Fails to install using pip - "lxml-version.h: No such file or directory"

[nijel]

This is a similar error as in #198, but not related to lxml==4.7.0, so I'm opening a separate issue for it.

For me, the builds started to fail this morning while having lxml version pinned to 4.6.4 (we do pin nearly everything).

• Working build 11 hours ago
• Broken build 1 hour ago

There are no code changes between and the only difference in the installed packages is amqp==5.0.7 instead of amqp==5.0.6 (this one is not pinned because we don't use it directly, but it's installed by Celery).

When playing with it a bit more, these seems to be something broken in the pip build. In the xmlsec sources python ./setup.py bdist_wheel works file, while pip install . fails:

$ pip install .
Processing /tmp/xmlsec-1.3.12
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: lxml>=3.8 in /tmp/.venv/lib/python3.9/site-packages (from xmlsec==1.3.12) (4.6.5)
Building wheels for collected packages: xmlsec
  Building wheel for xmlsec (pyproject.toml) ... error
  ERROR: Command errored out with exit status 1:
   command: /tmp/.venv/bin/python /tmp/.venv/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpw9sqs_at
       cwd: /tmp/xmlsec-1.3.12
  Complete output (26 lines):
  running bdist_wheel
  running build
  running build_py
  package init file 'src/xmlsec/__init__.py' not found (or not a regular file)
  creating build
  creating build/lib.linux-x86_64-3.9
  creating build/lib.linux-x86_64-3.9/xmlsec
  copying src/xmlsec/py.typed -> build/lib.linux-x86_64-3.9/xmlsec
  copying src/xmlsec/constants.pyi -> build/lib.linux-x86_64-3.9/xmlsec
  copying src/xmlsec/__init__.pyi -> build/lib.linux-x86_64-3.9/xmlsec
  copying src/xmlsec/tree.pyi -> build/lib.linux-x86_64-3.9/xmlsec
  copying src/xmlsec/template.pyi -> build/lib.linux-x86_64-3.9/xmlsec
  running build_ext
  building 'xmlsec' extension
  creating build/temp.linux-x86_64-3.9
  creating build/temp.linux-x86_64-3.9/tmp
  creating build/temp.linux-x86_64-3.9/tmp/xmlsec-1.3.12
  creating build/temp.linux-x86_64-3.9/tmp/xmlsec-1.3.12/src
  x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_NO_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO_OPENSSL=1 -DMODULE_NAME=xmlsec -DMODULE_VERSION=1.3.12 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -I/tmp/pip-build-env-g9fgz395/normal/lib/python3.9/site-packages/lxml/includes -I/tmp/pip-build-env-g9fgz395/normal/lib/python3.9/site-packages/lxml -I/tmp/pip-build-env-g9fgz395/normal/lib/python3.9/site-packages/lxml/includes/libxslt -I/tmp/pip-build-env-g9fgz395/normal/lib/python3.9/site-packages/lxml/includes/libexslt -I/tmp/pip-build-env-g9fgz395/normal/lib/python3.9/site-packages/lxml/includes/libxml -I/tmp/.venv/include -I/usr/include/python3.9 -c /tmp/xmlsec-1.3.12/src/constants.c -o build/temp.linux-x86_64-3.9/tmp/xmlsec-1.3.12/src/constants.o -g -std=c99 -fPIC -fno-strict-aliasing -Wno-error=declaration-after-statement -Werror=implicit-function-declaration -Os
  x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D__XMLSEC_FUNCTION__=__func__ -DXMLSEC_NO_SIZE_T -DXMLSEC_NO_GOST=1 -DXMLSEC_NO_GOST2012=1 -DXMLSEC_NO_CRYPTO_DYNAMIC_LOADING=1 -DXMLSEC_CRYPTO_OPENSSL=1 -DMODULE_NAME=xmlsec -DMODULE_VERSION=1.3.12 -I/usr/include/xmlsec1 -I/usr/include/libxml2 -I/tmp/pip-build-env-g9fgz395/normal/lib/python3.9/site-packages/lxml/includes -I/tmp/pip-build-env-g9fgz395/normal/lib/python3.9/site-packages/lxml -I/tmp/pip-build-env-g9fgz395/normal/lib/python3.9/site-packages/lxml/includes/libxslt -I/tmp/pip-build-env-g9fgz395/normal/lib/python3.9/site-packages/lxml/includes/libexslt -I/tmp/pip-build-env-g9fgz395/normal/lib/python3.9/site-packages/lxml/includes/libxml -I/tmp/.venv/include -I/usr/include/python3.9 -c /tmp/xmlsec-1.3.12/src/ds.c -o build/temp.linux-x86_64-3.9/tmp/xmlsec-1.3.12/src/ds.o -g -std=c99 -fPIC -fno-strict-aliasing -Wno-error=declaration-after-statement -Werror=implicit-function-declaration -Os
  In file included from /tmp/xmlsec-1.3.12/src/ds.c:15:
  /tmp/xmlsec-1.3.12/src/lxml.h:18:10: fatal error: lxml-version.h: Adresář nebo soubor neexistuje
     18 | #include <lxml-version.h>
        |          ^~~~~~~~~~~~~~~~
  compilation terminated.
  error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for xmlsec
Failed to build xmlsec
ERROR: Could not build wheels for xmlsec, which is required to install pyproject.toml-based projects

I've also verified that site-packages/lxml/includes/lxml-version.h is present.

[hoefling]

@nijel this may be related to build isolation, so the lxml installation is not used for building. Try pip install --no-build-isolation ., does it resolve it? If yes, it's a dupe of #198.

