ModuleNotFoundError: No module named 'Cython',/Users/zhangweilin/opt/anaconda3/bin/python: No module named flake8

[acse-wz19]

I have re-install it several times, but always module not found error happened. I do not know why and I attach the log file here firedrake-install.log

[acse-wz19]

this is the test error shown on my screen

[wence-]

The install went fine, but it looks like you haven't activated the firedrake virtual environment before running make alltest.

[acse-wz19]

Building extension modules Traceback (most recent call last): File "setup.py", line 5, in from Cython.Distutils import build_ext ModuleNotFoundError: No module named 'Cython' Linting firedrake codebase /Users/zhangweilin/opt/anaconda3/bin/python: No module named flake8 make: *** [lint] Error 1

[acse-wz19]

I hope you can help me figure out this problem, thanks

[acse-wz19]

Yes I will try it now,thanks

[acse-wz19]

is this all_test takes a very long time? and I can not use the function contained in this package.

[wence-]

It does take a long time, yes. Hopefully you are seeing lots of dots ...., or are you seeing many FFFFs?

[wence-]

I am confused that you don't see UnitSquareMesh though, since I would have expected that if the import did not fail, then the function should be available.

[acse-wz19]

but this problem happens on my notebook, and I can not import Thetis also. It is quite confusing me. Do you have any idea of this situation?

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发件人: Lawrence Mitchell notifications@github.com 发送时间: Thursday, June 4, 2020 11:07:18 PM 收件人: firedrakeproject/firedrake firedrake@noreply.github.com 抄送: Zhang, Weilin weilin.zhang19@imperial.ac.uk; Author author@noreply.github.com 主题: Re: [firedrakeproject/firedrake] ModuleNotFoundError: No module named 'Cython',/Users/zhangweilin/opt/anaconda3/bin/python: No module named flake8 (#1721)

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I am confused that you don't see UnitSquareMesh though, since I would have expected that if the import did not fail, then the function should be available.

― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/firedrakeproject/firedrake/issues/1721#issuecomment-638911316, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANLP5W7QYCDSMOFOIV4FNSLRU62CNANCNFSM4NSUSFKA.

[acse-wz19]

my test presently is .... rather than FFF

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发件人: Zhang, Weilin weilin.zhang19@imperial.ac.uk 发送时间: Thursday, June 4, 2020 11:30:17 PM 收件人: firedrakeproject/firedrake reply@reply.github.com; firedrakeproject/firedrake firedrake@noreply.github.com 抄送: Author author@noreply.github.com 主题: Re: [firedrakeproject/firedrake] ModuleNotFoundError: No module named 'Cython',/Users/zhangweilin/opt/anaconda3/bin/python: No module named flake8 (#1721)

but this problem happens on my notebook, and I can not import Thetis also. It is quite confusing me. Do you have any idea of this situation?

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发件人: Lawrence Mitchell notifications@github.com 发送时间: Thursday, June 4, 2020 11:07:18 PM 收件人: firedrakeproject/firedrake firedrake@noreply.github.com 抄送: Zhang, Weilin weilin.zhang19@imperial.ac.uk; Author author@noreply.github.com 主题: Re: [firedrakeproject/firedrake] ModuleNotFoundError: No module named 'Cython',/Users/zhangweilin/opt/anaconda3/bin/python: No module named flake8 (#1721)

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I am confused that you don't see UnitSquareMesh though, since I would have expected that if the import did not fail, then the function should be available.

― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/firedrakeproject/firedrake/issues/1721#issuecomment-638911316, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANLP5W7QYCDSMOFOIV4FNSLRU62CNANCNFSM4NSUSFKA.

