From ccd51d40ed6630f7fdc064812c0d2ae1e13c8958 Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Tue, 18 Apr 2023 12:20:07 +0200
Subject: [PATCH 01/14] allow direct input of

---
 ldndctools/cli/selector.py | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/ldndctools/cli/selector.py b/ldndctools/cli/selector.py
index 4d125b0..61c31d4 100644
--- a/ldndctools/cli/selector.py
+++ b/ldndctools/cli/selector.py
@@ -220,14 +220,18 @@ def ask(self):
 
 
 class CoordinateSelection:
-    def __init__(self, infile, lon_col="lon", lat_col="lat", id_col="ID"):
-        df = pd.read_csv(infile, delim_whitespace=True)
-
-        self.lons = df[lon_col].values
-        self.lats = df[lat_col].values
-        self.ids = (
-            df[id_col].values if id_col in list(df.columns) else range(len(self.lats))
-        )
+    
+    def __init__(self, infile=None, lon="lon", lat="lat", cid="ID"):
+        if infile:
+            df = pd.read_csv(infile, delim_whitespace=True)
+
+            self.lons = df[lon].values
+            self.lats = df[lat].values
+            self.ids  = df[cid].values if cid in list(df.columns) else range(len(self.lats))
+        else:
+            self.lons = [lon]
+            self.lats = [lat]
+            self.ids  = [cid]
 
     @property
     def selected(self):

From 18f618d1b206fa07412aca24b535ec7b35eb3d96 Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Tue, 18 Apr 2023 12:25:19 +0200
Subject: [PATCH 02/14] add arguments to main function

---
 ldndctools/dlsc.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/ldndctools/dlsc.py b/ldndctools/dlsc.py
index d300c3c..27624c8 100755
--- a/ldndctools/dlsc.py
+++ b/ldndctools/dlsc.py
@@ -41,12 +41,17 @@
     DPATH = Path(dpath)
 
 
-def main():
+def main( **kwargs):
     # parse args
     args = cli()
 
     # read config
-    cfg = get_config(args.config)
+    if 'config' in kwargs:
+        cfg = kwargs['config']
+        for k,v in cfg.items():
+            setattr(args, k, v)
+    else:
+        cfg = get_config(args.config)
 
     # write config
     if args.storeconfig:
@@ -81,7 +86,10 @@ def main():
 
     bbox = None
     if args.bbox:
-        x1, y1, x2, y2 = [float(x) for x in args.bbox.split(",")]
+        if type( args.bbox) == list:
+            x1, y1, x2, y2 = args.bbox
+        else: 
+            x1, y1, x2, y2 = [float(x) for x in args.bbox.split(",")]
         try:
             bbox = BoundingBox(x1=x1, y1=y1, x2=x2, y2=y2)
         except ValidationError:

From 975242289f18d46ecbc7a5f18a1dff2bfff8f065 Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Tue, 18 Apr 2023 12:26:37 +0200
Subject: [PATCH 03/14] change log message

---
 ldndctools/extra.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ldndctools/extra.py b/ldndctools/extra.py
index 64c176a..cfba563 100644
--- a/ldndctools/extra.py
+++ b/ldndctools/extra.py
@@ -91,7 +91,7 @@ def cfgfile_exists(cfgFile):
         cfgFile = _find_config()
 
         if not cfgfile_exists(cfgFile):
-            log.info("Copying config file")
+            log.info("Copying default config file")
             _copy_default_config()
             cfgFile = _find_config()
 

From 3b9350c967712f53f36d15410a0f160db210eee2 Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Tue, 18 Apr 2023 12:29:19 +0200
Subject: [PATCH 04/14] allow d selection

---
 ldndctools/io/xmlwriter.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/ldndctools/io/xmlwriter.py b/ldndctools/io/xmlwriter.py
index f0bc6ca..f67b2bf 100644
--- a/ldndctools/io/xmlwriter.py
+++ b/ldndctools/io/xmlwriter.py
@@ -71,9 +71,9 @@ def write(
         if status_widget:
             status_widget.warning("Preparing data")
 
-        if not all(v is None for v in [sample, id_selection, coords]):
-            # options currently not implemented
-            raise NotImplementedError
+        #if not all(v is None for v in [sample, id_selection, coords]):
+        #    # options currently not implemented
+        #    raise NotImplementedError
 
         ids: xr.DataArray = xr.zeros_like(self.mask, dtype=np.int32)
 
@@ -91,7 +91,10 @@ def write(
                         lat=self.soil.coords["lat"][j].values.item(),
                         lon=self.soil.coords["lon"][i].values.item(),
                     )
-                # print(cid)
+                if id_selection:
+                    if cid not in id_selection:
+                        continue
+
                 ids[j, i] = cid
                 Lcids.append(cid)
                 Lix.append(i)

