Merge branch 'master' of https://github.com/OpenDrift/opendrift into …

…dsd_options

.circleci/config.yml

@@ -18,7 +18,7 @@ commands:
             [[ "<<parameters.mpl>>" == "true" ]] && export MPL="--mpl"
 
             source activate opendrift
-            pytest --circleci-parallelize --junitxml=test-results/junit.xml --cov=opendrift --ignore=tests/benchmarks --ignore=tests/wps --run-slow $MPL --durations=50 --benchmark-disable -v --log-cli-level=debug
+            pytest --circleci-parallelize --junitxml=test-results/junit.xml --cov=opendrift --ignore=tests/benchmarks --ignore=tests/wps --run-slow $MPL --mpl-results-path=test-results/mpl_images --durations=50 --benchmark-disable -v --log-cli-level=debug
 
       - store_test_results:
           path: test-results
@@ -44,7 +44,7 @@ commands:
             cat envconfig
 
       - restore_cache:
-          key: v18-deps1-{{ checksum "environment.yml" }}-{{ checksum "envconfig" }}
+          key: v19-deps1-{{ checksum "environment.yml" }}-{{ checksum "envconfig" }}
 
       - run:
           name: Install requirements
@@ -54,14 +54,14 @@ commands:
               if [ -v PYTHON_VERSION ]; then
                 echo "Pinning python: ${PYTHON_VERSION}."
                 # pin python
-                conda create -c conda-forge -n opendrift -q -y "python=${PYTHON_VERSION}"
+                mamba create -c conda-forge -n opendrift -q -y "python=${PYTHON_VERSION}"
 
                 echo "python ${PYTHON_VERSION}.*" > /opt/conda/envs/opendrift/conda-meta/pinned
                 cat /opt/conda/envs/opendrift/conda-meta/pinned
 
-                conda env update -n opendrift -q -f environment.yml
+                mamba env update -n opendrift -q -f environment.yml
               else
-                conda env create -q --file environment.yml
+                mamba env create -q --file environment.yml
               fi
 
               source activate opendrift
@@ -70,14 +70,14 @@ commands:
             fi
 
       - save_cache:
-          key: v18-deps1-{{ checksum "environment.yml" }}-{{ checksum "envconfig" }}
+          key: v19-deps1-{{ checksum "environment.yml" }}-{{ checksum "envconfig" }}
           paths:
             - "/opt/conda/envs"
       - run:
           name: List environment
           command: |
             source activate opendrift
-            conda list
+            mamba list
 
   install_cartopy_shapes:
     steps:
@@ -99,7 +99,7 @@ commands:
 
 test-template: &test-template
   docker:
-    - image: continuumio/miniconda3
+    - image: condaforge/mambaforge
   resource_class: medium+
   steps:
     - checkout
@@ -114,7 +114,7 @@ test-template: &test-template
 jobs:
   build_package:
     docker:
-      - image: continuumio/miniconda3
+      - image: condaforge/mambaforge
     environment:
       - PYTHON_VERSION=3.9
 
@@ -142,7 +142,7 @@ jobs:
 
   publish_package:
     docker:
-      - image: continuumio/miniconda3
+      - image: condaforge/mambaforge
     environment:
       - PYTHON_VERSION=3.9
 
@@ -184,61 +184,18 @@ jobs:
     environment:
       - PYTHON_VERSION=3.8
 
-  python_37:
-    <<: *test-template
-    parallelism: 5
-    environment:
-      - PYTHON_VERSION=3.7
-
-  python_310_o_l_d:
-    docker:
-      - image: continuumio/miniconda3
-    parallelism: 5
-    environment:
-      - PYTHON_VERSION=3.10
-    steps:
-    - checkout
-
-    - install_conda_environment
-
-    - run:
-        name: Install opendrift-landmask-data and remove roaring-landmask
-        command: |
-          source activate opendrift
-          conda install -y -c conda-forge -c opendrift opendrift-landmask-data
-          pip uninstall -y roaring-landmask
-
-    - restore_cache:
-        key: v2-landmask
-
-    - run:
-        name: Generate landmask
-        command: |
-          source activate opendrift
-          python -c 'import opendrift_landmask_data as old; old.Landmask()'
-
-    - save_cache:
-        key: v2-landmask
-        paths:
-          - "/tmp/landmask"
-
-    - install_cartopy_shapes
-
-    - run_tests:
-        mpl: false
-
   docs-build-examples:
     docker:
-      - image: continuumio/miniconda3
+      - image: condaforge/mambaforge
     parallelism: 20
     steps:
       - checkout
       - run:
           name: Update packages
-          command: apt-get update
+          command: DEBIAN_FRONTEND=noninteractive apt-get -y update
       - run:
           name: Install packages
-          command: apt-get install -y build-essential jq curl
+          command: DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential jq curl
 
