CODEWITHSUNDEEP
python-3.xanacondapyscript
Jorge
Jorge

Reputation: 49

Does anyone know why I can't import and use the wheels from the biopython library in PyScript?

Hi I've recently been trying to import and use a wheel (downloaded from pypi) in PyScript. This wheel corresponds to the biopython library. However, I have been unable to see any results in this regard. Does anyone know why my code is not working?

<html>
  <head>
    <link rel="stylesheet" href="https://pyscript.net/alpha/pyscript.css" />
    <script defer src="https://pyscript.net/alpha/pyscript.js"></script>
  </head>


  <body>



  </body>

  
    <py-env>
      - './static/wheels/biopython-1.79-cp37-cp37m-win_amd64.whl'
    </py-env>


    <py-script>

    from Bio.Seq import Seq
    my_seq = Seq("AGTACACTGGT")

    print(my_seq)

    </py-script>



</html>

Below I show the error capture in my BRAVE browser console.

Uncaught (in promise) PythonError: Traceback (most recent call last):
  File "/lib/python3.10/asyncio/futures.py", line 201, in result
    raise self._exception
  File "/lib/python3.10/asyncio/tasks.py", line 234, in __step
    result = coro.throw(exc)
  File "/lib/python3.10/site-packages/micropip/_micropip.py", line 183, in install
    transaction = await self.gather_requirements(requirements, ctx, keep_going)
  File "/lib/python3.10/site-packages/micropip/_micropip.py", line 173, in gather_requirements
    await gather(*requirement_promises)
  File "/lib/python3.10/asyncio/futures.py", line 284, in __await__
    yield self  # This tells Task to wait for completion.
  File "/lib/python3.10/asyncio/tasks.py", line 304, in __wakeup
    future.result()
  File "/lib/python3.10/asyncio/futures.py", line 201, in result
    raise self._exception
  File "/lib/python3.10/asyncio/tasks.py", line 232, in __step
    result = coro.send(None)
  File "/lib/python3.10/site-packages/micropip/_micropip.py", line 243, in add_requirement
    raise ValueError(f"'{wheel['filename']}' is not a pure Python 3 wheel")
ValueError: 'biopython-1.79-cp37-cp37m-win_amd64.whl' is not a pure Python 3 wheel

    at new_error (pyodide.asm.js:14:238191)
    at pyodide.asm.wasm:0xedbcb
    at pyodide.asm.wasm:0xf1a0e
    at method_call_trampoline (pyodide.asm.js:14:238105)
    at pyodide.asm.wasm:0x134c2c
    at pyodide.asm.wasm:0x217a84
    at pyodide.asm.wasm:0x174a14
    at pyodide.asm.wasm:0x135149
    at pyodide.asm.wasm:0x135243
    at pyodide.asm.wasm:0x1352e6
    at pyodide.asm.wasm:0x1fff83
    at pyodide.asm.wasm:0x1f98b5
    at pyodide.asm.wasm:0x135329
    at pyodide.asm.wasm:0x201f1b
    at pyodide.asm.wasm:0x1ff9ff
    at pyodide.asm.wasm:0x1f98b5
    at pyodide.asm.wasm:0x135329
    at pyodide.asm.wasm:0xf16d8
    at Object.Module.callPyObjectKwargs (pyproxy.gen.ts:360:23)
    at Object.Module.callPyObject (pyproxy.gen.ts:384:17)
    at wrapper (pyodide.asm.js:14:205222)

Upvotes: 0

Views: 967

Answers (1)

Jorge
Jorge

Reputation: 49

I found a way to do it but without the ".whl". The problem is that biopython is not a pure Python wheel, in this sense you have to notify the pyodide team so that they add it. The pyodide team only adds popular projects like biopython. I still feel like we still need a tool that gives us freedom like pip in the case of PyScript.

Solution below, We just need to import "-Bio"

    <py-env>
- Bio
    </py-env>


    <py-script>

from Bio.Seq import Seq
my_seq = Seq("AGTACACTGGT")

print(my_seq)

print(my_seq.find("ACT"))

    </py-script>

Upvotes: 2

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