fix images in docstrings

AugustinMortier · Sep 22, 2024 · 4e6eb85 · 4e6eb85
1 parent da281ac
commit 4e6eb85
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Showing 13 changed files with 42 additions and 99 deletions.
diff --git a/aprofiles/detection/clouds.py b/aprofiles/detection/clouds.py
@@ -41,11 +41,7 @@ def detect_clouds(profiles, time_avg=1., zmin=0., thr_noise=5., thr_clouds=4., m
         profiles.plot(show_clouds=True, vmin=1e-2, vmax=1e1, log=True)
         ```
 
-        .. figure:: ../../examples/images/clouds.png
-            :scale: 50 %
-            :alt: clouds detection
-
-            Clouds detection.
+        ![Clouds detection](../../assets/images/clouds.png)
     """
 
     def _detect_clouds_from_rcs(data, zmin, thr_noise, thr_clouds, min_snr):

diff --git a/aprofiles/detection/foc.py b/aprofiles/detection/foc.py
@@ -56,11 +56,7 @@ def detect_foc(profiles, method="cloud_base", var="attenuated_backscatter_0", z_
         profiles.plot(show_foc=True, zmax=6000., vmin=1e-2, vmax=1e1, log=True)
         ```
 
-        .. figure:: ../../examples/images/foc.png
-            :scale: 50 %
-            :alt: foc detection
-
-            Fog or condensation (foc) detection.
+        ![Fog or condensation (foc) detection](../../assets/images/foc.png)
     """
 
     if method == "cloud_base":

diff --git a/aprofiles/detection/pbl.py b/aprofiles/detection/pbl.py
@@ -49,11 +49,7 @@ def detect_pbl(
         profiles.plot(show_pbl=True, zmax=6000., vmin=1e-2, vmax=1e1, log=True)
         ```
 
-        .. figure:: ../../examples/images/pbl.png
-            :scale: 50 %
-            :alt: clouds detection
-
-            Planetary Boundary Layer Height detection.
+        ![Planetary Boundary Layer Height detection](../../assets/images/pbl.png)
     """
 
     from scipy.ndimage.filters import uniform_filter1d

diff --git a/aprofiles/plot/image.py b/aprofiles/plot/image.py
@@ -150,7 +150,7 @@ def plot(
         # attenuated backscatter image
         profiles.plot(vmin=1e-2, vmax=1e1, log=True)
         ```
-        ![Image of attenuated backscatter profiles](assets/images/attenuated_backscatter.png){: style="width: 50%;" }
+        ![Image of attenuated backscatter profiles](../../assets/images/attenuated_backscatter.png)
     """
 
     # calculates max value from data

diff --git a/aprofiles/plot/profile.py b/aprofiles/plot/profile.py
@@ -132,7 +132,8 @@ def plot(
     show_fig=True,
     save_fig=None
 ):
-    """Plot single profile of selected variable from :class:`aprofiles.profiles.ProfilesData` object.
+    """
+    Plot single profile of selected variable from (aprofiles.profiles.ProfilesData): object.
 
     Args:
         da (xarray.DataArray): DataArray.
@@ -164,11 +165,7 @@ def plot(
         profiles.plot(datetime=datetime, vmin=-1, vmax=10, zmax=12000, show_clouds=True, show_pbl=True)
         ```
 
-        .. figure:: ../../docs/assets/images/Profile-Oslo-20210909T212005.png
-            :scale: 80 %
-            :alt: profile
-
-            Single profile of attenuated backscatter.
+        ![Single profile of attenuated backscatter](../../assets/images/Profile-Oslo-20210909T212005.png){: style="width: 60%;" }
     """
 
     if datetime is None:

diff --git a/aprofiles/plot/timeseries.py b/aprofiles/plot/timeseries.py
@@ -10,7 +10,8 @@
 
 
 def plot(da, var="aod", show_fig=True, save_fig=None, **kwargs):
-    """Plot time series of selected variable from :class:`aprofiles.profiles.ProfilesData` object.
+    """
+    Plot time series of selected variable from (aprofiles.profiles.ProfilesData): object.
 
