Merge branch 'main' into pfs_repr_html

.devcontainer/devcontainer.json

@@ -1,21 +1,27 @@
 {
-	"name": "Miniconda (Python 3)",
-	"build": {
-		"context": "..",
-		"dockerfile": "Dockerfile"
-	},
-	"features": {
-		"ghcr.io/devcontainers-contrib/features/black:1": {},
-		"ghcr.io/devcontainers-contrib/features/flake8:1": {}
-	},
-	// Features to add to the dev container. More info: https://containers.dev/features.
-	// "features": {},
-	// Use 'forwardPorts' to make a list of ports inside the container available locally.
-	// "forwardPorts": [],
-	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip install -e ."
-	// Configure tool-specific properties.
-	// "customizations": {},
-	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
-	// "remoteUser": "root"
-}
+	"name": "Python 3",
+	"image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye",
+	"postCreateCommand": "pip3 install --user -e .'[dev,test,notebooks]'",
+	"customizations": {
+        "vscode": {
+            "extensions": [
+                "ms-python.python",
+                "ms-toolsai.jupyter",
+                "GitHub.vscode-pull-request-github",
+                "charliermarsh.ruff"
+
+            ],
+            "settings": {
+                "editor.formatOnSave": true,
+                "[python]": {
+                    "editor.formatOnSave": true,
+                    "editor.codeActionsOnSave": {
+                      "source.fixAll": true,
+                      "source.organizeImports": true
+                    }
+                  },
+                  "python.formatting.provider": "black"
+            }
+        }
+    }
+}

.github/workflows/build_docs.yml

@@ -0,0 +1,33 @@
+name: Build documentation (don't publish)
+
+on:
+  push:
+    pull_request:
+      branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.10"
+
+    - name: Install MIKE IO
+      run: |
+        pip install .[dev]
+    
+    - name: Sphinx Build
+      run: |
+        cd docs
+        make html
+
+    - name: Upload documentation
+      uses: actions/upload-artifact@v2
+      with:
+        name: html
+        path: docs/_build/html

.github/workflows/downstream_test.yml

@@ -23,9 +23,9 @@ jobs:
     - name: Install mikeio
       run: |
         pip install .
-    - name: Test fmskill from github
+    - name: Test modelskill from github
       run: |
-        git clone --depth 1 https://github.com/DHI/fmskill.git
-        cd fmskill
+        git clone --depth 1 https://github.com/DHI/modelskill.git
+        cd modelskill
         pip install .[test]
         pytest

.github/workflows/full_test.yml

@@ -18,7 +18,7 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest]
 
-        python-version: [3.8, 3.9, "3.10","3.11"]
+        python-version: [3.8, "3.11"]
 
     steps:
     - uses: actions/checkout@v3
@@ -47,5 +47,5 @@ jobs:
         pytest --cov=mikeio tests --ignore tests/performance/ --ignore tests/notebooks/ --disable-warnings
     - name: Test docstrings with doctest
       run: make doctest
-    #- name: Static type check
-    #  run: make typecheck
+    - name: Static type check
+      run: make typecheck

.github/workflows/python-publish.yml

@@ -22,6 +22,10 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install build wheel twine
+    - name: Install mikeio
+      run: pip install .[test]
+    - name: Test
+      run: pytest
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}

.gitignore

@@ -25,4 +25,5 @@ cov_annotate
 htmlcov
 
 docs/_build
-\tmp
+\tmp
+.venv/

CITATION.cff

@@ -0,0 +1,16 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it as below.
+authors:
+- family-names: Andersson
+  given-names: Johan Henrik
+  affiliation: DHI
+- family-names: Mariegaard
+  given-names: Jesper Sandvig
+  affiliation: DHI
+title: "MIKE IO"
+license: BSD-3-Clause
+repository-code: 'https:///github.com/DHI/mikeio'
+url: "https://dhi.github.io/mikeio/"
+version: 1.6.1
+date-released: 2023-06-09
+

Makefile

@@ -14,7 +14,7 @@ perftest:
 	pytest tests/performance/ --durations=0
 
 typecheck:
-	mypy mikeio/dataset/*.py
+	mypy mikeio/
 
 coverage: 
 	pytest --cov-report html --cov=mikeio tests/

README.md

@@ -10,9 +10,9 @@ Read, write and manipulate dfs0, dfs1, dfs2, dfs3, dfsu and mesh files.
 
 MIKE IO facilitates common data processing workflows for [MIKE files in Python](https://www.mikepoweredbydhi.com/products/mike-for-developers#io).
 
-[![YouTube](images/youtube1.png)](http://www.youtube.com/watch?v=Jm0iAeK8QW0)
+[![YouTube](https://raw.githubusercontent.com/DHI/mikeio/main/images/youtube1.png)](http://www.youtube.com/watch?v=Jm0iAeK8QW0)
 
-[![YouTube](images/youtube2.png)](http://www.youtube.com/watch?v=0oVedpx9zAQ)
+[![YouTube](https://raw.githubusercontent.com/DHI/mikeio/main/images/youtube2.png)](http://www.youtube.com/watch?v=0oVedpx9zAQ)
 
 ## Requirements
 * Windows or Linux operating system
@@ -90,8 +90,8 @@ TOTAL                              8696    756    91%
 
 It is possible to run MIKE IO in your favorite cloud notebook environment e.g. [Deepnote](https://deepnote.com/), [Google Colab](https://colab.research.google.com/), etc...
 
