Merge pull request #89 from jkrasting/thermocline-analysis

raphaeldussin · web-flow · commit 16e62b841f1e · 2022-03-16T08:19:32.000-04:00
diff --git a/ci/environment-py38esmf800.yml b/ci/environment-py38esmf800.yml
@@ -9,6 +9,7 @@ dependencies:
   - intake-xarray
   - esmf=8.0.0
   - esmpy=8.0.0
+  - gsw
   - matplotlib
   - netcdf4
   - numpy
@@ -17,6 +18,7 @@ dependencies:
   - pip
   - pip:
     - git+https://github.com/jkrasting/cmip_basins.git
+    - git+https://github.com/jkrasting/xcompare.git
     - git+https://github.com/raphaeldussin/static_downsampler.git
     - git+https://github.com/raphaeldussin/xoverturning
   - pyshp
diff --git a/ci/environment.yml b/ci/environment.yml
@@ -8,6 +8,7 @@ dependencies:
   - cartopy
   - cmocean
   - dask
+  - gsw
   - intake-xarray
   - esmf=8.0.0
   - esmpy=8.0.0
@@ -31,5 +32,6 @@ dependencies:
     - git+https://github.com/jkrasting/cmip_basins.git
     - git+https://github.com/raphaeldussin/static_downsampler.git
     - git+https://github.com/raphaeldussin/xoverturning
+    - git+https://github.com/jkrasting/xcompare.git
     - git+https://github.com/jkrasting/xwavelet.git
     - git+https://github.com/jkrasting/xcompare.git
diff --git a/ci/environment_test.yml b/ci/environment_test.yml
@@ -8,6 +8,7 @@ dependencies:
   - cartopy
   - cmocean
   - dask
+  - gsw
   - intake-xarray
   - esmf=8.0.0
   - esmpy=8.0.0
@@ -31,5 +32,6 @@ dependencies:
     - git+https://github.com/jkrasting/cmip_basins.git
     - git+https://github.com/raphaeldussin/static_downsampler.git
     - git+https://github.com/raphaeldussin/xoverturning
+    - git+https://github.com/jkrasting/xcompare.git
     - git+https://github.com/jkrasting/xwavelet.git
     - git+https://github.com/jkrasting/xcompare.git
diff --git a/ci/requirements.txt b/ci/requirements.txt
@@ -1,6 +1,7 @@
 black
 cmocean
 dask
+gsw
 intake-xarray
 matplotlib
 netcdf4
@@ -14,4 +15,5 @@ scipy
 shapely
 six
 xarray
+xcompare
 xesmf
diff --git a/data/RoemmichGilson_ARGO_based_climatology.ipynb b/data/RoemmichGilson_ARGO_based_climatology.ipynb
@@ -103,7 +103,7 @@
    "outputs": [],
    "source": [
     "for f in glob(\"*.gz\"):\n",
-    "    sp.check_call(f\"gunzip --keep --force {f}\", shell=True)"
+    "    sp.check_call(f\"gunzip --force {f}\", shell=True)"
    ]
   },
   {
diff --git a/om4labs/catalogs/obs_catalog_gfdl.yml b/om4labs/catalogs/obs_catalog_gfdl.yml
@@ -3,6 +3,39 @@ plugins:
     - module: intake_xarray
 sources:
 
