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WIP Make cylc a module #2834

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wants to merge 12 commits into from
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WIP Make cylc a module #2834

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kinow
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@kinow kinow commented Nov 3, 2018

I created this branch some months ago, while in parallel started bothering the maintainers of isodatetime to include the setup.py file over there 😬 Showed it to @hjoliver some days ago, but it was a huge mess of commits (you know, the ol' break here, fix over there kind of commits).

After #1337, I thought it would be useful to open at least an WIP pull request so others could have a look at an example of a working setup.py for Cylc.

At the moment it is producing an egg file for Cylc with setuptools + distutils + some Python witchcraft.

$ python setup.py develop --user 
$ python
Python 2.7.15rc1 (default, Apr 15 2018, 21:51:34) 
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import cylc.version
>>> print(cylc.version.CYLC_VERSION)
7.7.1-310-g17393
>>> 

@kinow
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kinow commented Nov 3, 2018

This is still a work-in-progress branch, mainly waiting for:

  • isodatetime release, so that the dependency to a git commit can be removed, and instead point to a tag
  • another pull request to fix the compatibility issues with the new version of isodatetime. That is done in this branch in a single commit to this branch, which will be deleted (i.e. git rebase -i HEAD~4 and then mark that as dropped)
  • dependency groups are added, reflecting the modular design approach in cylc installation: packages for Debian, Red Hat, etc... #1337
  • final round of checks, also confirming if there's any work that could be done for packaging for Conda, RPM, Deb, tar.gz, etc.
  • documentation

@kinow
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kinow commented Nov 3, 2018

I started this more because I wanted to play with Cylc's API in Jupyter Notebooks (which I think maybe would interest @jonnyhtw too?). Here's one example which I maintain using the branch in this pull request (though one of the notebooks dates a few years ago I think):

https://github.com/kinow/cylc-notebooks

@matthewrmshin
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I suppose we can create a new isodatetime release without metomi/isodatetime#101? In which case I'll try and do that early next week, so we don't end up blocking progress on other stuffs.

@kinow
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kinow commented Nov 3, 2018

Did not want to put any pressure on that @matthewrmshin, sorry. I will have another look at that pull request during next week, but my hopes are not too high for finding a solution that doesn't break anything else.

I was thinking about discussing the setup.py file with others in Melbourne, to see if that sounded like a good idea, and if we could start experimenting with it... but I was planning on bothering you guys more with coverage first, once the release is out 😬 😁

Just raised this pull request to provide some example for the recent issue about packaging cylc. So feel free to focus on the Cylc release if you prefer, and leave the isodatetime for whenever you guys are ready to release 👍

@matthewrmshin matthewrmshin added this to the soon milestone Nov 3, 2018
@jonnyhtw
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jonnyhtw commented Nov 5, 2018

Hi there

Definitely interested in Jupyter integration. I'm a big fan!

Cheers

J

@kinow
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kinow commented Nov 12, 2018

Included a few more commits (will squash/edit later) to

  • use PyTest from setup.py (e.g. python setup.py test)
  • include files that are not just Python files, like the static files for Cylc Review
  • simplify dependency management by listing everything in setup.py only
  • added dependency groups, for [ssl], which includes dependencies necessary to support SSL in cylc, and [empy], as per name. Also included group [all] which is just the sum of both previous groups... it can be tested with pip install -e .[all]

Still a few more loose ends. Rebased onto master.

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kinow commented Nov 16, 2018

Note: Conda docs mention a way to upload via setup.py, but that generates a PYPI artifact, installed via pip and specifying the Conda PYPI repository. If we want to have a conda install cylc, then we need the meta.yml.

Had a go at uploading to Conda via PYPI and then realized it wouldn't resolve dependencies via conda.

via-pypi

python setup.py sdist
anaconda upload dist/*.tar.gz
# quite easy to remove it from your channel later
anaconda remove kinow/pccora/0.2

Next week will finish experimenting with Conda, and hopefully have a meta.yaml for Cylc to include in this pull request.

