BatDetect2 Version 2.0 Beta

.bumpversion.cfg

@@ -1,8 +1,10 @@
 [bumpversion]
-current_version = 1.3.1
+current_version = 1.1.1
 commit = True
 tag = True
 
-[bumpversion:file:batdetect2/__init__.py]
+[bumpversion:file:src/batdetect2/__init__.py]
 
 [bumpversion:file:pyproject.toml]
+
+[bumpversion:file:docs/source/conf.py]

.github/workflows/ci.yml

@@ -0,0 +1,79 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  checks:
+    name: Checks
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install just
+        uses: taiki-e/install-action@just
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+          cache-dependency-glob: |
+            pyproject.toml
+            uv.lock
+
+      - name: Install dependencies
+        run: uv sync --all-extras --all-groups
+
+      - name: Run formatting, lint, and type checks
+        run: just check
+
+  tests:
+    name: Tests (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version:
+          - "3.10"
+          - "3.11"
+          - "3.12"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install just
+        uses: taiki-e/install-action@just
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+          cache-dependency-glob: |
+            pyproject.toml
+            uv.lock
+
+      - name: Install dependencies
+        run: uv sync --all-extras --all-groups
+
+      - name: Run test suite
+        run: just test

.github/workflows/docs-pages.yml

@@ -0,0 +1,69 @@
+name: Docs Pages
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: docs-pages
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: Build Docs
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install just
+        uses: taiki-e/install-action@just
+
+      - name: Configure GitHub Pages
+        uses: actions/configure-pages@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+          cache-dependency-glob: |
+            pyproject.toml
+            uv.lock
+
+      - name: Install dependencies
+        run: uv sync --all-extras --all-groups
+
+      - name: Build docs
+        run: just check-docs
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v4
+        with:
+          path: docs/build
+
+  deploy:
+    name: Deploy Docs
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/publish-pypi.yml

@@ -0,0 +1,70 @@
+name: Publish PyPI
+
+on:
+  release:
+    types:
+      - published
+
+permissions:
+  contents: read
+
+concurrency:
+  group: publish-pypi
+  cancel-in-progress: false
+
+jobs:
+  build:
+    name: Build Distributions
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install just
+        uses: taiki-e/install-action@just
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+          cache-dependency-glob: |
+            pyproject.toml
+            uv.lock
+
+      - name: Install dependencies
+        run: just install-dev
+
+      - name: Build distributions
+        run: just build-dist
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    environment:
+      name: pypi
+      url: https://pypi.org/p/batdetect2
+
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v5
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -50,6 +50,7 @@ cover/
 
 # Sphinx documentation
 docs/_build/
+docs/build/
 
 # PyBuilder
 .pybuilder/
@@ -95,8 +96,15 @@ dmypy.json
 *.json
 plots/*
 
+!example_data/anns/*.json
+
 # Model experiments
 experiments/*
+DvcLiveLogger/checkpoints
+logs/
+mlruns/
+/outputs/
+notebooks/lightning_logs
 
 # Jupiter notebooks
 .virtual_documents
@@ -105,8 +113,24 @@ experiments/*
 
 # DO Include
 !batdetect2_notebook.ipynb
-!batdetect2/models/*.pth.tar
+!src/batdetect2/models/checkpoints/*.pth.tar
 !tests/data/*.wav
+!notebooks/*.ipynb
 !tests/data/**/*.wav
-notebooks/lightning_logs
+.aider*
+
+# Intermediate artifacts
 example_data/preprocessed
+
+# Dev notebooks
+notebooks/tmp
+/tmp
+/.agents/skills
+/notebooks
+/AGENTS.md
+/scripts
+/todo.md
+
+# Assets
+!assets/*
+/models