Merge branch 'main' into eleanor-patch-5

OceanGlidersCommunity · Oct 31, 2024 · 7d76da0 · 7d76da0
2 parents f9de956 + 8dff4a4
commit 7d76da0
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -35,7 +35,3 @@ jobs:
     - name: Full Tests
       run: |
         python -m pytest -rxs tests/
-
-    - name: run notebook
-      run: |
-        jupyter nbconvert --to notebook --execute notebooks/demo.ipynb --output=demo-output.ipynb
diff --git a/README.md b/README.md
@@ -4,8 +4,7 @@ This is a repo to diagnose issues in glider data such as CTD thermal lag.
 
 This is a work in progress, all contributions welcome!
 
-
-### Usage
+### Instal
 
 Install from PyPI with
 
@@ -21,6 +20,10 @@ pip install -e .
 ```
 This installs glidertest locally. -e ensures that any edits you make in the files will be picked up by scripts that import functions from glidertest.
 
+### Documentation
+
+Documentation website at [https://callumrollo.github.io/glidertest/](https://callumrollo.github.io/glidertest/)
+
 Check out the example notebook `notebooks/demo.ipynb` for example functionality
 
 As input, glidertest takes [OceanGliders format files](https://github.com/OceanGlidersCommunity/OG-format-user-manual)

diff --git a/docs/source/_static/glider.jpg b/docs/source/_static/glider.jpg
diff --git a/docs/source/_static/glider.png b/docs/source/_static/glider.png
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -11,7 +11,7 @@
 
 # General information about the project.
 project = 'glidertest'
-author = 'Callum Rollo'
+author = 'Eleanor Frajka-Williams, Chiara Monforte, Callum Rollo'
 copyright = f"{year}, {author}"
 release = 'v0.0.1'
 
@@ -39,3 +39,5 @@
 html_static_path = ['_static']
 
 source_suffix = [".rst", ".md"]
+
+html_logo = "_static/glider.png"
diff --git a/docs/source/glidertest.rst b/docs/source/glidertest.rst
@@ -4,4 +4,7 @@
 .. automodule:: glidertest.tools
    :members:
    :undoc-members:
-   :show-inheritance:
+
+.. automodule:: glidertest.fetchers
+   :members:
+   :undoc-members:
diff --git a/glidertest/fetchers.py b/glidertest/fetchers.py
@@ -10,14 +10,26 @@
         "sea076_20230906T0852_delayed.nc": "sha256:bd50b2c1019b49f8c14381de8f78aa67d66e9d9e89607bbcedff246be60e6c92",
         "sea055_20220104T1536_R.nc": "sha256:5687c9d7b383713ff730ad4a570689622fe6eb9807e340919d59a83a437773b9",
         "sea055_20220104T1536_delayed.nc": "sha256:7f72f8a0398c3d339687d7b7dcf0311036997f6855ed80cae5bbf877e09975a6",
+        "sea045_20230530T0832_delayed.nc": "sha256:9a97b5b212e9ad751909e175bc01fdc75fd7b7fd784cc59d8e9f29e8bdfb829f",
     },
 )
 
 
-def load_sample_dataset(dataset_name="sea076_20230906T0852_delayed.nc"):
+def load_sample_dataset(dataset_name="sea045_20230530T0832_delayed.nc"):
+    """Download sample datasets for use with glidertest
+
+    Args:
+        dataset_name (str, optional): _description_. Defaults to "sea076_20230906T0852_delayed.nc".
+
+    Raises:
+        ValueError: If the requests dataset is not known, raises a value error
+
+    Returns:
+        xarray.Dataset: Requested sample dataset
+    """
     if dataset_name in data_source_og.registry.keys():
         file_path = data_source_og.fetch(dataset_name)
         return xr.open_dataset(file_path)
     else:
-        msg = f"Requested sample dataset {dataset_name} not known"
+        msg = f"Requested sample dataset {dataset_name} not known. Specify one of the following available datasets: {list(data_source_og.registry.keys())}"
         raise ValueError(msg)
diff --git a/notebooks/demo.ipynb b/notebooks/demo.ipynb
@@ -60,7 +60,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds\n"
+    "ds"
    ]
   },
   {
@@ -101,7 +101,7 @@
    "outputs": [],
    "source": [
     "# Basic diagnostics of the watermass properties\n",
-    "tools.plot_ts_histograms(ds)\n"
+    "tools.plot_ts_histograms(ds)"
    ]
   },
   {
@@ -228,7 +228,7 @@
