Merge remote-tracking branch 'origin/main' into joss-submission

.circleci/config.yml

@@ -0,0 +1,136 @@
+version: 2.1
+
+jobs:
+  build_test:
+    docker:
+      - image: cimg/python:3.12
+    steps:
+      - checkout
+
+      - run:
+          name: Build (build_test)
+          command: python3 setup.py sdist bdist_wheel
+
+      - run:
+          name: Check if wheel file exists (build_test)
+          command: ls -l dist/
+
+      - run:
+          name: Set wheel filename (build_test)
+          command: |
+            export WHL_FILENAME=$(ls dist/*.whl)
+            echo "WHEEL FILE: $WHL_FILENAME"
+
+      - run:
+          name: Install dependencies (build_test)
+          command: |
+            python -m venv venv
+            . venv/bin/activate
+            pip install -r requirements.txt
+
+      - run:
+          name: Install package (build_test)
+          command: |
+            . venv/bin/activate
+            export WHL_FILENAME=$(ls dist/*.whl)
+            pip install $WHL_FILENAME
+
+      - run:
+          name: Install pytest (build_test)
+          command: |
+            . venv/bin/activate
+            pip install pytest
+
+      - run:
+          name: Run Tests (build_test)
+          command: |
+            . venv/bin/activate
+            pytest
+
+      - store_test_results:
+          path: test-reports
+
+  test_pypi_publish:
+    docker:
+      - image: cimg/python:3.12
+    steps:
+      - checkout
+
+      - run:
+          name: Create whl (test_pypi_publish)
+          command: python3 setup.py sdist bdist_wheel
+
+      - run:
+          name: Check if wheel file exists (test_pypi_publish)
+          command: ls -l dist/
+
+      - run:
+          name: Install dependencies (test_pypi_publish)
+          command: |
+            python -m venv venv
+            . venv/bin/activate
+            pip install -r requirements.txt
+
+      - run:
+          name: Install twine (test_pypi_publish)
+          command: |
+            . venv/bin/activate
+            pip install twine
+
+      - run:
+          name: Publish on TestPyPI
+          command: |
+            . venv/bin/activate
+            twine upload -u ${TESTPYPI_USERNAME} -p ${TESTPYPI_PASSWORD} --repository testpypi dist/* --verbose
+
+  pypi_publish:
+    docker:
+      - image: cimg/python:3.12
+    steps:
+      - checkout
+
+      - run:
+          name: Create whl (pypi_publish)
+          command: python3 setup.py sdist bdist_wheel
+
+      - run:
+          name: Check if wheel file exists (pypi_publish)
+          command: ls -l dist/
+
+      - run:
+          name: Install dependencies (pypi_publish)
+          command: |
+            python -m venv venv
+            . venv/bin/activate
+            pip install -r requirements.txt
+
+      - run:
+          name: Install twine (pypi_publish)
+          command: |
+            . venv/bin/activate
+            pip install twine
+
+      - run:
+          name: Publish on PyPI
+          command: |
+            . venv/bin/activate
+            twine upload -u ${PYPI_USERNAME} -p ${PYPI_PASSWORD} dist/* --verbose
+
+workflows:
+  build_test_publish:
+    jobs:
+      - build_test
+      - test_pypi_publish:
+          requires:
+            - build_test
+          filters:
+            branches:
+              only:
+                - develop
+      - pypi_publish:
+          requires:
+            - build_test
+          filters:
+            branches:
+              only:
+                - main

.github/workflows/deploy.yml

@@ -16,7 +16,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.12'
+        python-version: '3.12.4'
 
     - name: Install dependencies
       run: |

CHANGELOG.md

@@ -0,0 +1,29 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [1.0.3] - 2024-07-27
+### Bug Fixes
+- Deploying documentation
+
+## [1.0.2] - 2024-07-27
+### Added
+- Improved CI/CD pipeline by ensuring up-to-date gh-pages branch before deployment.
+- Updated installation instructions to include pip installation from PyPI.
+
+## [1.0.1] - 2024-07-27
+### Added
+- Added `CHANGELOG.md` file to document changes.
+- Published project to PyPI.
+- Integrated CircleCI for continuous integration and deployment.
+
+## [1.0.0] - 2024-07-16
+### Initial Release
+- Initial release of LorenzCycleToolkit.
+- Implemented core functionalities for calculating the Lorenz Energy Cycle (LEC) in specific atmospheric regions.
+- Added support for both Eulerian and Semi-Lagrangian frameworks.
+- Provided options for fixed and moving computational domains.
+- Generated detailed results in CSV format for energy, conversion, and generation terms.
+- Included automatic plot generation for spatial and temporal analysis.
+- Utilized Xarray, Dask, Pandas, and MetPy for data handling and computations.
+- Comprehensive documentation and usage examples.

