Accessor (#204)

* User-friendly error when setting manually ds.sections Solves #200 * User-friendly error when setting manually ds.sections Solves #200 * Revert accidental double implementation of sections.setter * Update documentation of datastore class * Removed numbagg from dependencies llvmlite is a pain to install with pip. Alternatively, it could be installed with conda * Explicitly pass sections to more functions * Format * Moving away from calibrate_double_ended() inplace self.update(out) is still in place at the end * Refactored calibrate_double_ended covariance calculation * Parallel testing * refactored variance functions * Include pyupgrade flag of ruff * Refactored single ended routine p_val to params and moved averaging routines * Update .gitignore * Refactored calibration routines In preparation of the accessor * Please ruff * Refactored Datastore class * Updated sections example notebook * Updated example notebooks * Add api to docs * Unfortenate formatting of notebooks * Estimate variance of stokes refactored * single_ended_calibration and single_conf_ints working * renamed conf_ints_single_ended to monte_carlo_single_ended and calibration_single_ended to calibrate_ssingle_ended * Removed DataStore from being used * removed renaming_labels test * conf_int_single renamed to monte_carlo_single * Initial commit monte_carlo_double_ended * Single and double ended calibration working and tested, including the monte carlo runs * Got several variance_tests working * Passing all variance tests * Passing all tests except lint and examples * Undo certain merge changes * Minor cleanup * Circumventing circular import DTSaccessor * Update 03Define_sections.ipynb * Update 04Calculate_variance_Stokes.ipynb * Update 07Calibrate_single_ended.ipynb * Update 08Calibrate_double_ended.ipynb * calibration_double_ended to calibrate_double_ended * Update 12Datastore_from_numpy_arrays.ipynb * Update 13Fixed_parameter_calibration.ipynb * Update 14Lossy_splices.ipynb * Update 16Averaging_temperatures.ipynb * Update 17Temperature_uncertainty_single_ended.ipynb * Formatting of the entire repository * Docs cleanup * Fixed variance test * Update test_variance_stokes.py * Update 15Matching_sections.ipynb * Updated 16Averaging notebook * Update test_examples.py * Update test_examples.py * Fixing weirdly failing notebooks * Update test_examples.py * Rewritten test_notebooks routine * Removed unused variable * Remove metadata from notebook 12 * Delete 02Common_DataStore_functions_slice_mean_max_std_resample.ipynb * Remove old reference to DataStore in notebooks * Removed references to ds.variance_*() from docs * Update src/dtscalibration/dts_accessor.py Co-authored-by: Bart Schilperoort <[email protected]> * Update test_examples.py * Update docs * Minimal attempt to fix docs * Update README.rst --------- Co-authored-by: Bart Schilperoort <[email protected]>
dtscalibration · Oct 27, 2023 · 588db04 · 588db04
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diff --git a/.gitignore b/.gitignore
@@ -57,6 +57,7 @@ output/*/index.html
 
 # Sphinx
 docs/_build
+**/generated/**/*
 
 .DS_Store
 *~

diff --git a/README.rst b/README.rst
@@ -93,6 +93,7 @@ Devices currently supported
 Documentation
 =============
 
+* A full calibration procedure for single-ended setups is presented in notebook `07Calibrate_single_ended.ipynb <https://github.com/dtscalibration/python-dts-calibration/blob/main/docs/notebooks/07Calibrate_single_ended.ipynb>`_ and for double-ended setups in `08Calibrate_double_ended.ipynb <https://github.com/dtscalibration/python-dts-calibration/blob/main/docs/notebooks/08Calibrate_double_ended.ipynb>`_.
 * Documentation at https://python-dts-calibration.readthedocs.io/ .
 * Example notebooks that work within the browser can be viewed `here <https://python-dts-calibration.readthedocs.io/en/latest/learn_by_examples.html>`_.
 

