imagepy #5450

yxdragon · 2018-03-20T17:37:28Z

No description provided.

yxdragon · 2018-03-20T17:47:03Z

@jbcrail sknw has been merged! That is imagepy, which need wxpython, I did not know if it can be solved!

mariusvniekerk · 2018-03-22T01:41:39Z

So the easiest way to get circle to run your tests after uostream things are merged is to just close and reopen this pull request. Barring that make an empty commit with git commit --allow-empty

conda-forge-linter · 2018-03-22T03:45:35Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/imagepy) and found it was in an excellent condition.

jakirkham · 2018-03-22T03:47:45Z

Took the liberty of merging this with conda-forge/master and pushed a commit to your branch to do just that, @yxdragon. Hope that is ok.

Appears to have addressed whatever CI issues and lingering recipe issues that were here.

jakirkham · 2018-03-22T03:52:40Z

recipes/imagepy/meta.yaml

+  home: https://github.com/Image-Py/imagepy
+  license: BSD 3-clause
+  license_family: BSD
+  license_file: ''


Added PR ( Image-Py/imagepy#16 ) upstream, which should ensure the license file can be included in packages in the future.

@jakirkham need I re upload to pypi first?

Yes, so now that you've merged that PR the next upload to PyPI will have the license file in it. If you want to do a patch release now that includes that, then you could update the recipe to use that version and set license_file: LICENSE. Otherwise you could just remember to do it for the next release.

Or could copy the license file over here for now, in which case it can be dropped from the recipe on the next update. Anyways lots of options to choose from here, feel free to pick what works best for you.

jakirkham · 2018-03-22T03:54:40Z

recipes/imagepy/meta.yaml

+  license_family: BSD
+  license_file: ''
+  summary: interactive python image-processing plugin framework
+  description: Image process framework based on plugin like imagej, it is esay to glue with scipy.ndimage, scikit-image, opencv, simpleitk, mayavi...and any libraries based on numpy


Would suggest wrapping the description. Here is a good example.

jakirkham · 2018-03-22T03:55:46Z

recipes/imagepy/meta.yaml

+
+build:
+  number: 0
+  script: python setup.py install  --single-version-externally-managed --record=record.txt


Apologies. The example is a bit outdated. We should fix that. Currently we encourage using pip for the install.

jakirkham · 2018-03-22T03:56:12Z

recipes/imagepy/meta.yaml

+requirements:
+  build:
+    - python
+    - setuptools


Also would change setuptools to pip.

jakirkham · 2018-03-22T03:57:37Z

recipes/imagepy/meta.yaml

+  sha256: {{ hash_value }}
+
+build:
+  number: 0


Is this a pure Python package? If so, would take a look at using noarch: python. This would build one universal Python package that users could install on Python 2/3 on all platforms.

yes, pure python package, (with numba, pure?)
@jakirkham I think it is the matter of wxpython, here: https://wxpython.org/pages/downloads/

"Because of the differences between Linux distributions (mainly different versions of the core libraries installed by default, but also platform architecture and etc.) it is not possible to host binary wheel files for Linux on PyPI..."

wxpython.org say pypi not work on linux, I do not know if conda can solve it? and is there any wx app on conda? I want to have a look!

@yxdragon conda-forge has a wxpython package: https://github.com/conda-forge/wxpython-feedstock. It should work fine.

If imagepy only has Python code in it, it can be noarch: python, even if it uses Numba / dependencies that aren't Python – it's just a question of whether imagepy itself installs any different files for different architectures, e.g. because it has to compile code.

Run time compilation via Numba still counts as pure Python. We are only concerned with compilation that occurs at build time and it sounds like imagepy doesn't do that. So imagepy counts as pure Python.

