Use geoviews everywhere + use pn.State for caching

This commit is quite messy, but we are still at an early stage of the
development and the API is not set yet. Anyhow, it mostly  addresses the
remarks made by @jbednar at:

#16 (comment)

In a nutshell:

- We follow the recommendation of the [FAQ](https://holoviews.org/FAQ.html)
  and we stop mixing holoviews and geoviews objects.
- We use `pn.State` in order to cache the `xr.Dataset` objects among
  different requests.
- We fix cartopy to < 0.20 since we are affected by this issue:
  holoviz/geoviews#529

Author: pmav99

README.md

@@ -9,15 +9,16 @@ You will need some data to visualize. If you don't have any you can download a s
 created with [pyposeidon](https://github.com/ec-jrc/pyPoseidon/):
 
 ```
-mkdir data
-wget -O data/dataset.nc    https://static.techrad.eu/thalassa/dataset.nc
+mkdir ./data
+wget -O data/dataset.nc https://static.techrad.eu/thalassa/dataset.nc
 ```
 
 ## Deploying on a server
 
 1. Install the binary dependencies:
 
 - `python 3.9`
+- `proj < 8`
 
 2. Install the python dependencies with
 

Thalassa.ipynb

@@ -48,6 +48,7 @@ netCDF4 = "^1.5"
 datashader = "^0.13"
 ruyaml = "^0.20.0"
 geoviews = "^1.9.2"
+Cartopy = "<0.20"  # due to https://github.com/holoviz/geoviews/issues/529
 
 [tool.poetry.group.dev.dependencies]
 black = "^21.9b0"

