ecmwf · mathleur · Jan 24, 2024 · Jan 24, 2024 · Jan 24, 2024 · Jan 24, 2024
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -0,0 +1,153 @@
+name: ci
+on:
+  # Trigger the workflow on push to master or develop, except tag creation
+  push:
+    branches:
+      - 'main'
+      - 'develop'
+  # Trigger the workflow on pull request
+  pull_request: ~
+  # Trigger the workflow manually
+  workflow_dispatch: ~
+  # Trigger after public PR approved for CI
+  pull_request_target:
+    types: [labeled]
+  release:
+    types: [created]
+jobs:
+  qa:
+    name: qa
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+        with:
+          repository: ${{ inputs.repository }}
+          ref: ${{ inputs.ref }}
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python_version }}
+
+      - name: Install Python Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install black flake8 isort
+      - name: Check isort
+        run: isort --check .
+
+      - name: Check black
+        run: black --check .
+
+      - name: Check flake8
+        run: flake8 .
+  setup:
+    name: setup
+    runs-on: ubuntu-20.04
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+      inputs: ${{ steps.prepare-inputs.outputs.inputs }}
+      inputs-for-ubuntu: ${{ steps.prepare-inputs.outputs.inputs-for-ubuntu }}
+    steps:
+      - name: Set Matrix
+        id: set-matrix
+        shell: bash -eux {0}
+        run: |
+          MATRIX=$(cat << 'EOS'
+          name:
+          - [email protected]
+          - [email protected]
+          include:
+          - name: [email protected]
+            os: ubuntu-22.04
+            compiler: gnu-11
+            compiler_cc: gcc-11
+            compiler_cxx: g++-11
+            compiler_fc: gfortran-11
+          - name: [email protected]
+            os: ubuntu-22.04
+            compiler: clang-14
+            compiler_cc: clang-14
+            compiler_cxx: clang++-14
+            compiler_fc: gfortran-11
+          # Xcode compiler requires empty environment variables, so we pass null (~) here
+          EOS
+          )
+          SKIP_MATRIX_JOBS=$(cat << 'EOS'
+          ${{ inputs.skip_matrix_jobs }}
+          EOS
+          )
+          SELECT_NAME_COND="1 != 1"
+          SELECT_INCLUDE_COND="1 != 1"
+          for skip_job in $SKIP_MATRIX_JOBS; do SELECT_NAME_COND="$SELECT_NAME_COND or . == \"$skip_job\""; SELECT_INCLUDE_COND="$SELECT_INCLUDE_COND or .name == \"$skip_job\""; done
+          echo matrix=$(echo "$MATRIX" | yq eval "del(.name[] | select($SELECT_NAME_COND)) | del(.include[] | select($SELECT_INCLUDE_COND))" --output-format json --indent 0 -) >> $GITHUB_OUTPUT
+      - name: Prepare build-package Inputs
+        id: prepare-inputs
+        shell: bash -eux {0}
+        run: |
+          echo inputs=$(echo "${{ inputs.build_package_inputs || '{}' }}" | yq eval '.' --output-format json --indent 0 -) >> $GITHUB_OUTPUT
+          echo inputs-for-ubuntu=$(echo "${{ inputs.build_package_inputs || '{}' }}" | yq eval '. * {"os":"ubuntu-20.04","compiler":"gnu-10","compiler_cc":"gcc-10","compiler_cxx":"g++-10","compiler_fc":"gfortran-10"}' --output-format json --indent 0 -) >> $GITHUB_OUTPUT
+  test:
+    name: test
+    needs:
+      - qa
+      - setup
+    strategy:
+      fail-fast: false
+      matrix: ${{ fromJson(needs.setup.outputs.matrix) }}
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ inputs.python_version }}
+
+      - name: Install Python Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install --upgrade pip setuptools wheel
+          python -m pip install pytest pytest-cov
+          python -m pip install -r requirements.txt 
+          python -m pip install -r ./tests/requirements_test.txt
+
+      - name: Verify Source Distribution
+        shell: bash -eux {0}
+        run: |
+          python setup.py sdist
+          python -m pip install dist/*
+      - name: Run Tests with Repository Code
+        env:
+          LD_LIBRARY_PATH: ${{ steps.install-dependencies.outputs.lib_path }}
+        shell: bash -eux {0}
+        run: |
+          DYLD_LIBRARY_PATH=${{ env.LD_LIBRARY_PATH }} python -m pytest -m "not data" tests --cov=./ --cov-report=xml
+          python -m coverage report
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          files: coverage.xml
+  deploy:
+    needs: test
+    if: ${{ github.event_name == 'release' }}
+    name: Upload to Pypi
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          python setup.py sdist
+          twine upload dist/*
diff --git a/README.md b/README.md
@@ -4,17 +4,6 @@ ECMWF library for encoding and decoding coerageJSON files/objects of meteorlogic
 
 * Encodes and decodes CoverageJSON objects
 
-* CoverageCollection(python dictionary)
-  * get_coverages()
-
-* Coverage()
-  * get_axes()
-  * get_metadata()
-  * get_ranges()
-  * get_parameters()
 
