Repository: ec-jrc/pyPoseidon (language: python)

Issue:
sort out cfgrib/eccodes dependency
cfgrib is pinned to 0.9.8.5 for now. See how to move pass that.
Follow pydata/xarray#5150


Discussion / hints:
This is resolved upstream with `eccodes>2.20`. It seems to be working. It will be closed with the next PL.

Fix patch:
diff --git a/environment.yml b/environment.yml
index ca8154eb..57d00b76 100644
--- a/environment.yml
+++ b/environment.yml
@@ -21,9 +21,8 @@ dependencies:
   - hvplot
   - descartes
   - netCDF4
-  - cfgrib <0.9.9
-  - eccodes=2.19.1
-  - libgfortran4
+  - cfgrib
+  - eccodes>2.20
   - moviepy
   - imageio-ffmpeg
   - bump2version
diff --git a/poetry.lock b/poetry.lock
index 49c4032d..ddd3f142 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -118,7 +118,7 @@ webencodings = "*"
 
 [[package]]
 name = "bokeh"
-version = "2.4.0"
+version = "2.4.1"
 description = "Interactive plots and applications in the browser from Python"
 category = "main"
 optional = false
@@ -182,7 +182,7 @@ python-versions = "*"
 
 [[package]]
 name = "cffi"
-version = "1.14.6"
+version = "1.15.0"
 description = "Foreign Function Interface for Python calling C code."
 category = "main"
 optional = false
@@ -211,7 +211,7 @@ xarray = ["xarray (>=0.15)"]
 
 [[package]]
 name = "cftime"
-version = "1.5.1"
+version = "1.5.1.1"
 description = "Time-handling functionality from netcdf4-python"
 category = "main"
 optional = false
@@ -222,7 +222,7 @@ numpy = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "2.0.6"
+version = "2.0.7"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 category = "main"
 optional = false
@@ -330,7 +330,7 @@ six = "*"
 
 [[package]]
 name = "coverage"
-version = "6.0.1"
+version = "6.1.1"
 description = "Code coverage measurement for Python"
 category = "dev"
 optional = false
@@ -341,18 +341,15 @@ toml = ["tomli"]
 
 [[package]]
 name = "cycler"
-version = "0.10.0"
+version = "0.11.0"
 description = "Composable style cycles"
 category = "main"
 optional = false
-python-versions = "*"
-
-[package.dependencies]
-six = "*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "dask"
-version = "2021.9.1"
+version = "2021.11.0"
 description = "Parallel PyData with Task Scheduling"
 category = "main"
 optional = false
@@ -361,7 +358,7 @@ python-versions = ">=3.7"
 [package.dependencies]
 bokeh = {version = ">=1.0.0,<2.0.0 || >2.0.0", optional = true, markers = "extra == \"complete\""}
 cloudpickle = ">=1.1.1"
-distributed = {version = "2021.09.1", optional = true, markers = "extra == \"complete\""}
+distributed = {version = "2021.11.0", optional = true, markers = "extra == \"complete\""}
 fsspec = ">=0.6.0"
 jinja2 = {version = "*", optional = true, markers = "extra == \"complete\""}
 numpy = {version = ">=1.18", optional = true, markers = "extra == \"complete\""}
@@ -373,11 +370,11 @@ toolz = ">=0.8.2"
 
 [package.extras]
 array = ["numpy (>=1.18)"]
-complete = ["bokeh (>=1.0.0,!=2.0.0)", "distributed (==2021.09.1)", "jinja2", "numpy (>=1.18)", "pandas (>=1.0)"]
+complete = ["bokeh (>=1.0.0,!=2.0.0)", "distributed (==2021.11.0)", "jinja2", "numpy (>=1.18)", "pandas (>=1.0)"]
 dataframe = ["numpy (>=1.18)", "pandas (>=1.0)"]
 diagnostics = ["bokeh (>=1.0.0,!=2.0.0)", "jinja2"]
-distributed = ["distributed (==2021.09.1)"]
-test = ["pytest", "pytest-rerunfailures", "pytest-xdist"]
+distributed = ["distributed (==2021.11.0)"]
+test = ["pytest", "pytest-rerunfailures", "pytest-xdist", "pre-commit"]
 
 [[package]]
 name = "datashader"
@@ -432,7 +429,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*"
 
 [[package]]
 name = "distributed"
-version = "2021.9.1"
+version = "2021.11.0"
 description = "Distributed scheduler for Dask"
 category = "main"
 optional = false
@@ -441,7 +438,7 @@ python-versions = ">=3.7"
 [package.dependencies]
 click = ">=6.6"
 cloudpickle = ">=1.5.0"
-dask = "2021.09.1"
+dask = "2021.11.0"
 jinja2 = "*"
 msgpack = ">=0.6.0"
 psutil = ">=5.0"
@@ -529,7 +526,7 @@ test = ["pytest (>=3)", "pytest-cov", "boto3 (>=1.2.4)", "mock"]
 
 [[package]]
 name = "fsspec"
-version = "2021.10.0"
+version = "2021.11.0"
 description = "File-system specification"
 category = "main"
 optional = false
@@ -559,7 +556,7 @@ ssh = ["paramiko"]
 
 [[package]]
 name = "geopandas"
-version = "0.10.1"
+version = "0.10.2"
 description = "Geographic pandas extensions"
 category = "main"
 optional = false
@@ -675,7 +672,7 @@ tests = ["coveralls", "nose", "flake8", "parameterized", "pytest", "nbsmoke (>=0
 
 [[package]]
 name = "idna"
-version = "3.2"
+version = "3.3"
 description = "Internationalized Domain Names in Applications (IDNA)"
 category = "main"
 optional = false
@@ -683,7 +680,7 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "imageio"
-version = "2.9.0"
+version = "2.10.3"
 description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
 category = "main"
 optional = false
@@ -691,14 +688,19 @@ python-versions = ">=3.5"
 
 [package.dependencies]
 numpy = "*"
-pillow = "*"
+pillow = ">=8.3.2"
 
 [package.extras]
-ffmpeg = ["imageio-ffmpeg"]
+build = ["wheel"]
+dev = ["invoke", "pytest", "pytest-cov", "black", "flake8"]
+docs = ["sphinx", "numpydoc", "pydata-sphinx-theme"]
+ffmpeg = ["imageio-ffmpeg", "psutil"]
 fits = ["astropy"]
-full = ["astropy", "gdal", "imageio-ffmpeg", "itk"]
+full = ["astropy", "black", "flake8", "gdal", "imageio-ffmpeg", "invoke", "itk", "numpydoc", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx", "wheel"]
 gdal = ["gdal"]
 itk = ["itk"]
+linting = ["black", "flake8"]
+test = ["invoke", "pytest", "pytest-cov"]
 
 [[package]]
 name = "imageio-ffmpeg"
@@ -712,7 +714,7 @@ python-versions = ">=3.4"
 name = "importlib-metadata"
 version = "4.8.1"
 description = "Read metadata from Python packages"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 
@@ -734,7 +736,7 @@ python-versions = "*"
 
 [[package]]
 name = "ipython"
-version = "7.28.0"
+version = "7.29.0"
 description = "IPython: Productive Interactive Computing"
 category = "main"
 optional = false
@@ -873,7 +875,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "mkdocs"
-version = "1.2.2"
+version = "1.2.3"
 description = "Project documentation with Markdown."
 category = "dev"
 optional = false
@@ -1015,7 +1017,7 @@ python-versions = "*"
 
 [[package]]
 name = "netcdf4"
-version = "1.5.7"
+version = "1.5.8"
 description = "Provides an object-oriented python interface to the netCDF version 4 library."
 category = "main"
 optional = false
@@ -1039,7 +1041,7 @@ numpy = ">=1.15"
 
 [[package]]
 name = "numpy"
-version = "1.21.2"
+version = "1.21.4"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
@@ -1047,25 +1049,29 @@ python-versions = ">=3.7,<3.11"
 
 [[package]]
 name = "packaging"
-version = "21.0"
+version = "21.2"
 description = "Core utilities for Python packages"
 category = "main"
 optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-pyparsing = ">=2.0.2"
+pyparsing = ">=2.0.2,<3"
 
 [[package]]
 name = "pandas"
-version = "1.3.3"
+version = "1.3.4"
 description = "Powerful data structures for data analysis, time series, and statistics"
 category = "main"
 optional = false
 python-versions = ">=3.7.1"
 
 [package.dependencies]
-numpy = ">=1.17.3"
+numpy = [
+    {version = ">=1.17.3", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""},
+    {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""},
+    {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""},
+]
 python-dateutil = ">=2.7.3"
 pytz = ">=2017.3"
 
@@ -1100,16 +1106,16 @@ tests = ["flake8", "parameterized", "pytest", "scipy", "nbsmoke (>=0.2.0)", "pyt
 
 [[package]]
 name = "param"
-version = "1.11.1"
+version = "1.12.0"
 description = "Make your Python code clearer and more reliable by declaring Parameters."
 category = "main"
 optional = false
 python-versions = ">=2.7"
 
 [package.extras]
-all = ["flake8", "graphviz", "myst-parser", "myst-nb (==0.12.2)", "nbconvert (<6.0)", "nbsite (>=0.6.1)", "nose", "pydata-sphinx-theme", "pygraphviz"]
-doc = ["pygraphviz", "nbsite (>=0.6.1)", "pydata-sphinx-theme", "myst-parser", "nbconvert (<6.0)", "graphviz", "myst-nb (==0.12.2)"]
-tests = ["nose", "flake8"]
+all = ["aiohttp", "flake8", "graphviz", "myst-parser", "myst-nb (==0.12.2)", "nbconvert (<6.0)", "nbsite (>=0.6.1)", "pandas", "panel", "pydata-sphinx-theme", "pygraphviz", "pytest", "pytest-cov", "sphinx-copybutton"]
+doc = ["pygraphviz", "nbsite (>=0.6.1)", "pydata-sphinx-theme", "myst-parser", "nbconvert (<6.0)", "graphviz", "myst-nb (==0.12.2)", "sphinx-copybutton", "aiohttp", "panel", "pandas"]
+tests = ["pytest", "pytest-cov", "flake8"]
 
 [[package]]
 name = "parso"
@@ -1167,7 +1173,7 @@ python-versions = "*"
 
 [[package]]
 name = "pillow"
-version = "8.3.2"
+version = "8.4.0"
 description = "Python Imaging Library (Fork)"
 category = "main"
 optional = false
@@ -1198,7 +1204,7 @@ tqdm = "*"
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.20"
+version = "3.0.22"
 description = "Library for building powerful interactive command lines in Python"
 category = "main"
 optional = false
@@ -1228,11 +1234,11 @@ python-versions = "*"
 
