Pre commit

.github/workflows/CI.yml

@@ -1,4 +1,4 @@
-# This file is autogenerated by maturin v1.7.0
+# This file is autogenerated by maturin v1.7.8
 # To update, run
 #
 #    maturin generate-ci github
@@ -11,7 +11,7 @@ on:
       - main
       - master
     tags:
-      - '*'
+      - "*"
   pull_request:
   workflow_dispatch:
 
@@ -24,17 +24,17 @@ jobs:
     strategy:
       matrix:
         platform:
-          - runner: ubuntu-latest
+          - runner: ubuntu-22.04
             target: x86_64
-          - runner: ubuntu-latest
+          - runner: ubuntu-22.04
             target: x86
-          - runner: ubuntu-latest
+          - runner: ubuntu-22.04
             target: aarch64
-          - runner: ubuntu-latest
+          - runner: ubuntu-22.04
             target: armv7
-          - runner: ubuntu-latest
+          - runner: ubuntu-22.04
             target: s390x
-          - runner: ubuntu-latest
+          - runner: ubuntu-22.04
             target: ppc64le
     steps:
       - uses: actions/checkout@v4
@@ -46,7 +46,7 @@ jobs:
         with:
           target: ${{ matrix.platform.target }}
           args: --release --out dist --find-interpreter
-          sccache: 'true'
+          sccache: "true"
           manylinux: auto
       - name: Upload wheels
         uses: actions/upload-artifact@v4
@@ -59,13 +59,13 @@ jobs:
     strategy:
       matrix:
         platform:
-          - runner: ubuntu-latest
+          - runner: ubuntu-22.04
             target: x86_64
-          - runner: ubuntu-latest
+          - runner: ubuntu-22.04
             target: x86
-          - runner: ubuntu-latest
+          - runner: ubuntu-22.04
             target: aarch64
-          - runner: ubuntu-latest
+          - runner: ubuntu-22.04
             target: armv7
     steps:
       - uses: actions/checkout@v4
@@ -77,7 +77,7 @@ jobs:
         with:
           target: ${{ matrix.platform.target }}
           args: --release --out dist --find-interpreter
-          sccache: 'true'
+          sccache: "true"
           manylinux: musllinux_1_2
       - name: Upload wheels
         uses: actions/upload-artifact@v4
@@ -105,7 +105,7 @@ jobs:
         with:
           target: ${{ matrix.platform.target }}
           args: --release --out dist --find-interpreter
-          sccache: 'true'
+          sccache: "true"
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
@@ -117,7 +117,7 @@ jobs:
     strategy:
       matrix:
         platform:
-          - runner: macos-12
+          - runner: macos-13
             target: x86_64
           - runner: macos-14
             target: aarch64
@@ -131,7 +131,7 @@ jobs:
         with:
           target: ${{ matrix.platform.target }}
           args: --release --out dist --find-interpreter
-          sccache: 'true'
+          sccache: "true"
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
@@ -156,11 +156,23 @@ jobs:
   release:
     name: Release
     runs-on: ubuntu-latest
-    if: "startsWith(github.ref, 'refs/tags/')"
+    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
     needs: [linux, musllinux, windows, macos, sdist]
+    permissions:
+      # Use to sign the release artifacts
+      id-token: write
+      # Used to upload release artifacts
+      contents: write
+      # Used to generate artifact attestation
+      attestations: write
     steps:
       - uses: actions/download-artifact@v4
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v1
+        with:
+          subject-path: "wheels-*/*"
       - name: Publish to PyPI
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
         uses: PyO3/maturin-action@v1
         env:
           MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/pre-commit.yml

@@ -2,9 +2,9 @@ name: pre-commit
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
 
 env:
   CARGO_TERM_COLOR: always
@@ -15,8 +15,8 @@ jobs:
     env:
       SKIP: no-commit-to-branch
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:  # run pre-commit on our oldest supported python version
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with: # run pre-commit on our oldest supported python version
           python-version: "3.10"
-    - uses: pre-commit/action@v3.0.1
+      - uses: pre-commit/action@v3.0.1