@kinow
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kinow commented Nov 20, 2018

Good primer on Python packaging: A tour on Python Packaging, Nick Mavrakis

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kinow commented Nov 21, 2018

Finished the tests on Conda, using that small Python utility as test experiment.

Notes:

  • PCCORA had one runtime dependency, construct, so I thought it would be super simple to upload it to Conda.... but turns out the maintainer of construct never uploaded it there... instead, two developers did so, but when uploading it, they used Python 2.7...
  • PCCORA required Python 3.3+, so Conda was unable to satisfy construct + Python 3.6. Looking around, found that others suggest to upload it to your own channel when that happens 😥
conda skeleton pypi construct
anaconda upload /home/kinow/Development/python/anaconda3/conda-bld/linux-64/construct-2.5.1-py37_0.tar.bz2

...
Upload complete

conda package located at:
https://anaconda.org/kinow/construct

After doing that, I had to include my own channel in the list of default channels, so that conda build for PCCORA would work too...

# file ~/.condarc
channels:
  - conda-forge
  - defaults
  - travis
  - kinow
anaconda_upload: false
  • We could create a new organisation in Anaconda, say, Cylc for example. That way users could use conda install -c cylc cylc
  • The conda skeleton is useful, but it doesn't work exactly like setup.py. For example, I can't use PYPI dependencies in the meta.yaml generated, they have to be duplicated, both in setup.py and in the generated meta.yaml
  • I had to manually include six library, and pytest-runner. The latter is a special dependency for setup.py, not automatically identified by conda skeleton, and six... well, that was just weird
  • It defaults to using the PYPI .tar.gz file + sha256... instead, I used a Git repo + Git tag... that way I can close the tag and use the tag to upload both PYPI and Conda artefacts, without having to commit any more changes
  • The final artefact in Conda was much bigger than the one in PYPI. I suspect because in PYPI case, I filtered what had to be included via setup.py (did not use a MANIFEST.MF, but we could have that too), while Conda probably doesn't use that information. For Cylc, we would have to investigate how to limit what is uploaded, so users don't end up with extra/unnecessary files.

Building the library and uploading it

After that, it finally worked to build and upload it (it does both by default, by I disabled that in my .condarc file.

kinow@kinow-VirtualBox:~$  conda install -c kinow pccora 
Solving environment: done

## Package Plan ##

  environment location: /home/kinow/Development/python/anaconda3

  added / updated specs: 
    - pccora


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    construct-2.5.1            |           py37_0         110 KB  kinow
    pccora-0.3                 |           py37_0        18.2 MB  kinow
    ------------------------------------------------------------
                                           Total:        18.3 MB

The following NEW packages will be INSTALLED:

    construct: 2.5.1-py37_0 kinow
    pccora:    0.3-py37_0   kinow

Proceed ([y]/n)? y


Downloading and Extracting Packages
construct-2.5.1      | 110 KB    | ######################################################################################################################################################################## | 100% 
pccora-0.3           | 18.2 MB   | ######################################################################################################################################################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
kinow@kinow-VirtualBox:~$ python
Python 3.7.0 (default, Jun 28 2018, 13:15:42) 
[GCC 7.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pccora
>>> p = pccora.PCCORAParser()
>>> p
<pccora.pccora.PCCORAParser object at 0x7f5e6a9a3a58>
>>> 

Conclusion

I think it is doable to generate a meta.yaml for Cylc, especially if we can use the setup.py from this pull request. But I will push for this to happen in another ticket, as it could involve some work on the meta.yaml file, and also gathering feedback of others about channel name, dependencies that we need, whether all dependencies work in all environments, etc 👍

@kinow
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kinow commented Nov 21, 2018

The only thing holding me from removing the WIP from the title here now, is that it requires some changes to our tests and other files. I included a pytest.ini here, but this file is already included in the #2765 report test coverage PR. I would like to see it getting included there first, then drop the commits here, and it should be finally ready for review 🏃‍♂️

@hjoliver
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Test coverage reporting is now in 🍾 so ... (as per your previous comment) ... this is almost ready to go?

@hjoliver
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(I guess we need to document clearly that package installation does not address the PyGTK dependency; for that users might still need to rely on the system Python 2).

