docs: refactoring documentation + adding new example

Loop3D · May 5, 2022 · d15ba6c · d15ba6c
1 parent dae9e92
commit d15ba6c
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Showing 20 changed files with 1,224 additions and 18 deletions.
diff --git a/.github/workflows/documentation.yml b/.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
diff --git a/.github/workflows/windows_CI.yml b/.github/workflows/windows_CI.yml
@@ -34,3 +34,23 @@ jobs:
         shell: bash -l {0}
         run: |
           pytest
+  documentation:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - 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
+          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 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
diff --git a/LoopStructural/modelling/input/process_data.py b/LoopStructural/modelling/input/process_data.py
@@ -90,7 +90,7 @@ def __init__(
             self.fault_properties = fault_properties
         elif fault_locations is not None:
             self.fault_properties = pd.DataFrame(
-                fault_locations["fault_name"].unique(), columns=["name"]
+                fault_locations["feature_name"].unique(), columns=["name"]
             ).set_index("name")
 
         if fault_edges is not None and fault_edge_properties is not None:
@@ -619,10 +619,15 @@ def fault_orientations(self, fault_orientations):
             fault_orientations[["gx", "gy", "gz"]] = strike_dip_vector(
                 fault_orientations["strike"], fault_orientations["dip"]
             )
-        if "feature_name" not in fault_orientations.columns and "fault_name" in fault_orientations.columns:
+        if (
+            "feature_name" not in fault_orientations.columns
+            and "fault_name" in fault_orientations.columns
+        ):
             fault_orientations["feature_name"] = fault_orientations["fault_name"]
         if "feature_name" not in fault_orientations.columns:
-            raise ValueError("Fault orientation data must contain feature_name or fault_name")
+            raise ValueError(
+                "Fault orientation data must contain feature_name or fault_name"
+            )
         self._fault_orientations = fault_orientations[
             ["X", "Y", "Z", "gx", "gy", "gz", "coord", "feature_name"]
         ]
@@ -645,7 +650,15 @@ def fault_locations(self, fault_locations):
         fault_locations = fault_locations.copy()
         fault_locations["coord"] = 0
         fault_locations["val"] = 0
-        fault_locations["feature_name"] = fault_locations["fault_name"]
+        if (
+            "feature_name" not in fault_locations.columns
+            and "fault_name" in fault_locations.columns
+        ):
+            fault_locations["feature_name"] = fault_locations["fault_name"]
+        if "feature_name" not in fault_locations.columns:
+            raise ValueError(
+                "Fault location data must contain feature_name or fault_name"
+            )
         self._fault_locations = fault_locations[
             ["X", "Y", "Z", "val", "feature_name", "coord"]
         ]
diff --git a/docs/source/about.rst → docs/source/getting_started/about.rst b/docs/source/about.rst → docs/source/getting_started/about.rst
diff --git a/docs/source/background.rst → docs/source/getting_started/background.rst b/docs/source/background.rst → docs/source/getting_started/background.rst
diff --git a/docs/source/contributors_guide.rst → ...ce/getting_started/contributors_guide.rst b/docs/source/contributors_guide.rst → ...ce/getting_started/contributors_guide.rst
diff --git a/docs/source/getting_started.rst → docs/source/getting_started/index.rst b/docs/source/getting_started.rst → docs/source/getting_started/index.rst
@@ -6,7 +6,7 @@ Getting Started
 
    installation
    background
-   auto_examples/index
-   contributors_guide
    about
+   contributors_guide
+   loopstructural_design
    CHANGELOG
diff --git a/docs/source/installation.rst → docs/source/getting_started/installation.rst b/docs/source/installation.rst → docs/source/getting_started/installation.rst
diff --git a/.../source/_static/loopstructural_design.rst → ...getting_started/loopstructural_design.rst b/.../source/_static/loopstructural_design.rst → ...getting_started/loopstructural_design.rst
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -28,7 +28,7 @@ and a wrapper for the generalised radial basis functions provided by Surfe :cite
 .. toctree::
    :hidden:
 
-   getting_started
+   getting_started/index
    auto_examples/index
    user_guide/index
 

diff --git a/examples/4_advanced/bbox.csv b/examples/4_advanced/bbox.csv
@@ -0,0 +1,2 @@
+origin, 519572.569,7489723.89,-4800.0
+maximum,551978.745,7516341.01,1200.0