README.md

@@ -28,40 +28,36 @@ The LorenzCycleToolkit is a tool for calculating the Lorenz Energy Cycle (LEC) i
 
 For detailed documentation and usage instructions, visit the [LorenzCycleToolkit Documentation](https://daniloceano.github.io/LorenzCycleToolkit/).
 
-## Installation
-To install the required dependencies, use the provided `requirements.txt` file:
-```sh
-pip install -r requirements.txt
-```
-
-## Basic Usage
-Run the toolkit with a sample NetCDF file:
-```sh
-python lorenzcycletoolkit.py samples/testdata_ERA5.nc -r -f
-```
-
-For more detailed usage instructions, including configuration options and examples, please refer to the documentation.
-
 ## Contributing
 Contributions are welcome! Please see the [contributing guide](CONTRIBUTING.md) for more details.
 
 ### Continuous Integration and Deployment
 
-This project uses GitHub Actions for Continuous Integration (CI) and Continuous Deployment (CD). 
+This project uses GitHub Actions and CircleCI for Continuous Integration (CI) and Continuous Deployment (CD). 
 
-- **CI Pipeline**: The CI pipeline is triggered on each push and pull request to the repository. It runs the following steps:
+- **CI Pipeline with GitHub Actions**: The CI pipeline is triggered on each push and pull request to the repository. It runs the following steps:
   - Sets up the Python environment.
   - Installs dependencies.
   - Formats code using autopep8.
   - Sorts imports using isort.
   - Lints code using flake8.
   - Runs tests using pytest.
 
+- **CI Pipeline with CircleCI**: CircleCI is used to build, test, and publish the package. The pipeline runs the following steps:
+  - Builds the package.
+  - Checks if the wheel file exists.
+  - Installs dependencies.
+  - Installs the package.
+  - Runs tests using pytest.
+  - Publishes the package to TestPyPI for the `develop` branch.
+  - Publishes the package to PyPI for the `main` branch.
+
 - **CD Pipeline**: The CD pipeline deploys the documentation to GitHub Pages whenever changes are pushed to the `main` branch.
 
 You can view the CI/CD configuration in the following files:
 - [python-app.yml](.github/workflows/python-app.yml)
 - [deploy-docs.yml](.github/workflows/deploy-docs.yml)
+- [config.yml](.circleci/config.yml)
 
 ## License
 This project is licensed under the MIT License. See the [LICENSE](LICENSE) file for details.

docs/source/installation.rst

@@ -4,26 +4,39 @@ Installation
 Prerequisites
 -------------
 - Python 3.12 or later
-- Required Python packages listed in `requirements.txt`
 
 Steps
 -----
-1. Clone the repository::
+
+1. Install via pip::
+
+   pip install LorenzCycleToolkit
+
+2. Alternatively, clone the repository::
 
    git clone https://github.com/daniloceano/lorenz-cycle.git
    cd lorenz-cycle
 
-2. Create and activate a virtual environment:
+3. Create a virtual environment and activate it::
+
+   python -m venv venv
+   source venv/bin/activate
+
+4. Install the dependencies::
 
-   - Using `venv`::
+   pip install -r requirements.txt
+
+For Conda users:
+
+1. Clone the repository::
 
-      python -m venv venv
-      source venv/bin/activate
+   git clone https://github.com/daniloceano/lorenz-cycle.git
+   cd lorenz-cycle
 
-   - Or using `conda`::
+2. Create a Conda environment and activate it::
 
-      conda create --name lorenz-cycle python=3.12
-      conda activate lorenz-cycle
+   conda create --name lorenzcycletoolkit python=3.12
+   conda activate lorenzcycletoolkit
 
 3. Install the dependencies::
 

setup.py

@@ -13,7 +13,7 @@ def read_requirements():
 
 setup(
     name='LorenzCycleToolkit',
-    version='1.0.0',
+    version='1.0.3',
     packages=find_packages(),
     include_package_data=True,
     install_requires=read_requirements(),