Unfortenate formatting of notebooks

docs/notebooks/03Define_sections.ipynb

@@ -23,7 +23,7 @@
    "source": [
     "import os\n",
     "\n",
-    "from dtscalibration import read_silixa_files\n"
+    "from dtscalibration import read_silixa_files"
    ]
   },
   {
@@ -40,7 +40,7 @@
    "outputs": [],
    "source": [
     "filepath = os.path.join(\"..\", \"..\", \"tests\", \"data\", \"double_ended2\")\n",
-    "ds = read_silixa_files(directory=filepath, timezone_netcdf=\"UTC\", file_ext=\"*.xml\")\n"
+    "ds = read_silixa_files(directory=filepath, timezone_netcdf=\"UTC\", file_ext=\"*.xml\")"
    ]
   },
   {
@@ -67,7 +67,7 @@
    "source": [
     "print(ds.timeseries_keys)  # list the available timeseeries\n",
     "ds.probe1Temperature.plot(figsize=(12, 8))\n",
-    "# plot one of the timeseries\n"
+    "# plot one of the timeseries"
    ]
   },
   {
@@ -116,7 +116,7 @@
     "sections = {\n",
     "    \"probe1Temperature\": [slice(7.5, 17.0), slice(70.0, 80.0)],  # cold bath\n",
     "    \"probe2Temperature\": [slice(24.0, 34.0), slice(85.0, 95.0)],  # warm bath\n",
-    "}\n"
+    "}"
    ]
   },
   {

docs/notebooks/04Calculate_variance_Stokes.ipynb

@@ -55,7 +55,7 @@
    "source": [
     "filepath = os.path.join(\"..\", \"..\", \"tests\", \"data\", \"double_ended2\")\n",
     "\n",
-    "ds = read_silixa_files(directory=filepath, timezone_netcdf=\"UTC\", file_ext=\"*.xml\")\n"
+    "ds = read_silixa_files(directory=filepath, timezone_netcdf=\"UTC\", file_ext=\"*.xml\")"
    ]
   },
   {
@@ -81,7 +81,7 @@
     "sections = {\n",
     "    \"probe1Temperature\": [slice(7.5, 17.0), slice(70.0, 80.0)],  # cold bath\n",
     "    \"probe2Temperature\": [slice(24.0, 34.0), slice(85.0, 95.0)],  # warm bath\n",
-    "}\n"
+    "}"
    ]
   },
   {
@@ -125,7 +125,7 @@
     "    \"is approximately {:.2f} on a {:.1f} sec acquisition time\".format(\n",
     "        I_var, ds.userAcquisitionTimeFW.data[0]\n",
     "    )\n",
-    ")\n"
+    ")"
    ]
   },
   {
@@ -152,7 +152,7 @@
     "    robust=True,\n",
     "    units=\"\",\n",
     "    method=\"single\",\n",
-    ")\n"
+    ")"
    ]
   },
   {
@@ -186,7 +186,7 @@
     "x = np.linspace(mean - 3 * sigma, mean + 3 * sigma, 100)\n",
     "approximated_normal_fit = scipy.stats.norm.pdf(x, mean, sigma)\n",
     "residuals.plot.hist(bins=50, figsize=(12, 8), density=True)\n",
-    "plt.plot(x, approximated_normal_fit)\n"
+    "plt.plot(x, approximated_normal_fit)"
    ]
   },
   {

docs/notebooks/07Calibrate_single_ended.ipynb

@@ -72,7 +72,7 @@
    "outputs": [],
    "source": [
     "filepath = os.path.join(\"..\", \"..\", \"tests\", \"data\", \"single_ended\")\n",
-    "ds = read_silixa_files(directory=filepath, timezone_netcdf=\"UTC\", file_ext=\"*.xml\")\n"
+    "ds = read_silixa_files(directory=filepath, timezone_netcdf=\"UTC\", file_ext=\"*.xml\")"
    ]
   },
   {
@@ -93,7 +93,7 @@
     "sections = {\n",
     "    \"probe1Temperature\": [slice(20, 25.5)],  # warm bath\n",
     "    \"probe2Temperature\": [slice(5.5, 15.5)],  # cold bath\n",
-    "}\n"
+    "}"
    ]
   },
   {
@@ -120,7 +120,7 @@
    "outputs": [],
    "source": [
     "st_var, resid = ds.variance_stokes_constant(sections=sections, st_label=\"st\")\n",
-    "ast_var, _ = ds.variance_stokes_constant(sections=sections, st_label=\"ast\")\n"
+    "ast_var, _ = ds.variance_stokes_constant(sections=sections, st_label=\"ast\")"
    ]
   },
   {
@@ -136,7 +136,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "resid.plot(figsize=(12, 4))\n"
+    "resid.plot(figsize=(12, 4))"
    ]
   },
   {
@@ -160,7 +160,7 @@
    },
    "outputs": [],
    "source": [
-    "ds.calibration_single_ended(sections=sections, st_var=st_var, ast_var=ast_var)\n"
+    "ds.calibration_single_ended(sections=sections, st_var=st_var, ast_var=ast_var)"
    ]
   },
   {
@@ -177,7 +177,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds.tmpf.plot(figsize=(12, 4))\n"
+    "ds.tmpf.plot(figsize=(12, 4))"
    ]
   },
   {
@@ -189,7 +189,7 @@
     "ds1 = ds.isel(time=0)\n",
     "ds1.tmpf.plot(figsize=(12, 4))\n",
     "(ds1.tmpf_var**0.5).plot(figsize=(12, 4))\n",
-    "plt.ylabel(\"$\\sigma$ ($^\\circ$C)\")\n"
+    "plt.ylabel(\"$\\sigma$ ($^\\circ$C)\")"
    ]
   },
   {
@@ -217,7 +217,7 @@
    "outputs": [],
    "source": [
     "ds1.st.plot(figsize=(12, 8))\n",
-    "ds1.ast.plot()\n"
+    "ds1.ast.plot()"
    ]
   },
   {

