Reading 'positive' attribute back to the depth dimension (#103)

Reordering the attributes of the dimensions, we considered that it was best to keep the attribute `positive`, to have it clear where the dimension depth points (down for depth, up for elevation).

README.md

@@ -22,43 +22,36 @@ The `copernicusmarine` offers capabilities through both **Command Line Interface
 
 ## Installation
 
-
 For installation, multiple options are available depending on your setup:
 
 ### Mamba | Conda
 
-
 A `conda` package is available on [Anaconda](https://anaconda.org/conda-forge/copernicusmarine).
 
 You can install it using `mamba` (or conda) through the `conda-forge` channel with the following command:
 
-
 ```bash
 mamba install conda-forge::copernicusmarine --yes
 ```
 
 To upgrade the Toolbox with mamba (or conda):
 
-
 ```bash
 mamba update --name copernicusmarine copernicusmarine --yes
 ```
 
 ### Docker
 
-
 A docker image is also available here: [https://hub.docker.com/r/copernicusmarine/copernicusmarine](https://hub.docker.com/r/copernicusmarine/copernicusmarine)
 
 First step is to pull the container image:
 
-
 ```bash
 docker pull copernicusmarine/copernicusmarine:latest
 ```
 
 Then run it:
 
-
 ```bash
 docker run -it --rm copernicusmarine/copernicusmarine --version
 ```
@@ -75,14 +68,12 @@ python -m pip install copernicusmarine
 
 And to **upgrade the package** to the newest available version, run:
 
-
 ```bash
 python -m pip install copernicusmarine --upgrade
 ```
 
 ## User Guide
 
-
 For more comprehensive details on how to use the `copernicusmarine` Toolbox, please refer to our [Help Center](https://help.marine.copernicus.eu/en/collections/9080063-copernicus-marine-toolbox). It ensures a smooth migration for existing users of legacy services such as MOTU, OPeNDAP or FTP.
 
 ### Network configuration
@@ -174,7 +165,6 @@ You can use the `--skip-if-user-logged-in` option to skip the configuration file
 
 #### Access points migration and evolution
 
-
 If you still have a configuration for legacy services (e.g. `~/motuclient/motuclient-python.ini`, `~/.netrc` or `~/_netrc`) in your home directory, it will automatically be taken into account with commands `get` and `subset` without the need for running the `login` command.
 If the configuration files are already available in another directory, when running commands `subset` or `get`, you can use the `--credentials-file` option to point to the files.
 

copernicusmarine/core_functions/credentials_utils.py

@@ -36,10 +36,12 @@
 # TODO: handle cache of the credentials without cachier
 
 
-class CredentialCannotBeNone(Exception): ...
+class CredentialCannotBeNone(Exception):
+    ...
 
 
-class InvalidUsernameOrPassword(Exception): ...
+class InvalidUsernameOrPassword(Exception):
+    ...
 
 
 def _load_credential_from_copernicus_marine_configuration_file(

copernicusmarine/download_functions/subset_xarray.py

@@ -377,7 +377,11 @@ def _update_dataset_coordinate_attributes(
                         coord.encoding["units"].replace("_", " ").title()
                     )
                     coordinate_attributes.remove("units")
-                elif coordinate_label in ["latitude", "depth", "elevation"]:
+                elif coordinate_label in ["depth", "elevation"]:
+                    attrs["valid_min"] = coord.values.min()
+                    attrs["valid_max"] = coord.values.max()
+                    coordinate_attributes.append("positive")
+                elif coordinate_label == "latitude":
                     attrs["valid_min"] = coord.values.min()
                     attrs["valid_max"] = coord.values.max()
                 elif coordinate_label == "longitude":

tests/test_command_line_interface.py

@@ -1011,24 +1011,27 @@ def then_I_have_correct_sign_for_depth_coordinates_values(
             assert dataset.elevation.min() >= -10
             assert dataset.elevation.max() <= 0
 
-    def then_I_have_correct_attribute_value(self, output_path, dimention_name):
+    def then_I_have_correct_attribute_value(
+        self, output_path, dimention_name, attribute_value
+    ):
         filepath = pathlib.Path(output_path, "data.zarr")
         dataset = xarray.open_dataset(filepath, engine="zarr")
         assert dataset[dimention_name].attrs["standard_name"] == dimention_name
+        assert dataset[dimention_name].attrs["positive"] == attribute_value
 
     def test_conversion_between_elevation_and_depth(self, tmp_path):
         self.when_I_request_subset_dataset_with_zarr_service(tmp_path, True)
         self.then_I_have_correct_sign_for_depth_coordinates_values(
             tmp_path, "positive"
         )
-        self.then_I_have_correct_attribute_value(tmp_path, "depth")
+        self.then_I_have_correct_attribute_value(tmp_path, "depth", "down")
 
     def test_force_no_conversion_between_elevation_and_depth(self, tmp_path):
         self.when_I_request_subset_dataset_with_zarr_service(tmp_path, False)
         self.then_I_have_correct_sign_for_depth_coordinates_values(
             tmp_path, "negative"
         )
-        self.then_I_have_correct_attribute_value(tmp_path, "elevation")
+        self.then_I_have_correct_attribute_value(tmp_path, "elevation", "up")
 
     def when_I_run_copernicus_marine_command_using_no_directories_option(
         self, tmp_path, force_service: GetServiceToTest, output_directory=None

tests/test_python_interface.py

@@ -227,6 +227,7 @@ def test_subset_modify_attr_for_depth(self):
         dataset = open_dataset(
             dataset_id="cmems_mod_arc_phy_anfc_6km_detided_P1D-m"
         )
+        assert dataset.depth.attrs["positive"] == "down"
         assert dataset.depth.attrs["standard_name"] == "depth"
         assert dataset.depth.attrs["long_name"] == "Depth"