Merge branch 'noaa-oar-arl:stable' into feature/viirs_aws_gridded

.github/workflows/ci.yml

@@ -9,6 +9,9 @@ on:
   schedule:
     - cron: "0 12 * * 1"
 
+env:
+  OPENAQ_API_KEY: "${{ secrets.OPENAQ_API_KEY }}"
+
 jobs:
   test:
     name: Test (Py ${{ matrix.python-version }})
@@ -42,14 +45,15 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
             attrs=22.2.0
+            aioitertools=0.11.0
 
       - name: Test with pytest
-        run: pytest -n auto -v -W "ignore:Downloading test file:UserWarning::"
+        run: pytest -n auto -v -rsx -W "ignore:Downloading test file:UserWarning::"
 
       - name: Test with pytspack installed
         run: |
           pip install https://github.com/noaa-oar-arl/pytspack/archive/master.zip
-          pytest -n auto -v -k with_pytspack
+          pytest -n auto -v -rsx -k with_pytspack
 
   docs:
     name: Check docs build

.pre-commit-config.yaml

@@ -6,6 +6,7 @@ repos:
         exclude: tdump\.[0-9]*
       - id: end-of-file-fixer
       - id: check-docstring-first
+        exclude: monetio/obs/openaq_v2\.py
       - id: check-yaml
 
   - repo: https://github.com/asottile/pyupgrade

monetio/__init__.py

@@ -1,10 +1,23 @@
 from . import grids
 from .models import camx, cmaq, fv3chem, hysplit, hytraj, ncep_grib, pardump, prepchem, raqms
-from .obs import aeronet, airnow, aqs, cems, crn, improve, ish, ish_lite, nadp, openaq, pams
+from .obs import (
+    aeronet,
+    airnow,
+    aqs,
+    cems,
+    crn,
+    improve,
+    ish,
+    ish_lite,
+    nadp,
+    openaq,
+    openaq_v2,
+    pams,
+)
 from .profile import geoms, gml_ozonesonde, icartt, tolnet
 from .sat import goes
 
-__version__ = "0.2.6"
+__version__ = "0.2.7"
 
 __all__ = [
     "__version__",
@@ -29,6 +42,7 @@
     "ish_lite",
     "nadp",
     "openaq",
+    "openaq_v2",
     "pams",
     #
     # profile obs

monetio/models/_camx_mm.py

@@ -68,8 +68,8 @@ def open_mfdataset(
                 dset = add_met_data_3D(dset, dset_met)
             if "alt_agl_m_mid" in dset.variables:
                 var_list = var_list + ["alt_agl_m_mid"]
-            if "layer_height_agl" in dset.variables:
-                var_list = var_list + ["layer_height_agl"]
+            if "dz_m" in dset.variables:
+                var_list = var_list + ["dz_m"]
             if "pres_pa_mid" in dset.variables:
                 var_list = var_list + ["pres_pa_mid"]
             if "temperature_k" in dset.variables:
@@ -206,7 +206,7 @@ def add_met_data_3D(d_chem, d_met):
             "var_desc": "pressure",
         }
     if ("z" in d_met.variables) or ("ZGRID_M" in d_met.variables):
-        d_chem["alt_agl_m_mid"], d_chem["layer_height_agl"] = _calc_midlayer_height_agl(d_met)
+        d_chem["alt_agl_m_mid"], d_chem["dz_m"] = _calc_midlayer_height_agl(d_met)
     else:
         warnings.warn("No altitude AGL was found.")
 
@@ -458,6 +458,12 @@ def _calc_midlayer_height_agl(dset):
     alt_agl_m_mid[:, :, :, :] = mid_layer_height
     alt_agl_m_mid.attrs["var_desc"] = "Layer height above ground level at midpoint"
     alt_agl_m_mid.attrs["long_name"] = "Height AGL at midpoint"
+
+    dz_m = xr.zeros_like(layer_height_agl)
+    dz_m[:, 0, :, :] = layer_height_agl[:, 0, :, :].values
+    dz_m[:, 1:, :, :] = layer_height_agl[:, 1:, :, :].values - layer_height_agl[:, :-1, :, :].values
+    dz_m.attrs["long_name"] = "dz in meters"
+    dz_m.attrs["var_desc"] = "Layer thickness in meters"
     return alt_agl_m_mid, layer_height_agl
 
 

monetio/models/_wrfchem_mm.py

@@ -102,6 +102,8 @@ def open_mfdataset(
             var_wrf = getvar(
                 wrflist, var, timeidx=ALL_TIMES, method="cat", squeeze=False, units="m"
             )
+            if var == "zstag":
+                var_wrf = var_wrf.rename("zstag")
         else:
             var_wrf = getvar(wrflist, var, timeidx=ALL_TIMES, method="cat", squeeze=False)
         var_wrf_list.append(var_wrf)

monetio/obs/__init__.py

@@ -10,6 +10,7 @@
     ish_lite,
     nadp,
     openaq,
+    openaq_v2,
     pams,
 )
 
@@ -25,6 +26,7 @@
     "cems_mod",
     "nadp",
     "openaq",
+    "openaq_v2",
     "pams",
 ]