Add/update python 3.7.6

[david]

No description provided.

[donald]

Requires some cleanup, doesn't it?

Are the new --prefix=$PREFIX on pip required? Why ?

[thomas]

pip has changed the default install behavior, so I guess this was choosen to be on the safe side. Also some parts have been developed/tested separately (boost/GL/tensorflaw), there the prefix was needed. So, yes it's worth checking what happens if the prefix is dropped P.S. I've noted 2 questions, and no cudos -- a bit poor according to the massive overhaul done by David :) Donald Buczek wrote:

…

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[david]

Requires some cleanup, doesn't it?
you mean my commit messages or ? I will clean this

Are the new --prefix=$PREFIX on pip required? Why ?

If the pythonpath not writable for the user, pip use dir in the homedirectory. To be on the safe side I have decide to add prefix on all pip commands.

[donald]

O, I just realized, that most of the changes to the build script are not in this PR but were already committed directly on the master beginning with 10307f6. Was this intended?

[pmenzel]

@david, thank you for the changes.

Were changes forcefully pushed to the master branch though?

e711d4d...6d5f768 master                  -> origin/master  (forced update)

[pmenzel]

*   e711d4d Merge pull request #104 from mariux64/rebuild-python3
|\  
| * 39a7b0b (origin/rebuild-python3) python3: Add libxml2-python3, scour, jupyterlab-git
| * bf941dc python3: Rebuild version 3.7.4
* | 10307f6 Python-3.7.6: Add package from https://github.molgen.mpg.de/mariux64/pkg-scripts/pull/104/files
|/  
* 96e2724 igv: Add version 2.8.0

So, commit 10307f6 (Python-3.7.6: Add package from https://github.molgen.mpg.de/mariux64/pkg-scripts/pull/104/files) is already in the (original) master branch.

[pmenzel]

This is the new origin/master, merge/pull request #104 was lost.

* 6d5f768 (origin/master, origin/HEAD) tensorflow: make sure tf use the right arch flags
* 9baa7f5 build hic2cool from github
* 4dd95b6 wish from Robert Schoepflin
* 0877565 latest cudaversion
* 7a1b908 bazel needs a lot of space
* 4225376 pucuda change lib path
* 65c3b73 remove is not need, the install part is enough
* bb877fc tensorflow build from source
* 10307f6 Python-3.7.6: Add package from https://github.molgen.mpg.de/mariux64/pkg-scripts/pull/104/files

[donald]

So the #104 merge was force-pushed away?

[donald]

#104 was the last PR, #105 and #106 are issues, #107 is this one. So we could reset the master to the merge commit of #104 which is e711d4d and rebase this branch on top of it. But we'd still have no commits, where python-3.7.6-0.build.sh came from. 10307f6 is a bit mysterious and the changes from the previous version ( like the --prefix for each pip install command) are already included. Anyway this would be a good basis to massage this PR into the most beautiful PR ever :-)

A pitty, it doesn't build, which propably is caused by some updated PiPy modules. I hate it... Maybe we should freeze all versions in the build scripts, but how to do updates then?

Successfully installed HiCMatrix-11 cooler-0.8.5 intervaltree-3.0.2 sortedcontainers-2.1.0
+ pip3 install --prefix=/dev/shm/python-3.7.6-0 pyGenomeTracks
Collecting pyGenomeTracks
  Downloading pyGenomeTracks-3.3-py2.py3-none-any.whl (80 kB)
Requirement already satisfied: numpy>=1.16 in /dev/shm/python-3.7.6-0/lib/python3.7/site-packages (from pyGenomeTracks) (1.18.2)
ERROR: Could not find a version that satisfies the requirement hicmatrix>=12 (from pyGenomeTracks) (from versions: 5, 7, 10, 11)
ERROR: No matching distribution found for hicmatrix>=12 (from pyGenomeTracks)

[donald]

Were changes forcefully pushed to the master branch though?

e711d4d...6d5f768 master                  -> origin/master  (forced update)

where did you get this line?

[pmenzel]

Were changes forcefully pushed to the master branch though?

e711d4d...6d5f768 master                  -> origin/master  (forced update)

where did you get this line?

It was printed by git remote update.

[thomas]

... to massage this PR into the most beautiful PR ever :-)
yeahhhh - even mild irony counts as acknowlegement (at least for me :) )

[david]

some commits are on the master. This was a mistake from me. I will clean this

[thomas]

Sorry for bothering, but to me the topic reads

'Add/update python 3.7.6'

The thread content now is about 'how did we loose a commit with git/git-hub' (LOL)

To me this deems nonconstructive and close to ridiculus, 'caus it doesn't make the build script any better -- so shouldn't this be moved to a place where the discussion can take place just for the people that are interested in themes like that?

(excuse the bad formatting, but this web-app doesn't seem to support my browser)

[donald]

I suggested to reset master to e711d4d, so that the commits which are already on the master, were only in this PRs branch and could be rewritten, e.g. to remove commits like 88aba68. This belongs to this PR, because until we decided and - if accepted - complete that, we can't merge this PR.

[david]

I cannot reset to this or mean you the last commit there 39a7b0b ?

schrader@bacon:~/git_zeug/pkg-scripts
[master]$ git reset e711d4d7d62308d8d33b1f529872be099afecc54
fatal: Could not parse object 'e711d4d7d62308d8d33b1f529872be099afecc54'.

[pmenzel]

Probably because you forgot to fetch the origin/master branch before you forced pushed. So you never got the git objects.

Anyway, I force pushed e711d4d to origin/master now, and put your commits in broken_master. But you should be able to simply rebase your branch/commits on origin/master.

$ git fetch all
$ git rebase origin/master

Then force push this to this merge/pull request,or close this merge/pull request and open a new one so to have a clean discussion.

[david]

ty Paul
I will make a new pull request