poetry.lock

@@ -1,4 +1,4 @@
-anyio==3.3.2; python_full_version >= "3.6.2" and python_version >= "3.6"
+anyio==3.3.3; python_full_version >= "3.6.2" and python_version >= "3.6"
 appnope==0.1.2; sys_platform == "darwin" and python_version >= "3.7" or platform_system == "Darwin" and python_version >= "3.7"
 argon2-cffi==21.1.0; python_version >= "3.6"
 astroid==2.8.2; python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.1"
@@ -9,12 +9,13 @@ backports.entry-points-selectable==1.1.0; python_version >= "2.7" and python_ful
 black==21.9b0; python_full_version >= "3.6.2"
 bleach==4.1.0; python_version >= "3.6"
 bokeh==2.4.0; python_version >= "3.7"
-certifi==2021.5.30; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" or python_version >= "3.7"
+cartopy==0.19.0.post1; python_version >= "3.5"
+certifi==2021.10.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" or python_version >= "3.7"
 cffi==1.14.6; implementation_name == "pypy" and python_version >= "3.6" or python_version >= "3.6"
 cfgv==3.3.1; python_full_version >= "3.6.1"
 cftime==1.5.1
-charset-normalizer==2.0.6; python_full_version >= "3.6.0" and python_version >= "3.6"
-click==8.0.1; python_version >= "3.6" and python_full_version >= "3.6.2" or python_version >= "3.7"
+charset-normalizer==2.0.7; python_full_version >= "3.6.0" and python_version >= "3.6"
+click==8.0.3; python_version >= "3.6" and python_full_version >= "3.6.2" or python_version >= "3.7"
 cloudpickle==2.0.0; python_version >= "3.7" or python_version >= "3.7"
 colorama==0.4.4; python_version >= "3.6" and python_full_version < "3.0.0" and platform_system == "Windows" or python_full_version >= "3.5.0" and python_version >= "3.6" and platform_system == "Windows" or python_version >= "3.6" and python_full_version >= "3.6.2" and platform_system == "Windows" or python_version >= "3.7" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.7" and python_full_version >= "3.5.0" or python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.1" and sys_platform == "win32"
 colorcet==2.0.6; python_version >= "2.7"
@@ -31,20 +32,21 @@ dodgy==0.2.1; python_full_version >= "3.6.1" and python_version < "4.0"
 entrypoints==0.3; python_full_version >= "3.6.1" and python_version >= "3.6" or python_version >= "3.6"
 filelock==3.3.0; python_version >= "3.6" and python_full_version >= "3.6.1"
 flake8-polyfill==1.0.2; python_full_version >= "3.6.1" and python_version < "4.0"
-flake8==3.9.2; python_full_version >= "3.6.1" and python_version < "4.0"
+flake8==2.3.0; python_full_version >= "3.6.1" and python_version < "4.0"
 fsspec==2021.10.0; python_version >= "3.7"
+geoviews==1.9.2; python_version >= "3.7"
 heapdict==1.0.1; python_version >= "3.7"
 holoviews==1.14.6; python_version >= "2.7"
 identify==2.3.0; python_full_version >= "3.6.1"
-idna==3.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" or python_full_version >= "3.6.2" and python_version >= "3.6"
+idna==3.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" or python_full_version >= "3.6.2" and python_version >= "3.6"
 ipykernel==6.4.1; python_version >= "3.7"
 ipython-genutils==0.2.0; python_version >= "3.6"
 ipython==7.28.0; python_version >= "3.7"
 isort==5.9.3; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.6"
 jedi==0.18.0; python_version >= "3.7"
 jinja2==3.0.2; python_version >= "3.7" or python_version >= "3.6"
 json5==0.9.6; python_version >= "3.6"
-jsonschema==4.0.1; python_version >= "3.7"
+jsonschema==4.1.0; python_version >= "3.7"
 jupyter-client==7.0.6; python_full_version >= "3.6.1" and python_version >= "3.6" or python_full_version >= "3.6.1" and python_version >= "3.7"
 jupyter-core==4.8.1; python_full_version >= "3.6.1" and python_version >= "3.6" or python_version >= "3.6"
 jupyter-server==1.11.1; python_version >= "3.6"
@@ -82,6 +84,7 @@ parso==0.8.2; python_version >= "3.7"
 partd==1.2.0; python_version >= "3.7"
 pathspec==0.9.0; python_full_version >= "3.6.2"
 pep8-naming==0.10.0; python_full_version >= "3.6.1" and python_version < "4.0"
+pep8==1.7.1; python_full_version >= "3.6.1" and python_version < "4.0"
 pexpect==4.8.0; sys_platform != "win32" and python_version >= "3.7"
 pickleshare==0.7.5; python_version >= "3.7"
 pillow==8.3.2; python_version >= "3.6"
@@ -93,7 +96,7 @@ prospector==1.5.1; python_full_version >= "3.6.1" and python_version < "4.0"
 psutil==5.8.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_version >= "3.7" and python_full_version >= "3.4.0"
 ptyprocess==0.7.0; sys_platform != "win32" and python_version >= "3.7" or os_name != "nt" and python_version >= "3.6"
 py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or implementation_name == "pypy" and python_version >= "3.6" and python_full_version >= "3.4.0"
-pycodestyle==2.7.0; python_full_version >= "3.6.1" and python_version < "4.0"
+pycodestyle==2.8.0; python_full_version >= "3.6.1" and python_version < "4.0"
 pycparser==2.20; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 pyct==0.4.8; python_version >= "2.7"
 pydocstyle==6.1.1; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.6"
@@ -107,14 +110,15 @@ pylint==2.11.1; python_version >= "3.6" and python_version < "4.0" and python_fu
 pyparsing==2.4.7; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.7"
 pyproj==3.2.1; python_version >= "3.7"
 pyrsistent==0.18.0; python_version >= "3.7"
+pyshp==2.1.3; python_version >= "3.7"
 python-dateutil==2.8.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "2.7" or python_full_version >= "3.7.1" and python_version >= "2.7" or python_full_version >= "3.6.1" and python_version >= "3.6"
 pytz==2021.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" or python_full_version >= "3.7.1" and python_version >= "2.7"
 pyviz-comms==2.1.0
-pywin32==301; sys_platform == "win32" and platform_python_implementation != "PyPy" and python_version >= "3.6"
+pywin32==302; sys_platform == "win32" and platform_python_implementation != "PyPy" and python_version >= "3.6"
 pywinpty==1.1.4; os_name == "nt" and python_version >= "3.6"
 pyyaml==5.4.1; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.7" or python_full_version >= "3.6.1" and python_version < "4.0" or python_full_version >= "3.6.1"
 pyzmq==22.3.0; python_full_version >= "3.6.1" and python_version >= "3.6" or python_version >= "3.6"
-regex==2021.9.30; python_full_version >= "3.6.2"
+regex==2021.10.8; python_full_version >= "3.6.2"
 requests-unixsocket==0.2.0; python_version >= "3.6"
 requests==2.26.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
 requirements-detector==0.7; python_full_version >= "3.6.1" and python_version < "4.0"
@@ -123,6 +127,7 @@ scipy==1.7.1; python_version >= "3.7" and python_version < "3.10"
 send2trash==1.8.0; python_version >= "3.6"
 setoptconf-tmp==0.3.1; python_full_version >= "3.6.1" and python_version < "4.0"
 setuptools==58.2.0; python_version >= "3.6" and python_version < "3.10" or python_version >= "3.6" or python_version >= "3.7" or python_version >= "3.6" and python_version < "4.0" and python_full_version >= "3.6.1"
+shapely==1.7.1; python_version >= "3.7"
 six==1.16.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6" or python_full_version >= "3.7.1" and python_version >= "2.7" or python_full_version >= "3.6.1" or python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "2.7"
 sniffio==1.2.0; python_full_version >= "3.6.2" and python_version >= "3.6"
 snowballstemmer==2.1.0; python_full_version >= "3.6.1" and python_version < "4.0" and python_version >= "3.6"

