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DONE: Functionality for dev-build #3
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looks good to me. Has been used to setup Ahsan's machine at PDBe |
Why are you installing scipy in the update script - and hardcoding a specific version? Is there a dependency that is broken? If so - that should be fixed - and comments around the code explaining the reason for doing this. Version 1.2.3 is available for python 2. For python 3, we should move to the 1.4 series. Is there a reason for 1.2.x - there are ways to code that without coding a specific version - and making it depend on python 2 only. If there is a reason not to trust dependencies or installing dependencies with our extra pip options messes things up, base_package/requirements.txt is the place - and you can see python version specific logic. |
scipy is pulled in by wwpdb-TEMPy for python2 which is part of the base install. There is also an assumption of what directory you are sitting in. open('../base_packages/requirements_wwpdb_dependencies.txt') |
Thanks for reviewing.
Yes there is a broken dependency.
So the logical step is to add this dependency in the So now there are essentially two set of constraints:
This I am not sure of. My reasons for the version was the video, where scipy was installed for 1.2.2 I know putting a package name and installing isn't the best way. Do you have a good way we can do this given the constraints I highlighted above? |
I am thinking two different base ones might be required.... I will play with it over the weekend... |
Yes
Oh yes. |
can we remove wwpdb-TEMPy and biopython from the requirements.txt? |
…ttps://github.com/wwPDB/onedep_admin into pvt-ahsant-dev-isntall-in-RunUpdate
fixed biopython version for python 2.7
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this branch works for a blank install where as master doesn't.
@epeisach over to you to approve
Need to lock at 1.73 of biopython for python 2. Until va package is updated to not lock down version - you will probably wind up installing 1.76, then not being backed down. With 1.76 installed - does "pip check" report any issues? |
And if biopython did not put n proper metadata to tell pip this is not the version you want - shame on them. This is the fourth package with the issue. Numpy got it right, but other packages have not. We wind up having to hardcode versions in setup.py which is unfortunate. |
can biopython be removed from requirements.txt? why does it need to be here? |
@epeisach can this be merged to master now? |
i've just used this to install 3 servers (production, staging and a development server with --edit). it worked for me. @epeisach can we merge please. |
I have merged your pull request, Looks correct to me. |
PR to add
dev-build
flag:git clone
andpip --edit install
of modules.Changes include:
pyenv
beforewebfe
)Dev-tested on
pdbe-ondep-test
machine