Merge pull request #179 from ec-jrc/dev

Dev

Tutorial/FORECAST.ipynb

@@ -241,7 +241,7 @@
    "source": [
     "## Setup a (re)forecast\n",
     "\n",
-    "Let's assume we have a forecasting cycle where new meteo forcings become available every `12H`."
+    "Let's assume we have a forecasting cycle where new meteo forcings become available every `12h`."
    ]
   },
   {
@@ -264,7 +264,7 @@
     "# creating a time sequence of the runs\n",
     "start_date = pd.to_datetime(\"2018-10-1 0:0:0\")\n",
     "end_date = pd.to_datetime(\"2018-10-2 12:0:0\")\n",
-    "date_list = pd.date_range(start_date, end_date, freq=\"12H\")\n",
+    "date_list = pd.date_range(start_date, end_date, freq=\"12h\")\n",
     "date_list"
    ]
   },

Tutorial/GSS.ipynb

@@ -112,7 +112,7 @@
     "model={'solver_name':'schism',\n",
     "     'mesh_file':'./test/global/hgrid.gr3',\n",
     "     'start_date':'2011-01-1 0:0:0',\n",
-    "     'time_frame':'12H',\n",
+    "     'time_frame':'12h',\n",
     "     'meteo_source' : ['./data/era5.grib'], #path to meteo files\n",
     "     'dem_source' : './data/dem.nc', #path to dem file\n",
     "     'rpath':'./test/global/schism/', #location of calc folder\n",

Tutorial/HINDCAST.ipynb

@@ -205,7 +205,7 @@
     "     'coastlines':ne_i,\n",
     "     'mesh_generator' : 'jigsaw', # set grid generator \n",
     "     'start_date':'2011-01-1 0:0:0',\n",
-    "     'time_frame':'12H',\n",
+    "     'time_frame':'12h',\n",
     "     'meteo_source' : './data/era5.grib', #path to meteo files\n",
     "     'dem_source' : './data/dem.nc', #path to dem file\n",
     "     'rpath':'./test/hindcast/20110101.00/', #location of calc folder\n",
@@ -258,7 +258,7 @@
    "source": [
     "## Setup a hindcast\n",
     "\n",
-    "Let's assume we want to split the hindcast on a `12H` splits. Doing a hindcast doesn't, in general, entail overlaping meteo forcing. However when more than one meteo file is needed one needs to be consistent into aligning the dates accordingly. There is an extra argument that provides that functionality (see documentation). \n",
+    "Let's assume we want to split the hindcast on a `12h` splits. Doing a hindcast doesn't, in general, entail overlaping meteo forcing. However when more than one meteo file is needed one needs to be consistent into aligning the dates accordingly. There is an extra argument that provides that functionality (see documentation). \n",
     "\n",
     "We setup the hindcast process as"
    ]
@@ -285,7 +285,7 @@
     "# creating a time sequence of the runs\n",
     "start_date = pd.to_datetime(\"2011-1-1 0:0:0\")\n",
     "end_date = pd.to_datetime(\"2011-1-2 0:0:0\")\n",
-    "date_list = pd.date_range(start_date, end_date, freq=\"12H\")\n",
+    "date_list = pd.date_range(start_date, end_date, freq=\"12h\")\n",
     "date_list"
    ]
   },

Tutorial/MODEL.ipynb

@@ -195,7 +195,7 @@
     "#     'tag':'schism', # optional tag \n",
     "     'mesh_generator' : 'jigsaw', # set mesh generator  \n",
     "     'start_date':'2017-10-1 0:0:0',\n",
-    "     'time_frame':'12H',\n",
+    "     'time_frame':'12h',\n",
     "     'meteo_source' : ['./data/erai.grib'], #path to meteo files\n",
     "     'dem_source' : './data/dem.nc', #path to dem file\n",
     "#     'ncores': 4 , # optional number of cores\n",