@kinow
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kinow commented Nov 25, 2018

@hjoliver

(I guess we need to document clearly that package installation does not address the PyGTK dependency; for that users might still need to rely on the system Python 2).

+1

And also need to figure out what to do about the release. That's, I think, the last pending issue for me.

isodatetime was easier to make a package as its use was mainly as a tool. But Cylc is used as an application, and the scripts part needs more testing I think (i.e. confirm they are correctly exported to the $PATH of users).

Furthermore, isodatetime, jinja2, and markupsafe were removed. Users would have to run python setup.py install to grab dependencies (assuming they can download/install dependencies in their sites), or we would need to investigate the option to create a complete package.

This complete package, would be Cylc with all its dependencies included (and the .git folder too), so technically, it would be the same as before, and users would just have to replace the binary. We could also add this release to GitHub, so users could just go to https://github.com/cylc/cylc/releases and grab it.

Rebased the work, removing what had been implemented in the coverage reports pull request and was redundant here.

@kinow kinow mentioned this pull request Nov 26, 2018
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kinow commented Jan 8, 2019

Rebased. Pending now Travis build.

I believe this is ready to go, but not in a 7.x release. This makes Cylc a module, and allows users to install it via pip.

However, it also removes dependencies, and users would have to change their installation process to comply with this change.

So it might be better to leave the WIP for now, and merge it when going Python 3, IMO.

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kinow commented Jan 8, 2019

Building with python setup.py bdist_rpm now produces a RPM with the following settings:

$ rpm -qp cylc-7.8.0_19_ge947e0_dirty-1.noarch.rpm --requires
/bin/bash
/usr/bin/python
python-jinja2
python-markupsafe
rpmlib(CompressedFileNames) <= 3.0.4-1
rpmlib(FileDigests) <= 4.6.0-1
rpmlib(PayloadFilesHavePrefix) <= 4.0-1

$ rpm -qp cylc-7.8.0_19_ge947e0_dirty-1.noarch.rpm --provides
cylc = 7.8.0_19_ge947e0_dirty-1