From 288099ef712e51d2eae5430a311271517749fee3 Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Tue, 18 Apr 2023 14:09:06 +0200
Subject: [PATCH 05/14] create bounding box from lat/lon pair

---
 ldndctools/dlsc.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/ldndctools/dlsc.py b/ldndctools/dlsc.py
index 27624c8..fc62101 100755
--- a/ldndctools/dlsc.py
+++ b/ldndctools/dlsc.py
@@ -85,6 +85,10 @@ def main( **kwargs):
     res = RES[args.resolution]
 
     bbox = None
+
+    if ('lat' in args) and ('lon' in args):
+       setattr(args, 'bbox', [float(args.lon-0.5), float(args.lat-0.5), float(args.lon+0.5), float(args.lat+0.5)]) 
+       log.info("Creating bounding box for coordinates specified.")
     if args.bbox:
         if type( args.bbox) == list:
             x1, y1, x2, y2 = args.bbox
@@ -93,9 +97,9 @@ def main( **kwargs):
         try:
             bbox = BoundingBox(x1=x1, y1=y1, x2=x2, y2=y2)
         except ValidationError:
-            print("Ilegal bounding box coordinates specified.")
-            print("required: x1,y1,x2,y2 [cond: x1<x2, y1<y2]")
-            print(f"given:    x1={x1},y1={y1},x2={x2},y2={y2}")
+            log.info("Ilegal bounding box coordinates specified.")
+            log.info("required: x1,y1,x2,y2 [cond: x1<x2, y1<y2]")
+            log.info(f"given:    x1={x1},y1={y1},x2={x2},y2={y2}")
             exit(1)
 
     if not args.outfile:

From c3754664c42074f1b7fe16bf74639502fd95bad4 Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Tue, 18 Apr 2023 14:38:40 +0200
Subject: [PATCH 06/14] create site input for slected coordinate only

---
 ldndctools/dlsc.py             |  2 +-
 ldndctools/misc/create_data.py | 17 ++++++++++++++---
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/ldndctools/dlsc.py b/ldndctools/dlsc.py
index fc62101..e9bf634 100755
--- a/ldndctools/dlsc.py
+++ b/ldndctools/dlsc.py
@@ -156,7 +156,7 @@ def main( **kwargs):
     log.info(selector.selected)
 
     with tqdm(total=1) as progressbar:
-        xml, nc = create_dataset(soil, selector, res, progressbar)
+        xml, nc = create_dataset(soil, selector, res, args, progressbar)
 
     open(cfg["outname"], "w").write(xml)
     ENCODING = {
diff --git a/ldndctools/misc/create_data.py b/ldndctools/misc/create_data.py
index 98d6dc2..3aaf10d 100644
--- a/ldndctools/misc/create_data.py
+++ b/ldndctools/misc/create_data.py
@@ -1,19 +1,25 @@
 from typing import Any, Optional, Union
 
+import logging
 import numpy as np
 import rioxarray  # noqa
 import xarray as xr
 
+from ldndctools.misc.geohash import coords2geohash_dec
 from ldndctools.cli.selector import CoordinateSelection, Selector
 from ldndctools.io.xmlwriter import SiteXmlWriter
 from ldndctools.misc.types import RES
 from ldndctools.sources.soil.soil_base import SoilDataset
 
+log = logging.getLogger(__name__)
+
+log.setLevel("DEBUG")
 
 def create_dataset(
     soil: SoilDataset,
     selector: Union[Selector, CoordinateSelection],
     res: RES,
+    args,
     progressbar: Optional[Any] = None,
     status_widget: Optional[Any] = None,
 ):
@@ -21,9 +27,9 @@ def create_dataset(
     # soil = soil.rio.write_crs(4326)
 
     if isinstance(selector, Selector):
-        print("Using Selector")
+        log.info("Using Selector")
         if selector.gdf_mask is None:
-            print("No valid data to process for this region/ bbox request.")
+            log.info("No valid data to process for this region/ bbox request.")
             exit(1)
 
         # clip region selection
@@ -36,7 +42,12 @@ def create_dataset(
         soil.clip_mask(selector.gdf_mask.geometry, all_touched=True)
 
         xmlwriter = SiteXmlWriter(soil, res=res)
-        site_xml = xmlwriter.write(progressbar=progressbar, status_widget=status_widget)
+        if ('lat' in args) and ('lon' in args):
+            sel = soil._soil.sel(lat=args.lat, lon=args.lon, method='nearest')
+            cid = coords2geohash_dec( lat=sel["lat"].values.item(), lon=sel["lon"].values.item())
+            site_xml = xmlwriter.write(progressbar=progressbar, status_widget=status_widget, id_selection=[cid])
+        else:
+            site_xml = xmlwriter.write(progressbar=progressbar, status_widget=status_widget)
 
     else:
         # WARNING: THIS BRANCH IS DEFUNCT!!!

