pyVPRM 3.0__tar.gz → 5.0__tar.gz

{pyvprm-3.0/pyVPRM.egg-info → pyvprm-5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyVPRM
-Version: 3.0
+Version: 5.0
 Summary: Vegetation Photosynthesis and Respiration Model
 Home-page: https://github.com/tglauch/pyVPRM/
 Author: Theo Glauch
@@ -36,5 +36,6 @@ Requires-Dist: lxml
 Requires-Dist: requests
 Requires-Dist: statsmodels
 Requires-Dist: loguru
+Requires-Dist: fiona
 
 A tool to calculate the CO2 exchange flux between atmosphere and terrestrial biosphere using the Vegetation Photosynthesis and Respiration Model

{pyvprm-3.0 → pyvprm-5.0}/README.md

@@ -47,7 +47,7 @@ conda install esmpy
 Afterwards install ```pyVPRM``` using pip via
 
 ```
-pip install git+https://github.com/tglauch/pyVPRM.git
+pip install pyVPRM
 ```
 
 ## Start your own project

{pyvprm-3.0 → pyvprm-5.0}/pyVPRM/VPRM.py

@@ -38,7 +38,7 @@ regridder_options["conservative"] = "conserve"
 
 class vprm:
     """
-    Class for the  Vegetation Photosynthesis and Respiration Model
+    Main class for the  Vegetation Photosynthesis and Respiration Model
     """
 
     def __init__(
@@ -617,9 +617,13 @@ class vprm:
                     )
                     src_grid.to_netcdf(src_temp_path)
                     ds_out.to_netcdf(dest_temp_path)
-                    exec_str = "ESMF_RegridWeightGen --source {} --destination {} --weight {} -m conserve -r --netcdf4 –src_regional –dest_regional ".format(
-                        src_temp_path, dest_temp_path, regridder_save_path
-                    )
+                    logger.debug(f"wrote source regridder: {src_temp_path}")
+                    logger.debug(f"wrote dest regridder: {dest_temp_path}")
+                    exec_str = (
+                        "ESMF_RegridWeightGen --source {} --destination {} "
+                        "--weight {} -m conserve -r --netcdf4 --src_regional"
+                        " --dest_regional --ignore_unmapped"
+                    ).format(src_temp_path, dest_temp_path, regridder_save_path)
                     if mpi is True:
                         exec_str = "mpirun -np {} ".format(n_cpus) + exec_str
                     if not logs:

pyvprm-5.0/pyVPRM/__init__.py

@@ -0,0 +1 @@
+__version__ = "4.0"

pyvprm-5.0/pyVPRM/lib/reproject_fiona.py

@@ -0,0 +1,64 @@
+"""antimeridian-aware geopandas GeoDataFrame reprojection tool using fiona
+
+This is an adaptation of this example from the geopandas documentation:
+https://geopandas.org/en/stable/docs/user_guide/reproject_fiona.html#fiona-example
+
+The main user-level function is transform_geodataframe(). Helper functions
+crs_to_fiona() and base_transform() are not expected to be called by end-users.
+"""
+
+from functools import partial
+
+import fiona
+import geopandas as gpd
+from fiona.transform import transform_geom
+from packaging import version
+from pyproj import CRS
+from pyproj.enums import WktVersion
+from shapely.geometry import mapping, shape
+
+
+# set up Fiona transformer
+def crs_to_fiona(proj_crs):
+    """translate a CRS definition to a format fiona can understand
+
+    from https://geopandas.org/en/stable/docs/user_guide/reproject_fiona.html#fiona-example
+
+    helper function for transform_geodataframe()
+    """
+    proj_crs = CRS.from_user_input(proj_crs)
+    if version.parse(fiona.__gdal_version__) < version.parse("3.0.0"):
+        fio_crs = proj_crs.to_wkt(WktVersion.WKT1_GDAL)
+    else:
+        # GDAL 3+ can use WKT2
+        fio_crs = proj_crs.to_wkt()
+    return fio_crs
+
+
+def base_transformer(geom, src_crs, dst_crs):
+    """transform a geometry from from one CRS to another
+
+    from https://geopandas.org/en/stable/docs/user_guide/reproject_fiona.html#fiona-example
+
+    helper function for transform_geodataframe()
+    """
+    return shape(
+        transform_geom(
+            src_crs=crs_to_fiona(src_crs),
+            dst_crs=crs_to_fiona(dst_crs),
+            geom=mapping(geom),
+            antimeridian_cutting=True,
+            antimeridian_offset=100.0,
+        )
+    )
+
+
+def transform_geodataframe(
+    gdf: gpd.GeoDataFrame, src_crs: str, dst_crs: str
+) -> gpd.GeoDataFrame:
+    forward_transformer = partial(base_transformer, src_crs=gdf.crs, dst_crs=dst_crs)
+    with fiona.Env(OGR_ENABLE_PARTIAL_REPROJECTION="YES"):
+        gdf_reproj = gdf.set_geometry(
+            gdf.geometry.apply(forward_transformer), crs=dst_crs
+        )
+    return gdf_reproj

