Mailman 3 January 2016 - yt-dev

PR Triage Hangout Link AND Poll
by Hilary Egan 12 Jan '16

12 Jan '16

Hi all, Here's the link for Monday's (1/11) PR triage hangout, usual time. Hangout <https://plus.google.com/u/0/b/107728486871834552760/events/cg6ibf3kc8fm0qs1…> Here's a link for a poll to check times for this spring. Although it has specific dates listed, treat it as your average week from now til ~May. If a new time/day is selected we'll switch the week after (1/18-1/22). Poll <http://doodle.com/poll/ys7ympfwci6demcq> Thanks everyone! -- Hilary Egan Astrophysical and Planetary Science Department University of Colorado Boulder _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

1 1

Issue #1159: Logarithmic Scaling for multiple 1d profiles (yt_analysis/yt)
by Miguel de Val-Borro 07 Jan '16

07 Jan '16

New issue 1159: Logarithmic Scaling for multiple 1d profiles https://bitbucket.org/yt_analysis/yt/issues/1159/logarithmic-scaling-for-mu… Miguel de Val-Borro: Axis scaling manipulation using the set_log() function does not work for multiple 1d profiles created using yt.create_profile ``` #!python #!/usr/bin/python import yt profiles = [] basename = "Sedov_3d/sedov_hdf5_chk" for i in [0, 1]: filename = "{0}_{1:04d}".format(basename, i) ds = yt.load(filename) sphere = ds.sphere([0., 0., 0.], (1, 'cm')) profile = yt.create_profile(sphere, "radius", ["radial_velocity_absolute"], logs = {"radius": False, "radial_velocity_absolute": False} ) profiles.append(profile) plot = yt.ProfilePlot.from_profiles(profiles) plot.set_log("radial_velocity_absolute", False) plot.save() ``` The traceback error obtained from this script is shown below: ``` #!python Traceback (most recent call last): File "./profiles_test.py", line 17, in <module> plot.set_log("radial_velocity_absolute", False) File "/home/mdevalbo/project/yt_analysis/yt/yt/visualization/plot_container.py", line 64, in newfunc rv = f(*args, **kwargs) File "/home/mdevalbo/project/yt_analysis/yt/yt/visualization/profile_plotter.py", line 468, in set_log field, = self.profiles[0].data_source._determine_fields([field]) File "/home/mdevalbo/project/yt_analysis/yt/yt/data_objects/data_containers.py", line 985, in _determine_fields finfo = self.ds._get_field_info("unknown", fname) ReferenceError: weakly-referenced object no longer exists ``` _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

1 0

97th percentile
by Sam Skillman 06 Jan '16

06 Jan '16

Well done, folks! http://www.nature.com/news/the-unsung-heroes-of-scientific-software-1.19100 _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

5 4

Issue #1158: data file not recognized IsolatedGalaxy (yt_analysis/yt)
by dan mckeown 06 Jan '16

06 Jan '16

New issue 1158: data file not recognized IsolatedGalaxy https://bitbucket.org/yt_analysis/yt/issues/1158/data-file-not-recognized-i… dan mckeown: Hello yt community, I have successfully reproduced the plot from tutorial 4 using data folder enzo_tiny_cosmology . this data file had no trouble being loaded into yt for plotting. However, IsolatedGalaxy is not recognized even though it is downloaded and unpacked. I went through the same process as enzo_tiny_cosmology but when I attempted to move the IsolatedGalaxy folder into my working directory I always receive the message "error no such file or directory" even though the file is clearly there. _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

1 0

Issue #1157: AttributeError when building docs with python 3 (yt_analysis/yt)
by Miguel de Val-Borro 05 Jan '16

05 Jan '16

New issue 1157: AttributeError when building docs with python 3 https://bitbucket.org/yt_analysis/yt/issues/1157/attributeerror-when-buildi… Miguel de Val-Borro: This is the error I get when I build the docs with `make html`: ``` #!python Exception occurred: File "/mnt/home/miguel/project/hydro/yt_analysis/yt/doc/extensions/notebook_sphinxext.py", line 61, in run dest_path_eval = string.replace(dest_path, '.ipynb', '_evaluated.ipynb') AttributeError: module 'string' has no attribute 'replace' The full traceback has been saved in /tmp/sphinx-err-shczw5mf.log, if you want to report the issue to the developers. Please also report this if it was a user error, so that a better error message can be provided next time. A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks! Makefile:50: recipe for target 'html' failed ``` _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

1 0

Issue #1156: trouble loading data (yt_analysis/yt)
by dan mckeown 05 Jan '16

05 Jan '16

New issue 1156: trouble loading data https://bitbucket.org/yt_analysis/yt/issues/1156/trouble-loading-data dan mckeown: I am unable to get data to load and receive the following message YTOutputNotIdentified: Supplied ('IsolatedGalaxy/galaxy0030/galaxy0030',) {}, but could not load! _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

1 0

Issue #1155: tips for data (yt_analysis/yt)
by dan mckeown 05 Jan '16

05 Jan '16

New issue 1155: tips for data https://bitbucket.org/yt_analysis/yt/issues/1155/tips-for-data dan mckeown: Hello all, I am new to yt and starting to work with sample datasets. I was wondering if any of you users have tips for where I could best store my data for use in yt. (in other words, what is the most fluid structure for data locations that you find works best. I will certainly experiment on my own but I was just curious for your insights. _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

1 0

Issue #1154: issue importing yt in canopy after install (yt_analysis/yt)
by dan mckeown 04 Jan '16

04 Jan '16

New issue 1154: issue importing yt in canopy after install https://bitbucket.org/yt_analysis/yt/issues/1154/issue-importing-yt-in-cano… dan mckeown: Hello, I am having difficulty getting yt to import into canopy Version: 1.5.2 after using pip to install yt. _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

1 0

Issue #1153: difficulty importing yt for Canopy Python 2.7.6 in OSX el Capitan (yt_analysis/yt)
by dan mckeown 04 Jan '16

04 Jan '16

New issue 1153: difficulty importing yt for Canopy Python 2.7.6 in OSX el Capitan https://bitbucket.org/yt_analysis/yt/issues/1153/difficulty-importing-yt-fo… dan mckeown: Hello all, I have been having a little difficulty getting yt to import. I installed it using a script that was written for osx el capitan called the get_yt.sh script Now, this script gives instructions for creating a PATH environment variable which isn't working for some reason. No error is given when I create the suggested variable which is: $ export PATH=/path/to/yt-conda:$PATH where /path/to is just /Users/myusername. However, when I try to import yt from canopy or at the command line it doesn't work. _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

1 0

Issue #1152: File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) (yt_analysis/yt)
by Anonymous 01 Jan '16

01 Jan '16

New issue 1152: File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) https://bitbucket.org/yt_analysis/yt/issues/1152/file-h5fpyx-line-70-in-h5p… Anonymous: I ran into this error some times (possibly randomly) using yt legacy version. File "start_SGE.py", line 28, in <module> File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 58, in get_snapshots File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 43, in get_redshift File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 218, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 165, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 57, in make_fid File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) Exception AttributeError: "'NoneType' object has no attribute 'close'" in ignored Please have a look. Thank you very much, Best, Dai _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

1 0