$ less cylc-7.8.0_19_ge947e0_dirty-1.noarch.rpm
cylc-7.8.0_19_ge947e0_dirty-1.noarch.rpm:
Name        : cylc
Version     : 7.8.0_19_ge947e0_dirty
Release     : 1
Architecture: noarch
Install Date: (not installed)
Group       : Development/Libraries
Size        : 10214370
License     : GPL
Signature   : (none)
Source RPM  : cylc-7.8.0_19_ge947e0_dirty-1.src.rpm
Build Date  : Wed 09 Jan 2019 12:12:46 NZDT
Build Host  : kinow-VirtualBox
Relocations : /usr 
Vendor      : Hilary Oliver <[email protected]>
URL         : https://cylc.github.io/cylc/
Summary     : Cylc ("silk") is a workflow engine for cycling systems - it orchestrates distributed suites of interdependent cycling tasks that may continue to run indefinitely.
Description :
.... # contents of README.md
*** Contents:
/usr/local/bin/cycl
/usr/local/bin/cylc
/usr/local/bin/cylc-5to6
/usr/local/bin/cylc-bcast
/usr/local/bin/cylc-broadcast
/usr/local/bin/cylc-browse
/usr/local/bin/cylc-cat-log
/usr/local/bin/cylc-cat-state
/usr/local/bin/cylc-check-software
/usr/local/bin/cylc-check-triggering
/usr/local/bin/cylc-check-versions
/usr/local/bin/cylc-checkpoint
/usr/local/bin/cylc-client
/usr/local/bin/cylc-compare
/usr/local/bin/cylc-conditions
/usr/local/bin/cylc-cycle-point
/usr/local/bin/cylc-cyclepoint
/usr/local/bin/cylc-cycletime
/usr/local/bin/cylc-datetime
/usr/local/bin/cylc-diff
/usr/local/bin/cylc-documentation
/usr/local/bin/cylc-dump
/usr/local/bin/cylc-edit
/usr/local/bin/cylc-email-suite
/usr/local/bin/cylc-email-task
/usr/local/bin/cylc-ext-trigger
/usr/local/bin/cylc-external-trigger
/usr/local/bin/cylc-function-run
/usr/local/bin/cylc-get-config
/usr/local/bin/cylc-get-contact
/usr/local/bin/cylc-get-cylc-version
/usr/local/bin/cylc-get-directory
/usr/local/bin/cylc-get-global-config
/usr/local/bin/cylc-get-gui-config
/usr/local/bin/cylc-get-host-metrics
/usr/local/bin/cylc-get-site-config
/usr/local/bin/cylc-get-suite-config
/usr/local/bin/cylc-get-suite-contact
/usr/local/bin/cylc-get-suite-version
/usr/local/bin/cylc-gpanel
/usr/local/bin/cylc-graph
/usr/local/bin/cylc-graph-diff
/usr/local/bin/cylc-grep
/usr/local/bin/cylc-gscan
/usr/local/bin/cylc-gsummary
/usr/local/bin/cylc-gui
/usr/local/bin/cylc-help
/usr/local/bin/cylc-hold
/usr/local/bin/cylc-import-examples
/usr/local/bin/cylc-insert
/usr/local/bin/cylc-jobs-kill
/usr/local/bin/cylc-jobs-poll
/usr/local/bin/cylc-jobs-submit
/usr/local/bin/cylc-jobscript
/usr/local/bin/cylc-kill
/usr/local/bin/cylc-list
/usr/local/bin/cylc-log
/usr/local/bin/cylc-ls
/usr/local/bin/cylc-ls-checkpoints
/usr/local/bin/cylc-message
/usr/local/bin/cylc-monitor
/usr/local/bin/cylc-nudge
/usr/local/bin/cylc-ping
/usr/local/bin/cylc-poll
/usr/local/bin/cylc-print
/usr/local/bin/cylc-profile-battery
/usr/local/bin/cylc-register
/usr/local/bin/cylc-release
/usr/local/bin/cylc-reload
/usr/local/bin/cylc-remote-init
/usr/local/bin/cylc-remote-tidy
/usr/local/bin/cylc-remove
/usr/local/bin/cylc-report-timings
/usr/local/bin/cylc-reset
/usr/local/bin/cylc-restart
/usr/local/bin/cylc-review
/usr/local/bin/cylc-run
/usr/local/bin/cylc-scan
/usr/local/bin/cylc-scp-transfer
/usr/local/bin/cylc-search
/usr/local/bin/cylc-set-verbosity
/usr/local/bin/cylc-show
/usr/local/bin/cylc-shutdown
/usr/local/bin/cylc-spawn
/usr/local/bin/cylc-start
/usr/local/bin/cylc-stop
/usr/local/bin/cylc-submit
/usr/local/bin/cylc-suite-state
/usr/local/bin/cylc-task-message
/usr/local/bin/cylc-test-battery
/usr/local/bin/cylc-trigger
/usr/local/bin/cylc-unhold
/usr/local/bin/cylc-upgrade-run-dir
/usr/local/bin/cylc-validate
/usr/local/bin/cylc-view
/usr/local/bin/cylc-warranty
/usr/local/bin/gcontrol
/usr/local/bin/gcycl
/usr/local/bin/gcylc
/usr/local/lib/python2.7/dist-packages/Jinja2Filters/duration_as.py
/usr/local/lib/python2.7/dist-packages/Jinja2Filters/duration_as.pyc
/usr/local/lib/python2.7/dist-packages/Jinja2Filters/duration_as.pyo
/usr/local/lib/python2.7/dist-packages/Jinja2Filters/pad.py
/usr/local/lib/python2.7/dist-packages/Jinja2Filters/pad.pyc
/usr/local/lib/python2.7/dist-packages/Jinja2Filters/pad.pyo
/usr/local/lib/python2.7/dist-packages/Jinja2Filters/strftime.py
/usr/local/lib/python2.7/dist-packages/Jinja2Filters/strftime.pyc
/usr/local/lib/python2.7/dist-packages/Jinja2Filters/strftime.pyo
/usr/local/lib/python2.7/dist-packages/cherrypy/LICENSE.txt
/usr/local/lib/python2.7/dist-packages/cherrypy/__init__.py
/usr/local/lib/python2.7/dist-packages/cherrypy/__init__.pyc
/usr/local/lib/python2.7/dist-packages/cherrypy/__init__.pyo
...