.github/workflows/rust.yml

@@ -2,9 +2,9 @@ name: Rust
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -15,12 +15,11 @@ env:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Build
-      run: cargo build --verbose
-    - name: Run tests
-      run: cargo test --verbose
+      - uses: actions/checkout@v4
+      - name: Build
+        run: cargo build --verbose
+      - name: Run tests
+        run: cargo test --verbose

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-ast
       - id: check-merge-conflict
@@ -18,12 +18,12 @@ repos:
     rev: 054bda51dbe278b3e86f27c890e3f3ac877d616c
     hooks:
       - id: validate-cff
-  - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: "v3.4.2"
     hooks:
-      - id: mdformat
+      - id: prettier
   - repo: https://github.com/crate-ci/typos
-    rev: v1.24.6
+    rev: v1.28.3
     hooks:
       - id: typos
   - repo: https://github.com/doublify/pre-commit-rust
@@ -32,13 +32,13 @@ repos:
       - id: fmt
       - id: cargo-check
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.8
+    rev: v0.8.3
     hooks:
       - id: ruff-format
       - id: ruff
-        args: [ --fix, --show-fixes ]
+        args: [--fix, --show-fixes]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.13.0
     hooks:
       - id: mypy
 

CHANGELOG.md

@@ -49,7 +49,7 @@ Patch release to fix distribution to PyPI.
 
 ## \[0.6.1\] -- 2023-10-05
 
-Patch release to fix distribution to PyPI.  The release is now happening
+Patch release to fix distribution to PyPI. The release is now happening
 automatically from GitHub CI.
 
 ## \[0.6.0\] -- 2023-10-05
@@ -84,7 +84,7 @@ API.
 ## \[0.5.0\] -- 2022-02-10
 
 The major change of this release is a change in the macro DSL to write
-reactions even more naturally, with `+` instead of `,`.  Example:
+reactions even more naturally, with `+` instead of `,`. Example:
 `translation: mRNA => mRNA + GFP @ trans_rate`.
 
 It comes also with some performance improvements, mostly on the API side (~5%).
@@ -93,7 +93,7 @@ It comes also with some performance improvements, mostly on the API side (~5%).
 
 - The Rngs can now be seeded.
 - `SRate::LMA2` was reintroduced, along with `SRate::LMAn`, implementing
-  2nd and nth-order LMA.  They cannot be implemented in terms of
+  2nd and nth-order LMA. They cannot be implemented in terms of
   `SRate::LMA`.
 - Added nth-order reactants and products to the macro DSL.
 - The libraries `rand` and `rand_distr` are now reexported to be more
@@ -115,7 +115,7 @@ as more performance improvements for the function-based API (20-35%).
 
 ### Changed
 
-- `Gillespie` no longer has a const parameter.  This breaking change
+- `Gillespie` no longer has a const parameter. This breaking change
   was necessary for the definition of a system at run-time (for
   Python bindings).
 
@@ -163,6 +163,6 @@ First release.
     time, and with several possible rate functions (Law of Mass Action
     but also Hill functions or Michaelis--Menten dynamics);
   - `define_system!` which requires that the system is defined at
-    compilation.  It only supports rate functions based on the Law
-    of Mass Action.  It runs typically three times as fast as the
+    compilation. It only supports rate functions based on the Law
+    of Mass Action. It runs typically three times as fast as the
     programmatic API.

CITATION.cff

@@ -10,9 +10,9 @@ type: software
 authors:
   - given-names: Virgile
     family-names: Andreani
-    orcid: 'https://orcid.org/0000-0002-2383-1478'
-repository-code: 'https://github.com/Armavica/rebop'
-url: 'https://armavica.github.io/rebop/'
+    orcid: "https://orcid.org/0000-0002-2383-1478"
+repository-code: "https://github.com/Armavica/rebop"
+url: "https://armavica.github.io/rebop/"
 abstract: Fast stochastic simulator for chemical reaction networks
 license: MIT
 version: 0.8.3