move logger

Dockerfile

@@ -2,7 +2,7 @@
 FROM python:3.10.13
 
 # install the toolbox runner tools
-RUN pip install json2args==0.6.1
+RUN pip install json2args==0.7.0
 
 # Install GDAL which will be used by geopandas
 RUN pip install --upgrade pip
@@ -45,6 +45,9 @@ RUN mkdir /src
 COPY ./src /src
 RUN mv /whitebox/WhiteboxTools_linux_amd64/WBT /src/WBT
 
+# copy the citation file - looks funny to make COPY not fail if the file is not there
+COPY ./CITATION.cf[f] /src/CITATION.cff
+
 # download a precompiled binary of duckdb
 #  first line checks the architecture, and replaces x86_64 with amd64, which is what duckdb uses
 RUN arch=$(uname -m | sed s/x86_64/amd64/) && \     

docker-compose.yml

@@ -1,4 +1,3 @@
-version: '3.8'
 services:
   db:
     image: postgis/postgis:15-3.4

src/aggregator.py

@@ -7,7 +7,7 @@
 import polars as pl
 
 from param import load_params
-from logger import logger
+from json2args.logger import logger
 from writer import dispatch_result_saver
 
 class AggregationMacros(TypedDict):

src/clip.py

@@ -9,7 +9,7 @@
 from pyproj import CRS
 from geocube.api.core import make_geocube
 
-from logger import logger
+from json2args.logger import logger
 from param import load_params
 
 

src/ingestor.py

@@ -9,7 +9,7 @@
 import duckdb
 from metacatalog.models import Entry
 
-from logger import logger
+from json2args.logger import logger
 from param import load_params
 
 SPATIAL_DIMENSIONS = ('lon', 'lat', 'z')

src/loader.py

@@ -11,7 +11,7 @@
 import geopandas as gpd
 import rasterio as rio
 
-from logger import logger
+from json2args.logger import logger
 from writer import dispatch_save_file, entry_metadata_saver
 from param import load_params, Params
 from utils import whitebox_log_handler
@@ -315,22 +315,22 @@ def error_handler(future):
     tiles = [future.result() for future in futures if future.result() is not None]
 
     # run the merge function and delete the other files
-    if len(tiles) > 1:
-        logger.debug('Starting WhitboxTools mosaic operation...')
-        _wbt_merge_raster(dataset_base_path, f"{entry.variable.name.replace(' ', '_')}_{entry.id}.tif")
+    # if len(tiles) > 1:
+    #     logger.debug('Starting WhitboxTools mosaic operation...')
+    #     _wbt_merge_raster(dataset_base_path, f"{entry.variable.name.replace(' ', '_')}_{entry.id}.tif")
 
-        # remove the tiles
-        for tile in tiles:
-            Path(tile).unlink()
+    #     # remove the tiles
+    #     for tile in tiles:
+    #         Path(tile).unlink()
 
-    # check if there is exactly one tile
-    elif len(tiles) == 1:
-        # rename the file
-        new_name = dataset_base_path / f"{entry.variable.name.replace(' ', '_')}_{entry.id}.tif"
-        Path(tiles[0]).rename(new_name)
-        tiles = [str(new_name)]
-    else:
-        logger.warning(f'No tiles were clipped for the reference area. It might not be covered by dataset <ID={entry.id}>')
+    # # check if there is exactly one tile
+    # elif len(tiles) == 1:
+    #     # rename the file
+    #     new_name = dataset_base_path / f"{entry.variable.name.replace(' ', '_')}_{entry.id}.tif"
+    #     Path(tiles[0]).rename(new_name)
+    #     tiles = [str(new_name)]
+    # else:
+    #     logger.warning(f'No tiles were clipped for the reference area. It might not be covered by dataset <ID={entry.id}>')
 
     # save the metadata
     metafile_name = str(params.dataset_path / f"{entry.variable.name.replace(' ', '_')}_{entry.id}.metadata.json")

src/reporter.py

@@ -5,7 +5,7 @@
 from ydata_profiling import ProfileReport
 
 from param import load_params
-from logger import logger
+from json2args.logger import logger
 
 
 def generate_profile_report(file_name: str) -> None:

src/run.py

@@ -13,7 +13,7 @@
 
 from param import load_params, Integrations
 from loader import load_entry_data
-from logger import logger
+from json2args.logger import logger
 import ingestor
 import aggregator
 import reporter

src/utils.py

@@ -1,4 +1,4 @@
-from logger import logger
+from json2args.logger import logger
 
 # define a handler for whiteboxgis tools verbose output
 def whitebox_log_handler(msg: str):

src/writer.py

@@ -13,7 +13,7 @@
 import pandas as pd
 import xarray as xr
 
-from logger import logger
+from json2args.logger import logger
 
 
 # create a union of all supported Dataframe types