Tutorial/VALIDATION.ipynb

@@ -300,7 +300,7 @@
     "     'coastlines':ne_i, # coastlines\n",
     "     'mesh_generator' : 'jigsaw', # set grid generator  \n",
     "     'start_date':'2017-10-1 0:0:0',\n",
-    "     'time_frame':'12H',\n",
+    "     'time_frame':'12h',\n",
     "     'meteo_source' : './data/erai.grib', #path to meteo files\n",
     "     'dem_source' : './data/dem.nc', #path to dem file\n",
     "     'rpath':'./test/validation/', #location of calc folder\n",

docs/model.md

@@ -9,10 +9,10 @@ A number of parameters is provided by the user :
 
 - *solver_name*:
 	Select the solver to be used e.g. *schism*.
-- *geometry*: 
+- *geometry*:
 	In the most simple case that is a lat/lon box that defines the area of interest.
 - *coastlines*:
-	A coastlines *GeoDataFrame* or *shapefile* providing boundaries to the mesh. 
+	A coastlines *GeoDataFrame* or *shapefile* providing boundaries to the mesh.
 - *mesh_generator*:
 	Set the backend for creating a mesh e.g. `jigsaw`.
 - *start_date*:
@@ -33,7 +33,7 @@ dic = {
     "coastlines": "/path/to/coastal/shapefile.shp",
     "mesh_generator": "jigsaw",
     "start_date": "2017-10-1 0:0:0",
-    "time_frame": "12H",
+    "time_frame": "12h",
     "meteo_source": ["/path/to/meteo/file.grib"],
     "dem_source": "./path/to/dem/file.nc",
 }
@@ -80,7 +80,7 @@ b.get_output_data() # integrate output
 ```
 
 and the data are available as
- 
+
 ```py
 b.data.Dataset # output Dataset
 ```
@@ -94,12 +94,12 @@ If a model is created by `pyposeidon` there is a `json` file that describes the
 a = pyposeidon.model.read('./path/to/schism_model.json')
 a.execute() #execute it again
 ```
- 
+
 When a model is created by other means, it can still be incorporated into `pyposeidon` with
 
 ```py
 c = pm.set(solver_name='schism', rfolder = './path/to/folder/',
  	 		load_mesh=True, load_meteo=True)
 c.mesh.Dataset
 c.meteo.Dataset
-```
+```

locks/requirements-ci.txt

@@ -49,7 +49,7 @@ importlib-metadata==7.1.0 ; python_version >= "3.9" and python_version < "3.12"
 importlib-resources==6.4.0 ; python_version >= "3.9" and python_version < "4.0"
 iniconfig==2.0.0 ; python_version >= "3.9" and python_version < "4"
 jinja2==3.1.3 ; python_version >= "3.9" and python_version < "4"
-joblib==1.3.2 ; python_version >= "3.9" and python_version < "4"
+joblib==1.4.0 ; python_version >= "3.9" and python_version < "4"
 kiwisolver==1.4.5 ; python_version >= "3.9" and python_version < "4"
 limits==3.10.1 ; python_version >= "3.9" and python_version < "4.0"
 llvmlite==0.42.0 ; python_version >= "3.9" and python_version < "4"
@@ -74,6 +74,7 @@ pydantic-core==2.16.3 ; python_version >= "3.9" and python_version < "4.0"
 pydantic==2.6.4 ; python_version >= "3.9" and python_version < "4.0"
 pydap==3.4.1 ; python_version >= "3.9" and python_version < "4"
 pykdtree==1.3.11 ; python_version >= "3.9" and python_version < "4"
+pyogrio==0.7.2 ; python_version >= "3.9" and python_version < "4"
 pyparsing==3.1.2 ; python_version >= "3.9" and python_version < "4"
 pyproj==3.6.1 ; python_version >= "3.9" and python_version < "4"
 pyresample==1.28.2 ; python_version >= "3.9" and python_version < "4"

locks/requirements-full.txt

@@ -82,7 +82,7 @@ itk-numerics==5.3.0 ; python_version >= "3.9" and python_version < "4"