@dougalsutherland
that is my CI build log, libgtk-x11-2.0, so I think wx does not work.

from wx.core import *
File "/home/conda/staged-recipes/build_artifacts/imagepy_1521691888499/_t_env/lib/python2.7/site-packages/wx/core.py", line 12, in
from ._core import *
ImportError: libgtk-x11-2.0.so.0: cannot open shared object file: No such file or directory

Ack. Sorry about that.

So we are not as cleanly separated from the OS as we would like. In some cases, particularly GUI packages, we rely on system backed things like Gtk and X11 to be provided for us. Ideally we would package things like X11 (we have done a lot of work in that direction) and Gtk, which we are working on in PR ( #3920 ). In cases where we rely on system packages, we notate this in a yum_requirements.txt file in the recipe like this one for wxpython.

Would just copy wxpython's yum_requirements.txt file and place it in your recipe here. This should install the needed Gtk and X11 libraries behind the scenes. In practice users will typically already have X11 and Gtk as they will be running on a Linux Desktop as opposed to a Docker image (which is where we are building this). In the future, we plan to do a better job of packaging these dependencies outright.

If you have any questions about this, please feel free to ask. :)

Went ahead and added yum_requirements.txt, which should fix this. Hope that is ok.

jakirkham · 2018-03-22T03:59:03Z

Overall this looks really good, @yxdragon. Thanks for adding this.

Added a few comments about, but they shouldn't be too difficult. Please let us know if you have any questions.

Thoughts from @conda-forge/staged-recipes?

conda-forge-linter · 2018-03-22T16:45:54Z

Hi! This is the friendly automated conda-forge-linting service.

I was trying to look for recipes to lint for you, but couldn't find any.
Please ping the 'conda-forge/core' team (using the @ notation in a comment) if you believe this is a bug.

conda-forge-linter · 2018-03-22T17:11:33Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/imagepy) and found it was in an excellent condition.

yxdragon · 2018-03-22T17:22:44Z

@jakirkham I did not know conda is so powerful! and we can also add a apt-get requirements?

yxdragon · 2018-03-22T17:30:18Z

@jakirkham 17 minutes has passed, I click the build detail, and I saw a tag "not runing", is it right?

djsutherland · 2018-03-22T17:39:37Z

@yxdragon Sometimes the CIs get a little busy and it takes a while. Patience. :)

Also: yum_requirements.txt is only used for building on the CIs – it has nothing to do with what users see. So apt-get requirements wouldn't do anything, and the package will still unfortunately break if the user doesn't have gtk / x11 installed.

yxdragon · 2018-03-22T17:43:12Z

@dougalsutherland so the "conda install wxpython" does not work on linux?

djsutherland · 2018-03-22T17:44:14Z

It does, as long as the user has gtk and x11 installed themselves. They usually will if they're on a desktop machine.

yxdragon · 2018-03-22T17:46:23Z

OK, I would try it after ImagePy is merged.

yxdragon · 2018-03-22T17:53:49Z

The CI is too busy, I would have a look tomorrow, you (members of canda-forge org) are so friendly and responsible, Thanks!

jakirkham · 2018-03-22T18:05:09Z

FWIW we are interested in packaging Gtk and it is in the last stages. There already is a cross platform set of X11 packages, but we are working out the details on how best to use them. So I think in the future we will just use these packages and not yum, which should be a bit cleaner.

patricksnape · 2018-03-23T11:46:13Z

recipes/imagepy/meta.yaml

+  summary: interactive python image-processing plugin framework
+  description: |
+    Image process framework based on plugin like imagej.
+    It is esay to glue with any libraries based on numpy.


esay -> easy

djsutherland · 2018-03-23T15:12:30Z

We don't need to wait for CIs to run again for this one-character change to the description. 😉

Merging; thanks @yxdragon!

yxdragon · 2018-03-23T15:18:54Z

@dougalsutherland thanks, I would try to install on py2/3 under win, mac, linux, If there are some question, may need your help! by the way, If I want to update, I will upload to pypi a new version, then what should I do to update conda-forge?

djsutherland · 2018-03-23T15:23:16Z

It'll take a moment for the build to show up on anaconda.org, but the home for the imagepy recipe is now https://github.com/conda-forge/imagepy-feedstock (which you should have gotten an automatic invitation to).

