Merge pull request #76 from rcaneill/doc_to_website

Add doc as website

.github/workflows/ci.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2
@@ -35,7 +35,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11"]
         poetry-version: ["1.3.2"]
     steps:
       - name: Checkout
@@ -53,24 +53,3 @@ jobs:
           poetry install --with test
       - name: Run tests with pytest
         run: poetry run pytest xnemogcm/test
-
-
-  test_notebooks:
-    name: test notebook doc
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.11
-    - name: Run poetry
-      uses: abatilo/actions-poetry@v2.0.0
-      with:
-        poetry-version: 1.3.2
-    - name: Install / build
-      run: poetry install --with dev,test
-    - name: Run nbconvert
-      run: poetry run jupyter nbconvert --to notebook --execute src_example/*.ipynb --stdout

.github/workflows/ci_upgrade_dependencies.yml

@@ -26,7 +26,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.8"]
+        python-version: ["3.9"]
         poetry-version: ["1.3.2"]
     steps:
       - name: Checkout

.gitignore

@@ -37,3 +37,4 @@ docs/_build
 # Dev
 dev/
 tmp/
+site/

.readthedocs.yaml

@@ -0,0 +1,27 @@
+# Read the Docs configuration file for MkDocs projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+  jobs:
+    post_create_environment:
+      # Install poetry
+      # https://python-poetry.org/docs/#installing-with-the-official-installer
+      - curl -sSL https://install.python-poetry.org | python3 -
+      # Tell poetry to not use a virtual environment
+      - $HOME/.local/bin/poetry config virtualenvs.create false
+    post_install:
+      # Install dependencies with 'docs' dependency group
+      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
+      - $HOME/.local/bin/poetry export --with docs --format requirements.txt > requirements.txt
+      - python -m pip install -r requirements.txt
+      - python -m pip install --no-deps .
+
+mkdocs:
+  configuration: mkdocs.yml

README.md

@@ -9,7 +9,6 @@ Interface to open NEMO ocean global circulation model output dataset and create
 NEMO 3.6, 4.0, and 4.2.0 are tested and supported. Any version between 3.6 and 4.2.0 should work,
 but in case of trouble, [please open an issue](https://github.com/rcaneill/xnemogcm/issues).
 
-This repository is mirrored at https://gitlab.com/open-ocean/xnemogcm.
 If you wish to contribute but don't have a github account, send me an email with your questions or comments: `romain [dot] caneill [at] ens-lyon [.] org`
 
 ## Usage
@@ -29,89 +28,5 @@ import xgcm
 grid = xgcm.Grid(ds, metrics=get_metrics(ds), periodic=False)
 ```
 
-See the [example](https://nbviewer.ipython.org/github/rcaneill/xnemogcm/blob/master/example/)
-directory for some jupyter notebook examples.
-xnemocgm is able to process xarray.Datasets (e.g. they could be retrieved from a remote server),
-and can get information of the variables grid points with multiple options
-(see [example/open_process_files.ipynb](https://nbviewer.ipython.org/github/rcaneill/xnemogcm/blob/master/example/open_process_files.ipynb).
-
-### Note
-
-`xnemogcm` is capable or recombining the domain_cfg and mesh_mask files output
-by multiple processors,
-the recombining tool from the NEMO toolbox is thus not needed here, see
-the [example/recombing_mesh_mask_domain_cfg.ipynb](https://nbviewer.ipython.org/github/rcaneill/xnemogcm/blob/master/example/recombing_mesh_mask_domain_cfg.ipynb)
-
-## Installation
-
-Installation via pip:
-```bash
-pip3 install xnemogcm
-```
-
-Installation via conda:
-```bash
-conda install -c conda-forge xnemogcm
-```
-
-## Requirements for dev
-
-We use *poetry* to set up a virtual environment containing all
-needed packages to run xnemogcm and the tests.
-To install all the dependencies, type `poetry install --with test,dev`
-after cloning the directory. This will create a new virtual environment.
-Typing `poetry shell` in the package directory will activate the virtual environment.
-
-### About test data
-
-Test data are based on the GYRE configuration, and produced by another repository:
-[rcaneill/xnemogcm_test_data](https://github.com/rcaneill/xnemogcm_test_data).
-Testing is built in a way that it is quite easy to add other nemo version to test.
-
-### About notebooks examples
-
-Sources for the notebooks are located in `src_example`. This is where to add / modify the
-examples. A github action is set to automatically build the notebook according to
-the latest version of the code, and publish them to `example` when commiting to master branch.
-
-
-## What's new
-
-### v0.4.2 (2023-08-07)
-* Allow additional dimension names occurring when variables on inner grid are diagnosed, e.g. `x_grid_U_inner` or `x_grid_U`.
-* Add coordinates into the DataArrays
-* Add some standard names and units in domcfg
-
-### v0.4.1 (2023-03-29)
-* Allow to open files if time bounds are missing
-* Minor bug correction for nemo 3.6 
-* Add nemo 3.6 and 4.2.0 test data
-* Update code to support nemo 3.6 and 4.2.0
-
-### v0.4.0 (2022-12-08)
-* Optimize speed
-* Add option to decode grid type from attributes
-* Shift from pipenv and setupy.py to poetry
-* Refactor data test to allow testing of multiple version of NEMO
-
-### v0.3.4 (2021-06-15)
-* Adding some example
-* Bug fixes
-* Add option to compute extra scale factors
-
-### v0.3.2 - v0.3.3 (2021-05-05)
-* By default adds the lat/lon/depth variables of domcfg as coordinates
-
-### v0.3.1 (2021-05-04)
-* Minor bug fix when merging
-* better squeezing of time in domcfg + nemo v3.6 compatibility
-
-### v0.3.0 (2021-04-13)
-* Cleaning the backend
-* Removing the saving options (that were useless and confusing)
-* Minor bug fixes
-* Tested with realistic regional configuration
-
-### v0.2.3 (2021-03-15)
-* Support for surface only files
-* Reshaping the data files for the tests (dev)
+[The full documentation is hosted online:
+[https://xnemogcm.readthedocs.io/](https://xnemogcm.readthedocs.io/)

docs/api.md

@@ -0,0 +1,3 @@
+# Reference
+
+::: xnemogcm

docs/dev.md

@@ -0,0 +1,13 @@
+## Requirements for dev
+
+We use *poetry* to set up a virtual environment containing all
+needed packages to run xnemogcm and the tests.
+To install all the dependencies, type `poetry install --with test,dev,docs`
+after cloning the directory. This will create a new virtual environment.
+Typing `poetry shell` in the package directory will activate the virtual environment.
+
+## About test data
+
+Test data are based on the GYRE configuration, and produced by another repository:
+[rcaneill/xnemogcm_test_data](https://github.com/rcaneill/xnemogcm_test_data).
+Testing is built in a way that it is quite easy to add other nemo version to test.