misc: Ruff manual changes

.github/actionlint.yaml

@@ -0,0 +1,5 @@
+self-hosted-runner:
+  labels:
+    - asv
+    - amdgpu
+    - nvidiagpu

.github/workflows/asv.yml

@@ -36,12 +36,12 @@ jobs:
 
     - name: Set VIRTUAL_ENV
       run: |
-        echo "VIRTUAL_ENV=$ENVHOME/asv" >> $GITHUB_ENV
-        echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> $GITHUB_ENV
+        echo "VIRTUAL_ENV=$ENVHOME/asv" >> "$GITHUB_ENV"
+        echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> "$GITHUB_ENV"
 
     - name: Set PATH
       run: |
-        echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> $GITHUB_ENV
+        echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> "$GITHUB_ENV"
 
     - name: Install dependencies
       run: |

.github/workflows/docker-bases.yml

@@ -114,10 +114,10 @@ jobs:
           TAG_BASE: ${{ format('cpu-gcc{0}', matrix.gcc) }}
         run: |
           docker buildx imagetools create \
-            --tag devitocodes/bases:${TAG_BASE} \
-            devitocodes/bases:${TAG_BASE}-amd64 \
-            devitocodes/bases:${TAG_BASE}-arm64
-          docker buildx imagetools inspect devitocodes/bases:${TAG_BASE}
+            --tag "devitocodes/bases:${TAG_BASE}" \
+            "devitocodes/bases:${TAG_BASE}-amd64" \
+            "devitocodes/bases:${TAG_BASE}-arm64"
+          docker buildx imagetools inspect "devitocodes/bases:${TAG_BASE}"
 
   #######################################################
   ############## Intel OneApi CPU #######################
@@ -296,10 +296,10 @@ jobs:
           FINAL_TAG: ${{ matrix.final_tag }}
         run: |
           docker buildx imagetools create \
-            --tag devitocodes/bases:${FINAL_TAG} \
-            devitocodes/bases:${FINAL_TAG}-amd64 \
-            devitocodes/bases:${FINAL_TAG}-arm64
-          docker buildx imagetools inspect devitocodes/bases:${FINAL_TAG}
+            --tag "devitocodes/bases:${FINAL_TAG}" \
+            "devitocodes/bases:${FINAL_TAG}-amd64" \
+            "devitocodes/bases:${FINAL_TAG}-arm64"
+          docker buildx imagetools inspect "devitocodes/bases:${FINAL_TAG}"
 
   #######################################################
   ##################### AMD #############################

.github/workflows/docker-devito.yml

@@ -113,7 +113,7 @@ jobs:
 
       - name: Set per‑runner variables
         run: |
-          echo "CONTAINER_NAME=testrun-${{ matrix.tag }}-${RUNNER_NAME// /_}" >> $GITHUB_ENV
+          echo "CONTAINER_NAME=testrun-${{ matrix.tag }}-${RUNNER_NAME// /_}" >> "$GITHUB_ENV"
 
       - name: Check event name
         run: echo ${{ github.event_name }}
@@ -246,8 +246,8 @@ jobs:
               refs="$refs devitocodes/devito:${tag}-${arch}"
             done
             echo "Creating manifest for devitocodes/devito:${tag} using:${refs}"
-            docker buildx imagetools create --tag devitocodes/devito:${tag} $refs
-            docker buildx imagetools inspect devitocodes/devito:${tag}
+            docker buildx imagetools create --tag "devitocodes/devito:${tag}" "$refs"
+            docker buildx imagetools inspect "devitocodes/devito:${tag}"
           done
 
   test-devito:
@@ -286,7 +286,7 @@ jobs:
 
       - name: Set per‑runner variables
         run: |
-          echo "CONTAINER_NAME=testrun-${{ matrix.tag }}-${RUNNER_NAME// /_}" >> $GITHUB_ENV
+          echo "CONTAINER_NAME=testrun-${{ matrix.tag }}-${RUNNER_NAME// /_}" >> "$GITHUB_ENV"
 
       - name: Run tests against multi-arch image
         run: |

.github/workflows/examples-mpi.yml

@@ -63,7 +63,7 @@ jobs:
     - name: Install dependencies
       run: |
         pip install --upgrade pip
-        pip install -e .[extras,mpi,tests]
+        pip install -e ".[extras,mpi,tests]"
         python3 scripts/clear_devito_cache.py
 
