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Dev #179

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Apr 9, 2024
Merged

Dev #179

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fe65df4
schism: Add `parse_staout()`
pmav99 Apr 9, 2024
9ca079e
schism: Support hotstart in `parse_mirror_out()`.
pmav99 Apr 9, 2024
7270aeb
fix: Remove a bunch of pandas FutureWarnings
pmav99 Apr 9, 2024
8002a13
deps: Add pyogrio as a primary dependency.
pmav99 Apr 9, 2024
ad6bf14
gmsh: Inline gmsh import
pmav99 Apr 9, 2024
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4 changes: 2 additions & 2 deletions Tutorial/FORECAST.ipynb
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Expand Up @@ -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`."
]
},
{
Expand All @@ -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"
]
},
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2 changes: 1 addition & 1 deletion Tutorial/GSS.ipynb
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Expand Up @@ -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",
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6 changes: 3 additions & 3 deletions Tutorial/HINDCAST.ipynb
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Expand Up @@ -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",
Expand Down Expand Up @@ -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"
]
Expand All @@ -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"
]
},
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2 changes: 1 addition & 1 deletion Tutorial/MODEL.ipynb
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Expand Up @@ -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",
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2 changes: 1 addition & 1 deletion Tutorial/VALIDATION.ipynb
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Expand Up @@ -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",
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12 changes: 6 additions & 6 deletions docs/model.md
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Expand Up @@ -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*:
Expand All @@ -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",
}
Expand Down Expand Up @@ -80,7 +80,7 @@ b.get_output_data() # integrate output
```

and the data are available as

```py
b.data.Dataset # output Dataset
```
Expand All @@ -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
```
```
3 changes: 2 additions & 1 deletion locks/requirements-ci.txt
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Expand Up @@ -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"
Expand All @@ -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"
Expand Down
3 changes: 2 additions & 1 deletion locks/requirements-full.txt
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Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand Down
5 changes: 2 additions & 3 deletions locks/requirements-viz.txt
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Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand Down
5 changes: 2 additions & 3 deletions locks/requirements.txt
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Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand All @@ -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"
Expand All @@ -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"
Expand Down
55 changes: 50 additions & 5 deletions poetry.lock
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7 changes: 6 additions & 1 deletion pyposeidon/mgmsh.py
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Expand Up @@ -16,7 +16,6 @@
import os
from tqdm.auto import tqdm
import sys
import gmsh
import subprocess
import shapely
import shlex
Expand Down Expand Up @@ -67,6 +66,8 @@ def get_ibounds(df, mm):


def read_msh(filename, **kwargs):
import gmsh

model = gmsh.model
factory = model.geo

Expand Down Expand Up @@ -800,6 +801,8 @@ def make_bgmesh(df, fpos, **kwargs):


def make_gmsh(df, **kwargs):
import gmsh

logger.info("Creating mesh")

model = gmsh.model
Expand Down Expand Up @@ -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
Expand Down
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