     Args:
         da (xarray.DataArray): DataArray
@@ -31,11 +32,7 @@ def plot(da, var="aod", show_fig=True, save_fig=None, **kwargs):
         profiles.plot(var="pbl" ymin=0., ymax=3000., min_snr=2.)
         ```
 
-        .. figure:: ../../docs/assets/images/time_series.png
-            :scale: 50 %
-            :alt: time series
-
-            Time series of Planetary Boundary Layer height.
+        ![Time series of Planetary Boundary Layer height](../../assets/images/time_series.png)
     """
 
     def __init__(self):

diff --git a/aprofiles/profiles.py b/aprofiles/profiles.py
@@ -111,11 +111,7 @@ def snr(self, var="attenuated_backscatter_0", step=4, verbose=False):
             profiles.plot(var='snr',vmin=0, vmax=3, cmap='Greys_r')
             ```
 
-            .. figure:: ../../docs/assets/images/snr.png
-                :scale: 50 %
-                :alt: snr
-
-                Signal to Noise Ratio.
+            ![Signal to Noise Ratio](../../assets/images/snr.png)
         """
 
         def _1D_snr(array, step):
@@ -174,17 +170,8 @@ def gaussian_filter(
             0.50
             ```
 
-            .. figure:: ../../docs/assets/images/attenuated_backscatter.png
-                :scale: 50 %
-                :alt: before filtering
-
-                Before gaussian filtering.
-
-            .. figure:: ../../docs/assets/images/gaussian_filter.png
-                :scale: 50 %
-                :alt: after gaussian filtering
-
-                After gaussian filtering (sigma=0.5).
+            ![Before gaussian filtering](../../assets/images/attenuated_backscatter.png)
+            ![After gaussian filtering (sigma=0.5)](../../assets/images/gaussian_filter.png)
         """
         import copy
 
@@ -271,17 +258,8 @@ def extrapolate_below(
             150
             ```
 
-            .. figure:: ../../docs/assets/images/lowest.png
-                :scale: 50 %
-                :alt: before extrapolation
-
-                Before extrapolation.
-
-            .. figure:: ../../docs/assets/images/lowest_extrap.png
-                :scale: 50 %
-                :alt: after desaturation
-
-                After extrapolation.
+            ![Before extrapolation](../../assets/images/lowest.png)
+            ![After extrapolation](../../assets/images/lowest_extrap.png)
         """
 
         # get index of z
@@ -381,17 +359,8 @@ def desaturate_below(self, var="attenuated_backscatter_0", z=4000.0, inplace=Fal
             True
             ```
 
-            .. figure:: ../../docs/assets/images/saturated.png
-                :scale: 50 %
-                :alt: before desaturation
-
-                Before desaturation.
-
-            .. figure:: ../../docs/assets/images/desaturated.png
-                :scale: 50 %
-                :alt: after desaturation
-
-                After desaturation.
+            ![Before desaturation](../../assets/images/saturated.png)
+            ![After desaturation](../../assets/images/desaturated.png)
         """
 
         imax = self._get_index_from_altitude_AGL(z)

diff --git a/aprofiles/retrieval/extinction.py b/aprofiles/retrieval/extinction.py
@@ -200,11 +200,7 @@ def inversion(
         profiles.plot(var='extinction', zmax=6000, vmin=0, vmax=5e-2)
         ```
 
-        .. figure:: ../../docs/assets/images/backward.png
-            :scale: 50 %
-            :alt: clouds detection
-
-            Extinction profiles retrieved with the backward method.
+        ![Extinction profiles retrieved with the backward method](../../assets/images/backward.png)
 
         Forward inversion
         ```python
@@ -214,11 +210,7 @@ def inversion(
         profiles.plot(var='extinction', zmax=6000, vmin=0, vmax=5e-2)
         ```
 