       - run:
           name: Get PR title
@@ -259,7 +216,7 @@ jobs:
           name: Install sphinx and friends
           command: |
             source activate opendrift
-            conda install -c conda-forge sphinx sphinx-autoapi sphinx-gallery>=0.7.0
+            mamba install -c conda-forge sphinx sphinx-autoapi sphinx-gallery>=0.7.0
             pip install sphinx-rtd-theme
 
       - run:
@@ -312,7 +269,7 @@ jobs:
             cd docs/
             make sharded-gallery SHARDS=${CIRCLE_NODE_TOTAL} SHARD=${CIRCLE_NODE_INDEX}
             ls -R source
-          no_output_timeout: 40m
+          no_output_timeout: 60m
 
       - store_test_results:
           path: docs/test-results
@@ -326,7 +283,7 @@ jobs:
 
   docs-build:
     docker:
-      - image: continuumio/miniconda3
+      - image: condaforge/mambaforge
     steps:
       - checkout
 
@@ -335,10 +292,10 @@ jobs:
 
       - run:
           name: Update packages
-          command: apt-get update
+          command: DEBIAN_FRONTEND=noninteractive apt-get -y update
       - run:
           name: Install packages
-          command: apt-get install -y build-essential gfortran libgeos-dev gdal-bin imagemagick jq curl
+          command: DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential gfortran libgeos-dev gdal-bin imagemagick jq curl
 
       - run:
           name: Get PR title
@@ -373,7 +330,7 @@ jobs:
           name: Install sphinx and friends
           command: |
             source activate opendrift
-            conda install -c conda-forge sphinx sphinx-autoapi sphinx-gallery>=0.7.0
+            mamba install -c conda-forge sphinx sphinx-autoapi sphinx-gallery>=0.7.0
             pip install sphinx-rtd-theme
 
       - save_cache:
@@ -454,8 +411,6 @@ workflows:
       - python_310
       - python_39
       - python_38
-      - python_37
-      - python_310_o_l_d
       - build_package
       - publish_package:
           requires:

docs/source/install.rst

@@ -16,10 +16,10 @@ Alternative 1: Using Miniconda and Git (recommended)
 
 .. code-block:: bash
 
-  $ conda config --add channels conda-forge  # recommended, but not necessary
+  $ conda config --add channels conda-forge
   $ conda env create -f environment.yml
   $ conda activate opendrift
-  $ pip install -e .
+  $ pip install --no-deps -e .
 
 This installs the OpenDrift package as an editable package. You can therefore directly make changes to the repository or fetch the newest changes with :code:`git pull`. You do not need to add OpenDrift to PYTHONPATH as long as you have the :code:`opendrift` environment activated.
 
@@ -33,39 +33,39 @@ Alternative 2: Using Miniconda
 ++++++++++++++++++++++++++++++
 
 1. Install `miniconda3 <https://docs.conda.io/en/latest/miniconda.html>`_
-2. Set up a *Python 3* environment for opendrift
+2. Set up a *Python 3* environment for opendrift and install opendrift
 
 .. code-block:: bash
 
-   $ conda config --add channels conda-forge  # recommended, but not necessary
-   $ conda create -n opendrift python=3
+   $ conda config --add channels conda-forge
+   $ conda create -n opendrift python=3 opendrift
    $ conda activate opendrift
 
-3. Install OpenDrift and dependencies
-
-.. code-block:: bash
-
-  $ conda install -c opendrift -c conda-forge -c noaa-orr-erd opendrift
-
 .. _source_install:
 
 Modify install to use Git version
 ---------------------------------
 
 If you later want to edit the OpenDrift source code, or be able to update from repository with `git pull`, the following two steps are necessary. This yields the same as Alternative 1.
 
-4. Clone OpenDrift:
+3. Clone OpenDrift:
 
 .. code-block:: bash
 
    $ git clone https://github.com/OpenDrift/opendrift.git
    $ cd opendrift/
 
+4. Remove original package:
+
+.. code-block:: bash
+
+   $ conda remove opendrift
+
 5. Install as editable:
 
 .. code-block:: bash
 
-   $ pip install -e .
+   $ pip install -e --no-deps .
 
 Building and using the Docker image
 +++++++++++++++++++++++++++++++++++

docs/source/references.rst

@@ -3,6 +3,10 @@ Publications
 
 Some papers using or mentioning OpenDrift:
 
+Rodríguez-Villegas C., Figueroa R.I, Pérez-Santos I, Molinet C., Saldías G.S., Rosales S.A, Álvarez G., Linford P., Díaz P.A., Continental shelf off northern Chilean Patagonia: A potential risk zone for the onset of Alexandrium catenella toxic bloom? Marine Pollution Bulletin 184 (2022) 114103, https://doi.org/10.1016/j.marpolbul.2022.11410
+
+Devis Morales A.D., Rubio E.R., Martínez D.R., Numerical modeling of oil spills in the Gulf of Morrosquillo, Colombian Caribean, Ciencia, Tecnologia y Futuro Vol 12, Num 1 June 2022. pages 69 - 83, https://doi.org/10.29047/01225383.396.
+
 Kotnik, J.; Žagar, D.; Novak, G.; Ličer, M.; Horvat, M. Dissolved Gaseous Mercury (DGM) in the Gulf of Trieste, Northern Adriatic Sea. J. Mar. Sci. Eng. 2022, 10, 587. https://doi.org/10.3390/jmse10050587
 
