GEOPY-2456: Solve warning issues raised by RTD

docs/content/user_guide/airborne_tem.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "# Airborne Time-Domain\n",
     "\n",
-    "This type of survey can be used to store airborne time-domain electromagnetic (ATEM) data defined by a fixed transmitter-receiver loop configuration. The survey is made up of two entities ([AirborneTEMTransmitters](../api/geoh5py.objects.surveys.electromagnetics.rst#geoh5py.objects.surveys.electromagnetics.airborne_tem.AirborneTEMTransmitters) and [AirborneTEMReceivers](../api/geoh5py.objects.surveys.electromagnetics.rst#geoh5py.objects.surveys.electromagnetics.airborne_tem.AirborneTEMReceivers)) linked by their metadata.\n",
+    "This type of survey can be used to store airborne time-domain electromagnetic (ATEM) data defined by a fixed transmitter-receiver loop configuration. The survey is made up of two entities ({py:class}`geoh5py.objects.surveys.electromagnetics.airborne_tem.AirborneTEMTransmitters` and {py:class}`geoh5py.objects.surveys.electromagnetics.airborne_tem.AirborneTEMReceivers`) linked by their metadata.\n",
     "\n",
     "The following example shows how to generate an airborne TEM survey with associated data stored in `geoh5` format and accessible from [Geoscience ANALYST](https://mirageoscience.com/mining-industry-software/geoscience-analyst/).\n",
     "\n",
@@ -169,9 +169,9 @@
    "source": [
     "### Property groups\n",
     "\n",
-    "List of [PropertyGroup](../api/geoh5py.groups.rst#module-geoh5py.groups.property_group)s defining the various data components (e.g. `dBzdt`, `Bz`, ...). It is expected that each component contains data channels at all times and in the same order as defined in `Channels`.\n",
+    "List of {py:class}`geoh5py.groups.property_group.PropertyGroup`s defining the various data components (e.g. `dBzdt`, `Bz`, ...). It is expected that each component contains data channels at all times and in the same order as defined in `Channels`.\n",
     "\n",
-    "The class method [add_component_data](../api/geoh5py.objects.surveys.electromagnetics.rst#geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.add_components_data) can help users add data from nested dictionaries. Below is an example using four components:"
+    "The class method {py:func}`geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.add_components_data` can help users add data from nested dictionaries. Below is an example using four components:"
    ]
   },
   {
@@ -220,7 +220,7 @@
    "id": "17",
    "metadata": {},
    "source": [
-    "Data channels associated with each component can be quickly accessed through the [BaseEMSurvey.components](../api/geoh5py.objects.surveys.electromagnetics.rst#geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.components) property:"
+    "Data channels associated with each component can be quickly accessed through the {py:func}`geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.components` property:"
    ]
   },
   {
@@ -398,7 +398,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "demo",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -412,7 +412,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.2"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,

docs/content/user_guide/data.ipynb

@@ -46,6 +46,7 @@
    "id": "2",
    "metadata": {},
    "source": [
+    "(float-section)=\n",
     "## Float\n",
     "\n",
     "Numerical `float` data can be attached to the various elements making up object. Data can be added to an `Object` entity using the `add_data` method."
@@ -119,7 +120,7 @@
    "source": [
     "## Integer\n",
     "\n",
-    "Same implementation as for [Float](#Float) data type but with values provided as integer (`int32`)."
+    "Same implementation as for [Float](float-section) data type but with values provided as integer (`int32`)."
    ]
   },
   {
@@ -209,7 +210,7 @@
    "id": "14",
    "metadata": {},
    "source": [
-    "We now have an array that contains a range of integer values for red, green, blue and alpha (RGBA) over the span of the data values. This array can be used to implicitly create a [MyColorMap](../api/geoh5py.data.rst#module-geoh5py.data.color_map) from the `EntityType`."
+    "We now have an array that contains a range of integer values for red, green, blue and alpha (RGBA) over the span of the data values. This array can be used to implicitly create a {py:class}`geoh5py.data.color_map.ColorMap` from the `EntityType`."
    ]
   },
   {
@@ -491,7 +492,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.2"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,

