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.h not found when building with uv but found when using pip and a virtual env #10052

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MalcolmMielle opened this issue Dec 20, 2024 · 3 comments
Open

.h not found when building with uv but found when using pip and a virtual env #10052

MalcolmMielle opened this issue Dec 20, 2024 · 3 comments
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compatibility Compatibility with a specification or another tool

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@MalcolmMielle
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I am trying to install the package petsc4py. When trying to build using uv I have the error:

$uv add petsc4py
× Failed to download and build `petsc4py==3.22.1`
  ╰─▶ Build backend failed to build wheel through `build_wheel` (exit status: 1)

      [stdout]
      running bdist_wheel
      running build
      running build_src
      running build_py
      copying src/petsc4py/PETSc.py -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/__init__.py -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/__main__.py -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/typing.py -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/lib/__init__.py -> build/lib.linux-x86_64-cpython-312/petsc4py/lib
      copying src/petsc4py/__init__.pyi -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/__main__.pyi -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/py.typed -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/PETSc.pxd -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/PETSc.h -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/PETSc_api.h -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/include/petsc4py/numpy.h ->
      build/lib.linux-x86_64-cpython-312/petsc4py/include/petsc4py
      copying src/petsc4py/include/petsc4py/petsc4py.h ->
      build/lib.linux-x86_64-cpython-312/petsc4py/include/petsc4py
      copying src/petsc4py/include/petsc4py/pybuffer.h ->
      build/lib.linux-x86_64-cpython-312/petsc4py/include/petsc4py
      copying src/petsc4py/include/petsc4py/pyscalar.h ->
      build/lib.linux-x86_64-cpython-312/petsc4py/include/petsc4py
      copying src/petsc4py/include/petsc4py/petsc4py.i ->
      build/lib.linux-x86_64-cpython-312/petsc4py/include/petsc4py
      copying src/petsc4py/lib/__init__.pyi -> build/lib.linux-x86_64-cpython-312/petsc4py/lib
      copying src/petsc4py/lib/__init__.pyi -> build/lib.linux-x86_64-cpython-312/petsc4py/lib
      copying src/petsc4py/lib/petsc.cfg -> build/lib.linux-x86_64-cpython-312/petsc4py/lib
      running build_ext
      PETSC_DIR:    /home/malcolm/.cache/uv/builds-v0/.tmpIYB9qQ/lib64/python3.12/site-packages/petsc
      PETSC_ARCH:
      version:      3.22.1 release
      integer-size: 32-bit
      scalar-type:  real
      precision:    double
      language:     CONLY
      compiler:     gcc
      linker:       gcc
      building 'PETSc' extension
      gcc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow
      -fstack-protector -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow
      -fstack-protector -g -O -fPIC -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG
      -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -DMPICH_SKIP_MPICXX=1
      -DOMPI_SKIP_MPICXX=1 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Isrc -Isrc/petsc4py/include
      -I/home/malcolm/.cache/uv/builds-v0/.tmpIYB9qQ/lib64/python3.12/site-packages/numpy/_core/include
      -I/home/malcolm/.cache/uv/sdists-v6/pypi/petsc/3.22.1/wE68-1CFx8eRBCppGL6ik/src/build/bdist.linux-x86_64/wheel/petsc/include
      -I/home/malcolm/.cache/uv/builds-v0/.tmpIYB9qQ/include -I/usr/include/python3.12 -c src/petsc4py/PETSc.c -o
      build/temp.linux-x86_64-cpython-312/src/petsc4py/PETSc.o

      [stderr]
      src/petsc4py/PETSc.c:1222:10: fatal error: petsc.h: No such file or directory
       1222 | #include <petsc.h>
            |          ^~~~~~~~~
      compilation terminated.
      error: command '/usr/bin/gcc' failed with exit code 1

      hint: This error likely indicates that you need to install a library that provides "petsc.h" for
      `[email protected]`
  help: `petsc4py` (v3.22.1) was included because `your-package` (v0.1.0) depends on `petsc4py`