From a86fdf084f031ba65f734f3f802869507784482a Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Wed, 19 Apr 2023 13:08:06 +0200
Subject: [PATCH 07/14] update requirements

---
 requirements.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 96988a1..d5071bd 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,10 +2,10 @@ aiohttp >= 3.8.1
 boto3 >= 1.20.49
 dask[distributed] >= 2022.2.0
 geopandas >= 0.10.2
-git+https://github.com/rasterio/rasterio.git
+rasterio
 #cython >= 0.29.22
 #cytoolz >= 0.11.2
-git+https://github.com/Toblerity/Fiona.git  # required for 3.10 compat
+fiona
 intake >= 0.6.5
 intake-geopandas >= 0.4.0
 intake-xarray >= 0.6.0

From a7642725023eafcef3f9b845646f63c8b90a427d Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Wed, 19 Apr 2023 15:44:17 +0200
Subject: [PATCH 08/14] change log level to info

---
 ldndctools/dlsc.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/ldndctools/dlsc.py b/ldndctools/dlsc.py
index e9bf634..f8f4198 100755
--- a/ldndctools/dlsc.py
+++ b/ldndctools/dlsc.py
@@ -30,8 +30,7 @@
 from ldndctools.sources.soil.soil_iscricwise import ISRICWISE_SoilDataset
 
 log = logging.getLogger(__name__)
-
-log.setLevel("DEBUG")
+log.setLevel("INFO")
 
 NODATA = "-99.99"
 

From 3fbfd3f30051417132b0f07af864fd4bcdfea166 Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Thu, 20 Apr 2023 14:05:09 +0200
Subject: [PATCH 09/14] continue testing if Pytest coverage comment fails

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 70c9793..556717f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -52,6 +52,7 @@ jobs:
           pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=ldndctools tests/ | tee pytest-coverage.txt
 
     - name: Pytest coverage comment
+      continue-on-error: true
       uses: MishaKav/pytest-coverage-comment@main
       if: ${{ matrix.python-version == '3.10' }}
       with:

From 83c5fe3ed3352de6d59c10f00eff9013a03fddf6 Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Fri, 9 Feb 2024 11:40:05 +0100
Subject: [PATCH 10/14] allow dask for lazy data

---
 ldndctools/cdgen.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ldndctools/cdgen.py b/ldndctools/cdgen.py
index f9e8430..7dbe92e 100644
--- a/ldndctools/cdgen.py
+++ b/ldndctools/cdgen.py
@@ -161,7 +161,7 @@ def inner_func(x, lat, lon):
 def geohash_xr(mask: xr.DataArray) -> xr.DataArray:
     lon_xr = mask.lon.broadcast_like(mask)
     lat_xr = mask.lat.broadcast_like(mask)
-    data = xr.apply_ufunc(inner_func, mask, lat_xr, lon_xr, output_dtypes=[np.int64])
+    data = xr.apply_ufunc(inner_func, mask, lat_xr, lon_xr, output_dtypes=[np.int64], dask="allowed")
     assert data.dtype == np.int64
     return data
 

From cc0d2e3e5df9b6c2dd6c67d1dcfa157b3b3236eb Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Fri, 9 Feb 2024 11:40:48 +0100
Subject: [PATCH 11/14] replace root_validator by model_validator

---
 ldndctools/misc/types.py | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/ldndctools/misc/types.py b/ldndctools/misc/types.py
index ced5896..74a290e 100644
--- a/ldndctools/misc/types.py
+++ b/ldndctools/misc/types.py
@@ -2,7 +2,7 @@
 from enum import Enum
 from typing import Optional
 
-from pydantic import BaseModel, confloat, conint, root_validator, ValidationError
+from pydantic import BaseModel, confloat, conint, model_validator, ValidationError
 from pydantic.dataclasses import dataclass
 from pydantic.json import pydantic_encoder
 
@@ -40,17 +40,15 @@ class BoundingBox:
     y1: confloat(ge=-90, le=90) = -90
     y2: confloat(ge=-90, le=90) = 90
 
-    @root_validator(allow_reuse=True)
+    @model_validator(mode='after')
     def check_x1_smaller_x2(cls, values):
-        x1, x2 = values.get("x1"), values.get("x2")
-        if x1 >= x2:
+        if values.x1 >= values.x2:
             raise ValidationError("x1 must be smaller x2")
         return values
 
-    @root_validator(allow_reuse=True)
+    @model_validator(mode='after')
     def check_y1_smaller_y2(cls, values):
-        y1, y2 = values.get("y1"), values.get("y2")
-        if y1 >= y2:
+        if values.y1 >= values.y2:
             raise ValidationError("y1 must be smaller y2")
         return values
 