docs/content/user_guide/direct_current.ipynb

@@ -21,7 +21,7 @@
    "source": [
     "## Current Electrode (transmitters)\n",
     "\n",
-    "The [CurrentElectrode](../api/geoh5py.objects.surveys.rst#geoh5py.objects.surveys.direct_current.CurrentElectrode) entity defines the A-B dipole pairs used to inject current into the ground. It is a sub-class of the [PotentialElectrode](../api/geoh5py.objects.surveys.rst#geoh5py.objects.surveys.direct_current.PotentialElectrode) object defined by vertices (poles) and cells (dipoles). Here we generate four (4) parallel EW lines with eight dipoles per line."
+    "The {py:class}`geoh5py.objects.surveys.direct_current.CurrentElectrode` entity defines the A-B dipole pairs used to inject current into the ground. It is a sub-class of the {py:class}`geoh5py.objects.surveys.direct_current.PotentialElectrode` object defined by vertices (poles) and cells (dipoles). Here we generate four (4) parallel EW lines with eight dipoles per line."
    ]
   },
   {
@@ -70,12 +70,12 @@
    "id": "4",
    "metadata": {},
    "source": [
-    "At this stage the `CurrentElectrode` object has segments (`cells`) connecting all poles in series along line. \n",
+    "At this stage, the `CurrentElectrode` object has segments (`cells`) connecting all poles in series along line. \n",
     "\n",
     "### AB Cell ID\n",
-    "A key element of the DCIP survey objects is the `ab_cell_id` property. This `ReferenceData` contains the map referencing each cell of the `CurrentElectrode` object to a unique A-B source identifier with name.\n",
+    "A key element of the DCIP survey objects is the `ab_cell_id` property. This `ReferenceData` contains the map referencing each cell of the `CurrentElectrode` object to a unique A-B source identifier with a name.\n",
     "\n",
-    "The utility function [add_default_ab_cell_id](../api/geoh5py.objects.surveys.rst#geoh5py.objects.surveys.direct_current.CurrentElectrode.add_default_ab_cell_id) can help generate this map with a simple name string incrementor."
+    "The utility function {py:func}`geoh5py.objects.surveys.direct_current.CurrentElectrode.add_default_ab_cell_id` can help generate this map with a simple name string incrementor."
    ]
   },
   {
@@ -115,9 +115,9 @@
    "source": [
     "## Potential Electrode (receivers)\n",
     "\n",
-    "The [PotentialElectrode](../api/geoh5py.objects.surveys.rst#geoh5py.objects.surveys.direct_current.PotentialElectrode) object defines the M-N dipole pairs used to measure the electric potential (receivers). It is a sub-class of the [Curve](../api/geoh5py.objects.rst#geoh5py.objects.curve.Curve) object defined by `vertices` (poles) and `cells` (dipoles). \n",
+    "The {py:class}`geoh5py.objects.surveys.direct_current.PotentialElectrode` object defines the M-N dipole pairs used to measure the electric potential (receivers). It is a subclass of the {py:class}`geoh5py.objects.curve.Curve` object defined by `vertices` (poles) and `cells` (dipoles). \n",
     "\n",
-    "Although poles could be set independently on the `CurrentElectrode` and `PotentialElectrode` objects, here we re-uses the same locations for simplicity.  We must also define the receiver dipoles. The following routine generates a maximum of six (6) receivers dipoles per injection currents along line."
+    "Although poles could be set independently on the `CurrentElectrode` and `PotentialElectrode` objects, here we reuse the same locations for simplicity.  We must also define the receiver dipoles. The following routine generates up to six (6) receiver dipoles per injection current along the line."
    ]
   },
   {
@@ -187,7 +187,7 @@
    "id": "13",
    "metadata": {},
    "source": [
-    "The link between the sources [CurrentElectrode](../api/geoh5py.objects.surveys.rst#geoh5py.objects.surveys.direct_current.CurrentElectrode) and the receivers [PotentialElectrode](../api/geoh5py.objects.surveys.rst#geoh5py.objects.surveys.direct_current.PotentialElectrode) is established by the `metadata`, shared by both entities. The connection can be made by assigning `current_electrodes` to the receivers: "
+    "The link between the sources `CurrentElectrode` and the receivers `PotentialElectrode` is established by the `metadata`, shared by both entities. The connection can be made by assigning `current_electrodes` to the receivers: "
    ]
   },
   {
@@ -312,7 +312,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.2"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,