pyproject.toml

@@ -1,9 +1,10 @@
 bleach==4.1.0; python_version >= "3.6"
 bokeh==2.4.0; python_version >= "3.7"
-certifi==2021.5.30; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" or python_version >= "3.7"
+cartopy==0.19.0.post1; python_version >= "3.5"
+certifi==2021.10.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" or python_version >= "3.7"
 cftime==1.5.1
-charset-normalizer==2.0.6; python_full_version >= "3.6.0" and python_version >= "3.6"
-click==8.0.1; python_version >= "3.7"
+charset-normalizer==2.0.7; python_full_version >= "3.6.0" and python_version >= "3.6"
+click==8.0.3; python_version >= "3.7"
 cloudpickle==2.0.0; python_version >= "3.7" or python_version >= "3.7"
 colorama==0.4.4; python_version >= "3.6" and python_full_version < "3.0.0" and platform_system == "Windows" or python_full_version >= "3.5.0" and python_version >= "3.6" and platform_system == "Windows" or python_version >= "3.7" and python_full_version < "3.0.0" and platform_system == "Windows" or python_version >= "3.7" and platform_system == "Windows" and python_full_version >= "3.5.0"
 colorcet==2.0.6; python_version >= "2.7"
@@ -13,9 +14,10 @@ datashape==0.5.2; python_version >= "2.7"
 distributed==2021.9.1; python_version >= "3.7"
 distro==1.6.0; python_version >= "3.6"
 fsspec==2021.10.0; python_version >= "3.7"
+geoviews==1.9.2; python_version >= "3.7"
 heapdict==1.0.1; python_version >= "3.7"
 holoviews==1.14.6; python_version >= "2.7"
-idna==3.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
+idna==3.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6"
 jinja2==3.0.2; python_version >= "3.7" or python_version >= "3.7"
 llvmlite==0.36.0; python_version >= "3.6" and python_version < "3.10"
 locket==0.2.1; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.7"
@@ -36,6 +38,7 @@ psutil==5.8.0; python_version >= "3.7" and python_full_version < "3.0.0" or pyth
 pyct==0.4.8; python_version >= "2.7"
 pyparsing==2.4.7; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.7"
 pyproj==3.2.1; python_version >= "3.7"
+pyshp==2.1.3; python_version >= "3.7"
 python-dateutil==2.8.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "2.7" or python_full_version >= "3.7.1" and python_version >= "2.7"
 pytz==2021.3; python_full_version >= "3.7.1" and python_version >= "2.7"
 pyviz-comms==2.1.0; python_version >= "2.7"
@@ -44,6 +47,7 @@ requests==2.26.0; python_version >= "3.6" and python_full_version < "3.0.0" or p
 ruyaml==0.20.0; python_version >= "3.6"
 scipy==1.7.1; python_version >= "3.7" and python_version < "3.10"
 setuptools==58.2.0; python_version >= "3.6" and python_version < "3.10" or python_version >= "3.6" or python_version >= "3.7"
+shapely==1.7.1; python_version >= "3.7"
 six==1.16.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6" or python_full_version >= "3.7.1" and python_version >= "2.7" or python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "2.7"
 sortedcontainers==2.4.0; python_version >= "3.7"
 tblib==1.7.0; python_version >= "3.7" and python_full_version < "3.0.0" or python_version >= "3.7" and python_full_version >= "3.5.0"

requirements/requirements-dev.txt

@@ -1,18 +1,18 @@
 from __future__ import annotations
 
-from .utils import coords_to_web_mercator
 from .utils import open_dataset
-from .utils import open_loaded_dataset
 from .utils import reload
+from .visuals import get_max_elevation
+from .visuals import get_tiles
 from .visuals import get_trimesh
-from .visuals import get_wireframe_and_max_elevation
+from .visuals import get_wireframe
 
 
 __all__: list[str] = [
-    "coords_to_web_mercator",
     "open_dataset",
-    "open_loaded_dataset",
     "reload",
     "get_trimesh",
-    "get_wireframe_and_max_elevation",
+    "get_tiles",
+    "get_wireframe",
+    "get_max_elevation",
 ]

requirements/requirements.txt

@@ -7,21 +7,12 @@
 import pathlib
 import sys
 
-import holoviews as hv
 import xarray as xr
 
 logger = logging.getLogger(__name__)
 
