       - name: Upload test results
+#         if: ${{ always() }} # Upload even on mypy error
+#         uses: actions/upload-artifact@v4
+#         with:
+#           name: Mypy report
+#           path: mypy-report

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -11,7 +11,7 @@ repos:
         types: [text]
         files: \.(json|ipynb)$
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.6
+    rev: v0.15.7
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -22,6 +22,6 @@ repos:
       - id: ruff-format
         types_or: [python, jupyter]
   - repo: https://github.com/rbubley/mirrors-prettier # Update mirror as official mirror is deprecated
-    rev: v3.5.1
+    rev: v3.8.1
     hooks:
       - id: prettier

README.md

@@ -44,7 +44,7 @@ VirtualShip is a command line simulator allowing students to plan and conduct a
 - Surface drifters
 - Argo float deployments
 
-<!-- TODO: future. Along the way students will encounter difficulties such as: -->
+Along the way, students will encounter realistic problems that may occur during an oceanographic expedition, requiring them to make decisions to adapt their plans accordingly. For example, delays due to equipment failures, pre-depature logistical issues or safety drills.
 
 ## Installation
 

docs/conf.py

@@ -80,6 +80,11 @@
     "user-guide/teacher-content/ILOs": "user-guide/_images/ILOs.jpg",
     "user-guide/teacher-content/UU-ocean-of-future/Tutorial1": "user-guide/_images/freepik_assignment.png",
     "user-guide/teacher-content/UU-ocean-of-future/Tutorial2": "user-guide/_images/freepik_assignment.png",
+    "user-guide/tutorials/surf_collaborative_setup": "user-guide/_images/freepik_research_vessel.jpg",
+    "user-guide/tutorials/surf_research_cloud_setup": "user-guide/_images/freepik_research_vessel.jpg",
+    "user-guide/tutorials/working_with_expedition_yaml": "user-guide/_images/AnnaWeber.jpeg",
+    "user-guide/teacher-content/UU-dyoc/example_expedition": "user-guide/_images/AnnaWeber.jpeg",
+    "user-guide/teacher-content/UU-dyoc/file_permissions": "user-guide/_images/AnnaWeber.jpeg",
 }
 
 sphinx_gallery_conf = {"default_thumb_file": "_static/virtual_ship_logo.png"}

docs/paper/paper.md

@@ -75,7 +75,7 @@ Moreover, the data ingestion system relies on Analysis-Ready and Cloud-Optimized
 
 The package opens space for many other research applications. It can support real-life expedition planning by letting users test sampling routes before going to sea. It also provides tooling to explore real-time adaptive strategies in which sampling plans shift as forecasts or observations update. The same workflow can also be used to investigate sampling efficiency, for example, examining how waypoint number or spacing shapes the ability to capture features of interest. Moreover, the software is well-suited for developing Observation System Simulation Experiments (OSSEs; e.g. @Errico2013) to test and optimise observational strategies in a cost- and time-efficient manner. This framework further enables instrument design experiments that are relevant to autonomous observing systems. There is potential for users to prototype and test control strategies for gliders, REMUS vehicles, and Saildrones, as well as explore concepts for new instruments at early stages of development. Future tutorials could demonstrate how to define custom instruments within the VirtualShip framework.
 
-Both the customisability of the `VirtualShip` platform and the exciting potential for new ARCO-based data hosting services in domains beyond oceanography (e.g., [atmospheric science](https://climate.copernicus.eu/work-progress-our-data-stores-turn-arco)) means there is potential to extend VirtualShip (or "VirtualShip-like" tools) to other domains in the future. Furthermore, as the `Parcels` underpinnings themselves continue to evolve, with a future (at time of writing) [v4.0 release](https://docs.oceanparcels.org/en/v4-dev/v4/) focusing on alignment with [Pangeo](https://pangeo.io/) standards and `Xarray` data structures [@Hoyer2017], `VirtualShip` will also benefit from these improvements, further enhancing its capabilities, extensibility and compatability with modern cloud-based data pipelines.
+Both the customisability of the `VirtualShip` platform and the exciting potential for new ARCO-based data hosting services in domains beyond oceanography (e.g., [atmospheric science](https://climate.copernicus.eu/work-progress-our-data-stores-turn-arco)) means there is potential to extend VirtualShip (or "VirtualShip-like" tools) to other domains in the future. Furthermore, as the `Parcels` underpinnings themselves continue to evolve, with a future (at time of writing) [v4.0 release](https://docs.oceanparcels.org/en/main/v4/) focusing on alignment with [Pangeo](https://pangeo.io/) standards and `Xarray` data structures [@Hoyer2017], `VirtualShip` will also benefit from these improvements, further enhancing its capabilities, extensibility and compatability with modern cloud-based data pipelines.
 
 # AI usage disclosure
 

docs/paper/plotting_functions.py

@@ -109,7 +109,7 @@ def plot_ctd(ds, ax, plot_variable, vmin, vmax, axes_labels=False):
     var_down = _ctd_descent_only(ctd_distance, MAP_VARNAMES[plot_variable])
 
     # 1d array of depth dimension (from deepest trajectory)
-    traj_idx, obs_idx = np.where(z_down == np.nanmin(z_down))
+    traj_idx, _ = np.where(z_down == np.nanmin(z_down))
     z1d = z_down.values[traj_idx[0], :]
 
     # distance as 1d array