 Keramea P, Kokkos N, Gikas GD, Sylaios G. Operational Modeling of North Aegean Oil Spills Forced by Real-Time Met-Ocean Forecasts. Journal of Marine Science and Engineering. 2022; 10(3):411. https://doi.org/10.3390/jmse10030411

environment.yml

@@ -3,7 +3,7 @@ channels:
   - opendrift
   - conda-forge
 dependencies:
-  - matplotlib>=3.1
+  - matplotlib>=3.5
   - numpy>=1.17
   - scipy>=1.6
   - netcdf4
@@ -29,7 +29,7 @@ dependencies:
   - coloredlogs
   - cmocean
   - utm
+  - roaring-landmask>=0.7
   - pip
   - pip:
     - motuclient
-    - roaring-landmask

examples/example_compare_oilbudgets.py

@@ -37,7 +37,7 @@
         b[ot] = o.get_oil_budget()
         # Get viscosity and density
         kin_viscosity = o.history['viscosity']
-        dyn_viscosity = kin_viscosity * o.history['density']
+        dyn_viscosity = kin_viscosity * o.history['density'] * 1000 # mPas
         viscosities[ot] = dyn_viscosity.mean(axis=0)
         densities[ot] = o.history['density'].mean(axis=0)
         water_fractions[ot] = o.history['water_fraction'].mean(axis=0)

examples/example_grid_time.py

@@ -18,8 +18,7 @@
 
 #%%
 # Landmask
-reader_landmask = reader_global_landmask.Reader(
-                    extent=[4.0, 5.5, 59.9, 61.2])
+reader_landmask = reader_global_landmask.Reader()
 
 o.add_reader([reader_landmask, reader_norkyst])
 

examples/example_rungekutta_norkyst.py

@@ -17,8 +17,7 @@
     '16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
 time = reader_norkyst.start_time
 
-reader_landmask = reader_global_landmask.Reader(
-                    extent=[4, 5.5, 59.9, 61.5])
+reader_landmask = reader_global_landmask.Reader()
 
 o.add_reader([reader_norkyst, reader_landmask])
 lon = 4.5; lat = 60.0;

examples/example_schism_native.py

@@ -20,15 +20,13 @@
 ###############################
 # Creating and adding reader using a native SCHISM netcdf output file
 # SCHISM reader
-reader_landmask = reader_global_landmask.Reader(
-                    llcrnrlon=171.5, llcrnrlat=-43.5,
-                    urcrnrlon=177.0, urcrnrlat=-38.0)
+reader_landmask = reader_global_landmask.Reader()
 
 # NZTM proj4 string found at https://spatialreference.org/ref/epsg/nzgd2000-new-zealand-transverse-mercator-2000/
 proj4str_nztm = '+proj=tmerc +lat_0=0 +lon_0=173 +k=0.9996 +x_0=1600000 +y_0=10000000 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs'
 schism_native = reader_schism_native.Reader(
-	filename = 'https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc', 
-	proj4 = proj4str_nztm, 
+	filename = 'https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc',
+	proj4 = proj4str_nztm,
 	use_3d = True)
 # schism_native.plot_mesh(variable = ['sea_floor_depth_below_sea_level']) # check reader was correctly loaded
 
@@ -48,12 +46,12 @@
 o.disable_vertical_motion()  #Deactivate any vertical processes/advection"""
 #%%
 # Running model
-o.run(time_step=900, 
+o.run(time_step=900,
 	  end_time = schism_native.start_time+timedelta(days=0.1))
 	  # outfile='schism_native_output.nc')
 
 # Print and plot results
 print(o)
 o.plot(fast=True)
 o.animation()
-o.animation_profile()
+o.animation_profile()

examples/example_sediments.py

@@ -7,13 +7,13 @@
 from datetime import timedelta, datetime
 from opendrift.models.sedimentdrift import SedimentDrift
 
-o = SedimentDrift(loglevel=50)  # 0 for debug output
+o = SedimentDrift(loglevel=0)  # 0 for debug output
 
 #%%
 # Source of sediments at Glomma river outlet
 lat=59.169194
 lon=10.962920
-o.seed_elements(lon=lon, lat=lat, number=10000, 
+o.seed_elements(lon=lon, lat=lat, number=10000,
                 time=[datetime.utcnow(), datetime.utcnow()+timedelta(hours=48)],
                 terminal_velocity=-.001)  # 1 mm/s settling speed