docs/content/user_guide/magnetotelluric.ipynb

@@ -57,7 +57,7 @@
    "source": [
     "## Metadata\n",
     "\n",
-    "Along with the [MTReceivers](../api/geoh5py.objects.surveys.electromagnetics.rst#module-geoh5py.objects.surveys.electromagnetics.magnetotellurics), the metadata contains all the necessary information to define the geophysical experiment."
+    "Along with the {py:class}`geoh5py.objects.surveys.electromagnetics.magnetotellurics.MTReceivers`, the metadata contains all the necessary information to define the geophysical experiment."
    ]
   },
   {
@@ -123,9 +123,9 @@
    "source": [
     "### Property groups\n",
     "\n",
-    "List of [PropertyGroup](../api/geoh5py.groups.rst#module-geoh5py.groups.property_group)s defining the various data components (e.g. `Zxx (real)`, `Zxy (imag)`, ...). It is not required to supply all components of the impedence tensor, but it is expected that each component contains a list of data channels of length and in the same order as the `Channels` (one `Data` per frequency).\n",
+    "List of {py:class}`module-geoh5py.groups.property_group.PropertyGroup`s defining the various data components (e.g. `Zxx (real)`, `Zxy (imag)`, ...). It is not required to supply all components of the impedance tensor, but it is expected that each component contains a list of data channels of length and in the same order as the `Channels` (one `Data` per frequency).\n",
     "\n",
-    "The class method [add_components_data](../api/geoh5py.objects.surveys.electromagnetics.rst#geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.add_components_data) can help users add data from nested dictionaries. Below is an example using four components:"
+    "The class method {py:func}`geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.add_components_data` can help users add data from nested dictionaries. Below is an example using four components:"
    ]
   },
   {
@@ -231,7 +231,7 @@
    "id": "12",
    "metadata": {},
    "source": [
-    "Data channels associated with each component can be quickly accessed through the [BaseEMSurvey.components](../api/geoh5py.objects.surveys.electromagnetics.rst#geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.components) property:"
+    "Data channels associated with each component can be quickly accessed through the {py:class}`geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.components` property:"
    ]
   },
   {
@@ -335,7 +335,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.2"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,

docs/content/user_guide/objects.ipynb

@@ -366,7 +366,7 @@
    "metadata": {},
    "source": [
     "### Geo-referencing\n",
-    "By default, the `GeoImage` object will be displayed at the origin (xy-plane) with dimensions equal to the pixel count. The utility function [GeoImage.georeference](../api/geoh5py.objects.rst#geoh5py.objects.geo_image.GeoImage.georeference) lets users geo-reference the image in 3D space based on at least three (3) input reference points (pixels) with associated world coordinates."
+    "By default, the `GeoImage` object will be displayed at the origin (xy-plane) with dimensions equal to the pixel count. The utility function {py:func}`geoh5py.objects.geo_image.GeoImage.georeference` lets users geo-reference the image in 3D space based on at least three (3) input reference points (pixels) with associated world coordinates."
    ]
   },
   {
@@ -616,7 +616,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.17"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,

docs/content/user_guide/tipper.ipynb

@@ -101,7 +101,7 @@
    "source": [
     "## Metadata\n",
     "\n",
-    "Along with the [TipperReceivers](../api/geoh5py.objects.surveys.electromagnetics.rst#geoh5py.objects.surveys.electromagnetics.tipper.TipperReceivers), the metadata contains all the necessary information to define the geophysical experiment."
+    "Along with the {py:class}`geoh5py.objects.surveys.electromagnetics.tipper.TipperReceivers`, the **metadata** contains all the necessary information to define the geophysical experiment."
    ]
   },
   {
@@ -151,9 +151,9 @@
    "source": [
     "### Property groups\n",
     "\n",
-    "List of [PropertyGroup](../api/geoh5py.groups.rst#module-geoh5py.groups.property_group)s defining the various data components (e.g. `Txz (real)`, `Tyz (imag)`, ...). It is not required to supply all components of the impedence tensor, but it is expected that each component contains a list of data channels of length and in the same order as the `Channels` (one `Data` per frequency).\n",
+    "List of {py:class}`geoh5py.groups.property_group.PropertyGroup` instances defining the various data components (e.g. `Txz (real)`, `Tyz (imag)`, ...). It is not required to supply all components of the impedence tensor, but it is expected that each component contains a list of data channels of length and in the same order as the `Channels` (one `Data` per frequency).\n",
     "\n",
-    "The class method [add_components_data](../api/geoh5py.objects.surveys.electromagnetics.rst#geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.add_components_data) can help users add data from nested dictionaries. Below is an example using four components:"
+    "The class method {py:func}`geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.add_components_data` can help users add data from nested dictionaries. Below is an example using four components:"
    ]
   },
   {
@@ -210,7 +210,7 @@
    "id": "16",
    "metadata": {},
    "source": [
-    "Data channels associated with each component can be quickly accessed through the [BaseEMSurvey.components](../api/geoh5py.objects.surveys.electromagnetics.rst#geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.components) property:"
+    "Data channels associated with each component can be quickly accessed through the {py:func}`geoh5py.objects.surveys.electromagnetics.base.BaseEMSurvey.components` property:"
    ]
   },
   {
@@ -230,7 +230,7 @@
    "source": [
     "### Receivers\n",
     "\n",
-    "Generic label used in the `geoh5` standard for EM survey to identify the [TipperReceivers](../api/geoh5py.objects.surveys.electromagnetics.rst#geoh5py.objects.surveys.electromagnetics.tipper.TipperReceivers) entity."
+    "Generic label used in the `geoh5` standard for EM survey to identify the {py:class}`geoh5py.objects.surveys.electromagnetics.tipper.TipperReceivers` entity."
    ]
   },
   {
@@ -240,7 +240,7 @@
    "source": [
     "### Base stations\n",
     "\n",
-    "Generic label used in the `geoh5` standard for EM survey to identify the [TipperBaseStations](../api/geoh5py.objects.surveys.electromagnetics.rst#geoh5py.objects.surveys.electromagnetics.tipper.TipperBaseStations) entity."
+    "Generic label used in the `geoh5` standard for EM survey to identify the {py:class}`geoh5py.objects.surveys.electromagnetics.tipper.TipperBaseStations` entity."
    ]
   },
   {
@@ -290,7 +290,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,