@@ -97,7 +95,7 @@ class LayerData(BaseModel):
     class Config:
         validate_assignment = True
 
-    # @root_validator
+    # @model_validator
     # def check_wcmin_smaller_wcmax(cls, values):
     #     wcmin, wcmax = values.get("wcmin"), values.get("wcmax")
     #     if None not in [wcmin, wcmax]:
@@ -105,7 +103,7 @@ class Config:
     #             raise ValidationError("wcmin must be smaller wcmax")
     #     return values
 
-    @root_validator(allow_reuse=True)
+    #@model_validator(mode='after')
     def check_texture_is_plausible(cls, values):
         sand, silt, clay = values.get("sand"), values.get("silt"), values.get("clay")
         args = [a for a in [sand, silt, clay] if a is not None]

From 792a9fb8e8d677c772920fbc1b09c60415bed850 Mon Sep 17 00:00:00 2001
From: David Kraus <david.kraus@kit.edu>
Date: Fri, 9 Feb 2024 11:43:24 +0100
Subject: [PATCH 12/14] update catalog: port, ignore metadata

---
 data/catalog.yml               | 13 +++++++------
 ldndctools/misc/create_data.py |  2 +-
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/data/catalog.yml b/data/catalog.yml
index fab0c3d..f729ce0 100644
--- a/data/catalog.yml
+++ b/data/catalog.yml
@@ -21,7 +21,8 @@ sources:
           anon: true
           default_fill_cache: false
           client_kwargs:
-            endpoint_url: 'https://s3.imk-ifu.kit.edu:8082'
+            endpoint_url: 'https://s3.imk-ifu.kit.edu:10443'
+            verify: False
         simplecache:
           cache_storage: '.cache'
           same_names: true
@@ -63,7 +64,7 @@ sources:
           anon: true
           default_fill_cache: false
           client_kwargs:
-            endpoint_url: 'https://s3.imk-ifu.kit.edu:8082'
+            endpoint_url: 'https://s3.imk-ifu.kit.edu:10443'
         simplecache:
           cache_storage: '.cache'
           same_names: true
@@ -73,12 +74,12 @@ sources:
     driver: zarr
     args:
       urlpath: 's3://era5land-zarr/data.zarr'
-      consolidated: True
+      consolidated: False
       storage_options:
-        use_ssl: False
+        use_ssl: True
         anon: True
         client_kwargs:
-          endpoint_url: 'https://s3.imk-ifu.kit.edu:8082'
+          endpoint_url: 'https://s3.imk-ifu.kit.edu:10443'
           verify: False
 
 
@@ -100,7 +101,7 @@ sources:
           anon: true
           default_fill_cache: false
           client_kwargs:
-            endpoint_url: 'https://s3.imk-ifu.kit.edu:8082'
+            endpoint_url: 'https://s3.imk-ifu.kit.edu:10443'
         simplecache:
           cache_storage: '.cache'
           same_names: true
diff --git a/ldndctools/misc/create_data.py b/ldndctools/misc/create_data.py
index 3aaf10d..780644a 100644
--- a/ldndctools/misc/create_data.py
+++ b/ldndctools/misc/create_data.py
@@ -22,7 +22,7 @@ def create_dataset(
     args,
     progressbar: Optional[Any] = None,
     status_widget: Optional[Any] = None,
-):
+    ):
     # soil = soil.load()
     # soil = soil.rio.write_crs(4326)
 

From 92f573f395fb29d6b50e0f3421f53a33b8d1c72d Mon Sep 17 00:00:00 2001
From: Kraus <kraus-d@GAP-L282A1.local>
Date: Thu, 22 May 2025 11:30:02 +0200
Subject: [PATCH 13/14] add examples

---
 data/catalog.yml                     | 29 ++++++++-
 data/ldndctools.conf                 |  4 +-
 examples/examples.conf               | 26 ++++++++
 examples/readme.txt                  |  2 +
 ldndctools/cdgen.py                  | 30 ++++++++-
 ldndctools/cli/cli.py                |  2 +-
 ldndctools/dlsc.py                   | 97 ++++++++++++++++------------
 ldndctools/misc/create_data.py       | 17 ++++-
 ldndctools/misc/types.py             |  2 +-
 ldndctools/sources/soil/soil_base.py |  8 +--
 10 files changed, 159 insertions(+), 58 deletions(-)
 create mode 100644 examples/examples.conf
 create mode 100644 examples/readme.txt

diff --git a/data/catalog.yml b/data/catalog.yml
index f729ce0..c7a0654 100644
--- a/data/catalog.yml
+++ b/data/catalog.yml
@@ -4,6 +4,30 @@ plugins:
     - module: intake_geopandas
 