On the other hand, using pip install --use-pep517 --force-reinstall --no-cache petsc4py in a python 3.12 environment works just fine:

$pip install --use-pep517 --force-reinstall --no-cache  petsc4py 
Collecting petsc4py
  Downloading petsc4py-3.22.1.tar.gz (428 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Collecting numpy>=1.19 (from petsc4py)
  Downloading numpy-2.2.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Collecting petsc<3.23,>=3.22 (from petsc4py)
  Downloading petsc-3.22.1.tar.gz (16.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.8/16.8 MB 2.6 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Downloading numpy-2.2.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.1/16.1 MB 4.3 MB/s eta 0:00:00
Building wheels for collected packages: petsc4py, petsc
  Building wheel for petsc4py (pyproject.toml) ... done
  Created wheel for petsc4py: filename=petsc4py-3.22.1-cp312-cp312-linux_x86_64.whl size=9602637 sha256=ec793de0818cd5906d6e93efd16fd1731c870c7f8ae9a583a28c403816dcf4ce
  Stored in directory: /tmp/pip-ephem-wheel-cache-p_h_edn5/wheels/a7/75/c4/ec901515d0c5d403c7a6427a4901783c107199972d0db5e327
  Building wheel for petsc (pyproject.toml) ... done
  Created wheel for petsc: filename=petsc-3.22.1-py3-none-linux_x86_64.whl size=71577168 sha256=8b6c91557f6fcdd00b2ee82e7eb8cf3db9bfc5a066dfbab6445b05ef218eec9a
  Stored in directory: /tmp/pip-ephem-wheel-cache-p_h_edn5/wheels/1f/d8/38/baccdf720fb3f9fba2099a252677d5e2ceca92c4c9c6045aa3
Successfully built petsc4py petsc
Installing collected packages: petsc, numpy, petsc4py
  Attempting uninstall: petsc
    Found existing installation: petsc 3.22.1
    Uninstalling petsc-3.22.1:
      Successfully uninstalled petsc-3.22.1
  Attempting uninstall: numpy
    Found existing installation: numpy 2.2.0
    Uninstalling numpy-2.2.0:
      Successfully uninstalled numpy-2.2.0
  Attempting uninstall: petsc4py
    Found existing installation: petsc4py 3.22.1
    Uninstalling petsc4py-3.22.1:
      Successfully uninstalled petsc4py-3.22.1
Successfully installed numpy-2.2.0 petsc-3.22.1 petsc4py-3.22.1

[notice] A new release of pip is available: 24.2 -> 24.3.1
[notice] To update, run: pip install --upgrade pip

My system is:

  • Fedora 41
  • uv: 0.5.11
  • python 3.12
@samypr100
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I also had a similar outcome. I haven't really looked at the documentation or the recommended ways to build it, but it's interesting that it does work with build isolation with pip and not uv pip.

~ uv pip install petsc4py==3.22.1
Resolved 3 packages in 3m 17s
  × Failed to build `petsc4py==3.22.1`
  ├─▶ The build backend returned an error
  ╰─▶ Call to `setuptools.build_meta.build_wheel` failed (exit status: 1)