-
-* TimeSeriesCoverage()
-  * set_axes()
-  * set_ranges()
-  * set_parameters()
+| :warning: This project is BETA and will be experimental for the foreseeable future. Interfaces and functionality are likely to change. DO NOT use this software in any project/software that is operational. |
+|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
diff --git a/eccovjson/Coverage.py b/eccovjson/Coverage.py
@@ -1,6 +1,3 @@
-import json
-
-
 class Coverage:
     def __init__(self, covjson):
         if isinstance(covjson, dict):

diff --git a/eccovjson/CoverageCollection.py b/eccovjson/CoverageCollection.py
@@ -1,6 +1,3 @@
-import json
-
-
 class CoverageCollection:
     def __init__(self, covjson):
         if isinstance(covjson, dict):
@@ -12,8 +9,6 @@ def __init__(self, covjson):
         if self.type == "CoverageCollection":
             print("Correct Type")
         elif self.type == "Coverage":
-            raise TypeError(
-                "CoverageCollection class takes CoverageCollection not Coverage"
-            )
+            raise TypeError("CoverageCollection class takes CoverageCollection not Coverage")
 
         self.coverages = self.coverage["coverages"]
diff --git a/eccovjson/__init__.py b/eccovjson/__init__.py
@@ -1,5 +1,5 @@
-import eccovjson.encoder.VerticalProfile
-import eccovjson.encoder.TimeSeries
-import eccovjson.decoder.VerticalProfile
-import eccovjson.decoder.TimeSeries
 import eccovjson.api
+import eccovjson.decoder.TimeSeries
+import eccovjson.decoder.VerticalProfile
+import eccovjson.encoder.TimeSeries
+import eccovjson.encoder.VerticalProfile
diff --git a/eccovjson/api.py b/eccovjson/api.py
@@ -1,13 +1,11 @@
-import json
-
+import eccovjson.decoder.BoundingBox
+import eccovjson.decoder.Frame
 import eccovjson.decoder.TimeSeries
 import eccovjson.decoder.VerticalProfile
-import eccovjson.encoder.TimeSeries
-import eccovjson.encoder.VerticalProfile
 import eccovjson.encoder.BoundingBox
-import eccovjson.decoder.BoundingBox
 import eccovjson.encoder.Frame
-import eccovjson.decoder.Frame
+import eccovjson.encoder.TimeSeries
+import eccovjson.encoder.VerticalProfile
 
 features_encoder = {
     "pointseries": eccovjson.encoder.TimeSeries.TimeSeries,

diff --git a/eccovjson/decoder/BoundingBox.py b/eccovjson/decoder/BoundingBox.py
@@ -1,7 +1,9 @@
-from .decoder import Decoder
-import xarray as xr
 import datetime as dt
 
+import xarray as xr
+
+from .decoder import Decoder
+
 
 class BoundingBox(Decoder):
     def __init__(self, covjson):
@@ -74,15 +76,9 @@ def to_xarray(self):
                 num = [int(coord[0][5]) for coord in coords]
                 coords_fc = coords[ind]
                 try:
-                    t = [
-                        dt.datetime.strptime(coord[4], "%Y-%m-%d %H:%M:%S")
-                        for coord in coords_fc
-                    ]
+                    t = [dt.datetime.strptime(coord[4], "%Y-%m-%d %H:%M:%S") for coord in coords_fc]
                 except ValueError:
-                    t = [
-                        dt.datetime.strptime(coord[4], "%Y-%m-%dT%H:%M:%S")
-                        for coord in coords_fc
-                    ]
+                    t = [dt.datetime.strptime(coord[4], "%Y-%m-%dT%H:%M:%S") for coord in coords_fc]
 
                 param_coords = {"x": xs, "y": ys, "z": zs, "number": num, "t": t}
                 dataarray = xr.DataArray(
@@ -93,12 +89,8 @@ def to_xarray(self):
                 )
 
                 dataarray.attrs["type"] = self.get_parameter_metadata(parameter)["type"]
-                dataarray.attrs["units"] = self.get_parameter_metadata(parameter)[
-                    "unit"
-                ]["symbol"]
-                dataarray.attrs["long_name"] = self.get_parameter_metadata(parameter)[
-                    "description"
-                ]
+                dataarray.attrs["units"] = self.get_parameter_metadata(parameter)["unit"]["symbol"]
+                dataarray.attrs["long_name"] = self.get_parameter_metadata(parameter)["description"]
                 dataarraydict[dataarray.attrs["long_name"]] = dataarray
 
         ds = xr.Dataset(dataarraydict)

diff --git a/eccovjson/decoder/Frame.py b/eccovjson/decoder/Frame.py
@@ -1,7 +1,9 @@
-from .decoder import Decoder
-import xarray as xr
 import datetime as dt
 
