Add init command

.github/CONTRIBUTING.md

@@ -1 +1 @@
-See the following [contributing guide](../docs/contributing.md).
+See the following [contributing guide](https://virtualship.oceanparcels.org/en/latest/contributing.html).

.github/workflows/ci.yml

@@ -21,13 +21,6 @@ env:
   FORCE_COLOR: 3
 
 jobs:
-  # pylint:
-  #   name: Format
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Run PyLint
-  #       run: pipx run nox -s pylint -- --output-format=github
-
   tests:
     name: tests (${{ matrix.runs-on }} | Python ${{ matrix.python-version }})
     runs-on: ${{ matrix.runs-on }}
@@ -48,7 +41,7 @@ jobs:
           create-args: >-
             python=${{matrix.python-version}}
 
-      - run: pip install . --no-deps --no-build-isolation
+      - run: pip install . --no-deps
 
       - name: Test package
         run: >-

.gitignore

@@ -175,3 +175,4 @@ cython_debug/
 src/virtualship/_version_setup.py
 
 .vscode/
+.DS_Store

.readthedocs.yaml

@@ -10,7 +10,7 @@ build:
   jobs:
     pre_build:
       - pip install .
-      # - sphinx-build -b linkcheck docs/ _build/linkcheck
+      - sphinx-build -b linkcheck docs/ _build/linkcheck
       - sphinx-apidoc -o docs/api/ --module-first --no-toc --force src/virtualship
 
 conda:

README.md

@@ -7,6 +7,13 @@
 
 <!-- Badges -->
 
+[![Anaconda-release](https://anaconda.org/conda-forge/virtualship/badges/version.svg)](https://anaconda.org/conda-forge/virtualship/)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/virtualship)
+[![unit-tests](https://github.com/OceanParcels/virtualship/actions/workflows/ci.yml/badge.svg)](https://github.com/OceanParcels/virtualship/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/OceanParcels/virtualship/graph/badge.svg?token=SLGLN8QBLW)](https://codecov.io/gh/OceanParcels/virtualship)
+
+<!-- Zenodo badge -->
+
 ---
 
 <!-- SPHINX-START -->
@@ -45,7 +52,7 @@ conda activate ship
 
 which creates an environment named `ship` with the latest version of `virtualship`. You can replace `ship` with any name you like.
 
-For a development installation, please follow the instructions detailed in the [contributing page](.github/CONTRIBUTING.md).
+For a development installation, please follow the instructions detailed in the [contributing page](https://virtualship.oceanparcels.org/en/latest/contributing.html).
 
 ## Usage
 
@@ -101,3 +108,7 @@ For examples, see [the tutorials section of our documentation](https://virtualsh
 ## Input data
 
 The scripts are written to work with [A-grid ocean data from the Copernicus Marine Service](https://data.marine.copernicus.eu/product/GLOBAL_ANALYSISFORECAST_PHY_001_024/description).
+
+## Source code
+
+The code for this project is [hosted on GitHub](https://github.com/OceanParcels/virtualship).

codecov.yml

@@ -0,0 +1,11 @@
+coverage:
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true
+comment: false
+# When modifying this file, please validate using
+# curl -X POST --data-binary @codecov.yml https://codecov.io/validate

docs/conf.py

@@ -47,15 +47,13 @@
     "source_repository": "https://github.com/OceanParcels/virtualship",
     "source_branch": "main",
     "source_directory": "docs/",
-}
-
-html_static_path = ["_static"]
-html_theme_options = {
     "light_logo": "virtual_ship_logo.png",
     "dark_logo": "virtual_ship_logo_inverted.png",
     "sidebar_hide_name": True,
 }
 
+html_static_path = ["_static"]
+
 myst_enable_extensions = [
     "colon_fence",
 ]

docs/index.md

@@ -8,6 +8,7 @@ Home <self>
 quickstart
 tutorials/index
 contributing
+OceanParcels <https://oceanparcels.org>
 ```
 
 ```{include} ../README.md

environment.yml

@@ -10,6 +10,7 @@ dependencies:
   - numpy >=1, < 2
   - pydantic >=2, <3
   - pip
+  - pyyaml
 
