Merge pull request #21 from sybila/daemontus/chore/deps-and-ci-update

Dependencies and CI update

Author: daemontus

.github/workflows/build.yml

@@ -1,101 +1,22 @@
 name: build
 
-# This should ensure that the workflow won't run on `dev-*` branches, but will
-# otherwise execute on any other branch and any pull request (including PRs
-# from dev branches).
+# This should ensure that the workflow won't run on `feat/*`, `fix/*` and `chore/*` branches, but will
+# otherwise execute on any other branch and any pull request.
 on:
   push:
     branches-ignore:
-      - 'dev-*'
+      - '**/feat/*'
+      - '**/fix/*'
+      - '**/chore/*'
   pull_request:
     branches:
       - '*'
 
-env:
-  # A fixed version used for testing, so that the builds don't
-  # spontaneously break after a few years.
-  # Make sure to update this from time to time.
-  RUST_VERSION: "1.86.0"
 jobs:
-  # Checks syntax formatting.
-  fmt:
-    name: Rustfmt
-    runs-on: ubuntu-latest
-    env:
-      RUSTFLAGS: "-D warnings"
-    steps:
-      - uses: actions/checkout@v4
-      - uses: dtolnay/rust-toolchain@stable
-        with:
-          toolchain: ${{ env.RUST_VERSION }}
-          components: rustfmt
-      - run: cargo fmt --all -- --check
-
-  # Run basic code validity check.
-  check:
-    needs: fmt
-    name: Check
-    runs-on: ubuntu-latest
-    env:
-      RUSTFLAGS: "-D warnings"
-    steps:
-      - uses: actions/checkout@v4
-      - uses: dtolnay/rust-toolchain@stable
-        with:
-          toolchain: ${{ env.RUST_VERSION }}
-      - run: cargo check --all-features
-
-  # Run tests.
-  test:
-    needs: check
-    name: Test Suite (linux)
-    runs-on: ubuntu-latest
-    env:
-      RUSTFLAGS: "-D warnings"
-    steps:
-      - uses: actions/checkout@v4
-      - uses: dtolnay/rust-toolchain@stable
-        with:
-          toolchain: ${{ env.RUST_VERSION }}
-          components: rustfmt
-      - run: cargo test --all-features
-
-  # Checks code style.
-  clippy:
-    needs: check
-    name: Clippy
-    runs-on: ubuntu-latest
-    env:
-      RUSTFLAGS: "-D warnings"
-    steps:
-      - uses: actions/checkout@v4
-      - uses: dtolnay/rust-toolchain@stable
-        with:
-          toolchain: ${{ env.RUST_VERSION }}
-          components: clippy
-      - run: cargo clippy --all-features
-
-  # Compute code coverage
-  codecov:
-    needs: test
-    name: Code coverage
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: dtolnay/rust-toolchain@stable
-        with:
-          toolchain: ${{ env.RUST_VERSION }}
-      # Install action using cargo-binstall, which is faster because we don't have to compile tarpaulin every time.
-      - uses: taiki-e/install-action@v2
-        with:
-          tool: cargo-tarpaulin
-      - run: cargo tarpaulin --verbose --lib --examples --all-features --out xml
-      - name: Upload to codecov.io
-        uses: codecov/codecov-action@v4
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-      - name: Archive code coverage results
-        uses: actions/upload-artifact@v4
-        with:
-          name: code-coverage-report
-          path: cobertura.xml
+  validate:
+    uses: sybila/github-workflows/.github/workflows/rust-build-and-check.yml@main
+    with:
+      rust-version: "1.90.0"
+      min-rust-version: "1.88.0"
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/release.yml

@@ -0,0 +1,16 @@
+on:
+  push:
+    tags:
+      - 'v*.*.*'
+
+name: Publish to crates.io and generate release info
+
+jobs:
+  deploy:
+    uses: sybila/github-workflows/.github/workflows/rust-release-and-publish.yml@main
+    with:
+      min-rust-version: "1.88.0"
+      repository-url: "https://github.com/sybila/biodivine-hctl-model-checker"
+    secrets:
+      GEMINI_API_KEY: ${{ secrets.GEMINI_API_KEY }}
+      CRATES_IO_API_TOKEN: ${{ secrets.CRATES_IO_API_TOKEN }}

.releasenotes.yml

@@ -0,0 +1,6 @@
+project_type: library
+public_api_command: "cargo public-api --omit blanket-impls,auto-trait-impls,auto-derived-impls"
+gemini_model: "gemini-2.5-pro"
+diff_exclude_paths:
+  - benchmark_models/**
+  - test/**

