Merge pull request #144 from promised-ai/release/0.5.0

WIP 0.5.0 release candidate

.github/scripts/run_code_in_mdfile.py

@@ -43,10 +43,10 @@ def process_file(file, language, version):
         elif args.language == "rust":
             rust_script_contents = f"""//! ```cargo
         //! [dependencies]
-        //! lace = {{ path = ".", version="{version}" }}
-        //! polars = {{ version = "0.33", features=["csv"] }}
-        //! rand = "0.8"
-        //! rand_xoshiro = "0.6"
+        //! lace = {{ path = ".", version="{version}", features = ["examples", "ctrlc_handler"] }}
+        //! polars = {{ version = "0.34", default_features=false, features=["csv", "dtype-i8", "dtype-i16", "dtype-u8", "dtype-u16"] }}
+        //! rand = {{version="0.8", features=["serde1"]}}
+        //! rand_xoshiro = {{ version="0.6", features = ["serde1"] }}
         //! ```
         fn main() {{
         {code}

.github/workflows/cli-build-test.yaml

@@ -0,0 +1,143 @@
+name: 'CLI: Build and Test'
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  workflow_dispatch:
+  pull_request:
+    paths:
+      - 'cli/**'
+      - 'lace/**'
+      - '.github/workflows/cli-build-test.yaml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  features:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Cache Rust
+        uses: Swatinem/rust-cache@v2
+        with:
+          workspaces: . -> cli/target
+
+      - name: Install dependencies
+        run: cargo install cargo-hack
+
+      - name: Run cargo check on all features
+        working-directory: cli
+        run: cargo hack check --each-feature --all-targets
+
+  lint:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: cli
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Rust
+        uses: dtolnay/rust-toolchain@stable
+        with:
+          components: rustfmt, clippy
+
+      - name: Cache Rust
+        uses: Swatinem/rust-cache@v2
+        with:
+          workspaces: . -> cli/target
+
+      - name: Run rustfmt
+        working-directory: cli
+        run: cargo fmt --all -- --check
+
+      - name: Run clippy
+        working-directory: cli
+        env:
+          RUSTFLAGS: -C debuginfo=0
+        run: |
+          cargo clippy --all-features
+
+      - name: Install audit
+        run: cargo install cargo-audit
+
+      - name: Run audit
+        working-directory: cli
+        # Note: Both `polars` and `arrow2` trigger this security violation
+        #       due to their reliance on `chrono`, which is the ultimate source of the violation
+        #       as of 2/21/23, no version of `chrono` has been published that fixes the issue
+        #       and thus neither `polars` or `arrow2` can pass `audit` checks
+        run: cargo audit -f Cargo.lock --ignore RUSTSEC-2020-0071
+
+  test:
+    runs-on: ${{ matrix.os }}
+    needs: ["lint", "features"]
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+    defaults:
+      run:
+        working-directory: cli
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Rust
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Cache Rust
+        uses: Swatinem/rust-cache@v2
+        with:
+          workspaces: . -> cli/target
+
+      - name: Regen Examples
+        env:
+          RUSTFLAGS: -C debuginfo=0
+        run: cargo run -- regen-examples
+
+      - name: Run tests
+        env:
+          RUSTFLAGS: -C debuginfo=0
+        run: cargo test 
+
+  # semver-checks:
+  #   runs-on: ubuntu-latest
+  #   needs: ["features", "lint", "test"]
+  #   steps:
+  #     - name: Checkout branch
+  #       uses: actions/checkout@v3
+  #       with:
+  #         path: branch
+
+  #     - name: Checkout master
+  #       uses: actions/checkout@v3
+  #       with:
+  #         ref: master
+  #         path: master
+
+  #     - name: Set up Rust
+  #       uses: dtolnay/rust-toolchain@stable
+
+  #     - name: Cache Rust
+  #       uses: Swatinem/rust-cache@v2
+  #       with:
+  #         workspaces: . -> lace/target
+
+  #     - name: Install extra cargo tools
+  #       run: cargo install cargo-semver-checks --locked
+
+  #     - name: Check for semver-incompatibilities
+  #       run: cargo semver-checks check-release --manifest-path branch/lace/Cargo.toml --baseline-root master/lace --verbose

.github/workflows/rust-build-test.yaml

@@ -107,14 +107,15 @@ jobs:
           workspaces: . -> lace/target
 
       - name: Regen Examples
+        working-directory: cli
         env:
           RUSTFLAGS: -C debuginfo=0
         run: cargo run -- regen-examples
 
