fix: Removing cython dependency (#168)

* fix: adding json exports

* fix: moving and renaming conversion functions

also adding some type hints and a generic numeric type

* tests: adding tests for conversions

need to add some better tests not just 0 and 1s

* fix: remove process_map2loop

not required, can be done using processor

* fix: adding synthetic horizontal layers model

* fix: adding corners property to bounding box

* fix: substituting pli for p1

same interpolator but this implementation uses numpy instead of cython

* tests: test that horizontal layers are working

* fix: making structured tetra compatible with p1 interp

* fix: making p1 interpolator work

* fix: cast input to np array

* fix: adding type enums

* fix: adding sparse matrix neighbour calculator

this means no more cython code

* fix: adding some type hints

* refactor: ➖ removing model builder

there is no real advantage to using a builder design pattern for loopstructural

* fix: ✨ adding ability to calculate normalised value of a feature

this just makes it easier to scale scalar field between 0 and 1

* fix: adding map for interpolator to support type

* fix: enabling support builder with interpolator factory

* fix: updating imports for maths functions

* fix: adding support creator from bbox

* fix: when reset clear the constraints dictionary

* fix: reset when setting up interpolator

* fix: removing old pli interpolator

* fix: fixing tetra indexing and masks

* fix: removing unused imports

* fix: speeding up element getter

* fix: adding onGeometryChange function for supports

* fix: reset change number of constraints

* fix: adding gradient orthogonal to p1interpolator

* fix: changing instrusion example to rescale points

* fix: setting model tolerance using new bounding box

* fix: updating fold to use p1 interpolator

* fix: renaming variables

* fix: adding name and vector args to min edge jumps

* fix: removing old imports

* fix: fixing orthogonal constraints for p1

* fix: moving fault setup into fault builder frm model

* fix: flake8 error

* fix: add bb origin to surfaces

* fix: fold constraints added in setup interpolator

this allows for interpolator to be reset
and doesn't remove the fold constraints when resetting

* fix: temp fix for issue with np types

* Replace reqs with correct theme

Theme being loaded by requirements.txt was wrong (an old one?) So have updated with the pydata_sphinx_theme so now builds correctly

* Adding PyPI custom link to navigation

* Replacing square icon with (nicer) round icon

* Adding navbar options and metadata

Image is a placeholder for now, but this is an (onvs opinionated) view on a nicer format. Adds a limit to the number of nav items, adds a logo, changes the title to look cleaner (and not say "documentation" at the end), adds metadata

* Fixing svg img

* Updating the contributors docs

* removing accidental tab

* docs: fixing missing automodule

* fix: adding length to bbox

* fix: removing dof and name from interpolator json

* docs: adding explicit imports for submodules

Without explicit import of submodules and using __ALL__ the majority of the code isn't imported so sphinx doesn't document it.

* docs: adding citations to documentation

* fix: removing reference to dtm creator and using get interpolator correctly

* fix: face table resize when geometry reset

* fix: elements property for base structured support

* fix: adding imports to api

* fix: changing from interpolator type string to enum

* fix: removing cython

* fix: only axial foliation is constrained by fold frame

* Update release-please.yml

* Update release-please.yml

* Update release-please.yml

* ci: updating to use pip wheel .

* Update release-please.yml

* fix: disable progress bar for model update

* ci: remove numpy version for conda

* fix: changing to interpolator factory

required changing how fold interpolator is setup. Rather than
initialising with a fold, the fold is added to the interpolator
added map between stringinterpolator names and the interpolatortypes enum

* fix: identify points that fall on face of shared tetras. Automatically chooses the second one.