 [[package]]
 name = "py"
-version = "1.10.0"
+version = "1.11.0"
 description = "library with cross-python path, ini-parsing, io, code, log facilities"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "pycparser"
@@ -1289,10 +1295,9 @@ tests = ["pytest (>=3.6)", "pytest-cov", "pytest-attrib", "beautifulsoup4", "req
 [package.source]
 type = "url"
 url = "https://github.com/pydap/pydap/archive/3f6aa190c59e3bbc6c834377a61579b20275ff69.zip"
-
 [[package]]
 name = "pygeos"
-version = "0.10.2"
+version = "0.11.1"
 description = "GEOS wrapped in numpy ufuncs"
 category = "main"
 optional = false
@@ -1356,14 +1361,15 @@ certifi = "*"
 
 [[package]]
 name = "pyresample"
-version = "1.21.1"
+version = "1.22.0"
 description = "Geospatial image resampling in Python"
 category = "main"
 optional = false
-python-versions = ">=3.4"
+python-versions = ">=3.7"
 
 [package.dependencies]
 configobj = "*"
+importlib-metadata = "*"
 numpy = ">=1.10.0"
 pykdtree = ">=1.3.1"
 pyproj = ">=2.2"
@@ -1374,8 +1380,9 @@ cf = ["xarray"]
 dask = ["dask (>=0.16.1)"]
 gradient_search = ["shapely"]
 numexpr = ["numexpr"]
-quicklook = ["matplotlib", "cartopy", "pillow"]
+quicklook = ["matplotlib", "cartopy (>=0.20.0)", "pillow"]
 rasterio = ["rasterio"]
+tests = ["rasterio", "dask", "xarray", "cartopy", "pillow", "matplotlib", "scipy", "zarr", "pytest-lazy-fixtures"]
 xarray_bilinear = ["xarray", "dask", "zarr"]
 
 [[package]]
@@ -1504,11 +1511,11 @@ tests = ["flake8", "nose"]
 
 [[package]]
 name = "pyyaml"
-version = "5.4.1"
+version = "6.0"
 description = "YAML parser and emitter for Python"
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "pyyaml-env-tag"
@@ -1523,7 +1530,7 @@ pyyaml = "*"
 
 [[package]]
 name = "rasterio"
-version = "1.2.9"
+version = "1.2.10"
 description = "Fast and direct raster I/O for use with Numpy and SciPy"
 category = "main"
 optional = false
@@ -1540,7 +1547,7 @@ numpy = "*"
 snuggs = ">=1.4.1"
 
 [package.extras]
-all = ["pytest (>=2.8.2)", "sphinx-rtd-theme", "hypothesis", "packaging", "shapely", "sphinx", "boto3 (>=1.2.4)", "matplotlib", "numpydoc", "ghp-import", "pytest-cov (>=2.2.0)", "ipython (>=2.0)"]
+all = ["numpydoc", "hypothesis", "matplotlib", "pytest-cov (>=2.2.0)", "sphinx", "ipython (>=2.0)", "boto3 (>=1.2.4)", "shapely", "pytest (>=2.8.2)", "packaging", "sphinx-rtd-theme", "ghp-import"]
 docs = ["ghp-import", "numpydoc", "sphinx", "sphinx-rtd-theme"]
 ipython = ["ipython (>=2.0)"]
 plot = ["matplotlib"]
@@ -1549,7 +1556,7 @@ test = ["boto3 (>=1.2.4)", "hypothesis", "packaging", "pytest-cov (>=2.2.0)", "p
 
 [[package]]
 name = "regex"
-version = "2021.10.8"
+version = "2021.11.2"
 description = "Alternative regular expression module, to replace re."
 category = "dev"
 optional = false
@@ -1575,25 +1582,25 @@ use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
 
 [[package]]
 name = "scipy"
-version = "1.7.1"
+version = "1.7.2"
 description = "SciPy: Scientific Library for Python"
 category = "main"
 optional = false
-python-versions = ">=3.7,<3.10"
+python-versions = ">=3.7,<3.11"
 
 [package.dependencies]
 numpy = ">=1.16.5,<1.23.0"
 
 [[package]]
 name = "shapely"
-version = "1.7.1"
+version = "1.8.0"
 description = "Geometric objects, predicates, and operations"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 
 [package.extras]
-all = ["numpy", "pytest", "pytest-cov"]
+all = ["pytest", "pytest-cov", "numpy"]
 test = ["pytest", "pytest-cov"]
 vectorized = ["numpy"]
 
@@ -1630,7 +1637,7 @@ python-versions = "*"
 
 [[package]]
 name = "soupsieve"
-version = "2.2.1"
+version = "2.3"
 description = "A modern CSS selector implementation for Beautiful Soup."
 category = "main"
 optional = false
@@ -1654,7 +1661,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "toolz"
-version = "0.11.1"
+version = "0.11.2"
 description = "List processing tools and functional utilities"
 category = "main"
 optional = false
@@ -1686,7 +1693,7 @@ telegram = ["requests"]
 
 [[package]]
 name = "traitlets"
-version = "5.1.0"
+version = "5.1.1"
 description = "Traitlets Python configuration system"
 category = "main"
 optional = false
@@ -1765,15 +1772,15 @@ testing = ["pytest (>=3.1.0)", "coverage", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "xarray"
-version = "0.19.0"
+version = "0.20.1"
 description = "N-D labeled arrays and datasets in Python"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.dependencies]
-numpy = ">=1.17"
-pandas = ">=1.0"
+numpy = ">=1.18"
+pandas = ">=1.1"
 
 [package.extras]
 accel = ["scipy", "bottleneck", "numbagg"]
@@ -1798,7 +1805,7 @@ heapdict = "*"
 name = "zipp"
 version = "3.6.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "dev"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 
@@ -1852,8 +1859,8 @@ bleach = [
     {file = "bleach-4.1.0.tar.gz", hash = "sha256:0900d8b37eba61a802ee40ac0061f8c2b5dee29c1927dd1d233e075ebf5a71da"},
 ]
 bokeh = [
-    {file = "bokeh-2.4.0-py3-none-any.whl", hash = "sha256:91a7c3b8a42d9275df26f13269859a1add82dc9e5dda316f7476ad76a5a10851"},
-    {file = "bokeh-2.4.0.tar.gz", hash = "sha256:6fa00ed8baab5cca33f4175792c309fa2536eaae7e90abee884501ba8c90fddb"},
+    {file = "bokeh-2.4.1-py3-none-any.whl", hash = "sha256:b270d6ef899598fe26e64b6ae08e30f8d67a177baa1f5bfe18e1979a81bb7c4d"},
+    {file = "bokeh-2.4.1.tar.gz", hash = "sha256:d0410717d743a0ac251e62480e2ea860a7341bdcd1dbe01499a904f233c90512"},
 ]
 branca = [
     {file = "branca-0.4.2-py3-none-any.whl", hash = "sha256:62c2e777f074fc1830cd40ba9e650beb941861075980babafead8d97856b1a4b"},
@@ -1871,90 +1878,91 @@ certifi = [
     {file = "certifi-2021.10.8.tar.gz", hash = "sha256:78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872"},
 ]
 cffi = [
-    {file = "cffi-1.14.6-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:22b9c3c320171c108e903d61a3723b51e37aaa8c81255b5e7ce102775bd01e2c"},
-    {file = "cffi-1.14.6-cp27-cp27m-manylinux1_i686.whl", hash = "sha256:f0c5d1acbfca6ebdd6b1e3eded8d261affb6ddcf2186205518f1428b8569bb99"},
-    {file = "cffi-1.14.6-cp27-cp27m-manylinux1_x86_64.whl", hash = "sha256:99f27fefe34c37ba9875f224a8f36e31d744d8083e00f520f133cab79ad5e819"},
-    {file = "cffi-1.14.6-cp27-cp27m-win32.whl", hash = "sha256:55af55e32ae468e9946f741a5d51f9896da6b9bf0bbdd326843fec05c730eb20"},
-    {file = "cffi-1.14.6-cp27-cp27m-win_amd64.whl", hash = "sha256:7bcac9a2b4fdbed2c16fa5681356d7121ecabf041f18d97ed5b8e0dd38a80224"},
-    {file = "cffi-1.14.6-cp27-cp27mu-manylinux1_i686.whl", hash = "sha256:ed38b924ce794e505647f7c331b22a693bee1538fdf46b0222c4717b42f744e7"},
-    {file = "cffi-1.14.6-cp27-cp27mu-manylinux1_x86_64.whl", hash = "sha256:e22dcb48709fc51a7b58a927391b23ab37eb3737a98ac4338e2448bef8559b33"},
-    {file = "cffi-1.14.6-cp35-cp35m-macosx_10_9_x86_64.whl", hash = "sha256:aedb15f0a5a5949ecb129a82b72b19df97bbbca024081ed2ef88bd5c0a610534"},
-    {file = "cffi-1.14.6-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:48916e459c54c4a70e52745639f1db524542140433599e13911b2f329834276a"},
-    {file = "cffi-1.14.6-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:f627688813d0a4140153ff532537fbe4afea5a3dffce1f9deb7f91f848a832b5"},
-    {file = "cffi-1.14.6-cp35-cp35m-win32.whl", hash = "sha256:f0010c6f9d1a4011e429109fda55a225921e3206e7f62a0c22a35344bfd13cca"},
-    {file = "cffi-1.14.6-cp35-cp35m-win_amd64.whl", hash = "sha256:57e555a9feb4a8460415f1aac331a2dc833b1115284f7ded7278b54afc5bd218"},
-    {file = "cffi-1.14.6-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:e8c6a99be100371dbb046880e7a282152aa5d6127ae01783e37662ef73850d8f"},
-    {file = "cffi-1.14.6-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:19ca0dbdeda3b2615421d54bef8985f72af6e0c47082a8d26122adac81a95872"},
-    {file = "cffi-1.14.6-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:d950695ae4381ecd856bcaf2b1e866720e4ab9a1498cba61c602e56630ca7195"},
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 ]
 typed-ast = [
     {file = "typed_ast-1.4.3-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:2068531575a125b87a41802130fa7e29f26c09a2833fea68d9a40cf33902eba6"},
@@ -3039,8 +3059,8 @@ webob = [
     {file = "WebOb-1.8.7.tar.gz", hash = "sha256:b64ef5141be559cfade448f044fa45c2260351edcb6a8ef6b7e00c7dcef0c323"},
 ]
 xarray = [
-    {file = "xarray-0.19.0-py3-none-any.whl", hash = "sha256:da0f0d7719b5ee95143a34804e3afb82cb8abbe5c10f9750a9dbed156ad30f00"},
-    {file = "xarray-0.19.0.tar.gz", hash = "sha256:3a365ce09127fc841ba88baa63f37ca61376ffe389a6c5e66d52f2c88c23a62b"},
+    {file = "xarray-0.20.1-py3-none-any.whl", hash = "sha256:2812691033fdf8ef1fc5675b4883587521d11d02ce8a9fbbe9a4172c77924d0a"},
+    {file = "xarray-0.20.1.tar.gz", hash = "sha256:9c0bffd8b55fdef277f8f6c817153eb51fa4e58653a7ad92eaed9984164b7bdb"},
 ]
 zict = [
     {file = "zict-2.0.0-py3-none-any.whl", hash = "sha256:26aa1adda8250a78dfc6a78d200bfb2ea43a34752cf58980bca75dde0ba0c6e9"},
diff --git a/pyposeidon/boundary.py b/pyposeidon/boundary.py
index ed2b148f..ce2f5f79 100644
--- a/pyposeidon/boundary.py
+++ b/pyposeidon/boundary.py
@@ -33,6 +33,7 @@ def simplify(geo):
             geo_ = [geo.buffer(0).unary_union]
 
         geo = gp.GeoDataFrame(geometry=geo_)
+        geo = gp.GeoDataFrame(geometry=geo.buffer(0))
 
     return geo
 
diff --git a/pyposeidon/d3d.py b/pyposeidon/d3d.py
index a82e1f89..8d9a9ca4 100644
--- a/pyposeidon/d3d.py
+++ b/pyposeidon/d3d.py
@@ -30,7 +30,7 @@
 import pyposeidon.dem as pdem
 from pyposeidon.utils.get_value import get_value
 from pyposeidon.utils.converter import myconverter
-from pyposeidon.utils.data import data
+from pyposeidon.utils import data
 import logging
 
 logger = logging.getLogger("pyposeidon")
@@ -1057,4 +1057,4 @@ def get_data(self, **kwargs):
 
         dic.update(kwargs)
 
