Merge branch 'master' of https://github.com/Loop3D/LoopStructural

Author: lachlangrose

.github/workflows/documentation.yml

@@ -1,15 +1,14 @@
 name: Build documentation and deploy
 
 on:
-  release:
-    types: [edited, created]
+  push:
 
 jobs:
   documentation:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2.0.0
+      - uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           auto-activate-base: true
           installer-url: https://github.com/conda-forge/miniforge/releases/download/4.10.1-0/Miniforge-pypy3-4.10.1-0-Linux-x86_64.sh
@@ -20,14 +19,8 @@ jobs:
         env:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         run: |
-            conda install -c conda-forge theano cython numpy pandas imageio scipy matplotlib  sphinx=3.5.4 sphinx-gallery sphinxcontrib-bibtex sphinx_rtd_theme myst-parser scikit-learn scikit-image pyamg flake8 pytest networkx -y
+            conda install -c conda-forge theano cython numpy pandas imageio scipy matplotlib  sphinx sphinx-gallery sphinxcontrib-bibtex pydata-sphinx-theme myst-parser scikit-learn scikit-image pyamg flake8 pytest networkx python=3.9   -y
             pip install lavavu-osmesa 
             python setup.py install build_ext --inplace
             cd docs
-            make html
-
-      - name: Deploy 🚀
-        uses: JamesIves/github-pages-deploy-action@4.1.3
-        with:
-          branch: gh-pages # The branch the action should deploy to.
-          folder: docs/build/html # The folder the action should deploy.
+            make html

.github/workflows/release-please.yml

@@ -4,8 +4,51 @@ on:
       - master
 name: release-please
 jobs:
+  continuous-integration:
+    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: ["3.7","3.8","3.9"]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          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 numba statsmodels scikit-fmm 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 
+        shell: bash -l {0}
+        run: |
+          pip install .
+      - name: pytest
+        shell: bash -l {0}
+        run: |
+          pytest
+  documentation-test:
+    runs-on: ubuntu-latest
+    #needs: continuous-integration
+    steps:
+      - uses: actions/checkout@v2
+      - run: |
+          docker build . -t=lsdocs -f docs/Dockerfile 
+          docker run -v $(pwd):/LoopStructural lsdocs bash LoopStructural/docs/build_docs.sh
+      
+
   release-please:
     runs-on: ubuntu-latest
+    needs: documentation-test
     steps:
       - uses: GoogleCloudPlatform/release-please-action@v2
         id: release
@@ -21,22 +64,9 @@ jobs:
     if: ${{ needs.release-please.outputs.release_created }}
     steps:
       - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2.0.0
-        with:
-          auto-activate-base: true
-          installer-url: https://github.com/conda-forge/miniforge/releases/download/4.10.1-0/Miniforge-pypy3-4.10.1-0-Linux-x86_64.sh
-          channels: anaconda,conda-forge,loop3d,conda-forge/label/cf202003
-          python-version: 3.8
-      - name: Build documentation 
-        shell: bash -l {0}
-        env:
-          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
-        run: |
-            conda install -c conda-forge theano cython numpy pandas imageio scipy matplotlib  sphinx sphinx-gallery sphinxcontrib-bibtex sphinx_rtd_theme myst-parser scikit-learn scikit-image pyamg flake8 pytest networkx python=3.9   -y
-            pip install lavavu-osmesa 
-            python setup.py install build_ext --inplace
-            cd docs
-            make html
+      - run: |
+          docker build . -t=lsdocs -f docs/Dockerfile 
+          docker run -v $(pwd):/LoopStructural lsdocs bash LoopStructural/docs/build_docs.sh
       - name: Deploy 🚀
         uses: JamesIves/github-pages-deploy-action@4.1.3
         with:

