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Fixes to python test environment #58

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merged 10 commits into from
Oct 27, 2023
Merged

Fixes to python test environment #58

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dd9bfcb
next try
AaronDavidSchneider Oct 24, 2023
6ab7bbe
next try
AaronDavidSchneider Oct 25, 2023
2e47c33
update to mambaforge
AaronDavidSchneider Oct 25, 2023
1094d73
extra pip install
AaronDavidSchneider Oct 25, 2023
f51d351
upgrade only if needed
AaronDavidSchneider Oct 25, 2023
47c5c99
remove hdf5 again
AaronDavidSchneider Oct 25, 2023
b34fced
go all in with conda
AaronDavidSchneider Oct 25, 2023
5fde57c
not all available
AaronDavidSchneider Oct 25, 2023
d356923
less requirements
AaronDavidSchneider Oct 26, 2023
3f8210f
use Z instead of Z_l
AaronDavidSchneider Oct 26, 2023
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8 changes: 6 additions & 2 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ jobs:
fail-fast: false
matrix:
os: [ "ubuntu-latest" ]
python-version: [ "3.8", "3.9", "3.10" ]
python-version: [ "3.9", "3.10" ]
steps:
- uses: actions/checkout@v2
- name: Cache conda
Expand All @@ -34,13 +34,16 @@ jobs:
- uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: test_env # Defined in ci/environment*.yml
auto-update-conda: false
miniforge-variant: Mambaforge
miniforge-version: latest
use-mamba: true
python-version: ${{ matrix.python-version }}
environment-file: ci/environment-${{ matrix.python-version }}.yml
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
- name: Set up conda environment
shell: bash -l {0}
run: |
python -m pip install --no-deps molmass miepython git+https://github.com/MITgcm/xmitgcm.git petitRADTRANS==2.4.9 prt-phasecurve
python -m pip install -e .
conda list
- name: Run Tests
Expand Down Expand Up @@ -75,6 +78,7 @@ jobs:
- name: Set up conda environment
shell: bash -l {0}
run: |
python -m pip install --no-deps molmass miepython git+https://github.com/MITgcm/xmitgcm.git petitRADTRANS==2.4.9 prt-phasecurve
python -m pip install -e .
conda list
- name: Run Tests
Expand Down
23 changes: 14 additions & 9 deletions ci/environment-3.10.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,15 +6,20 @@ dependencies:
- cubedsphere
- pytest
- codecov
- xmitgcm
- pytest-cov
- xarray
- h5py
- numpy=1.21.5
- setuptools=61.2.0
- matplotlib
- astropy
- numpy
- scipy
- setuptools
- netcdf4
- pandas
- numba
- corner
- tqdm
- h5py
- pre-commit
- pymultinest
- seaborn
- pip
- pip:
- git+https://github.com/MITgcm/xmitgcm.git
- miepython
- petitRADTRANS==2.4.9
- prt-phasecurve
20 changes: 0 additions & 20 deletions ci/environment-3.8.yml
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This file was deleted.

26 changes: 15 additions & 11 deletions ci/environment-3.9.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,16 +6,20 @@ dependencies:
- cubedsphere
- pytest
- codecov
- xmitgcm
- pytest-cov
- xarray
- h5py
- numpy=1.21.5
- setuptools=61.2.0
- matplotlib
- astropy
- numpy
- scipy
- setuptools
- netcdf4
- pip
- pip:
- git+https://github.com/MITgcm/xmitgcm.git
- miepython
- petitRADTRANS==2.4.9
- prt-phasecurve

- pandas
- numba
- corner
- tqdm
- h5py
- pre-commit
- pymultinest
- seaborn
- pip
21 changes: 14 additions & 7 deletions ci/environment-xarraymaster.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,15 +6,22 @@ dependencies:
- cubedsphere
- pytest
- codecov
- xmitgcm
- pytest-cov
- h5py
- numpy=1.21.5
- setuptools=61.2.0
- matplotlib
- astropy
- numpy
- scipy
- setuptools
- netcdf4
- pandas
- numba
- corner
- tqdm
- h5py
- pre-commit
- pymultinest
- seaborn
- pip
- pip:
- git+https://github.com/MITgcm/xmitgcm.git
- git+https://github.com/pydata/xarray.git
- miepython
- petitRADTRANS==2.4.9
- prt-phasecurve
44 changes: 27 additions & 17 deletions gcm_toolkit/tests/test_interface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,15 +43,21 @@ def test_prt_interface(petitradtrans_testdata, all_raw_testdata):
)