 itkwidgets==0.32.6 ; python_version >= "3.9" and python_version < "4"
 jedi==0.19.1 ; python_version >= "3.9" and python_version < "4"
 jinja2==3.1.3 ; python_version >= "3.9" and python_version < "4"
-joblib==1.3.2 ; python_version >= "3.9" and python_version < "4"
+joblib==1.4.0 ; python_version >= "3.9" and python_version < "4"
 jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "4"
 jsonschema==4.21.1 ; python_version >= "3.9" and python_version < "4"
 jupyter-client==8.6.1 ; python_version >= "3.9" and python_version < "4"
@@ -150,6 +150,7 @@ pyface==8.0.0 ; python_version >= "3.9" and python_version < "4"
 pygments==2.17.2 ; python_version >= "3.9" and python_version < "4"
 pykdtree==1.3.11 ; python_version >= "3.9" and python_version < "4"
 pymdown-extensions==10.7.1 ; python_version >= "3.9" and python_version < "4"
+pyogrio==0.7.2 ; python_version >= "3.9" and python_version < "4"
 pyparsing==3.1.2 ; python_version >= "3.9" and python_version < "4"
 pyproj==3.6.1 ; python_version >= "3.9" and python_version < "4"
 pyresample==1.28.2 ; python_version >= "3.9" and python_version < "4"

locks/requirements-viz.txt

@@ -12,7 +12,6 @@ beautifulsoup4==4.12.3 ; python_version >= "3.9" and python_version < "4"
 bleach==6.1.0 ; python_version >= "3.9" and python_version < "4"
 bokeh==3.4.0 ; python_version >= "3.9" and python_version < "4"
 cartopy==0.22.0 ; python_version >= "3.9" and python_version < "4"
-catalogue==2.0.10 ; python_version >= "3.9" and python_version < "4"
 certifi==2024.2.2 ; python_version >= "3.9" and python_version < "4"
 cffi==1.16.0 ; python_version >= "3.9" and python_version < "4"
 cfgrib==0.9.11.0 ; python_version >= "3.9" and python_version < "4"
@@ -75,7 +74,7 @@ itk-numerics==5.3.0 ; python_version >= "3.9" and python_version < "4"
 itkwidgets==0.32.6 ; python_version >= "3.9" and python_version < "4"
 jedi==0.19.1 ; python_version >= "3.9" and python_version < "4"
 jinja2==3.1.3 ; python_version >= "3.9" and python_version < "4"
-joblib==1.3.2 ; python_version >= "3.9" and python_version < "4"
+joblib==1.4.0 ; python_version >= "3.9" and python_version < "4"
 jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "4"
 jsonschema==4.21.1 ; python_version >= "3.9" and python_version < "4"
 jupyter-client==8.6.1 ; python_version >= "3.9" and python_version < "4"
@@ -132,6 +131,7 @@ pydap==3.4.1 ; python_version >= "3.9" and python_version < "4"
 pyface==8.0.0 ; python_version >= "3.9" and python_version < "4"
 pygments==2.17.2 ; python_version >= "3.9" and python_version < "4"
 pykdtree==1.3.11 ; python_version >= "3.9" and python_version < "4"
+pyogrio==0.7.2 ; python_version >= "3.9" and python_version < "4"
 pyparsing==3.1.2 ; python_version >= "3.9" and python_version < "4"
 pyproj==3.6.1 ; python_version >= "3.9" and python_version < "4"
 pyresample==1.28.2 ; python_version >= "3.9" and python_version < "4"
@@ -159,7 +159,6 @@ sniffio==1.3.1 ; python_version >= "3.9" and python_version < "4.0"
 snuggs==1.4.7 ; python_version >= "3.9" and python_version < "4"
 soupsieve==2.5 ; python_version >= "3.9" and python_version < "4"
 spatialpandas==0.4.10 ; python_version >= "3.9" and python_version < "4"
-srsly==2.4.8 ; python_version >= "3.9" and python_version < "4"
