chore: Configure pre-commit, update the justfile (#890)

Setups `pre-commit` instead of the ad-hoc `.github/pre-commit` file, and
cleans up the `just` recipes.

The main benefit of this is to avoid running both codebase tests on each
commit, since `pre-commit` filters the required checks based on the
modified files.

Updates `DEVELOPMENT.md` with the new commands. It should be a bit more
straightforward now.

drive-by: Fixes for the `trailing-whitespace` and `end-of-file-fixer`
hooks.

.github/workflows/drop-cache.yml

@@ -10,18 +10,18 @@ jobs:
     steps:
       - name: Check out code
         uses: actions/checkout@v4
-        
+
       - name: Cleanup
         run: |
           gh extension install actions/gh-actions-cache
-          
+
           REPO=${{ github.repository }}
           BRANCH="refs/pull/${{ github.event.pull_request.number }}/merge"
 
           echo "Fetching list of cache key"
           cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH | cut -f 1 )
 
-          ## Setting this to not fail the workflow while deleting cache keys. 
+          ## Setting this to not fail the workflow while deleting cache keys.
           set +e
           echo "Deleting caches..."
           for cacheKey in $cacheKeysForPR

.github/workflows/pr-title.yml

@@ -3,7 +3,7 @@ name: Check Conventional Commits format
 on:
   pull_request_target:
     branches:
-      - main 
+      - main
     types:
       - opened
       - edited
@@ -69,4 +69,4 @@ jobs:
           # labels change, you might want to use the `labeled` and `unlabeled`
           # event triggers in your workflow.
           ignoreLabels: |
-            ignore-semantic-pull-request
+            ignore-semantic-pull-request

.github/workflows/unsoundness.yml

@@ -3,7 +3,7 @@ name: Unsoundness checks
 on:
   push:
     branches:
-      - main 
+      - main
   workflow_dispatch: {}
 
 concurrency:

.gitignore

@@ -20,9 +20,6 @@ proptest-regressions/
 .devenv*
 devenv.local.nix
 
-# managed by devenv
-.pre-commit-config.yaml
-
 # Coverage report
 lcov.info
 

.pre-commit-config.yaml

@@ -0,0 +1,65 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0 # Use the ref you want to point at
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-vcs-permalinks
+      - id: check-yaml
+      - id: detect-private-key
+      - id: end-of-file-fixer
+        exclude: ^specification/schema/
+      - id: trailing-whitespace
+      - id: fix-byte-order-marker
+      - id: mixed-line-ending
+      # Python-specific
+      - id: check-ast
+      - id: check-docstring-first
+      - id: debug-statements
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.0
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.9.0
+    hooks:
+      - id: mypy
+        additional_dependencies: [pydantic]
+
+  - repo: local
+    hooks:
+      - id: cargo-fmt
+        name: cargo format
+        description: Format rust code with `cargo fmt`.
+        entry: cargo fmt --all -- --check
+        language: system
+        files: \.rs$
+        pass_filenames: false
+      - id: cargo-check
+        name: cargo check
+        description: Check rust code with `cargo check`.
+        entry: cargo check --all --all-features --workspace
+        language: system
+        files: \.rs$
+        pass_filenames: false
+      - id: cargo-test
+        name: cargo test
+        description: Run tests with `cargo test`.
+        entry: cargo test --all-features --workspace
+        language: system
+        files: \.rs$
+        pass_filenames: false
+      - id: cargo-clippy
+        name: cargo clippy
+        description: Run clippy lints with `cargo clippy`.
+        entry: cargo clippy --all-features --workspace -- -D warnings
+        language: system
+        files: \.rs$
+        pass_filenames: false

DEVELOPMENT.md

@@ -32,27 +32,24 @@ To setup the environment manually you will need:
 - Just: https://just.systems/
 - Poetry: https://python-poetry.org/
 
-You can use the git hook in [`.github/pre-commit`](.github/pre-commit) to automatically run the test and check formatting before committing.
-To install it, run:
+Once you have these installed, you can install the required python dependencies and setup pre-commit hooks with:
 
 ```bash
-ln -s .github/pre-commit .git/hooks/pre-commit
-# Or, to check before pushing instead
-ln -s .github/pre-commit .git/hooks/pre-push
+just setup
 ```
 
 ## 🏃 Running the tests
 
-To compile and test the rust code, run:
+To compile and test the code, run:
 
 ```bash
-# Rust tests
-just test # or `cargo test`
-# Python tests
-just pytest
+just test
+# or, to test only the rust code or the python code
+just test rust
+just test python
 ```
 
-Run the benchmarks with:
+Run the rust benchmarks with:
 
 ```bash
 cargo bench
@@ -75,7 +72,6 @@ The rustfmt tool is used to enforce a consistent rust coding style. The CI will
 To format your code, run:
 
 ```bash
-# Format rust code
 just format
 ```
 
@@ -89,6 +85,9 @@ To quickly fix common issues, run:
 