* fix: rename surface vtk property to vtk from pyvista

* fix: add docstring and cast isinside to an array

* docs: adding docs to surface datatype

* fix: removing cython code

* fix: removing model api for time being

* build: adding conda builds to git ignore

* typo

* ci: using conda convert to create osx

* ci: removing cython

* ci: typo in yml

* ci: again

* ci: again

---------

Co-authored-by: Sam <samuel.joseph.roberts@hotmail.co.uk>

Author: lachlangrose

.github/workflows/release-please.yml

@@ -3,30 +3,30 @@ on:
 name: release-please
 jobs:
   continuous-integration:
-    name: Continuous integration ${{ matrix.os }} python ${{ matrix.python-version }} 
+    name: Continuous integration ${{ matrix.os }} python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest",  "windows-latest"] #"macos-latest",
-        python-version: ["3.8","3.9","3.10"]
+        os: ${{ fromJSON(vars.BUILD_OS)}}
+        python-version: ${{ fromJSON(vars.PYTHON_VERSIONS)}}
     steps:
       - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: ${{ matrix.python }} 
+          python-version: ${{ matrix.python }}
       - name: Installing dependencies
         shell: bash -l {0}
         run: |
           conda install -c conda-forge cython numpy scipy scikit-image scikit-learn pyamg flake8 pytest networkx osqp matplotlib -y
       - name: Checking formatting of code
         shell: bash -l {0}
         run: |
-            # stop the build if there are Python syntax errors or undefined names
-            flake8 LoopStructural --count --select=E9,F63,F7,F82 --show-source --statistics
-            # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-            flake8 LoopStructural --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-      - name: Building and install 
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 LoopStructural --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 LoopStructural --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Building and install
         shell: bash -l {0}
         run: |
           python setup.py install build_ext --inplace
@@ -78,109 +78,88 @@ jobs:
         with:
           branch: gh-pages # The branch the action should deploy to.
           folder: docs/build/html # The folder the action should deploy.
-          
+
   conda-deploy:
     name: Uploading to Loop3d for python ${{ matrix.os }})
     needs: ["documentation-test", "continuous-integration"]
-    runs-on: ${{ matrix.os }}
+    runs-on: ${{matrix.os}}
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest",  "windows-latest"]
-        python-version: ["3.10","3.9","3.8"]
+        os: ["ubuntu-latest"]
+        python-version: ${{ fromJSON(vars.PYTHON_VERSIONS)}}
     steps:
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
-    
+
       - uses: actions/checkout@v2
       - name: update submodules
-#       shell: bash -l {0}
+        #       shell: bash -l {0}
         run: |
-            git submodule update --init --recursive
-      - name: Add msbuild to PATH
-        if: matrix.os == 'windows-latest'
-        uses: microsoft/setup-msbuild@v1.0.2  
-      - name: Conda build'
+          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 scikit-build numpy cython anaconda-client -y
-           conda build -c anaconda -c conda-forge -c loop3d --output-folder conda conda --numpy 1.21
-           conda install anaconda-client -y
+          conda install -c conda-forge conda-build scikit-build numpy cython anaconda-client -y
+          conda build -c anaconda -c conda-forge -c loop3d --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@v3
         with:
           name: conda
           path: conda
-     
 
   make_sdist:
     needs: ["documentation-test", "continuous-integration"]
     name: Make SDist
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-      
-    - name: Build SDist
-      run: |
-        pip install numpy cython
-        python setup.py sdist
+      - uses: actions/checkout@v3
 
-    - uses: actions/upload-artifact@v3
-      with:
-        name: dist
-        path: dist/*.tar.gz
-        
-  build_wheels:
-    needs: ["documentation-test", "continuous-integration"]
-    name: Build wheels
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-    steps:
-      - uses: actions/checkout@v2
+      - name: Build SDist
+        run: |
+          pip install numpy
+          python setup.py sdist
+          pip wheel -w wheelhouse .
 
