Merge pull request #225 from BradyAJohnston/dev-tests

Dev: Add Initial testing suite

Now that a [recent version of bpy](https://pypi.org/project/bpy/) is built and available on PyPi, this enables testing of the addon through `pytest` like other python-based projects. 

I have set up the workflows for running automatic testing on Windows and Linux machines, but there is a `segfault` error on macOS machines when running on GitHub actions. The tests run fine on my own 2017 MacBook pro, but I haven't looked into it much what the error might be.

In previously having discussion with the Blender devs, applying the modifiers and then comparing vertices might be the best strategy for doing snapshot tests. I have a couple of tests so far, which do exactly that for the regular import, cartoon and ribbon methods. There is also a method which tests importing via `.pdb` / `.cif` and downloading from the PDB and ensures their verts are the same. 

Currently these tests are just positionally based, though the other attributes will also be testable. Best to get some initial tests added and put into the workflow so that potentially others can contribute also. 

There are errors with importing `pyopenvdb` when using the `bpy` addon. It seems that the library isn't installed into the local python, and instead is called from within the addon itself to load volume files. This currently limits the ability to write any tests involving the volumetric import, but something to work on in the future.

.github/workflows/docs.yml

@@ -1,4 +1,4 @@
-name: Documentation
+name: docs-build-deploy
 
 on:
   workflow_dispatch:

.github/workflows/tests.yml

@@ -0,0 +1,43 @@
+name: test-addon
+
+on: 
+  push:
+    branches: 
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 4
+      fail-fast: false
+      matrix:
+        blender-version: ["3.5.0"]
+        os: [ubuntu-latest, windows-latest]
+        # os: [ubuntu-latest]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+      - run: pip install bpy==${{ matrix.blender-version }}
+      - run: pip install -r requirements.txt
+
+      - name: Install MolecularNodes
+        run: pip install .
+
+      - name: Run Tests
+        run: pytest --verbose --cov=MolecularNodes --cov-report=xml:coverage.xml
+
+      - name: Expose coverage as a CI download # Related to test_addon_blender_advanced.py
+        uses: actions/upload-artifact@v1
+        with:
+          name: coverage.xml
+          path: coverage.xml
+      # setup ssh to check on file system state
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3

.gitignore

@@ -7,3 +7,5 @@ logs/side-packages-install.log
 *.pyc
 .Rproj.user
 /.quarto/
+*egg*/*
+build/*

MANIFEST.in

@@ -0,0 +1 @@
+include MolecularNodes/assets/*

Makefile

@@ -1,3 +1,7 @@
 docs-build:
 	cd docs && quartodoc build
 	quarto render docs
+
+test:
+	pip3 install .
+	pytest -vv

MolecularNodes/density.py

@@ -1,9 +1,9 @@
 import bpy
-import pyopenvdb as vdb
+# import pyopenvdb as vdb
 import numpy as np
 import os
 
-def map_to_grid(file: str, invert: bool = False) -> vdb.FloatGrid:
+def map_to_grid(file: str, invert: bool = False):
     """Reads an MRC file and converts it into a pyopenvdb FloatGrid object.
 
     This function reads a file in MRC format, and converts it into a pyopenvdb FloatGrid object,
@@ -18,6 +18,8 @@ def map_to_grid(file: str, invert: bool = False) -> vdb.FloatGrid:
         pyopenvdb.FloatGrid: A pyopenvdb FloatGrid object containing the density data.
     """
     import mrcfile
+    import pyopenvdb as vdb
+
     volume = mrcfile.read(file)
 
     dataType = volume.dtype
@@ -68,6 +70,8 @@ def map_to_vdb(file: str, invert: bool = False, world_scale=0.01, overwrite=Fals
         str: The path to the converted .vdb file.
     """
     import mrcfile
+    import pyopenvdb as vdb
+
     file_path = path_to_vdb(file)
 
     # If the map has already been converted to a .vdb and overwrite is False, return that instead

MolecularNodes/load.py

@@ -353,7 +353,7 @@ def create_molecule(mol_array,
     # remove the solvent from the structure if requested
     if del_solvent:
         try:
-            mol_array = mol_array[np.invert(struc.filter_solvent(mol_array))]
+            mol_array = mol_array[0][np.invert(struc.filter_solvent(mol_array))]
         except TypeError:
             pass
 

docs/.gitignore

@@ -1 +1,4 @@
-/.quarto/
+/.quarto/
+reference/*
+_build/*
+objects.json

pyproject.toml

@@ -0,0 +1,25 @@
+[build-system]
+requires = ["setuptools>=45", "wheel", "setuptools_scm>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+markers = [
+]
+testpaths = [
+    "tests"
+]
+
+[project]
+name = "MolecularNodes"
+version = "2.6.2"
+
+[tool.setuptools.packages.find]
+where = ["."]
+
+[tool.setuptools]
+# ...
+# By default, include-package-data is true in pyproject.toml, so you do
+# NOT have to specify this line.
+include-package-data = true
+
+[tool.setuptools_scm]

requirements.txt

@@ -0,0 +1,8 @@
+pytest
+pytest-snapshot
+pytest-cov
+biotite==0.37.0     # General parsing of structural files.
+MDAnalysis==2.2.0   # Reading of molecular dynamics trajectories.
+mrcfile==1.4.3      # Importing EM density files.
+starfile==0.4.11    # Importing star files.
+eulerangles==1.0.1  # Handling euler angle in starfiles.