Hi, sorry to bother you guys, but I encountered some assertion errors when executing the py.test command after I install the LASIF_2.0 through pyenv(not anaconda).
I'm a rookie at Seismology. And I'm not sure what's wrong with my installation.
Here is some info about my env.
platform MacOS Monterey
Python 3.7.13
Python packages:
alabaster 0.7.12
appnope 0.1.3
attrs 22.2.0
Babel 2.11.0
backcall 0.2.0
Cartopy 0.20.3
certifi 2022.12.7
charset-normalizer 2.1.1
click 8.1.3
cmasher 1.6.3
colorama 0.4.6
colorspacious 1.1.2
cycler 0.11.0
debugpy 1.6.4
decorator 5.1.1
dill 0.3.6
docutils 0.17.1
e13tools 0.9.6
entrypoints 0.4
exceptiongroup 1.1.0
Flask 2.2.2
Flask-Cache 0.13.1
fonttools 4.38.0
geographiclib 2.0
geojson 2.5.0
greenlet 2.0.1
h5py 3.7.0
idna 3.4
imagesize 1.4.1
importlib-metadata 6.0.0
iniconfig 1.1.1
ipydatawidgets 4.3.2
ipykernel 6.16.2
ipython 7.34.0
ipywidgets 8.0.4
isodate 0.6.1
itsdangerous 2.1.2
jedi 0.18.2
Jinja2 3.1.2
joblib 1.2.0
jupyter_client 7.4.8
jupyter_core 4.12.0
jupyterlab-widgets 3.0.5
kiwisolver 1.4.4
lasif 0.0.1 /Users/yanghaote2/Documents/code/LASIF_2.0
lxml 4.9.2
MarkupSafe 2.1.1
matplotlib 3.5.3
matplotlib-inline 0.1.6
mock 5.0.0
nest-asyncio 1.5.6
networkx 2.6.3
nose 1.3.7
numexpr 2.8.4
numpy 1.21.6
obspy 1.3.1
packaging 22.0
pandas 1.3.5
parso 0.8.3
pathlib 1.0.1
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.4.0
pip 22.3.1
pluggy 1.0.0
progressbar 2.5
prompt-toolkit 3.0.36
prov 2.0.0
psutil 5.9.4
ptyprocess 0.7.0
pyasdf 0.7.5
Pygments 2.14.0
pyparsing 3.0.9
pyproj 3.2.1
PyQt5 5.15.7
PyQt5-Qt5 5.15.2
PyQt5-sip 12.11.0
pyqtgraph 0.12.4
pyshp 2.3.1
pytest 7.2.0
python-dateutil 2.8.2
pythreejs 2.4.1
pytz 2022.7
pyzmq 24.0.1
rdflib 6.2.0
requests 2.28.1
scipy 1.7.3
seaborn 0.12.2
setuptools 47.1.0
Shapely 1.8.5
six 1.16.0
snowballstemmer 2.2.0
Sphinx 5.3.0
sphinx-rtd-theme 1.1.1
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
SQLAlchemy 1.4.46
toml 0.10.2
tomli 2.0.1
tornado 6.2
tqdm 4.64.1
traitlets 5.8.0
traittypes 0.2.1
typing_extensions 4.4.0
urllib3 1.26.13
wcwidth 0.2.5
Werkzeug 2.2.2
widgetsnbextension 4.0.4
zipp 3.11.0
AssertionError:
$LASIF_2.0 git:(master) py.test 3.7.13
Exception ignored in: <function Popen.__del__ at 0x10e332dd0>
Traceback (most recent call last):
File "/Users/yanghaote2/.pyenv/versions/3.7.13/lib/python3.7/subprocess.py", line 883, in __del__
ResourceWarning, source=self)
ResourceWarning: subprocess 75182 is still running
Exception ignored in: <function Popen.__del__ at 0x10e332dd0>
Traceback (most recent call last):
File "/Users/yanghaote2/.pyenv/versions/3.7.13/lib/python3.7/subprocess.py", line 883, in __del__
ResourceWarning, source=self)
ResourceWarning: subprocess 75183 is still running
============================================ test session starts ============================================
platform darwin -- Python 3.7.13, pytest-7.2.0, pluggy-1.0.0
rootdir: /Users/yanghaote2/Documents/code/LASIF_2.0, configfile: pytest.ini
collected 207 items
lasif/rotations.py .... [ 1%]
lasif/utils.py ... [ 3%]
lasif/window_selection.py . [ 3%]
lasif/components/events.py .. [ 4%]
lasif/components/iterations.py . [ 5%]
lasif/function_templates/process_data.py s [ 5%]
lasif/function_templates/window_picking_function.py s [ 6%]
lasif/tests/test_adjoint_sources.py .... [ 8%]
lasif/tests/test_api.py ............................. [ 22%]
lasif/tests/test_cli_interface.py .................s...... [ 33%]
lasif/tests/test_code_formatting.py s [ 34%]
lasif/tests/test_domain.py .......................................................................... [ 70%]
....................... [ 81%]
lasif/tests/test_rotations.py .. [ 82%]
lasif/tests/test_utils.py . [ 82%]
lasif/tests/test_window_selection.py . [ 83%]
lasif/tests/components/test_adjoint_sources_component.py .FF. [ 85%]
lasif/tests/components/test_downloads_component.py . [ 85%]
lasif/tests/components/test_events_component.py ...... [ 88%]
lasif/tests/components/test_iterations_component.py .... [ 90%]
lasif/tests/components/test_project_component.py F... [ 92%]
lasif/tests/components/test_query_component.py ... [ 93%]
lasif/tests/components/test_validator_component.py .. [ 94%]
lasif/tests/components/test_visualization_component.py ssssssss [ 98%]
