docs: skeleton of code reference

docs/sec_code_reference.rst

@@ -7,11 +7,106 @@ Code reference
 
 
 
-.. _sec_ref_definitions:
+.. _sec_ref_alias:
 
-
-module-level methods
+Module level aliases
 ====================
-autofunction ...
+For user convenience, the following objects are available
+at the module level.
+
+.. class:: nanite.Indentation
+
+    alias of :class:`nanite.indent.Indentation`
+
+.. class:: nanite.IndentationDataSet
+
+    alias of :class:`nanite.dataset.IndentationDataSet`
+
+.. class:: nanite.IndentationRater
+
+    alias of :class:`nanite.rate.IndentationRater`
+
+.. class:: nanite.QMap
+
+    alias of :class:`nanite.qmap.QMap`
+
+
+.. _sec_ref_indent:
+
+Force-indentation data
+======================
+
+.. automodule:: nanite.indent
+   :members:
+   :undoc-members:
+
+
+.. _sec_ref_dataset:
+
+Datasets
+========
+
+.. automodule:: nanite.dataset
+   :members:
+   :undoc-members:
+
+
+.. _sec_ref_read:
+
+Loading data
+============
+
+.. automodule:: nanite.read
+   :members:
+   :undoc-members:
+
+
+.. _sec_ref_preproc:
+
+Preprocessing
+=============
+
+.. automodule:: nanite.preproc
+   :members:
+   :undoc-members:
+
+
+.. _sec_ref_model:
+
+Modeling
+========
+
+.. automodule:: nanite.model
+   :members:
+   :undoc-members:
+
+
+.. _sec_ref_fit:
+
+Fitting
+=======
+
+.. automodule:: nanite.fit
+   :members:
+   :undoc-members:
+
+
+.. _sec_ref_rate:
+
+Rating
+======
+
+.. automodule:: nanite.rate
+   :members:
+   :undoc-members:
+
+
+.. _sec_ref_qmap:
+
+Quantitative maps
+=================
 
+.. automodule:: nanite.qmap
+   :members:
+   :undoc-members:
 

nanite/fit.py

@@ -49,12 +49,14 @@ class FitProperties(dict):
     and dynamically manage resets due to new initial parameters.
 
     Dynamic properties include:
+
     - set "params_initial" to `None` if the "model_key" changes
     - remove all keys except those in `FP_DEFAULT` if a key that is
       in `FP_DEFAULT` changes (All other keys are considered to be
       obsolete fitting results).
 
     Additional attributes:
+
     - "segment_bool": bool
         `False` for "approach" and `True` for "retract"
     """
@@ -121,6 +123,7 @@ def __init__(self, data_set, **kwargs):
             The range for fitting, see `range_type` below.
         range_type: str
             One of:
+
             - absolute:
                 Set the absolute fitting range in values
                 given by the `x_axis`.
@@ -290,6 +293,7 @@ def compute_opt_mindelta(emoduli, indentations):
         """Determine the plateau of an emodulus-indentation curve
 
         The following procedure is performed:
+
         1. Smooth the emodulus data with a Butterworth filter
         2. Label sequences that have similar values by binning
            into ten regions between the min and max.

nanite/indent.py

@@ -24,6 +24,7 @@ def __init__(self, approach, retract, metadata, path, enum=0):
         approach, retract: [1d ndarray, unit, title]
             The respective curves obtained by the `readfiles` module.
             The columns must be available:
+
               - "time" [s]
               - "force" [N]
               - "height (measured)" [m]
@@ -167,14 +168,14 @@ def estimate_contact_point_index(self):
         that one which returns the smallest index is returned.
 
         Method 1: baseline deviation
-        ----------------------------
+
         1. Obtain the baseline (initial 10% of the approach curve)
         2. Compute average and maximum deviation of the baseline
         3. The CP is the index of the approach curve where it exceeds
            twice of the maximum deviation
 
         Method 2: sign of gradient
-        ----------------------------
+
         1. Perform a median filter on the approach curve
         2. Compute the gradient
         3. Cut off trailing 10 points from the gradient (noise)
@@ -247,6 +248,7 @@ def fit_model(self, **kwargs):
             The range for fitting, see `range_type` below.
         range_type: str
             One of:
+
             - absolute:
                 Set the absolute fitting range in values
                 given by the `x_axis`.

nanite/qmap.py

@@ -16,7 +16,7 @@ def __init__(self, path_or_dataset, callback=None):
 
         Parameters
         ----------
-        path_or_dataset: str or IndentationDataSet
+        path_or_dataset: str or nanite.IndentationDataSet
             The path to the data file. The data format is determined
             using the extension of the file and the data is loaded
             with the correct method.