Merge pull request #278 from kujaku11/patches

kujaku11 · web-flow · commit c8219dedc0d4 · 2026-02-17T22:09:57.000-08:00
Updated EMTFXML Location to include datum and declination information.
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -73,7 +73,7 @@ jobs:
 
       - name: Generate changelog
         run: |
-          git cliff -o CHANGELOG.md
+          git cliff --unreleased --tag v${{ steps.version.outputs.version }} -o CHANGELOG.md
           echo "Generated changelog for version ${{ steps.version.outputs.version }}"
 
       - name: Update HISTORY.rst
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,2 +1,3 @@
-Changelog
-All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.All notable changes to this project will be documented in this file.
+# Changelog
+
+All notable changes to this project will be documented in this file.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,29 +1,4 @@
-Changelog All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.All notable changes to this project will be documented in this
-file.
+Changelog
+=========
+
+All notable changes to this project will be documented in this file.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -280,3 +280,7 @@ file.All notable changes to this project will be documented in this
 file.All notable changes to this project will be documented in this
 file.All notable changes to this project will be documented in this
 file.
+Changelog
+=========
+
+All notable changes to this project will be documented in this file.
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# mt_metadata version 1.0.3
+# mt_metadata version 1.0.4
  Standard MT metadata
 
 [![PyPi version](https://img.shields.io/pypi/v/mt_metadata.svg)](https://pypi.python.org/pypi/mt-metadata)
@@ -28,7 +28,7 @@ MT Metadata is a project led by [IRIS-PASSCAL MT Software working group](https:/
 
 Most people will be using the transfer functions, but a lot of that metadata comes from the time series metadata.  This module supports both and has tried to make them more or less seamless to reduce complication.
 
-* **Version**: 1.0.3
+* **Version**: 1.0.4
 * **Free software**: MIT license
 * **Documentation**: https://mt-metadata.readthedocs.io.
 * **Examples**: Click the `Binder` badge above and Jupyter Notebook examples are in **mt_metadata/examples/notebooks** and **docs/source/notebooks**
diff --git a/cliff.toml b/cliff.toml
@@ -1,15 +1,17 @@
 [changelog]
-header = """# Changelog
+header = """
+# Changelog
 
 All notable changes to this project will be documented in this file.
 """
 
 body = """
 {% for group, commits in commits | group_by(attribute="group") %}
-    ## {{ group | upper_first }}
-    {% for commit in commits %}
-        - {% if commit.breaking %}[**BREAKING**] {% endif %}{{ commit.message | upper_first }} ([{{ commit.id | truncate(length=7, end="") }}]({{ commit.id }}))
-    {% endfor %}
+## {{ group | upper_first }}
+{% for commit in commits %}
+- {% if commit.breaking %}[**BREAKING**] {% endif %}{{ commit.message | upper_first }} ([{{ commit.id | truncate(length=7, end="") }}](https://github.com/kujaku11/mth5/commit/{{ commit.id }}))
+{% endfor %}
+
 {% endfor %}
 """
 
