Add SWOPP3 analysis script and violations module

.github/copilot-instructions.md

@@ -0,0 +1,36 @@
+# Copilot Instructions for routetools
+
+This repository implements weather-routing optimization with JAX and CMA-ES. Keep changes focused, reproducible, and validated.
+
+Write and reason in English.
+
+## Required Workflow
+
+1. Read relevant source files and matching tests before editing.
+2. Make the smallest change that satisfies the request.
+
+## Code Conventions
+
+- Use the repository toolchain (`uv` via `make` targets).
+- Preserve existing public APIs unless the request explicitly requires a breaking change.
+- Follow `ruff` and `pytest` settings in `pyproject.toml`.
+- Keep docstrings in NumPy style for public functions.
+- Prefer vectorized/JAX-friendly implementations in performance-sensitive code paths.
+
+## Testing Conventions
+
+- Place tests in `tests/` near the relevant domain file.
+- Keep tests deterministic and lightweight unless a larger benchmark is explicitly requested.
+
+## Data and Artifacts
+
+- Do not commit large generated outputs.
+- Treat `data/` contents as potentially large and optional in local environments.
+- Fail with clear error messages when optional datasets are missing.
+
+## Permissions
+
+- Make sure you have the necessary permissions to push to the repository. If you do not have permissions, stop and ask for them, guiding the user to the appropriate process to gain access.
+- You can add, commit and push changes to this repository. Never commit to 'main' or 'swopp' branches directly.
+- If you are on 'main' or 'swopp', create a new branch for your changes and open a pull request for review.
+- Do small commits, preferably one per logical change. This makes it easier to review and understand the history of changes.

.github/workflows/pre-commit-pr.yml

@@ -1,14 +1,14 @@
-name: pre-commit-pr
+name: post-commit-push
 
 on:
-  pull_request:
+  push:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
-  pre-commit:
+  post-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -30,5 +30,5 @@ jobs:
           uv pip install pip
       - uses: pre-commit/action@v3.0.1
         with:
-          # Ejecutar solo en ficheros que hayan cambiado https://github.com/pre-commit/action/issues/7
-          extra_args: --color=always --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}
+          # Run hooks after commits are pushed
+          extra_args: --color=always --all-files --hook-stage post-commit

.gitignore

@@ -167,3 +167,17 @@ output*
 # User files
 nohup.out
 *.zip
+output/
+
+# CodaBench competition — large data & build artifacts
+codabench/reference_data/*.nc
+codabench/reference_data/*.shp
+codabench/reference_data/*.shx
+codabench/reference_data/*.dbf
+codabench/reference_data/*.prj
+codabench/logo/
+codabench/test_submission/
+
+# Separate repo
+routingviz/
+*.whl

README.md

@@ -22,6 +22,10 @@ Tools:
 - [prettier](https://prettier.io/): format YAML and Markdown
 - [codespell](https://github.com/codespell-project/codespell): check spelling in source code
 
+## Documentation
+
+- [Parametric Performance Model](docs/parametric_model.md) — closed-form RISE model for ship power prediction (hull, wind, wave, and wingsail components).
+
 ## Installation
 
 ### Application
@@ -38,7 +42,18 @@ Install package and pinned dependencies with the [`uv`](https://docs.astral.sh/u
    uv sync
    ```
 
-4. Run any command or Python script with `uv run`, for instance:
+4. (Optional) Install the SWOPP3 performance model:
+
+   ```{bash}
+   uv sync --extra swopp3 --find-links release_package/wheels
+   ```
+
+   If the pre-built wheels are available locally in `release_package/wheels/`,
+   `uv` will resolve `swopp3-performance-model` from that directory. Wheels are
+   available for Python 3.10 – 3.13 on Linux (manylinux) and Windows
+   (win_amd64).
+
+5. Run any command or Python script with `uv run`, for instance:
 
    ```{bash}
    uv run routetools/cmaes.py
@@ -50,63 +65,6 @@ Install package and pinned dependencies with the [`uv`](https://docs.astral.sh/u
    source .venv/bin/activate
    ```
 