I will package isodatetime as a RPM as well, then try to install it on a blank centos7 container. These RPM's are being built on Ubuntu after installing rpmbuild.

If that works, will start trying deb too.

@kinow
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kinow commented Jan 9, 2019

Testing the RPM:

[root@4c921bbd54db rpms]# rpm -ivh cylc-7.8.0_20_g1f592-1.noarch.rpm 
error: Failed dependencies:
	python-jinja2 is needed by cylc-7.8.0_20_g1f592-1.noarch
	python-markupsafe is needed by cylc-7.8.0_20_g1f592-1.noarc

To install with dependencies, we can just fake-use yum (note: most containers are built as small as possible, without including tools like vim, less, 'which', etc... cylc does not work without less nor without which!):

[root@4c921bbd54db rpms]# yum -y --nogpgcheck localinstall cylc*noarch.rpm 
Loaded plugins: fastestmirror, ovl
Examining cylc-7.8.0_20_g1f592_dirty-1.noarch.rpm: cylc-7.8.0_20_g1f592_dirty-1.noarch
Marking cylc-7.8.0_20_g1f592_dirty-1.noarch.rpm to be installed
Resolving Dependencies
--> Running transaction check
---> Package cylc.noarch 0:7.8.0_20_g1f592_dirty-1 will be installed
--> Processing Dependency: less for package: cylc-7.8.0_20_g1f592_dirty-1.noarch
Loading mirror speeds from cached hostfile
 * base: mirror.ventraip.net.au
 * extras: mirror.optus.net
 * updates: ftp.swin.edu.au
--> Processing Dependency: python-jinja2 for package: cylc-7.8.0_20_g1f592_dirty-1.noarch
--> Processing Dependency: python-markupsafe for package: cylc-7.8.0_20_g1f592_dirty-1.noarch
--> Running transaction check
---> Package less.x86_64 0:458-9.el7 will be installed
---> Package python-jinja2.noarch 0:2.7.2-2.el7 will be installed
---> Package python-markupsafe.x86_64 0:0.11-10.el7 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

===================================================================================================================================================================================================================
 Package                                        Arch                                Version                                                Repository                                                         Size
===================================================================================================================================================================================================================
Installing:
 cylc                                           noarch                              7.8.0_20_g1f592_dirty-1                                /cylc-7.8.0_20_g1f592_dirty-1.noarch                              9.7 M
Installing for dependencies:
 less                                           x86_64                              458-9.el7                                              base                                                              120 k
 python-jinja2                                  noarch                              2.7.2-2.el7                                            base                                                              515 k
 python-markupsafe                              x86_64                              0.11-10.el7                                            base                                                               25 k

Transaction Summary
===================================================================================================================================================================================================================
Install  1 Package (+3 Dependent packages)

Total size: 10 M
Total download size: 660 k
Installed size: 13 M
Downloading packages:
(1/3): less-458-9.el7.x86_64.rpm                                                                                                                                                            | 120 kB  00:00:00     
(2/3): python-markupsafe-0.11-10.el7.x86_64.rpm                                                                                                                                             |  25 kB  00:00:00     
(3/3): python-jinja2-2.7.2-2.el7.noarch.rpm                                                                                                                                                 | 515 kB  00:00:00     
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                                                                                              906 kB/s | 660 kB  00:00:00     
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
  Installing : python-markupsafe-0.11-10.el7.x86_64                                                                                                                                                            1/4 
  Installing : python-jinja2-2.7.2-2.el7.noarch                                                                                                                                                                2/4 
  Installing : less-458-9.el7.x86_64                                                                                                                                                                           3/4 
  Installing : cylc-7.8.0_20_g1f592_dirty-1.noarch                                                                                                                                                             4/4 
  Verifying  : cylc-7.8.0_20_g1f592_dirty-1.noarch                                                                                                                                                             1/4 
  Verifying  : python-jinja2-2.7.2-2.el7.noarch                                                                                                                                                                2/4 
  Verifying  : less-458-9.el7.x86_64                                                                                                                                                                           3/4 
  Verifying  : python-markupsafe-0.11-10.el7.x86_64                                                                                                                                                            4/4 

