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util/visual.h: include <cstdint> for uint32_t. func/primlist.h: remove operator<< of VelocityPrimitive, which refers to nonexistent members and fails with -Wtemplate-body.
Build and test on Ubuntu 24.04 with OpenMPI and parallel HDF5, without hypre and the Cubism backend.
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Add tools/format which runs a pinned clang-format via uvx on tracked sources, excluding doc/ and bundled src/CubismNoCopy/ and src/overlap/.
tools/format now also runs ruff 0.17.2 on tracked *.py files and
scripts with a Python shebang; --check also runs the linter. ruff.toml
follows the config used in other projects (E, W, F, I), targets
Python 3.8, and ignores star imports, bare except and lambda
assignment. Replaces yapf.
Fixes found by the linter:
- doc/sphinx/includecode.py: GetStruct() used undefined `filename`.
- src/test/{hdf,partstr}/bgen: undefined GetEmptyCluster().
- src/test/advection/plot.py: PlotPart is in aphros.plot.
- examples/102_mean_curv_flow/ref/2_detect.py: recolor() used
undefined nx, ny.
- examples/105_sharp/tools/raw2img: wrong number of % arguments.
- deploy/scripts/task: usage text lacked the placeholder for the
program name.
- examples/213_electrochem: duplicate dict key in colorbar.py.
- Remove unused variables, compare types with `is`, None with `is`.
np.float and np.int are replaced with the builtins, as recommended by NumPy. Enable ruff rule NPY001 to catch them.
Many tests rely on the default backend cubismnc or the default linear solver hypre (deploy/scripts/sim_base.conf) and abort without them. Register them only if USE_BACKEND_CUBISM or USE_HYPRE is on. test/inner expects the inner-blocks-first order of cubismnc.
Exact comparison fails with -march=native, which allows contraction to FMA. Print the value on failure.
Split examples/Makefile into DIRS_BUILD and DIRS_SIM. The simulations use the default backend cubismnc, which is disabled in CI.
The number of subdomains is computed as ranks / threads, which is zero with more threads than ranks, and the test aborts.
Only the diagonal coefficient was set, others were uninitialized and appeared in the output.
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CircleCI is no longer active. This adds a minimal GitHub Actions workflow and removes
.circleci/.format:tools/format --check(clang-format 23.1.3 and ruff 0.17.2, pinned viauvx)linux: Ubuntu 24.04, OpenMPI, parallel HDF5 (libhdf5-openmpi-dev); buildsdeployandsrcwithout hypre and the Cubism backend, runsctest, builds the examplestools/formatformats tracked C/C++ sources (excludingdoc/,src/CubismNoCopy/,src/overlap/) and Python files (*.pyand scripts with a Python shebang);ruff.tomlreplaces.style.yapfcubismncor the default linear solverhypreare registered only ifUSE_BACKEND_CUBISMorUSE_HYPREis on (58 of 122 tests remain in this configuration)<cstdint>inutil/visual.h, broken unusedoperator<<infunc/primlist.h)np.float,np.int)test/reconstcompared floating-point results exactly, which fails with FMAtest/commmapprinted uninitialized coefficients of the systemtest/commmapruns withOMP_NUM_THREADS=1; with more threads than ranks it abortsmake build_nosim)aphros.TestBaseprints a diff of text files that differ from the reference