diff --git a/docs/api/dtscalibration.DataStore.rst b/docs/api/dtscalibration.DataStore.rst
diff --git a/docs/api/dtscalibration.check_dims.rst b/docs/api/dtscalibration.check_dims.rst
diff --git a/docs/api/dtscalibration.check_timestep_allclose.rst b/docs/api/dtscalibration.check_timestep_allclose.rst
diff --git a/docs/api/dtscalibration.get_netcdf_encoding.rst b/docs/api/dtscalibration.get_netcdf_encoding.rst
diff --git a/docs/api/dtscalibration.merge_double_ended.rst b/docs/api/dtscalibration.merge_double_ended.rst
diff --git a/docs/api/dtscalibration.open_datastore.rst b/docs/api/dtscalibration.open_datastore.rst
diff --git a/docs/api/dtscalibration.open_mf_datastore.rst b/docs/api/dtscalibration.open_mf_datastore.rst
diff --git a/docs/api/dtscalibration.plot_accuracy.rst b/docs/api/dtscalibration.plot_accuracy.rst
diff --git a/docs/api/dtscalibration.plot_location_residuals_double_ended.rst b/docs/api/dtscalibration.plot_location_residuals_double_ended.rst
diff --git a/docs/api/dtscalibration.plot_residuals_reference_sections.rst b/docs/api/dtscalibration.plot_residuals_reference_sections.rst
diff --git a/docs/api/dtscalibration.plot_residuals_reference_sections_single.rst b/docs/api/dtscalibration.plot_residuals_reference_sections_single.rst
diff --git a/docs/api/dtscalibration.plot_sigma_report.rst b/docs/api/dtscalibration.plot_sigma_report.rst
diff --git a/docs/api/dtscalibration.read_apsensing_files.rst b/docs/api/dtscalibration.read_apsensing_files.rst
diff --git a/docs/api/dtscalibration.read_sensornet_files.rst b/docs/api/dtscalibration.read_sensornet_files.rst
diff --git a/docs/api/dtscalibration.read_sensortran_files.rst b/docs/api/dtscalibration.read_sensortran_files.rst
diff --git a/docs/api/dtscalibration.read_silixa_files.rst b/docs/api/dtscalibration.read_silixa_files.rst
diff --git a/docs/api/dtscalibration.shift_double_ended.rst b/docs/api/dtscalibration.shift_double_ended.rst
diff --git a/docs/api/dtscalibration.suggest_cable_shift_double_ended.rst b/docs/api/dtscalibration.suggest_cable_shift_double_ended.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,7 +1,11 @@
-# -*- coding: utf-8 -*-
-from datetime import date
 import os
+from datetime import date
+
+from xarray import Dataset  # noqa: E402
+import sphinx_autosummary_accessors
 
+import dtscalibration  # noqa: E402
+from dtscalibration.dts_accessor import DtsAccessor  # noqa: E402
 
 extensions = [
     "sphinx_rtd_theme",
@@ -15,6 +19,7 @@
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
     "sphinx.ext.autosectionlabel",
+    "sphinx_autosummary_accessors",
     "nbsphinx",
     "sphinx.ext.mathjax",
     "sphinx.ext.intersphinx",
@@ -41,11 +46,11 @@
 project = "dtscalibration"
 year = str(date.today().year)
 author = "Bas des Tombe and Bart Schilperoort"
-copyright = "{0}, {1}".format(year, author)
+copyright = f"{year}, {author}"
 version = release = "2.0.0"
 
 pygments_style = "trac"
-templates_path = ["."]
+templates_path = [".", sphinx_autosummary_accessors.templates_path]
 extlinks = {
     "issue": (
         "https://github.com/dtscalibration/python-dts-calibration/issues" "/%s",
@@ -63,7 +68,7 @@
 html_sidebars = {
     "**": ["searchbox.html", "globaltoc.html", "sourcelink.html"],
 }
-html_short_title = "%s-%s" % (project, version)
+html_short_title = f"{project}-{version}"
 
 napoleon_use_ivar = True
 napoleon_use_rtype = False

diff --git a/docs/notebooks/01Load_xml_measurement_files.ipynb b/docs/notebooks/01Load_xml_measurement_files.ipynb
@@ -7,13 +7,13 @@
    "source": [
     "# 1. Load your first measurement files\n",
     "\n",
-    "The goal of this notebook is to show the different options of loading measurements from raw DTS files. These files are loaded into a `DataStore` object. This object has various methods for calibration, plotting. The current supported devices are:\n",
+    "The goal of this notebook is to show the different options of loading measurements from raw DTS files. These files are loaded into a `xarray.Dataset` object. This object has various methods for calibration, plotting. Both single-ended and double-ended measurements are supported. The current supported devices are:\n",
     "- Silixa\n",
     "- Sensornet\n",
+    "- AP Sensing\n",
+    "- Sensortran\n",
     "\n",
-    "This example loads Silixa files. Both single-ended and double-ended measurements are supported. The first step is to load the correct read routine from `dtscalibration`.\n",
-    "- Silixa -> `dtscalibration.read_silixa_files`\n",
-    "- Sensornet -> `dtscalibration.read_sensornet_files`"
+    "See notebooks A2, A3, and A4."
    ]
   },
   {
@@ -125,20 +125,6 @@
    "source": [
     "print(ds)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -157,7 +143,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.5"
+   "version": "3.10.10"
   }
  },
  "nbformat": 4,