 sources:
+
+  soil_national:
+    name: 'SOIL national'
+    description: 'Default soil data for ldndctools (site file generation)'
+    driver: netcdf
+    parameters:
+      res:
+        default: 'LR'
+        allowed: ['LR', 'MR', 'HR']
+        description: 'Resolution (LR, MR or HR).'
+        type: str
+    args:
+      urlpath: 'simplecache::s3://ldndcdata/GLOBAL_WISESOIL_S1_{{res}}.nc'
+      storage_options:
+        s3:
+          anon: true
+          default_fill_cache: false
+          client_kwargs:
+            endpoint_url: 'https://s3.imk-ifu.kit.edu:{{port}}'
+            verify: False
+        simplecache:
+          cache_storage: '.cache'
+          same_names: true
+
   soil:
     name: 'SOIL'
     description: 'Default soil data for ldndctools (site file generation)'
@@ -21,7 +45,7 @@ sources:
           anon: true
           default_fill_cache: false
           client_kwargs:
-            endpoint_url: 'https://s3.imk-ifu.kit.edu:10443'
+            endpoint_url: 'https://s3.imk-ifu.kit.edu:{{port}}'
             verify: False
         simplecache:
           cache_storage: '.cache'
@@ -40,7 +64,7 @@ sources:
         description: 'Resolution (10, 50 or 110m).'
         type: int
     args:
-      urlpath: 'simplecache::https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/{{scale}}m/cultural/ne_{{scale}}m_admin_0_countries.zip'
+      urlpath: '/Users/kraus-d/projects/ldndctools-kraus/data/ne_50m_admin_0_countries.zip'
       use_fsspec: True
       storage_options:
         simplecache:
@@ -74,7 +98,6 @@ sources:
     driver: zarr
     args:
       urlpath: 's3://era5land-zarr/data.zarr'
-      consolidated: False
       storage_options:
         use_ssl: True
         anon: True
diff --git a/data/ldndctools.conf b/data/ldndctools.conf
index 603455b..6557650 100644
--- a/data/ldndctools.conf
+++ b/data/ldndctools.conf
@@ -4,8 +4,8 @@
 
 # author info
 info:
-    author: Christian Werner
-    email: christian.werner@kit.edu
+    author: David Kraus
+    email: david.kraus@kit.edu
     institution: IMK-IFU, Karlsruhe Institut of Technology, Garmisch-Partenkirchen, Germany
 
 # project info
diff --git a/examples/examples.conf b/examples/examples.conf
new file mode 100644
index 0000000..8d66824
--- /dev/null
+++ b/examples/examples.conf
@@ -0,0 +1,26 @@
+# default ldndctools.conf file
+#
+#
+
+# author info
+info:
+    author: David Kraus
+    email: david.kraus@kit.edu
+
+# project info
+project:
+    dataset: test
+    version: 0.1
+    source: IMK-IFU, KIT
+
+soil: national
+output: file #stream
+outfile: test_out.xml
+bbox: 44,44,45,45
+gui: False
+file: None 
+interactive: False
+resolution: 'HR' #LR
+rcode: None
+storeconfig: False
+verbose: False
diff --git a/examples/readme.txt b/examples/readme.txt
new file mode 100644
index 0000000..c5032aa
--- /dev/null
+++ b/examples/readme.txt
@@ -0,0 +1,2 @@
+Run on your terminal:
+dlsc -c examples.conf
\ No newline at end of file
diff --git a/ldndctools/cdgen.py b/ldndctools/cdgen.py
index 7dbe92e..e87a1a2 100644
--- a/ldndctools/cdgen.py
+++ b/ldndctools/cdgen.py
@@ -14,7 +14,7 @@
 import pandas as pd
 import urllib3
 import xarray as xr
-from dask.distributed import Client
+from dask.distributed import LocalCluster, Client
 from pydantic import ValidationError
 
 from ldndctools.misc.geohash import coords2geohash_dec
@@ -50,9 +50,22 @@ def subset_climate_data(
 
     with resources.path("data", "catalog.yml") as cat:
         catalog = intake.open_catalog(str(cat))
+        #load the data into a Dask Dataset
         ds = catalog["climate_era5land_hr"].to_dask()
-
+        ds = xr.open_zarr(
+            store="s3://era5land-zarr/data.zarr",
+            consolidated=True,
+            storage_options={
+                "anon": True,
+                "client_kwargs": {
+                    "endpoint_url": "https://s3.imk-ifu.kit.edu:10443",
+                    "verify": False
+                },
+                "use_ssl": True,
+            },
+        )
         if mask is not None:
+            #match the latitude and longitude coordinates of ds
             mask = mask.interp(lat=ds["lat"], lon=ds["lon"])
             ds = ds.where(mask>0)
 