-        self.data = data(**dic)
+        self.data = data.get_output(**dic)
diff --git a/pyposeidon/grid.py b/pyposeidon/grid.py
index 2ad74107..82f27923 100644
--- a/pyposeidon/grid.py
+++ b/pyposeidon/grid.py
@@ -165,7 +165,7 @@ class tri2d:
     def __init__(self, **kwargs):
 
         grid_file = kwargs.get("grid_file", None)
-        grid_generator = kwargs.get("grid_generator", "jigsaw")
+        grid_generator = kwargs.get("grid_generator", None)
         geo = kwargs.pop("geometry", None)
         coasts = kwargs.pop("coastlines", None)
         boundary = kwargs.pop("boundary", None)
diff --git a/pyposeidon/jigsaw.py b/pyposeidon/jigsaw.py
index 96911eee..e5878341 100644
--- a/pyposeidon/jigsaw.py
+++ b/pyposeidon/jigsaw.py
@@ -183,9 +183,14 @@ def make_bgmesh(boundary, **kwargs):
         lat_min = contours.bounds.miny.min()
         lat_max = contours.bounds.maxy.max()
 
-    dem = pdem.dem(lon_min=lon_min, lon_max=lon_max, lat_min=lat_min, lat_max=lat_max, **kwargs)
-
     kwargs_ = kwargs.copy()
+    kwargs_.pop("lon_min", None)
+    kwargs_.pop("lon_max", None)
+    kwargs_.pop("lat_min", None)
+    kwargs_.pop("lat_max", None)
+
+    dem = pdem.dem(lon_min=lon_min, lon_max=lon_max, lat_min=lat_min, lat_max=lat_max, **kwargs_)
+
     res_min = kwargs_.pop("resolution_min", 0.01)
     res_max = kwargs_.pop("resolution_max", 0.5)
     dhdx = kwargs_.pop("dhdx", 0.15)
diff --git a/pyposeidon/model.py b/pyposeidon/model.py
index 463275c7..6f971dd8 100644
--- a/pyposeidon/model.py
+++ b/pyposeidon/model.py
@@ -81,7 +81,7 @@
 nm = ["Z", "A"]
 
 
-def model(solver=None, atm=True, tide=False, **kwargs):
+def set(solver=None, atm=True, tide=False, **kwargs):
     """
     Construct a hydrodynamic model based on different solvers.
 
@@ -95,7 +95,7 @@ def model(solver=None, atm=True, tide=False, **kwargs):
 
     Example:
 
-    model = pyposeidon.model(solver='d3d)
+    model = pyposeidon.set(solver='d3d)
 
     """
 
@@ -106,7 +106,7 @@ def model(solver=None, atm=True, tide=False, **kwargs):
         return schism(**kwargs)
 
 
-def read_model(filename, **kwargs):
+def read(filename, **kwargs):
 
     end = filename.split(".")[-1]
 
@@ -119,4 +119,4 @@ def read_model(filename, **kwargs):
         logger.error("Model file should be .txt or .json")
         sys.exit(0)
 
-    return model(**info)
+    return set(**info)
diff --git a/pyposeidon/schism.py b/pyposeidon/schism.py
index fdbf8c8b..40b8fc73 100644
--- a/pyposeidon/schism.py
+++ b/pyposeidon/schism.py
@@ -38,7 +38,7 @@
 from pyposeidon.utils.vals import obs
 from pyposeidon.utils.cpoint import closest_node
 from pyposeidon.utils.unml import unml
-from pyposeidon.utils.data import data
+from pyposeidon.utils import data
 
 import logging
 
@@ -161,7 +161,7 @@ def __init__(self, **kwargs):
                 self.time_frame = self.end_date - self.start_date
 
         if not hasattr(self, "date"):
-            self.date = self.start_date
+            self.date = get_value(self, kwargs, "date", self.start_date)
 
         if not hasattr(self, "end_date"):
             # ---------------------------------------------------------------------
@@ -465,7 +465,6 @@ def output(self, **kwargs):
         # open boundaries
         number_of_open_boundaries = bs.loc[bs.type == "open"].id.max()
         number_of_open_boundaries_nodes = bs.loc[bs.type == "open"].shape[0]
-        print(number_of_open_boundaries)
 
         with open(path + "bctides.in", "w") as f:
             f.write("Header\n")
@@ -1734,6 +1733,11 @@ def set_obs(self, **kwargs):
         stations["z"] = 0
         stations.index += 1
         stations["gindex"] = grid_index
+        stations["name"] = tg.locations.Name.values
+        stations["id"] = tg.locations.ID.values
+        stations["group"] = tg.locations.Group.values
+        stations["longitude"] = tg.locations.longitude.values
+        stations["latitude"] = tg.locations.latitude.values
 
         if coastal_monitoring:
             ## FOR COASTAL MONITORING
@@ -1808,7 +1812,7 @@ def get_station_data(self, **kwargs):
                 logger.error("No station.in file present")
             return
 
-        dstamp = kwargs.get("dstamp", self.start_date)
+        dstamp = kwargs.get("dstamp", self.date)
 
         dfs = []
         for idx in vals.index:
@@ -1821,16 +1825,22 @@ def get_station_data(self, **kwargs):
             pindex = pd.MultiIndex.from_product([df.T.columns, df.T.index])
 
             r = pd.DataFrame(df.values.flatten(), index=pindex, columns=[vals.loc[idx, "variable"]])
-            r.index.names = ["time", "index"]
+            r.index.names = ["time", "node"]
+
+            r.index = r.index.set_levels(r.index.levels[1] - 1, level=1)
 
             dfs.append(r.to_xarray())
 
         self.time_series = xr.combine_by_coords(dfs)
 
-    def get_data(self, **kwargs):
+    def get_output_data(self, **kwargs):
 
         dic = self.__dict__
 
         dic.update(kwargs)
 
-        self.data = data(**dic)
+        self.data = data.get_output(**dic)
+
+    def open_thalassa(self, **kwargs):
+        # open a Thalassa instance to visualize the output
+        return
diff --git a/pyposeidon/utils/cast.py b/pyposeidon/utils/cast.py
index 86dc9a54..2110e481 100644
--- a/pyposeidon/utils/cast.py
+++ b/pyposeidon/utils/cast.py
@@ -3,10 +3,15 @@
 
 """
 # Copyright 2018 European Union
-# This file is part of pyposeidon, a software written by George Breyiannis (JRC E.1)
+# This file is part of pyposeidon.
 # Licensed under the EUPL, Version 1.2 or – as soon they will be approved by the European Commission - subsequent versions of the EUPL (the "Licence").
 # Unless required by applicable law or agreed to in writing, software distributed under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the Licence for the specific language governing permissions and limitations under the Licence.
+import pyposeidon
+import pyposeidon.model as pm
+import pyposeidon.grid as pgrid
+from pyposeidon.utils.get_value import get_value
+
 
 import numpy as np
 import errno
@@ -15,10 +20,8 @@
 import os, errno
 from shutil import copy2
 import glob
-import pyposeidon.model as pmodel
-import pyposeidon.grid as pgrid
-from pyposeidon.utils.get_value import get_value
 import pandas as pd
+import pathlib
 
 # from pyposeidon.utils import data
 import subprocess
@@ -27,7 +30,7 @@
 logger = logging.getLogger("pyposeidon")
 
 
-def cast(solver=None, **kwargs):
+def set(solver=None, **kwargs):
     if solver == "d3d":
         return dcast(**kwargs)
     elif solver == "schism":
@@ -40,7 +43,7 @@ def __init__(self, **kwargs):
         for attr, value in kwargs.items():
             setattr(self, attr, value)
 
-    def set(self, **kwargs):
+    def run(self, **kwargs):
 
         if isinstance(self.model, str):
             self.model = pyposeidon.read_model(self.model)
@@ -103,9 +106,7 @@ def set(self, **kwargs):
         if self.restart_step:
             info["restart_step"] = self.restart_step
 
-        #            for attr, value in self.items():
-        #                setattr(info, attr, value)
-        m = pmodel(**info)
+        m = pm.set(**info)
 
         # copy/link necessary files
         logger.debug("copy necessary files")
@@ -128,13 +129,16 @@ def set(self, **kwargs):
             ipath = glob.glob(self.origin + filename)
             if ipath:
                 try:
-                    os.symlink(ipath[0], rpath + filename)
+                    os.symlink(pathlib.Path(ipath[0]).resolve(strict=True), rpath + filename)
                 except OSError as e:
                     if e.errno == errno.EEXIST:
                         logger.warning("Restart link present\n")
                         logger.warning("overwriting\n")
                         os.remove(rpath + filename)
-                        os.symlink(ipath[0], rpath + filename)
+                        os.symlink(
+                            pathlib.Path(ipath[0]).resolve(strict=True),
+                            rpath + filename,
+                        )
         logger.debug(".. done")
 
         copy2(ppath + m.tag + ".mdf", rpath)  # copy the mdf file
@@ -147,14 +151,20 @@ def set(self, **kwargs):
 
         #  copy2(ppath+inresfile,rpath+'tri-rst.'+outresfile)
         try:
-            os.symlink(ppath + "/" + inresfile, rpath + "tri-rst." + outresfile)
+            os.symlink(
+                pathlib.Path(ppath + "/" + inresfile).resolve(strict=True),
+                rpath + "tri-rst." + outresfile,
+            )
             logger.debug("symlink {} to {}".format(ppath + "/" + inresfile, rpath + "tri-rst." + outresfile))
         except OSError as e:
             if e.errno == errno.EEXIST:
                 logger.warning("Restart symlink present\n")
                 logger.warning("overwriting\n")
                 os.remove(rpath + "tri-rst." + outresfile)
-                os.symlink(ppath + "/" + inresfile, rpath + "tri-rst." + outresfile)
+                os.symlink(
+                    pathlib.Path(ppath + "/" + inresfile).resolve(strict=True),
+                    rpath + "tri-rst." + outresfile,
+                )
             else:
                 raise e
 
