chore: update dependencies

.flake8

@@ -16,3 +16,6 @@ ignore =
 
     # Unused imports - pb with import_and_args.py
     # F401
+per-file-ignores =
+    # __init__ files
+    dataset_product_mapping.py: E501

.github/workflows/binaries.yml

@@ -0,0 +1,56 @@
+name: Create Binaries
+
+on:
+  push:
+    branches:
+       - main
+       - 'pre-releases/**'
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, ubuntu-latest, macos-13]
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 20
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: '1.5.6-0'
+        micromamba-binary-path: ${{ runner.temp }}/bin/micromamba
+        environment-file: conda_environment_binary.yaml
+        environment-name: copernicusmarine-binary
+        condarc-file: .condarc
+        cache-environment: true
+        post-cleanup: 'all'
+
+    - name: Build with PyInstaller
+      shell: micromamba-shell {0}
+      run: |
+        make run-using-pyinstaller-${{ matrix.os }}
+
+    - name: Set VERSION environment variable
+      id: set-version
+      shell: micromamba-shell {0}
+      run: echo "VERSION=$(poetry version --short)" >> $GITHUB_OUTPUT
+
+    - name: Upload binaries to macos or ubuntu
+      shell: micromamba-shell {0}
+      env:
+        GH_TOKEN: ${{ github.token }}
+      run: |
+        if [ "${{ matrix.os }}" == "macos-latest" ]; then
+          ARCH="macos-arm64"
+        elif [ "${{ matrix.os }}" == "macos-13" ]; then
+          ARCH="macos-x86_64"
+        elif [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
+          ARCH="linux"
+        fi
+          gh release upload v${{steps.set-version.outputs.VERSION}} dist/copernicusmarine_${ARCH}.cli#copernicusmarine-binary-${ARCH}-for-v${{steps.set-version.outputs.VERSION}}

.github/workflows/binary-windows.yml

@@ -0,0 +1,45 @@
+name: Create Binaries
+
+on:
+  push:
+    branches:
+       - main
+       - 'pre-releases/**'
+
+jobs:
+  build:
+    runs-on: windows-latest
+    timeout-minutes: 20
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: '1.5.6-0'
+        micromamba-binary-path: ${{ runner.temp }}\Scripts\micromamba.exe
+        environment-file: conda_environment_binary.yaml
+        environment-name: copernicusmarine-binary
+        condarc-file: .condarc
+        cache-environment: true
+        post-cleanup: 'all'
+
+    - name: Build with PyInstaller
+      shell: bash -el {0}
+      run: |
+        make run-using-pyinstaller-windows-latest
+
+    - name: Set VERSION environment variable
+      id: set-version
+      shell: bash -el {0}
+      run: echo "VERSION=$(poetry version --short)" >> $GITHUB_OUTPUT
+
+    - name: Upload binaries to windows
+      shell: bash -el {0}
+      env:
+        GH_TOKEN: ${{ github.token }}
+      run: |
+          gh release upload v${{steps.set-version.outputs.VERSION}} dist/copernicusmarine.exe#copernicusmarine-binary-windows-for-v${{steps.set-version.outputs.VERSION}}

.github/workflows/tests.yml

@@ -2,7 +2,10 @@ name: Run tests
 
 on:
   pull_request:
-    branches: [ "main", "copernicusmarine-toolbox-v2" ]
+    branches:
+      - "main"
+      - "copernicusmarine-toolbox-v2"
+      - "pre-releases/**"
 
 jobs:
   tests:

.gitignore

@@ -8,3 +8,9 @@ copernicusmarine/**/__pycache__/
 **/.DS_Store
 __debug.py
 dist/
+
+# Sphinx documentation html build
+doc/_build/
+
+# Jupyter notebook checkpoints
+**/.ipynb_checkpoints/

.pre-commit-config.yaml

@@ -28,6 +28,7 @@ repos:
         args: [--pytest-test-first]
         exclude: ^tests/resources/
       - id: pretty-format-json
+        exclude: ^doc/usage/quickoverview.ipynb
   - repo: https://github.com/pre-commit/mirrors-isort
     rev: v5.10.1
     hooks:

.readthedocs.yaml

@@ -0,0 +1,38 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-22.9"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: doc/conf.py
+
+conda:
+  environment: conda_environment_sphinx.yaml
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - method: pip
+      path: .
+
+#TODO: add environment variables if we want to build the notebook when building the documentation
+# https://docs.readthedocs.io/en/stable/environment-variables.html

CONTRIBUTION.md

@@ -112,3 +112,40 @@ First, here is the link to the conda-forge feedstock repository: [https://github
 All the conda-forge informations about this repository are available [here in the README](https://github.com/orgs/conda-forge/teams/copernicusmarine). To update it (new version, new maintainer...), please follow the indicated procedure.
 
