Merge branch 'NCAR:stable' into develop_satellite

.github/workflows/ci.yml

@@ -25,21 +25,26 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Set up Python (micromamba)
-        uses: mamba-org/provision-with-micromamba@v13
+        uses: mamba-org/provision-with-micromamba@v15
         with:
           environment-file: environment-dev.yml
           cache-env: true
           extra-specs: |
             python=${{ matrix.python-version }}
 
       - name: Test with pytest
-        run: pytest -n auto -v
+        run: pytest -n auto -v -k 'not aqs'
 
       - 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
 
+      - name: Downgrade OpenSSL and test AQS
+        run: |
+          micromamba install 'openssl <3'
+          pytest -n auto -v -k aqs
+
   docs:
     name: Check docs build
     runs-on: ubuntu-latest
@@ -52,11 +57,14 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Set up Python (micromamba)
-        uses: mamba-org/provision-with-micromamba@v13
+        uses: mamba-org/provision-with-micromamba@v15
         with:
           environment-file: docs/environment-docs.yml
           cache-env: true
 
+      - name: Downgrade OpenSSL (for AQS URL linkcheck)
+        run: micromamba install 'openssl <3'
+
       - name: linkcheck
         run: sphinx-build -b linkcheck docs docs/_build/linkcheck
 

.pre-commit-config.yaml

@@ -1,30 +1,30 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.3.0"
+    rev: "v4.4.0"
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-docstring-first
       - id: check-yaml
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: "v2.38.0"
+    rev: "v3.3.1"
     hooks:
       - id: pyupgrade
         args: [--py36-plus]
 
   - repo: https://github.com/PyCQA/isort
-    rev: "5.10.1"
+    rev: "5.12.0"
     hooks:
       - id: isort
 
   - repo: https://github.com/psf/black
-    rev: "22.8.0"
+    rev: "23.1.0"
     hooks:
       - id: black
 
   - repo: https://github.com/PyCQA/flake8
-    rev: "5.0.4"
+    rev: "6.0.0"
     hooks:
       - id: flake8
 

docs/conf.py

@@ -56,6 +56,11 @@
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"
 
+linkcheck_ignore = [
+    "https://doi.org/10.1080/10473289.2005.10464718",
+    "https://www.camx.com",
+]
+
 # -- Extension configuration -------------------------------------------------
 
 extlinks = {

docs/tutorial/improve_trends_kmeans.rst

@@ -67,7 +67,7 @@ Now we will load the data (in this case the file is
       self._setitem_with_indexer(indexer, value)
 
 
-Lets look at the dataframe
+Let's look at the dataframe.
 
 .. code-block:: python
 
@@ -438,8 +438,8 @@ Lets look at the dataframe
 
 
 
-Now this is in the long pandas format. Lets use the
-monet.util.tools.long_to_wide utility to reformat the dataframe into a
+Now this is in the long pandas format. Let's use the
+``monet.util.tools.long_to_wide`` utility to reformat the dataframe into a
 wide format.
 
 .. code-block:: python
@@ -622,7 +622,7 @@ wide format.
 
 
 
-Lets now plot some of the different measurements with time from a site.
+Let's now plot some of the different measurements with time from a site.
 In this case we will look at the PHOE1 site in Phoenix, Arizona.
 
 .. code-block:: python
@@ -828,7 +828,7 @@ Let’s look at SIf as an example from ACAD1.
 .. image:: improve_trends_kmeans_files/improve_trends_kmeans_11_1.png
 
 
-Now this is good but lets resample to see if we can see a trend.
+Now this is good, but let's resample to see if we can see a trend.
 
 .. code-block:: python
 
@@ -840,10 +840,10 @@ Now this is good but lets resample to see if we can see a trend.
 .. image:: improve_trends_kmeans_files/improve_trends_kmeans_13_0.png
 
 
-Simply resampling is fine but lets try to get a signal out using a
-kolmogorov-zerbenko filter. See
-https://www.tandfonline.com/doi/pdf/10.1080/10473289.2005.10464718 for
-more information
+Simply resampling is fine, but let's try to get a signal out using a
+Kolmogorov--Zurbenko filter. See
+https://doi.org/10.1080/10473289.2005.10464718 for
+more information.
 
 .. code-block:: python
 
@@ -878,7 +878,7 @@ some tools from sklearn to use in our analysis.
 
 .. code-block:: python
 
-    from sklearn.preprocessing import RobustScaler #to scale our data
+    from sklearn.preprocessing import RobustScaler # to scale our data
     from sklearn.cluster import KMeans # clustering algorithm
 
 First we want to separate out different variables that may be useful
@@ -968,7 +968,7 @@ NaN values so let us go ahead and do that.
 
 
 Usually, with sklearn it is better to scale the data first before
-putting it through the algorithm. We will use th RobustScaler to do
+putting it through the algorithm. We will use the RobustScaler to do
 this.
 
 .. code-block:: python
@@ -983,14 +983,14 @@ analysis.
 
     km = KMeans(n_clusters=2).fit(X_scaled)
 
-The clusters can be found under km.labels\_ . These are integers
+The clusters can be found under ``km.labels_``. These are integers
 representing the different clusters.
 
 .. code-block:: python
 
     clusters = km.labels_
 
-Lets plot this so that we can see where there is dust.
+Let's plot this so that we can see where there is dust.
 
 .. code-block:: python
 

environment-dev.yml

@@ -16,6 +16,7 @@ dependencies:
   #
   # optional
   - joblib
+  - lxml
   - pyhdf
   - requests
   #

monetio/__init__.py

@@ -4,7 +4,7 @@
 from .profile import geoms, icartt, tolnet
 from .sat import goes
 
-__version__ = "0.2.2"
+__version__ = "0.2.3"
 
 __all__ = [
     "__version__",

monetio/models/_wrfchem_mm.py

@@ -189,7 +189,7 @@ def open_mfdataset(
     if "pm25_om" in list_calc_sum:
         dset = add_lazy_om_pm25(dset, dict_sum)
 
-    dset = dset.reset_index(["XTIME", "datetime"], drop=True)
+    dset = dset.reset_coords(["XTIME", "datetime"], drop=True)
     if not surf_only_nc:
         # Reset more variables
         dset = dset.rename(

monetio/models/cdump2netcdf.py

@@ -114,7 +114,6 @@ def handle_levels(levlist):
 
 # def cdump2awips(flist, outname, format='NETCDF4', d1=None, d2=None):
 def cdump2awips(xrash1, dt, outname, mscale=1, munit="unit", format="NETCDF4", d1=None, d2=None):
-
     # mass loading should be in g/m2 to compare to satellite.
     # concentration should be in mg/m3 to compare to threshold levels.