@@ -184,7 +194,6 @@ def set(self, **kwargs):
         m.config_file = rpath + m.tag + ".mdf"
 
         os.chdir(rpath)
-        # subprocess.call(rpath+'run_flow2d3d.sh',shell=True)
         m.save()
 
         if execute:
@@ -193,10 +202,6 @@ def set(self, **kwargs):
         # cleanup
         os.remove(rpath + "tri-rst." + outresfile)
 
-        # save compiled nc file
-
-        # out = data(**{'solver':m.solver,'rpath':rpath,'savenc':True})
-
         logger.info("done for date :" + datetime.datetime.strftime(self.date, "%Y%m%d.%H"))
 
         os.chdir(pwd)
@@ -208,7 +213,7 @@ def __init__(self, **kwargs):
         for attr, value in kwargs.items():
             setattr(self, attr, value)
 
-    def set(self, **kwargs):
+    def run(self, **kwargs):
 
         if isinstance(self.model, str):
             self.model = pyposeidon.read_model(self.model)
@@ -217,7 +222,7 @@ def set(self, **kwargs):
             if not hasattr(self, attr):
                 setattr(self, attr, value)
 
-        execute = get_value(self, kwargs, "execute", False)
+        execute = get_value(self, kwargs, "execute", True)
 
         pwd = os.getcwd()
 
@@ -257,12 +262,13 @@ def set(self, **kwargs):
             sys.exit(1)
 
         ppath = self.ppath
-        # create the folder/run path
+        # create the new folder/run path
         rpath = self.cpath
 
         if not os.path.exists(rpath):
             os.makedirs(rpath)
 
+        tag = kwargs.get("tag", "schism")
         copy2(ppath + self.tag + "_model.json", rpath)  # copy the info file
 
         # load model
@@ -271,27 +277,34 @@ def set(self, **kwargs):
             info[info.isnull().values] = None
             info = info.to_dict()[0]
 
-        args = set(kwargs.keys()).intersection(info.keys())  # modify dic with kwargs
-        for attr in list(args):
-            info[attr] = kwargs[attr]
+        try:
+            args = set(kwargs.keys()).intersection(info.keys())  # modify dic with kwargs
+            for attr in list(args):
+                info[attr] = kwargs[attr]
+        except:
+            pass
 
         info["config_file"] = ppath + "param.nml"
 
         # update the properties
 
-        info["start_date"] = self.date
+        info["date"] = self.date0
+        info["start_date"] = self.sdate
         info["time_frame"] = self.time_frame
-        info["end_date"] = self.date + pd.to_timedelta(self.time_frame)
+        info["end_date"] = self.sdate + pd.to_timedelta(self.time_frame)
         info["meteo_source"] = self.meteo
         info["rpath"] = rpath
-        #            info['grid_file'] = ppath + '/hgrid.gr3'
-
-        #            for attr, value in self.items():
-        #                setattr(info, attr, value)
 
-        m = pmodel(**info)
+        m = pm.set(**info)
 
         # Grid
+        gfile = glob.glob(ppath + "hgrid.gr3")
+        if gfile:
+            info["grid_file"] = gfile[0]
+            self.grid_file = gfile[0]
+            info["grid_generator"] = None
+            self.grid_generator = None
+
         m.grid = pgrid.grid(type="tri2d", **info)
 
         # get lat/lon from file
@@ -330,46 +343,29 @@ def set(self, **kwargs):
                     copy2(ppath + filename, rpath + filename)
         logger.debug(".. done")
 
-        # symlink the station files
-        # logger.debug('symlink station files')
-        # for filename in station_files:
-
-        #   ipath = glob.glob(self.path+self.folders[0] + filename)
-        #   if ipath:
-
-        #        if not os.path.exists(rpath + '/outputs/'):
-        #            os.makedirs(rpath + '/outputs/')
-
-        #        try:
-        #            os.symlink(ipath[0],rpath + filename)
-        #        except OSError as e:
-        #            if e.errno == errno.EEXIST:
-        #                logger.warning('Restart link present\n')
-        #                logger.warning('overwriting\n')
-        #                os.remove(rpath + filename)
-        #                os.symlink(ipath[0],rpath + filename)
-        # logger.debug('.. done')
-
         # symlink the big files
         logger.debug("symlink model files")
         for filename in files_sym:
             ipath = glob.glob(self.origin + filename)
             if ipath:
                 try:
-                    os.symlink(ipath[0], rpath + filename)
+                    os.symlink(pathlib.Path(ipath[0]).resolve(strict=True), rpath + filename)
                 except OSError as e:
                     if e.errno == errno.EEXIST:
                         logger.warning("Restart link present\n")
                         logger.warning("overwriting\n")
                         os.remove(rpath + filename)
-                        os.symlink(ipath[0], rpath + filename)
+                        os.symlink(
+                            pathlib.Path(ipath[0]).resolve(strict=True),
+                            rpath + filename,
+                        )
         logger.debug(".. done")
 
         # create restart file
         logger.debug("create restart file")
 
         # check for combine hotstart
-        hotout = int((self.date - self.date0).total_seconds() / info["params"]["core"]["dt"])
+        hotout = int((self.sdate - self.date0).total_seconds() / info["params"]["core"]["dt"])
         logger.debug("hotout_it = {}".format(hotout))
 
         resfile = glob.glob(ppath + "/outputs/hotstart_it={}.nc".format(hotout))
@@ -379,7 +375,7 @@ def set(self, **kwargs):
                 ph = pd.read_json(f, lines=True).T
                 ph[ph.isnull().values] = None
                 ph = ph.to_dict()[0]
-            p = pmodel(**ph)
+            p = pm.set(**ph)
             p.hotstart(it=hotout)
 
         # link restart file
@@ -389,13 +385,16 @@ def set(self, **kwargs):
         logger.info("set restart\n")
 
         try:
-            os.symlink(ppath + inresfile, rpath + outresfile)
+            os.symlink(pathlib.Path(ppath + inresfile).resolve(strict=True), rpath + outresfile)
         except OSError as e:
             if e.errno == errno.EEXIST:
                 logger.warning("Restart link present\n")
                 logger.warning("overwriting\n")
                 os.remove(rpath + outresfile)
-                os.symlink(ppath + inresfile, rpath + outresfile)
+                os.symlink(
+                    pathlib.Path(ppath + inresfile).resolve(strict=True),
+                    rpath + outresfile,
+                )
             else:
                 raise e
 
@@ -433,7 +432,7 @@ def set(self, **kwargs):
             logger.warning("meteo files present\n")
 
         # modify param file
-        rnday_new = (self.date - self.date0).total_seconds() / (3600 * 24.0) + pd.to_timedelta(
+        rnday_new = (self.sdate - self.date0).total_seconds() / (3600 * 24.0) + pd.to_timedelta(
             self.time_frame
         ).total_seconds() / (3600 * 24.0)
         hotout_write = int(rnday_new * 24 * 3600 / info["params"]["core"]["dt"])
@@ -448,24 +447,15 @@ def set(self, **kwargs):
             }
         )
 
-        m.config(output=True, **info)
+        m.config(output=True, **info)  # save param.nml
 
         m.config_file = rpath + "param.nml"
 
-        os.chdir(rpath)
-        # subprocess.call(rpath+'run_flow2d3d.sh',shell=True)
         m.save()
 
         if execute:
             m.run()
 
-        # cleanup
-        #            os.remove(rpath+'hotstart.nc')
-
-        # save compiled nc file
-
-        # out = data(**{'solver':m.solver,'rpath':rpath,'savenc':True})
-
-        logger.info("done for date :" + datetime.datetime.strftime(self.date, "%Y%m%d.%H"))
+        logger.info("done for date :" + datetime.datetime.strftime(self.sdate, "%Y%m%d.%H"))
 
         os.chdir(pwd)
diff --git a/pyposeidon/utils/data.py b/pyposeidon/utils/data.py
index 5458b856..475fc360 100644
--- a/pyposeidon/utils/data.py
+++ b/pyposeidon/utils/data.py
@@ -23,7 +23,7 @@
 logger = logging.getLogger("pyposeidon")
 
 
-def data(**kwargs):
+def get_output(**kwargs):
 
     solver = kwargs.get("solver", None)
     if solver == "d3d":
@@ -176,7 +176,7 @@ def __init__(self, **kwargs):
             xdat.sort(key=lambda f: int("".join(filter(str.isdigit, f))))
 
             if len(xdat) > 0:
-                datai.extend(xdat)  # append to list
+                datai.append(xdat)  # append to list
 
             else:  # run merge output
 
@@ -185,7 +185,7 @@ def __init__(self, **kwargs):
                     info[info.isnull().values] = None
                     info = info.to_dict()[0]
 
-                p = pm.model(**info)
+                p = pm.set(**info)
 
                 p.misc = misc
 
@@ -196,88 +196,47 @@ def __init__(self, **kwargs):
                 xdat = glob.glob(folder + "/outputs/schout_[!0]*.nc")
                 xdat.sort(key=lambda f: int("".join(filter(str.isdigit, f))))
 
-                datai.extend(xdat)  # append to list
+                datai.append(xdat)  # append to list
 
-        self.Dataset = xr.open_mfdataset(datai, combine="by_coords", data_vars="minimal")
+        merge = kwargs.get("merge", True)
 
-        with open(self.folders[-1] + "/" + tag + "_model.json", "r") as f:
-            info = pd.read_json(f, lines=True).T
-            info[info.isnull().values] = None
-            info = info.to_dict()[0]
-
-        p = pm.model(**info)
-
-        logger.info("Retrieve station timeseries if any\n")
+        if merge:
 
-        dstamp = kwargs.get("dstamp", info["date"])
-        try:
-            p.get_station_data(dstamp=dstamp)
-            self.time_series = p.time_series
+            datai = [j for i in datai for j in i]
+            self.Dataset = xr.open_mfdataset(datai, combine="by_coords", data_vars="minimal")
 
-            dic = {}
+            with open(self.folders[-1] + "/" + tag + "_model.json", "r") as f:
+                info = pd.read_json(f, lines=True).T
+                info[info.isnull().values] = None
+                info = info.to_dict()[0]
 
-            try:
-
-                with open(self.folders[0] + "/" + tag + "_model.json", "r") as f:
-                    info = pd.read_json(f, lines=True).T
-                    info[info.isnull().values] = None
-                    self.info = info.to_dict()[0]
+            p = pm.set(**info)
 
-                dic = self.info.copy()  # start with x's keys and values
-                dic.update(kwargs)  # modifies z with y's keys and values & returns None
+            if hasattr(p, "stations"):
 
-            except:
-                pass
+                logger.info("Retrieve station timeseries\n")
 
-            if "sa_date" not in dic.keys():
-                dic.update({"sa_date": self.time_series.time.values[0]})
+                dstamp = kwargs.get("dstamp", info["date"])
 
-            if "se_date" not in dic.keys():
-                dic.update({"se_date": self.Dataset.time.values[-1]})
+                p.get_station_data(dstamp=dstamp)
+                self.time_series = p.time_series
 