@@ -26,11 +28,16 @@ commit_parsers = [
   { message = "^refactor", group = "Refactor" },
   { message = "^style", group = "Styling" },
   { message = "^test", group = "Testing" },
-  { message = "^chore\\(release\\): prepare for", skip = true },
-  { message = "^chore\\(deps\\)", skip = true },
-  { message = "^chore\\(pr\\)", skip = true },
-  { message = "^chore\\(pull\\)", skip = true },
+  { message = "^chore(release): prepare for", skip = true },
+  { message = "^chore(deps)", skip = true },
+  { message = "^chore(pr)", skip = true },
+  { message = "^chore(pull)", skip = true },
+  { message = "^chore|^ci", skip = true },
   { message = "^chore", group = "Miscellaneous Tasks" },
   { body = ".*security", group = "Security" },
   { message = "^revert", group = "Revert" },
 ]
+
+# Skip commits that only bump versions
+filter_commits = true
+skip_tags = "v0.1.0-beta.1"
diff --git a/code.json b/code.json
@@ -3,20 +3,20 @@
     "name": "mt-metadata",
     "organization": "U.S. Geological Survey",
     "description": "A Python module to handle/validate/read/write metadata in general but mainly for magnetotelluric data including time series, transfer functions, and Fourier coefficients. Formats include JSON, XML, text files.",
-    "version": "v1.0.3",
+    "version": "v1.0.4",
     "status": "Production",
     "permissions": {
       "usageType": "openSource",
       "licenses": [
         {
           "name": "MIT",
-          "URL": "https://code.usgs.gov/gmeg/mt-metadata/-/raw/v1.0.3/LICENSE.md"
+          "URL": "https://code.usgs.gov/gmeg/mt-metadata/-/raw/v1.0.4/LICENSE.md"
         }
       ]
     },
     "homepageURL": "https://code.usgs.gov/gmeg/mt_metadata",
-    "downloadURL": "https://code.usgs.gov/gmeg/mt-metadata/-/archive/v1.0.3/mt-metadata-v1.0.3.zip",
-    "disclaimerURL": "https://code.usgs.gov/gmeg/mt-metadata/-/raw/v1.0.3/DISCLAIMER.md",
+    "downloadURL": "https://code.usgs.gov/gmeg/mt-metadata/-/archive/v1.0.4/mt-metadata-v1.0.4.zip",
+    "disclaimerURL": "https://code.usgs.gov/gmeg/mt-metadata/-/raw/v1.0.4/DISCLAIMER.md",
     "repositoryURL": "https://code.usgs.gov/gmeg/mt_metadata.git",
     "tags": [
       "magnetotellurics",
diff --git a/mt_metadata/__init__.py b/mt_metadata/__init__.py
@@ -39,7 +39,7 @@
 
