_after_setup hook for setup_properties

.github/workflows/black.yml

@@ -0,0 +1,10 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: psf/black@stable

.gitignore

@@ -0,0 +1,171 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# configs/ # commented as new configs can be added as a part of a feature
+
+/.idea
+/data
+/logs
+/results_buffer
+electra_pretrained.ckpt
+.isort.cfg
+/.vscode

chebai_graph/preprocessing/datasets/chebi.py

@@ -1,26 +1,26 @@
-from typing import Optional, List, Callable
+import importlib
+import os
+from typing import Callable, List, Optional
 
+import pandas as pd
+import torch
+import tqdm
+from chebai.preprocessing.datasets.base import XYBaseDataModule
 from chebai.preprocessing.datasets.chebi import (
     ChEBIOver50,
     ChEBIOver100,
     ChEBIOverXPartial,
 )
-from chebai.preprocessing.datasets.base import XYBaseDataModule
 from lightning_utilities.core.rank_zero import rank_zero_info
+from torch_geometric.data.data import Data as GeomData
 
-from chebai_graph.preprocessing.reader import GraphReader, GraphPropertyReader
+import chebai_graph.preprocessing.properties as graph_properties
 from chebai_graph.preprocessing.properties import (
     AtomProperty,
     BondProperty,
     MolecularProperty,
 )
-import pandas as pd
-from torch_geometric.data.data import Data as GeomData
-import torch
-import chebai_graph.preprocessing.properties as graph_properties
-import importlib
-import os
-import tqdm
+from chebai_graph.preprocessing.reader import GraphPropertyReader, GraphReader
 
 
 class ChEBI50GraphData(ChEBIOver50):
@@ -84,18 +84,20 @@ def _setup_properties(self):
         for file in file_names:
             # processed_dir_main only exists for ChEBI datasets
             path = os.path.join(
-                self.processed_dir_main
-                if hasattr(self, "processed_dir_main")
-                else self.raw_dir,
+                (
+                    self.processed_dir_main
+                    if hasattr(self, "processed_dir_main")
+                    else self.raw_dir
+                ),
                 file,
             )
             raw_data += list(self._load_dict(path))
         idents = [row["ident"] for row in raw_data]
         features = [row["features"] for row in raw_data]
 
         # use vectorized version of encode function, apply only if value is present
-        enc_if_not_none = (
-            lambda encode, value: [encode(atom_v) for atom_v in value]
+        enc_if_not_none = lambda encode, value: (
+            [encode(atom_v) for atom_v in value]
             if value is not None and len(value) > 0
             else None
         )
@@ -134,11 +136,14 @@ def get_property_path(self, property: MolecularProperty):
             f"{property.name}_{property.encoder.name}.pt",
         )
 
-    def setup(self, **kwargs):
-        super().setup(keep_reader=True, **kwargs)
-        self._setup_properties()
+    def _after_setup(self, **kwargs):
+        """
+        Finalize the setup process after ensuring the processed data is available.
 
-        self.reader.on_finish()
+        This method performs post-setup tasks like finalizing the reader and setting internal properties.
+        """
+        self._setup_properties()
+        super()._after_setup(**kwargs)
 
     def _merge_props_into_base(self, row):
         geom_data = row["features"]