Merge branch 'dev'

.github/workflows/release-please.yml

@@ -0,0 +1,154 @@
+on: [push, pull_request]
+name: release-please
+jobs:
+  linting:
+    name: Linting
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black ruff
+      - name: Autoformat with black
+        run: |
+          black .
+      - name: Lint with ruff
+        run: |
+          ruff check LoopDataConverter --fix
+      - uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: "style: style fixes by ruff and autoformatting by black"
+
+  continuous-integration:
+    name: Continuous integration ${{ matrix.os }} python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ${{ fromJSON(vars.BUILD_OS)}}
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Installing dependencies
+        shell: bash -l {0}
+        run: |
+          conda install -c conda-forge numpy scipy pytest dill beartype pandas geopandas shapely validators sqlite -y
+      - name: Building and install
+        shell: bash -l {0}
+        run: |
+          pip install . --user
+      - name: Testing
+        shell: bash -l {0}
+        run: |
+          pytest
+
+  release-please:
+    runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/dev'
+    steps:
+      - uses: GoogleCloudPlatform/release-please-action@v4
+        id: release
+        with:
+          release-type: python
+          package-name: LoopDataConverter
+          version-file: LoopDataConverter/version.py
+    outputs:
+      release_created: ${{ steps.release.outputs.release_created }}
+  # if a release is created then run the deploy scripts for github.io, conda, pypi and docker
+
+  conda-deploy:
+    name: Building conda package for python ${{ matrix.os }})
+    needs: "continuous-integration"
+    runs-on: ${{matrix.os}}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/checkout@v4
+      - name: update submodules
+        #       shell: bash -l {0}
+        run: |
+          git submodule update --init --recursive
+      - name: Conda build
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN  }}
+        shell: bash -l {0}
+        run: |
+          conda install -c conda-forge conda-build pytest numpy scipy pandas geopandas sqlite shapely validators anaconda-client -y
+          conda build -c anaconda -c conda-forge --output-folder conda conda 
+          conda convert -p all conda/linux-64/*.tar.bz2 -f -o conda
+          conda install anaconda-client -y
+      - name: upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: conda-${{ matrix.os }}-${{ matrix.python-version }}
+          path: conda
+
+  make_sdist:
+    needs: "continuous-integration"
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build SDist
+        run: |
+          pip install build
+          python -m build
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  upload_to_conda:
+    needs: ["release-please", "conda-deploy"]
+    runs-on: ${{matrix.os}}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    if: ${{ needs.release-please.outputs.release_created }}
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: conda-${{ matrix.os }}-${{ matrix.python-version }}
+          path: conda
+      - uses: conda-incubator/setup-miniconda@v3
+      - name: upload all files to conda-forge
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN  }}
+        run: |
+          conda install -c anaconda anaconda-client -y
+          anaconda upload --label main conda/*/*.tar.bz2
+
+  upload_to_pypi:
+    needs: ["release-please", "conda-deploy"]
+    runs-on: "ubuntu-latest"
+
+    if: ${{ needs.release-please.outputs.release_created }}
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip_existing: true
+          verbose: true
+          user: ${{ secrets.PYPI_USERNAME }}
+          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -1,5 +1,5 @@
-LoopDataConverter.egg-info/dependency_links.txt
-LoopDataConverter.egg-info/PKG-INFO
+LoopDataConverter.egg-info/top_level.txt
 LoopDataConverter.egg-info/requires.txt
 LoopDataConverter.egg-info/SOURCES.txt
-LoopDataConverter.egg-info/top_level.txt
+LoopDataConverter.egg-info/PKG-INFO
+LoopDataConverter.egg-info/dependency_links.txt

LoopDataConverter/converters/__init__.py

@@ -0,0 +1,14 @@
+from .base_converter import BaseConverter
+from .ntgs_converter import NTGSConverter
+from ..datatypes import SurveyName
+
+converter_map = {
+    SurveyName.NTGS: NTGSConverter,
+    SurveyName.GA: "",
+    SurveyName.GSQ: "",
+    SurveyName.GSWA: "",
+    SurveyName.GSSA: "",
+    SurveyName.GSV: "",
+    SurveyName.MRT: "",
+    SurveyName.GSNSW: "",
+}

LoopDataConverter/converters/base_converter.py

@@ -0,0 +1,26 @@
+from abc import ABC, abstractmethod
+
+
+class BaseConverter(ABC):
+
+    def __init__(self):
+        self._type_label = "BaseTypeConverter"
+
+    def type(self):
+        return self._type_label
+
+    @abstractmethod
+    def convert_fold_map(self):
+        pass
+
+    @abstractmethod
+    def convert_fault_map(self):
+        pass
+
+    @abstractmethod
+    def convert_structure_map(self):
+        pass
+
+    @abstractmethod
+    def convert(self):
+        pass