 stack-data==0.6.3 ; python_version >= "3.9" and python_version < "4"
 terminado==0.18.1 ; python_version >= "3.9" and python_version < "4"
 tinycss2==1.2.1 ; python_version >= "3.9" and python_version < "4"

locks/requirements.txt

@@ -5,7 +5,6 @@ asciitree==0.3.3 ; python_version >= "3.9" and python_version < "4"
 attrs==23.2.0 ; python_version >= "3.9" and python_version < "4"
 beautifulsoup4==4.12.3 ; python_version >= "3.9" and python_version < "4"
 cartopy==0.22.0 ; python_version >= "3.9" and python_version < "4"
-catalogue==2.0.10 ; python_version >= "3.9" and python_version < "4"
 certifi==2024.2.2 ; python_version >= "3.9" and python_version < "4"
 cffi==1.16.0 ; python_version >= "3.9" and python_version < "4"
 cfgrib==0.9.11.0 ; python_version >= "3.9" and python_version < "4"
@@ -44,7 +43,7 @@ idna==3.6 ; python_version >= "3.9" and python_version < "4"
 importlib-metadata==7.1.0 ; python_version >= "3.9" and python_version < "3.12"
 importlib-resources==6.4.0 ; python_version >= "3.9" and python_version < "4.0"
 jinja2==3.1.3 ; python_version >= "3.9" and python_version < "4"
-joblib==1.3.2 ; python_version >= "3.9" and python_version < "4"
+joblib==1.4.0 ; python_version >= "3.9" and python_version < "4"
 kiwisolver==1.4.5 ; python_version >= "3.9" and python_version < "4"
 limits==3.10.1 ; python_version >= "3.9" and python_version < "4.0"
 llvmlite==0.42.0 ; python_version >= "3.9" and python_version < "4"
@@ -66,6 +65,7 @@ pydantic-core==2.16.3 ; python_version >= "3.9" and python_version < "4.0"
 pydantic==2.6.4 ; python_version >= "3.9" and python_version < "4.0"
 pydap==3.4.1 ; python_version >= "3.9" and python_version < "4"
 pykdtree==1.3.11 ; python_version >= "3.9" and python_version < "4"
+pyogrio==0.7.2 ; python_version >= "3.9" and python_version < "4"
 pyparsing==3.1.2 ; python_version >= "3.9" and python_version < "4"
 pyproj==3.6.1 ; python_version >= "3.9" and python_version < "4"
 pyresample==1.28.2 ; python_version >= "3.9" and python_version < "4"
@@ -84,7 +84,6 @@ six==1.16.0 ; python_version >= "3.9" and python_version < "4"
 sniffio==1.3.1 ; python_version >= "3.9" and python_version < "4.0"
 snuggs==1.4.7 ; python_version >= "3.9" and python_version < "4"
 soupsieve==2.5 ; python_version >= "3.9" and python_version < "4"
-srsly==2.4.8 ; python_version >= "3.9" and python_version < "4"
 toolz==0.12.1 ; python_version >= "3.9" and python_version < "4"
 tqdm==4.66.2 ; python_version >= "3.9" and python_version < "4"
 typing-extensions==4.11.0 ; python_version >= "3.9" and python_version < "4.0"

pyposeidon/mgmsh.py

@@ -16,7 +16,6 @@
 import os
 from tqdm.auto import tqdm
 import sys
-import gmsh
 import subprocess
 import shapely
 import shlex
@@ -67,6 +66,8 @@ def get_ibounds(df, mm):
 
 
 def read_msh(filename, **kwargs):
+    import gmsh
+
     model = gmsh.model
     factory = model.geo
 
@@ -800,6 +801,8 @@ def make_bgmesh(df, fpos, **kwargs):
 
 
 def make_gmsh(df, **kwargs):
+    import gmsh
+
     logger.info("Creating mesh")
 
     model = gmsh.model
@@ -1006,6 +1009,8 @@ def make_gmsh(df, **kwargs):
 
 
 def make_gmsh_3d(df, **kwargs):
+    import gmsh
+
     logger.info("Creating global mesh")
 
     model = gmsh.model