Merge pull request #6 from DroneML/1-python-template

add content from python template

.copier-answers.yml

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+# Changes here will be overwritten by Copier
+SelectCitation:
+- AddCitationFile_flag
+- AddCFFConvert_flag
+SelectCodeQualityFeatures:
+- AddLocalTests_flag
+- SelectGitHubActions_flag
+- AddLinting_flag
+SelectCommunityFeatures: []
+SelectDocumentationFeatures:
+- AddOnlineDocumentation_flag
+- AddDevDoc_flag
+- AddGitHubActionDocumentation_flag
+SelectGitHubActions:
+- AddGitHubActionBuild_flag
+- AddLinkCheck_flag
+SelectPublishReleaseFeatures:
+- SelectCitation_flag
+- AddZenodo_flag
+_commit: 0.6.1
+_src_path: https://github.com/nlesc/python-template.git
+copyright_holder: Christiaan Meijer
+email: [email protected]
+full_name: Christiaan Meijer
+github_organization: DroneML
+keywords: Segmentation, UNet, Active learning, Drone, Raster data, Spatial data
+license: Apachev2
+package_name: segmentmytiff
+package_short_description: Segment (georeferenced) raster data in an interactive fashion.
+    Retrain models in seconds. Only small amounts of labeled data necessary because
+    of our use of pretrained base models as feature extractors.
+template_profile: ask
+version: 0.1.0

.github/workflows/build.yml

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+name: Python package
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+jobs:
+
+  build:
+    name: Build for (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        python-version: ['3.10', '3.11', '3.12']
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Python info
+        shell: bash -e {0}
+        run: |
+          which python
+          python --version
+      - name: Upgrade pip and install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          python -m pip install .[dev,publishing]
+      - name: Run unit tests
+        run: python -m pytest -v
+      - name: Verify that we can build the package
+        run: python -m build
+  lint:
+    name: Linting build
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
+      - name: Python info
+        shell: bash -e {0}
+        run: |
+          which python
+          python --version
+      - name: Upgrade pip and install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          python -m pip install .[dev,publishing]
+      - name: Check style against standards using ruff
+        run: |
+          ruff check
+          ruff format --check

.github/workflows/cffconvert.yml

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+name: cffconvert
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+jobs:
+
+  verify:
+    name: "cffconvert"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        name: Check out a copy of the repository
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/[email protected]
+        with:
+          args: "--validate"

.github/workflows/documentation.yml

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+name: documentation
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+
+jobs:
+  build-documentation:
+    name: Build documentation
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
+      - name: Python info
+        shell: bash -e {0}
+        run: |
+          which python
+          python --version
+      - name: Upgrade pip and install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          python -m pip install .[dev,publishing]
+      - name: Install pandoc using apt
+        run: sudo apt install pandoc        
+      - name: Build documentation
+        run: make coverage doctest html
+        working-directory: docs

.github/workflows/link-check.yml

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+name: link-check
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+    - main
+  pull_request:
+    branches:
+    - main
+  schedule:
+  - cron: '0 0 1 * *' # first day of every month at midnight
+
+permissions:
+  contents: read
+  issues: write
+
+jobs:
+  linkChecker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Link Checker
+        id: lychee
+        uses: lycheeverse/lychee-action@v1
+
+      - name: Set Issue Title
+        id: set_title
+        run: echo "ISSUE_TITLE=Link Checker Report - $(date '+%Y-%m-%d')" >> $GITHUB_ENV
+
+      - name: Create Issue From File
+        if: env.lychee_exit_code != 0
+        uses: peter-evans/create-issue-from-file@v5
+        with:
+          title: ${{ env.ISSUE_TITLE }}
+          content-filepath: ./lychee/out.md
+          labels: report, automated issue

.gitignore

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+# Byte-compiled / optimized / DLL files
+*.py[cod]
+*$py.class
+__pycache__
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# jupyter notebook
+.ipynb_checkpoints
+
+# Unit test / coverage reports
+htmlcov/
+.coverage
+.coverage.*
+coverage.xml
+.cache
+.pytest_cache
+.tox/
+
+# Sphinx documentation
+docs/_build
+
+# ide
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+.spyderproject
+.spyproject
+
+# Mac
+.DS_Store
+
+# virtual environments
+env
+.env
+env3
+.env3
+venv
+.venv
+venv3
+.venv3
+ENV/
+env.bak/
+venv.bak/
+
+# vim
+*.swp
+*.swo
+*.orig

.readthedocs.yaml

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+version: 2
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

CITATION.cff

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+# YAML 1.2
+---
+cff-version: "1.2.0"
+title: "segmentmytiff"
+authors:
+  - family-names: Meijer
+    given-names: Christiaan
+    orcid: "https://orcid.org/0000-0000-0000-0000"
+date-released: 2024-10-08
+version: "0.1.0"
+repository-code: "https://github.com/DroneML/segmentmytiff"
+keywords:
+  - "Segmentation"
+  - " UNet"
+  - " Active learning"
+  - " Drone"
+  - " Raster data"
+  - " Spatial data"
+message: "If you use this software, please cite it using these metadata."