Merge branch 'main' of github.com:ARM-DOE/ACT

act/plotting/timeseriesdisplay.py

@@ -9,11 +9,14 @@
 from copy import deepcopy
 from re import search, search as re_search
 
+import numpy as np
+import pandas as pd
+from scipy import stats
 import matplotlib as mpl
 import matplotlib.dates as mdates
 import matplotlib.pyplot as plt
-import numpy as np
-import pandas as pd
+from matplotlib.patches import Rectangle
+from matplotlib.collections import PatchCollection
 from matplotlib import colors as mplcolors
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 from scipy.interpolate import NearestNDInterpolator
@@ -1847,3 +1850,130 @@ def fill_between(
         ax.set_title(set_title)
         self.axes[subplot_index] = ax
         return self.axes[subplot_index]
+
+    def plot_stripes(
+        self,
+        field,
+        dsname=None,
+        subplot_index=(0,),
+        set_title=None,
+        reference_period=None,
+        cmap='bwr',
+        cbar_label=None,
+        colorbar=True,
+        **kwargs,
+    ):
+        """
+        Makes a climate stripe plot with or without a baseline period specified
+
+        Parameters
+        ----------
+        field : str
+            The name of the field to plot.
+        dsname : None or str
+            If there is more than one datastream in the display object the
+            name of the datastream needs to be specified. If set to None and
+            there is only one datastream ACT will use the sole datastream
+            in the object.
+        subplot_index : 1 or 2D tuple, list, or array
+            The index of the subplot to set the x range of.
+        set_title : str
+            The title for the plot.
+        reference_period : list
+            List of a start and end date for a reference period ['2020-01-01', '2020-04-01']
+            If this is set, the plot will subtract the mean of the reference period from the
+            field to create an anomaly calculation.
+        cmap : string
+            Colormap to use for plotting.  Defaults to bwr
+        cbar_label : str
+            Option to overwrite default colorbar label.
+        colorbar : boolean
+            Option to not plot the colorbar. Default is to plot it
+        **kwargs : keyword arguments
+            The keyword arguments for :func:`plt.plot` (1D timeseries) or
+            :func:`plt.pcolormesh` (2D timeseries).
+
+        Returns
+        -------
+        ax : matplotlib axis handle
+            The matplotlib axis handle of the plot.
+
+        """
+        if dsname is None and len(self._ds.keys()) > 1:
+            raise ValueError(
+                'You must choose a datastream when there are 2 '
+                'or more datasets in the TimeSeriesDisplay '
+                'object.'
+            )
+        elif dsname is None:
+            dsname = list(self._ds.keys())[0]
+
+        # Get data and dimensions
+        data = self._ds[dsname][field]
+        dim = list(self._ds[dsname][field].dims)
+        xdata = self._ds[dsname][dim[0]]
+
+        start = int(mdates.date2num(xdata.values[0]))
+        end = int(mdates.date2num(xdata.values[-1]))
+        delta = stats.mode(xdata.diff('time').values)[0] / np.timedelta64(1, 'D')
+
+        # Calculate mean for reference period and subtract from the data
+        if reference_period is not None:
+            reference = data.sel(time=slice(reference_period[0], reference_period[1])).mean('time')
+            data.values = data.values - reference.values
+
+        # Get the current plotting axis, add day/night background and plot data
+        if self.fig is None:
+            self.fig = plt.figure()
+
+        if self.axes is None:
+            self.axes = np.array([plt.axes()])
+            self.fig.add_axes(self.axes[0])
+
+        # Set ax to appropriate axis
+        ax = self.axes[subplot_index]
+
+        # Plot up data using rectangles
+        col = PatchCollection(
+            [Rectangle((y, 0), delta, 1) for y in np.arange(start, end + 1, delta)]
+        )
+        col.set_array(data)
+        col.set_cmap(cmap)
+        col.set_clim(np.nanmin(data), np.nanmax(data))
+        ax.add_collection(col)
+
+        locator = mdates.AutoDateLocator(minticks=3)
+        formatter = mdates.AutoDateFormatter(locator)
+        ax.xaxis.set_major_locator(locator)
+        ax.xaxis.set_major_formatter(formatter)
+
+        ax.set_ylim(0, 1)
+        ax.set_yticks([])
+        ax.set_xlim(start, end + 1)
+
+        # Set Title
+        if set_title is None:
+            set_title = ' '.join(
+                [
+                    dsname,
+                    field,
+                    'Stripes on',
+                    dt_utils.numpy_to_arm_date(self._ds[dsname].time.values[0]),
+                ]
+            )
+        ax.set_title(set_title)
+
+        # Set Colorbar
+        if colorbar:
+            if 'units' in data.attrs:
+                ytitle = ''.join(['(', data.attrs['units'], ')'])
+            else:
+                ytitle = field
+            if cbar_label is None:
+                cbar_title = ytitle
+            else:
+                cbar_title = ''.join(['(', cbar_label, ')'])
+            self.add_colorbar(col, title=cbar_title, subplot_index=subplot_index)
+
+        self.axes[subplot_index] = ax
+        return self.axes[subplot_index]