-      - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.0
-        env:
-          CIBW_ARCHS_MACOS: x86_64 universal2
-          CIBW_BUILD: "cp36-* cp37-* cp38-* cp39-* cp310*"
-          CIBW_BEFORE_BUILD: "pip install numpy cython" #make sure numpy is the same version as required by LS
       - uses: actions/upload-artifact@v3
         with:
           name: dist
-          path: ./wheelhouse/*.whl
-          
+          path: dist/*.tar.gz
+      - uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: wheelhouse/*.whl
+
   upload_to_pypi:
-    needs: ["release-please","build_wheels","make_sdist","conda-deploy"]
+    needs: ["release-please", "make_sdist", "conda-deploy"]
     runs-on: ubuntu-latest
     if: ${{ needs.release-please.outputs.release_created }}
     steps:
-    - uses: actions/download-artifact@v3
-      with:
+      - uses: actions/download-artifact@v3
+        with:
           name: dist
           path: dist
-    - uses: actions/download-artifact@v3
-      with:
+      - uses: actions/download-artifact@v3
+        with:
           name: conda
           path: conda
-    - uses: pypa/gh-action-pypi-publish@v1.6.4
-      with:
-        skip_existing: true
-        verbose: true
-        user: ${{ secrets.PYPI_USERNAME }}
-        password: ${{ secrets.PYPI_PASSWORD }}
-    - uses: conda-incubator/setup-miniconda@v2
-    - 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 
-    
+      - uses: pypa/gh-action-pypi-publish@v1.6.4
+        with:
+          skip_existing: true
+          verbose: true
+          user: ${{ secrets.PYPI_USERNAME }}
+          password: ${{ secrets.PYPI_PASSWORD }}
+      - uses: conda-incubator/setup-miniconda@v2
+      - 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

.gitignore

@@ -132,3 +132,7 @@ examples/*.png
 dev/scalar_field
 dev/unconf
 docs/source/sg_execution_times.rst
+conda/index.html
+conda/channeldata.json
+conda/noarch
+conda/win-64

LoopStructural/__init__.py

@@ -1,6 +1,6 @@
 """
-LoopStructural API
-=======================
+LoopStructural
+==============
 
 """
 

LoopStructural/api/__init__.py

@@ -0,0 +1,2 @@
+from ._interpolate import LoopInterpolator
+from ._surface import LoopIsosurfacer

LoopStructural/api/_interpolate.py

@@ -6,6 +6,7 @@
 from LoopStructural.interpolators import (
     GeologicalInterpolator,
     InterpolatorFactory,
+    InterpolatorType,
 )
 from LoopStructural.utils import BoundingBox
 from LoopStructural.utils import getLogger
@@ -18,7 +19,7 @@ def __init__(
         self,
         bounding_box: BoundingBox,
         dimensions: int = 3,
-        type: str = "FDI",
+        type=InterpolatorType.FINITE_DIFFERENCE,
         nelements: int = 1000,
     ):
         """Scikitlearn like interface for LoopStructural interpolators

LoopStructural/api/_surface.py

@@ -1,5 +1,6 @@
-from typing import Optional, Union
+from typing import Optional, Union, Callable
 import numpy as np
+import numpy.typing as npt
 from LoopStructural.utils import getLogger
 
 logger = getLogger(__name__)
@@ -13,23 +14,81 @@
 from LoopStructural.utils import BoundingBox
 from LoopStructural.datatypes import Surface
 
-surface_list = dict[str, tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]]
+surface_list = dict[
+    str, tuple[npt.ArrayLike, npt.ArrayLike, npt.ArrayLike, npt.ArrayLike]
+]
 
 
 class LoopIsosurfacer:
-    def __init__(self, bounding_box: BoundingBox, interpolator: GeologicalInterpolator):
+    def __init__(
+        self,
+        bounding_box: BoundingBox,
+        interpolator: Optional[GeologicalInterpolator] = None,
+        callable: Optional[Callable[[npt.ArrayLike], npt.ArrayLike]] = None,
+    ):
+        """Extract isosurfaces from a geological interpolator or a callable function.
+
+
+        Parameters
+        ----------
+        bounding_box : BoundingBox
+            _description_
+        interpolator : Optional[GeologicalInterpolator], optional
+            interpolator object, by default None
+        callable : Optional[Callable[[npt.ArrayLike], npt.ArrayLike]], optional
+            callable object, by default None
+
+        Raises
+        ------
+        ValueError
+            _description_
+        ValueError
+            _description_
+        ValueError
+            _description_
+        """
         self.bounding_box = bounding_box
-        self.interpolator = interpolator
+        self.callable = callable
+        if interpolator is None and callable is None:
+            raise ValueError("Must specify either interpolator or callable")
+        if interpolator is not None and self.callable is not None:
+            raise ValueError("Must specify either interpolator or callable")
+
+        if interpolator is not None:
+            self.callable = interpolator.evaluate_value
+        if self.callable is None:
+            raise ValueError("Must specify either interpolator or callable")
 