-![DeepNote](images/deepnote.png)
+![DeepNote](https://raw.githubusercontent.com/DHI/mikeio/main/images/deepnote.png)
 
-![Colab](images/colab.png)
+![Colab](https://raw.githubusercontent.com/DHI/mikeio/main/images/colab.png)
 
 

docs/conf.py

@@ -18,8 +18,8 @@
 # -- Project information -----------------------------------------------------
 
 project = "MIKE IO"
-copyright = "2022, Henrik Andersson, Jesper Mariegaard, Marc Ridler,"
-author = "Henrik Andersson, Jesper Mariegaard, Marc Ridler"
+copyright = "2023, DHI"
+author = "Henrik Andersson, Jesper Mariegaard"
 release = ""
 
 # -- General configuration ---------------------------------------------------
@@ -37,6 +37,19 @@
     "myst_parser",
 ]
 
+# inspired by https://github.com/pydata/xarray/blob/main/doc/conf.py
+
+autodoc_typehints = "none"
+
+# Napoleon configurations
+
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_use_param = False
+napoleon_use_rtype = False
+napoleon_preprocess_types = True
+
+
 # Configuration to include links to other project docs when referencing
 # functions/classes
 intersphinx_mapping = {

docs/data-structures.md

@@ -2,8 +2,8 @@
 
 MIKE IO has these primary data structures: 
 
-* [Dataset](Dataset) - a collection of DataArrays corresponding to the contents of a dfs file; typically obtained from {py:meth}`mikeio.read`
-* [DataArray](DataArray) - data and metadata corresponding to one "item" in a dfs file. 
+* [**Dataset**](Dataset) - a collection of DataArrays corresponding to the contents of a dfs file; typically obtained from {py:meth}`mikeio.read`
+* [**DataArray**](DataArray) - data and metadata corresponding to one "item" in a dfs file. 
 * **Geometry** - spatial description of the data in a dfs file; comes in different flavours: [Grid1D](Grid1D), [Grid2D](Grid2D), [Grid3D](Grid3D), [GeometryFM](GeometryFM), [GeometryFM3D](GeometryFM3D), etc. corresponding to different types of dfs files. 
-* **Dfs** - an object returned by `dfs = mikeio.open()` containing the metadata (=header) of a dfs file ready for reading the data (which can be done with `dfs.read()`); exists in different specialized versions: [Dfs0](Dfs0), [Dfs1](Dfs1), [Dfs2](Dfs2), [Dfs3](Dfs3), [Dfsu2DH](Dfsu2DH), [Dfsu3D](Dfsu3D), [Dfsu2DV](Dfsu2DV), [DfsuSpectral](DfsuSpectral), 
+* **Dfs** - an object returned by `dfs = mikeio.open()` containing the metadata (=header) of a dfs file ready for reading the data (which can be done with `dfs.read()`); exists in different specialized versions: [Dfs0](Dfs0), [Dfs1](Dfs1), [Dfs2](Dfs2), [Dfs3](Dfs3), [Dfsu2DH](Dfsu2DH), [Dfsu3D](Dfsu3D), [Dfsu2DV](Dfsu2DV), [DfsuSpectral](DfsuSpectral).
 

docs/dataarray.md

@@ -1,6 +1,6 @@
 # DataArray
 
-The [DataArray](DataArray) is the common MIKE IO data structure 
+The [DataArray](mikeio.DataArray) is the common MIKE IO data structure 
 for *item* data from dfs files. 
 The {py:meth}`mikeio.read` methods returns a Dataset as a container of DataArrays (Dfs items)
 
@@ -98,7 +98,7 @@ The plotting of a DataArray is context-aware meaning that plotting behaviour dep
 >>> da.plot.mesh()
 ```
 
-See details in the [API specification](_DatasetPlotter) below and in the bottom of the relevant pages e.g. [DataArray Plotter Grid2D API](_DataArrayPlotterGrid2D) on the dfs2 page.
+See details in the [API specification](mikeio.dataset._data_plot._DataArrayPlotter) below and in the bottom of the relevant pages e.g. [DataArray Plotter Grid2D API](dfs2.md#dataarray-plotter-grid2d-api) on the dfs2 page.
 
 
 
@@ -175,7 +175,7 @@ Other methods that also return a DataArray:
 A DataArray `da` can be plotted using `da.plot`. 
 
 ```{eval-rst}
-.. autoclass:: mikeio.dataarray._DataArrayPlotter
+.. autoclass:: mikeio.dataset._data_plot._DataArrayPlotter
 	:members:
 ```
 

docs/dataset.md

@@ -1,8 +1,8 @@
 # Dataset
 
-The [Dataset](Dataset) is the MIKE IO data structure 
+The [Dataset](mikeio.Dataset) is the MIKE IO data structure 
 for data from dfs files. 
-The {py:meth}`mikeio.read` methods returns a Dataset as a container of [DataArrays](dataarray) (Dfs items). Each DataArray has the properties, *item*, *time*, *geometry* and *values*. The time and geometry are common to all DataArrays in the Dataset. 
+The {py:meth}`mikeio.read` methods returns a Dataset as a container of [DataArrays](mikeio.DataArray) (Dfs items). Each DataArray has the properties, *item*, *time*, *geometry* and *values*. The time and geometry are common to all DataArrays in the Dataset. 
 
 The Dataset has the following primary properties: 
 
@@ -113,7 +113,7 @@ In most cases, you will *not* plot the Dataset, but rather it's DataArrays. But
 * dfs0-Dataset : plot all items as timeseries with ds.plot()
 * scatter : compare two items using ds.plot.scatter(x="itemA", y="itemB")
 
-See details in the [API specification](_DatasetPlotter) below.
+See details in the [API specification](Dataset Plotter API) below.
 
 
 ## Properties
@@ -189,7 +189,7 @@ Other methods that also return a Dataset:
 ## Dataset Plotter API
 
 ```{eval-rst}
-.. autoclass:: mikeio.dataset._DatasetPlotter
+.. autoclass:: mikeio.dataset._data_plot._DatasetPlotter
 	:members:
 ```