     "# Let's visually check a section of chlorphyll and see if we observe any NPQ\n",
     "fig, ax = plt.subplots(1, 1, figsize=(15, 5))\n",
     "\n",
-    "tools.plot_section_with_srss(ds, 'CHLA', ax, start_time = '2023-09-06', end_time = '2023-09-10', ylim=35)"
+    "tools.plot_section_with_srss(ds, 'CHLA', ax, start_time = '2023-06-04', end_time = '2023-06-06', ylim=35)"
    ]
   },
   {
@@ -239,9 +239,9 @@
    "outputs": [],
    "source": [
     "# Compute day and night average for chlorophylla and temeparture\n",
-    "dayT, nightT = tools.day_night_avg(ds, sel_var='TEMP',start_time = '2023-09-06', end_time = '2023-09-10')\n",
-    "dayS, nightS = tools.day_night_avg(ds, sel_var='PSAL',start_time = '2023-09-06', end_time = '2023-09-10')\n",
-    "dayC, nightC = tools.day_night_avg(ds, sel_var='CHLA',start_time = '2023-09-06', end_time = '2023-09-10')"
+    "dayT, nightT = tools.day_night_avg(ds, sel_var='TEMP',start_time = '2023-06-03', end_time = '2023-06-07')\n",
+    "dayS, nightS = tools.day_night_avg(ds, sel_var='PSAL',start_time = '2023-06-03', end_time = '2023-06-07')\n",
+    "dayC, nightC = tools.day_night_avg(ds, sel_var='CHLA',start_time = '2023-06-03', end_time = '2023-06-07')"
    ]
   },
   {
@@ -253,9 +253,9 @@
    "source": [
     "fig, ax = plt.subplots(1, 3, figsize=(15, 5))\n",
     "\n",
-    "tools.plot_daynight_avg( dayT, nightT, ax[0],sel_day='2023-09-08', xlabel='Temperature [C]')\n",
-    "tools.plot_daynight_avg( dayS, nightS, ax[1],sel_day='2023-09-08', xlabel='Salinity [PSU]')\n",
-    "tools.plot_daynight_avg( dayC, nightC, ax[2],sel_day='2023-09-08', xlabel='Chlorophyll [mg m-3]')"
+    "tools.plot_daynight_avg( dayT, nightT, ax[0],sel_day='2023-06-04', xlabel='Temperature [C]')\n",
+    "tools.plot_daynight_avg( dayS, nightS, ax[1],sel_day='2023-06-04', xlabel='Salinity [PSU]')\n",
+    "tools.plot_daynight_avg( dayC, nightC, ax[2],sel_day='2023-06-04', xlabel='Chlorophyll [mg m-3]')"
    ]
   },
   {
@@ -372,7 +372,7 @@
     "\n",
     "*  Check for any possible drift in the data that might look suspicious. The great temporal and spatial variability may not allow for such check to be succesful. Evaluation using reference CTD cast data or any other data available in the stufy area is recommended.\n",
     "\n",
-    "Oxygen SOP provides a great summary of the needed processing of salinity data and the vaious difference based on sensor modela nd platform type https://oceangliderscommunity.github.io/Salinity_SOP/sections/salinity_dmqc.html"
+    "Oxygen SOP provides a great summary of the needed processing of salinity data and the vaious difference based on sensor model and platform type https://oceangliderscommunity.github.io/Salinity_SOP/sections/salinity_dmqc.html"
    ]
   },
   {

diff --git a/tests/test_tools.py b/tests/test_tools.py
@@ -26,10 +26,10 @@ def test_quench_sequence():
     if not "TIME" in ds.indexes.keys():
         ds = ds.set_xindex('TIME')
     fig, ax = plt.subplots()
-    tools.plot_section_with_srss(ds, 'CHLA', ax,start_time = '2023-09-06', end_time = '2023-09-10', ylim=35)
-    dayT, nightT = tools.day_night_avg(ds, sel_var='TEMP',start_time = '2023-09-06', end_time = '2023-09-10')
+    tools.plot_section_with_srss(ds, 'CHLA', ax,start_time = '2023-06-04', end_time = '2023-06-06', ylim=35)
+    dayT, nightT = tools.day_night_avg(ds, sel_var='TEMP',start_time = '2023-06-04', end_time = '2023-06-06')
     fig, ax = plt.subplots()
-    tools.plot_daynight_avg( dayT, nightT,ax,sel_day='2023-09-08', xlabel='Temperature [C]') 
+    tools.plot_daynight_avg( dayT, nightT,ax,sel_day='2023-06-04', xlabel='Temperature [C]') 
 
 def test_temporal_drift():
     ds = fetchers.load_sample_dataset()
@@ -42,4 +42,4 @@ def test_temporal_drift():
 def test_profile_check():
     ds = fetchers.load_sample_dataset()
     tools.check_monotony(ds.PROFILE_NUMBER)
-    tools.plot_profIncrease(ds)
+    tools.plot_profIncrease(ds)