Refactor morphology to metrics and add gh workflow to publish docs

.github/workflows/docs.yml

@@ -0,0 +1,43 @@
+# This is a basic workflow to help you get started with Actions
+
+name: Build-sphinx-docs
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+           python-version: "3.10"
+
+      - name: Install dependencies
+        run: | 
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+      - name: Build HTML
+        run: | 
+          cd docs/
+          make html
+      - name: Run ghp-import
+        run: | 
+          ghp-import -n -p -f docs/_build/html

docs/dpm_tools.morphology.rst → docs/dpm_tools.metrics.rst

@@ -7,15 +7,15 @@ Submodules
 dpm\_tools.morphology.features module
 -------------------------------------
 
-.. automodule:: dpm_tools.morphology.features
+.. automodule:: dpm_tools.metrics.features
    :members:
    :undoc-members:
    :show-inheritance:
 
 Module contents
 ---------------
 
-.. automodule:: dpm_tools.morphology
+.. automodule:: dpm_tools.metrics
    :members:
    :undoc-members:
    :show-inheritance:

docs/dpm_tools.rst

@@ -8,7 +8,7 @@ Subpackages
    :maxdepth: 4
 
    dpm_tools.io
-   dpm_tools.morphology
+   dpm_tools.metrics
    dpm_tools.visualization
 
 Module contents

docs/modules/generated/dpm_tools.morphology.features.rst → docs/modules/generated/dpm_tools.metrics.features.rst

@@ -1,7 +1,7 @@
-dpm\_tools.morphology.features
-==============================
+dpm\_tools.metrics.features
+===========================
 
-.. automodule:: dpm_tools.morphology.features
+.. automodule:: dpm_tools.metrics.features
 
 
 

docs/modules/generated/dpm_tools.metrics.rst

@@ -0,0 +1,31 @@
+dpm\_tools.metrics
+==================
+
+.. automodule:: dpm_tools.metrics
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+
+   dpm_tools.metrics.features
+

docs/modules/index.rst

@@ -11,5 +11,5 @@ Modules
       :recursive:
 
       dpm_tools.io
-      dpm_tools.morphology
+      dpm_tools.metrics
       dpm_tools.visualization

dpm_tools/__init__.py

@@ -1,6 +1,6 @@
 from time import perf_counter_ns
 
-from . import morphology
+from . import metrics
 from . import io
 from . import visualization
 

dpm_tools/morphology/features.py → dpm_tools/metrics/features.py

@@ -4,8 +4,7 @@
 from typing import Tuple, Literal
 
 def slicewise_edt(data) -> np.ndarray:
-    """
-    Compute the Euclidean distance transform map of each slice individually and stacks them into a single 3D array.
+    """ Compute the Euclidean distance transform map of each slice individually and stacks them into a single 3D array.
     :param data: Image dataclass
     :return: Euclidean distance transform map of each slice
     :rtype: numpy.ndarray

examples/morphological_features.py

@@ -1,4 +1,4 @@
 import numpy as np
-from dpm_tools.morphology import chords
+from dpm_tools.metrics import chords
 from dpm_tools.io import ImageFromFile