-            if "lon_min" not in dic.keys():
-                dic.update({"lon_min": self.Dataset.SCHISM_hgrid_node_x.values.min()})
-
-            if "lon_max" not in dic.keys():
-                dic.update({"lon_max": self.Dataset.SCHISM_hgrid_node_x.values.max()})
-
-            if "lat_min" not in dic.keys():
-                dic.update({"lat_min": self.Dataset.SCHISM_hgrid_node_y.values.min()})
-
-            if "lat_max" not in dic.keys():
-                dic.update({"lat_max": self.Dataset.SCHISM_hgrid_node_y.values.max()})
-
-            logger.info("Retrieve observations info\n")
-
-            self.obs = obs(**dic)
+        else:
+            self.Dataset = [xr.open_mfdataset(x, combine="by_coords", data_vars="minimal") for x in datai]
 
-            ret = kwargs.get("online", False)
+            ts = []
 
-            if ret is True:
-                logger.info("collect observational data")
-                tgs = self.obs.locations.loc[self.obs.locations.Group == "TD UNESCO"]
+            for folder in self.folders:
 
-                dic = {}
-                for i in tgs.index:
-                    #            print(i, tgs.loc[i].Name.strip())
-                    while True:
-                        p = self.obs.iloc(i)
-                        if p is not None:
-                            if p.shape[0] > 1:
-                                p = p.dropna()
-                            break
-                    dic.update({tgs.loc[i].Name.strip(): p})
+                p = pm.read_model(folder + "/{}_model.json".format(tag))  # read model
 
-                tg = pd.concat(dic, axis=0, sort=True)
+                if hasattr(p, "stations"):
 
-                try:
-                    tg = tg.drop("TimeUTC", axis=1)
-                except:
-                    pass
+                    logger.info("Retrieve station timeseries\n")
 
-                tg.to_csv(self.folders[0] + "/" + "obs.csv")
+                    dstamp = kwargs.get("dstamp", p.date)
 
-                self.obs.dataframe = tg
+                    p.get_station_data(dstamp=dstamp)
+                    ts.append(p.time_series)
 
-        except:
-            logger.info("no station data loaded")
+            self.time_series = ts
diff --git a/pyposeidon/utils/global_bgmesh.py b/pyposeidon/utils/global_bgmesh.py
index a9bcef6f..98bc7c92 100644
--- a/pyposeidon/utils/global_bgmesh.py
+++ b/pyposeidon/utils/global_bgmesh.py
@@ -67,7 +67,7 @@ def make_bgmesh_global(b, fpos, dem, **kwargs):
     elif grid_generator == "jigsaw":
 
         dh = xr.Dataset(
-            {"z": (["longitude", "latitude"], nodes.d2.values.reshape(ui.shape))},
+            {"h": (["longitude", "latitude"], nodes.d2.values.reshape(ui.shape))},
             coords={
                 "longitude": ("longitude", d1.flatten()),
                 "latitude": ("latitude", d2.flatten()),
diff --git a/pyposeidon/utils/hfun.py b/pyposeidon/utils/hfun.py
index e3982bc1..c742faa0 100644
--- a/pyposeidon/utils/hfun.py
+++ b/pyposeidon/utils/hfun.py
@@ -16,14 +16,17 @@ def get_hfun(dem, path=".", tag="jigsaw", resolution_min=0.01, resolution_max=0.
 
     # scale bathymetry
     try:
-        b = dem.adjusted.to_dataframe()
+        b = dem.Dataset.adjusted.to_dataframe()
     except:
-        b = dem.elevation.to_dataframe()
+        b = dem.Dataset.elevation.to_dataframe()
+
+    b = b.reset_index()
+    b.columns = ["longitude", "latitude", "z"]
 
     nodes = scale_dem(b, resolution_min, resolution_max, **kwargs)
 
-    x = dem.longitude.values
-    y = dem.latitude.values
+    x = dem.Dataset.longitude.values
+    y = dem.Dataset.latitude.values
 
     tria = MakeTriangleFaces(y.shape[0], x.shape[0])
 
@@ -47,7 +50,7 @@ def get_hfun(dem, path=".", tag="jigsaw", resolution_min=0.01, resolution_max=0.
     cfun = fun.flatten().reshape((y.shape[0], x.shape[0]))
 
     dh = xr.Dataset(
-        {"h": (["longitude", "latitude"], cfun)},
+        {"h": (["latitude", "longitude"], cfun)},
         coords={"longitude": ("longitude", x), "latitude": ("latitude", y)},
     )
 
@@ -139,7 +142,7 @@ def to_hfun_grid(dh, fhfun):
         np.savetxt(f, dh.latitude.values)
 
     with open(fhfun, "a") as f:
-        f.write("VALUE={};1\n".format(dh.z.size))
+        f.write("VALUE={};1\n".format(dh.h.size))
 
     with open(fhfun, "a") as f:
-        np.savetxt(f, dh.z.values.flatten())
+        np.savetxt(f, dh.h.T.values.flatten())
diff --git a/pyposeidon/utils/hplot.py b/pyposeidon/utils/hplot.py
index 2935b95c..89cdaddd 100644
--- a/pyposeidon/utils/hplot.py
+++ b/pyposeidon/utils/hplot.py
@@ -81,7 +81,12 @@ def contourf(self, var="depth", it=None, tiles=False, **kwargs):
             )
         else:
             return rasterize(trimesh, aggregator="mean").opts(
-                colorbar=True, cmap="Viridis", padding=0.1, tools=["hover"], width=width, height=height
+                colorbar=True,
+                cmap="Viridis",
+                padding=0.1,
+                tools=["hover"],
+                width=width,
+                height=height,
             )
 
     def meteo(self, **kwargs):
@@ -218,10 +223,66 @@ def time_mesh(time):
         meshes = hv.DynamicMap(time_mesh, kdims=["Time"]).redim.values(Time=times)
 
         imesh = rasterize(meshes, aggregator="mean").opts(
-            cmap="viridis", colorbar=True, padding=0.1, tools=["hover"], clim=(zmin, zmax)
+            cmap="viridis",
+            colorbar=True,
+            padding=0.1,
+            tools=["hover"],
+            clim=(zmin, zmax),
         )
 
         if tiles:
             return hv.output(tile * imesh, holomap="scrubber", fps=1)
         else:
             return hv.output(imesh.opts(width=width, height=height), holomap="scrubber", fps=1)
+
+
+# from https://pandas.pydata.org/pandas-docs/stable/development/extending.html
+@pd.api.extensions.register_dataframe_accessor("hplot")
+class BoundaryAccessor:
+    def __init__(self, pandas_obj):
+        self._validate(pandas_obj)
+        self._obj = pandas_obj
+
+    @staticmethod
+    def _validate(obj):
+        # verify there is a column latitude and a column longitude
+        if "lat" not in obj.columns or "lon" not in obj.columns:
+            raise AttributeError("Must have 'lat' and 'lon'.")
+
+    @property
+    def center(self):
+        # return the geographic center point of this DataFrame
+        lat = self._obj.lat
+        lon = self._obj.lon
+        return (float(lon.mean()), float(lat.mean()))
+
+    def show(self, **kwargs):
+        width = kwargs.get("width", 800)
+        height = kwargs.get("height", 600)
+        opts.defaults(opts.WMTS(width=width, height=height))
+
+        tile = gv.WMTS("https://b.tile.openstreetmap.org/{Z}/{X}/{Y}.png")
+
+        ps = [tile]
+
+        # external
+        ds = self._obj.loc["line0"]
+        ds = ds.append(ds.iloc[0]).reset_index(drop=True)
+
+        dland = ds.loc[ds.tag == "land"]
+        dland_ = np.split(dland, np.flatnonzero(np.diff(dland.index) != 1) + 1)
+        for seg in dland_:
+            ps.append(seg.hvplot.paths(x="lon", y="lat", geo=True, color="brown"))
+
+        dwater = ds.loc[ds.tag == "open"]
+        dwater_ = np.split(dwater, np.flatnonzero(np.diff(dwater.index) != 1) + 1)
+        for seg in dwater_:
+            ps.append(seg.hvplot.paths(x="lon", y="lat", geo=True, color="blue"))
+
+        # islands
+        for line in self._obj.index.levels[0][1:]:
+            ds = self._obj.loc[line]
+            ds = ds.append(ds.iloc[0]).reset_index(drop=True)
+            ps.append(ds.hvplot.paths(x="lon", y="lat", geo=True, color="green"))
+
+        return hv.Overlay(ps)
diff --git a/pyposeidon/utils/mplot.py b/pyposeidon/utils/mplot.py
index b77ee68f..3a37aa80 100644
--- a/pyposeidon/utils/mplot.py
+++ b/pyposeidon/utils/mplot.py
@@ -10,12 +10,14 @@
 
 from mayavi import mlab
 
+mlab.options.offscreen = True
 from mayavi.sources.builtin_surface import BuiltinSurface
 import xarray as xr
 import numpy as np
 import pandas as pd
 import subprocess
-
+from pyposeidon.utils.stereo import to_3d
+from itkwidgets import view
 import os
 import sys
 
@@ -102,7 +104,16 @@ def contourf(self, **kwargs):
         self.globe(R - 0.002, bcolor=bcolor)
         # 3D triangular mesh surface (like trisurf)
         grd = mlab.triangular_mesh(
-            px, py, pz, tri3, representation=rep, opacity=1.0, scalars=z, colormap=cmap, vmin=vmin, vmax=vmax
+            px,
+            py,
+            pz,
+            tri3,
+            representation=rep,
+            opacity=1.0,
+            scalars=z,
+            colormap=cmap,
+            vmin=vmin,
+            vmax=vmax,
         )
 
         grd.actor.mapper.scalar_visibility = True
@@ -156,7 +167,16 @@ def animate(self, **kwargs):
         self.globe(R - 0.002, bcolor=bcolor)
         # 3D triangular mesh surface (like trisurf)
         grd = mlab.triangular_mesh(
-            px, py, pz, tri3, representation=rep, opacity=1.0, scalars=z[0, :], colormap=cmap, vmin=vmin, vmax=vmax
+            px,
+            py,
+            pz,
+            tri3,
+            representation=rep,
+            opacity=1.0,
+            scalars=z[0, :],
+            colormap=cmap,
+            vmin=vmin,
+            vmax=vmax,
         )
 
         grd.actor.mapper.scalar_visibility = True
@@ -228,7 +248,16 @@ def to_file(self, **kwargs):
         self.globe(R - 0.002, bcolor=bcolor)
         # 3D triangular mesh surface (like trisurf)
         grd = mlab.triangular_mesh(
-            px, py, pz, tri3, representation=rep, opacity=1.0, scalars=z[0, :], colormap=cmap, vmin=vmin, vmax=vmax
+            px,
+            py,
+            pz,
+            tri3,
+            representation=rep,
+            opacity=1.0,
+            scalars=z[0, :],
+            colormap=cmap,
+            vmin=vmin,
+            vmax=vmax,
         )
 
         grd.actor.mapper.scalar_visibility = True
@@ -311,13 +340,8 @@ def grid(self, **kwargs):
         R = kwargs.get("R", 1.0)
 
         if dim == "3D":
-
-            px = np.cos(y / 180 * np.pi) * np.cos(x / 180 * np.pi) * R
-            py = np.cos(y / 180 * np.pi) * np.sin(x / 180 * np.pi) * R
-            pz = np.sin(y / 180 * np.pi) * R
-
+            px, py, pz = to_3d(x, y, R=R)
         else:
-
             px = x
             py = y
             pz = np.zeros(x.shape[0])
@@ -335,10 +359,13 @@ def grid(self, **kwargs):
 
         if coast is not None:
             try:
-                del kwargs["coastlines", "R"]
+                del kwargs["coastlines"]
+            except:
+                pass
+            try:
+                del kwargs["R"]
             except:
                 pass
-
             src, lines = self.c3d(coast, R=R, **kwargs)
             mlab.pipeline.surface(src, color=(1, 0, 0), line_width=10, opacity=0.8)
 