+  Argo_Climatology:
+    description: "Gridded in-situ temperature and salinity derived from Argo profiles"
+    driver: netcdf
+    args:
+      urlpath: '/archive/Raphael.Dussin/datasets/Roemmich_Gilson_ARGO_TS_Clim/RG_ArgoClim_Extended_200401-202112_annual_clim_ptemp+salt.nc'
+      chunks: {'time': 1}
+      xarray_kwargs:
+        decode_times: False
+    metadata:
+      origin_url: ''
+
+  Argo_Temp:
+    description: "Gridded in-situ temperature derived from Argo profiles"
+    driver: netcdf
+    args:
+      urlpath: '/archive/Raphael.Dussin/datasets/Roemmich_Gilson_ARGO_TS_Clim/RG_ArgoClim_Extended_200401-202112_annual_clim_ptemp+salt.nc'
+      chunks: {'time': 1}
+      xarray_kwargs:
+        decode_times: False
+    metadata:
+      origin_url: ''
+
+  Argo_Psal:
+    description: "Gridded in-situ practical salinity derived from Argo profiles"
+    driver: netcdf
+    args:
+      urlpath: '/archive/Raphael.Dussin/datasets/Roemmich_Gilson_ARGO_TS_Clim/RG_ArgoClim_Extended_200401-202112_annual_clim_ptemp+salt.nc'
+      chunks: {'time': 1}
+      xarray_kwargs:
+        decode_times: False
+    metadata:
+      origin_url: ''
+
   WOA13_annual_TS:
     description: "World Ocean Atlas 2013 annual climatology T/S"
     driver: netcdf
diff --git a/om4labs/catalogs/obs_catalog_testing.yml b/om4labs/catalogs/obs_catalog_testing.yml
@@ -3,6 +3,39 @@ plugins:
     - module: intake_xarray
 sources:
 
+  Argo_Climatology:
+    description: "Gridded in-situ temperature and salinity derived from Argo profiles"
+    driver: netcdf
+    args:
+      urlpath: 'test_data/obs/RG_ArgoClim_Extended_200401-202112_annual_clim_ptemp+salt.nc'
+      chunks: {'time': 1}
+      xarray_kwargs:
+        decode_times: False
+    metadata:
+      origin_url: ''
+
+  Argo_Temp:
+    description: "Gridded in-situ temperature derived from Argo profiles"
+    driver: netcdf
+    args:
+      urlpath: 'test_data/obs/RG_ArgoClim_Extended_200401-202112_annual_clim_ptemp+salt.nc'
+      chunks: {'time': 1}
+      xarray_kwargs:
+        decode_times: False
+    metadata:
+      origin_url: ''
+
+  Argo_Psal:
+    description: "Gridded in-situ practical salinity derived from Argo profiles"
+    driver: netcdf
+    args:
+      urlpath: 'test_data/obs/RG_ArgoClim_Extended_200401-202112_annual_clim_ptemp+salt.nc'
+      chunks: {'time': 1}
+      xarray_kwargs:
+        decode_times: False
+    metadata:
+      origin_url: ''
+
   WOA13_annual_TS:
     description: "World Ocean Atlas 2013 annual climatology T/S"
     driver: netcdf
diff --git a/om4labs/diags/__init__.py b/om4labs/diags/__init__.py
@@ -11,6 +11,7 @@
 from . import sst_annual_bias_1x1deg
 from . import sss_annual_bias_1x1deg
 from . import seaice
+from . import stratification
 from . import stress_curl
 from . import thetao_yz_annual_bias_1x1deg
 from . import section_transports
diff --git a/om4labs/diags/stratification/__init__.py b/om4labs/diags/stratification/__init__.py
@@ -0,0 +1,7 @@
+from .stratification import parse, read, calculate, plot, run, parse_and_run
+
+__description__ = "Evaluate stratification parameters in z-coordinates"
+__ppstreams__ = [
+    "ocean_annual_z_1x1deg/av",
+]
+__ppvars__ = ["thetao"]
diff --git a/om4labs/diags/stratification/stratification.py b/om4labs/diags/stratification/stratification.py
diff --git a/setup.cfg b/setup.cfg

Original file line number	Diff line number	Diff line change
`@@ -103,7 +103,7 @@`
`103`	`103`	`"outputs": [],`
`104`	`104`	`"source": [`
`105`	`105`	`"for f in glob(\"*.gz\"):\n",`
`106`		`- " sp.check_call(f\"gunzip --keep --force {f}\", shell=True)"`
	`106`	`+ " sp.check_call(f\"gunzip --force {f}\", shell=True)"`
`107`	`107`	`]`
`108`	`108`	`},`
`109`	`109`	`{`