 ```bash
 just fix
+# or, to fix only the rust code or the python code
+just fix rust
+just fix python
 ```
 
 ## 📈 Code Coverage
@@ -98,18 +97,14 @@ line-by-line coverage report on
 [codecov](https://app.codecov.io/gh/CQCL/hugr/commits?branch=All%20branches).
 
 To run the coverage checks locally, first install `cargo-llvm-cov`.
-
 ```bash
 cargo install cargo-llvm-cov
 ```
 
 Then run the tests:
 
 ```bash
-# Rust test coverage
 just coverage
-# Python test 
-just pycoverage
 ```
 
 and open it with your favourite coverage viewer. In VSCode, you can use
@@ -140,4 +135,4 @@ We accept the following contribution types:
 - test: Adding missing tests, refactoring tests; no production code change.
 - ci: CI related changes. These changes are not published in the changelog.
 - chore: Updating build tasks, package manager configs, etc. These changes are not published in the changelog.
-- revert: Reverting previous commits.
+- revert: Reverting previous commits.

LICENCE

@@ -198,4 +198,4 @@
    distributed under the License is distributed on an "AS IS" BASIS,
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
-   limitations under the License.
+   limitations under the License.

devenv.nix

@@ -4,7 +4,7 @@ let
 in
 {
   # https://devenv.sh/packages/
-  # on macos frameworks have to be explicitly specified 
+  # on macos frameworks have to be explicitly specified
   # otherwise a linker error ocurs on rust packages
   packages = [
     pkgs.just
@@ -46,12 +46,6 @@ in
     components = [ "rustc" "cargo" "clippy" "rustfmt" "rust-analyzer" ];
   };
 
-  # https://devenv.sh/pre-commit-hooks/
-  pre-commit.hooks.clippy.enable = true;
-  pre-commit.tools.clippy = lib.mkForce config.languages.rust.toolchain.clippy;
-  pre-commit.hooks.rustfmt.enable = true;
-  pre-commit.tools.rustfmt = lib.mkForce config.languages.rust.toolchain.rustfmt;
-
   # https://devenv.sh/processes/
   # processes.ping.exec = "ping example.com";
 

devenv.yaml

@@ -5,4 +5,4 @@ inputs:
     url: github:nix-community/fenix
     inputs:
       nixpkgs:
-        follows: nixpkgs
+        follows: nixpkgs

justfile

@@ -2,40 +2,70 @@
 help:
     @just --list --justfile {{justfile()}}
 
-# Run all the rust tests
-test:
-    cargo test --all-features
+# Prepare the environment for development, installing all the dependencies and
+# setting up the pre-commit hooks.
+setup:
+    poetry install
+    poetry run pre-commit install -t pre-commit
 
-# Auto-fix all clippy warnings
-fix:
-    cargo clippy --all-targets --all-features --workspace --fix --allow-staged
-    poetry run ruff check --fix
-
-# Run the pre-commit checks
+# Run the pre-commit checks.
 check:
-    ./.github/pre-commit
+    poetry run pre-commit run --all-files
 
-# Format the code
-format:
-    cargo fmt
-    poetry run ruff format
+# Run all the tests.
+test language="[rust|python]": (_run_lang language \
+        "cargo test --all-features" \
+        "poetry run pytest"
+    )
 
-# Generate a test coverage report
-coverage:
-    cargo llvm-cov --lcov > lcov.info
+# Run all the benchmarks.
+bench language="[rust|python]": (_run_lang language \
+        "cargo bench" \
+        "true"
+    )
 
-# Load a poetry shell with the dependencies installed
-pyshell:
-    poetry shell
+# Auto-fix all clippy warnings.
+fix language="[rust|python]": (_run_lang language \
+        "cargo clippy --all-targets --all-features --workspace --fix --allow-staged --allow-dirty" \
+        "poetry run ruff check --fix"
+    )
+
+# Format the code.
+format language="[rust|python]": (_run_lang language \
+        "cargo fmt" \
+        "poetry run ruff format"
+    )
 
-# Run the python tests
-pytest:
-    poetry run pytest
+# Generate a test coverage report.
+coverage language="[rust|python]": (_run_lang language \
+        "cargo llvm-cov --lcov > lcov.info" \
+        "poetry run pytest --cov=./ --cov-report=html"
+    )
 
-# Generate a python test coverage report
-pycoverage:
-    poetry run pytest --cov=./ --cov-report=html
+# Load a shell with all the dependencies installed
+shell:
+    poetry shell
 
-# Update the HUGR schema
+# Update the HUGR schema.
 update-schema:
     poetry run python scripts/generate_schema.py specification/schema/
+
+
+# Runs a rust and a python command, depending on the `language` variable.
+#
+# If `language` is set to `rust` or `python`, only run the command for that language.
+# Otherwise, run both commands.
+_run_lang language rust_cmd python_cmd:
+    #!/usr/bin/env bash
+    set -euo pipefail
+    if [ "{{ language }}" = "rust" ]; then
+        set -x
+        {{ rust_cmd }}
+    elif [ "{{ language }}" = "python" ]; then
+        set -x
+        {{ python_cmd }}
+    else
+        set -x
+        {{ rust_cmd }}
+        {{ python_cmd }}
+    fi