 __author__ = """Jared Peacock"""
 __email__ = "jpeacock@usgs.gov"
-__version__ = "1.0.3"
+__version__ = "1.0.4"
 
 # =============================================================================
 # Imports
diff --git a/mt_metadata/transfer_functions/io/emtfxml/emtfxml.py b/mt_metadata/transfer_functions/io/emtfxml/emtfxml.py
@@ -1193,6 +1193,9 @@ def station_metadata(self, station_metadata: Station) -> None:
         self.site.location.latitude = sm.location.latitude
         self.site.location.longitude = sm.location.longitude
         self.site.location.elevation = sm.location.elevation
+        self.site.location.declination.value = sm.location.declination.value
+        self.site.location.declination.epoch = sm.location.declination.epoch
+        self.site.location.declination.model = sm.location.declination.model
         self.site.orientation.angle_to_geographic_north = (
             sm.orientation.angle_to_geographic_north
             if sm.orientation.angle_to_geographic_north is not None
diff --git a/mt_metadata/transfer_functions/io/emtfxml/metadata/__init__.py b/mt_metadata/transfer_functions/io/emtfxml/metadata/__init__.py
@@ -27,6 +27,7 @@
 from .data_quality_notes import DataQualityNotes
 from .data_quality_warnings import DataQualityWarnings
 from .orientation import Orientation
+from .location import Location
 from .site import Site
 from .instrument import Instrument
 from .electrode import Electrode
@@ -61,6 +62,7 @@
     "DataQualityNotes",
     "DataQualityWarnings",
     "Orientation",
+    "Location",
     "Site",
     "Instrument",
     "Electrode",
diff --git a/mt_metadata/transfer_functions/io/emtfxml/metadata/location.py b/mt_metadata/transfer_functions/io/emtfxml/metadata/location.py
@@ -0,0 +1,62 @@
+from typing import Annotated
+from xml.etree import ElementTree as et
+
+from pydantic import Field
+
+from mt_metadata.common import BasicLocation, Declination
+from mt_metadata.transfer_functions.io.emtfxml.metadata.helpers import element_to_string
+
+
+class Location(BasicLocation):
+    declination: Annotated[
+        Declination,
+        Field(
+            default_factory=Declination,  # type: ignore
+            description="Declination at the location in degrees",
+            alias=None,
+            json_schema_extra={
+                "units": "degrees",
+                "required": False,
+                "examples": ["10.0"],
+            },
+        ),
+    ]
+
+    def to_xml(self, string=False, required=True):
+        """
+        Overwrite to XML to follow EMTF XML format
+
+        Parameters
+        -------------
+
+        string: bool
+            If True, return the XML as a string. If False, return an ElementTree Element. Defaults to False.
+        required: bool
+            If True, include all required fields in the XML. Defaults to True.
+
+        Returns
+        -----------
+            XML representation of the BasicLocationDeclination object as a string or ElementTree Element.
+
+        """
+        if self.datum is None:
+            self.datum = "WGS84"
+        if self.declination.epoch is None:
+            self.declination.epoch = "1995"
+
+        root = et.Element(self.__class__.__name__.capitalize(), {"datum": self.datum})
+        lat = et.SubElement(root, "Latitude")
+        lat.text = f"{self.latitude:.6f}"
+        lon = et.SubElement(root, "Longitude")
+        lon.text = f"{self.longitude:.6f}"
+        elev = et.SubElement(root, "Elevation", {"units": "meters"})
+        elev.text = f"{self.elevation:.3f}"
+        dec = et.SubElement(
+            root, "Declination", {"epoch": self.declination.epoch.split(".", 1)[0]}
+        )
+        dec.text = f"{self.declination.value:.3f}"
+
+        if not string:
+            return root
+        else:
+            return element_to_string(root)
diff --git a/mt_metadata/transfer_functions/io/emtfxml/metadata/site.py b/mt_metadata/transfer_functions/io/emtfxml/metadata/site.py
@@ -9,9 +9,9 @@
 from pydantic import Field, field_validator
 
 from mt_metadata.base import MetadataBase
-from mt_metadata.common import BasicLocationNoDatum, Comment
+from mt_metadata.common import Comment
 from mt_metadata.common.mttime import MTime
-from mt_metadata.transfer_functions.io.emtfxml.metadata import helpers
+from mt_metadata.transfer_functions.io.emtfxml.metadata import helpers, Location
 
 from . import DataQualityNotes, DataQualityWarnings, Orientation
 
@@ -204,15 +204,17 @@ class Site(MetadataBase):
     ]
 
     location: Annotated[
-        BasicLocationNoDatum,
+        Location,
         Field(
-            default_factory=BasicLocationNoDatum,  # type: ignore
+            default_factory=Location,  # type: ignore
             description="Location of the site",
             alias=None,
             json_schema_extra={
                 "units": None,
                 "required": False,
-                "examples": ["BasicLocation('latitude=60.0, longitude=-135.0')"],
+                "examples": [
+                    "Location('latitude=60.0, longitude=-135.0, declination=10.0')"
+                ],
             },
         ),
     ]
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "mt_metadata"
-version = "1.0.3"
+version = "1.0.4"
 description = "Metadata for magnetotelluric data"
 readme = {file = "README.md", content-type = "text/markdown"}
 license = {file = "LICENSE"}
@@ -98,7 +98,7 @@ ignore-init-module-imports = true
 in-place = true
 
 [tool.bumpversion]
-current_version = "1.0.3"
+current_version = "1.0.4"
 commit = true
 tag = true
 
diff --git a/tests/transfer_functions/io/emtfxml/metadata/test_site.py b/tests/transfer_functions/io/emtfxml/metadata/test_site.py
@@ -9,7 +9,7 @@
 The Site class is the most complex basemodel with:
 - String fields: project, survey, country, id, name, acquired_by
 - MTime fields: start, end, year_collected
-- Complex object fields: location (BasicLocationNoDatum), orientation (Orientation),
+- Complex object fields: location (Location), orientation (Orientation),
   comments (Comment), data_quality_notes/warnings (DataQuality*)
 - List field: run_list
 - Multiple field validators and custom serialization methods
@@ -24,11 +24,12 @@
 
