build: updated setup (pyproject.toml, ruff, tox, trusted publishing)

.github/dependabot.yaml

@@ -0,0 +1,11 @@
+# Config for Dependabot updates. See Documentation here:
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  # Update GitHub actions in workflows
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    # Check for updates to GitHub Actions every weekday
+    schedule:
+      interval: "daily"

.github/workflows/release.yml

@@ -0,0 +1,131 @@
+name: release
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  build_sdist:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      - name: install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: build source tarball
+        run: |
+          python -m build --sdist
+          twine check --strict dist/*
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*
+
+  build_wheels:
+    name: wheel on ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # temporarily ignoring binary wheels for windows until pythran issues are fixed
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      # see https://github.com/pypa/cibuildwheel/issues/933
+      # - uses: pypa/cibuildwheel@v2
+
+      # Used to host cibuildwheel
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      - name: install cibuildwheel
+        run: python -m pip install
+
+      - name: build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+
+      - name: upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          path: wheelhouse/*.whl
+
+  publish_dev_build:
+    needs: [build_sdist, build_wheels]
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://pypi.org/p/detectree
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - name: publish to test pypi
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
+
+  release:
+    needs: [publish_dev_build]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/detectree
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+      # see https://github.com/softprops/action-gh-release/issues/236
+      contents: write
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      - name: generate change log
+        uses: heinrichreimer/[email protected]
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          issues: true
+          issuesWoLabels: true
+          pullRequests: true
+          prWoLabels: true
+          unreleased: true
+          addSections: '{"documentation":{"prefix":"**Documentation:**","labels":["documentation"]}}'
+          sinceTag: v0.1.0
+          output: RELEASE-CHANGELOG.md
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - name: create github release
+        uses: softprops/action-gh-release@v1
+        with:
+          body_path: ./RELEASE-CHANGELOG.md
+          files: dist/*.whl
+          draft: false
+          prerelease: false
+
+      - name: publish to pypi
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yml

@@ -0,0 +1,47 @@
+name: tests
+
+on:
+  pull_request:
+    branches:
+      - "*"
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        include:
+          - os: macos-latest
+            python-version: "3.12"
+          - os: windows-latest
+            python-version: "3.12"
+
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pip
+
+      - name: install dependencies
+        run: pip install tox tox-gh-actions
+
+      - name: test with tox
+        run: tox
+        env:
+          CONDA_EXE: mamba
+
+      - name: upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+
+      - name: list files
+        run: ls -l .

.pre-commit-config.yaml

@@ -1,38 +1,55 @@
-exclude: 'docs|node_modules|migrations|.tox'
-default_stages: [commit]
-fail_fast: true
+ci:
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes from pre-commit hooks"
+  autoupdate_commit_msg: "style(pre-commit.ci): pre-commit autoupdate"
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
 
-  - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.18.2
+  - repo: https://github.com/commitizen-tools/commitizen
+    rev: v3.15.0
     hooks:
-      - id: check-github-workflows
+      - id: commitizen
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.1.0
+    hooks:
+      - id: prettier
+        additional_dependencies: [prettier, prettier-plugin-toml, prettier-plugin-ini]
+        types: ["ini", "toml", "yaml"]
 
-  - repo: https://github.com/psf/black
-    rev: 22.10.0
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.17 # Use the ref you want to point at
     hooks:
-      - id: black
+      - id: mdformat
+        # Optionally add plugins
+        additional_dependencies:
+          - mdformat-gfm
+          - mdformat-black
 
-  - repo: https://github.com/timothycrosley/isort
-    rev: 5.10.1
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.35.1
     hooks:
-      - id: isort
+      - id: yamllint
+        args: ["-d relaxed"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.28.0
+    hooks:
+      - id: check-github-workflows
 
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 5.0.4
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
     hooks:
-      - id: flake8
-        additional_dependencies: [flake8-isort]
+      - id: pyupgrade
 
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: 6.1.1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.2.2
     hooks:
-      - id: pydocstyle
-        files: ^detectree
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format

.readthedocs.yml

@@ -1,8 +1,11 @@
 version: 2
 
+build:
+    os: ubuntu-22.04
+    tools:
+        python: mambaforge-4.10
+
 python:
-  install:
-    - requirements: requirements.txt
-    - requirements: requirements-dev.txt
-    - method: pip
-      path: .
+    install:
+        - method: pip
+          path: .