      [stdout]
      running bdist_wheel
      running build
      running build_src
      using Cython 3.0.11
      cythonizing 'petsc4py/PETSc.pyx' -> 'petsc4py/PETSc.c'
      running build_py
      creating build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/__init__.py -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/PETSc.py -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/typing.py -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/__main__.py -> build/lib.linux-x86_64-cpython-312/petsc4py
      creating build/lib.linux-x86_64-cpython-312/petsc4py/lib
      copying src/petsc4py/lib/__init__.py -> build/lib.linux-x86_64-cpython-312/petsc4py/lib
      copying src/petsc4py/__init__.pyi -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/__main__.pyi -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/py.typed -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/PETSc.pxd -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/PETSc.h -> build/lib.linux-x86_64-cpython-312/petsc4py
      copying src/petsc4py/PETSc_api.h -> build/lib.linux-x86_64-cpython-312/petsc4py
      creating build/lib.linux-x86_64-cpython-312/petsc4py/include/petsc4py
      copying src/petsc4py/include/petsc4py/pyscalar.h -> build/lib.linux-x86_64-cpython-312/petsc4py/include/petsc4py
      copying src/petsc4py/include/petsc4py/pybuffer.h -> build/lib.linux-x86_64-cpython-312/petsc4py/include/petsc4py
      copying src/petsc4py/include/petsc4py/numpy.h -> build/lib.linux-x86_64-cpython-312/petsc4py/include/petsc4py
      copying src/petsc4py/include/petsc4py/petsc4py.h -> build/lib.linux-x86_64-cpython-312/petsc4py/include/petsc4py
      copying src/petsc4py/include/petsc4py/petsc4py.i -> build/lib.linux-x86_64-cpython-312/petsc4py/include/petsc4py
      copying src/petsc4py/lib/__init__.pyi -> build/lib.linux-x86_64-cpython-312/petsc4py/lib
      copying src/petsc4py/lib/__init__.pyi -> build/lib.linux-x86_64-cpython-312/petsc4py/lib
      copying src/petsc4py/lib/petsc.cfg -> build/lib.linux-x86_64-cpython-312/petsc4py/lib
      running build_ext
      PETSC_DIR:    /root/.cache/uv/builds-v0/.tmpYkB4Yy/lib/python3.12/site-packages/petsc
      PETSC_ARCH:
      version:      3.22.1 release
      integer-size: 32-bit
      scalar-type:  real
      precision:    double
      language:     CONLY
      compiler:     clang
      linker:       clang
      building 'PETSc' extension
      creating build/temp.linux-x86_64-cpython-312/src/petsc4py
      clang -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wconversion -Wno-sign-conversion -Wno-float-conversion
      -Wno-implicit-float-conversion -fstack-protector -Qunused-arguments -Wall -Wwrite-strings
      -Wno-unknown-pragmas -Wconversion -Wno-sign-conversion -Wno-float-conversion -Wno-implicit-float-conversion
      -fstack-protector -Qunused-arguments -g -O3 -fPIC -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3
      -Wall -DMPICH_SKIP_MPICXX=1 -DOMPI_SKIP_MPICXX=1 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Isrc
      -Isrc/petsc4py/include -I/root/.cache/uv/builds-v0/.tmpYkB4Yy/lib/python3.12/site-packages/numpy/_core/include
      -I/root/.cache/uv/sdists-v6/pypi/petsc/3.22.1/hJkKH1sasJwoixz03FvId/src/build/bdist.linux-x86_64/wheel/petsc/include
      -I/root/.cache/uv/builds-v0/.tmpYkB4Yy/include -I/usr/local/include/python3.12 -c src/petsc4py/PETSc.c -o
      build/temp.linux-x86_64-cpython-312/src/petsc4py/PETSc.o

      [stderr]
      src/petsc4py/PETSc.c:1222:10: fatal error: 'petsc.h' file not found
      #include <petsc.h>
               ^~~~~~~~~
      1 error generated.
      error: command '/usr/bin/clang' failed with exit code 1

      hint: This error likely indicates that you need to install a library that provides "petsc.h" for
      `[email protected]`

@samypr100
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samypr100 commented Dec 22, 2024 •
edited
Loading

Looking at their setup.py I notice they leverage PEP517_BUILD_BACKEND environment variable being set to patch the include files (this variable seems to be set by pip). I think this would be set to setuptools.build_meta for this project and using_build_backend will be True in their build script. When using uv this would be False as those environment variables will not be set.

TL;DR try setting PEP517_BUILD_BACKEND=setuptools.build_meta before your commands.

CC @konstin

@samypr100 samypr100 added the compatibility Compatibility with a specification or another tool label Dec 22, 2024
@MalcolmMielle
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I'll have a try when I'm back from holidays. Thanks!

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