       - name: Run tests
         env:
           RUSTFLAGS: -C debuginfo=0
-        run: cargo test 
+        run: cargo test --all-features
 
   # semver-checks:
   #   runs-on: ubuntu-latest
@@ -217,7 +218,7 @@ jobs:
           test "$DEPLOYING_VERSION" = "$MAIN_VERSION"
       - name: Install dependencies
         run: cargo install cargo-crate
-      - name: Publish Updated Crates to Crates.io
+      - name: Publish Updated Library Crates to Crates.io
         working-directory: lace
         env:
           CRATES_TOKEN: ${{ secrets.CRATES_TOKEN }}
@@ -239,3 +240,14 @@ jobs:
               cargo publish --token "${CRATES_TOKEN}" -p $PACKAGE_NAME
             fi
           done
+      - name: Publish Updated CLI Crate to Crates.io
+        working-directory: cli
+        env:
+          CRATES_TOKEN: ${{ secrets.CRATES_TOKEN }}
+        run: |
+          PACKAGE_VERSION=$(tomlq .package.version Cargo.toml)
+          ALREADY_PUBLISHED=$(cargo crate info lace-cli --json --max-versions 100 | jq '[.krate.versions[].num] | any(. == '$PACKAGE_VERSION')')
+          if [ "$ALREADY_PUBLISHED" == 'false' ]
+          then
+            cargo publish --token "${CRATES_TOKEN}" -p lace-cli
+          fi

.gitignore

@@ -7,3 +7,4 @@ Pipfile
 pybraid/.github
 *.ini
 .vscode/
+.helix

CHANGELOG.md

@@ -7,6 +7,37 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [python-0.5.0] - 2023-11-20
+
+### Added
+
+- Codebook.value_map fn and iterator
+
+### Changed
+
+- Added common transitions sets by name to `Engine.update` transition argument.
+
+## [rust-0.5.0] - 2023-11-20
+
+### Added
+
+- Lace can now be compiled to Wasm
+
+### Changed
+
+- Moved CLI into its own crate
+- Moved `DataSource` variants for Parquet, IPC (Arrow), and JSON data types into the `formats` feature flag.
+- Moved the `CtrlC` `UpdateHandler` into `ctrlc_handler` feature flag
+- Moved `Bencher` into the `bencher` feature flag
+- Moved `Example` code into the `examples` feature flag (on by default)
+- Replaced instances of `once_cell::sync::OnceCell` with `syd::sync::OnceLock`
+- Renamed all files/methods with the name `feather` to `arrow`
+- Renamed `Builder` to `EngineBuilder`
+
+### Fixed
+
+- Fixed typo `UpdateHandler::finialize` is now `UpdateHandler::finalize`
+
 ## [python-0.4.1] - 2023-10-19
 
 ### Fixed
@@ -152,7 +183,9 @@ Initial release on [PyPi](https://pypi.org/)
 
 Initial release on [crates.io](https://crates.io/)
 
-[unreleased]: https://github.com/promised-ai/lace/compare/python-0.4.1...HEAD
+[unreleased]: https://github.com/promised-ai/lace/compare/python-0.5.0...HEAD
+[python-0.5.0]: https://github.com/promised-ai/lace/compare/python-0.4.1...python-0.5.0
+[rust-0.5.0]: https://github.com/promised-ai/lace/compare/rust-0.4.1...rust-0.5.0
 [python-0.4.1]: https://github.com/promised-ai/lace/compare/python-0.4.0...python-0.4.1
 [rust-0.4.1]: https://github.com/promised-ai/lace/compare/rust-0.4.0...rust-0.4.1
 [python-0.4.0]: https://github.com/promised-ai/lace/compare/python-0.3.1...python-0.4.0

CITATION.cff

@@ -0,0 +1,38 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: 'Lace: Bayesian Tabular Analysis for Scientific Discovery'
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Baxter
+    family-names: Eaves
+    name-suffix: Jr
+    email: [email protected]
+    affiliation: Redpoll
+  - given-names: Michael
+    family-names: Schmidt
+    email: [email protected]
+    affiliation: Redpoll
+  - given-names: Ken
+    family-names: Swanson
+    email: [email protected]
+    affiliation: Redpoll
+identifiers:
+  - type: url
+    value: 'https://github.com/promised-ai/lace'
+    description: Github repository
+repository-code: 'https://github.com/promised-ai/lace'
+url: 'https://lace.dev'
+abstract: >-
+  Lace is a probabilistic cross-categorization engine
+  written in rust.
+keywords:
+  - Bayesian
+  - Machine Learning
+license: BSL-1.1
+version: 0.5.0
+date-released: '2023-11-17'