Problem about buliding about turgon

[yungyuc]

@yufang-hu could you post the error log here?

and then

[yungyuc]

It is not a good way to post image for textual log. Any further processing requires typing by the image. I cannot quote and respond where there is an issue. Please use mark-down format to post the original textual message next time.

None of xtl, xsimd, xtensor, and xtensor-python is found. Where do you install those headers to?

I got your advice. Thanks a lot.
I install those packages using conda ,and they are all intstalled to the path /Users/huyufang/anaconda3/envs/turgon/include.
Following is the error log.

-- BUILD_GTESTS: ON
-- HIDE_SYMBOL: OFF
-- DEBUG_SYMBOL: ON
-- not use clang-tidy
-- pybind11_INCLUDE_DIRS: /Users/huyufang/anaconda3/envs/turgon/include/python3.7m;/Users/huyufang/anaconda3/envs/turgon/include/python3.7m
-- NUMPY_INCLUDE_DIR: /Users/huyufang/anaconda3/envs/turgon/lib/python3.7/site-packages/numpy/core/include
-- xtl_INCLUDE_DIR: not found
-- xsimd_INCLUDE_DIR: not found
-- xtensor_INCLUDE_DIR: not found
-- xtensor-python_INCLUDE_DIR: not found
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/huyufang/Desktop/turgon/spacetime/gtests/googletest-download
[100%] Built target googletest
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/huyufang/Desktop/turgon/spacetime

[yungyuc]

Thanks for updating the textual log. Have you tried to give cmake the path hint, e.g., https://github.com/yungyuc/turgon/blob/master/spacetime/cmake/Findxtl.cmake#L9 ? It can be provided through cmake command line like cmake -Dxtl_ROOT=/where/you/install/xtl.

It seems that I have successfully build it.

$ make
[ 25%] Built target _libst
[ 50%] Built target gtest
[ 75%] Built target gtest_main
[100%] Built target libst_gtests

then I run libst_gtests

$ ./libst_gtests
[==========] Running 3 tests from 2 test cases.
[----------] Global test environment set-up.
[----------] 2 tests from CopyTest
[ RUN      ] CopyTest.Grid
[       OK ] CopyTest.Grid (0 ms)
[ RUN      ] CopyTest.Solver
[       OK ] CopyTest.Solver (0 ms)
[----------] 2 tests from CopyTest (0 ms total)

[----------] 1 test from SolverTest
[ RUN      ] SolverTest.Celm
[       OK ] SolverTest.Celm (0 ms)
[----------] 1 test from SolverTest (0 ms total)

[----------] Global test environment tear-down
[==========] 3 tests from 2 test cases ran. (0 ms total)
[  PASSED  ] 3 tests.

I'm not sure whether I do the wrong step.
Can I ask the proper steps to build this project?

[yungyuc]

In the Makefile in spacetime/, there are 2 targets for testing: gtest and pytest (test depends on both). Could you please run both and see the results? If both pass then you are doing it correctly.

After that we should arrange a lecture for the premise of the CESE method for you to start hacking.

So is it means that the Makefile in spacetime/ will create 2 target call gtest and pytest and I will see two executable file and I should run them respectively?
But after I make I just see one executable file called libst_gtests in spacetime/gtests/and it run as my previously paste.
Have I done gtest part?

[yungyuc]

The Makefile has two targets. But it is not accurate to say it creates two targets. And, although gtest has a corresponding executable, pytest does not. pytest uses a Python extension module, which is a shared library.

You did the gtest part. But you had the pytest missing.

I see _libst.cpython-37m-darwin.so in spacename/. I think it is the python extension module I need if I want to run the five python files in tests/ because they all import libst.
When I run pytest it come out the error:

ImportError while importing test module '/Users/huyufang/Desktop/turgon/spacetime/tests/test_celm_selm.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_celm_selm.py:8: in <module>
    import libst
E   ModuleNotFoundError: No module named 'libst'

Then I move _libst.cpython-37m-darwin.so to tests/ but it still doesn't work.
I think it might be problem in the filename so I move out the _ at the beginning of _libst.cpython-37m-darwin.so although I don't know if it is appropriate to do that and then try to run it again, it come out another error:

ImportError while importing test module '/Users/huyufang/Desktop/turgon/spacetime/tests/test_celm_selm.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_celm_selm.py:8: in <module>
    import libst
E   ImportError: dynamic module does not define module export function (PyInit_libst)

How can I solve this problem?

[yungyuc]

Please print your exact commands and output for running pytest. If you literally executed pytest, you should get that error message, because of the way Python3 discovers modules. The fix is easy.

