Merge branch 'main' into zarr-prop-tests

* main: (167 commits)
  Bump actions/checkout from 2 to 4 in the actions group (#305)
  update zarr pin to v3.0.0b1 (#302)
  Fix non-conformant "attributes" metadata (#303)
  Implement branch reset functionality (#301)
  README minor tune up: syntax and other very minor typos etc (#300)
  remove awaits in icechunk notebook (#298)
  Add missing permission to release action (#295)
  Minor changes to virtual docs (#293)
  Add changelogs (#291)
  Install cargo release (#290)
  Update python ci (#289)
  GHA workflow to release Rust (#288)
  Release 0.1.0-alpha.3 to the Rust world (#287)
  `ByteRange` can do last n bytes now (#285)
  Introduce `Store::list_dir_items` (#286)
  [Docs] Improve virtual ref docs (#284)
  [Docs] correct output dimensions in xr example (#283)
  [Docs] add note for requirements of tutorial data download (#282)
  [Docs] correct module calls to match imports (#281)
  fix(docs): Docs postlaunch fixes (#278)
  ...

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git*,*.svg,*.lock,*.css,.codespellrc
+check-hidden = true
+ignore-regex = ^\s*"image/\S+": ".*|\bND\b
+ignore-words-list = crate

.gitattributes

@@ -0,0 +1 @@
+*.ipynb linguist-detectable=false

.github/dependabot.yml

@@ -18,3 +18,7 @@ updates:
       day: "monday"
       time: "05:00"
       timezone: "US/Pacific"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/codespell.yml

@@ -0,0 +1,25 @@
+# Codespell configuration is within .codespellrc
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/deploy-docs.yaml

@@ -0,0 +1,67 @@
+name: deploy-docs 
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+permissions:
+  contents: write
+jobs:
+  deploy:
+    defaults:
+      run:
+        working-directory: ./docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+
+      - name: Load cached Poetry installation
+        id: cached-poetry
+        uses: actions/cache@v4
+        with:
+          path: ~/.local  # the path depends on the OS
+          key: poetry-0  # increment to reset cache
+
+      - name: Install Poetry
+        if: steps.cached-poetry.outputs.cache-hit != 'true'
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          virtualenvs-path: .venv
+          installer-parallel: true
+
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Install dependencies (with cache)
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+
+      - name: Install project
+        run: poetry install --no-interaction
+
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
+
+      - name: Setup Cache for MkDocs
+        uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      
+      - name: Deploy to gh-pages
+        run: poetry run mkdocs gh-deploy --force

.github/workflows/publish-rust-library.yml

@@ -0,0 +1,64 @@
+name: publish rust library
+
+env:
+  CARGO_INCREMENTAL: 0
+  CARGO_NET_RETRY: 10
+  CI: 1
+  RUST_BACKTRACE: short
+  RUSTFLAGS: "-D warnings -W unreachable-pub -W bare-trait-objects"
+  RUSTUP_MAX_RETRIES: 10
+  RUST_CHANNEL: 'stable'
+
+on:
+  workflow_dispatch:
+
+jobs:
+  publish:
+    name: Check and publish
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Stand up MinIO
+        run: |
+          docker compose up -d minio
+      - name: Wait for MinIO to be ready
+        run: |
+          for i in {1..10}; do
+              if curl --silent --fail http://minio:9000/minio/health/live; then
+              break
+              fi
+              sleep 3
+          done
+          docker compose exec -T minio mc alias set minio http://minio:9000 minio123 minio123
+
+      - name: Install Just
+        run: sudo snap install --edge --classic just
+
+      - name: Install Rust toolchain
+        run: |
+          rustup update --no-self-update ${{ env.RUST_CHANNEL }}
+          rustup component add --toolchain ${{ env.RUST_CHANNEL }} rustfmt rust-src clippy
+          rustup default ${{ env.RUST_CHANNEL }}
+
+      - name: Cache Dependencies
+        uses: Swatinem/rust-cache@v2
+        with:
+          # workspaces: "rust -> target"
+          key: ${{ env.RUST_CHANNEL }}
+
+      - name: Install cargo-deny
+        run: cargo install --locked cargo-deny
+
+      - name: Check
+        if: matrix.os == 'ubuntu-latest' || github.event_name == 'push'
+        run: |
+          just pre-commit
+
+      - name: Install cargo-release
+        run: cargo install --locked cargo-release
+
+      - name: publish to crates
+        run: cargo release --tag-prefix icechunk-rust --execute
+        env:
+          CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}

.github/workflows/python-check.yaml

@@ -0,0 +1,95 @@
+name: Python Check
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    paths:
+      - 'icechunk/**'
+      - 'icechunk-python/**'
+      - '.github/workflows/python-check.yaml'
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+defaults:
+  run:
+    working-directory: ./icechunk-python
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Stand up MinIO
+        run: |
+          docker compose up -d minio
+      - name: Wait for MinIO to be ready
+        run: |
+          for _ in {1..10}; do
+              if curl --silent --fail http://minio:9000/minio/health/live; then
+              break
+              fi
+              sleep 3
+          done
+          docker compose exec -T minio mc alias set minio http://minio:9000 minio123 minio123
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          working-directory: icechunk-python
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: 'true'
+          manylinux: ${{ matrix.platform.manylinux }} # https://github.com/PyO3/maturin-action/issues/245
+      - name: mypy
+        shell: bash
+        working-directory: icechunk-python
+        run: |
+          set -e
+          python3 -m venv .venv
+          source .venv/bin/activate
+          pip install icechunk['test'] --find-links dist --force-reinstall
+          mypy python
+      - name: ruff
+        shell: bash
+        working-directory: icechunk-python
+        run: |
+          set -e
+          python3 -m venv .venv
+          source .venv/bin/activate
+          pip install icechunk['test'] --find-links dist --force-reinstall
+          ruff check
+      - name: Restore cached hypothesis directory
+        id: restore-hypothesis-cache
+        uses: actions/cache/restore@v4
+        with:
+          path: icechunk-python/.hypothesis/
+          key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}
+          restore-keys: |
+            cache-hypothesis-
+      - name: pytest
+        shell: bash
+        working-directory: icechunk-python
+        run: |
+          set -e
+          python3 -m venv .venv
+          source .venv/bin/activate
+          pip install icechunk['test'] --find-links dist --force-reinstall
+          pytest
+      # explicitly save the cache so it gets updated, also do this even if it fails.
+      - name: Save cached hypothesis directory
+        id: save-hypothesis-cache
+        if: always()
+        uses: actions/cache/save@v4
+        with:
+          path: icechunk-python/.hypothesis/
+          key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}