Merge pull request #153 from SciTools-incubator/unstructured_scheme

Merge unstructured scheme feature branch

Author: bjlittle

.cirrus.yml

@@ -20,7 +20,7 @@ env:
   SKIP_TEST_TASK: ""
   SKIP_BENCHMARK_TASK: ""
   # Maximum cache period (in weeks) before forcing a new cache upload.
-  CACHE_PERIOD: "2"
+  CACHE_PERIOD: "0"
   # Increment the build number to force new conda cache upload.
   CONDA_CACHE_BUILD: "0"
   # Increment the build number to force new nox cache upload.
@@ -31,6 +31,27 @@ env:
   PIP_CACHE_PACKAGES: "pip setuptools wheel nox pyyaml"
   # Conda packages to be installed.
   CONDA_CACHE_PACKAGES: "nox pip pyyaml"
+  # Use specific custom iris source feature branch.
+  IRIS_SOURCE: "github:main"
+  # Git commit hash for iris test data.
+  IRIS_TEST_DATA_VERSION: "2.2"
+  # Base directory for the iris-test-data.
+  IRIS_TEST_DATA_DIR: ${HOME}/iris-test-data
+  OVERRIDE_TEST_DATA_REPOSITORY: ${IRIS_TEST_DATA_DIR}/test_data
+
+
+#
+# YAML alias for the iris-test-data cache.
+#
+iris_test_data_template: &IRIS_TEST_DATA_TEMPLATE
+  data_cache:
+    folder: ${IRIS_TEST_DATA_DIR}
+    fingerprint_script:
+      - echo "iris-test-data v${IRIS_TEST_DATA_VERSION}"
+    populate_script:
+      - wget --quiet https://github.com/SciTools/iris-test-data/archive/v${IRIS_TEST_DATA_VERSION}.zip -O iris-test-data.zip
+      - unzip -q iris-test-data.zip
+      - mv iris-test-data-${IRIS_TEST_DATA_VERSION} ${IRIS_TEST_DATA_DIR}
 
 
 #
@@ -88,10 +109,6 @@ test_task:
   only_if: ${SKIP_TEST_TASK} == ""
   auto_cancellation: true
   matrix:
-    env:
-      PY_VER: "3.6"
-    env:
-      PY_VER: "3.7"
     env:
       PY_VER: "3.8"
       COVERAGE: "true"
@@ -104,6 +121,7 @@ test_task:
       - echo "${CIRRUS_TASK_NAME}"
       - echo "${NOX_CACHE_BUILD}"
       - if [ -n "${IRIS_SOURCE}" ]; then echo "${IRIS_SOURCE}"; fi
+  << : *IRIS_TEST_DATA_TEMPLATE
   test_script:
     - export CONDA_OVERRIDE_LINUX="$(uname -r | cut -d'+' -f1)"
     - nox --session tests -- --verbose

README.md

@@ -7,3 +7,59 @@
 [![License](https://img.shields.io/github/license/SciTools-incubator/iris-esmf-regrid)](https://github.com/SciTools-incubator/iris-esmf-regrid/blob/main/LICENSE)
 [![Contributors](https://img.shields.io/github/contributors/SciTools-incubator/iris-esmf-regrid)](https://github.com/SciTools-incubator/iris-esmf-regrid/graphs/contributors)
 ![Mark stale issues and pull requests](https://github.com/SciTools-incubator/iris-esmf-regrid/workflows/Mark%20stale%20issues%20and%20pull%20requests/badge.svg)
+
+---
+
+## Overview
+
+This project aims to provide a bridge between [Iris](https://github.com/SciTools/iris)
+and [ESMF](https://github.com/esmf-org/esmf). This takes the form of regridder classes
+which take Iris cubes as their arguments and use ESMF to perform regridding
+calculations. These classes are designed to perform well on cubes which have multiple
+non-horizontal dimensions and lazy ([Dask](https://github.com/dask/dask)) data.
+Both rectilinear and curvilinear grids as well as UGRID meshes have been supported.
+
+## Regridding Example
+
+There are a range of regridder classes (e.g `MeshToGridESMFRegridder` and
+`GridToMeshESMFRegridder`). For an example of the regridding process, the
+`MeshToGridESMFRegridder` class works as follows:
+
+```python
+import iris
+from iris.experimental.ugrid import PARSE_UGRID_ON_LOAD
+from esmf_regrid.experimental.unstructured_scheme import MeshToGridESMFRegridder
+
+# An example such a file can be found at:
+# https://github.com/SciTools/iris-test-data/blob/master/test_data/NetCDF/unstructured_grid/data_C4.nc
+with PARSE_UGRID_ON_LOAD.context():
+    source_mesh_cube = iris.load_cube("mesh_cube.nc")
+
+# An example of such a file can be found at:
+# https://github.com/SciTools/iris-test-data/blob/master/test_data/NetCDF/global/xyt/SMALL_hires_wind_u_for_ipcc4.nc
+target_grid_cube = iris.load_cube("grid_cube.nc")
+
+# Initialise the regridder with a source mesh and target grid.
+regridder = MeshToGridESMFRegridder(source_mesh_cube, target_grid_cube)
+
+# use the initialised regridder to regrid the data from the source cube
+# onto a cube with the same grid as `target_grid_cube`.
+result = regridder(source_mesh_cube)
+```
+
+Note that this pattern allows the reuse of an initialised regridder, saving
+significant amounts of time when regridding. To make use of this efficiency across
+sessions, we support the saving of certain regridders. We can do this as follows:
+
+```python
+from esmf_regrid.experimental.io import load_regridder, save_regridder
+
+# Save the regridder.
+save_regridder(regridder, "saved_regridder.nc")
+
+# Load saved regridder.
+loaded_regridder = load_regridder("saved_regridder.nc")
+
+# Use loaded regridder.
+result = loaded_regridder(source_mesh_cube)
+```

benchmarks/benchmarks/__init__.py

@@ -1 +1,44 @@
 """Benchmark tests for iris-esmf-regrid"""
+
+
+def disable_repeat_between_setup(benchmark_object):
+    """
+    Decorator for benchmarks where object persistence would be inappropriate.
+
+    E.g:
+        * Data is realised during testing.
+
+    Can be applied to benchmark classes/methods/functions.
+
+    https://asv.readthedocs.io/en/stable/benchmarks.html#timing-benchmarks
+
+    """
+    # Prevent repeat runs between setup() runs - object(s) will persist after 1st.
+    benchmark_object.number = 1
+    # Compensate for reduced certainty by increasing number of repeats.
+    #  (setup() is run between each repeat).
+    #  Minimum 5 repeats, run up to 30 repeats / 20 secs whichever comes first.
+    benchmark_object.repeat = (5, 30, 20.0)
+    # ASV uses warmup to estimate benchmark time before planning the real run.
+    #  Prevent this, since object(s) will persist after first warmup run,
+    #  which would give ASV misleading info (warmups ignore ``number``).
+    benchmark_object.warmup_time = 0.0
+
+    return benchmark_object
+
+
+def skip_benchmark(benchmark_object):
+    """
+    Decorator for benchmarks skipping benchmarks.
+    """
+
+    def setup_cache(self):
+        pass
+
+    def setup(*args):
+        raise NotImplementedError
+
+    benchmark_object.setup_cache = setup_cache
+    benchmark_object.setup = setup
+
+    return benchmark_object