LoopDataConverter/converters/conversion_manager.py

@@ -0,0 +1,44 @@
+from .ntgs_converter import NTGSConverter
+from ..datatypes import SurveyName
+from ..file_readers import LoopGisReader
+from ..input import InputData
+
+
+class LoopConverter:
+    """
+    LoopConverter class use the LoopGisReader to look up the correct file
+    reader for the input file type and then converting the data to
+    Map2Loop or LoopStrucural formats using the adequate converter
+    """
+
+    def __init__(self, survey_name: SurveyName, data: InputData, layer: str = None):
+        self._fileData = data
+        self._layer = layer
+        self._survey_name = survey_name
+        self._converters = {
+            SurveyName.NTGS: NTGSConverter,
+            SurveyName.GA: "",
+            SurveyName.GSQ: "",
+            SurveyName.GSWA: "",
+            SurveyName.GSSA: "",
+            SurveyName.GSV: "",
+            SurveyName.GSNSW: "",
+            SurveyName.MRT: "",
+        }
+
+    def read_file(self):
+        """
+        read the file using the correct file reader
+        """
+        file_reader = LoopGisReader(self._fileData)
+        file_reader.read(self._fileData, self._layer)
+        return file_reader.data
+
+    def get_converter(self):
+        return self._converters[self._survey_name]
+
+    def convert(self):
+        data = self.read_file()
+        converter = self.get_converter()
+        converter(data)
+        self.data = converter._data

LoopDataConverter/converters/ntgs_converter.py

@@ -0,0 +1,68 @@
+# internal imports
+from .base_converter import BaseConverter
+from ..utils import (
+    convert_dipdir_terms,
+    convert_dip_terms,
+    convert_tightness_terms,
+    convert_displacement_terms,
+)
+
+# external imports
+import pandas
+import numpy
+
+
+class NTGSConverter(BaseConverter):
+    # TODO: modify class to take fold, fault, and structure layers as arguments
+    def __init__(self, data: pandas.DataFrame):
+        self.raw_data = data.copy()
+        self._type_label = "NTGSConverter"
+        self._data = None
+
+    def type(self):
+        return self._type_label
+
+    def convert_fold_map(self):
+        # convert dip direction terms to degrees
+        self.raw_data["AxialPlaneDipDir"] = self.raw_data["AxialPlaneDipDir"].apply(
+            lambda x: convert_dipdir_terms(x)
+        )
+        # convert dip terms to degrees
+        self.raw_data["AxialPlaneDip"] = self.raw_data["AxialPlaneDip"].apply(
+            lambda x: convert_dip_terms(x, type="fold")
+        )
+        # convert tightness terms to degrees
+        self.raw_data["InterlimbAngle"] = self.raw_data["InterlimbAngle"].apply(
+            lambda x: convert_tightness_terms(x)
+        )
+
+    def convert_fault_map(self):
+        # convert dip direction terms to degrees
+        self.raw_data["DipDirection"] = self.raw_data["DipDirection"].apply(
+            lambda x: convert_dipdir_terms(x)
+        )
+        # convert dip terms to degrees
+        self.raw_data["Dip"] = self.raw_data["Dip"].apply(
+            lambda x: convert_dip_terms(x, type="fault")
+        )
+        self.raw_data["Displacement"] = self.raw_data["Displacement"].apply(
+            lambda x: convert_displacement_terms(x)
+        )
+
+    def convert_structure_map(self):
+        # discard any rows that has a dip value of -99 and does not have any esimated dip value
+        condition = (self.raw_data["Dip"] != -99) & (self.raw_data["DipEstimate"] != numpy.nan)
+        self.raw_data = self.raw_data[condition]
+        # convert dip estimate to float (average of the range)
+        condition = self.raw_data["Dip"] == -99
+        self.raw_data.loc[condition, "DipEstimate"] = self.raw_data.loc[
+            condition, "DipEstimate"
+        ].apply(lambda x: sum(map(float, x.split("-"))) / 2)
+        self.raw_data[condition, "Dip"] = self.raw_data[condition, "DipEstimate"]
+
+    def convert(self):
+        self.convert_fold_map()
+        self.convert_fault_map()
+        self.convert_structure_map()
+
+        self._data = self.raw_data.copy()

LoopDataConverter/datatypes/__init__.py

@@ -0,0 +1 @@
+from .enums import Datatype, SurveyName, Filetype

LoopDataConverter/datatypes/enums.py

@@ -0,0 +1,31 @@
+from enum import IntEnum
+
+
+class Datatype(IntEnum):
+    GEOLOGY = 0
+    STRUCTURE = 1
+    FAULT = 2
+    FOLD = 3
+    DTM = 4
+    FAULT_ORIENTATION = 5
+
+
+class SurveyName(IntEnum):
+
+    GA = 0
+    NTGS = 1
+    GSQ = 2
+    GSWA = 3
+    GSSA = 4
+    GSV = 5
+    MRT = 6
+    GSNSW = 7
+
+
+class Filetype(IntEnum):
+
+    CSV = 0
+    GEOJSON = 1
+    SHP = 2
+    GPKG = 3
+    ZIP = 4

LoopDataConverter/fields/_ntgs/__init__.py

@@ -0,0 +1 @@
+from ._ntgs_config import NtgsConfig