@@ -249,7 +262,14 @@ def conf():
 
 
 def main():
-    client = Client(dashboard_address=":1234")
+
+    # Create a LocalCluster with 2 workers and set the dashboard address
+    cluster = LocalCluster(n_workers=2, memory_limit="2GB", dashboard_address=":1234")
+
+    # Connect a Client to the LocalCluster
+    client = Client(cluster)
+
+    #client = Client(dashboard_address=":1234")
 
     print(f"NOTE: You can see progress at {platform.node()}:1234 if bokeh is installed")
 
@@ -258,6 +278,7 @@ def main():
     bbox = get_boundingbox(args.bbox)
     mask = get_mask(args.mask)
 
+    print("subset climate")
     # mask = xr.open_dataset("VN_MISC5_V2.nc")["rice_rot"]
     # mask = xr.where(mask > 0, 1, np.nan)
     ds = subset_climate_data(
@@ -268,6 +289,7 @@ def main():
         date_max=args.date_max,
     )
 
+    print("group")
     tavg_year = ds.tavg.groupby("time.year").mean(dim="time").mean(dim="year")
     tamp_year = ds.tavg.groupby("time.year").apply(amplitude).mean(dim="year")
     prec_year = ds.prec.groupby("time.year").sum(dim="time").mean(dim="year")
@@ -307,6 +329,7 @@ def main():
     # match coords (usually means take lat/ lon from ref dataset)
     ds = ds.assign_coords({"lat": stats.lat, "lon": stats.lon})
 
+    print("df stats")
     df_stats = (
         stats.to_dataframe()
         .dropna(subset=["tavg", "tamp", "wind"], how="all")
@@ -314,6 +337,7 @@ def main():
     )
     # ignore prec for now
 
+    print("lookup")
     lookup: Dict[int, ClimateSiteStats] = {}
     for _, row in df_stats.iterrows():
         lookup[int(row["geohash"])] = ClimateSiteStats(
diff --git a/ldndctools/cli/cli.py b/ldndctools/cli/cli.py
index c71bf61..4feb956 100644
--- a/ldndctools/cli/cli.py
+++ b/ldndctools/cli/cli.py
@@ -28,7 +28,7 @@ def __call__(self, parser, namespace, values=None, option_string=None):
         handlers = logging.getLogger().handlers
         for handler in handlers:
             if type(handler) is logging.StreamHandler:
-                handler.setLevel(logging.DEBUG)
+                handler.setLevel(logging.INFO)
         setattr(namespace, self.dest, True)
 
 
diff --git a/ldndctools/dlsc.py b/ldndctools/dlsc.py
index f8f4198..ed5528c 100755
--- a/ldndctools/dlsc.py
+++ b/ldndctools/dlsc.py
@@ -28,6 +28,7 @@
 from ldndctools.misc.create_data import create_dataset
 from ldndctools.misc.types import BoundingBox, RES
 from ldndctools.sources.soil.soil_iscricwise import ISRICWISE_SoilDataset
+from ldndctools.sources.soil.soil_national import NATIONAL_SoilDataset
 
 log = logging.getLogger(__name__)
 log.setLevel("INFO")
@@ -36,8 +37,8 @@
 
 # TODO: there has to be a better way here...
 #       also, tqdm takes no effect
-with resources.path("data", "") as dpath:
-    DPATH = Path(dpath)
+#with resources.path("data", "") as dpath:
+#    DPATH = Path(dpath)
 
 
 def main( **kwargs):
@@ -47,14 +48,13 @@ def main( **kwargs):
     # read config
     if 'config' in kwargs:
         cfg = kwargs['config']
-        for k,v in cfg.items():
-            setattr(args, k, v)
     else:
         cfg = get_config(args.config)
 
     # write config
-    if args.storeconfig:
-        set_config(cfg)
+    #if args.storeconfig:
+    #    set_config(cfg)
+
 
     # def _get_cfg_item(group, item, save="na"):
     #     return cfg[group].get(item, save)
@@ -69,9 +69,12 @@ def main( **kwargs):
     #     SOURCE=_get_cfg_item("project", "source"),
     # )
 
-    if (args.rcode is not None) or (args.file is not None):
+    if False: #(args.rcode is not None) or (args.file is not None):
         log.info("Non-interactive mode...")
         cfg["interactive"] = False
+    else:
+        pass
+        #log.info("Interactive mode...")
 
