Cleanup dependencies (#51)

* remove dependency on data.utils.annotations.extras

* test: fix tests

* chore: delete data.utils.annotations.extras

* chore: cleanup pyproject.toml

* chore: fix linting

* chore: remove extras.py test

* chore: cleanup src/plinder/data/structure/atoms.py

* chore: remove src/plinder/data/structure/models.py

* chore: cleanup tests/test_annotations.py

* chore: cleanup tests/test_atoms.py

* chore: update pip-compile for removed deps

* fix: add tabulate back for networkit bumpversion minor

---------

Co-authored-by: Thomas Duignan <thomas.j.duignan@gmail.com>

Author: yusuf1759

dockerfiles/base/requirements.txt

@@ -74,7 +74,9 @@ def get_version_bump(base_tag: str | None = None) -> str:
             ),
             text=True,
         ).strip()
-        if log and "origin/main" in log:
+        # origin/main hack was to get around docs branch but isn'try:
+        # present before pushing the tag back to main so just search for PR number
+        if log and "(#" in log:
             bump = token.split()[1]
             break
     if bump == "skip":

flows/docker.py

@@ -12,15 +12,8 @@ dependencies = [
     "nbformat",
     "google-cloud-storage",
     "gcsfs",
-    "tabulate",
     "gemmi",
     "rdkit==2023.9.5",
-    "pytest",
-    "pdb2pqr",
-    "molecular-rectifier",
-    "hydride",
-    "pdbeccdutils",
-    "oddt",
     "pyarrow",
     "omegaconf",
     "mmcif",

pyproject.toml

@@ -1,3 +1,4 @@
   networkit >= 11.0
+  tabulate
   pdb-validation @ git+https://git.scicore.unibas.ch/schwede/ligand-validation.git
   mmpdb @ git+https://github.com/rdkit/mmpdb.git