     - name: Test mpi notebooks

.github/workflows/examples.yml

@@ -101,4 +101,4 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        name: ${{ matrix.name }}
+        name: Examples

.github/workflows/lint.yml

@@ -47,7 +47,7 @@ jobs:
     name: "Spellcheck everything"
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
@@ -69,7 +69,7 @@ jobs:
     # #example-error-annotation-on-github-actions
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
       - name: Check workflow files
         uses: docker://rhysd/actionlint:latest
         with:
@@ -81,9 +81,9 @@ jobs:
     container:
       image: hadolint/hadolint:latest-alpine
       env:
-        HADOLINT_IGNORE: "DL3005,DL3007,DL3008,DL3015,DL3059"
+        HADOLINT_IGNORE: "DL3003,DL3004,DL3005,DL3007,DL3008,DL3009,DL3013,DL3015,DL3042,DL3059,SC2103,SC2046,SC2086"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
       - name: Lint dockerfiles inside hadolint container
         run: |
           for DOCKERFILE in docker/Dockerfile.*; \

.github/workflows/pytest-core-nompi.yml

@@ -153,9 +153,9 @@ jobs:
     - name: Set run prefix
       run: |
           if [[ "${{ matrix.name }}" =~ "docker" ]]; then
-              echo "RUN_CMD=docker run --init -t --rm -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} --name testrun devito_img"  >> $GITHUB_ENV
+              echo "RUN_CMD=docker run --init -t --rm -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} --name testrun devito_img"  >> "$GITHUB_ENV"
           else
-              echo "RUN_CMD=" >> $GITHUB_ENV
+              echo "RUN_CMD=" >> "$GITHUB_ENV"
           fi
       id: set-run
 
@@ -168,7 +168,7 @@ jobs:
       run : |
           if [ "${{ runner.os }}" == 'macOS' ]; then
             brew install llvm libomp
-            echo "/opt/homebrew/opt/llvm/bin" >> $GITHUB_PATH
+            echo "/opt/homebrew/opt/llvm/bin" >> "$GITHUB_PATH"
           fi
       id: set-tests
 
@@ -178,14 +178,14 @@ jobs:
           major=${ver%%.*}
           minor=${ver#*.}; minor=${minor%%.*}
           if [ "$major" -eq 3 ] && [ "$minor" -ge 12 ]; then
-            echo "PIPFLAGS='--break-system-packages'" >> $GITHUB_ENV
+            echo "PIPFLAGS='--break-system-packages'" >> "$GITHUB_ENV"
           fi
 
     - name: Install dependencies
       if: "!contains(matrix.name, 'docker')"
       run: |
         python3 -m pip install ${{ env.PIPFLAGS }} --upgrade pip
-        python3 -m pip install ${{ env.PIPFLAGS }} -e .[tests,extras]
+        python3 -m pip install ${{ env.PIPFLAGS }} -e ".[tests,extras]"
         python3 -m pip install ${{ env.PIPFLAGS }} sympy==${{matrix.sympy}}
 
     - name: Check Docker image Python version

.github/workflows/pytest-gpu.yml

@@ -79,8 +79,8 @@ jobs:
 
       - name: Set per-runner tags
         run: |
-          echo "DOCKER_IMAGE=${{ matrix.name }}-${RUNNER_NAME// /_}" >> $GITHUB_ENV
-          echo "CONTAINER_BASENAME=testrun-${{ matrix.name }}-${RUNNER_NAME// /_}-${{ github.sha }}" >> $GITHUB_ENV
+          echo "DOCKER_IMAGE=${{ matrix.name }}-${RUNNER_NAME// /_}" >> "$GITHUB_ENV"
+          echo "CONTAINER_BASENAME=testrun-${{ matrix.name }}-${RUNNER_NAME// /_}-${{ github.sha }}" >> "$GITHUB_ENV"
 
       - name: Ensure buildx builder
         run: |
@@ -93,7 +93,7 @@ jobs:
           docker buildx build . \
             --builder "${RUNNER_NAME// /_}" \
             --load \
-            --label ci-run=$GITHUB_RUN_ID \
+            --label ci-run="$GITHUB_RUN_ID" \
             --rm --pull \
             --file docker/Dockerfile.devito \
             --tag "${DOCKER_IMAGE}" \
@@ -107,7 +107,7 @@ jobs:
           # Make sure CUDA_VISIBLE_DEVICES is at least *something* on NVIDIA
           # runners; fall back to "all" so the driver probe does not fail.
           if [[ "${{ matrix.runner_label }}" == "nvidiagpu" && -z "${CUDA_VISIBLE_DEVICES:-}" ]]; then
-            echo "CUDA_VISIBLE_DEVICES=all" >> $GITHUB_ENV
+            echo "CUDA_VISIBLE_DEVICES=all" >> "$GITHUB_ENV"
           fi
 
