Explore Updating Biotite and other deps.

.github/workflows/local.yml

@@ -0,0 +1,24 @@
+name: test-in-blender
+
+on:
+  push:
+    branches: ["main", "20250211-biotite1"]
+  pull_request:
+    branches: ["main", "4.2", "4.3", "20250211-biotite1"]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 4
+      fail-fast: false
+      matrix:
+        version: ["4.3.2", "daily"]
+        os: [ubuntu-latest, macos-14, windows-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up pixi
+        uses: prefix-dev/[email protected]
+      - name: Run Tests
+        run: |
+          pixi run pytest

.github/workflows/test-daily.yml

@@ -1,25 +1,27 @@
 name: Test Daily Build
 
 on:
-  schedule:
-    - cron: '0 0 * * *'
+  push:
+    branches: ["20250211-biotite1"]
+  pull_request:
+    branches: ["20250211-biotite1"]
 jobs:
-    build:
-        runs-on: ${{ matrix.os }}
-        strategy:
-            max-parallel: 4
-            fail-fast: false
-            matrix:
-              version: ["daily"]
-              os: [ubuntu-latest, macos-14, windows-latest]
-        steps:
-            - uses: actions/checkout@v4
-            - uses: BradyAJohnston/[email protected]
-              with:
-                version: ${{ matrix.version }}
-            - name: Install in Blender
-              run: |
-                blender -b -P tests/python.py -- -m pip install ".[test]"
-            - name: Run Tests
-              run: |
-                blender -b -P tests/run.py -- -vv tests --cov --cov-report=xml
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 4
+      fail-fast: false
+      matrix:
+        version: ["daily"]
+        os: [ubuntu-latest, macos-14, windows-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: BradyAJohnston/[email protected]
+        with:
+          version: ${{ matrix.version }}
+      - name: Install in Blender
+        run: |
+          blender -b -P tests/python.py -- -m pip install ".[test]"
+      - name: Run Tests
+        run: |
+          blender -b -P tests/run.py -- -vv tests --cov --cov-report=xml

.gitignore

@@ -33,3 +33,7 @@ docs/nodes/*.qmd
 /.luarc.json
 tests/data/starfile/montage.tiff
 tests/data/cellpack/petworld/*.cif
+
+# pixi environments
+.pixi
+*.egg-info

molecularnodes/entities/molecule/oldcif.py

@@ -19,7 +19,8 @@ def __init__(self, file_path, extra_fields=None, sec_struct=True):
         self.n_atoms = self.array.array_length()
 
     def _read(self, file_path):
-        return pdbx.legacy.PDBxFile.read(file_path)
+        # return pdbx.legacy.PDBxFile.read(file_path)
+        return pdbx.CIFFile().read(file_path)
 
     def _get_structure(self, extra_fields: str = None, sec_struct=True, bonds=True):
         fields = ["b_factor", "charge", "occupancy", "atom_id"]

molecularnodes/entities/molecule/pdbx.py

@@ -266,7 +266,6 @@ def _ss_label_to_int(label):
     else:
         return 3
 
-
 class CIF(PDBX):
     def __init__(self, file_path):
         super().__init__(file_path)
@@ -299,6 +298,7 @@ def list_assemblies(self):
         return list(pdbx.list_assemblies(self._file).keys())
 
     def get_transformations(self, assembly_id):
+
         assembly_gen_category = self._file.block["pdbx_struct_assembly_gen"]
 
         struct_oper_category = self._file.block["pdbx_struct_oper_list"]
@@ -341,7 +341,6 @@ def get_transformations(self, assembly_id):
                         "pdb_model_num": pdb_model_num,
                     }
                 )
-
         return matrices
 
     def get_assemblies(self):

molecularnodes/entities/molecule/ui.py

@@ -9,8 +9,8 @@
 
 from ...download import FileDownloadPDBError, download, CACHE_DIR
 from ...blender import path_resolve
-from .oldcif import OldCIF
 from .molecule import Molecule
+from .oldcif import OldCIF
 from .pdb import PDB
 from .pdbx import BCIF, CIF
 from .sdf import SDF
@@ -92,6 +92,7 @@ def load_local(
     style="spheres",
     build_assembly=False,
 ):
+    print("loading local")
     mol = parse(file_path)
     mol.create_object(
         name=name,

pixi.toml

@@ -0,0 +1,42 @@
+[workspace]
+channels = [
+    "conda-forge",
+    "https://prefix.dev/pixi-build-backends",
+    "https://prefix.dev/conda-forge",
+]
+platforms = ["osx-arm64", "linux-64", "win-64"]
+preview = ["pixi-build"]
+
+
+[package]
+name = "molecularnodes"
+version = "0.1.0"
+
+[package.build]
+backend = { name = "pixi-build-python", version = "*" }
+
+[package.host-dependencies]
+hatchling = "==1.26.3"
+python = "==3.11"
+
+
+[package.run-dependencies]
+python = "==3.11"
+
+
+[tasks]
+
+[dependencies]
+python = "==3.11"
+ipython = "*"
+molecularnodes = { path = "." }
+
+[pypi-dependencies]
+bpy = "*"
+databpy = "*"
+pytest = "*"
+syrupy = "*"
+MDAnalysis = "*"
+biotite = "*"
+mrcfile = "*"
+starfile = "*"

pyproject.toml

@@ -3,18 +3,22 @@ name = "molecularnodes"
 version = "4.2.11"
 description = "Toolbox for molecular animations with Blender and Geometry Nodes."
 readme = "README.md"
-dependencies = ["databpy", "MDAnalysis>=2.7.0", "biotite~=0.40", "mrcfile", "starfile"]
-maintainers = [
-    {name = "Brady Johnston",    email = "[email protected]"}
-    ]
+dependencies = [
+    "databpy>=0.0.8",
+    "MDAnalysis>=2.7.0",
+    "biotite>=1.1",
+    "mrcfile",
+    "starfile",
+]
+maintainers = [{ name = "Brady Johnston", email = "[email protected]" }]
 