{pyvprm-3.0 → pyvprm-5.0}/pyVPRM/meteorologies/era5_monthly_xr.py

@@ -13,9 +13,30 @@ import datetime
 from pyVPRM.meteorologies.met_base_class import met_data_handler_base
 from loguru import logger
 
+
 class met_data_handler(met_data_handler_base):
 
-    def __init__(self, year, month, day, hour, bpath, mpi=False, keys=[]):
+    def __init__(
+        self,
+        year,
+        month,
+        day,
+        hour,
+        bpath,
+        fname_fmt_str="{year}_{month}.nc",
+        mpi=False,
+        keys=[],
+    ):
+        """construct a met_data_handler instance for monthly ERA5 data
+
+        ARGS:
+        fname_fmt_str (str): specifies the file name syntax. Must have
+           placeholders for year and month.
+           valid examples:
+              '{year}_{month}.nc'
+              'ERA5_2mT_msdswrf_ssrd_NZ_{year:04d}_{month:02d}.nc'
+        """
+
         super().__init__()
         # Init with year, month, day, hour and the required era5 keys as given in the
         #  keys_dict above
@@ -23,6 +44,7 @@ class met_data_handler(met_data_handler_base):
         self.this_month = 0
         self.this_year = 0
         self.bpath = bpath
+        self.fname_fmt_str = fname_fmt_str
         self.ds_in_t = None
         self.regridder = None
         self.mpi = mpi
@@ -109,23 +131,41 @@ class met_data_handler(met_data_handler_base):
     def _init_data_for_day(self):
         if (self.this_month != self.month) | (self.this_year != self.year):
             self.data = xr.open_dataset(
-                os.path.join(self.bpath, "{}_{}.nc".format(self.year, self.month))
+                os.path.join(
+                    self.bpath,
+                    self.fname_fmt_str.format(year=self.year, month=self.month),
+                )
             )
             self.this_month = self.month
             self.this_year = self.year
             self.in_era5_grid = True
 
         if self.ds_in_t is None:
+            # determine whether data uses "lat" or "latitude"
+            if "lat" in self.data.coords:
+                latvar = "lat"
+            elif "latitude" in self.data.coords:
+                latvar = "latitude"
+            else:
+                raise ValueError("cannot locate 'lat' or 'latitude' values")
+            # determine whether data uses "lon" or "longitude"
+            if "lon" in self.data.coords:
+                lonvar = "lon"
+            elif "longitude" in self.data.coords:
+                lonvar = "longitude"
+            else:
+                raise ValueError("cannot locate 'lon' or 'longitude' values")
+
             self.ds_in_t = xr.Dataset(
                 {
                     "lat": (
                         ["lat"],
-                        self.data["lat"].values,
+                        self.data[latvar].values,
                         {"units": "degrees_north"},
                     ),
                     "lon": (
                         ["lon"],
-                        self.data["lon"].values,
+                        self.data[lonvar].values,
                         {"units": "degrees_east"},
                     ),
                 }

{pyvprm-3.0 → pyvprm-5.0}/pyVPRM/vprm_configs/copernicus_land_cover.yaml

@@ -5,10 +5,10 @@ Evergreen Forest:
         - 112
         - 121
         - 122
-    tmin: -5
-    topt: 20
-    tmax: 40    
-    tlow: 1
+    tmin: -4
+    topt: 15
+    tmax: 38
+    tlow: -3  
 
 Deciduous Forest:
     vprm_class: 2
@@ -17,11 +17,11 @@ Deciduous Forest:
         - 114
         - 123
         - 124
-    tmin: 0
-    topt: 20
-    tmax: 40
-    tlow: 5
-
+    tmin: 1
+    topt: 21
+    tmax: 37
+    tlow: 0 
+    
 Mixed Forest:
     vprm_class: 3
     class_numbers:
@@ -29,19 +29,19 @@ Mixed Forest:
         - 126
         - 116
         - 125
-    tmin: -3
-    topt: 20
-    tmax: 40    
-    tlow: 2
+    tmin: -1
+    topt: 18
+    tmax: 38
+    tlow: 0     
 
 Shrubland:
     vprm_class: 4
     class_numbers:
         - 20
-    tmin: 2
-    topt: 20
-    tmax: 40    
-    tlow: 0
+    tmin: -1
+    topt: 19
+    tmax: 44
+    tlow: 2   
 
 Savannas:
     vprm_class: 5
@@ -49,27 +49,27 @@ Savannas:
         - 999
     tmin: 0
     topt: 20
-    tmax: 40  
-    tlow: 0
-
+    tmax: 40
+    tlow: 0   
+    
 Cropland:
     vprm_class: 6
     class_numbers:
         - 40
-    tmin: -2
-    topt: 22
-    tmax: 40
-    tlow: 2
-
+    tmin: -3
+    topt: 16
+    tmax: 50
+    tlow: -3
+     
 Grassland:
     vprm_class: 7
     class_numbers:
         - 30
         - 100
-    tmin: -3
-    topt: 18
-    tmax: 40
-    tlow: 0
+    tmin: -2
+    topt: 17
+    tmax: 36
+    tlow: -2
 