lasif/tests/data/example_project/FUNCTIONS/process_data.py s [ 99%]
lasif/tests/data/example_project/FUNCTIONS/window_picking_function.py s [ 99%]
lasif/tools/adjoint/utils.py . [100%]
================================================= FAILURES ==================================================
_________________________________________ test_get_misfit_for_event _________________________________________
comm = <lasif.components.communicator.Communicator object at 0x13831f9d0>
def test_get_misfit_for_event(comm):
events = lasif.api.list_events(comm, output=True)
iteration = lasif.api.list_iterations(comm, output=True)[0]
lasif.api.calculate_adjoint_sources_multiprocessing(comm, iteration, "A")
misfit = comm.adj_sources.get_misfit_for_event(
event=events[0], iteration=iteration
)
> np.testing.assert_almost_equal(misfit, 1.301670132868937)
E AssertionError:
E Arrays are not almost equal to 7 decimals
E ACTUAL: 1.3016674437258846
E DESIRED: 1.301670132868937
/Users/yanghaote2/Documents/code/LASIF_2.0/lasif/tests/components/test_adjoint_sources_component.py:57: AssertionError
------------------------------------------- Captured stdout call --------------------------------------------
===========================================================
Starting adjoint source calculation for event 1 of 2...
===========================================================
Writing adjoint sources...
1 Adjoint sources are in your file.
Finalizing adjoint sources...
===========================================================
Starting adjoint source calculation for event 2 of 2...
===========================================================
Writing adjoint sources...
1 Adjoint sources are in your file.
Finalizing adjoint sources...
------------------------------------------- Captured stderr call --------------------------------------------
100%|██████████| 4/4 [00:00<00:00, 43.20it/s]
100%|██████████| 4/4 [00:00<00:00, 17.19it/s]
______________________________________ test_calculate_adjoint_sources _______________________________________
comm = <lasif.components.communicator.Communicator object at 0x1383f58d0>
def test_calculate_adjoint_sources(comm):
events = lasif.api.list_events(comm, output=True)
file = (
comm.project.paths["adjoint_sources"]
/ "ITERATION_1"
/ events[0]
/ "auxiliary_adjoint.npy"
)
should_be = np.load(file)
lasif.api.calculate_adjoint_sources_multiprocessing(comm, "1", "A", weight_set="sw_1")
output = (
comm.project.paths["adjoint_sources"]
/ "ITERATION_1"
/ events[0]
/ "adjoint_source_auxiliary.h5"
)
with pyasdf.ASDFDataSet(output) as ds:
adj = ds.auxiliary_data.AdjointSources.HT_ALN.Channel__HHZ.data[()]
> np.testing.assert_array_almost_equal(should_be, adj)
E AssertionError:
E Arrays are not almost equal to 6 decimals
E
E (shapes (30002,), (30001,) mismatch)
E x: array([0., 0., 0., ..., 0., 0., 0.])
E y: array([0., 0., 0., ..., 0., 0., 0.])
/Users/yanghaote2/Documents/code/LASIF_2.0/lasif/tests/components/test_adjoint_sources_component.py:103: AssertionError
------------------------------------------- Captured stdout call --------------------------------------------
===========================================================
Starting adjoint source calculation for event 1 of 2...
===========================================================
Writing adjoint sources...
1 Adjoint sources are in your file.
Finalizing adjoint sources...
===========================================================
Starting adjoint source calculation for event 2 of 2...
===========================================================
Writing adjoint sources...
1 Adjoint sources are in your file.
Finalizing adjoint sources...
------------------------------------------- Captured stderr call --------------------------------------------
100%|██████████| 4/4 [00:00<00:00, 47.66it/s]
100%|██████████| 4/4 [00:00<00:00, 17.33it/s]
___________________________________ test_config_file_creation_and_parsing ___________________________________
tmpdir = local('/private/var/folders/_4/17zvg8wd3vbf51txxcqystc00000gq/T/pytest-of-yanghaote2/pytest-3/test_config_file_creation_and_0')
def test_config_file_creation_and_parsing(tmpdir):
"""
Tests the creation of a default config file and the reading of the file.