Cargo.toml

@@ -2,7 +2,7 @@
 name = "biodivine-hctl-model-checker"
 version = "0.3.3"
 authors = ["Ondřej Huvar <xhuvar@fi.muni.cz>", "Samuel Pastva <sam.pastva@gmail.com>"]
-edition = "2021"
+edition = "2024"
 description = "Library for symbolic HCTL model checking on partially defined Boolean networks."
 documentation = "https://docs.rs/biodivine-hctl-model-checker/latest/"
 homepage = "https://github.com/sybila/biodivine-hctl-model-checker"
@@ -11,6 +11,8 @@ readme = "README.md"
 keywords = ["hctl", "model-checking", "boolean-network", "symbolic", "systems-biology"]
 categories = ["science", "simulation"]
 license = "MIT"
+# If you are increasing this, update it in both CI workflows.
+rust-version = "1.88.0"
 exclude = ["benchmark_models", ".github", ".githooks"]
 
 [profile.test]
@@ -25,9 +27,11 @@ name = "convert-aeon-to-bnet"
 path = "src/bin/convert_aeon_to_bnet.rs"
 
 [dependencies]
-biodivine-lib-bdd = ">=0.5.22, <1.0.0"
-biodivine-lib-param-bn = ">=0.5.13, <1.0.0"
-clap = { version = "4.1.4", features = ["derive"] }
-rand = "0.8.5"
-termcolor = "1.1.2"
-zip = "0.6.3"
+biodivine-lib-bdd = ">=0.6.1, <1.0.0"
+biodivine-lib-param-bn = ">=0.6.1, <1.0.0"
+clap = { version = "4.5", features = ["derive"] }
+# `rand` cannot be updated because `lib-bdd` uses it to generate random `big-int` values
+# and this is not yet supported for `0.9` or newer.
+rand = "0.8"
+termcolor = "1.4"
+zip = "0.6"

src/_aeon_algorithms/algo_xie_beerel.rs

@@ -1,8 +1,8 @@
 use crate::_aeon_algorithms::saturated_reachability::{reach_bwd, reachability_step};
 
+use biodivine_lib_param_bn::VariableId;
 use biodivine_lib_param_bn::biodivine_std::traits::Set;
 use biodivine_lib_param_bn::symbolic_async_graph::{GraphColoredVertices, SymbolicAsyncGraph};
-use biodivine_lib_param_bn::VariableId;
 
 /// Uses a simplified Xie-Beerel algorithm adapted to coloured setting to find all bottom
 /// SCCs in the given `universe` set. It only tests transitions using `active_variables`.

src/_aeon_algorithms/itgr/_impl_extended_component_process.rs

@@ -1,6 +1,6 @@
+use biodivine_lib_param_bn::VariableId;
 use biodivine_lib_param_bn::biodivine_std::traits::Set;
 use biodivine_lib_param_bn::symbolic_async_graph::{GraphColoredVertices, SymbolicAsyncGraph};
-use biodivine_lib_param_bn::VariableId;
 
 use crate::_aeon_algorithms::itgr::{BwdProcess, ExtendedComponentProcess, Process, Scheduler};
 use crate::_aeon_algorithms::saturated_reachability::reach_bwd;

src/_aeon_algorithms/itgr/_impl_reachable_process.rs

@@ -1,6 +1,6 @@
+use biodivine_lib_param_bn::VariableId;
 use biodivine_lib_param_bn::biodivine_std::traits::Set;
 use biodivine_lib_param_bn::symbolic_async_graph::{GraphColoredVertices, SymbolicAsyncGraph};
-use biodivine_lib_param_bn::VariableId;
 
 use crate::_aeon_algorithms::itgr::{
     ExtendedComponentProcess, FwdProcess, Process, ReachableProcess, Scheduler,

src/_aeon_algorithms/itgr/_impl_scheduler.rs

@@ -1,6 +1,6 @@
+use biodivine_lib_param_bn::VariableId;
 use biodivine_lib_param_bn::biodivine_std::traits::Set;
 use biodivine_lib_param_bn::symbolic_async_graph::{GraphColoredVertices, SymbolicAsyncGraph};
-use biodivine_lib_param_bn::VariableId;
 
 use crate::_aeon_algorithms::itgr::{Process, Scheduler};
 

src/_aeon_algorithms/itgr/mod.rs

@@ -5,8 +5,8 @@
 //! a very reasonable amount of time.
 //!
 
-use biodivine_lib_param_bn::symbolic_async_graph::{GraphColoredVertices, SymbolicAsyncGraph};
 use biodivine_lib_param_bn::VariableId;
+use biodivine_lib_param_bn::symbolic_async_graph::{GraphColoredVertices, SymbolicAsyncGraph};
 
 mod _impl_extended_component_process;
 mod _impl_fwd_bwd_process;

src/_aeon_algorithms/saturated_reachability.rs

@@ -1,6 +1,6 @@
+use biodivine_lib_param_bn::VariableId;
 use biodivine_lib_param_bn::biodivine_std::traits::Set;
 use biodivine_lib_param_bn::symbolic_async_graph::{GraphColoredVertices, SymbolicAsyncGraph};
-use biodivine_lib_param_bn::VariableId;
 
 /// Performs one reachability step using the saturation scheme.
 ///