 Other:
     vprm_class: 8
@@ -82,13 +82,13 @@ Other:
     tmin: 2
     topt: 18
     tmax: 40
-    tlow: 0
+    tlow: -2
 
 Wetland:
     vprm_class: 9
     class_numbers:
         - 90
-    tmin: 0
-    topt: 20
+    tmin: -2
+    topt: 26
     tmax: 40
     tlow: 0

{pyvprm-3.0 → pyvprm-5.0}/pyVPRM/vprm_configs/esa_world_cover.yaml

@@ -2,59 +2,66 @@ Evergreen Forest:
     vprm_class: 1
     class_numbers:
         - -1
-    tmin: 0
-    topt: 20
-    tmax: 40    
+    tmin: -4
+    topt: 15
+    tmax: 38
+    tlow: -3      
 
 Deciduous Forest:
     vprm_class: 2
     class_numbers:
         - -1
-    tmin: 0
-    topt: 20
-    tmax: 40
+    tmin: 1
+    topt: 21
+    tmax: 37
+    tlow: 0 
     
 
 Mixed Forest:
     vprm_class: 3
     class_numbers:
         - 10
-    tmin: 0
-    topt: 20
-    tmax: 40    
+    tmin: -1
+    topt: 18
+    tmax: 38
+    tlow: 0     
 
 
 Shrubland:
     vprm_class: 4
     class_numbers:
         - 20
-    tmin: 2
-    topt: 20
-    tmax: 40    
+    tmin: -1
+    topt: 19
+    tmax: 44
+    tlow: 2   
 
 Savannas:
     vprm_class: 5
     class_numbers:
-        - 126
-    tmin: 2
+        - 999
+    tmin: 0
     topt: 20
-    tmax: 40  
+    tmax: 40
+    tlow: 0  
     
 Cropland:
     vprm_class: 6
     class_numbers:
         - 40
-    tmin: 5
-    topt: 22
-    tmax: 40
+    tmin: -3
+    topt: 16
+    tmax: 50
+    tlow: -3
      
 Grassland:
     vprm_class: 7
     class_numbers:
         - 30
-    tmin: 2
-    topt: 18
-    tmax: 40
+    tmin: -2
+    topt: 17
+    tmax: 36
+    tlow: -2
 
 Other:
     vprm_class: 8
@@ -63,9 +70,18 @@ Other:
         - 60
         - 70
         - 80
-        - 90
         - 95
         - 100
     tmin: 2
     topt: 18
     tmax: 40
+    tlow: -2
+
+Wetland:
+    vprm_class: 9
+    class_numbers:
+        - 90
+    tmin: -2
+    topt: 26
+    tmax: 40
+    tlow: 0

{pyvprm-3.0 → pyvprm-5.0/pyVPRM.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyVPRM
-Version: 3.0
+Version: 5.0
 Summary: Vegetation Photosynthesis and Respiration Model
 Home-page: https://github.com/tglauch/pyVPRM/
 Author: Theo Glauch
@@ -36,5 +36,6 @@ Requires-Dist: lxml
 Requires-Dist: requests
 Requires-Dist: statsmodels
 Requires-Dist: loguru
+Requires-Dist: fiona
 
 A tool to calculate the CO2 exchange flux between atmosphere and terrestrial biosphere using the Vegetation Photosynthesis and Respiration Model

{pyvprm-3.0 → pyvprm-5.0}/pyVPRM.egg-info/SOURCES.txt

@@ -15,6 +15,7 @@ pyVPRM/lib/downmodis.py
 pyVPRM/lib/fancy_plot.py
 pyVPRM/lib/flux_tower_class.py
 pyVPRM/lib/functions.py
+pyVPRM/lib/reproject_fiona.py
 pyVPRM/lib/fluxnet_info/fluxnet_sites.pkl
 pyVPRM/lib/fluxnet_info/site_infos.txt
 pyVPRM/meteorologies/__init__.py

{pyvprm-3.0 → pyvprm-5.0}/pyVPRM.egg-info/requires.txt

@@ -21,3 +21,4 @@ lxml
 requests
 statsmodels
 loguru
+fiona

{pyvprm-3.0 → pyvprm-5.0}/setup.py

@@ -8,7 +8,7 @@ def readme():
 
 setup(
     name="pyVPRM",
-    version="3.0",
+    version="5.0",
     description="Vegetation Photosynthesis and Respiration Model",
     long_description="A tool to calculate the CO2 exchange flux between atmosphere and terrestrial biosphere using the Vegetation Photosynthesis and Respiration Model",
     classifiers=[
@@ -48,6 +48,7 @@ setup(
         "requests",
         "statsmodels",
         "loguru",
+        "fiona",
     ],
     include_package_data=True,
     zip_safe=False,

pyvprm-3.0/pyVPRM/__init__.py

@@ -1 +0,0 @@
-__version__ = "3.0"