.github/workflows/windows_CI.yml

@@ -1,5 +1,63 @@
 # Changelog
 
+### [1.4.10](https://www.github.com/Loop3D/LoopStructural/compare/v1.4.9...v1.4.10) (2022-07-20)
+
+
+### Bug Fixes
+
+* :bug: unconformities weren't working. ([304335d](https://www.github.com/Loop3D/LoopStructural/commit/304335d0421297ca026fa26a2e6fed2e4c16332b))
+* adding loopjson encoder ([ec1b84e](https://www.github.com/Loop3D/LoopStructural/commit/ec1b84e7881977d7ec1fec7ecf00b45770f5d832))
+* adding more informative errors to p2 tetra ([c63cae7](https://www.github.com/Loop3D/LoopStructural/commit/c63cae7e9c03be10b566d4b5b85987956d164a78))
+* adding python alternatives for cg and fold cg ([5ffef3b](https://www.github.com/Loop3D/LoopStructural/commit/5ffef3b482e1fedaaf2ec6a6c8c44a392d6def6f))
+* catch all exceptions, raise import ([a071416](https://www.github.com/Loop3D/LoopStructural/commit/a071416cb602db135c9fa9d67d99ceb79ddb0407))
+* catch dfi import error ([f9c8aa0](https://www.github.com/Loop3D/LoopStructural/commit/f9c8aa0b04996dd5ad887871b950b2851c4310bb))
+* catch modulenotfound raise importerror ([836ee84](https://www.github.com/Loop3D/LoopStructural/commit/836ee843f418956fc9bd578868030eba537960e2))
+* don't add unconformity if base feature is None ([be4d8ac](https://www.github.com/Loop3D/LoopStructural/commit/be4d8ac220d1fe9a58738652ccf823631cab607e))
+* faults enabled bug, ~ does not flip boolean, changing to not ([0c68788](https://www.github.com/Loop3D/LoopStructural/commit/0c6878837e8eeb24b2ca9009cced0a8ecb6750ac))
+* feature type enums renaming ([616b554](https://www.github.com/Loop3D/LoopStructural/commit/616b55440944055d284484381ace2d068e5259c1))
+* featuretype enum ([c256746](https://www.github.com/Loop3D/LoopStructural/commit/c2567465855b9a8ae6a97c1ded5972ec18a89b30))
+* fold cg ([a35f41a](https://www.github.com/Loop3D/LoopStructural/commit/a35f41a0a1f2be50e9d15ae8d4e2d92877526eff))
+* lavavu.camera bug when keys are missing ([b554c3c](https://www.github.com/Loop3D/LoopStructural/commit/b554c3c143b27e592672f87d1982ae455779aade))
+* missing enum ([bc34bb4](https://www.github.com/Loop3D/LoopStructural/commit/bc34bb4e8cb07a006529c26a7982b3e2b3ea0241))
+* model plotter uses BaseFeature to check type ([a2bd0f0](https://www.github.com/Loop3D/LoopStructural/commit/a2bd0f01a7c297ecf01fc0c612dc0d123ac16702))
+* pli import is optional ([6347742](https://www.github.com/Loop3D/LoopStructural/commit/6347742847460821a11ce840af51972f0b5df43b))
+* raise error if cython can't be imported ([f5b82eb](https://www.github.com/Loop3D/LoopStructural/commit/f5b82ebf96e7b93052693f99af783ea18511aa48))
+* recursive error fix ([f3180f3](https://www.github.com/Loop3D/LoopStructural/commit/f3180f3beaae36a424be1de7f2512800fbe39022))
+* renaming enums to be consistent with calls ([57ed443](https://www.github.com/Loop3D/LoopStructural/commit/57ed44349c5b8f04e967d049f55aa35f1440e324))
+* unconformities causing nan slicing due to recurvsive error ([728fc5f](https://www.github.com/Loop3D/LoopStructural/commit/728fc5f053345ae6901631bf60bd1d2457574d66))
+
+
+### Documentation
+
+* :memo: added example for plotting unconformities ([bad53a0](https://www.github.com/Loop3D/LoopStructural/commit/bad53a01e21e39dcdbdc3a5c218e9c9957050f9b))
+* fixing new documentation so that data can be loaded ([7ac5a0d](https://www.github.com/Loop3D/LoopStructural/commit/7ac5a0d1752c6aad2e8f5112ec4d6efeaa93dd20))
+* missing variable ([7df88a2](https://www.github.com/Loop3D/LoopStructural/commit/7df88a2111c259de367b734a095452a747b8a019))
+* renaming cython to _cython so its not included in docs ([27e88a1](https://www.github.com/Loop3D/LoopStructural/commit/27e88a1d4f3c8f3461481972fc1b13fda7513f0d))
+* trying to ignore cython ([6582d0c](https://www.github.com/Loop3D/LoopStructural/commit/6582d0c8381588e8f59c623641c7d8ce451891fc))
+* updating documentation ([493beea](https://www.github.com/Loop3D/LoopStructural/commit/493beeac3ade0b35c49895d91c64aa8926d9a3b7))
+* using docker to build docs ([f499aae](https://www.github.com/Loop3D/LoopStructural/commit/f499aae76107e09e15d2b9ce56e75fa9b2e0560b))
+
+### [1.4.9](https://www.github.com/Loop3D/LoopStructural/compare/v1.4.8...v1.4.9) (2022-05-05)
+
+
+### Documentation
+
+* fixing docs ci ([2e0d472](https://www.github.com/Loop3D/LoopStructural/commit/2e0d47292ccc20c071256cbb51ac8736c6851f9e))
+
+### [1.4.8](https://www.github.com/Loop3D/LoopStructural/compare/v1.4.7...v1.4.8) (2022-05-05)
+
+
+### Bug Fixes
+
+* :bug: faults where feature name given not fault_name were crashing ([dae9e92](https://www.github.com/Loop3D/LoopStructural/commit/dae9e92f4b2f94ebcaefe85dfc419bfdef69b43a))
+
+
+### Documentation
+
+* adding geopandas to doc test ([b6613a9](https://www.github.com/Loop3D/LoopStructural/commit/b6613a91fd158405ac01d8c9675618bcb6e6af12))
+* fixing fault network example ([6f4f2fc](https://www.github.com/Loop3D/LoopStructural/commit/6f4f2fcba8e1e708c17acfa569d6592f0a33c9d6))
+* refactoring documentation + adding new example ([d15ba6c](https://www.github.com/Loop3D/LoopStructural/commit/d15ba6c391af889e0a0e57f4eced126fe6521461))
+
 ### [1.4.7](https://www.github.com/Loop3D/LoopStructural/compare/v1.4.6...v1.4.7) (2022-05-04)
 