Installed:
  cylc.noarch 0:7.8.0_20_g1f592_dirty-1                                                                                                                                                                            

Dependency Installed:
  less.x86_64 0:458-9.el7                                      python-jinja2.noarch 0:2.7.2-2.el7                                      python-markupsafe.x86_64 0:0.11-10.el7                                     

Complete!

Interestingly... if you do not install less or which, then cylc check-software crashes (exception). If you install pygtk, then it crashes too for trying to use a display.

[root@ead3bc7d5ffe /]# cylc check-software
Checking your software...

Individual results:
==========================================================================================
Package (version requirements)                                     Outcome (version found)
==========================================================================================
                                   *REQUIRED SOFTWARE*                                   
Python (2.6+, <3).................................FOUND & min. version MET (2.7.5.final.0)

             *OPTIONAL SOFTWARE for the GUI & dependency graph visualisation*             
Traceback (most recent call last):
  File "/usr/bin/cylc-check-software", line 335, in <module>
    main()
  File "/usr/bin/cylc-check-software", line 317, in main
    functionality_print(tag)
  File "/usr/bin/cylc-check-software", line 255, in functionality_print
    opt_result[module] = check_py_module_ver(module, ver_req)
  File "/usr/bin/cylc-check-software", line 168, in check_py_module_ver
    import gtk
  File "/usr/lib64/python2.7/site-packages/gtk-2.0/gtk/__init__.py", line 64, in <module>
    _init()
  File "/usr/lib64/python2.7/site-packages/gtk-2.0/gtk/__init__.py", line 52, in _init
    _gtk.init_check()
RuntimeError: could not open display

And to fix that in Docker.

[root@ead3bc7d5ffe /]# yum install xorg-x11-server-Xvfb
[root@ead3bc7d5ffe /]# Xvfb :1 -screen 0 1024x768x16 &> xvfb.log  &
[1] 771
[root@ead3bc7d5ffe /]# ps aux | grep X
root       771  0.3  0.2  99432 12508 pts/0    S    03:22   0:00 Xvfb :1 -screen 0 1024x768x16
root       774  0.0  0.0   9100   816 pts/0    S+   03:22   0:00 grep --color=auto X
[root@ead3bc7d5ffe /]# DISPLAY=:1.0
[root@ead3bc7d5ffe /]# export DISPLAY
[root@ead3bc7d5ffe /]# cylc check-software
....

Now cylc gui is failing with:

[root@ead3bc7d5ffe /]# cylc gui
Failed to open file “/usr/lib/python2.7/images/icon.png”: No such file or directory

We are getting closer to a working RPM, that installs Cylc and all dependencies, built from sources. But the icon.png will be probably tricky, so will start working on it tomorrow morning.

@kinow
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kinow commented Jan 9, 2019

Blocking work on the modules, until #2918 is sorted out. Need to include the images in the package too... unless we want to go without building pygtk/pygraphviz, but instead ditching all GUI, and working only on the new module. If that's the case, #2918 can be closed, but this will be still blocked until Python3 work starts 👍

@hjoliver
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I'll create a "blocked" label for PRs like this...

@hjoliver hjoliver added the BLOCKED This can't happen until something else does label Jan 10, 2019
@kinow
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kinow commented Jan 10, 2019

Good idea, thanks @hjoliver !

@hjoliver
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@kinow - did you mean to close this?

@kinow kinow removed this from the cylc-8-alpha-1 milestone Mar 12, 2019
@kinow kinow removed the BLOCKED This can't happen until something else does label Mar 12, 2019
@kinow kinow mentioned this pull request Mar 12, 2019
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4 participants