 
-def coords_to_web_mercator(ds: xr.Dataset, longitude_var: str, latitude_var: str) -> xr.Dataset:
-    lons = ds[longitude_var]
-    lats = ds[latitude_var]
-    x, y = hv.util.transform.lon_lat_to_easting_northing(lons, lats)
-    ds = ds.assign({longitude_var: x, latitude_var: y})
-    return ds
-
-
-def open_dataset(path: str | pathlib.Path) -> xr.Dataset:
+def open_dataset(path: str | pathlib.Path, load: bool = False) -> xr.Dataset:
     path = pathlib.Path(path)
     if path.suffix == ".nc":
         ds = xr.open_dataset(path, mask_and_scale=True)
@@ -30,14 +21,9 @@ def open_dataset(path: str | pathlib.Path) -> xr.Dataset:
     # TODO: extend with GeoTiff, Grib etc
     else:
         raise ValueError(f"Don't know how to handle this: {path}")
-    return ds
-
-
-def open_loaded_dataset(path: str, reproject: bool, longitude_var: str, latitude_var: str) -> xr.Dataset:
-    ds = open_dataset(path=path)
-    if reproject:
-        ds = coords_to_web_mercator(ds, longitude_var, latitude_var)
-    ds.load()
+    if load:
+        # load dataset to memory
+        ds.load()
     return ds
 
 

thalassa/__init__.py

@@ -4,7 +4,6 @@
 import holoviews as hv  # type: ignore
 import pandas as pd  # type: ignore
 import xarray as xr
-from holoviews import opts as hvopts
 from holoviews.operation.datashader import dynspread  # type: ignore
 from holoviews.operation.datashader import rasterize  # type: ignore
 
@@ -19,34 +18,41 @@ def get_trimesh(
     elevation_var: str,
     simplices_var: str,
     time_var: str,
-) -> hv.TriMesh:
-    # Prepare the data
+) -> gv.TriMesh:
+    # local aliases
     lons = ds[longitude_var].values
     lats = ds[latitude_var].values
     simplices = ds[simplices_var].values
-    elevation = ds[elevation_var].max(dim=time_var).values
+    # get max elevation
+    max_elevation = ds[elevation_var].max(dim=time_var).values
     # Create holoviews objects
-    points_df = pd.DataFrame(dict(longitude=lons, latitude=lats, elevation=elevation))
-    points_hv = hv.Points(points_df, kdims=["longitude", "latitude"], vdims="elevation")
-    trimesh = hv.TriMesh((simplices, points_hv))
+    points_df = pd.DataFrame(dict(lons=lons, lats=lats, max_elevation=max_elevation))
+    points_gv = gv.Points(points_df, kdims=["lons", "lats"], vdims="max_elevation")
+    trimesh = gv.TriMesh((simplices, points_gv))
     return trimesh
 
 
-def get_wireframe_and_max_elevation(trimesh: hv.TriMesh) -> hv.Layout:
-    # pylint: disable=no-member
-    # tiles = hv.Tiles("http://c.tile.openstreetmap.org/{Z}/{X}/{Y}.png")
+def get_tiles() -> gv.Tiles:
     tiles = gv.WMTS("http://c.tile.openstreetmap.org/{Z}/{X}/{Y}.png")
-    # tiles = hv.element.tiles.tile_sources["EsriStreet"]()
-    wireframe = dynspread(rasterize(trimesh.edgepaths)).opts(title="Wireframe")
-    elevation = rasterize(trimesh).opts(
+    return tiles
+
+
+def get_wireframe(trimesh: gv.TriMesh) -> hv.Layout:
+    # If we want the wireframe plot to be connected to the main plot
+    # we need create the overlay with tiles too.
+    # That being said, we might be able to use a more lightweight tile for the wireframe
+    tiles = get_tiles()
+    wireframe = dynspread(rasterize(trimesh.edgepaths, precompute=True))
+    wireframe = wireframe.opts(title="Wireframe")  # pylint: disable=no-member
+    return tiles * wireframe
+
+
+def get_max_elevation(trimesh: gv.TriMesh) -> hv.Layout:
+    tiles = get_tiles()
+    elevation = rasterize(trimesh, precompute=True).opts(  # pylint: disable=no-member
         title="Max Elevation",
         colorbar=True,
         clabel="meters",
         show_legend=True,
     )
-    layout = (tiles * elevation + tiles * wireframe).cols(1)
-    layout = layout.opts(
-        hvopts.Image(width=800, height=400, show_title=True, tools=["hover"]),
-        hvopts.Layout(toolbar="right"),
-    )
-    return layout
+    return tiles * elevation