@@ -346,8 +373,8 @@ def grid(self, **kwargs):
         scene = engine.scenes[0]
         scene.scene.z_plus_view()
 
-        mlab.show()
-        return
+        # mlab.show()
+        return view(actors=grd, rotate=True, ui_collapsed=True)
 
     @staticmethod
     def c3d(coastlines, R=1, **kwargs):
@@ -416,7 +443,14 @@ def c3d(coastlines, R=1, **kwargs):
             # of the final set of points once all lines have been combined
             # together, this is why we need to keep track of the total number of
             # points already created (index)
-            connections.append(np.vstack([np.arange(index, index + N - 1.5), np.arange(index + 1, index + N - 0.5)]).T)
+            connections.append(
+                np.vstack(
+                    [
+                        np.arange(index, index + N - 1.5),
+                        np.arange(index + 1, index + N - 0.5),
+                    ]
+                ).T
+            )
             index += N
 
         # Now collapse all positions, scalars and connections in big arrays
diff --git a/pyposeidon/utils/post.py b/pyposeidon/utils/post.py
new file mode 100644
index 00000000..37423d0e
--- /dev/null
+++ b/pyposeidon/utils/post.py
@@ -0,0 +1,108 @@
+import os
+import pandas as pd
+import xarray as xr
+import numpy as np
+
+import pyposeidon
+from pyposeidon.utils import data
+from pyposeidon.utils.vals import obs
+from pyposeidon.utils.statistics import get_stats
+
+import logging
+
+logger = logging.getLogger("pyposeidon")
+
+
+def to_thalassa(folders, freq=None, **kwargs):
+
+    # Retrieve data
+    tag = kwargs.get("tag", "schism")
+    rpath = kwargs.get("rpath", "./thalassa/")
+
+    if not os.path.exists(rpath):
+        os.makedirs(rpath)
+
+    # Get simulation data
+    c = []
+
+    for folder in folders:
+
+        b = pyposeidon.read(folder + "/{}_model.json".format(tag))
+        b.get_output_data()
+        st = b.data.time_series
+        b.data.Dataset.to_netcdf(rpath + "/{}.nc".format(b.start_date.strftime("%Y%m%d%H")))  # save netcdf
+
+        h = []
+        for l in range(freq):
+            from_date = b.start_date + pd.to_timedelta("{}H".format(l * 12)) + pd.to_timedelta("1S")
+            to_date = b.start_date + pd.to_timedelta("{}H".format((l + 1) * 12))
+            h.append(st.sel(time=slice(from_date, to_date), drop=True))
+
+        dr = xr.concat(h, dim="level")
+
+        c.append(dr)
+
+    cc = xr.concat(c, dim="time")
+
+    # Observation/Stats
+    logger.info("Retrieve observation data for station points\n")
+    odata = obs(**b.__dict__, sa_date=b.date, se_date=b.end_date)
+
+    logger.info("Compute general statistics for station points\n")
+    tgs = []
+    sts = []
+    for idx, val in odata.locations.iterrows():
+
+        obs_ = odata.iloc(idx)  # Get observational data
+
+        sim = st.isel(node=idx).elev.to_dataframe().drop("node", axis=1)
+
+        stable = get_stats(sim, obs_)  # Do general statitics
+
+        tgs.append(obs_.Surge)  # store
+        sts.append(stable)
+
+    logger.info("Construct station data output\n")
+    # Construct Thalassa file
+    stations = pd.DataFrame(b.stations)
+    stations = stations.reset_index(drop=True)
+    stations.index.name = "node"
+    stations["id"] = odata.locations.ID.values
+    stations["group"] = odata.locations.Group.values
+    stations["longitude"] = odata.locations.longitude.values
+    stations["latitude"] = odata.locations.latitude.values
+
+    sd = b.data.time_series.rename({"elev": "elevation"})
+
+    oo = pd.concat(tgs, keys=np.arange(len(tgs)), names=["node", "time"])
+    oo.name = "observation"
+
+    stats = pd.DataFrame(sts)
+    stats.index.name = "node"
+
+    cf = cc.rename({"elev": "forecast", "time": "ftime"})
+
+    vdata = xr.merge([oo.to_xarray(), stats.to_xarray(), stations.to_xarray(), sd, cf])
+
+    logger.info("Save station data output\n")
+    vdata.to_netcdf(rpath + "/fskill.nc")
+    logger.info("..done\n")
+
+
+def fskill(dset, var, node):
+
+    lstat = []
+
+    for l in dset.level.values:
+
+        obs_ = dset.sel(node=node).observation  # Get observational data
+        obs_ = obs_.to_dataframe().drop("node", axis=1)
+
+        sim = dset.isel(node=node).forecast.sel(level=l).to_dataframe().drop("node", axis=1)
+
+        stable = get_stats(sim, obs_)  # Do general statitics
+
+        lstat.append(stable[var])
+
+    # match values to scale
+    return lstat
diff --git a/pyposeidon/utils/pplot.py b/pyposeidon/utils/pplot.py
index b419ec8f..8ffaef81 100644
--- a/pyposeidon/utils/pplot.py
+++ b/pyposeidon/utils/pplot.py
@@ -16,6 +16,7 @@
 import cartopy.feature as cfeature
 import xarray as xr
 import geopandas as gp
+import pandas as pd
 import shapely
 from pyposeidon.utils.quads2tr import quads_to_tris
 
@@ -74,7 +75,15 @@ def contourf(self, x=None, y=None, z=None, tname="time", **kwargs):
         ax.set_aspect("equal")
         ims = []
         for i in range(len(t)):
-            im = ax.contourf(grid_x, grid_y, z_[i, :, :], vrange, vmin=vmin, vmax=vmax, transform=ccrs.PlateCarree())
+            im = ax.contourf(
+                grid_x,
+                grid_y,
+                z_[i, :, :],
+                vrange,
+                vmin=vmin,
+                vmax=vmax,
+                transform=ccrs.PlateCarree(),
+            )
             #        im = ax.contourf(x,y,z[i,:,:],v,vmin=v1,vmax=v2,latlon=True)
             add_arts = im.collections
             text = "time={}".format(t[i])
@@ -125,11 +134,21 @@ def quiver(self, x=None, y=None, z=None, tname="time", **kwargs):
         ax.set_aspect("equal")
 
         land_50m = cfeature.NaturalEarthFeature(
-            "physical", "land", "50m", edgecolor="face", facecolor=cfeature.COLORS["land"], zorder=0
+            "physical",
+            "land",
+            "50m",
+            edgecolor="face",
+            facecolor=cfeature.COLORS["land"],
+            zorder=0,
         )
 
         sea_50m = cfeature.NaturalEarthFeature(
-            "physical", "ocean", "50m", edgecolor="face", facecolor=cfeature.COLORS["water"], zorder=0
+            "physical",
+            "ocean",
+            "50m",
+            edgecolor="face",
+            facecolor=cfeature.COLORS["water"],
+            zorder=0,
         )
 
         title = kwargs.get("title", None)
@@ -163,25 +182,17 @@ def quiver(self, x=None, y=None, z=None, tname="time", **kwargs):
         # you need to set blit=False, or the first set of arrows never gets
         # cleared on subsequent frames
         v = animation.FuncAnimation(
-            fig, update_quiver, fargs=(Q, U, V, step), frames=range(0, np.size(t)), blit=False, repeat=False
+            fig,
+            update_quiver,
+            fargs=(Q, U, V, step),
+            frames=range(0, np.size(t)),
+            blit=False,
+            repeat=False,
         )  # , interval=1)
 
         return v
 
 
-def to_html5(fname, mimetype):
-    """Load the video in the file `fname`, with given mimetype, and display as HTML5 video."""
-    from IPython.display import HTML
-    import base64
-
-    video = open(fname, "rb").read()
-    video_encoded = base64.b64encode(video)
-    video_tag = '<video controls alt="test" src="data:video/{0};base64,{1}">'.format(
-        mimetype, video_encoded.decode("ascii")
-    )
-    return HTML(data=video_tag)
-
-
 def update_qframes(num, Q, U, V):
     """updates the horizontal and vertical vector components by a
     fixed increment on each frame
@@ -248,7 +259,21 @@ def contour(self, it=None, **kwargs):
             z = np.ma.masked_array(z, mask)
             z = z.filled(fill_value=-99999)
 
-        for val in ["x", "y", "t", "it", "vmin", "vmax", "title", "nv", "tes", "mask", "xy", "z", "var"]:
+        for val in [
+            "x",
+            "y",
+            "t",
+            "it",
+            "vmin",
+            "vmax",
+            "title",
+            "nv",
+            "tes",
+            "mask",
+            "xy",
+            "z",
+            "var",
+        ]:
             try:
                 del kwargs[val]
             except:
@@ -319,7 +344,22 @@ def contourf(self, it=None, **kwargs):
 
         xy = kwargs.get("xy", (0.3, 1.05))
 
-        for val in ["x", "y", "t", "it", "z", "vmin", "vmax", "title", "nv", "tes", "mask", "xy", "var", "figure"]:
+        for val in [
+            "x",
+            "y",
+            "t",
+            "it",
+            "z",
+            "vmin",
+            "vmax",
+            "title",
+            "nv",
+            "tes",
+            "mask",
+            "xy",
+            "var",
+            "figure",
+        ]:
             try:
                 del kwargs[val]
             except:
@@ -368,7 +408,21 @@ def quiver(self, it=None, u=None, v=None, title=None, scale=0.1, color="k", **kw
             v = v.filled(fill_value=-99999)
             u = u.filled(fill_value=-99999)
 
-        for val in ["x", "y", "t", "it", "u", "v", "title", "tes", "xy", "scale", "mask", "color", "var"]:
+        for val in [
+            "x",
+            "y",
+            "t",
+            "it",
+            "u",
+            "v",
+            "title",
+            "tes",
+            "xy",
+            "scale",
+            "mask",
+            "color",
+            "var",
+        ]:
             try:
                 del kwargs[val]
             except:
@@ -454,7 +508,17 @@ def qframes(self, u=None, v=None, scale=0.01, color="k", **kwargs):
 
         step = kwargs.get("step", 1)  # change accordingly to fit your needs
 
-        Q = ax.quiver(x, y, u[0, :], v[0, :], pivot="mid", color=color, angles="xy", scale_units="xy", scale=scale)
+        Q = ax.quiver(
+            x,
+            y,
+            u[0, :],
+            v[0, :],
+            pivot="mid",
+            color=color,
+            angles="xy",
+            scale_units="xy",
+            scale=scale,
+        )
 