-### Git credentials for VCS dependencies
-
-When `uv` installs a package from a git repository (VCS dependency), Git may need credentials to fetch the remote. On non-interactive environments this commonly fails with:
-
-```bash
-fatal: could not read Username for 'https://github.com': terminal prompts disabled
-```
-
-Use one of the following approaches to make VCS fetches non-interactive.
-
-**Option A: SSH (preferred)**
-
-Generate an SSH key (WSL / Linux):
-
-```bash
-ssh-keygen -t ed25519 -C "your_email@example.com" -f ~/.ssh/id_ed25519 -N ""
-eval "$(ssh-agent -s)"
-ssh-add ~/.ssh/id_ed25519
-cat ~/.ssh/id_ed25519.pub
-```
-
-Add the printed public key to GitHub (Settings → SSH and GPG keys). Test access:
-
-```bash
-ssh -T git@github.com
-git ls-remote git@github.com:Weather-Routing-Research/weather-routing-benchmarks.git refs/heads/main
-```
-
-Then use an SSH pip URL when adding or declaring the dependency:
-
-```bash
-uv add 'git+ssh://git@github.com/Weather-Routing-Research/weather-routing-benchmarks.git@main#egg=wrr_bench'
-uv sync
-```
-
-If you run `uv` from PowerShell on Windows, ensure the Windows SSH agent is running and the key is loaded (Start-Service ssh-agent; ssh-add $env:USERPROFILE\\.ssh\\id_ed25519), or run `uv` from WSL where the key was created.
-
-**Option B: HTTPS with credentials (fallback)**
-
-Use Git Credential Manager or GitHub CLI to cache credentials so Git won't prompt:
-
-PowerShell (Windows):
-
-```powershell
-git config --global credential.helper manager-core
-gh auth login --hostname github.com --git-protocol https
-```
-
-WSL / Linux (use gh or configure a credential helper that works in your environment):
-
-```bash
-gh auth login --hostname github.com --git-protocol https
-# or configure `git config --global credential.helper cache` for short-term caching
-```
-
-After configuring credentials, retry the `uv add` / `uv sync` command.
-
 ### Library
 
 Install a specific version of the package with `pip` or `uv pip`:
@@ -157,6 +115,102 @@ If your computer does not have a GPU, you can force JAX to use the CPU with `JAX
 JAX_PLATFORMS=cpu uv run scripts/single_run.py
 ```
 
+### ERA5 weather data pipeline
+
+The `routetools.era5` module provides real-world ERA5 wind and wave fields
+for weather routing. Two download backends are available:
+
+- **GCS** (default) — Google Cloud archive, no API key required.
+- **CDS** — Copernicus Climate Data Store (requires `cdsapi` + API key).
+
+**1. Download ERA5 data** for the Atlantic corridor (USNYC ↔ DEHAM):
+
+```bash
+uv run scripts/download_era5.py --corridor atlantic --year 2023
+```
+
+This creates `data/era5/era5_wind_atlantic_2023.nc` and
+`data/era5/era5_waves_atlantic_2023.nc`.
+
+**2. Run the real-world benchmark** (New York → Hamburg, Jan 8 2023):
+
+```bash
+uv run scripts/era5_benchmark.py --departure 2023-01-08T00:00:00
+```
+
+See `scripts/download_era5.py --help` and `scripts/era5_benchmark.py --help`
+for all available options.
+
+### SWOPP3 ERA5 pipeline
+
+The default SWOPP3 competition pipeline is:
+
+```bash
+uv run scripts/download_era5.py
+uv run scripts/swopp3_run.py
+```
+
+These two commands line up without extra path flags. The downloader writes the
+four default 2024 files that `scripts/swopp3_run.py` expects:
+
+```text
+data/era5/era5_wind_atlantic_2024.nc
+data/era5/era5_waves_atlantic_2024.nc
+data/era5/era5_wind_pacific_2024.nc
+data/era5/era5_waves_pacific_2024.nc
+```
+
+`scripts/swopp3_run.py` validates these files before running any case. If one
+or more inputs are missing, it exits immediately with a precise error message
+instead of silently substituting a great-circle route or running without
+weather data. This is intentional:
+
+- GC cases still require wind and wave data for SWOPP3 energy evaluation.
+- Optimised cases require wind data for the CMA-ES vectorfield and wind/wave
+  data for the final SWOPP3 energy evaluation.
+
+If you download a different year or only one corridor, pass matching
+`--wind-path*` and `--wave-path*` options to `scripts/swopp3_run.py`.
+
+### Reproducible SWOPP3 experiment profiles
+
+`scripts/swopp3_run.py` supports named experiment profiles stored in
+`config.toml`.
+
+Run a named experiment:
+
+```bash
+uv run scripts/swopp3_run.py k15_p400_w1000
+```
+
+Use another TOML file if needed:
+
+```bash
+uv run scripts/swopp3_run.py k15_p400_w1000 --config-path path/to/experiments.toml
+```
+
+Relative paths inside a profile are resolved from the directory that contains
+the TOML file, not from your current working directory.
+
+Each profile can define shared defaults plus one or more runs.
+
+The runner writes a resolved manifest to:
+
+```text
+output/<experiment>/experiment_manifest.json
+```
+
+This records the experiment name, config file, source script, and resolved run
+parameters used for the launch.
+
+To add a new experiment:
+
+1. Add a new `[swopp3.experiments.<name>]` section to `config.toml`.
+2. Put shared parameters under `[swopp3.experiments.<name>.defaults]`.
+3. Add one or more `[[swopp3.experiments.<name>.runs]]` entries.
+4. Set `source_script` to the script or workflow the profile replaces.
+5. Run `uv run scripts/swopp3_run.py <name>`.
+
 ## Reproduce the results (paper)
 
 To reproduce the results from the paper, run the following command: