Ruff formatting for most files. Black for notebooks

Matplotlib inline is not needed enymore with recent versions of jupyter and was conflicting with black formatter

docs/notebooks/03Define_sections.ipynb

@@ -65,7 +65,7 @@
    "outputs": [],
    "source": [
     "# The following command adds the .dts accessor to the xarray Dataset.\n",
-    "from dtscalibration import DtsAccessor   # noqa: E401\n",
+    "from dtscalibration import DtsAccessor  # noqa: E401\n",
     "\n",
     "print(ds.dts.get_timeseries_keys())  # list the available timeseeries\n",
     "ds.probe1Temperature.plot(figsize=(12, 8))"

docs/notebooks/04Calculate_variance_Stokes.ipynb

@@ -35,11 +35,9 @@
     "warnings.simplefilter(\"ignore\")  # Hide warnings to avoid clutter in the notebook\n",
     "\n",
     "from dtscalibration import read_silixa_files\n",
-    "from dtscalibration import DtsAccessor   # noqa: E401\n",
+    "from dtscalibration import DtsAccessor  # noqa: E401\n",
     "from dtscalibration.variance_stokes import variance_stokes_constant\n",
-    "from matplotlib import pyplot as plt\n",
-    "\n",
-    "%matplotlib inline"
+    "from matplotlib import pyplot as plt"
    ]
   },
   {

docs/notebooks/07Calibrate_single_ended.ipynb

@@ -43,11 +43,9 @@
     "import os\n",
     "\n",
     "from dtscalibration import read_silixa_files\n",
-    "from dtscalibration import DtsAccessor   # noqa: E401\n",
+    "from dtscalibration import DtsAccessor  # noqa: E401\n",
     "from dtscalibration.variance_stokes import variance_stokes_constant\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "%matplotlib inline"
+    "import matplotlib.pyplot as plt"
    ]
   },
   {

docs/notebooks/08Calibrate_double_ended.ipynb

@@ -45,13 +45,12 @@
     "    suggest_cable_shift_double_ended,\n",
     "    shift_double_ended,\n",
     ")\n",
-    "from dtscalibration import DtsAccessor   # noqa: E401\n",
+    "from dtscalibration import DtsAccessor  # noqa: E401\n",
     "from dtscalibration.variance_stokes import variance_stokes_constant\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "\n",
-    "warnings.simplefilter(\"ignore\")  # Hide warnings to avoid clutter in the notebook\n",
-    "%matplotlib inline"
+    "warnings.simplefilter(\"ignore\")  # Hide warnings to avoid clutter in the notebook"
    ]
   },
   {

docs/notebooks/12Datastore_from_numpy_arrays.ipynb

@@ -27,7 +27,7 @@
     "import xarray as xr\n",
     "\n",
     "from dtscalibration import read_silixa_files\n",
-    "from dtscalibration import DtsAccessor   # noqa: E401\n",
+    "from dtscalibration import DtsAccessor  # noqa: E401\n",
     "from dtscalibration.variance_stokes import variance_stokes_constant"
    ]
   },

docs/notebooks/13Fixed_parameter_calibration.ipynb

@@ -26,12 +26,10 @@
     "import os\n",
     "\n",
     "from dtscalibration import read_silixa_files\n",
-    "from dtscalibration import DtsAccessor   # noqa: E401\n",
+    "from dtscalibration import DtsAccessor  # noqa: E401\n",
     "from dtscalibration.variance_stokes import variance_stokes_constant\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "%matplotlib inline\n",
-    "\n",
     "filepath = os.path.join(\"..\", \"..\", \"tests\", \"data\", \"single_ended\")\n",
     "\n",
     "ds = read_silixa_files(directory=filepath, timezone_netcdf=\"UTC\", file_ext=\"*.xml\")\n",

docs/notebooks/14Lossy_splices.ipynb

@@ -44,11 +44,9 @@
     "import os\n",
     "\n",
     "from dtscalibration import read_silixa_files\n",
-    "from dtscalibration import DtsAccessor   # noqa: E401\n",
+    "from dtscalibration import DtsAccessor  # noqa: E401\n",
     "from dtscalibration.variance_stokes import variance_stokes_constant\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "%matplotlib inline"
+    "import matplotlib.pyplot as plt"
    ]
   },
   {

docs/notebooks/15Matching_sections.ipynb

@@ -40,12 +40,10 @@
     "import os\n",
     "\n",
     "from dtscalibration import read_silixa_files\n",
-    "from dtscalibration import DtsAccessor   # noqa: E401\n",
+    "from dtscalibration import DtsAccessor  # noqa: E401\n",
     "from dtscalibration.variance_stokes import variance_stokes_constant\n",
     "\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "%matplotlib inline"
+    "import matplotlib.pyplot as plt"
    ]
   },
   {

docs/notebooks/16Averaging_temperatures.ipynb

@@ -37,11 +37,9 @@
     "import os\n",
     "\n",
     "from dtscalibration import read_silixa_files\n",
-    "from dtscalibration import DtsAccessor   # noqa: E401\n",
+    "from dtscalibration import DtsAccessor  # noqa: E401\n",
     "from dtscalibration.variance_stokes import variance_stokes_constant\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
-    "%matplotlib inline"
+    "import matplotlib.pyplot as plt"
    ]
   },
   {

docs/notebooks/17Temperature_uncertainty_single_ended.ipynb

@@ -24,7 +24,7 @@
     "import os\n",
     "\n",
     "from dtscalibration import read_silixa_files\n",
-    "from dtscalibration import DtsAccessor   # noqa: E401\n",
+    "from dtscalibration import DtsAccessor  # noqa: E401\n",
     "from dtscalibration.variance_stokes import variance_stokes_constant\n",
     "import matplotlib.pyplot as plt\n",
     "\n",

pyproject.toml

@@ -107,11 +107,11 @@ features = ["dev"]
 [tool.hatch.envs.default.scripts]
 lint = [
   "ruff check src/ tests/ examples/",
-  "black --check src/ tests/ examples/",
+  "black --check docs/notebooks",
   "isort --check-only --diff src/ tests/ examples/",
   "mypy src/",
 ]
-format = ["isort src/ tests/ examples/", "ruff check src/ tests/ examples/ --fix", "ruff format src/ tests/ examples/", "black src/ tests/ examples/", "lint",]
+format = ["isort src/ tests/ examples/", "ruff check src/ tests/ examples/ --fix", "ruff format src/ tests/ examples/", "black docs/notebooks", "lint",]
 test = ["pytest ./src/ ./tests/",]
 fast-test = ["pytest ./tests/ -m \"not slow\"",]
 coverage = [

src/dtscalibration/calibrate_utils.py

@@ -392,9 +392,7 @@ def calibration_single_ended_solver(  # noqa: MC0001
 
         w = (
             1
-            / (
-                ds_sec.st**-2 * st_var_sec + ds_sec.ast**-2 * ast_var_sec
-            ).values.ravel()
+            / (ds_sec.st**-2 * st_var_sec + ds_sec.ast**-2 * ast_var_sec).values.ravel()
         )
 
         if np.any(matching_indices):
@@ -1232,15 +1230,10 @@ def calibrate_double_ended_solver(  # noqa: MC0001
     rst_var_sec = parse_st_var(ds.rst, rst_var).isel(x=ix_sec).values
     rast_var_sec = parse_st_var(ds.rast, rast_var).isel(x=ix_sec).values
 
-    w_F = (
-        1
-        / (ds_sec.st**-2 * st_var_sec + ds_sec.ast**-2 * ast_var_sec).values.ravel()
-    )
+    w_F = 1 / (ds_sec.st**-2 * st_var_sec + ds_sec.ast**-2 * ast_var_sec).values.ravel()
     w_B = (
         1
-        / (
-            ds_sec.rst**-2 * rst_var_sec + ds_sec.rast**-2 * rast_var_sec
-        ).values.ravel()
+        / (ds_sec.rst**-2 * rst_var_sec + ds_sec.rast**-2 * rast_var_sec).values.ravel()
     )
 
     if not np.any(matching_indices):
@@ -1369,12 +1362,8 @@ def calibrate_double_ended_solver(  # noqa: MC0001
         rast_var_mnc = parse_st_var(ds.rast, rast_var).isel(x=ix_match_not_cal).values
 
         w_eq1 = 1 / (
-            (
-                ds_hix.st**-2 * st_var_hix + ds_hix.ast**-2 * ast_var_hix
-            ).values.ravel()
-            + (
-                ds_tix.st**-2 * st_var_tix + ds_tix.ast**-2 * ast_var_tix
-            ).values.ravel()
+            (ds_hix.st**-2 * st_var_hix + ds_hix.ast**-2 * ast_var_hix).values.ravel()
+            + (ds_tix.st**-2 * st_var_tix + ds_tix.ast**-2 * ast_var_tix).values.ravel()
         )
         w_eq2 = 1 / (
             (
@@ -2346,16 +2335,15 @@ def match_sections(ds, matching_sections):
         hxs = ds.x.sel(x=hslice).size
         txs = ds.x.sel(x=tslice).size
 
-        assert (
-            hxs == txs
-        ), "the two sections do not have matching " "number of items: " + str(
-            hslice
-        ) + "size: " + str(
-            hxs
-        ) + str(
-            tslice
-        ) + "size: " + str(
-            txs
+        assert hxs == txs, (
+            "the two sections do not have matching "
+            "number of items: "
+            + str(hslice)
+            + "size: "
+            + str(hxs)
+            + str(tslice)
+            + "size: "
+            + str(txs)
         )
 
     hix = ds.dts.ufunc_per_section(

src/dtscalibration/datastore_utils.py

@@ -36,17 +36,15 @@ def check_dims(
         assert len(labels) > 1, "Define the correct dimensions"
 
         for li in labels[1:]:
-            assert (
-                ds[labels[0]].dims == ds[li].dims
-            ), li + " does not have the correct dimensions." " Should be " + str(
-                ds[labels[0]].dims
+            assert ds[labels[0]].dims == ds[li].dims, (
+                li + " does not have the correct dimensions."
+                " Should be " + str(ds[labels[0]].dims)
             )
     else:
         for li in labels:
-            assert (
-                ds[li].dims == correct_dims
-            ), li + " does not have the correct dimensions. " "Should be " + str(
-                correct_dims
+            assert ds[li].dims == correct_dims, (
+                li + " does not have the correct dimensions. "
+                "Should be " + str(correct_dims)
             )
 
 

src/dtscalibration/io/apsensing.py

@@ -72,9 +72,9 @@ def read_apsensing_files(
         filepathlist = sorted(Path(directory).glob(file_ext))
 
         # Make sure that the list of files contains any files
-        assert (
-            len(filepathlist) >= 1
-        ), "No measurement files found in provided " "directory: \n" + str(directory)
+        assert len(filepathlist) >= 1, (
+            "No measurement files found in provided " "directory: \n" + str(directory)
+        )
 
     # Make sure that the list of files contains any files
     assert len(filepathlist) >= 1, (

src/dtscalibration/io/sensortran.py

@@ -46,9 +46,10 @@ def read_sensortran_files(
     filepathlist_dts = sorted(Path(directory).glob("*BinaryRawDTS.dat"))
 
     # Make sure that the list of files contains any files
-    assert (
-        len(filepathlist_dts) >= 1
-    ), "No RawDTS measurement files found " "in provided directory: \n" + str(directory)
+    assert len(filepathlist_dts) >= 1, (
+        "No RawDTS measurement files found "
+        "in provided directory: \n" + str(directory)
+    )
 
     filepathlist_temp = [
         Path(str(f).replace("RawDTS", "Temp")) for f in filepathlist_dts

src/dtscalibration/io/silixa.py

@@ -61,9 +61,9 @@ def read_silixa_files(
         filepathlist = sorted(Path(directory).glob(file_ext))
 
         # Make sure that the list of files contains any files
-        assert (
-            len(filepathlist) >= 1
-        ), "No measurement files found in provided " "directory: \n" + str(directory)
+        assert len(filepathlist) >= 1, (
+            "No measurement files found in provided " "directory: \n" + str(directory)
+        )
 
     elif filepathlist is None and zip_handle:
         filepathlist = ziphandle_to_filepathlist(fh=zip_handle, extension=file_ext)

tests/test_datastore.py

@@ -665,6 +665,6 @@ def test_merge_double_ended_times(inotinfw, inotinbw, inotinout):
         plot_result=False,
         verbose=False,
     )
-    assert ds.time.size == len(iout) and np.all(
-        ds.st.isel(x=0) == iout
+    assert (
+        ds.time.size == len(iout) and np.all(ds.st.isel(x=0) == iout)
     ), f"FW:{ifw} & BW:{ibw} should lead to {iout} but instead leads to {ds.st.isel(x=0).values}"