 

CHANGELOG.md

@@ -1,6 +1,7 @@
 from skimage.measure import marching_cubes
 import pandas as pd
 import numpy as np
+from LoopStructural.modelling.features import FeatureType
 
 from LoopStructural.utils import getLogger
 
@@ -26,7 +27,7 @@ def calculate_fault_intersections(model, threshold=0.001):
     """
     fault_names = []
     for f in model.features:
-        if f.type == "fault":
+        if f.type == FeatureType.FAULT:
             fault_names.append(f.name)
     fault_matrix = pd.DataFrame(columns=fault_names)
     for f in fault_names:

LoopStructural/analysis/_fault_intersection.py

@@ -17,3 +17,4 @@
 from ._base import load_unconformity
 from ._base import load_duplex
 from ._base import load_tabular_intrusion
+from ._base import load_geological_map_data

LoopStructural/datasets/__init__.py

@@ -157,3 +157,71 @@ def load_tabular_intrusion():
     data = pd.read_csv(join(module_path, Path("data/tabular_intrusion.csv")))
     bb = np.array([[0, 0, 0], [5, 5, 5]])
     return data, bb
+
+
+def load_geological_map_data():
+    module_path = dirname(__file__)
+    contacts = pd.read_csv(
+        join(module_path, Path("data/geological_map_data/contacts.csv"))
+    )
+    stratigraphic_orientations = pd.read_csv(
+        join(
+            module_path, Path("data/geological_map_data/stratigraphic_orientations.csv")
+        )
+    )
+    stratigraphic_thickness = pd.read_csv(
+        join(module_path, Path("data/geological_map_data/stratigraphic_thickness.csv")),
+        skiprows=1,
+        names=["name", "thickness"],
+    )
+    stratigraphic_order = pd.read_csv(
+        join(module_path, Path("data/geological_map_data/stratigraphic_order.csv")),
+        skiprows=1,
+        names=["order", "unit name"],
+    )
+    bbox = pd.read_csv(
+        join(module_path, Path("data/geological_map_data/bbox.csv")),
+        index_col=0,
+        header=None,
+        names=["X", "Y", "Z"],
+    )
+    fault_properties = pd.read_csv(
+        join(module_path, Path("data/geological_map_data/fault_displacement.csv")),
+        index_col=0,
+    )
+    fault_edges = []
+    with open(
+        join(module_path, Path("data/geological_map_data/fault_edges.txt")), "r"
+    ) as f:
+        for l in f.read().split("\n"):
+            faults = l.split(",")
+            if len(faults) == 2:
+                fault_edges.append((faults[0], faults[1]))
+    fault_locations = pd.read_csv(
+        join(module_path, Path("data/geological_map_data/fault_locations.csv"))
+    )
+    fault_orientations = pd.read_csv(
+        join(module_path, Path("data/geological_map_data/fault_orientations.csv"))
+    )
+    return (
+        contacts,
+        stratigraphic_orientations,
+        stratigraphic_thickness,
+        stratigraphic_order,
+        bbox,
+        fault_locations,
+        fault_orientations,
+        fault_properties,
+        fault_edges,
+    )
+
+
+def load_fault_trace():
+    import geopandas
+
+    module_path = dirname(__file__)
+
+    fault_trace = geopandas.read_file(
+        join(module_path, Path("data/fault_trace/fault_trace.shp"))
+    )
+    return fault_trace