docs/notebooks/08Calibrate_double_ended.ipynb

@@ -70,7 +70,7 @@
     "\n",
     "ds_notaligned = read_silixa_files(\n",
     "    directory=filepath, timezone_netcdf=\"UTC\", file_ext=\"*.xml\"\n",
-    ")\n"
+    ")"
    ]
   },
   {
@@ -102,7 +102,7 @@
    },
    "outputs": [],
    "source": [
-    "ds_notaligned = ds_notaligned.sel(x=slice(0, 100))  # only calibrate parts of the fiber\n"
+    "ds_notaligned = ds_notaligned.sel(x=slice(0, 100))  # only calibrate parts of the fiber"
    ]
   },
   {
@@ -124,7 +124,7 @@
     "    plot_result=True,\n",
     "    figsize=(12, 6),\n",
     ")\n",
-    "print(suggested_shift)\n"
+    "print(suggested_shift)"
    ]
   },
   {
@@ -140,7 +140,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds = shift_double_ended(ds_notaligned, suggested_shift[0])\n"
+    "ds = shift_double_ended(ds_notaligned, suggested_shift[0])"
    ]
   },
   {
@@ -160,7 +160,7 @@
     "sections = {\n",
     "    \"probe1Temperature\": [slice(7.5, 17.0), slice(70.0, 80.0)],  # cold bath\n",
     "    \"probe2Temperature\": [slice(24.0, 34.0), slice(85.0, 95.0)],  # warm bath\n",
-    "}\n"
+    "}"
    ]
   },
   {
@@ -189,7 +189,7 @@
     "st_var, resid = ds.variance_stokes_constant(sections=sections, st_label=\"st\")\n",
     "ast_var, _ = ds.variance_stokes_constant(sections=sections, st_label=\"ast\")\n",
     "rst_var, _ = ds.variance_stokes_constant(sections=sections, st_label=\"rst\")\n",
-    "rast_var, _ = ds.variance_stokes_constant(sections=sections, st_label=\"rast\")\n"
+    "rast_var, _ = ds.variance_stokes_constant(sections=sections, st_label=\"rast\")"
    ]
   },
   {
@@ -212,7 +212,7 @@
    },
    "outputs": [],
    "source": [
-    "resid.plot(figsize=(12, 4))\n"
+    "resid.plot(figsize=(12, 4))"
    ]
   },
   {
@@ -242,7 +242,7 @@
     "    ast_var=ast_var,\n",
     "    rst_var=rst_var,\n",
     "    rast_var=rast_var,\n",
-    ")\n"
+    ")"
    ]
   },
   {
@@ -258,7 +258,7 @@
    },
    "outputs": [],
    "source": [
-    "ds.tmpw.plot(figsize=(12, 4))\n"
+    "ds.tmpw.plot(figsize=(12, 4))"
    ]
   },
   {
@@ -296,7 +296,7 @@
     "ds.tmpw_var.plot(figsize=(12, 4))\n",
     "ds1 = ds.isel(time=-1)  # take only the first timestep\n",
     "(ds1.tmpw_var**0.5).plot(figsize=(12, 4))\n",
-    "plt.gca().set_ylabel(\"Standard error ($^\\circ$C)\")\n"
+    "plt.gca().set_ylabel(\"Standard error ($^\\circ$C)\")"
    ]
   },
   {
@@ -333,7 +333,7 @@
     "    mc_sample_size=500,\n",
     ")  # < increase sample size for better approximation\n",
     "\n",
-    "ds.tmpw_mc_var.plot(figsize=(12, 4))\n"
+    "ds.tmpw_mc_var.plot(figsize=(12, 4))"
    ]
   },
   {
@@ -353,7 +353,7 @@
     "ds1.tmpw.plot(linewidth=0.7, figsize=(12, 4))\n",
     "ds1.tmpw_mc.isel(CI=0).plot(linewidth=0.7, label=\"CI: 2.5%\")\n",
     "ds1.tmpw_mc.isel(CI=1).plot(linewidth=0.7, label=\"CI: 97.5%\")\n",
-    "plt.legend(fontsize=\"small\")\n"
+    "plt.legend(fontsize=\"small\")"
    ]
   },
   {
@@ -382,7 +382,7 @@
     "(ds1.tmpb_var**0.5).plot()\n",
     "(ds1.tmpw_var**0.5).plot()\n",
     "(ds1.tmpw_mc_var**0.5).plot()\n",
-    "plt.ylabel(\"$\\sigma$ ($^\\circ$C)\")\n"
+    "plt.ylabel(\"$\\sigma$ ($^\\circ$C)\")"
    ]
   },
   {

docs/notebooks/12Datastore_from_numpy_arrays.ipynb

@@ -26,7 +26,7 @@
     "import matplotlib.pyplot as plt\n",
     "import xarray as xr\n",
     "\n",
-    "from dtscalibration import DataStore, read_silixa_files\n"
+    "from dtscalibration import DataStore, read_silixa_files"
    ]
   },
   {
@@ -61,7 +61,7 @@
    "source": [
     "filepath = os.path.join(\"..\", \"..\", \"tests\", \"data\", \"single_ended\")\n",
     "\n",
-    "ds_silixa = read_silixa_files(directory=filepath, silent=True)\n"
+    "ds_silixa = read_silixa_files(directory=filepath, silent=True)"
    ]
   },
   {
@@ -89,7 +89,7 @@
     "x = ds_silixa.x.values\n",
     "time = ds_silixa.time.values\n",
     "ST = ds_silixa.st.values\n",
-    "AST = ds_silixa.ast.values\n"
+    "AST = ds_silixa.ast.values"
    ]
   },
   {
@@ -116,7 +116,7 @@
     "ds[\"x\"] = (\"x\", x)\n",
     "ds[\"time\"] = (\"time\", time)\n",
     "ds[\"st\"] = ([\"x\", \"time\"], ST)\n",
-    "ds[\"ast\"] = ([\"x\", \"time\"], AST)\n"
+    "ds[\"ast\"] = ([\"x\", \"time\"], AST)"
    ]
   },
   {
@@ -133,7 +133,7 @@
    "outputs": [],
    "source": [
     "ds = DataStore(ds)\n",
-    "print(ds)\n"
+    "print(ds)"
    ]
   },
   {
@@ -169,7 +169,7 @@
     "ds[\"temp1\"] = ds_silixa[\"probe1Temperature\"]\n",
     "ds[\"temp2\"] = ds_silixa[\"probe2Temperature\"]\n",
     "\n",
-    "ds.attrs[\"isDoubleEnded\"] = \"0\"\n"
+    "ds.attrs[\"isDoubleEnded\"] = \"0\""
    ]
   },
   {
@@ -202,7 +202,7 @@
     "ast_var, _ = ds.variance_stokes_constant(sections=sections, st_label=\"ast\")\n",
     "ds.calibration_single_ended(sections=sections, st_var=st_var, ast_var=ast_var)\n",
     "\n",
-    "ds.isel(time=0).tmpf.plot()\n"
+    "ds.isel(time=0).tmpf.plot()"
    ]
   },
   {
@@ -211,7 +211,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds\n"
+    "ds"
    ]
   },
   {

docs/notebooks/13Fixed_parameter_calibration.ipynb

@@ -76,7 +76,7 @@
     "    ast_var=ast_var,\n",
     "    fix_gamma=fix_gamma,\n",
     "    fix_dalpha=fix_dalpha,\n",
-    ")\n"
+    ")"
    ]
   },
   {
@@ -100,7 +100,7 @@
    "outputs": [],
    "source": [
     "print(\"gamma used in calibration:\", ds100.gamma.values)\n",
-    "print(\"dalpha used in calibration:\", ds100.dalpha.values)\n"
+    "print(\"dalpha used in calibration:\", ds100.dalpha.values)"
    ]
   },
   {
@@ -132,7 +132,7 @@
     "    linewidth=1, label=\"Device calibrated\"\n",
     ")  # plot the temperature calibrated by the device\n",
     "plt.title(\"Temperature at the first time step\")\n",
-    "plt.legend()\n"
+    "plt.legend()"
    ]
   },
   {