When a new version comes out, you can either (a) wait for the auto-tick bot to send a PR updating the version (< a day after it's up on PyPI; example: conda-forge/tmux-feedstock#6), or (b) send a PR yourself. (Do the PR from your own fork, rather than a branch on the conda-forge feedstock: branches automatically get uploaded also!) In the PR, all you should have to do is bump the version variable, update the sha256 (which you can get from https://pypi.org/project/imagepy/#files), and update any dependencies if they changed. The bot PR will do the first two parts for you, but you'll still have to edit it if any dependencies or anything else about the recipe changed.

jakirkham · 2018-03-23T15:42:55Z

Thanks all. Thanks @yxdragon for submitting. Feel free to submit plugin packages if you like as well.

yxdragon · 2018-03-23T17:36:18Z

@jakirkham ImagePy's plugins is managed in menus, tools, widgets folder, and parse these plugins to generate UI, I will think about how to manage imagepy's plugin more elegantly, and more convenient to publish, search and download, maybe a package named ipy_xxx, put the plugins file in, and with a catlog file to show which parent menus this plugin belong, Is there a interface I can search conda-forge's packages and list those start with 'ipy_'?

yxdragon · 2018-03-23T17:44:14Z

@jakirkham @dougalsutherland
I try run on Ubuntu 16.4, but got some error, (wxpython)
......
ImportError: libiconv.so.2: cannot open shared object file: No such file or directory

see https://wxpython.org/pages/downloads/, we must download the whl according to the linux core and version. I think conda can solve this promblem, but if should I open a issue to wxpython orgnization?
Next, I want to build a web based ImagePy. qt/wx is too heavy, difficult to install...

jakirkham · 2018-03-23T18:20:47Z

Do you already gtk2 and webkitgtk installed from apt-get? gtk2 should pull that in as a dependency.

jakirkham · 2018-03-23T18:26:38Z

Ah ok. Thanks for the info about the plugins.

Might want to chat with Jupyter and/or Spyder developers who have thought more about plugin architecture. Expect they will have some good advice that would be useful as you look into this more.

cc @minrk @ccordoba12

minrk · 2018-03-26T08:59:14Z

We've explored afew extension mechanisms over the years in IPython/Jupyter:

placing files in $PREFIX/share/jupyter for jupyter extensions. This works for us because Jupyter extensions may not be Python specific (often they are purely javascript), but has management downsides since things may not be pure Python packages
%load_ext <pythonmodule> in IPython, calls pythonmodule.load_ipython_extension(self). This works well, but has no mechanism for discovery.
using setuptools entrypoints, e.g. for registering nbconvert exporters

I think for a Python package, entrypoints are the way to go because they make discovery really simple and efficient. Just make sure to use the entrypoints package for runtime discovery instead of pkg_resources, since pkg_resources does wildly inefficient imports on load.

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Merge remote-tracking branch 'conda-forge/master' into 'Image-Py/master'

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jakirkham reviewed Mar 22, 2018

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recipes/imagepy/meta.yaml Outdated

requirements:

build:

- python

- setuptools

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Also would change setuptools to pip.

jakirkham reviewed Mar 22, 2018

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yxdragon added 2 commits March 23, 2018 00:32

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yxdragon closed this Mar 22, 2018

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yxdragon reopened this Mar 22, 2018

yxdragon closed this Mar 22, 2018

yxdragon reopened this Mar 22, 2018

Include yum requirements for wxpython

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jakirkham approved these changes Mar 22, 2018

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patricksnape reviewed Mar 23, 2018

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easy

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djsutherland merged commit 8b7a6b8 into conda-forge:master Mar 23, 2018

imagepy #5450

imagepy #5450

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yxdragon commented Mar 20, 2018

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