Re: [typhon] Typhon setup issue

[Oliver Lemke]

Hi Reno,

Are you using cmake to generate an Xcode project and compile ARTS inside Xcode? 
In that case yes, Xcode does put compiled files directly inside the 
Debug/Release directory with no additional src subdirectory. According to your 
previous log file, you had a libarts_api.so in build/build/Debug/src. Can't see 
it in your current ls output below. Did you copy it there and removed it now? 

I strongly recommend to not compile ARTS with Xcode and the Apple clang 
compiler except for ARTS development. The main reason being that the clang 
C/C++ compiler provided by Apple/Xcode does not support OpenMP. This will make 
your ARTS runs a lot slower. Look into a package manager such as MacPorts that 
provides compilers such as GCC or Clang with OpenMP. MacPorts also provides 
convenient access to up to date versions of cmake, git, subversion etc.

If you have MacPorts, you can then configure ARTS to use its GCC compiler like 
this:

cmake -DCMAKE_C_COMPILER=gcc-mp-7 -DCMAKE_CXX_COMPILER=g++-mp-7 -DCMAKE_C_API=1 
..

Apart from that, I agree that typhon should search in ARTS_BUILD_PATH/ and 
ARTS_BUILD_PATH/src for the library. This will be added in an upcoming patch.

Cheers,
Oliver


> On 13 Mar 2018, at 13:48, Reno Choi  wrote:
> 
> 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.xmltest_gridded_fields*   
> test_quantum*
> libartscore.a  outfile.xml.bintest_integration*  
> test_readpp*
> libmatpack.a   quantum.xmltest_interpolation*
> test_sorting*
> libmethods.a   sdata1.xml test_legendre* 
> test_sparse*
> libmicrohttpd.asdata2.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.

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Re: [typhon] Typhon setup issue

[Reno Choi]

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.xmltest_gridded_fields*
 test_quantum*
libartscore.a  outfile.xml.bintest_integration*
test_readpp*
libmatpack.a   quantum.xmltest_interpolation*
test_sorting*
libmethods.a   sdata1.xml test_legendre*
 test_sparse*
libmicrohttpd.asdata2.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  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  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, tutoria

Re: [typhon] Typhon setup issue

[Oliver Lemke]

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  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 
> + "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/f1/2flhkrrj7f739kk364dqx1l8gn/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 
> . 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.