act/qc/qc_summary.py

@@ -143,7 +143,7 @@ def create_qc_summary(
 
             history_value = (
                 f"Quality control summary implemented by ACT-{version} at "
-                f"{datetime.datetime.utcnow().replace(microsecond=0)} UTC"
+                f"{datetime.datetime.now(datetime.timezone.utc).replace(microsecond=0)} UTC"
             )
 
             if 'history' in list(return_ds.attrs.keys()):

act/utils/data_utils.py

@@ -112,9 +112,10 @@ def change_units(
                     self._ds[var_name].attrs = attrs
             except (
                 KeyError,
+                TypeError,
                 pint.errors.DimensionalityError,
                 pint.errors.UndefinedUnitError,
-                np.core._exceptions.UFuncTypeError,
+                np._core._exceptions.UFuncTypeError,
             ):
                 if raise_error:
                     raise ValueError(

docs/environment_docs.yml

@@ -7,36 +7,31 @@ dependencies:
   - pyproj
   - numpy
   - scipy
-  - matplotlib>=3.5.1
+  - matplotlib
   - netcdf4
   - dask
   - xarray
   - ipython
   - notebook
-  - pint=0.8.1
   - skyfield
   - scikit-posthocs
-  - pip
-  - shapely<1.8.3
   - moviepy
+  - cmweather
+  - metpy
+  - sphinx-design
+  - nbsphinx
+  - arm_pyart
+  - sphinx<7.2
+  - sphinx-gallery
+  - sphinx-copybutton
+  - pydata-sphinx-theme
+  - myst-nb
+  - nbsphinx
+  - pip
   - pip:
     - mpl2nc
     - lazy_loader
-    - metpy>=1.2
-    - arm-pyart
-    - sphinx<7.2
-    - sphinx_gallery
-    - sphinx-copybutton
-    - pydata-sphinx-theme<0.9.0
-    - myst_nb
     - ablog
-    - sphinx_design
-    - nbsphinx
     - pooch
     - icartt
-    - cmweather
-    - sphinxcontrib-devhelp==1.0.5
-    - sphinxcontrib-htmlhelp==2.0.4
-    - sphinxcontrib-qthelp==1.0.6
-    - sphinxcontrib-serializinghtml==1.1.9
     - git+https://github.com/ARM-DOE/arm-test-data.git

docs/source/_static/act-theme.css

@@ -3,144 +3,47 @@
     font-family: Poppins, sans-serif;
   }
 
- /* ARM header color */
- .bg-arm {
-     background-color: #182b55;
- }
-
- :root {
-     --pst-color-navbar-link: 255, 255, 255;
-     --pst-color-text-base: 24, 43, 85;
-     --pst-color-h3: var(--pst-color-text-base);
-     --pst-color-h4: var(--pst-color-text-base);
-     --pst-color-h5: var(--pst-color-text-base);
-     --pst-color-h6: var(--pst-color-text-base);
-     --pst-color-paragraph: var(--pst-color-text-base);
- }
-
-/* Override the default color set in the original theme for title */
-.navbar-brand>.title {
-    color: rgba(255, 255, 255) !important;
-    font-weight: 400 !important;
-    font-style: bold;
+/* Define "ARM Blue" RGB values */
+:root {
+    --arm-blue-rgb: 18, 65, 117;
 }
 
- /* Override the default color set in the original theme */
- .navbar-nav>.active>.nav-link {
-     color: rgba(255, 255, 255) !important;
-     font-weight: 400 !important;
-     font-style: italic;
- }
-
- .fa-github-square:before {
-     color: rgba(255, 255, 255) !important;
-     font-weight: 400 !important;
- }
-
- .fa-twitter-square:before {
-     color: rgba(255, 255, 255) !important;
-     font-weight: 400 !important;
- }
-
- /* Override the default logo height */
- .navbar-brand {
-     height: 50px;
- }
-
- /* Enhance the links to function docs in the gallery examples */
- div[class^="highlight"] a {
-     background-color: #EEEEEE;
- }
-
- /* Control the appearance of the version alert banner */
- #banner .alert-version, .alert-news {
-     margin: 1em;
-     padding: 0.5em;
-     font-family: "Work Sans", sans-serif;
-     font-weight: 600; font-size: 16px;
- }
-
- .intro-card {
-     background: #d8e5e8;
-     border: none;
-     border-radius: 0;
-     padding: 30px 10px 10px 10px;
-     margin: 10px 0px;
- }
-
- .intro-card .card-text {
-     margin: 20px 0px;
- }
-
- .card-button {
-     background-color: #fafafa;
-     border: none;
-     color: #484848;
-     text-align: center;
-     text-decoration: none;
-     display: inline-block;
-     font-size: 0.9rem;
-     border-radius: 0.5rem;
-     max-width: 220px;
-     padding: 0.5rem 0rem;
-     margin-top: auto;
- }
-
- .card-button a {
-     color: #484848;
- }
-
- .card-button p {
-     margin-top: 0;
-     margin-bottom: 0rem;
-     color: #484848;
- }
-
- /* Tweaks to the appearance of the sidebars */
- .bd-sidebar {
-     flex: 0 0 20%;
-     border-right: none;
- }
-
- .bd-toc .tocsection {
-     border-left: none;
- }
-
- .bd-toc .section-nav {
-     border-left: none;
- }
-
- /* Can remove once theme releases new version */
- /* xarray output display in bootstrap */
- .xr-wrap[hidden] {
- display: block !important;
+ /* ARM header color */
+ .bg-header {
+     background: rgb(var(--arm-blue-rgb))
  }
 
- .xr-var-data pre {
-   border: none;
-   box-shadow: none;
- }
+ .theme-switch-button {
+    border-color: rgb(var(--arm-blue-rgb)) !important;
+}
 
+.bd-header .navbar-nav>.nav-item>.nav-link,
+.bd-header .dropdown-toggle,
 
- /* Styling the API Changes Table */
- .api-table tr:nth-child(3n + 1){
-     background: #EEF5F5;
- }
+ .navbar-nav .dropdown-menu {
+    background-color: var(--pst-color-background);
+}
 
- .api-table tr:nth-child(3n + 2){
-     opacity: 0.65;
- }
+/* Increase contrast of links in code snippets */
+div[class^="highlight"] a {
+    background-color: rgb(var(--arm-blue-rgb), 0.2);
+    color: var(--pst-color-text-muted);
+}
 
- code.literal:not(.xref) span.pre {
-     color: #000;
- }
+/* Control the appearance of the version alert banner */
+#banner .alert-version, .alert-news {
+    margin: 1em;
+    padding: 0.5em;
+    font-family: "Work Sans", sans-serif;
+    font-weight: 600; font-size: 16px;
+}
 
- .api-table tr:nth-child(3n + 2)>td span:first-child::before{
-     content: url(old.png);
-     zoom: 0.25;
- }
+/* Tweaks to the appearance of the sidebars */
+.bd-sidebar {
+    flex: 0 0 20%;
+    border-right: none;
+}
 
- .api-table tr:nth-child(3n + 3)>td span:first-child::before{
-     content: url(new.png);
-     zoom: 0.21;
- }
+.bd-sidebar-secondary div {
+    border-left: none;
+}