 Please also take a look at [this conda-forge documentation](https://conda-forge.org/docs/maintainer/updating_pkgs/#example-workflow-for-updating-a-package) for more information about the update procedure.
+
+## Documentation
+
+We use sphinx and read the docs to respectively build and distribute the documentation of the toolbox.
+
+### Sphinx
+
+We use:
+
+- autodoc: to create the documentation from the docstrings of the Python interface or the comments in the models
+- numpydoc: to convert numpydoc documentation to restructuresText
+- sphinx-click: to generate the documentation from the click CLI
+- furo: as a base template
+
+The configuration of sphinx can be found in the `doc/conf.py` file and the versions are in the `conda_environment_sphinx.yaml` file. The `_build` folder is gitignored.
+
+To build the documentation do:
+
+```bash
+cd doc/
+make html
+```
+
+### ReadTheDocs
+
+Please see the admin page of the toolbox: [here](https://readthedocs.org/projects/copernicusmarine/).
+
+To access admin rights, you need to be added to the readthedocs project (after creating an account). For the moment Mathis and Simon are the admin of this page.
+
+Example: [toolbox documentation](https://copernicusmarine.readthedocs.io)
+
+Readthedocs have a webhook on the copernicusmarine repo and is triggered when: a commit is pushed, a tag is created and other events.
+
+We defined some automatisation processes that listen to these events and trigger some actions.
+
+- If a tag of a release is pushed (eg v1.3.3) then the doc is built and the v1.3.3 will be available and the default documentation ie any user going to the root of the documentation [https://copernicusmarine.readthedocs.io](https://copernicusmarine.readthedocs.io) will be directed to the newest version: `copernicusmarine.readthedocs.io/en/v1.3.3`.
+- If a tag of a pre-release is pushed (eg v2.0.0a1) then the doc is built and the v2.0.0a1 is available but won't be the default one.

Makefile

@@ -54,6 +54,23 @@ run-tests-dependencie-versions:
 	${ACTIVATE_ENVIRONMENT}
 	tox run
 
+run-using-pyinstaller-windows-latest:
+	pip install -e .
+	python -m PyInstaller --copy-metadata copernicusmarine --icon=toolbox_icon.png --copy-metadata xarray --name copernicusmarine.exe --add-data "C:\Users\runneradmin\micromamba\envs\copernicusmarine-binary\Lib\site-packages\distributed\distributed.yaml;.\distributed" copernicusmarine/command_line_interface/copernicus_marine.py --onefile
+
+run-using-pyinstaller-macos-latest:
+	pip install -e .
+	python -m PyInstaller --collect-all tzdata --copy-metadata copernicusmarine --name copernicusmarine_macos-arm64.cli --icon=toolbox_icon.png copernicusmarine/command_line_interface/copernicus_marine.py --onefile --target-architecture=arm64
+
+run-using-pyinstaller-macos-13:
+	pip install -e .
+	python -m PyInstaller --collect-all tzdata --copy-metadata copernicusmarine --name copernicusmarine_macos-x86_64.cli --icon=toolbox_icon.png copernicusmarine/command_line_interface/copernicus_marine.py --onefile --target-architecture=x86_64
+
+run-using-pyinstaller-ubuntu-latest:
+	pip install -e .
+	python3 -m PyInstaller --collect-all tzdata --copy-metadata copernicusmarine --icon=toolbox_icon.png --name copernicusmarine_linux.cli --add-data="/home/runner/micromamba/envs/copernicusmarine-binary/lib/python3.12/site-packages/distributed/distributed.yaml:./distributed"  copernicusmarine/command_line_interface/copernicus_marine.py --onefile --path /opt/hostedtoolcache/Python/3.12.6/x64/lib/python3.12/site-packages --copy-metadata xarray
+	chmod +rwx /home/runner/work/copernicus-marine-toolbox/copernicus-marine-toolbox/dist/copernicusmarine_linux.cli
+
 release: SELECTED_ENVIRONMENT_NAME = ${ENVIRONMENT_NAME}
 release:
 	${ACTIVATE_ENVIRONMENT}
@@ -90,3 +107,14 @@ build-and-publish-dockerhub-image:
 	docker build --ulimit nofile=65536:65536 --tag copernicusmarine/copernicusmarine:$${VERSION} --tag copernicusmarine/copernicusmarine:latest -f Dockerfile.dockerhub --build-arg VERSION="$${VERSION}" .
 	docker push copernicusmarine/copernicusmarine:$${VERSION}
 	docker push copernicusmarine/copernicusmarine:latest
+
+build-and-prepare-for-binary:
+	python -m pip install --upgrade pip
+	pip install pyinstaller
+	pip install -e .
+	pip install poetry
+	pip install distributed
+	echo "VERSION=$$(poetry version --short)" >> ${GITHUB_OUTPUT}
+
+update-snapshots-tests:
+	pytest --snapshot-update tests/test_command_line_interface.py::TestCommandLineInterface::test_describe_including_datasets