Merge pull request #49 from xylar/add_github_actions

Improve code quality and CI

.github/workflows/build_workflow.yml

@@ -0,0 +1,98 @@
+name: CI/CD Build Workflow
+
+on:
+  push:
+    branches: [main]
+
+  pull_request:
+    branches: [main]
+
+  workflow_dispatch:
+
+env:
+  CANCEL_OTHERS: true
+  PATHS_IGNORE: '["**/README.md", "**/docs/**", "**/examples/**"]'
+
+jobs:
+  pre-commit-hooks:
+    runs-on: ubuntu-latest
+    timeout-minutes: 2
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
+        with:
+          cancel_others: ${{ env.CANCEL_OTHERS }}
+          paths_ignore: ${{ env.PATHS_IGNORE }}
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Checkout Code Repository
+        uses: actions/checkout@v3
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        # Run all pre-commit hooks on all the files.
+        # Getting only staged files can be tricky in case a new PR is opened
+        # since the action is run on a branch in detached head state
+        name: Install and Run Pre-commit
+        uses: pre-commit/[email protected]
+
+  build:
+    name: Build (Python ${{ matrix.python-version }})
+    runs-on: "ubuntu-latest"
+    timeout-minutes: 20
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
+        with:
+          cancel_others: ${{ env.CANCEL_OTHERS }}
+          paths_ignore: ${{ env.PATHS_IGNORE }}
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        uses: actions/checkout@v3
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Cache Conda
+        uses: actions/cache@v3
+        env:
+          # Increase this value to reset cache if conda-env/ci.yml has not changed in the workflow
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            ${{ runner.os }}-${{ matrix.python-version }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('conda-env/dev.yml') }}
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Set up Conda Environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: "pyremap_ci"
+          channel-priority: strict
+          auto-update-conda: true
+          # IMPORTANT: This needs to be set for caching to work properly!
+          use-only-tar-bz2: true
+          python-version: ${{ matrix.python-version }}
+        run: mamba install --file dev-spec.txt
+
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Install pyremap
+        run: python -m pip install .
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Run Tests
+        env:
+          CHECK_IMAGES: False
+        run: pytest --pyargs pyremap
+

.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+exclude: "docs|ci|.git|examples|licenses|conda/meta.yaml"
+default_stages: [commit]
+fail_fast: true
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+
+  # Can run individually with `pre-commit run isort --all-files`
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+
+  # Can run individually with `pre-commit run flake8 --all-files`
+  # Need to use flake8 GitHub mirror due to CentOS git issue with GitLab
+  # https://github.com/pre-commit/pre-commit/issues/1206
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        args: ["--config=setup.cfg"]
+        additional_dependencies: [flake8-isort]

dev-spec.txt

@@ -15,6 +15,9 @@ xarray >=0.10.0
 # Development
 pip
 pytest
+isort
+flake8
+pre-commit
 
 # Documentation
 mock

pyremap/__init__.py

@@ -1,10 +1,14 @@
-from pyremap.descriptor import MpasMeshDescriptor, MpasEdgeMeshDescriptor,\
-    LatLonGridDescriptor, LatLon2DGridDescriptor, ProjectionGridDescriptor, \
-    PointCollectionDescriptor, get_lat_lon_descriptor
-
+from pyremap.descriptor import (
+    LatLon2DGridDescriptor,
+    LatLonGridDescriptor,
+    MpasEdgeMeshDescriptor,
+    MpasMeshDescriptor,
+    PointCollectionDescriptor,
+    ProjectionGridDescriptor,
+    get_lat_lon_descriptor,
+)
+from pyremap.polar import get_polar_descriptor, get_polar_descriptor_from_file
 from pyremap.remapper import Remapper
 
-from pyremap.polar import get_polar_descriptor_from_file, get_polar_descriptor
-
 __version_info__ = (0, 0, 15)
 __version__ = '.'.join(str(vi) for vi in __version_info__)

pyremap/descriptor/__init__.py

@@ -9,17 +9,23 @@
 # distributed with this code, or at
 # https://raw.githubusercontent.com/MPAS-Dev/pyremap/main/LICENSE
 