 [project.urls]
 Homepage = "https://bradyajohnston.github.io/MolecularNodes"
 Repository = "https://github.com/bradyajohnston/MolecularNodes"
 Documentation = "https://bradyajohnston.github.io/MolecularNodes"
 
 [project.optional-dependencies]
-bpy =  ["bpy>=4.2"]
+bpy = ["bpy>=4.2"]
 dev = ["pytest", "pytest-cov", "syrupy", "scipy", "fake-bpy-module"]
 test = ["pytest", "pytest-cov", "syrupy", "scipy"]
 docs = ["quartodoc", "tomlkit", "nodepad"]

tests/test_assembly.py

@@ -5,11 +5,12 @@
 import biotite.structure.io.pdb as biotite_pdb
 import biotite.structure.io.pdbx as biotite_cif
 import molecularnodes.entities.molecule.pdb as pdb
-import molecularnodes.entities.molecule.oldcif as oldcif
+import molecularnodes.entities.molecule.pdbx as pdbx
 
 
 DATA_DIR = join(dirname(realpath(__file__)), "data")
 
+print(DATA_DIR)
 
 @pytest.mark.parametrize(
     "pdb_id, format", itertools.product(["1f2n", "5zng"], ["pdb", "cif"])
@@ -26,22 +27,42 @@ def test_get_transformations(pdb_id, format):
         ref_assembly = biotite_pdb.get_assembly(pdb_file, model=1)
         test_parser = pdb.PDBAssemblyParser(pdb_file)
     elif format == "cif":
-        cif_file = biotite_cif.PDBxFile.read(path)
+        cif_file = biotite_cif.CIFFile().read(path)
         atoms = biotite_cif.get_structure(
             # Make sure `label_asym_id` is used instead of `auth_asym_id`
             cif_file,
             model=1,
             use_author_fields=False,
         )
         ref_assembly = biotite_cif.get_assembly(cif_file, model=1)
-        test_parser = oldcif.CIFAssemblyParser(cif_file)
+        test_parser = pdbx.CIFAssemblyParser(cif_file)
+
     else:
         raise ValueError(f"Format '{format}' does not exist")
 
+
     assembly_id = test_parser.list_assemblies()[0]
     test_transformations = test_parser.get_transformations(assembly_id)
 
-    check_transformations(test_transformations, atoms, ref_assembly)
+    if format == "pdb":
+        # for idx, (chain_list, matrix_list ) in  enumerate(test_transformations):
+        #     if idx == 5:
+        #         break
+        #     print(format)
+        #     print(chain_list, matrix_list)
+        check_transformations(test_transformations, atoms, ref_assembly)
+    elif format == "cif":
+
+        for idx, tdict  in  enumerate(test_transformations):
+            if idx == 5:
+                break
+            print(format)
+            print(tdict['chain_ids'], tdict['matrix'])
+        test_transformations2 = [( transformation['chain_ids'], transformation['matrix']) for transformation in test_transformations]
+        check_transformations(test_transformations2, atoms, ref_assembly)
+    else:
+        raise ValueError(f"Format '{format}' does not exist")
+
 
 
 @pytest.mark.parametrize("assembly_id", [str(i + 1) for i in range(5)])
@@ -53,7 +74,7 @@ def test_get_transformations_cif(assembly_id):
     In this case all assemblies from a structure with more complex
     operation expressions are tested
     """
-    cif_file = biotite_cif.PDBxFile.read(join(DATA_DIR, "1f2n.cif"))
+    cif_file = biotite_cif.CIFFile.read(join(DATA_DIR, "1f2n.cif"))
     atoms = biotite_cif.get_structure(
         # Make sure `label_asym_id` is used instead of `auth_asym_id`
         cif_file,
@@ -62,10 +83,12 @@ def test_get_transformations_cif(assembly_id):
     )
     ref_assembly = biotite_cif.get_assembly(cif_file, model=1, assembly_id=assembly_id)
 
-    test_parser = oldcif.CIFAssemblyParser(cif_file)
+    test_parser = pdbx.CIFAssemblyParser(cif_file)
+
     test_transformations = test_parser.get_transformations(assembly_id)
 
-    check_transformations(test_transformations, atoms, ref_assembly)
+    test_transformations2 = [( transformation['chain_ids'], transformation['matrix']) for transformation in test_transformations]
+    check_transformations(test_transformations2, atoms, ref_assembly)
 
 
 def check_transformations(transformations, atoms, ref_assembly):
@@ -75,6 +98,7 @@ def check_transformations(transformations, atoms, ref_assembly):
     """
     test_assembly = None
     for chain_ids, matrix in transformations:
+
         matrix = np.array(matrix)
         translation = matrix[:3, 3]
         rotation = matrix[:3, :3]

tests/test_load.py

@@ -151,6 +151,7 @@ def test_rcsb_nmr(snapshot_custom, del_hydrogen):
 
 
 def test_load_small_mol(snapshot_custom):
+
     mol = mn.entities.load_local(data_dir / "ASN.cif")
     for att in ["position", "bond_type"]:
         assert snapshot_custom == mol.named_attribute(att).tolist()