Hi Oliver,

With your support, (I believe) I managed to clean up Typhon with my
Anaconda. Test run of Typhon looks normal at the beginning,

>>> import typhon
>>> typhon.test()
===================================== test session starts
======================================
platform darwin -- Python 3.6.3, pytest-3.2.1, py-1.4.34, pluggy-0.4.0
rootdir: /Users/reno/Downloads/typhon-master, inifile:
collected 197 items
:
blah blah...
:
E           Exception: ARTS executable not found at:
/Users/reno/OneDrive/Models/arts-2.2.64/build/build/Debug/src/arts

typhon/arts/common.py:62: Exception
======================= 1 failed, 182 passed, 14 skipped in 1.64 seconds
=======================
1

Obviously, Typhon itself is settled well, not with proper link with my Arts
v2.2.64 missing "libarts_api.so". I guess it's Arts issue from now on
rather than Typhon.

Thanks again your thorough tip.

Reno

P.S. In my MacBook, Arts executables are located in
../arts-2.2.64/build/build/Debug/
without src/ directory there.

reno@Renos-MacBook:~/OneDrive/Models/arts-2.2.64/build/build/Debug$ ls
arts*                  outfile.xml            test_gridded_fields*
 test_quantum*
libartscore.a          outfile.xml.bin        test_integration*
test_readpp*
libmatpack.a           quantum.xml            test_interpolation*
test_sorting*
libmethods.a           sdata1.xml             test_legendre*
 test_sparse*
libmicrohttpd.a        sdata2.xml             test_linalg*
 test_tensor*
make_auto_md_cc*       test_binaryio*         test_matpack*
test_xml*
make_auto_md_h*        test_cia*              test_omp*
make_auto_workspace_h* test_complex*          test_poly*

I wonder if it's just me not having ../arts-2.2.64/build/build/Debug/src/
after compilation.


On 13 March 2018 at 16:26, Oliver Lemke <oliver.le...@uni-hamburg.de> wrote:

> Hi Reno,
>
> The error messages you get there don't make sense to me. It finds the api
> in 
> '/Users/reno/OneDrive/Models/arts-2.2.64/build/build/Debug/src/libarts_api.so',
> so the ARTS_BUILD_PATH settings seem to be okay. No clue why directly
> afterwards it fails. I have the suspicion that something got mixed up in
> your typhon installation. Also, before rebuilding the documentation after
> updating typhon run 'make clean'. Otherwise sphinx might get confused with
> leftover files from an older build.
>
> Is this the current master branch version of typhon or did you download
> the latest stable release? For the arts-api it is best to use the latest
> development version of typhon since it is a very new and experimental
> feature.
>
> Try to make a clean installation of typhon with the current github master
> branch.
>
> 1) Checkout out the latest version (make sure there is no typhon directory
> in the current directory):
>
> git clone https://github.com/atmtools/typhon.git
>
> 2) Then install it using pip as a development version. I strongly advise
> against installing python packages with 'python setup.py install' into your
> system path. There is no clean way of getting rid of them again despite
> removing the files manually. Also, on every update of the source code, you
> need to reinstall the package. It is much better to use pip to install it
> as a development version. This way only a link to your source directory is
> created in the python site-packages directory and you can be sure that
> you're always using the current checked out version of typhon. The --user
> option is also a good way to not mess with your system installation. It
> installs the package into your home directory.
>
> In the typhon directory run:
>
> pip install --user --no-deps -e .
>
> Then, outside the typhon directory run:
>
> python3 -c "import typhon;print(typhon.__path__)"
>
> This should output the path to the directory where you cloned the typhon
> sources.
>
> Hope this helps.
>
> Cheers,
> Oliver
>
> P.S.: The best way to keep a clean Python installation is to use the
> Anaconda Platform. It gives you a way to install a complete Python
> environment in a standalone directory, provides a very good package manager
> and comes with hundreds of prebuilt packages. The command-line installer is
> very easy to use. And the conda package manager makes it easy to keep your
> python installation up to date. Maybe give it a try:
> https://www.anaconda.com/download/
>
>
> > On 12 Mar 2018, at 16:05, Reno Choi <renoc...@gmail.com> wrote:
> >
> > Hello,
> >
> > While pretty new to both arts and typhon, let alone python, and I'm
> trying to make Typhon working with my Arts.
> >
> > Installing Typhon through "python setup.py install" (seems successful)
> from Github repository, following error message appears for building
> documents,
> >
> > $ cd doc
> > $ make html
> > sphinx-build -b html -d _build/doctrees   . _build/html
> > Running Sphinx v1.6.3
> > loading pickled environment... not yet created
> > [autosummary] generating autosummary for: developer.rst, faq.rst,
> faq/atm_fields_compact_construction.rst, faq/import_without_x_server.rst,
> index.rst, modules.rst, tutorials.rst, tutorials/collocations.rst,
> tutorials/dataset.rst, tutorials/handlers.rst, ..., typhon.math.rst,
> typhon.oem.rst, typhon.physics.rst, typhon.physics.units.rst,
> typhon.plots.cm.rst, typhon.plots.rst, typhon.spareice.rst,
> typhon.spectroscopy.rst, typhon.trees.rst, typhon.utils.rst
> > Failed to import 'typhon.spareice.handlers.cloudsat': no module named
> typhon.spareice.handlers.cloudsat
> > Failed to import 'typhon.datasets': no module named typhon.datasets
> > Failed to import 'typhon.datasets.dataset': no module named
> typhon.datasets.dataset
> > Failed to import 'typhon.datasets.model': no module named
> typhon.datasets.model
> > Failed to import 'typhon.datasets.tovs': no module named
> typhon.datasets.tovs
> > Loading ARTS API from: /Users/reno/OneDrive/Models/
> arts-2.2.64/build/build/Debug/src/libarts_api.so
> >
> > Exception occurred:
> >   File 
> > "/Users/reno/anaconda3/lib/python3.6/site-packages/typhon/arts/workspace/api.py",
> line 52, in <module>
> >     + "Did you install it?")
> > OSError: Could not find ARTS API in your ARTS build path. Did you
> install it?
> > The full traceback has been saved in /var/folders/f1/
> 2flhkrrj7f739kk364dqx1l80000gn/T/sphinx-err-25q9_o1s.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!
> > make: *** [html] Error 1
> >
> > There are two issues according to the message above,
> >
> > 1. It searches "libarts_api.so" in my ARTS_BUILD_PATH (from
> "../typhon/arts/workspace/api.py", which presumably requires more recent
> version of Arts;
> > 2. In "api.py" (line 52), only searches ARTS_BUILD_PATH (e.g.
> ../arts/build/) + src/ while ARTS_BUILD_PATH for mac osx is in
> ../arts/build/build/Debug, which I may be able to modify.
> >
> > Reno
>
>


-- 
Dr. Reno K.-Y. Choi

T.     (+44 0)1225 719 478
T.     (+44 0)20 8133 9066
T.     (+82 0)70 7893 2756
M.     (+44 0)7909 612 846
M.     (+82 0)10 4570 9066
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