# add cloud properties
dsi_clouds = tools.get_models('0')
tmp = np.ones((len(dsi_clouds['time']), len(dsi_clouds['lat']),
len(dsi_clouds['lon']), len(dsi_clouds['Z_l'])))
dsi_clouds['ClAb'] = (('time', 'lat', 'lon', 'Z_l'), tmp*1e-5)
dsi_clouds['ClDs'] = (('time', 'lat', 'lon', 'Z_l'), tmp*1e2)
dsi_clouds['ClDr'] = (('time', 'lat', 'lon', 'Z_l'), tmp*1e3)
dsi_clouds['ClVf_Test1[s]'] = (('time', 'lat', 'lon', 'Z_l'), tmp*0.5)
dsi_clouds['ClVf_Test2[s]'] = (('time', 'lat', 'lon', 'Z_l'), tmp*0.5)
tools._replace_model('0', dsi_clouds)
dsi_clouds = tools.get_models("0")
tmp = np.ones(
(
len(dsi_clouds["time"]),
len(dsi_clouds["lat"]),
len(dsi_clouds["lon"]),
len(dsi_clouds["Z"]),
)
)
dsi_clouds["ClAb"] = (("time", "lat", "lon", "Z"), tmp * 1e-5)
dsi_clouds["ClDs"] = (("time", "lat", "lon", "Z"), tmp * 1e2)
dsi_clouds["ClDr"] = (("time", "lat", "lon", "Z"), tmp * 1e3)
dsi_clouds["ClVf_Test1[s]"] = (("time", "lat", "lon", "Z"), tmp * 0.5)
dsi_clouds["ClVf_Test2[s]"] = (("time", "lat", "lon", "Z"), tmp * 0.5)
tools._replace_model("0", dsi_clouds)
Comment on lines -46 to +60
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@Kiefersv, could you comment on these changes I had to make? I think the Z_l here is strange?!

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@Kiefersv Kiefersv Oct 27, 2023 •
edited
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I double checked and you are indeed right that it should be Z. No idea why it worked before with Z_l. Did this cause the problems?

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No. Its likely problems related to xarray's master branch. But this looked odd to me.


phases = np.linspace(0, 1, 50)
interface = tools.get_prt_interface(pRT)
Expand Down Expand Up @@ -113,9 +119,11 @@ def test_prt_interface(petitradtrans_testdata, all_raw_testdata):
)

# test transit calculation set up
interface.set_data(time=expected["times"][-1], terminator_avg=True, lon_resolution=60)
assert (interface.dsi['lon'].values == [-90, 90]).all()
assert interface.dsi['lat'].values == [0]
interface.set_data(
time=expected["times"][-1], terminator_avg=True, lon_resolution=60
)
assert (interface.dsi["lon"].values == [-90, 90]).all()
assert interface.dsi["lat"].values == [0]

# test transit calculation
interface.chem_from_poorman("T", co_ratio=0.55, feh_ratio=0.0)
Expand All @@ -129,7 +137,9 @@ def test_prt_interface(petitradtrans_testdata, all_raw_testdata):

# test transit calculation
interface.chem_from_poorman("T", co_ratio=0.55, feh_ratio=0.0)
wave, spectra = interface.calc_transit_spectrum(mmw=2.33, clouds=True, use_bruggemann=True)
wave, spectra = interface.calc_transit_spectrum(
mmw=2.33, clouds=True, use_bruggemann=True
)
assert sum(spectra) == 45237213620.53514

# Test if Pa works
Expand Down Expand Up @@ -253,7 +263,7 @@ def test_PAC_interface(all_nc_testdata):
pac2d.set_data(time=expected["times"][-1])

with pytest.raises(OSError):
pac1d.write_inputfile('non/existent/path')
pac2d.write_inputfile('non/existent/path')
pac2d.generate_lptfile('non/existent/path')
pac2d.generate_aptfiles('non/existent/path')
pac1d.write_inputfile("non/existent/path")
pac2d.write_inputfile("non/existent/path")
pac2d.generate_lptfile("non/existent/path")
pac2d.generate_aptfiles("non/existent/path")
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