Unable to install ruamel.yaml.clib

[ns-rse]

Encountered an issue with pyodide whereby the wheel for ruamel.yaml.clib fails to install as there is no pure Python wheel available (unsurprising as its a C library).

When trying to %pip install pgfinder it fails with the following

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[1], line 3
      1 await __import__("piplite").install(**{'requirements': ['ipywidgets']})
      2 await __import__("piplite").install(**{'requirements': ['ipysheet']})
----> 3 await __import__("piplite").install(**{'requirements': ['pgfinder']})
      4 #micropip.install(pgfinder, keep_going=True)

File /lib/python3.11/site-packages/piplite/piplite.py:103, in _install(requirements, keep_going, deps, credentials, pre)
    101 """Invoke micropip.install with a patch to get data from local indexes"""
    102 with patch("micropip._micropip._get_pypi_json", _get_pypi_json):
--> 103     return await _micropip.install(
    104         requirements=requirements,
    105         keep_going=keep_going,
    106         deps=deps,
    107         credentials=credentials,
    108         pre=pre,
    109     )

File /lib/python3.11/site-packages/micropip/_micropip.py:576, in install(requirements, keep_going, deps, credentials, pre)
    566 wheel_base = Path(getsitepackages()[0])
    568 transaction = Transaction(
    569     ctx=ctx,
    570     ctx_extras=[],
   (...)
    574     fetch_kwargs=fetch_kwargs,
    575 )
--> 576 await transaction.gather_requirements(requirements)
    578 if transaction.failed:
    579     failed_requirements = ", ".join([f"'{req}'" for req in transaction.failed])

File /lib/python3.11/site-packages/micropip/_micropip.py:342, in Transaction.gather_requirements(self, requirements)
    339 for requirement in requirements:
    340     requirement_promises.append(self.add_requirement(requirement))
--> 342 await gather(*requirement_promises)

File /lib/python3.11/site-packages/micropip/_micropip.py:349, in Transaction.add_requirement(self, req)
    346     return await self.add_requirement_inner(req)
    348 if not urlparse(req).path.endswith(".whl"):
--> 349     return await self.add_requirement_inner(Requirement(req))
    351 # custom download location
    352 wheel = WheelInfo.from_url(req)

File /lib/python3.11/site-packages/micropip/_micropip.py:457, in Transaction.add_requirement_inner(self, req)
    452 if self.check_version_satisfied(req):
    453     # Maybe while we were downloading pypi_json some other branch
    454     # installed the wheel?
    455     return
--> 457 await self.add_wheel(wheel, req.extras)

File /lib/python3.11/site-packages/micropip/_micropip.py:472, in Transaction.add_wheel(self, wheel, extras)
    470 await wheel.download(self.fetch_kwargs)
    471 if self.deps:
--> 472     await self.gather_requirements(wheel.requires(extras))
    474 self.wheels.append(wheel)

File /lib/python3.11/site-packages/micropip/_micropip.py:342, in Transaction.gather_requirements(self, requirements)
    339 for requirement in requirements:
    340     requirement_promises.append(self.add_requirement(requirement))
--> 342 await gather(*requirement_promises)

File /lib/python3.11/site-packages/micropip/_micropip.py:346, in Transaction.add_requirement(self, req)
    344 async def add_requirement(self, req: str | Requirement) -> None:
    345     if isinstance(req, Requirement):
--> 346         return await self.add_requirement_inner(req)
    348     if not urlparse(req).path.endswith(".whl"):
    349         return await self.add_requirement_inner(Requirement(req))

File /lib/python3.11/site-packages/micropip/_micropip.py:457, in Transaction.add_requirement_inner(self, req)
    452 if self.check_version_satisfied(req):
    453     # Maybe while we were downloading pypi_json some other branch
    454     # installed the wheel?
    455     return
--> 457 await self.add_wheel(wheel, req.extras)

File /lib/python3.11/site-packages/micropip/_micropip.py:472, in Transaction.add_wheel(self, wheel, extras)
    470 await wheel.download(self.fetch_kwargs)
    471 if self.deps:
--> 472     await self.gather_requirements(wheel.requires(extras))
    474 self.wheels.append(wheel)

File /lib/python3.11/site-packages/micropip/_micropip.py:342, in Transaction.gather_requirements(self, requirements)
    339 for requirement in requirements:
    340     requirement_promises.append(self.add_requirement(requirement))
--> 342 await gather(*requirement_promises)

File /lib/python3.11/site-packages/micropip/_micropip.py:346, in Transaction.add_requirement(self, req)
    344 async def add_requirement(self, req: str | Requirement) -> None:
    345     if isinstance(req, Requirement):
--> 346         return await self.add_requirement_inner(req)
    348     if not urlparse(req).path.endswith(".whl"):
    349         return await self.add_requirement_inner(Requirement(req))

File /lib/python3.11/site-packages/micropip/_micropip.py:444, in Transaction.add_requirement_inner(self, req)
    441 metadata = await _get_pypi_json(req.name, self.fetch_kwargs)
    443 try:
--> 444     wheel = find_wheel(metadata, req)
    445 except ValueError:
    446     self.failed.append(req)

File /lib/python3.11/site-packages/micropip/_micropip.py:312, in find_wheel(metadata, req)
    309     if best_wheel is not None:
    310         return wheel
--> 312 raise ValueError(
    313     f"Can't find a pure Python 3 wheel for '{req}'.\n"
    314     f"See: {FAQ_URLS['cant_find_wheel']}\n"
    315     "You can use `micropip.install(..., keep_going=True)`"
    316     "to get a list of all packages with missing wheels."
    317 )

ValueError: Can't find a pure Python 3 wheel for 'ruamel-yaml-clib>=0.2.7; platform_python_implementation == "CPython" and python_version < "3.12"'.
See: https://pyodide.org/en/stable/usage/faq.html#micropip-can-t-find-a-pure-python-wheel
You can use `micropip.install(..., keep_going=True)`to get a list of all packages with missing wheels.

This is known issue and documented at #3034 which suggests some work to solve this has been done already, but its not currently in pyodide-0.23.0.

One option may be to work around this and change the read_yaml() function in pgfinder to use the standard pyYAML library instead which does install under Pyodide.

In the Pyodide console...

%pip install pyyaml
import yaml
print(yaml.__version__)
6.0

[ns-rse]

Closing as removed the dependency on ruamel.yaml in the above issue.