           # Run a simple driver-probe command (nvidia-smi / rocm-smi)
@@ -124,7 +124,7 @@ jobs:
 
           # Run the test suite using the matrix-defined flags
           docker run ${{ matrix.flags }} \
-            ${ci_env} \
+            "${ci_env}" \
             -e CI=true \
             -e PYTHONFAULTHANDLER=1 \
             -e DEVITO_LOGGING=DEBUG \
@@ -152,7 +152,7 @@ jobs:
           docker rmi -f "${DOCKER_IMAGE}" || true
 
           # Classic image layers created in this job
-          docker image prune -f --filter label=ci-run=$GITHUB_RUN_ID
+          docker image prune -f --filter label=ci-run="$GITHUB_RUN_ID"
 
           # BuildKit cache: target the per-runner builder explicitly
           docker builder prune --builder "${RUNNER_NAME// /_}" \

.github/workflows/tutorials.yml

@@ -78,17 +78,17 @@ jobs:
     - name: Set run prefix
       run: |
           if [ "${{ matrix.name }}" == 'tutos-docker-gcc-py310' ]; then
-              echo "RUN_CMD=docker run --init -t --rm --name testrun devito_img" >> $GITHUB_ENV
+              echo "RUN_CMD=docker run --init -t --rm --name testrun devito_img" >> "$GITHUB_ENV"
           else
-              echo "RUN_CMD=" >> $GITHUB_ENV
+              echo "RUN_CMD=" >> "$GITHUB_ENV"
           fi
       id: set-run
 
     - name: Install dependencies
       if: matrix.name != 'tutos-docker-gcc-py310'
       run: |
         python -m pip install --upgrade pip
-        pip install -e .[tests,extras]
+        pip install -e ".[tests,extras]"
         pip install blosc
 
     - name: Check Docker image Python version

.pre-commit-config.yaml

@@ -13,13 +13,18 @@ repos:
     hooks:
       # Run isort to check only (don't modify files)
       - id: isort
-        args: [ --check-only ]
+        args: [--check-only, --filter-files]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
     rev: v0.14.4
     hooks:
       # Run the linter to check only (don't modify files)
       - id: ruff-check
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.3.0
+    hooks:
+      - id: flake8
+        additional_dependencies: [flake8-pyproject]
   - repo: https://github.com/crate-ci/typos
     rev: v1.39.1
     hooks:
@@ -33,3 +38,4 @@ repos:
     rev: v2.12.0
     hooks:
       - id: hadolint-docker
+        entry: -e HADOLINT_IGNORE=DL3003,DL3004,DL3005,DL3007,DL3008,DL3009,DL3013,DL3015,DL3042,DL3059,SC2103,SC2046,SC2086 ghcr.io/hadolint/hadolint hadolint

FAQ.md

@@ -64,7 +64,7 @@ Focus on modeling and math — Devito handles the performance.
 
 
 ## What Devito is not
-As is hopefully implied by the preceeding section, Devito is *not* a seismic modelling or imaging framework, nor is it a set of pre-baked solvers. Whilst Devito is often associated with seismic imaging, this is just one application domain. Our RTM and FWI examples use Devito under the hood, but the engine itself is physics-agnostic. There’s no built-in assumption about waves, seismics, or domains — you provide the physics, and Devito delivers efficient, architecture-aware implementations.
+As is hopefully implied by the preceding section, Devito is *not* a seismic modelling or imaging framework, nor is it a set of pre-baked solvers. Whilst Devito is often associated with seismic imaging, this is just one application domain. Our RTM and FWI examples use Devito under the hood, but the engine itself is physics-agnostic. There’s no built-in assumption about waves, seismics, or domains — you provide the physics, and Devito delivers efficient, architecture-aware implementations.
 
