Merge pull request #169 from mcflugen/mcflugen/fix-warnings-errors-in…

…-docs-build

Fix warnings and errors in docs build

.github/workflows/build.yml

@@ -58,7 +58,7 @@ jobs:
     - name: Install dependencies
       run: |
         pip install -r requirements-docs.txt
-        sudo apt update -y && sudo apt install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended dvipng
+        sudo apt update -y && sudo apt install -y latexmk texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended dvipng ffmpeg
     - name: Install DeltaMetrics
       run: |
         pip install .

deltametrics/mobility.py

@@ -1,11 +1,11 @@
 """Functions for channel mobility metrics.
 
 Current available mobility metrics include:
-    - Dry fraction decay from [Cazanacli et al 2002]_
-    - Planform overlap from [Wickert et al 2013]_
-    - Reworking index from [Wickert et al 2013]_
-    - Channel abandonment from [Liang et al 2016]_
-    - Channelized response variance from [Jarriel et al 2019]_
+- Dry fraction decay from [Cazanacli et al 2002]_
+- Planform overlap from [Wickert et al 2013]_
+- Reworking index from [Wickert et al 2013]_
+- Channel abandonment from [Liang et al 2016]_
+- Channelized response variance from [Jarriel et al 2019]_
 
 Also included are functions to fit curves to the output from the mobility
 functions, allowing for decay constants and timescales to be quantified.
@@ -330,7 +330,7 @@ def calculate_planform_overlap(chmap, landmap,
     where :math:`K_B` and :math:`K_T` are the channel mask values at the base
     and target maps, respectively.
 
-    :math:`\Phi` is calculated as:
+    :math:`\\Phi` is calculated as:
 
     .. math::
 
@@ -736,18 +736,19 @@ def calculate_channelized_response_variance(
                   arr, threshold=0.2, normalize_input=False,
                   normalize_output=False):
     """
-    Calculate the Channelized Response Variance (CRV) [1]_.
+    Calculate the Channelized Response Variance (CRV).
 
-    This function takes a t-x-y array and calculates its directional CRV.
+    This function takes a t-x-y array and calculates its directional CRV [1]_.
     In short, the function does the following:
-        1. Normalizes the array at each time slice if desired.
-        2. Calculates the CRV magnitude (aka variance along time-axis) and
-           normalizes this array if desired.
-        3. Does linear regressions through time for each pixel and returns
-           the slopes.
-        4. Calculates the directional CRV using a slope threshold value.
-        5. Returns the CRV magnitude, slopes, and directional CRV
-           values
+
+    1. Normalizes the array at each time slice if desired.
+    2. Calculates the CRV magnitude (aka variance along time-axis) and
+       normalizes this array if desired.
+    3. Does linear regressions through time for each pixel and returns
+       the slopes.
+    4. Calculates the directional CRV using a slope threshold value.
+    5. Returns the CRV magnitude, slopes, and directional CRV
+       values
 
     .. [1] Jarriel, Teresa, Leo F. Isikdogan, Alan Bovik, and Paola
            Passalacqua. "Characterization of deltaic channel morphodynamics

deltametrics/utils.py

@@ -155,9 +155,10 @@ def curve_fit(data, fit='harmonic'):
     fit : :obj:`str`, optional
         A string specifying the type of function to be fit. Options are as
         follows:
-          * `exponential`, which evaluates :code:`(a - b) * np.exp(-c * x) + b`
-          * `harmonic`, (default) which evaluates :code:`a / (1 + b * x)`
-          * `linear`, which evaluates :code:`a * x + b`
+
+        * `exponential`, which evaluates :code:`(a - b) * np.exp(-c * x) + b`
+        * `harmonic`, (default) which evaluates :code:`a / (1 + b * x)`
+        * `linear`, which evaluates :code:`a * x + b`
 
     Returns
     -------

docs/Makefile

@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
-SPHINXOPTS    ?=
+SPHINXOPTS    ?= -W
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = source
 BUILDDIR      = build

docs/source/guides/examples/computations/computing_sedimentograph.rst

@@ -81,7 +81,7 @@ Using the sedimentograph to evaluate time distribution in subsurface
     :include-source:
     :context: close-figs
 
-    time_bins = np.linspace(0, golfcube.t[-1], num=7)
+    time_bins = np.linspace(0, float(golfcube.t[-1]), num=7)
     (time_sedimentograph,
         time_radii,
         _) = dm.strat.compute_sedimentograph(

docs/source/guides/examples/computations/radial_growth_pattern.rst

@@ -57,7 +57,7 @@ Now plot
           golf.meta['N0'].data *
           golf.meta['dx'].data *
           (golf.meta['C0_percent'][0].data / 100))  # sediment input, m3/s
-    t = np.linspace(0, golf.t[time_idxs[-1]], num=100)
+    t = np.linspace(0, float(golf.t[time_idxs[-1]]), num=100)
 
     # make the figure
     fig, ax = plt.subplots()

docs/source/pyplots/guides/userguide_section_type_demos.py

@@ -21,7 +21,7 @@
 axs = [fig.add_subplot(spec[i, j]) for i, j in zip(
     np.repeat(np.arange(1, 4), 2), np.tile(np.arange(2), (4,)))]
 
-t10cmap = plt.cm.get_cmap('tab10')
+t10cmap = plt.get_cmap('tab10')
 golfcube.quick_show('eta', idx=-1, ax=ax0, ticks=True)
 for i, s in enumerate([_strike, _dip, _path, _circ, _rad]):
     s.show_trace('--', color=t10cmap(i), ax=ax0)