     # query environment or command flags for selection (non-interactive mode)
     args.rcode = os.environ.get("DLSC_REGION", args.rcode)
@@ -81,18 +84,20 @@ def main( **kwargs):
         log.error(f"Wrong resolution: {args.resolution}. Use HR, MR or LR.")
         exit(-1)
 
-    res = RES[args.resolution]
+    res = RES[cfg["resolution"]]
 
-    bbox = None
 
-    if ('lat' in args) and ('lon' in args):
-       setattr(args, 'bbox', [float(args.lon-0.5), float(args.lat-0.5), float(args.lon+0.5), float(args.lat+0.5)]) 
+    bbox = None
+    if  ('lat' in cfg) and ('lon' in cfg):
+       cfg['bbox'] = [float(cfg["lon"]-1.0), float(cfg["lat"]-1.0), 
+                      float(cfg["lon"]+1.0), float(cfg["lat"]+1.0)]
        log.info("Creating bounding box for coordinates specified.")
-    if args.bbox:
-        if type( args.bbox) == list:
-            x1, y1, x2, y2 = args.bbox
-        else: 
-            x1, y1, x2, y2 = [float(x) for x in args.bbox.split(",")]
+
+    if cfg["bbox"]:
+        if type( cfg["bbox"]) == list:
+            x1, y1, x2, y2 = cfg["bbox"]
+        else:
+            x1, y1, x2, y2 = [float(x) for x in cfg["bbox"].split(",")]
         try:
             bbox = BoundingBox(x1=x1, y1=y1, x2=x2, y2=y2)
         except ValidationError:
@@ -100,19 +105,16 @@ def main( **kwargs):
             log.info("required: x1,y1,x2,y2 [cond: x1<x2, y1<y2]")
             log.info(f"given:    x1={x1},y1={y1},x2={x2},y2={y2}")
             exit(1)
+        log.info(f"given:    x1={x1},y1={y1},x2={x2},y2={y2}")
+        
+    if "outfile" not in cfg:
+        cfg["outfile"] = f"sites_{res.name}.xml"
 
-    if not args.outfile:
-        cfg["outname"] = f"sites_{res.name}.xml"
-    else:
-        cfg["outname"] = args.outfile
-        if all([x.value not in cfg["outname"] for x in RES.members()]):
-            if cfg["outname"].endswith(".xml"):
-                cfg["outname"] = f'{cfg["outname"][:-4]}_{res.name}.xml'
-            else:
-                cfg["outname"] = f'{cfg["outname"]}_{res.name}.xml'
+    if not cfg["outfile"].endswith(".xml"):
+        cfg["outfile"] = f'{cfg["outfile"]}.xml'
 
     log.info(f"Soil resolution: {res.name} {res.value}")
-    log.info(f'Outfile name:    {cfg["outname"]}')
+    log.info(f'Outfile name:    {cfg["outfile"]}')
 
     res_scale_mapper = {RES.LR: 50, RES.MR: 50, RES.HR: 10}
 
@@ -120,25 +122,32 @@ def main( **kwargs):
         catalog = intake.open_catalog(str(cat))
 
     df = catalog.admin(scale=res_scale_mapper[res]).read()
-    soil_raw = catalog.soil(res=res.name).read()
-
-    soil = ISRICWISE_SoilDataset(soil_raw)
+    
+    print("config ", cfg)
+    if "soil" in cfg and cfg["soil"] == "national":
+        soil_raw = catalog.soil_national(res=res.name, port=8082).read()
+        print("soil_raw ",soil_raw)
+        soil = NATIONAL_SoilDataset( soil_raw)
+    else:
+        soil_raw = catalog.soil(res=res.name, port=8082).read()
+        soil = ISRICWISE_SoilDataset( soil_raw)
 
-    if args.file:
+    if False: #args.file:
         selector = CoordinateSelection(args.file)
     else:
         selector = Selector(df)
 
-    if args.interactive:
+    if False: #args.interactive:
         res = ask_for_resolution(cfg)
         selector.ask()
-    else:
-        if rcode:
-            selector.set_region(rcode)
+    #else:
+    #    if rcode:
+    #        selector.set_region(rcode)
 
     if bbox:
         log.info(f"Setting bounding box to {bbox}")
         selector.set_bbox(bbox)
+        log.info(f"Setting bounding box to {bbox}")
     else:
         if isinstance(selector, Selector):
             log.info("Adjusting bounding box to selection extent")
@@ -152,18 +161,20 @@ def main( **kwargs):
             )
             selector.set_bbox(new_bbox)
 
-    log.info(selector.selected)
+    #log.info(selector.selected)
 
     with tqdm(total=1) as progressbar:
-        xml, nc = create_dataset(soil, selector, res, args, progressbar)
-
-    open(cfg["outname"], "w").write(xml)
-    ENCODING = {
-        "siteid": {"dtype": "int32", "_FillValue": -1, "zlib": True},
-        "soilmask": {"dtype": "int32", "_FillValue": -1, "zlib": True},
-    }
-    nc.to_netcdf(cfg["outname"].replace(".xml", ".nc"), encoding=ENCODING)
+        xml, nc = create_dataset(soil, selector, res, cfg, progressbar)
 
