Move to hatch for building the package, and test/style/doc build scripts. Update READMEs (#11)

* Moved build action to hatch, updated dev readme

* Set up hatch environments for tests, styling and docs.

* Updated the documentation build action to use checkout & python setup v3. Setup ReadTheDocs.

* Updated bumpversion config

* Updated README.md to include a reference to s2spy, along with some stray s2spy uses

* Updated readme and dev readme to include up to date hatch instructions

* Removed prospector. Linting is now handled by Flake8

* Set up Sonarcloud

Co-authored-by: Peter Kalverla <[email protected]>

Author: BSchilperoort

.bumpversion.cfg

@@ -1,17 +1,13 @@
 [bumpversion]
-current_version = 0.2.0
+current_version = 0.2.1
 
 [comment]
-comment = The contents of this file cannot be merged with that of setup.cfg until https://github.com/c4urself/bump2version/issues/185 is resolved
+comment = The contents of this file cannot be merged with that of pyproject.toml until https://github.com/c4urself/bump2version/issues/42 is resolved
 
-[bumpversion:file:s2spy/__init__.py]
+[bumpversion:file:lilio/__init__.py]
 search = __version__ = "{current_version}"
 replace = __version__ = "{new_version}"
 
-[bumpversion:file:setup.cfg]
-search = version = {current_version}
-replace = version = {new_version}
-
 [bumpversion:file:CITATION.cff]
 search = version: "{current_version}"
 replace = version: "{new_version}"

.github/workflows/build.yml

@@ -18,6 +18,8 @@ jobs:
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
         python-version: ['3.8', '3.9', '3.10']
+    env:
+      MPLBACKEND: Agg  # https://github.com/orgs/community/discussions/26434
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -29,14 +31,13 @@ jobs:
         run: |
           which python3
           python3 --version
-      - name: Upgrade pip and install dependencies
+      - name: Upgrade pip and install hatch
         run: |
-          python3 -m pip install --upgrade pip
-          python3 -m pip install .[dev]
+          python3 -m pip install --upgrade pip hatch
       - name: Run unit tests
-        run: pytest -v
+        run: hatch run test
       - name: Verify that we can build the package
-        run: python3 -m build
+        run: hatch build
 
   lint:
     name: Linting build
@@ -54,11 +55,7 @@ jobs:
         run: |
           which python3
           python3 --version
-      - name: Upgrade pip and install dependencies
-        run: |
-          python3 -m pip install --upgrade pip setuptools
-          python3 -m pip install .[dev,publishing]
-      - name: Check style against standards using prospector
-        run: prospector
-      - name: Check import order
-        run: isort --check-only lilio --diff
+      - name: Upgrade pip and install hatch
+        run: python3 -m pip install --upgrade pip hatch
+      - name: Check style against standards
+        run: hatch run lint

.github/workflows/documentation.yml

@@ -15,22 +15,20 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
         with:
-          python-version: 3.9
+          python-version: "3.10"
       - name: Python info
         shell: bash -l {0}
         run: |
           which python3
           python3 --version
-      - name: Upgrade pip and install dependencies
+      - name: Upgrade pip and install hatch
         run: |
-          python3 -m pip install --upgrade pip setuptools
-          python3 -m pip install .[dev,publishing]
+          python3 -m pip install --upgrade pip hatch
       - name: Install pandoc using apt
         run: sudo apt install pandoc
       - name: Build documentation
-        run: make coverage doctest html
-        working-directory: docs
+        run: hatch run docs:build

.github/workflows/sonarcloud.yml

@@ -27,12 +27,10 @@ jobs:
         run: |
           which python3
           python3 --version
-      - name: Install dependencies
-        run: python3 -m pip install .[dev]
-      - name: Check style against standards using prospector
-        run: prospector --zero-exit --output-format grouped --output-format pylint:pylint-report.txt
+      - name: Install hatch
+        run: python3 -m pip install hatch
       - name: Run unit tests with coverage
-        run: pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml tests/
+        run: hatch run coverage
       - name: Correct coverage paths
         run: sed -i "s+$PWD/++g" coverage.xml
       - name: SonarCloud Scan

.prospector.yml

@@ -10,4 +10,4 @@ python:
     - method: pip
       path: .
       extra_requirements:
-        - dev
+        - docs

.readthedocs.yaml

@@ -39,4 +39,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 - Implemented resampling data to the advent calendar.
 - Example notebooks on how to use the calendar and resampling functionalities.
 
-[Unreleased]: https://github.com/AI4S2S/s2spy
+[Unreleased]: https://github.com/AI4S2S/lilio

CHANGELOG.md

@@ -1,30 +1,28 @@
 # lilio: Calendar generator for machine learning with timeseries data
 
-<img align="right" width="160" alt="Logo" src="https://raw.githubusercontent.com/AI4S2S/s2spy/main/docs/assets/images/ai4s2s_logo.png">
+<img align="right" width="160" alt="Logo" src="https://raw.githubusercontent.com/AI4S2S/lilio/main/docs/assets/images/ai4s2s_logo.png">
 