"""
# Create a new project.
pr = Project(
project_root_path=pathlib.Path(str(tmpdir)).absolute(),
init_project="TestProject",
)
del pr
# Init it once again.
pr = Project(pathlib.Path(str(tmpdir)).absolute())
# Assert the config file will test the creation of the default file and the
# reading.
assert pr.lasif_config["project_name"] == "TestProject"
assert pr.lasif_config["description"] == ""
assert pr.lasif_config["download_settings"]["channel_priorities"] == [
"BH?",
"LH[Z,N,E]",
"HH[Z,N,E]",
"EH[Z,N,E]",
"MH[Z,N,E]",
]
assert pr.lasif_config["download_settings"]["location_priorities"] == [
"",
"00",
"10",
"20",
"01",
"02",
]
assert pr.lasif_config["download_settings"]["networks"] == "None"
assert (
pr.lasif_config["download_settings"]["interstation_distance_in_m"]
== 1000.0
)
assert (
pr.lasif_config["download_settings"]["seconds_after_event"] == 3600.0
)
assert (
pr.lasif_config["download_settings"]["seconds_before_event"] == 300.0
)
> assert not pr.salvus_settings["attenuation"]
E assert not True
/Users/yanghaote2/Documents/code/LASIF_2.0/lasif/tests/components/test_project_component.py:80: AssertionError
========================================== short test summary info ==========================================
FAILED lasif/tests/components/test_adjoint_sources_component.py::test_get_misfit_for_event - AssertionError:
FAILED lasif/tests/components/test_adjoint_sources_component.py::test_calculate_adjoint_sources - AssertionError:
FAILED lasif/tests/components/test_project_component.py::test_config_file_creation_and_parsing - assert not True
================================ 3 failed, 190 passed, 14 skipped in 24.60s =================================
Hi, sorry to bother you guys, but I encountered some assertion errors when executing the py.test command after I install the LASIF_2.0 through pyenv(not anaconda).
I'm a rookie at Seismology. And I'm not sure what's wrong with my installation.
Here is some info about my env.
platform MacOS Monterey
Python 3.7.13
Python packages:
alabaster 0.7.12
appnope 0.1.3
attrs 22.2.0
Babel 2.11.0
backcall 0.2.0
Cartopy 0.20.3
certifi 2022.12.7
charset-normalizer 2.1.1
click 8.1.3
cmasher 1.6.3
colorama 0.4.6
colorspacious 1.1.2
cycler 0.11.0
debugpy 1.6.4
decorator 5.1.1
dill 0.3.6
docutils 0.17.1
e13tools 0.9.6
entrypoints 0.4
exceptiongroup 1.1.0
Flask 2.2.2
Flask-Cache 0.13.1
fonttools 4.38.0
geographiclib 2.0
geojson 2.5.0
greenlet 2.0.1
h5py 3.7.0
idna 3.4
imagesize 1.4.1
importlib-metadata 6.0.0
iniconfig 1.1.1
ipydatawidgets 4.3.2
ipykernel 6.16.2
ipython 7.34.0
ipywidgets 8.0.4
isodate 0.6.1
itsdangerous 2.1.2
jedi 0.18.2
Jinja2 3.1.2
joblib 1.2.0
jupyter_client 7.4.8
jupyter_core 4.12.0
jupyterlab-widgets 3.0.5
kiwisolver 1.4.4
lasif 0.0.1 /Users/yanghaote2/Documents/code/LASIF_2.0
lxml 4.9.2
MarkupSafe 2.1.1
matplotlib 3.5.3
matplotlib-inline 0.1.6
mock 5.0.0
nest-asyncio 1.5.6
networkx 2.6.3
nose 1.3.7
numexpr 2.8.4
numpy 1.21.6
obspy 1.3.1
packaging 22.0
pandas 1.3.5
parso 0.8.3
pathlib 1.0.1
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.4.0
pip 22.3.1
pluggy 1.0.0
progressbar 2.5
prompt-toolkit 3.0.36
prov 2.0.0
psutil 5.9.4
ptyprocess 0.7.0
pyasdf 0.7.5
Pygments 2.14.0
pyparsing 3.0.9
pyproj 3.2.1
PyQt5 5.15.7
PyQt5-Qt5 5.15.2
PyQt5-sip 12.11.0
pyqtgraph 0.12.4
pyshp 2.3.1
pytest 7.2.0
python-dateutil 2.8.2
pythreejs 2.4.1
pytz 2022.7
pyzmq 24.0.1
rdflib 6.2.0
requests 2.28.1
scipy 1.7.3
seaborn 0.12.2
setuptools 47.1.0
Shapely 1.8.5
six 1.16.0
snowballstemmer 2.2.0
Sphinx 5.3.0
sphinx-rtd-theme 1.1.1
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
SQLAlchemy 1.4.46
toml 0.10.2
tomli 2.0.1
tornado 6.2
tqdm 4.64.1
traitlets 5.8.0
traittypes 0.2.1
typing_extensions 4.4.0
urllib3 1.26.13
wcwidth 0.2.5
Werkzeug 2.2.2
widgetsnbextension 4.0.4
zipp 3.11.0
AssertionError: