Add tests

.copyright.tmpl

@@ -0,0 +1,15 @@
+Copyright ${years} ${owner}.
+
+This file is part of ${projectname}.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

.github/actions/setup/action.yaml

@@ -0,0 +1,50 @@
+name: 'venv setup'
+description: 'configures venv, python and caches'
+
+inputs:
+  python-version:
+    description: "Python version to use"
+    required: true
+  cache-dependency-path:
+    description: "Requirement files to install. Can be a glob pattern."
+    default: '**/requirements*.txt'
+  venv-dir:
+    default: '.venv'
+
+outputs:
+  cache-hit:
+    description: "A boolean value to indicate if a cache was restored"
+    value: ${{ steps.cache-venv.outputs.cache-hit }}
+
+runs:
+  using: 'composite'
+  steps:
+    - run: cp .env.example .env
+      shell: bash
+
+    - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c  # v5.0.0
+      id: setup-python
+      with:
+        python-version: ${{ inputs.python-version }}
+
+    - run: echo '::remove-matcher owner=python::'
+      shell: bash
+
+    - uses: actions/cache@13aacd865c20de90d75de3b17ebe84f7a17d57d2  # v4.0.0
+      id: cache-venv
+      with:
+        path: ${{ inputs.venv-dir }}
+        key: setup-venv-${{ runner.os }}-py-${{ steps.setup-python.outputs.python-version }}-${{ steps.setup-python.outputs.python-path }}-${{ hashFiles(inputs.cache-dependency-path) }}-${{ inputs.install-cmd }}
+
+    - run: python3 -m venv ${{ inputs.venv-dir }}
+      if: steps.cache-venv.outputs.cache-hit != 'true'
+      shell: bash
+
+    - run: |
+        source ${{ inputs.venv-dir }}/bin/activate
+        python -m pip install -r requirements.txt
+        python -m pip install -r requirements-dev.txt
+        echo "VIRTUAL_ENV=${VIRTUAL_ENV}" >> $GITHUB_ENV
+        echo "${VIRTUAL_ENV}/bin" >> $GITHUB_PATH
+
+      shell: bash

.github/workflows/ci.yaml

@@ -0,0 +1,29 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+    tags: ['v*']
+
+jobs:
+
+  tests:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ "ubuntu-latest" ]
+        python-version: [ "3.10" ]
+    runs-on: "${{ matrix.os }}"
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - uses: ./.github/actions/setup
+        with:
+          python-version: "${{ matrix.python-version }}"
+          venv-id: "tests-${{ runner.os }}"
+      - name: Run tests
+        run: |
+          pytest -r a -v tests
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3

.gitignore

@@ -4,10 +4,15 @@ inputs
 intermediates
 experiments
 .env
+.idea
 
 !outputs/README.md
 !inputs/README.md
 !intermediates/README.md
 .vscode/launch.json
 .vscode/settings.json
 domain.ipynb
+
+# Virtual environment
+venv
+.venv

Makefile

@@ -0,0 +1,3 @@
+.PHONY: update-licenseheaders
+update-licenseheaders:  ## add or update license headers in all python files
+	licenseheaders --current-year --owner "The Superpower Institute Ltd" --projname "OpenMethane" --tmpl .copyright.tmpl --ext .py -x "venv/*"

README.md

@@ -10,6 +10,14 @@ Copy the `.env.example` file to `.env` and customise the paths as you need.
 
