Updated libraries and tests so that everything is passing (#9)

CHANGELOG.md

@@ -5,15 +5,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+### Changed
+- Project migrated to https://github.com/podaac/net2cog
 
+## [0.2.0-alpha.15] - 26 July 2023
 ### Added
 - PCESA-2309 - Implemented the harmony-service-lib interface so that I can be run in the Harmony ngap account
 ### Changed
-- PCESA-2309 - Updated Jenkins to include building and pushing to ECC_NEXUS 
-### Deprecated
-### Removed
-### Fixed
-### Security
+- PCESA-2309 - Updated Jenkins to include building and pushing to ECC_NEXUS
 
 ## [0.2.0-alpha.14] - 3 September 2020
 ### Changed 

podaac/netcdf_converter/netcdf_convert.py → net2cog/netcdf_convert.py

@@ -8,12 +8,15 @@
 """
 
 import os
+import pathlib
 from os.path import join as pjoin, basename, dirname, exists, splitext
 import subprocess
 from subprocess import check_call
 
 import logging
 import tempfile
+from typing import List
+
 import xarray as xr
 import rasterio
 import rasterio.crs
@@ -61,7 +64,7 @@ def get_gtiff_name(output_file):
     out_fname = pjoin(dir_path, rel_path)
     if not exists(out_fname):
         os.makedirs(out_fname)
-    return out_fname
+    return pjoin(out_fname, rel_path)
 
 
 def _write_cogtiff(out_f_name, nc_xarray):
@@ -135,31 +138,22 @@ def rioxr_swapdims(netcdf_xarray):
                 dst_profile = cog_profiles.get("deflate")
                 cog_translate(src_dst, out_fname, dst_profile)
 
-            # cog validation method
-            # cogtif_val = [
-            #     'rio',
-            #     'cogeo',
-            #     'validate',
-            #     out_fname
-            #     ]
-            # run_command(cogtif_val, dirname(out_f_name))
-
             cogs_generated.append(out_fname)
             LOGGER.info("Finished conversion, writing variable: %s", out_fname)
     LOGGER.info("NetCDF conversion complete. Returning COGs generated.")
     return cogs_generated
 
 
-def netcdf_converter(input_nc_file, output_cog_pathname, var_list=None):
+def netcdf_converter(input_nc_file: pathlib.Path, output_cog_pathname: pathlib.Path, var_list: list = ()) -> List[str]:
     """
     Primary function for beginning NetCDF conversion using rasterio,
     rioxarray and xarray
 
     Parameters
     ----------
-    input_nc_file : string
+    input_nc_file : pathlib.Path
         Path to  NetCDF file to process
-    output_cog_pathname : string
+    output_cog_pathname : pathlib.Path
         COG Output path and NetCDF filename, filename converted to cog variable
         filename (.tif)
             ex: tests/data/tmpygj2vgxf/
@@ -189,7 +183,7 @@ def netcdf_converter(input_nc_file, output_cog_pathname, var_list=None):
             # used to invert y axis
             # xds_reversed = xds.reindex(lat=xds.lat[::-1])
             LOGGER.info("Writing COG to %s", basename(gtiff_fname))
-            if var_list is not None and var_list != '':
+            if var_list:
                 xds = xds[var_list]
             return _write_cogtiff(gtiff_fname, xds)
         LOGGER.error("%s: NetCDF file does not contain spatial dimensions such as lat / lon "

podaac/netcdf_converter/netcdf_convert_harmony.py → net2cog/netcdf_convert_harmony.py

@@ -13,17 +13,15 @@
 import pathlib
 
 import harmony
-import harmony.util
-from harmony import BaseHarmonyAdapter
 
-from podaac.netcdf_converter import netcdf_convert
+from net2cog import netcdf_convert
 
 DATA_DIRECTORY_ENV = "DATA_DIRECTORY"
 
 
-class NetcdfConverterService(BaseHarmonyAdapter):
+class NetcdfConverterService(harmony.BaseHarmonyAdapter):
     """
-    See https://git.earthdata.nasa.gov/projects/HARMONY/repos/harmony-service-lib-py/browse
+    See https://github.com/nasa/harmony-service-lib-py
     for documentation and examples.
     """