Add tests

.git-hooks/pre-push

@@ -0,0 +1,60 @@
+#!/bin/sh
+
+# An example hook script to verify what is about to be pushed.  Called by "git
+# push" after it has checked the remote status, but before anything has been
+# pushed.  If this script exits with a non-zero status nothing will be pushed.
+#
+# This hook is called with the following parameters:
+#
+# $1 -- Name of the remote to which the push is being done
+# $2 -- URL to which the push is being done
+#
+# If pushing without using a named remote those arguments will be equal.
+#
+# Information about the commits which are being pushed is supplied as lines to
+# the standard input in the form:
+#
+#   <local ref> <local oid> <remote ref> <remote oid>
+#
+# This sample shows how to prevent push of commits where the log message starts
+# with "WIP" (work in progress).
+
+remote="$1"
+url="$2"
+
+# Run Ruff check first
+echo "Running ruff check on src/..."
+ruff check src
+
+if [ $? -ne 0 ]; then
+	echo "❌ Ruff check failed. Push aborted."
+	exit 1
+fi
+
+# Prepare to check for WIP commits
+zero=$(git hash-object --stdin </dev/null | tr '[0-9a-f]' '0')
+
+while read local_ref local_oid remote_ref remote_oid; do
+	if test "$local_oid" = "$zero"; then
+		# Handle delete
+		:
+	else
+		if test "$remote_oid" = "$zero"; then
+			# New branch, examine all commits
+			range="$local_oid"
+		else
+			# Update to existing branch, examine new commits
+			range="$remote_oid..$local_oid"
+		fi
+
+		# Check for WIP commit
+		commit=$(git rev-list -n 1 --grep '^WIP' "$range")
+		if test -n "$commit"; then
+			echo >&2 "Found WIP commit in $local_ref, not pushing"
+			exit 1
+		fi
+	fi
+done
+
+echo "✅ All checks passed. Proceeding with push."
+exit 0

.gitattributes

@@ -4,4 +4,7 @@
 *.fits binary
 *.h5   binary
 *.pxt  binary
-*.nc   binary
+*.nc   binary
+*.ipynb filter=nbstripout
+*.zpln filter=nbstripout
+*.ipynb diff=ipynb

.github/workflows/python-app.yml

@@ -0,0 +1,61 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - "3.11"
+          - "3.12"
+          - "3.13"
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: eifinger/setup-uv@v3
+
+      - name: Set up Python
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install libhdf5-dev by apt
+        run: |
+          sudo apt -y update
+          sudo apt -y install libhdf5-dev libnetcdf-dev make pandoc ffmpeg
+
+      - name: uv sync
+        run: |
+          uv sync --all-extras --dev
+
+      - name: test with uv
+        run: uv run pytest -vv --color=yes --cov=./  --cov-report=xml
+
+      - name: Build docs
+        run: |
+          source .venv/bin/activate
+          cd docs
+          make html
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true # optional (default = false)
+          files: ./coverage.xml
+          flags: unittests # optional
+          name: codecov-umbrella # optional
+          token: ${{ secrets.CODECOV_TOKEN }} # required
+          verbose: true # optional (default = false)

.github/workflows/ruff.yml

@@ -0,0 +1,16 @@
+name: Ruff
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v1
+        with:
+          src: "./src"

.gitignore

@@ -2,6 +2,10 @@
 *.code-workspace
 .vscode/
 
+# rye generated
+requirements-dev.lock
+requirements.lock
+
 # JS Ecosystem
 node_modules/
 
@@ -29,17 +33,14 @@ junit/
 build/
 docs/source/generated/
 docs/source/notebooks/logs/
-docs/source/notebooks/img/
 
 cache/*.nc
 cache/*.json
 cache/*.keep
 
 .idea/
 
-TODO.md
-
-local_config.py
+src/local_config.py
 
 !datasets/Misc
 !experiments/Misc
@@ -113,6 +114,7 @@ target/
 
 # Jupyter Notebook
 .ipynb_checkpoints
+.virtual_documents/
 
 # pyenv
 .python-version
@@ -176,3 +178,4 @@ com_crashlytics_export_strings.xml
 crashlytics.properties
 crashlytics-build.properties
 fabric.properties
+uv.lock

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "stubs"]
+	path = stubs
+	url = git@github.com:microsoft/python-type-stubs

.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+      # Run the linter
+      - id: ruff
+        types_or: [python]
+      #  args: [ --fix ]
+      # Run the formatter
+      - id: ruff-format
+        types_or: [python]