revert workaround (#1077)

* reverted temporary hycom workaround

* updated comments in notebook and test script

* updated installation docs

Author: veenstrajelmer

docs/CONTRIBUTING.md

@@ -13,7 +13,7 @@
 ## Setup local developer environment
 
 - python 3.11 is recommended, [python>=3.9 is required](https://github.com/Deltares/dfm_tools/issues/267), [python 3.13 not yet supported](https://github.com/Deltares/dfm_tools/issues/559)
-- download Miniforge3 from [the miniforge github](https://github.com/conda-forge/miniforge?tab=readme-ov-file#download) and install it with the recommended settings.
+- download Miniforge3 from [conda-forge.org](https://conda-forge.org/miniforge) and install it with the recommended settings.
 - open Miniforge Prompt and navigate to the local checkout folder of the repository
 - `conda create --name dfm_tools_env python=3.11 git spyder -y` (`git` and `spyder` are optional)
 - `conda activate dfm_tools_env`

docs/installation.md

@@ -6,7 +6,7 @@
 
 ## Recommended installation
 
-- download Miniforge3 from [the miniforge github](https://github.com/conda-forge/miniforge?tab=readme-ov-file#download) and install it with the recommended settings.
+- download Miniforge3 from [conda-forge.org](https://conda-forge.org/miniforge) and install it with the recommended settings.
 - open Miniforge Prompt
 - `conda create --name dfm_tools_env python=3.12 git spyder -y` (`git` and `spyder` are optional)
 - `conda activate dfm_tools_env`

docs/notebooks/modelbuilder_example.ipynb

@@ -1065,7 +1065,7 @@
     "        \n",
     "    mdu.physics.iniwithnudge = 2 # support for initial sal/tem fields via iniwithnudge (requires a 3D model)\n",
     "    mdu.physics.salinity = 1 # enable salinity\n",
-    "    mdu.physics.temperature = 5 # composite ocean model\n",
+    "    mdu.physics.temperature = 5 # composite ocean model. This is automatically set to 1 if additional ERA5 variables are not provided.\n",
     "    mdu.physics.initialsalinity = 30 # for coastal models (default is 0)\n",
     "    mdu.physics.heat_eachstep = 1 # compute heatflux model on each timestep\n",
     "    mdu.physics.rhoairrhowater = 1 # better wind/water interaction\n",

tests/test_download.py

@@ -254,7 +254,7 @@ def test_copernicusmarine_get_dataset_id():
 @pytest.mark.unittest
 def test_download_cmems_my(tmp_path):
     # deliberately take inconvenient time/spatial subset to test if
-    # coordinates_selection_method='outside'
+    # coordinates_selection_method='outside' works properly
     date_min = '2010-01-01 01:00'
     date_max = '2010-01-01 23:00'
     longitude_min, longitude_max, latitude_min, latitude_max =    2.001,   3.001,  51.001, 52.001 #test domain
@@ -330,7 +330,6 @@ def test_download_hycom(tmp_path):
         dataset_url = [f'https://tds.hycom.org/thredds/dodsC/GLBu0.08/expt_19.1/{year}' for year in period_range_years] #list is possible with hycom, since it uses xr.open_mfdataset()
         # temporary fix to avoid RuntimeError: NetCDF: file not found
         # https://github.com/Deltares/dfm_tools/issues/1048
-        dataset_url = dataset_url[0]
         file_prefix = 'hycom_'
         dfmt.download_OPeNDAP(dataset_url=dataset_url,
                               varkey=varkey,