+from pyremap.descriptor.lat_lon_2d_grid_descriptor import (
+    LatLon2DGridDescriptor,
+)
+from pyremap.descriptor.lat_lon_grid_descriptor import (
+    LatLonGridDescriptor,
+    get_lat_lon_descriptor,
+)
 from pyremap.descriptor.mesh_descriptor import MeshDescriptor
+from pyremap.descriptor.mpas_edge_mesh_descriptor import MpasEdgeMeshDescriptor
 from pyremap.descriptor.mpas_mesh_descriptor import MpasMeshDescriptor
-from pyremap.descriptor.mpas_edge_mesh_descriptor import \
-    MpasEdgeMeshDescriptor
-from pyremap.descriptor.lat_lon_grid_descriptor import LatLonGridDescriptor, \
-    get_lat_lon_descriptor
-from pyremap.descriptor.lat_lon_2d_grid_descriptor import \
-    LatLon2DGridDescriptor
-from pyremap.descriptor.projection_grid_descriptor import \
-    ProjectionGridDescriptor
-from pyremap.descriptor.point_collection_descriptor import \
-    PointCollectionDescriptor
-from pyremap.descriptor.utility import interp_extrap_corner, \
-    interp_extrap_corners_2d
+from pyremap.descriptor.point_collection_descriptor import (
+    PointCollectionDescriptor,
+)
+from pyremap.descriptor.projection_grid_descriptor import (
+    ProjectionGridDescriptor,
+)
+from pyremap.descriptor.utility import (
+    interp_extrap_corner,
+    interp_extrap_corners_2d,
+)

pyremap/descriptor/lat_lon_2d_grid_descriptor.py

@@ -9,14 +9,19 @@
 # distributed with this code, or at
 # https://raw.githubusercontent.com/MPAS-Dev/pyremap/main/LICENSE
 
+import sys
+
 import netCDF4
 import numpy
-import sys
 import xarray
 
 from pyremap.descriptor.mesh_descriptor import MeshDescriptor
-from pyremap.descriptor.utility import interp_extrap_corners_2d, \
-    create_scrip, unwrap_corners, round_res
+from pyremap.descriptor.utility import (
+    create_scrip,
+    interp_extrap_corners_2d,
+    round_res,
+    unwrap_corners,
+)
 
 
 class LatLon2DGridDescriptor(MeshDescriptor):

pyremap/descriptor/lat_lon_grid_descriptor.py

@@ -9,14 +9,19 @@
 # distributed with this code, or at
 # https://raw.githubusercontent.com/MPAS-Dev/pyremap/main/LICENSE
 
+import sys
+
 import netCDF4
 import numpy
-import sys
 import xarray
 
 from pyremap.descriptor.mesh_descriptor import MeshDescriptor
-from pyremap.descriptor.utility import interp_extrap_corner, \
-    create_scrip, unwrap_corners, round_res
+from pyremap.descriptor.utility import (
+    create_scrip,
+    interp_extrap_corner,
+    round_res,
+    unwrap_corners,
+)
 
 
 def get_lat_lon_descriptor(dLon, dLat, lonMin=-180., lonMax=180., latMin=-90.,

pyremap/descriptor/mesh_descriptor.py

@@ -61,7 +61,8 @@ def to_scrip(self, scripFileName):
         scripFileName : str
             The path to which the SCRIP file should be written
         """
-        raise NotImplemented('to_scrip is not implemented for this descriptor')
+        raise NotImplementedError(
+            'to_scrip is not implemented for this descriptor')
 
     def to_esmf(self, esmfFileName):
         """
@@ -73,4 +74,5 @@ def to_esmf(self, esmfFileName):
         esmfFileName : str
             The path to which the ESMF mesh file should be written
         """
-        raise NotImplemented('to_esmf is not implemented for this descriptor')
+        raise NotImplementedError(
+            'to_esmf is not implemented for this descriptor')

pyremap/descriptor/mpas_edge_mesh_descriptor.py

@@ -9,9 +9,10 @@
 # distributed with this code, or at
 # https://raw.githubusercontent.com/MPAS-Dev/pyremap/main/LICENSE
 