 import pytest
 
-from mt_metadata.common import BasicLocationNoDatum, Comment
+from mt_metadata.common import Comment
 from mt_metadata.common.mttime import MTime
 from mt_metadata.transfer_functions.io.emtfxml.metadata import (
     DataQualityNotes,
     DataQualityWarnings,
+    Location,
     Orientation,
     Site,
 )
@@ -76,7 +77,7 @@ def full_site():
 @pytest.fixture
 def complex_site():
     """Create a Site instance with complex object fields."""
-    location = BasicLocationNoDatum()
+    location = Location()
     location.latitude = 60.0
     location.longitude = -135.0
 
@@ -210,7 +211,7 @@ def test_default_instantiation(self, default_site):
         assert isinstance(default_site.end, MTime)
         assert default_site.year_collected is None
         assert default_site.run_list == []
-        assert isinstance(default_site.location, BasicLocationNoDatum)
+        assert isinstance(default_site.location, Location)
         assert isinstance(default_site.orientation, Orientation)
         assert isinstance(default_site.comments, Comment)
         assert isinstance(default_site.data_quality_notes, DataQualityNotes)
@@ -245,7 +246,7 @@ def test_full_instantiation(self, full_site):
     def test_complex_instantiation(self, complex_site):
         """Test Site instantiation with complex object fields."""
         assert complex_site.project == "ComplexTest"
-        assert isinstance(complex_site.location, BasicLocationNoDatum)
+        assert isinstance(complex_site.location, Location)
         assert complex_site.location.latitude == 60.0
         assert complex_site.location.longitude == -135.0
         assert isinstance(complex_site.orientation, Orientation)
@@ -368,22 +369,22 @@ class TestSiteComplexObjects:
     """Test Site complex object field interactions."""
 
     def test_location_integration(self):
-        """Test BasicLocationNoDatum integration."""
-        # Test with BasicLocationNoDatum object
-        location = BasicLocationNoDatum()
+        """Test Location integration."""
+        # Test with Location object
+        location = Location()
         location.latitude = 45.0
         location.longitude = -120.0
         location.elevation = 1000.0
 
         site = Site(location=location)
-        assert isinstance(site.location, BasicLocationNoDatum)
+        assert isinstance(site.location, Location)
         assert site.location.latitude == 45.0
         assert site.location.longitude == -120.0
         assert site.location.elevation == 1000.0
 
         # Test with default factory
         site_default = Site()
-        assert isinstance(site_default.location, BasicLocationNoDatum)
+        assert isinstance(site_default.location, Location)
 
     def test_orientation_integration(self):
         """Test Orientation integration."""
@@ -641,7 +642,7 @@ class TestSiteIntegration:
     # )
     def test_site_with_all_dependencies(self):
         """Test Site with all dependency objects populated."""
-        location = BasicLocationNoDatum()
+        location = Location()
         location.latitude = 45.123
         location.longitude = -120.456
         location.elevation = 1234.5
@@ -676,7 +677,7 @@ def test_site_with_all_dependencies(self):
 
         # Verify all objects are properly integrated
         assert site.project == "IntegrationTest"
-        assert isinstance(site.location, BasicLocationNoDatum)
+        assert isinstance(site.location, Location)
         assert site.location.latitude == 45.123
         assert isinstance(site.orientation, Orientation)
         assert site.orientation.angle_to_geographic_north == 45.0
diff --git a/tests/transfer_functions/io/emtfxml/test_tf_write_complete_remote_info.py b/tests/transfer_functions/io/emtfxml/test_tf_write_complete_remote_info.py
diff --git a/tests/transfer_functions/io/emtfxml/test_tf_write_poor.py b/tests/transfer_functions/io/emtfxml/test_tf_write_poor.py