         #        if cr is not None:
         #            try:
@@ -471,7 +535,12 @@ def qframes(self, u=None, v=None, scale=0.01, color="k", **kwargs):
         # you need to set blit=False, or the first set of arrows never gets
         # cleared on subsequent frames
         v = animation.FuncAnimation(
-            fig, update_qframes, fargs=(Q, u, v), blit=False, repeat=False, frames=range(0, np.size(t))
+            fig,
+            update_qframes,
+            fargs=(Q, u, v),
+            blit=False,
+            repeat=False,
+            frames=range(0, np.size(t)),
         )
 
         plt.close()
@@ -567,3 +636,58 @@ def frames(self, **kwargs):
         plt.close()
 
         return v
+
+
+# https://pandas.pydata.org/pandas-docs/stable/development/extending.html
+@pd.api.extensions.register_dataframe_accessor("geo")
+class GeoAccessor:
+    def __init__(self, geopandas_obj):
+        dic = {}
+        tag = 0
+        for l in range(geopandas_obj.shape[0]):
+            lon = []
+            lat = []
+            try:
+                contour = geopandas_obj.loc[l].geometry.boundary
+            except:
+                contour = geopandas_obj.loc[l].geometry
+
+            if contour.type == "LineString":
+                for x, y in contour.coords[:]:
+                    lon.append(x)
+                    lat.append(y)
+                dic.update({"line{}".format(tag): {"longitude": lon, "latitude": lat}})
+                tag += 1
+            elif contour.type == "MultiLineString":
+                for m in range(len(contour)):
+                    lon = []
+                    lat = []
+                    for x, y in contour[l].coords[:]:
+                        lon.append(x)
+                        lat.append(y)
+                    dic.update({"line{}".format(tag): {"longitude": lon, "latitude": lat}})
+                    tag += 1
+
+        dict_of_df = {k: pd.DataFrame(v) for k, v in dic.items()}
+        df = pd.concat(dict_of_df, axis=0)
+        df = df.drop_duplicates()  # drop the repeat value on closed boundaries
+        self._validate(df)
+        self._obj = df
+
+    @staticmethod
+    def _validate(obj):
+        # verify there is a column latitude and a column longitude
+        if "latitude" not in obj.columns or "longitude" not in obj.columns:
+            raise AttributeError("Must have 'latitude' and 'longitude'.")
+
+    @property
+    def center(self):
+        # return the geographic center point of this DataFrame
+        lat = self._obj.latitude
+        lon = self._obj.longitude
+        return (float(lon.mean()), float(lat.mean()))
+
+    def plot(self):
+        # plot this array's data on a map, e.g., using Cartopy
+        self._obj.plot.scatter(x="longitude", y="latitude")
+        pass
diff --git a/pyposeidon/utils/scale.py b/pyposeidon/utils/scale.py
index 48f9de3a..3ede6ead 100644
--- a/pyposeidon/utils/scale.py
+++ b/pyposeidon/utils/scale.py
@@ -4,7 +4,7 @@
 
 def scale_dem(b, res_min, res_max, **kwargs):
 
-    b.columns = ["z"]
+    #    b.columns = ["z"]
 
     b[b.z >= -10] = -1.0e-4  # normalize to only negative values
 
diff --git a/pyposeidon/utils/statistics.py b/pyposeidon/utils/statistics.py
index 0658cc34..4d626668 100755
--- a/pyposeidon/utils/statistics.py
+++ b/pyposeidon/utils/statistics.py
@@ -3,6 +3,9 @@
 import numpy as np
 import pandas as pd
 import warnings
+import logging
+
+logger = logging.getLogger("pyposeidon")
 
 
 def get_stats(sim_, obs_):
@@ -13,10 +16,26 @@ def get_stats(sim_, obs_):
         obs_ = obs_.loc[:end]
         sim_ = sim_.loc[:end]
         obs_ = obs_.reindex(sim_.index, method="nearest")  # sample on simulation times
+        return vtable(obs_.values, sim_.values)
     except:
-        pass
-
-    return vtable(obs_.values, sim_.values)
+        if obs_.dropna().empty:
+            logger.warning("Observation data not available for this station")
+            stats = pd.Series(
+                index={
+                    "Mean Absolute Error",
+                    "RMSE",
+                    "Scatter Index",
+                    "percentage RMSE",
+                    "BIAS or mean error",
+                    "Standard deviation of residuals",
+                    "Correlation Coefficient",
+                    "R^2",
+                    "Nash-Sutcliffe Coefficient",
+                    "lamda index",
+                },
+                dtype="float64",
+            )
+            return stats
 
 
 def vtable(obsrv, model):
diff --git a/pyposeidon/utils/vals.py b/pyposeidon/utils/vals.py
index 334aa99b..6e226ceb 100644
--- a/pyposeidon/utils/vals.py
+++ b/pyposeidon/utils/vals.py
@@ -196,7 +196,7 @@ def webcritech(self, **kwargs):
                         "Level-Tide m": np.nan,
                     },
                     index=[0],
-                )
+                ).set_index("TimeUTC")
             tg.index.name = "time"
             tg.columns = ["Total", "Tide", "Surge"]
             return tg


Test patch:
diff --git a/tests/test_d3d.py b/tests/test_d3d.py
index e6e099e8..a71121d1 100644
--- a/tests/test_d3d.py
+++ b/tests/test_d3d.py
@@ -4,8 +4,6 @@
 import os
 import multiprocessing
 
-NCORES = max(1, multiprocessing.cpu_count() - 1)
-
 from . import DATA_DIR
 
 # define in a dictionary the properties of the model..
@@ -17,7 +15,6 @@
     "resolution": 0.2,  # grid resoltuion
     "map_step": 20,  # step for output of map field in d3d
     "restart_step": 60,  # when to output restart file
-    "ncores": NCORES,  # number of cores
     "meteo_source": [(DATA_DIR / "uvp_2018100100.grib").as_posix()],
     "dem_source": (DATA_DIR / "dem.nc").as_posix(),
     #     'update':['all'] # optional to select update quantities
@@ -28,14 +25,14 @@ def d3d(tmpdir, dic):
     # initialize a model
     rpath = str(tmpdir) + "/"
     dic.update({"rpath": rpath})  # use tmpdir for running the model
-    b = pyposeidon.model(**dic)
+    b = pyposeidon.model.set(**dic)
 
     try:
         b.execute()
-        out = data.data(**dic)
-        a = pyposeidon.read_model(rpath + "d3d_model.json")  # read model
+        out = data.get_output(**dic)
+        a = pyposeidon.read(rpath + "d3d_model.json")  # read model
         a.execute()
-        out = data.data(**dic)
+        out = data.get_output(**dic)
         return True
     except:
         return False
diff --git a/tests/test_d3d_cast.py b/tests/test_d3d_cast.py
index ef05dc32..6c359ba0 100644
--- a/tests/test_d3d_cast.py
+++ b/tests/test_d3d_cast.py
@@ -8,8 +8,6 @@
 import numpy as np
 import multiprocessing
 
-NCORES = max(1, multiprocessing.cpu_count() - 1)
-
 from . import DATA_DIR
 
 GRIB_FILES_1 = [(DATA_DIR / filename).as_posix() for filename in ("uvp_2018100100.grib", "uvp_2018100112.grib")]
@@ -33,7 +31,6 @@
     "resolution": 0.1,  # grid resoltuion
     "map_step": 60,  # step for output of map field in d3d
     "restart_step": 720,  # when to output restart file
-    "ncores": NCORES,  # number of cores
     "meteo_source": GRIB_FILES_1,
     "meteo_merge": "last",  # combine meteo
     "meteo_combine_by": "nested",
@@ -50,7 +47,6 @@
     "resolution": 0.1,  # grid resoltuion
     "map_step": 60,  # step for output of map field in d3d
     "restart_step": 720,  # when to output restart file
-    "ncores": NCORES,  # number of cores
     "dem_source": DEM_FILE,
     "meteo_source": GRIB_FILES_2,
     "meteo_merge": "last",  # combine meteo
@@ -64,7 +60,7 @@ def d3d(tmpdir):
     # initialize a model
     rpath = str(tmpdir) + "/d3d/"
     case.update({"rpath": rpath + "/20181001.00/"})  # use tmpdir for running the model
-    b = pyposeidon.model(**case)
+    b = pyposeidon.model.set(**case)
 
     b.execute()
 
@@ -89,7 +85,7 @@ def d3d(tmpdir):
 
     # set cast
     for l in range(len(rpaths) - 1):
-        h = cast.cast(
+        h = cast.set(
             solver="d3d",
             model=b,
             ppath=rpaths[l],
@@ -97,16 +93,16 @@ def d3d(tmpdir):
             meteo=meteo[l + 1],
             date=date_list[l + 1],
         )
-        h.set(execute=True)  # execute
+        h.run(execute=True)  # execute
 
     # Run check case - Total duration
     check.update({"rpath": rpath + "check/"})  # use tmpdir for running the model
-    c = pyposeidon.model(**check)
+    c = pyposeidon.model.set(**check)
     c.execute()
 
     # COMPARE
-    output = data.data(folders=rpaths, solver="d3d")
-    total = data.data(folders=[rpath + "check/"], solver="d3d")
+    output = data.get_output(folders=rpaths, solver="d3d")
+    total = data.get_output(folders=[rpath + "check/"], solver="d3d")
 
     test = True
     rb = []
diff --git a/tests/test_dem_fix.py b/tests/test_dem_fix.py
index 27c54745..d03fbe37 100644
--- a/tests/test_dem_fix.py
+++ b/tests/test_dem_fix.py
@@ -47,7 +47,13 @@ def test_dem_adjust(natural_earth, dem_source, window):
 @DEM_SOURCES
 @WINDOWS
 def test_schism_grid(tmpdir, natural_earth, dem_source, window):
-    grid = pg.grid(type="tri2d", geometry=window, coastlines=natural_earth, rpath=str(tmpdir) + "/")
+    grid = pg.grid(
+        type="tri2d",
+        geometry=window,
+        coastlines=natural_earth,
+        grid_generator="jigsaw",
+        rpath=str(tmpdir) + "/",
+    )
     xg = grid.Dataset.SCHISM_hgrid_node_x.values
     yg = grid.Dataset.SCHISM_hgrid_node_y.values
     df = pdem.dem(**window, grid_x=xg, grid_y=yg, dem_source=dem_source)  # get dem
@@ -62,7 +68,7 @@ def test_schism_grid(tmpdir, natural_earth, dem_source, window):
 def test_d3d_grid(tmpdir, natural_earth, dem_source, window):
     grid = pg.grid(type="r2d", geometry=window, resolution=0.1, rpath=str(tmpdir) + "/")
     gr = grid.Dataset
-    xp, yp = gr.lons, gr.lats
+    xp, yp = gr.lons.values, gr.lats.values
     df = pdem.dem(**window, grid_x=xp, grid_y=yp, dem_source=dem_source)
     df.adjust(natural_earth)
     assert np.isnan(df.Dataset.fval.values).sum() == 0
diff --git a/tests/test_dem_io.py b/tests/test_dem_io.py
index 936f43fc..95eb41d0 100644
--- a/tests/test_dem_io.py
+++ b/tests/test_dem_io.py
@@ -74,7 +74,7 @@ def d3d(tmpdir, dem_source, kwargs):
     pdem.to_output(df.Dataset, solver="d3d", rpath=rpath)
 
