Merge branch 'main' into trans_update

exorad · Oct 27, 2023 · 5e148aa · 5e148aa
2 parents 09b6450 + d462282
commit 5e148aa
Show file tree

Hide file tree

Showing 6 changed files with 76 additions and 67 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -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
@@ -34,18 +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 petitRADTRANS
-        shell: bash -l {0}
-        run: |
-          python -m pip install petitRADTRANS==2.4.9
-          python -m pip install prt-phasecurve
       - 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
@@ -77,14 +75,10 @@ jobs:
           auto-update-conda: false
           environment-file: ci/environment-xarraymaster.yml
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-      - name: Set up petitRADTRANS
-        shell: bash -l {0}
-        run: |
-          python -m pip install petitRADTRANS==2.4.9
-          python -m pip install prt-phasecurve
       - 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

diff --git a/ci/environment-3.10.yml b/ci/environment-3.10.yml
@@ -6,13 +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
diff --git a/ci/environment-3.8.yml b/ci/environment-3.8.yml
diff --git a/ci/environment-3.9.yml b/ci/environment-3.9.yml
@@ -6,13 +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
+  - pandas
+  - numba
+  - corner
+  - tqdm
+  - h5py
+  - pre-commit 
+  - pymultinest
+  - seaborn
+  - pip
diff --git a/ci/environment-xarraymaster.yml b/ci/environment-xarraymaster.yml
@@ -6,13 +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
diff --git a/gcm_toolkit/tests/test_interface.py b/gcm_toolkit/tests/test_interface.py
@@ -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)
 
     phases = np.linspace(0, 1, 50)
     interface = tools.get_prt_interface(pRT)
@@ -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)
@@ -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
@@ -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")