[acse-wz19]

it also contains ssss

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发件人: Zhang, Weilin weilin.zhang19@imperial.ac.uk 发送时间: Thursday, June 4, 2020 11:38:55 PM 收件人: firedrakeproject/firedrake reply@reply.github.com; firedrakeproject/firedrake firedrake@noreply.github.com 抄送: Author author@noreply.github.com 主题: Re: [firedrakeproject/firedrake] ModuleNotFoundError: No module named 'Cython',/Users/zhangweilin/opt/anaconda3/bin/python: No module named flake8 (#1721)

my test presently is .... rather than FFF

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发件人: Zhang, Weilin weilin.zhang19@imperial.ac.uk 发送时间: Thursday, June 4, 2020 11:30:17 PM 收件人: firedrakeproject/firedrake reply@reply.github.com; firedrakeproject/firedrake firedrake@noreply.github.com 抄送: Author author@noreply.github.com 主题: Re: [firedrakeproject/firedrake] ModuleNotFoundError: No module named 'Cython',/Users/zhangweilin/opt/anaconda3/bin/python: No module named flake8 (#1721)

but this problem happens on my notebook, and I can not import Thetis also. It is quite confusing me. Do you have any idea of this situation?

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---

发件人: Lawrence Mitchell notifications@github.com 发送时间: Thursday, June 4, 2020 11:07:18 PM 收件人: firedrakeproject/firedrake firedrake@noreply.github.com 抄送: Zhang, Weilin weilin.zhang19@imperial.ac.uk; Author author@noreply.github.com 主题: Re: [firedrakeproject/firedrake] ModuleNotFoundError: No module named 'Cython',/Users/zhangweilin/opt/anaconda3/bin/python: No module named flake8 (#1721)

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I am confused that you don't see UnitSquareMesh though, since I would have expected that if the import did not fail, then the function should be available.

― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/firedrakeproject/firedrake/issues/1721#issuecomment-638911316, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANLP5W7QYCDSMOFOIV4FNSLRU62CNANCNFSM4NSUSFKA.

[danshapero]

The .... indicates how many tests have run, which suggests that your installation worked. The sssss indicates that some tests are skipped because they're for special optional features that you might not have installed, so that's nothing to worry about.

To use Firedrake from a jupyter notebook, you have to install a jupyter kernel first. If you just want to make sure that Firedrake is working, can you try:

1. activate the Firedrake virtual environment
2. pip3 install ipython and run ipython
3. from the ipython interpreter, from firedrake import * and then mesh = UnitSquareMesh(10, 10)

Hopefully this will actually work. If it does, then you can do the following to install a jupyter kernel for Firedrake:

1. activate the virtual environment
2. pip3 install ipykernel
3. python3 -m ipykernel install --user --name=firedrake

When you want to use Firedrake in a new jupyter notebook, you might have to go into the "kernel" menu and selected "firedrake" for it to work properly.

[acse-wz19]

Thanks, this is very helpful.

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发件人: Daniel Shapero notifications@github.com 发送时间: Thursday, June 4, 2020 11:47:14 PM 收件人: firedrakeproject/firedrake firedrake@noreply.github.com 抄送: Zhang, Weilin weilin.zhang19@imperial.ac.uk; Author author@noreply.github.com 主题: Re: [firedrakeproject/firedrake] ModuleNotFoundError: No module named 'Cython',/Users/zhangweilin/opt/anaconda3/bin/python: No module named flake8 (#1721)

This email from notifications@github.com originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders listhttps://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address.

The .... indicates how many tests have run, which suggests that your installation worked. The sssss indicates that some tests are skipped because they're for special optional features that you might not have installed, so that's nothing to worry about.

To use Firedrake from a jupyter notebook, you have to install a jupyter kernel first. If you just want to make sure that Firedrake is working, can you try:

1. activate the Firedrake virtual environment
2. pip3 install ipython and run ipython
3. from the ipython interpreter, from firedrake import * and then mesh = UnitSquareMesh(10, 10)

Hopefully this will actually work. If it does, then you can do the following to install a jupyter kernel for Firedrake:

1. activate the virtual environment
2. pip3 install ipykernel
3. python3 -m ipykernel install --user --name=firedrake

When you want to use Firedrake in a new jupyter notebook, you might have to go into the "kernel" menu and selected "firedrake" for it to work properly.

― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/firedrakeproject/firedrake/issues/1721#issuecomment-638939975, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANLP5W2ZRHEAHKUDXEZZTITRU66YFANCNFSM4NSUSFKA.

[danshapero]

Happy to help! Let us know if everything worked so we can close the issue.

[danshapero]

I'm closing this issue, but if it's still a problem then feel free to re-open.