+import sys
+
 import netCDF4
 import numpy as np
-import sys
 import xarray as xr
 
 from pyremap.descriptor.mesh_descriptor import MeshDescriptor
@@ -104,7 +105,7 @@ def to_scrip(self, scripFileName):
         grid_area = outFile.createVariable('grid_area', 'f8', ('grid_size',))
         grid_area.units = 'radian^2'
         # a triangle if there is 1 valid cell and a diamond if there are 2
-        areaEdge = 0.5*validCellsOnEdge*dcEdge*dvEdge
+        areaEdge = 0.5 * validCellsOnEdge * dcEdge * dvEdge
         # SCRIP uses square radians
         grid_area[:] = areaEdge[:] / (sphereRadius**2)
 
@@ -118,12 +119,12 @@ def to_scrip(self, scripFileName):
         grid_corner_lat = np.zeros((nEdges, 4))
 
         # start by repeating vertices, since these always exist
-        vertices = verticesOnEdge[:, 0]-1
+        vertices = verticesOnEdge[:, 0] - 1
         grid_corner_lon[:, 0] = lonVertex[vertices]
         grid_corner_lat[:, 0] = latVertex[vertices]
         grid_corner_lon[:, 1] = lonVertex[vertices]
         grid_corner_lat[:, 1] = latVertex[vertices]
-        vertices = verticesOnEdge[:, 1]-1
+        vertices = verticesOnEdge[:, 1] - 1
         grid_corner_lon[:, 2] = lonVertex[vertices]
         grid_corner_lat[:, 2] = latVertex[vertices]
         grid_corner_lon[:, 3] = lonVertex[vertices]
@@ -165,7 +166,7 @@ def to_esmf(self, esmfFileName):
         with xr.open_dataset(self.fileName) as ds:
 
             nCells = ds.sizes['nCells']
-            nodeCount = nCells+ds.sizes['nVertices']
+            nodeCount = nCells + ds.sizes['nVertices']
             elementCount = ds.sizes['nEdges']
             coordDim = 2
 
@@ -193,7 +194,7 @@ def to_esmf(self, esmfFileName):
         for vertex in range(3):
             # swap -1 value until they're at the end
             mask = elementConn[:, vertex] == -1
-            elementConn[mask, vertex] = elementConn[mask, vertex+1]
+            elementConn[mask, vertex] = elementConn[mask, vertex + 1]
             elementConn[mask, vertex + 1] = -1
 
         numElementConn = np.sum((elementConn != -1), axis=1).astype(np.byte)

pyremap/descriptor/mpas_mesh_descriptor.py

@@ -9,9 +9,10 @@
 # distributed with this code, or at
 # https://raw.githubusercontent.com/MPAS-Dev/pyremap/main/LICENSE
 
+import sys
+
 import netCDF4
 import numpy
-import sys
 import xarray
 
 from pyremap.descriptor.mesh_descriptor import MeshDescriptor

pyremap/descriptor/point_collection_descriptor.py

@@ -9,9 +9,10 @@
 # distributed with this code, or at
 # https://raw.githubusercontent.com/MPAS-Dev/pyremap/main/LICENSE
 
+import sys
+
 import netCDF4
 import numpy
-import sys
 import xarray
 
 from pyremap.descriptor.mesh_descriptor import MeshDescriptor
@@ -129,7 +130,7 @@ def to_esmf(self, esmfFileName):
         nPoints = len(self.lat)
 
         elementCount = nPoints
-        nodeCount = 3*nPoints
+        nodeCount = 3 * nPoints
         coordDim = 2
         maxNodePElement = 3
 

pyremap/descriptor/projection_grid_descriptor.py

@@ -9,15 +9,19 @@
 # distributed with this code, or at
 # https://raw.githubusercontent.com/MPAS-Dev/pyremap/main/LICENSE
 
+import sys
+
 import netCDF4
 import numpy
-import sys
 import pyproj
 import xarray
 
 from pyremap.descriptor.mesh_descriptor import MeshDescriptor
-from pyremap.descriptor.utility import interp_extrap_corner, \
-    create_scrip, unwrap_corners
+from pyremap.descriptor.utility import (
+    create_scrip,
+    interp_extrap_corner,
+    unwrap_corners,
+)
 
 
 class ProjectionGridDescriptor(MeshDescriptor):