   # linting
   - pre-commit

pyproject.toml

@@ -32,6 +32,7 @@ dependencies = [
     "opensimplex == 0.4.5",
     "numpy >=1, < 2",
     "pydantic >=2, <3",
+    "PyYAML",
 ]
 
 [project.urls]
@@ -41,9 +42,12 @@ Documentation = "https://virtualship.oceanparcels.org/"
 "Bug Tracker" = "https://github.com/OceanParcels/virtualship/issues"
 Changelog = "https://github.com/OceanParcels/virtualship/releases"
 
+
 [tool.setuptools.packages.find]
 where = ["src"]
 
+[tool.setuptools.package-data]
+virtualship = ["*.yaml"]
 
 [tool.setuptools_scm]
 version_file = "src/virtualship/_version_setup.py"

src/virtualship/cli/commands.py

@@ -2,7 +2,9 @@
 
 import click
 
+from virtualship import utils
 from virtualship.expedition.do_expedition import do_expedition
+from virtualship.utils import SCHEDULE, SHIP_CONFIG
 
 
 @click.command(
@@ -11,11 +13,29 @@
 @click.argument(
     "path",
     type=click.Path(exists=False, file_okay=False, dir_okay=True),
-    # help="Expedition directory",
 )
 def init(path):
     """Entrypoint for the tool."""
-    raise NotImplementedError("Not implemented yet.")
+    path = Path(path)
+    path.mkdir(exist_ok=True)
+
+    config = path / SHIP_CONFIG
+    schedule = path / SCHEDULE
+
+    if config.exists():
+        raise FileExistsError(
+            f"File '{config}' already exist. Please remove it or choose another directory."
+        )
+
+    if schedule.exists():
+        raise FileExistsError(
+            f"File '{schedule}' already exist. Please remove it or choose another directory."
+        )
+
+    config.write_text(utils.get_example_config())
+    schedule.write_text(utils.get_example_schedule())
+
+    click.echo(f"Created '{config.name}' and '{schedule.name}' at {path}.")
 
 
 @click.command(

src/virtualship/expedition/do_expedition.py

@@ -6,6 +6,8 @@
 
 import pyproj
 
+from virtualship.utils import CHECKPOINT, SCHEDULE, SHIP_CONFIG
+
 from .checkpoint import Checkpoint
 from .expedition_cost import expedition_cost
 from .input_data import InputData
@@ -109,7 +111,7 @@ def do_expedition(expedition_dir: str | Path) -> None:
 
 
 def _get_ship_config(expedition_dir: Path) -> ShipConfig | None:
-    file_path = expedition_dir.joinpath("ship_config.yaml")
+    file_path = expedition_dir.joinpath(SHIP_CONFIG)
     try:
         return ShipConfig.from_yaml(file_path)
     except FileNotFoundError:
@@ -129,7 +131,7 @@ def _load_input_data(expedition_dir: Path, ship_config: ShipConfig) -> InputData
 
 
 def _get_schedule(expedition_dir: Path) -> Schedule | None:
-    file_path = expedition_dir.joinpath("schedule.yaml")
+    file_path = expedition_dir.joinpath(SCHEDULE)
     try:
         return Schedule.from_yaml(file_path)
     except FileNotFoundError:
@@ -138,13 +140,13 @@ def _get_schedule(expedition_dir: Path) -> Schedule | None:
 
 
 def _load_checkpoint(expedition_dir: Path) -> Checkpoint | None:
-    file_path = expedition_dir.joinpath("checkpoint.yaml")
+    file_path = expedition_dir.joinpath(CHECKPOINT)
     try:
         return Checkpoint.from_yaml(file_path)
     except FileNotFoundError:
         return None
 
 
 def _save_checkpoint(checkpoint: Checkpoint, expedition_dir: Path) -> None:
-    file_path = expedition_dir.joinpath("checkpoint.yaml")
+    file_path = expedition_dir.joinpath(CHECKPOINT)
     checkpoint.to_yaml(file_path)

src/virtualship/static/__init__.py

@@ -0,0 +1 @@
+"""Module to put static assets. Should not be used for data."""

