Spring python problem - installation issue

[Dawid Zyla]

Hello,

First of all thank you for accepting me to the group. I am working on helical structures called pili and recently I wanted to test your software to check whether Spring is giving me similar result as Relion. I am using CentOS 7. The problem is that during the installation there is some python problem and script is ending with errors and warnings. I was following the instructions on the website, so after unpacking tar archive I have run  ./patches/binary_install_linux.sh:

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 ---------------------- Running binary_install_linux.sh --------------------------

This script will quickly install Spring from binary. Once you move the binaries 

you will need to re-run the script in the new location for it work.

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Check pre-requisites: whether current directory is a Spring build directory.

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Prepare install by re-instating virtualenv and buildout environment.

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1. Re-install pip

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New python executable in ./bin/python

Installing setuptools.................done.

Installing pip.............done.

Overwriting ./bin/activate with new content

Overwriting ./bin/activate.fish with new content

Overwriting ./bin/activate.csh with new content

--2018-04-09 10:26:49--  https://bootstrap.pypa.io/get-pip.py

Resolving bootstrap.pypa.io (bootstrap.pypa.io)... 151.101.36.175

Connecting to bootstrap.pypa.io (bootstrap.pypa.io)|151.101.36.175|:443... connected.

HTTP request sent, awaiting response... 200 OK

Length: 1780465 (1.7M) [text/x-python]

Saving to: ‘get-pip.py’

100%[===================================================================================================================>] 1,780,465   5.66MB/s   in 0.3s   

2018-04-09 10:26:49 (5.66 MB/s) - ‘get-pip.py’ saved [1780465/1780465]

/tmp/tmpm2vKgQ/pip.zip/pip/_vendor/urllib3/util/ssl_.py:339: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings

/tmp/tmpm2vKgQ/pip.zip/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings

Requirement already up-to-date: pip in ./lib/python2.7/site-packages

/tmp/tmpm2vKgQ/pip.zip/pip/_vendor/urllib3/util/ssl_.py:137: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings

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2. Re-install latest setuptools

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/localhome/dawid/Downloads/spring_v0-86-1661/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:318: SNIMissingWarning: An HTTPSrequest has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incrrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urlib3.readthedocs.io/en/latest/security.html#snimissingwarning.

  SNIMissingWarning

/localhome/dawid/Downloads/spring_v0-86-1661/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A rue SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrde to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning.

  InsecurePlatformWarning

Requirement already up-to-date: pip in ./lib/python2.7/site-packages

/localhome/dawid/Downloads/spring_v0-86-1661/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A rue SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrde to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning.

  InsecurePlatformWarning

Requirement already up-to-date: setuptools in ./lib/python2.7/site-packages

/localhome/dawid/Downloads/spring_v0-86-1661/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A rue SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrde to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning.

  InsecurePlatformWarning

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3. Reinstate virtualenv and buildout environement

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New python executable in ./bin/python

Installing setuptools.................done.

Installing pip.............done.

/localhome/dawid/Downloads/spring_v0-86-1661/lib/python2.7/site-packages/pkg_resources/__init__.py:193: RuntimeWarning: You have iterated over the result ofpkg_resources.parse_version. This is a legacy behavior which is inconsistent with the new version class introduced in setuptools 8.0. In most cases, converson to a tuple is unnecessary. For comparison of versions, sort the Version instances directly. If you have another use case requiring the tuple, please filea bug with the setuptools project describing that need.

  stacklevel=1,

Creating directory '/localhome/dawid/Downloads/spring_v0-86-1661/develop-eggs'.

Generated script '/localhome/dawid/Downloads/spring_v0-86-1661/bin/buildout'.

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4. Install latest Python dependencies for Spring

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Installing springpython.

Couldn't find index page for 'emspring' (maybe misspelled?)

Getting distribution for 'emspring'.

Couldn't find index page for 'emspring' (maybe misspelled?)

While:

  Installing springpython.

  Getting distribution for 'emspring'.

Error: Couldn't find a distribution for 'emspring'.

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Install done. Check whether Spring was successfully installed by brief testing.

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./patches/binary_install_linux.sh: ./bin/nosetests: /struct/sachse/software/springbox_2017-12/spring_v0-86-1661/bin/python: bad interpreter: No such file ordirectory

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Testing done. If 4 quick tests ran OK Spring was correctly installed.

Install done. Please type to add the following line to your .cshrc:

echo setenv PATH:/localhome/dawid/Downloads/spring_v0-86-1661/bin:$PATH >> ~/.cshrc

or your favorite Bourne shell rc file (e.g. .bashrc, .zshrc):

echo export PATH:/localhome/dawid/Downloads/spring_v0-86-1661/bin:$PATH >> ~/.bashrc

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I have tried to update python manually in bin folder and in EMAN2 folder but it didn't work. All scripts in bin folder cannot start because the python exe is not in the proper directory (/struct/sachse/software/springbox_2017-12/spring_v0-86-1661/bin/python) and even changing this line to Spring python library also doesn't work. I would be very grateful for some hints how to fix that. I look forward to hearing from you soon!

All the best,

Dawid Zyla

ETH Zurich

[Carsten Sachse]

Dear Dawid,

Thanks for your message. We will look into the installation issue asap and keep you posted.

Best wishes,

Carsten

[Carsten Sachse]

Dear David,

Again, thanks for pointing out the issue. The issue is related to higher security settings in the Pypi servers. 

I provide a patch to fix the SSL connection issue you were reporting.

You can run it in the following way:

%patch -u binary_install_linux.sh  install_fix180416.patch

Now re-run:

% sh patches/binary_install_linux.sh

Please let me know if this works.

Best wishes,

Carsten

[Carsten Sachse]

Dear all,

David has confirmed that it works. Please, be aware I included the patched binary_install_linux.sh in the latest downloadable binary. No need to apply the patch yourself.

Best wishes,

Carsten