README.md

@@ -1,7 +1,7 @@
 [![PyPI version fury.io](https://badge.fury.io/py/detectree.svg)](https://pypi.python.org/pypi/detectree/)
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/detectree.svg)](https://anaconda.org/conda-forge/detectree)
 [![Documentation Status](https://readthedocs.org/projects/detectree/badge/?version=latest)](https://detectree.readthedocs.io/en/latest/?badge=latest)
-[![Build Status](https://github.com/martibosch/detectree/workflows/tests/badge.svg?branch=main)](https://github.com/martibosch/detectree/actions?query=workflow%3A%22tests%22)
+[![tests](https://github.com/martibosch/detectree/actions/workflows/tests.yml/badge.svg)](https://github.com/martibosch/detectree/blob/main/.github/workflows/tests.yml)
 [![codecov](https://codecov.io/gh/martibosch/detectree/branch/main/graph/badge.svg?token=ZTZK2LFR6T)](https://codecov.io/gh/martibosch/detectree)
 [![GitHub license](https://img.shields.io/github/license/martibosch/detectree.svg)](https://github.com/martibosch/detectree/blob/master/LICENSE)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.02172/status.svg)](https://doi.org/10.21105/joss.02172)
@@ -11,7 +11,7 @@
 
 ## Overview
 
-DetecTree is a Pythonic library to classify tree/non-tree pixels from aerial imagery, following the methods of Yang et al. [1]. The target audience is researchers and practitioners in GIS that are interested in two-dimensional aspects of trees, such as their proportional abundance and spatial distribution throughout a region of study. These measurements can be used to assess important aspects of urban planning such as the provision of urban ecosystem services. The approach is of special relevance when LIDAR data is not available or it is too costly in monetary or computational terms.
+DetecTree is a Pythonic library to classify tree/non-tree pixels from aerial imagery, following the methods of Yang et al. \[1\]. The target audience is researchers and practitioners in GIS that are interested in two-dimensional aspects of trees, such as their proportional abundance and spatial distribution throughout a region of study. These measurements can be used to assess important aspects of urban planning such as the provision of urban ecosystem services. The approach is of special relevance when LIDAR data is not available or it is too costly in monetary or computational terms.
 
 ```python
 import detectree as dtr
@@ -48,7 +48,7 @@ A full example application of DetecTree to predict a tree canopy map for the Aus
 
 Bosch M. 2020. “DetecTree: Tree detection from aerial imagery in Python”. *Journal of Open Source Software, 5(50), 2172.* [doi.org/10.21105/joss.02172](https://doi.org/10.21105/joss.02172)
 
-Note that DetecTree is based on the methods of Yang et al. [1], therefore it seems fair to reference their work too. An example citation in an academic paper might read as follows:
+Note that DetecTree is based on the methods of Yang et al. \[1\], therefore it seems fair to reference their work too. An example citation in an academic paper might read as follows:
 
 > The classification of tree pixels has been performed with the Python library DetecTree (Bosch, 2020), which is based on the approach of Yang et al. (2009).
 
@@ -58,29 +58,29 @@ Note that DetecTree is based on the methods of Yang et al. [1], therefore it see
 
 The easiest way to install `detectree` is with conda as in:
 
-``` bash
+```bash
 conda install -c conda-forge detectree
 ```
 
 ### With pip
 
 You can install `detectree` with pip as in:
 
-``` bash
+```bash
 pip install detectree
 ```
 
-If you want to be able to read compressed LAZ files, you will need [the Python bindings for `laszip`](https://github.com/tmontaigu/laszip-python). Note that the latter require [`laszip`], which can be installed using conda (which is automatically handled when installing `detectree` with conda as shown above) or downloaded from [laszip.org](https://laszip.org/). Then, detectree and the Python bindings for `laszip` can be installed with pip as in:
+If you want to be able to read compressed LAZ files, you will need [the Python bindings for `laszip`](https://github.com/tmontaigu/laszip-python). Note that the latter require \[`laszip`\], which can be installed using conda (which is automatically handled when installing `detectree` with conda as shown above) or downloaded from [laszip.org](https://laszip.org/). Then, detectree and the Python bindings for `laszip` can be installed with pip as in:
 
-``` bash
+```bash
 pip install detectree[laszip]
 ```
 
 ### Development install
 
 To install a development version of detectree, you can first use conda to create an environment with all the dependencies - with the [`environment-dev.yml` file](https://github.com/martibosch/detectree/blob/main/environment-dev.yml) - and activate it as in:
 
-``` bash
+```bash
 conda env create -f environment-dev.yml
 conda activate detectree-dev
 ```
@@ -101,12 +101,12 @@ pre-commit install
 
 ## See also
 
-* [lausanne-tree-canopy](https://github.com/martibosch/lausanne-tree-canopy): example computational workflow to get the tree canopy of Lausanne with DetecTree
-* [A video of a talk about DetecTree](https://www.youtube.com/watch?v=USwF2KyxVjY) in the [Applied Machine Learning Days of EPFL (2020)](https://appliedmldays.org/) and [its respective slides](https://martibosch.github.io/detectree-amld-2020)
+- [lausanne-tree-canopy](https://github.com/martibosch/lausanne-tree-canopy): example computational workflow to get the tree canopy of Lausanne with DetecTree
+- [A video of a talk about DetecTree](https://www.youtube.com/watch?v=USwF2KyxVjY) in the [Applied Machine Learning Days of EPFL (2020)](https://appliedmldays.org/) and [its respective slides](https://martibosch.github.io/detectree-amld-2020)
 
 ## Acknowledgments
 
-* With the support of the École Polytechnique Fédérale de Lausanne (EPFL)
+- With the support of the École Polytechnique Fédérale de Lausanne (EPFL)
 
 ## References