 Furthermore, the examples provided with Devito are often conflated with the core DSL and compiler. However, the purpose of this collection of tutorials, code samples, and helper functions is fourfold:
 

benchmarks/regression/benchmarks/arguments.py

@@ -10,9 +10,9 @@ class Processing:
     def setup(self):
         grid = Grid(shape=(5, 5, 5))
 
-        funcs = [Function(name='f%d' % n, grid=grid) for n in range(30)]
-        tfuncs = [TimeFunction(name='u%d' % n, grid=grid) for n in range(30)]
-        stfuncs = [SparseTimeFunction(name='su%d' % n, grid=grid, npoint=1, nt=100)
+        funcs = [Function(name=f'f{n}', grid=grid) for n in range(30)]
+        tfuncs = [TimeFunction(name=f'u{n}', grid=grid) for n in range(30)]
+        stfuncs = [SparseTimeFunction(name=f'su{n}', grid=grid, npoint=1, nt=100)
                    for n in range(30)]
         v = TimeFunction(name='v', grid=grid, space_order=2)
 

benchmarks/user/advisor/README.md

@@ -7,7 +7,7 @@ We recommend going through tutorial [02_advisor_roofline.ipynb](https://github.c
 * Support is guaranteed only for Intel oneAPI 2025; earlier versions may not work.
 You may download Intel oneAPI [here](https://www.intel.com/content/www/us/en/developer/tools/oneapi/base-toolkit-download.html?packages=oneapi-toolkit&oneapi-toolkit-os=linux&oneapi-lin=apt).
 
-* Add Advisor (advixe-cl) and compilers (icx) in the path. The right env variables should be sourced along the lines of (depending on your isntallation folder):
+* Add Advisor (advixe-cl) and compilers (icx) in the path. The right env variables should be sourced along the lines of (depending on your installation folder):
 ```sh
 source /opt/intel/oneapi/advisor/latest/env/vars.sh
 source /opt/intel/oneapi/compiler/latest/env/vars.sh

benchmarks/user/advisor/advisor_logging.py

@@ -9,18 +9,18 @@ def check(cond, msg):
 
 
 def err(msg):
-    print('\033[1;37;31m%s\033[0m' % msg)  # print in RED
+    print(f'\033[1;37;31m{msg}\033[0m')  # print in RED
 
 
 def log(msg):
-    print('\033[1;37;32m%s\033[0m' % msg)  # print in GREEN
+    print(f'\033[1;37;32m{msg}\033[0m')  # print in GREEN
 
 
 @contextmanager
 def progress(msg):
-    print('\033[1;37;32m%s ... \033[0m' % msg, end='', flush=True)  # print in GREEN
+    print(f'\033[1;37;32m{msg} ... \033[0m', end='', flush=True)  # print in GREEN
     yield
-    print('\033[1;37;32m%s\033[0m' % 'Done!')
+    print('\033[1;37;32m{}\033[0m'.format('Done!'))
 
 
 def log_process(process, logger):

benchmarks/user/advisor/roofline.py

@@ -205,7 +205,7 @@ def roofline(name, project, scale, precision, mode, th):
     log(f'\nFigure saved in {figpath}{name}.pdf.')
 
     # Save the JSON file
-    with open('%s.json' % name, 'w') as f:
+    with open(f'{name}.json', 'w') as f:
         f.write(json.dumps(roofline_data))
 
     log(f'\nJSON file saved as {name}.json.')

benchmarks/user/advisor/run_advisor.py

@@ -132,17 +132,16 @@ def run_with_advisor(path, output, name, exec_args):
     # Before collecting the `survey` and `tripcounts` a "pure" python run
     # to warmup the jit cache is preceded
 
-    log('Starting Intel Advisor\'s `roofline` analysis for `%s`' % name)
+    log(f'Starting Intel Advisor\'s `roofline` analysis for `{name}`')
     dt = datetime.datetime.now()
 
     # Set up a file logger that will track the output of the advisor profiling
     advixe_logger = logging.getLogger('run_advisor_logger')
     advixe_logger.setLevel(logging.INFO)
 
     advixe_formatter = logging.Formatter('%(asctime)s: %(message)s')
-    logger_datetime = '%d.%d.%d.%d.%d.%d' % (dt.year, dt.month,
-                                             dt.day, dt.hour, dt.minute, dt.second)
-    advixe_handler = logging.FileHandler('%s/%s_%s.log' % (output, name, logger_datetime))
+    logger_datetime = f'{dt.year}.{dt.month}.{dt.day}.{dt.hour}.{dt.minute}.{dt.second}'
+    advixe_handler = logging.FileHandler(f'{output}/{name}_{logger_datetime}.log')
     advixe_handler.setFormatter(advixe_formatter)
     advixe_logger.addHandler(advixe_handler)