src/virtualship/static/schedule.yaml

@@ -0,0 +1,16 @@
+waypoints:
+  - instrument: CTD
+    location:
+      latitude: 0
+      longitude: 0
+    time: 2023-01-01 00:00:00
+  - instrument: DRIFTER
+    location:
+      latitude: 0.01
+      longitude: 0.01
+    time: 2023-01-01 01:00:00
+  - instrument: ARGO_FLOAT
+    location:
+      latitude: 0.02
+      longitude: 0.02
+    time: 2023-01-01 02:00:00

src/virtualship/static/ship_config.yaml

@@ -0,0 +1,21 @@
+ship_speed_meter_per_second: 5.14
+adcp_config:
+  num_bins: 40
+  max_depth_meter: -1000.0
+  period_minutes: 5.0
+argo_float_config:
+  cycle_days: 10.0
+  drift_days: 9.0
+  drift_depth_meter: -1000.0
+  max_depth_meter: -2000.0
+  min_depth_meter: 0.0
+  vertical_speed_meter_per_second: -0.1
+ctd_config:
+  max_depth_meter: -2000.0
+  min_depth_meter: -11.0
+  stationkeeping_time_minutes: 20.0
+drifter_config:
+  depth_meter: 0.0
+  lifetime_minutes: 40320.0
+ship_underwater_st_config:
+  period_minutes: 5.0

src/virtualship/utils.py

@@ -0,0 +1,23 @@
+from functools import lru_cache
+from importlib.resources import files
+
+SCHEDULE = "schedule.yaml"
+SHIP_CONFIG = "ship_config.yaml"
+CHECKPOINT = "checkpoint.yaml"
+
+
+def load_static_file(name: str) -> str:
+    """Load static file from the ``virtualship.static`` module by file name."""
+    return files("virtualship.static").joinpath(name).read_text(encoding="utf-8")
+
+
+@lru_cache(None)
+def get_example_config() -> str:
+    """Get the example configuration file."""
+    return load_static_file(SHIP_CONFIG)
+
+
+@lru_cache(None)
+def get_example_schedule() -> str:
+    """Get the example schedule file."""
+    return load_static_file(SCHEDULE)

tests/test_cli.py

@@ -0,0 +1,41 @@
+from pathlib import Path
+
+import pytest
+from click.testing import CliRunner
+
+from virtualship.cli.commands import init
+from virtualship.utils import SCHEDULE, SHIP_CONFIG
+
+
+def test_init():
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        result = runner.invoke(init, ["."])
+        assert result.exit_code == 0
+        config = Path(SHIP_CONFIG)
+        schedule = Path(SCHEDULE)
+
+        assert config.exists()
+        assert schedule.exists()
+
+
+def test_init_existing_config():
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        config = Path(SHIP_CONFIG)
+        config.write_text("test")
+
+        with pytest.raises(FileExistsError):
+            result = runner.invoke(init, ["."])
+            raise result.exception
+
+
+def test_init_existing_schedule():
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        schedule = Path(SCHEDULE)
+        schedule.write_text("test")
+
+        with pytest.raises(FileExistsError):
+            result = runner.invoke(init, ["."])
+            raise result.exception

tests/test_utils.py

@@ -0,0 +1,26 @@
+from virtualship.expedition import Schedule, ShipConfig
+from virtualship.utils import get_example_config, get_example_schedule
+
+
+def test_get_example_config():
+    assert len(get_example_config()) > 0
+
+
+def test_get_example_schedule():
+    assert len(get_example_schedule()) > 0
+
+
+def test_valid_example_config(tmp_path):
+    path = tmp_path / "test.yaml"
+    with open(path, "w") as file:
+        file.write(get_example_config())
+
+    ShipConfig.from_yaml(path)
+
+
+def test_valid_example_schedule(tmp_path):
+    path = tmp_path / "test.yaml"
+    with open(path, "w") as file:
+        file.write(get_example_schedule())
+
+    Schedule.from_yaml(path)