 
 [![github repo badge](https://img.shields.io/badge/github-repo-000.svg?logo=github&labelColor=gray&color=blue)](https://github.com/AI4S2S/lilio)
 [![github license badge](https://img.shields.io/github/license/AI4S2S/lilio)](https://github.com/AI4S2S/lilio)
 [![fair-software badge](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu)
-<!--
 [![Documentation Status](https://readthedocs.org/projects/ai4s2s/badge/?version=latest)](https://ai4s2s.readthedocs.io/en/latest/?badge=latest)
 [![build](https://github.com/AI4S2S/lilio/actions/workflows/build.yml/badge.svg)](https://github.com/AI4S2S/lilio/actions/workflows/build.yml)
 [![sonarcloud](https://github.com/AI4S2S/lilio/actions/workflows/sonarcloud.yml/badge.svg)](https://github.com/AI4S2S/lilio/actions/workflows/sonarcloud.yml)
-[![workflow scc badge](https://sonarcloud.io/api/project_badges/measure?project=AI4S2S_ai4s2s&metric=coverage)](https://sonarcloud.io/dashboard?id=AI4S2S_ai4s2s)
--->
+[![workflow scc badge](https://sonarcloud.io/api/project_badges/measure?project=AI4S2S_lilio&metric=coverage)](https://sonarcloud.io/dashboard?id=AI4S2S_lilio)
+
+A python package for generating calendars to resample timeseries into training and target data for machine learning. Named after [the inventor](https://en.wikipedia.org/wiki/Aloysius_Lilius) of the [Gregorian Calendar](https://en.wikipedia.org/wiki/Gregorian_calendar).
 
-A python package for generating calendars to resample timeseries into training and target data for machine learning.
+Lilio was originally designed for use in [`s2spy`](https://github.com/AI4S2S/s2spy), a high-level python package integrating expert knowledge and artificial intelligence to boost (sub) seasonal forecasting.
 
 ## Installation
-<!--
 [![workflow pypi badge](https://img.shields.io/pypi/v/lilio.svg?colorB=blue)](https://pypi.python.org/project/lilio/)
 [![supported python versions](https://img.shields.io/pypi/pyversions/lilio)](https://pypi.python.org/project/lilio/)
 
 To install the latest release of lilio, do:
 ```console
 python3 -m pip install lilio
 ```
--->
 
 To install the in-development version from the GitHub repository, do:
 
@@ -33,24 +31,26 @@ python3 -m pip install git+https://github.com/AI4S2S/lilio.git
 ```
 
 ### Configure the package for development and testing
+A more extensive developer guide can be found [here](./docs/README.dev.md).
+
 The testing framework used here is [pytest](https://pytest.org). Before running the test, we get a local copy of the source code and install `lilio` via the command:
 
 ```py
 git clone https://github.com/AI4S2S/lilio.git
 cd lilio
-python3 -m pip install -e .
+python3 -m pip install -e .[dev]
 ```
 
 Then, run tests:
 ```py
-python3 -m pytest
+hatch run test
 ```
 
 ## How the lilio calendars work
 In a typical ML-based timeseries analysis, the first step is always data processing.  A calendar-based datetime module `time` is implemented for time operations. For instance, a user is looking for predictors for winter climate at seasonal timescales (~180 days). First, a `calendar` object is created using `AdventCalendar`:
 
 ```py
->>> calendar = s2spy.time.AdventCalendar(anchor="11-30", freq='180d')
+>>> calendar = lilio.time.AdventCalendar(anchor="11-30", freq='180d')
 >>> calendar = calendar.map_years(2020, 2021)
 >>> calendar.show()
 i_interval                         -1                         1
@@ -63,7 +63,7 @@ Now, the user can load the data `input_data` (e.g. `pandas` `DataFrame`) and res
 
 ```py
 >>> calendar = calendar.map_to_data(input_data)
->>> bins = s2spy.time.resample(calendar, input_data)
+>>> bins = lilio.time.resample(calendar, input_data)
 >>> bins
   anchor_year  i_interval                  interval  mean_data  target
 0        2020          -1  [2020-06-03, 2020-11-30)      275.5    True
@@ -78,11 +78,11 @@ Depending on data preparations, we can choose different types of calendars e.g.
 ## Tutorials
 `lilio` supports operations that are common in a machine learning pipeline of sub-seasonal to seasonal forecasting research. Tutorials covering supported methods and functionalities are listed in [notebooks](https://github.com/AI4S2S/lilio/tree/main/notebooks). To check these notebooks, users need to install [`Jupyter lab`](https://jupyter.org/). More details about each method can be found in this [API reference documentation](https://ai4s2s.readthedocs.io/en/latest/autoapi/index.html).
 
+-->
 ## Documentation
-[![Documentation Status](https://readthedocs.org/projects/ai4s2s/badge/?version=latest)](https://ai4s2s.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/lilio/badge/?version=latest)](https://lilio.readthedocs.io/en/latest/?badge=latest)
 
-For detailed information on using `s2spy` package, visit the [documentation page](https://ai4s2s.readthedocs.io/en/latest/) hosted at Readthedocs.
--->
+For detailed information on using `lilio` package, visit the [documentation page](https://lilio.readthedocs.io/en/latest/) hosted at Readthedocs.
 
 ## Contributing
 

MANIFEST.in

@@ -61,8 +61,8 @@ This section is for maintainers of the package.
 
 9. Create a PyPI release.
 
-    1. Create distribution archives with `python3 -m build`.
-    2. Upload archives to PyPI with `twine upload dist/*` (use your
+    1. Create distribution archives with `hatch build`.
+    2. Upload archives to PyPI with `hatch publish` (use your
         personal PyPI account).
 
 10. Verify