Merge pull request #19 from MOchiara/chiara-patch-12

Prepare for tests

.github/workflows/tests.yml

@@ -0,0 +1,39 @@
+name: Tests
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  run:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.10", "3.12"]
+        os: [windows-latest, ubuntu-latest, macos-latest]
+      fail-fast: true
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Setup Micromamba
+      uses: mamba-org/setup-micromamba@v1
+
+    - name: Python ${{ matrix.python-version }}
+      shell: bash -l {0}
+      run: >
+        micromamba create --name TEST python=${{ matrix.python-version }} pytest --file requirements-dev.txt --channel conda-forge
+        && micromamba activate TEST
+    - name: Install glidertest
+      shell: bash -l {0}
+      run: >
+        micromamba activate TEST
+        && python -m pip install -e . --no-deps --force-reinstall
+    - name: Tests
+      shell: bash -l {0}
+      run: >
+        micromamba activate TEST
+        && python -m pytest -rxs tests/

glidertest/tools.py

@@ -26,7 +26,7 @@ def grid2d(x, y, v, xi=1, yi=1):
     return grid, XI, YI
 
 
-def test_updown_bias(ds, axis, var='PSAL', v_res=0, return_val=False):
+def updown_bias(ds, axis, var='PSAL', v_res=0, return_val=False):
     p = 1  # Horizontal resolution
     z = v_res  # Vertical resolution
     varG, profG, depthG = grid2d(ds.PROFILE_NUMBER, ds.DEPTH, ds[var], p, z)
@@ -156,7 +156,7 @@ def chl_first_check(ds):
     ax.set(ylim=(np.nanpercentile(bottom_chl_data, 0.1), np.nanpercentile(bottom_chl_data, 99.9)),
            xlabel='Measurements',
            ylabel='Chla')
-    plt.show()
+
     if slope >= 0.00001:
         print(
             'Data from the deepest 10% of data has been analysed and data does not seem stable. An alternative solution for dark counts has to be considered. \nMoreover, it is recommended to check the sensor has this may suggest issues with the sensor (i.e water inside the sensor, temporal drift etc)')
@@ -313,8 +313,8 @@ def check_npq(ds, offset=np.timedelta64(1, "h"), start_time='2024-04-18', end_ti
     Two plots: a chlorphyll section and a comparison of day and night average chlorphyll over depth for the selcted day
 
     """
-
-
+    if not "TIME" in ds.indexes.keys():
+        ds = ds.set_xindex('TIME')
     ds_sel = ds.sel(TIME=slice(start_time, end_time))
     sunrise, sunset = sunset_sunrise(ds_sel.TIME, ds_sel.LATITUDE, ds_sel.LONGITUDE)
 

notebooks/demo.ipynb

@@ -79,10 +79,10 @@
    "outputs": [],
    "source": [
     "fig, ax = plt.subplots(1,4,figsize=(15, 5))\n",
-    "tools.test_updown_bias(ds, ax[0],var='PSAL',v_res=0.1)\n",
-    "tools.test_updown_bias(ds,ax[1], var='CHLA',v_res=0.1)\n",
-    "tools.test_updown_bias(ds, ax[2], var='TEMP',v_res=0.1)\n",
-    "tools.test_updown_bias(ds, ax[3], var='DOXY',v_res=0.1)"
+    "tools.updown_bias(ds, ax[0],var='PSAL',v_res=0.1)\n",
+    "tools.updown_bias(ds,ax[1], var='CHLA',v_res=0.1)\n",
+    "tools.updown_bias(ds, ax[2], var='TEMP',v_res=0.1)\n",
+    "tools.updown_bias(ds, ax[3], var='DOXY',v_res=0.1)"
    ]
   },
   {
@@ -171,7 +171,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -14,9 +14,11 @@ license = { file = "LICENSE" }
 maintainers = [
   { name = "Callum Rollo", email = "[email protected]" },
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.8"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",

requirements-dev.txt

@@ -1,5 +1,13 @@
-jupyterlab
-matplotlib
 netcdf4
 pooch
 xarray
+numpy
+matplotlib
+pandas
+seaborn
+scipy
+cmocean
+skyfield
+tqdm
+jupyterlab
+pytest

tests/test_fetchers.py

@@ -0,0 +1,6 @@
+from glidertest import fetchers
+
+
+def test_demo_datasets():
+    for remote_ds_name in fetchers.data_source_og.registry.keys():
+        ds = fetchers.load_sample_dataset(dataset_name=remote_ds_name)

tests/test_tools.py

@@ -0,0 +1,25 @@
+from glidertest import fetchers, tools
+import matplotlib.pyplot as plt
+
+
+def test_plots():
+    ds = fetchers.load_sample_dataset()
+    tools.plot_basic_vars(ds, end_prof=int(ds.PROFILE_NUMBER.max()))
+
+
+def test_up_down_bias():
+    ds = fetchers.load_sample_dataset()
+    fig, ax = plt.subplots()
+    tools.updown_bias(ds, ax, var='PSAL', v_res=0.1)
+
+
+def test_chl():
+    ds = fetchers.load_sample_dataset()
+    tools.chl_first_check(ds)
+
+
+def test_quench():
+    ds = fetchers.load_sample_dataset()
+    if not "TIME" in ds.indexes.keys():
+        ds = ds.set_xindex('TIME')
+    tools.check_npq(ds, start_time='2023-09-06', end_time='2023-09-08', sel_day=0)