     # read again dem
-    m = pmodel(solver="d3d")
+    m = pmodel.set(solver="d3d")
     rd = m.from_dep(rpath + "d3d.dep")
 
     # compare
diff --git a/tests/test_meteo_grib.py b/tests/test_meteo_grib.py
index a5bca366..2c1a18af 100644
--- a/tests/test_meteo_grib.py
+++ b/tests/test_meteo_grib.py
@@ -45,7 +45,7 @@ def d3d(tmpdir, name):
     df.to_output(solver="d3d", rpath=rpath)
 
     # read again meteo
-    m = pmodel(solver="d3d")
+    m = pmodel.set(solver="d3d")
 
     p = m.from_force(rpath + "p.amp", "msl")
     u = m.from_force(rpath + "u.amu", "u10")
diff --git a/tests/test_schism.py b/tests/test_schism.py
index 87c888e3..2af81b05 100644
--- a/tests/test_schism.py
+++ b/tests/test_schism.py
@@ -3,8 +3,6 @@
 import os
 import multiprocessing
 
-NCORES = max(1, multiprocessing.cpu_count() - 1)
-
 from . import DATA_DIR
 
 
@@ -22,7 +20,6 @@
     "time_frame": "12H",
     "meteo_source": [(DATA_DIR / "erai.grib").as_posix()],  # meteo file
     "dem_source": DEM_FILE,
-    "ncores": NCORES,  # number of cores
     "update": ["all"],  # update only meteo, keep dem
     "parameters": {
         "dt": 400,
@@ -45,7 +42,6 @@
     "end_date": "2017-10-2 0:0:0",  # optional instead of time_frame
     "dem_source": DEM_FILE,
     "meteo_source": [(DATA_DIR / "erai.grib").as_posix()],  # meteo file
-    "ncores": NCORES,  # number of cores
     "update": ["all"],  # update only meteo, keep dem
     "parameters": {
         "dt": 400,
@@ -69,7 +65,6 @@
     "time_frame": "12H",
     "meteo_source": [(DATA_DIR / "era5.grib").as_posix()],  # meteo file
     "dem_source": DEM_FILE,
-    "ncores": NCORES,  # number of cores
     "update": ["all"],  # update only meteo, keep dem
     "parameters": {
         "dt": 400,
@@ -88,16 +83,18 @@ def schism(tmpdir, dic):
     rpath = str(tmpdir) + "/"
     dic.update({"rpath": rpath})  # use tmpdir for running the model
 
-    b = pyposeidon.model(**dic)
+    b = pyposeidon.model.set(**dic)
 
-    try:
-        b.execute()
-        b.results()
-        a = pyposeidon.read_model(rpath + "test_model.json")  # read model
+    b.execute()
+    b.results()
+    err_file = b.rpath + "/outputs/fatal.error"
+    if os.stat(err_file).st_size == 0:
+        a = pyposeidon.model.read(rpath + "test_model.json")  # read model
         a.execute()
         a.results()
-        return True
-    except:
+        err_file = a.rpath + "/outputs/fatal.error"
+        return os.stat(err_file).st_size == 0
+    else:
         return False
 
 
diff --git a/tests/test_schism_cast.py b/tests/test_schism_cast.py
index eaafbd44..881a2f23 100644
--- a/tests/test_schism_cast.py
+++ b/tests/test_schism_cast.py
@@ -6,9 +6,6 @@
 import datetime
 import os
 import numpy as np
-import multiprocessing
-
-NCORES = max(1, multiprocessing.cpu_count() - 1)
 
 from . import DATA_DIR
 
@@ -41,7 +38,6 @@
     "meteo_merge": "last",  # combine meteo
     "meteo_combine_by": "nested",
     "meteo_xr_kwargs": {"concat_dim": "step"},
-    "ncores": NCORES,  # number of cores
     "update": ["all"],  # update only meteo, keep dem
     "parameters": {
         "dt": 400,
@@ -68,7 +64,6 @@
     "meteo_merge": "last",  # combine meteo
     "meteo_combine_by": "nested",
     "meteo_xr_kwargs": {"concat_dim": "step"},
-    "ncores": NCORES,  # number of cores
     "update": ["all"],  # update only meteo, keep dem
     "parameters": {
         "dt": 400,
@@ -87,7 +82,7 @@ def schism(tmpdir):
     rpath = str(tmpdir) + "/schism/"
     case.update({"rpath": rpath + "20181001.00/"})  # use tmpdir for running the model
 
-    b = pyposeidon.model(**case)
+    b = pyposeidon.model.set(**case)
 
     b.execute()
 
@@ -112,27 +107,28 @@ def schism(tmpdir):
 
     # set cast
     for l in range(len(rpaths) - 1):
-        h = cast.cast(
+        h = cast.set(
             solver="schism",
             model=b,
             ppath=rpaths[l],
             cpath=rpaths[l + 1],
             meteo=meteo[l + 1],
-            date=date_list[l + 1],
+            sdate=date_list[l + 1],
         )
-        h.set(execute=True)  # execute
+
+        h.run(execute=True)  # execute
 
     # Run check case - Total duration
     check.update({"rpath": rpath + "check/"})  # use tmpdir for running the model
 
-    c = pyposeidon.model(**check)
+    c = pyposeidon.model.set(**check)
 
     c.execute()
 
     # COMPARE
-    output = data.data(folders=rpaths, solver="schism")
+    output = data.get_output(folders=rpaths, solver="schism")
 
-    total = data.data(folders=[rpath + "check/"], solver="schism")
+    total = data.get_output(folders=[rpath + "check/"], solver="schism")
 
     rb = []
     for var in total.Dataset.data_vars:
diff --git a/tests/test_schism_reforecast.py b/tests/test_schism_reforecast.py
index 0609eaa8..15a3d5d0 100644
--- a/tests/test_schism_reforecast.py
+++ b/tests/test_schism_reforecast.py
@@ -8,9 +8,6 @@
 import os
 import numpy as np
 import xarray as xr
-import multiprocessing
-
-NCORES = max(1, multiprocessing.cpu_count() - 1)
 
 from . import DATA_DIR
 
@@ -43,7 +40,6 @@
     "meteo_merge": "first",  # combine meteo
     "meteo_combine_by": "nested",
     "meteo_xr_kwargs": {"concat_dim": "step"},
-    "ncores": NCORES,  # number of cores
     "update": ["all"],  # update only meteo, keep dem
     "parameters": {
         "dt": 400,
@@ -67,7 +63,6 @@
     "start_date": "2018-10-1 0:0:0",
     "time_frame": "36H",
     "dem_source": DEM_FILE,
-    "ncores": NCORES,  # number of cores
     "update": ["all"],  # update only meteo, keep dem
     "parameters": {
         "dt": 400,
@@ -86,7 +81,7 @@ def schism(tmpdir):
     rpath = str(tmpdir) + "/schism/"
     case.update({"rpath": rpath + "20181001.00/"})  # use tmpdir for running the model
 
-    b = pyposeidon.model(**case)
+    b = pyposeidon.model.set(**case)
 
     b.execute()
 
@@ -111,15 +106,15 @@ def schism(tmpdir):
 
     # set cast
     for l in range(len(rpaths) - 1):
-        h = cast.cast(
+        h = cast.set(
             solver="schism",
             model=b,
             ppath=rpaths[l],
             cpath=rpaths[l + 1],
             meteo=meteo[l + 1],
-            date=date_list[l + 1],
+            sdate=date_list[l + 1],
         )
-        h.set(execute=True)  # execute
+        h.run(execute=True)  # execute
 
     # Run check case - Total duration
     check.update({"rpath": rpath + "check/"})  # use tmpdir for running the model
@@ -143,14 +138,14 @@ def schism(tmpdir):
     # saving
     check.update({"meteo_source": meteo})
 
-    c = pyposeidon.model(**check)
+    c = pyposeidon.model.set(**check)
 
     c.execute()
 
     # COMPARE
-    output = data.data(folders=rpaths, solver="schism")
+    output = data.get_output(folders=rpaths, solver="schism")
 
-    total = data.data(folders=[rpath + "check/"], solver="schism")
+    total = data.get_output(folders=[rpath + "check/"], solver="schism")
 
     r = output.Dataset.isel(time=slice(0, 36))
 
diff --git a/tests/test_schism_total.py b/tests/test_schism_total.py
index e3e24213..daa69a18 100644
--- a/tests/test_schism_total.py
+++ b/tests/test_schism_total.py
@@ -3,8 +3,6 @@
 import os
 import multiprocessing
 
-NCORES = max(1, multiprocessing.cpu_count() - 1)
-
 from . import DATA_DIR
 
 DEM_FILE = DATA_DIR / "dem.nc"
@@ -30,7 +28,9 @@
 case4 = {"lon_min": -25.0, "lon_max": -10.0, "lat_min": 60.0, "lat_max": 68.0}
 
 
-def schism(tmpdir, case):
+@pytest.mark.schism
+@pytest.mark.parametrize("case", [case0, case2])  # , case1, case3])
+def test_schism(tmpdir, case):
     # initialize a model
     dic = {
         "solver": "schism",
@@ -40,9 +40,9 @@ def schism(tmpdir, case):
         "tag": "test",
         "start_date": "2017-10-1 0:0:0",
         "time_frame": "12H",
+        "grid_generator": "jigsaw",
         "meteo_source": [DATA_DIR / "erai.grib"],  # meteo file
         "dem_source": DEM_FILE,
-        "ncores": NCORES,  # number of cores
         "update": ["all"],  # update only meteo, keep dem
         "parameters": {
             "dt": 400,
@@ -58,17 +58,10 @@ def schism(tmpdir, case):
     rpath = str(tmpdir) + "/"
     dic.update({"rpath": rpath})  # use tmpdir for running the model
 
-    b = pyposeidon.model(**dic)
+    b = pyposeidon.model.set(**dic)
 
-    try:
-        b.execute()
-        b.results()
-        return True
-    except:
-        return False
+    b.execute()
+    b.results()
 
-
-@pytest.mark.schism
-@pytest.mark.parametrize("case", [case0, case2])  # , case1, case3])
-def test_answer(tmpdir, case):
-    assert schism(tmpdir, case) == True
+    err_file = b.rpath + "/outputs/fatal.error"
+    assert os.stat(err_file).st_size == 0