     def fit(self, values: Union[list, int, float]) -> surface_list:
+        """Extract isosurfaces from the interpolator
+
+        Parameters
+        ----------
+        values : Union[list, int, float]
+            Either a list of values to extract isosurfaces for, or a single value
+            to extract a single isosurface for, or an integer to extract that many
+            isosurfaces evenly spaced between the minimum and maximum values of the
+            interpolator.
+
+        Returns
+        -------
+        surface_list
+            a dictionary containing the extracted isosurfaces
+        """
+        if not callable(self.callable):
+            raise ValueError("No interpolator of callable function set")
         surfaces = {}
-        all_values = self.interpolator.evaluate_value(self.bounding_box.regular_grid())
+        all_values = self.callable(self.bounding_box.regular_grid())
         if isinstance(values, list):
             isovalues = values
         elif isinstance(values, float):
             isovalues = [values]
         elif isinstance(values, int):
-            isovalues = np.linspace(np.min(all_values), np.max(all_values), values)
+            isovalues = np.linspace(
+                np.min(all_values) + np.finfo(float).eps,
+                np.max(all_values) + np.finfo(float).eps,
+                values,
+            )
         for isovalue in isovalues:
             verts, faces, normals, values = marching_cubes(
                 all_values.reshape(self.bounding_box.nsteps, order="C"),
@@ -38,7 +97,7 @@ def fit(self, values: Union[list, int, float]) -> surface_list:
             )
             values = np.zeros(verts.shape[0]) + isovalue
             surfaces[f"surface_{isovalue}"] = Surface(
-                vertices=verts,
+                vertices=verts + self.bounding_box.origin,
                 triangles=faces,
                 normals=normals,
                 name=f"surface_{isovalue}",

LoopStructural/api/model.py

@@ -19,3 +19,4 @@
 from ._base import load_tabular_intrusion
 from ._base import load_geological_map_data
 from ._base import load_fault_trace
+from ._base import load_horizontal

LoopStructural/datasets/__init__.py

@@ -1,9 +1,46 @@
 from os.path import dirname, join
 from pathlib import Path
+from typing import Tuple
 import numpy as np
 import pandas as pd
 
 
+def load_horizontal() -> Tuple[pd.DataFrame, np.ndarray]:
+    """Synthetic model for horizontal layers
+
+    Returns
+    -------
+    Tuple[pd.DataFrame, np.ndarray]
+        dataframe with feature_name 'strati', bounding box array
+    """
+    bb = np.array([[0, 0, 0], [10, 10, 10]])
+    xy = np.mgrid[0:10, 0:10].reshape(2, -1).T
+    data = pd.DataFrame(
+        np.vstack(
+            [
+                np.hstack(
+                    [
+                        xy,
+                        np.zeros(xy.shape[0])[:, None] + 2,
+                        np.zeros(xy.shape[0])[:, None] + 2,
+                    ]
+                ),
+                np.hstack(
+                    [
+                        xy,
+                        np.zeros(xy.shape[0])[:, None] + 3,
+                        np.zeros(xy.shape[0])[:, None] + 3,
+                    ]
+                ),
+            ]
+        ),
+        columns=["X", "Y", "Z", "val"],
+    )
+
+    data["feature_name"] = "strati"
+    return data, bb
+
+
 def load_claudius():
     """Model dataset sampled from 3D seismic data