+import xarray as xr
+
+from .decoder import Decoder
+
 
 class Frame(Decoder):
     def __init__(self, covjson):
@@ -71,15 +73,9 @@ def to_xarray(self):
                 num = [int(coord[0][5]) for coord in coords]
                 coords_fc = coords[ind]
                 try:
-                    t = [
-                        dt.datetime.strptime(coord[4], "%Y-%m-%d %H:%M:%S")
-                        for coord in coords_fc
-                    ]
+                    t = [dt.datetime.strptime(coord[4], "%Y-%m-%d %H:%M:%S") for coord in coords_fc]
                 except ValueError:
-                    t = [
-                        dt.datetime.strptime(coord[4], "%Y-%m-%dT%H:%M:%S")
-                        for coord in coords_fc
-                    ]
+                    t = [dt.datetime.strptime(coord[4], "%Y-%m-%dT%H:%M:%S") for coord in coords_fc]
 
                 param_coords = {"x": xs, "y": ys, "z": zs, "number": num, "t": t}
                 dataarray = xr.DataArray(
@@ -90,12 +86,8 @@ def to_xarray(self):
                 )
 
                 dataarray.attrs["type"] = self.get_parameter_metadata(parameter)["type"]
-                dataarray.attrs["units"] = self.get_parameter_metadata(parameter)[
-                    "unit"
-                ]["symbol"]
-                dataarray.attrs["long_name"] = self.get_parameter_metadata(parameter)[
-                    "description"
-                ]
+                dataarray.attrs["units"] = self.get_parameter_metadata(parameter)["unit"]["symbol"]
+                dataarray.attrs["long_name"] = self.get_parameter_metadata(parameter)["description"]
                 dataarraydict[dataarray.attrs["long_name"]] = dataarray
 
         ds = xr.Dataset(dataarraydict)

diff --git a/eccovjson/decoder/TimeSeries.py b/eccovjson/decoder/TimeSeries.py
@@ -1,7 +1,9 @@
-from .decoder import Decoder
-import xarray as xr
 import datetime as dt
 
+import xarray as xr
+
+from .decoder import Decoder
+
 
 class TimeSeries(Decoder):
     def __init__(self, covjson):
@@ -75,15 +77,9 @@ def to_xarray(self):
                 num = [int(coord[0][5]) for coord in coords]
                 coords_fc = coords[ind]
                 try:
-                    t = [
-                        dt.datetime.strptime(coord[4], "%Y-%m-%d %H:%M:%S")
-                        for coord in coords_fc
-                    ]
+                    t = [dt.datetime.strptime(coord[4], "%Y-%m-%d %H:%M:%S") for coord in coords_fc]
                 except ValueError:
-                    t = [
-                        dt.datetime.strptime(coord[4], "%Y-%m-%dT%H:%M:%S")
-                        for coord in coords_fc
-                    ]
+                    t = [dt.datetime.strptime(coord[4], "%Y-%m-%dT%H:%M:%S") for coord in coords_fc]
 
                 param_coords = {"x": x, "y": y, "z": z, "number": num, "t": t}
                 dataarray = xr.DataArray(
@@ -94,12 +90,8 @@ def to_xarray(self):
                 )
 
                 dataarray.attrs["type"] = self.get_parameter_metadata(parameter)["type"]
-                dataarray.attrs["units"] = self.get_parameter_metadata(parameter)[
-                    "unit"
-                ]["symbol"]
-                dataarray.attrs["long_name"] = self.get_parameter_metadata(parameter)[
-                    "description"
-                ]
+                dataarray.attrs["units"] = self.get_parameter_metadata(parameter)["unit"]["symbol"]
+                dataarray.attrs["long_name"] = self.get_parameter_metadata(parameter)["description"]
                 dataarraydict[dataarray.attrs["long_name"]] = dataarray
 
         ds = xr.Dataset(dataarraydict)
@@ -110,7 +102,7 @@ def to_xarray(self):
         return ds
 
 
-"""   
+"""
     def to_xarray(self):
         dims = ["x", "y", "z", "fct", "t"]
         dataarraydict = {}

diff --git a/eccovjson/decoder/VerticalProfile.py b/eccovjson/decoder/VerticalProfile.py
@@ -1,6 +1,7 @@
-from .decoder import Decoder
 import xarray as xr
 
+from .decoder import Decoder
+
 
 class VerticalProfile(Decoder):
     def __init__(self, covjson):
@@ -79,12 +80,8 @@ def to_xarray(self):
                     name=parameter,
                 )
                 dataarray.attrs["type"] = self.get_parameter_metadata(parameter)["type"]
-                dataarray.attrs["units"] = self.get_parameter_metadata(parameter)[
-                    "unit"
-                ]["symbol"]
-                dataarray.attrs["long_name"] = self.get_parameter_metadata(parameter)[
-                    "description"
-                ]
+                dataarray.attrs["units"] = self.get_parameter_metadata(parameter)["unit"]["symbol"]
+                dataarray.attrs["long_name"] = self.get_parameter_metadata(parameter)["description"]
                 dataarraydict[dataarray.attrs["long_name"]] = dataarray
 
         ds = xr.Dataset(dataarraydict)