+    if ('output' in cfg) and cfg['output'] == 'stream':
+        return xml
+    else:
+        open( cfg["outfile"], "w").write(xml)
+        ENCODING = {
+            "siteid": {"dtype": "int32", "_FillValue": -1, "zlib": True},
+            "soilmask": {"dtype": "int32", "_FillValue": -1, "zlib": True},
+        }
+        nc.to_netcdf(cfg["outfile"].replace(".xml", ".nc"), encoding=ENCODING)
 
 if __name__ == "__main__":
     main()
diff --git a/ldndctools/misc/create_data.py b/ldndctools/misc/create_data.py
index 780644a..bbbab8b 100644
--- a/ldndctools/misc/create_data.py
+++ b/ldndctools/misc/create_data.py
@@ -43,13 +43,28 @@ def create_dataset(
 
         xmlwriter = SiteXmlWriter(soil, res=res)
         if ('lat' in args) and ('lon' in args):
-            sel = soil._soil.sel(lat=args.lat, lon=args.lon, method='nearest')
+            delta = 0
+            found = False
+            while not found:
+                for la in [-1,1]:
+                    for lo in [-1,1]:
+                        if not found:
+                            sel = soil._soil.sel(lat=args["lat"]+la*delta, lon=args["lon"]+lo*delta, method='nearest')
+                            if sel['TopDep'].mean() > 0:
+                                found = True
+                delta += 0.1
+                if delta > 10:
+                    log.info("No valid data to process for this region/ bbox request.")
+                    exit(1)
+
             cid = coords2geohash_dec( lat=sel["lat"].values.item(), lon=sel["lon"].values.item())
             site_xml = xmlwriter.write(progressbar=progressbar, status_widget=status_widget, id_selection=[cid])
         else:
             site_xml = xmlwriter.write(progressbar=progressbar, status_widget=status_widget)
 
     else:
+        log.info("Incorrect selector.")
+        exit(1)
         # WARNING: THIS BRANCH IS DEFUNCT!!!
         soil.clip_mask_box(
             minx=min(selector.lons),
diff --git a/ldndctools/misc/types.py b/ldndctools/misc/types.py
index 74a290e..95a00f8 100644
--- a/ldndctools/misc/types.py
+++ b/ldndctools/misc/types.py
@@ -56,7 +56,7 @@ def check_y1_smaller_y2(cls, values):
 NODATA = -99.99
 
 
-# map from isiric-wise fields and units to ldndc
+# map from isric-wise fields and units to ldndc
 # ldndcname, conversion, significant digits
 nmap = {
     "TOTC": ("corg", 0.001, 5),
diff --git a/ldndctools/sources/soil/soil_base.py b/ldndctools/sources/soil/soil_base.py
index abd112f..c0356c5 100644
--- a/ldndctools/sources/soil/soil_base.py
+++ b/ldndctools/sources/soil/soil_base.py
@@ -85,10 +85,6 @@ def mask(self) -> Union[xr.DataArray, None]:
     @property
     def mask_3d(self) -> xr.DataArray:
         """return 3d mask to clip soildata"""
-        lev_max_idx = self.layer_mask.max(skipna=True).astype(int).item()
-        mask = (self.layer_mask.values >= np.arange(lev_max_idx)[:, None, None]).astype(
-            int
-        )
 
         for v in self.original.data_vars:
             if len(self.original[v].squeeze(drop=True).shape) == 3:
@@ -100,6 +96,10 @@ def mask_3d(self) -> xr.DataArray:
         mask_3d = xr.ones_like(
             self.original[v].sel(lat=self.layer_mask.lat, lon=self.layer_mask.lon)
         )
+
+        lev_max_idx = np.shape(mask_3d)[0] #self.layer_mask.max(skipna=True).astype(int).item()
+        mask = (self.layer_mask.values >= np.arange(lev_max_idx)[:, None, None]).astype(int)
+
         mask_3d[:] = mask
         mask_3d = mask_3d.where(mask_3d == 1)
         return mask_3d

From 42069ecdd8b63764ea6752307b3a4d22270582db Mon Sep 17 00:00:00 2001
From: Kraus <kraus-d@GAP-L282A1.local>
Date: Thu, 22 May 2025 11:35:49 +0200
Subject: [PATCH 14/14] add documentation

---
 examples/examples.conf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/examples.conf b/examples/examples.conf
index 8d66824..5090c3b 100644
--- a/examples/examples.conf
+++ b/examples/examples.conf
@@ -16,11 +16,11 @@ project:
 soil: national
 output: file #stream
 outfile: test_out.xml
-bbox: 44,44,45,45
+bbox: 105,28,106,29 #[lon1,lat1,lon2,lat2]
 gui: False
 file: None 
 interactive: False
-resolution: 'HR' #LR
+resolution: 'LR' #HR
 rcode: None
 storeconfig: False
 verbose: False