-        .. figure:: ../../docs/assets/images/forward.png
-            :scale: 50 %
-            :alt: clouds detection
-
-            Extinction profiles retrieved with the forward method.
+        ![Extinction profiles retrieved with the forward method](../../assets/images/forward.png)
     """
 
     # we work on profiles averaged in time to reduce the noise

diff --git a/aprofiles/retrieval/mass_conc.py b/aprofiles/retrieval/mass_conc.py
@@ -44,12 +44,7 @@ def concentration_profiles(profiles, method):
         profiles.plot(var='mass_concentration:urban', zmax=6000, vmin=0, vmax=100)
         ```
 
-        .. figure:: ../../docs/assets/images/mass_conc-urban.png
-            :scale: 50 %
-            :alt: mass concentration
-
-            Mass concentration profiles in the case of urban particles.
-
+        ![Mass concentration profiles in the case of urban particles](../../assets/images/mass_conc-urban.png)
     """
 
     # read aer_properties.json files

diff --git a/aprofiles/simulation/ext2back.py b/aprofiles/simulation/ext2back.py
@@ -35,11 +35,7 @@ class ExtinctionToAttenuatedBackscatter:
         sim_profiles.plot('extinction_model')
         ```
 
-        .. figure:: ../../docs/assets/images/simulation_step-model.png
-            :scale: 80 %
-            :alt: simlation step model
-
-            Simulation of aerosol extinction using a step model.
+        ![Simulation of aerosol extinction using a step model](../../assets/images/simulation_step-model.png)
     """    
     # get the right reading class
     def __init__(self, model, wavelength, lidar_ratio, noise):

diff --git a/aprofiles/size_distribution.py b/aprofiles/size_distribution.py
@@ -102,12 +102,7 @@ def plot(self, show_fig=True):
             sd.plot()
             ```
 
-            .. figure:: ../../docs/assets/images/urban_sd.png
-                :scale: 80 %
-                :alt: urban size distribution
-
-                Size distributions for urban particles.
-
+            ![Size distributions for urban particles](../../assets/images/urban_sd.png)
         """
         fig, ax = plt.subplots(1, 1, figsize=(6, 6))
 

diff --git a/docs/assets/css/custom.css b/docs/assets/css/custom.css
@@ -30,4 +30,11 @@ a.download {
   a.download::before {
     content: "⇩ ";  /* Adding a download icon before the text */
   }
-
+
+  .md-header-nav__icon .vprofiles {
+    background-image: url('../assets/images/vprofiles-bold.ico');
+    background-size: cover;
+    width: 24px;
+    height: 24px;
+    display: inline-block;
+}
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -12,6 +12,8 @@ theme:
   features:
     - navigation.instant
     - navigation.tracking
+    - navigation.sections
+    #- navigation.expand   # Automatically expands sections
   palette:
     - media: "(prefers-color-scheme: light)"
       scheme: default
@@ -38,8 +40,13 @@ theme:
 
 # To set logos for different color schemes, use:
 extra:
-  logo_default: assets/images/A-Profiles-white.png
-  logo_slate: assets/images/A-Profiles.png
+  social:
+    - icon: fontawesome/solid/globe
+      link: https://vprofiles.met.no
+      name: V-Profiles
+  # Optional: Support for dark/light mode with custom logos
+  logo_light: assets/images/A-Profiles-white.png  # Logo for light mode
+  logo_dark: assets/images/A-Profiles.png         # Logo for dark mode
 
 # Repository information (replaces the 'icon_links' feature in Sphinx)
 repo_name: "AugustinMortier/A-Profiles"
@@ -93,7 +100,7 @@ extra_css:
 extra_javascript:
   - assets/js/custom.js
 
-extra_files:
-  - aprofiles/cli/aprocess.py
-  - aprofiles/cli/utils/workflow.py
+#extra_files:
+#  - aprofiles/cli/aprocess.py
+#  - aprofiles/cli/utils/workflow.py