 ### Installation
 
+To avoid conflicts with other Python projects, it is recommended to create a virtual environment for this project. To do this, run:
+
+
+```console
+python -m venv venv
+source venv/bin/activate
+```
+
 Install required modules:
 
 ```console

__init__.py

@@ -0,0 +1,17 @@
+#
+# Copyright 2024 The Superpower Institute Ltd.
+#
+# This file is part of OpenMethane.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#

omAgLulucfWasteEmis.py

@@ -1,11 +1,23 @@
-"""
-omAgLulucfWasteEmis.py
+#
+# Copyright 2024 The Superpower Institute Ltd.
+#
+# This file is part of OpenMethane.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 
-Copyright 2023 The Superpower Institute Ltd
-Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
-You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
-Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and limitations under the License.
+"""
+Process livestock methane emissions
 """
 
 import csv

omCreateDomainInfo.py

@@ -1,11 +1,23 @@
-"""
-omCreateDomainInfo.py
+#
+# Copyright 2024 The Superpower Institute Ltd.
+#
+# This file is part of OpenMethane.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 
-Copyright 2023 The Superpower Institute Ltd
-Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
-You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
-Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and limitations under the License.
+"""
+Generate domain file from example domain
 """
 
 from omInputs import domainPath, geomFilePath, croFilePath, dotFilePath

omDownloadInputs.py

@@ -1,18 +1,36 @@
+#
+# Copyright 2024 The Superpower Institute Ltd.
+#
+# This file is part of OpenMethane.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
 """
-omDownloadInputs.py
+Download required input files
 
-Copyright 2023 The Superpower Institute Ltd
-Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
-You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
-Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and limitations under the License.
+This downloads the input files that rarely change and can be cached between runs.
 """
 
-from omInputs import electricityPath, fugitivesPath, landUsePath, sectoralEmissionsPath, sectoralMappingsPath, ntlPath, auShapefilePath, livestockDataPath, termitePath, wetlandPath, coalPath, oilGasPath
+from omInputs import (electricityPath,
+                      # fugitivesPath,
+                      landUsePath, sectoralEmissionsPath, sectoralMappingsPath, ntlPath, auShapefilePath, livestockDataPath, termitePath, wetlandPath, coalPath, oilGasPath)
 import requests
 import os
 from omUtils import getenv
 
+root_path = os.path.dirname(os.path.realpath(__file__))
+
 remote = getenv("PRIOR_REMOTE")
 
 electricityFile = getenv("CH4_ELECTRICITY")
@@ -27,6 +45,7 @@
 wetlandFile = getenv("WETLANDS")
 coalFile = getenv("COAL")
 oilGasFile = getenv("OILGAS")
+
 downloads = [
     [electricityFile, electricityPath],
     [coalFile, coalPath],
@@ -41,15 +60,23 @@
     [wetlandFile, wetlandPath]
 ]
 
-for filename, filepath in downloads:
-    url = f"{remote}{filename}"
+def download_input_files(root_path, downloads, remote):
+    for filename, filepath in downloads:
+        filepath = os.path.join(root_path, filepath)
+        print(filepath)
+        url = f"{remote}{filename}"
+
+        if not os.path.exists(filepath):
+            print(f"Downloading {filename} to {filepath} from {url}")
 
-    if not os.path.exists(filepath):
-        print(f"Downloading {filename} to {filepath} from {url}")
+            with requests.get(url, stream=True) as response:
+                with open(filepath, mode="wb") as file:
+                    for chunk in response.iter_content(chunk_size=10 * 1024):
+                        file.write(chunk)
+        else:
+            print(f"Skipping {filename} beacuse it already exists at {filepath}")
 
-        with requests.get(url, stream=True) as response:
-            with open(filepath, mode="wb") as file:
-                for chunk in response.iter_content(chunk_size=10 * 1024):
-                    file.write(chunk)
-    else:
-        print(f"Skipping {filename} beacuse it already exists at {filepath}")
+if __name__ == '__main__':
+    download_input_files(root_path=root_path,
+                         downloads=downloads,
+                         remote=remote)

omElectricityEmis.py

@@ -1,11 +1,23 @@
-"""
-omEelctricityEmis.py
+#
+# Copyright 2024 The Superpower Institute Ltd.
+#
+# This file is part of OpenMethane.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 
-Copyright 2023 The Superpower Institute Ltd
-Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
-You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
-Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and limitations under the License.
+"""
+Process emissions from the electricity sector
 """
 
 import numpy as np

omFugitiveEmis.py

@@ -1,11 +1,23 @@
-"""
-omFugitiveEmis.py
+#
+# Copyright 2024 The Superpower Institute Ltd.
+#
+# This file is part of OpenMethane.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 
-Copyright 2023 The Superpower Institute Ltd
-Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
-You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
-Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and limitations under the License.
+"""
+Process fugitive Methane emissions
 """
 
 import numpy as np

omGFASEmis.py

@@ -1,11 +1,27 @@
+#
+# Copyright 2024 The Superpower Institute Ltd.
+#
+# This file is part of OpenMethane.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
 """
-omGFASEmis.py
+Download and process GFAS data
 
-Copyright 2023 The Superpower Institute Ltd
-Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
-You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
-Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and limitations under the License.
+This downloads files from [ADS](https://atmosphere.copernicus.eu/data).
+See the project readme for more information about configuring
+the required credentials.
 """
 
 import numpy as np