[regisb]

I can confirm that this issue is related to build isolation. During setup, lxml==4.7.0 was being installed because xmlsec has setup_requires=[..., 'lxml>=3.8'].

[nijel]

Ah, that could explain it. It works without isolation (after installing pkgconfig):

$ pip install --no-build-isolation .
Processing /tmp/xmlsec-1.3.12
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: lxml>=3.8 in /tmp/.venv/lib/python3.9/site-packages (from xmlsec==1.3.12) (4.6.5)
Building wheels for collected packages: xmlsec
  Building wheel for xmlsec (pyproject.toml) ... error
  ERROR: Command errored out with exit status 1:
   command: /tmp/.venv/bin/python /tmp/.venv/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmp7hyjw4x1
       cwd: /tmp/xmlsec-1.3.12
  Complete output (45 lines):
  running bdist_wheel
  running build
  running build_py
  package init file 'src/xmlsec/__init__.py' not found (or not a regular file)
  running build_ext
  Traceback (most recent call last):
    File "/tmp/.venv/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
      main()
    File "/tmp/.venv/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/tmp/.venv/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 261, in build_wheel
      return _build_backend().build_wheel(wheel_directory, config_settings,
    File "/tmp/.venv/lib/python3.9/site-packages/setuptools/build_meta.py", line 230, in build_wheel
      return self._build_with_temp_dir(['bdist_wheel'], '.whl',
    File "/tmp/.venv/lib/python3.9/site-packages/setuptools/build_meta.py", line 215, in _build_with_temp_dir
      self.run_setup()
    File "/tmp/.venv/lib/python3.9/site-packages/setuptools/build_meta.py", line 267, in run_setup
      super(_BuildMetaLegacyBackend,
    File "/tmp/.venv/lib/python3.9/site-packages/setuptools/build_meta.py", line 158, in run_setup
      exec(compile(code, __file__, 'exec'), locals())
    File "setup.py", line 400, in <module>
      setup(
    File "/tmp/.venv/lib/python3.9/site-packages/setuptools/__init__.py", line 153, in setup
      return distutils.core.setup(**attrs)
    File "/usr/lib/python3.9/distutils/core.py", line 148, in setup
      dist.run_commands()
    File "/usr/lib/python3.9/distutils/dist.py", line 966, in run_commands
      self.run_command(cmd)
    File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/tmp/.venv/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 299, in run
      self.run_command('build')
    File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/usr/lib/python3.9/distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
    File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "setup.py", line 45, in run
      import pkgconfig
  ModuleNotFoundError: No module named 'pkgconfig'
  ----------------------------------------
  ERROR: Failed building wheel for xmlsec
Failed to build xmlsec
ERROR: Could not build wheels for xmlsec, which is required to install pyproject.toml-based projects
$ pip install pkgconfig
Collecting pkgconfig
  Using cached pkgconfig-1.5.5-py3-none-any.whl (6.7 kB)
Installing collected packages: pkgconfig
Successfully installed pkgconfig-1.5.5
$ pip install --no-build-isolation .
Processing /tmp/xmlsec-1.3.12
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: lxml>=3.8 in /tmp/.venv/lib/python3.9/site-packages (from xmlsec==1.3.12) (4.6.5)
Building wheels for collected packages: xmlsec
  Building wheel for xmlsec (pyproject.toml) ... done
  Created wheel for xmlsec: filename=xmlsec-1.3.12-cp39-cp39-linux_x86_64.whl size=152195 sha256=e81e973c8e74d0daa69bf062bafe93f9e8e02c51017ca770a4413352d5b2bc59
  Stored in directory: /home/nijel/.cache/pip/wheels/50/34/39/5d7943b98340d3f270c17c5ee9181358b1bd8347f3325595b2
Successfully built xmlsec
Installing collected packages: xmlsec
  Attempting uninstall: xmlsec
    Found existing installation: xmlsec 1.3.12
    Uninstalling xmlsec-1.3.12:
      Successfully uninstalled xmlsec-1.3.12
Successfully installed xmlsec-1.3.12

That opens up another question - won't that cause issues if xmlsec is built against a different lxml version than is used in the runtime? Or to ask differently - is build isolation really desired in this case?

[hoefling]

I guess this is best to be answered by pip maintainers - if a package is required both as build and runtime dependency, the dependency resolver should take it into account and use the resolved version for both stages.

[nijel]

Allowing different versions is actually the reason for build isolation, so it IMHO works as intended.

[bmwant]

are there any plans of releasing a new version with the fix included cf38b52 soon?

[hoefling]

@bmwant lxml==4.7.0 is now yanked, so it shouldn't be an issue anyway. If you are still hitting this, try cleaning your pip cache and retry.

[hoefling]

@nijel again, IMO this isn't something that the package itself should be responsible for. Surely, you may get issues if you are building against lxml==X and executing against lxml==Y and X and Y are not ABI compatible. However, IMO this version discrepancy should be caught by the build backend, with either stopping the installation or issuing a warning about differences between build and runtime.
The only option I see to mitigate this on the package configuration side is a strict pin of lxml in both build and runtime deps, which won't help anyone either. I can also compare lxml versions at runtime and raise an error, just as it is done with xmlsec1 already. The check only makes sense for xmlsec1 though because its installation is not handled by pip, so it's fine. For lxml, it feels like doing the work which a build backend should do for me, even if PEP 517 doesn't explicitly state anything about it.

[nijel]

Okay, I've created pypa/pip#10731 to discuss this at pip. I don't see a good solution there and avoiding build isolation might be the least bad solution...