geoh5py/groups/base.py

@@ -71,7 +71,7 @@ def copy(
 
         if copy_children and new_entity is not None:
             for child in self.children:
-                if hasattr(child, "complement") and child.type != "Receivers":
+                if hasattr(child, "complement") and child.type_name != "Receivers":
                     continue
 
                 child.copy(

geoh5py/objects/surveys/base.py

@@ -117,7 +117,7 @@ def parent(self, parent: EntityContainer):
 
     @property
     @abstractmethod
-    def type(self):
+    def type_name(self):
         """Survey element type"""
 
     @property
@@ -158,13 +158,13 @@ def _copy_complement(
 
         setattr(
             new_entity,
-            self.type_map[self.complement.type],
+            self.type_map[self.complement.type_name],
             new_complement,
         )
 
         setattr(
             new_complement,
-            self.type_map[new_entity.type],
+            self.type_map[new_entity.type_name],
             new_entity,
         )
 

geoh5py/objects/surveys/direct_current.py

@@ -299,7 +299,7 @@ def potential_electrodes(self):
         return self
 
     @property
-    def type(self):
+    def type_name(self):
         """Survey element type"""
         return self.__TYPE
 
@@ -399,6 +399,6 @@ def add_default_ab_cell_id(self):
         self._ab_cell_id = ab_cell_id
 
     @property
-    def type(self):
+    def type_name(self):
         """Survey element type"""
         return self.__TYPE

geoh5py/objects/surveys/electromagnetics/airborne_app_con.py

@@ -210,7 +210,7 @@ def complement(self):
         return self.base_stations
 
     @property
-    def type(self):
+    def type_name(self):
         """Survey element type"""
         return self.__TYPE
 
@@ -230,6 +230,6 @@ def complement(self):
         return self.receivers
 
     @property
-    def type(self):
+    def type_name(self):
         """Survey element type"""
         return self.__TYPE

geoh5py/objects/surveys/electromagnetics/airborne_fem.py

@@ -92,7 +92,7 @@ def complement(self):
         return self.transmitters
 
     @property
-    def type(self):
+    def type_name(self):
         """Survey element type"""
         return self.__TYPE
 
@@ -111,6 +111,6 @@ def complement(self):
         return self.receivers
 
     @property
-    def type(self):
+    def type_name(self):
         """Survey element type"""
         return self.__TYPE

geoh5py/objects/surveys/electromagnetics/airborne_tem.py

@@ -92,7 +92,7 @@ def complement(self):
         return self.transmitters
 
     @property
-    def type(self):
+    def type_name(self):
         """Survey element type"""
         return self.__TYPE
 
@@ -111,6 +111,6 @@ def complement(self):
         return self.receivers
 
     @property
-    def type(self):
+    def type_name(self):
         """Survey element type"""
         return self.__TYPE

geoh5py/objects/surveys/electromagnetics/base.py

@@ -468,7 +468,7 @@ def tx_id_property(self, value: uuid.UUID | ReferencedData | np.ndarray | None):
 
         self._tx_id_property = value
 
-        if self.type == "Receivers":
+        if self.type_name == "Receivers":
             self.edit_em_metadata({"Tx ID property": getattr(value, "uid", None)})
         else:
             self.edit_em_metadata({"Tx ID tx property": getattr(value, "uid", None)})
@@ -498,8 +498,8 @@ def validate_em_metadata(self, values: dict | np.ndarray | bytes | None) -> dict
         if values is None:
             metadata = self.default_metadata
 
-            if self.type is not None:
-                metadata["EM Dataset"][self.type] = self.uid
+            if self.type_name is not None:
+                metadata["EM Dataset"][self.type_name] = self.uid
 
             values = metadata
 
@@ -593,7 +593,7 @@ def _fetch_transmitter_id(self) -> ReferencedData | IntegerData | None:
         Utility method to retrieve the transmitter ID property, either from
         metadata or from list of children Data.
         """
-        if self.type == "Receivers":
+        if self.type_name == "Receivers":
             uid = self.metadata["EM Dataset"].get("Tx ID property", None)
         else:
             uid = self.metadata["EM Dataset"].get("Tx ID tx property", None)