Here is the commands and output for running pytest on test_celm_selm.py
Now _libst.cpython-37m-darwin.so is in spacetime/

$pytest tests/test_celm_selm.py

============================= test session starts ==============================
platform darwin -- Python 3.7.5, pytest-5.2.4, py-1.8.0, pluggy-0.13.0
rootdir: /Users/huyufang/Desktop/turgon/spacetime
collected 0 items / 1 errors

==================================== ERRORS ====================================
___________________ ERROR collecting tests/test_celm_selm.py ___________________
ImportError while importing test module '/Users/huyufang/Desktop/turgon/spacetime/tests/test_celm_selm.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_celm_selm.py:8: in <module>
    import libst
E   ModuleNotFoundError: No module named 'libst'
=============================== warnings summary ===============================
tests/test_celm_selm.py:101
  /Users/huyufang/Desktop/turgon/spacetime/tests/test_celm_selm.py:101: DeprecationWarning: invalid escape sequence \(
    "Celm\(xindex=2\)::move_at\(offset=-1\): xindex = 1 "

tests/test_celm_selm.py:102
  /Users/huyufang/Desktop/turgon/spacetime/tests/test_celm_selm.py:102: DeprecationWarning: invalid escape sequence \[
    "outside the interval \[2, 23\)",

tests/test_celm_selm.py:109
  /Users/huyufang/Desktop/turgon/spacetime/tests/test_celm_selm.py:109: DeprecationWarning: invalid escape sequence \(
    "Celm\(xindex=22\)::move_at\(offset=1\): xindex = 23 "

tests/test_celm_selm.py:110
  /Users/huyufang/Desktop/turgon/spacetime/tests/test_celm_selm.py:110: DeprecationWarning: invalid escape sequence \[
    "outside the interval \[2, 23\)",

tests/test_celm_selm.py:244
  /Users/huyufang/Desktop/turgon/spacetime/tests/test_celm_selm.py:244: DeprecationWarning: invalid escape sequence \(
    "Selm\(xindex=1\)::move_at\(offset=-1\): xindex = 0 "

tests/test_celm_selm.py:245
  /Users/huyufang/Desktop/turgon/spacetime/tests/test_celm_selm.py:245: DeprecationWarning: invalid escape sequence \[
    "outside the interval \[1, 24\)",

tests/test_celm_selm.py:252
  /Users/huyufang/Desktop/turgon/spacetime/tests/test_celm_selm.py:252: DeprecationWarning: invalid escape sequence \(
    "Selm\(xindex=23\)::move_at\(offset=1\): xindex = 24 "

tests/test_celm_selm.py:253
  /Users/huyufang/Desktop/turgon/spacetime/tests/test_celm_selm.py:253: DeprecationWarning: invalid escape sequence \[
    "outside the interval \[1, 24\)",

-- Docs: https://docs.pytest.org/en/latest/warnings.html
!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!
========================= 8 warnings, 1 error in 1.14s =========================

[yungyuc]

You should type

make pytest

This is the output on my machine:

$ make pytest
env PYTHONPATH=/Users/yungyuc/hack/code/turgon/spacetime /Users/yungyuc/hack/usr/opt37_190418/bin/pytest  tests/
==================================================================== test session starts =====================================================================
platform darwin -- Python 3.7.4+, pytest-4.4.1, py-1.8.0, pluggy-0.9.0
rootdir: /Users/yungyuc/hack/code/turgon/spacetime
collected 51 items

tests/test_celm_selm.py .............................                                                                                                  [ 56%]
tests/test_grid.py ....                                                                                                                                [ 64%]
tests/test_inviscid_burgers.py ..                                                                                                                      [ 68%]
tests/test_linear_scalar.py ......                                                                                                                     [ 80%]
tests/test_solution.py ..........                                                                                                                      [100%]

================================================================= 51 passed in 0.36 seconds ==================================================================

The trick is, Python 3 doesn't automatically search the current directory for modules if . isn't in PYTHONPATH.

I see the target pytest in the original Makefile in spacetime/.
After I build it on my machine, the Makefile it create will replace the original one, and there is no target pytest in it (but target gtest is in). I don't know why.
But I think I can deal with this problem later.
I add ~/turgon/spacetime/ to PATHONPATH and successfully pass the tests!

$ pytest tests
============================= test session starts ==============================
platform darwin -- Python 3.7.5, pytest-5.2.4, py-1.8.0, pluggy-0.13.0
rootdir: /Users/huyufang/Desktop/turgon/spacetime
collected 51 items

tests/test_celm_selm.py .............................                    [ 56%]
tests/test_grid.py ....                                                  [ 64%]
tests/test_inviscid_burgers.py ..                                        [ 68%]
tests/test_linear_scalar.py ......                                       [ 80%]
tests/test_solution.py ..........                                        [100%]

============================== 51 passed in 0.65s ==============================