Python 3.8 compatibility (GT4SD#152)

* fix: wheel tensorboard version conflict (closes GT4SD#146)

* feat: python 3.8 support

* Install (GT4SD#1)

* refactor: importlib instead of pkg_resources

* fix: importlib pin

* wip: mypy python 3.8 checks, lower lightning

* wip: restore new lightning version

* docs: updating python version upper bound

* chore: import cleanup

* chore: remove unused import from init

Co-authored-by: Matteo Manica <[email protected]>

README.md

@@ -25,7 +25,7 @@ For full details on the library API and examples see the [docs](https://gt4sd.gi
 
 Currently `gt4sd` relies on:
 
-- python>=3.7,<3.8
+- python>=3.7,<3.9
 - pip>=19.1,<20.3
 
 We are actively working on relaxing these, so stay tuned or help us with this by [contributing](./CONTRIBUTING.md) to the project.

conda.yml

@@ -5,7 +5,7 @@ channels:
   - https://conda.anaconda.org/pyg
   - https://conda.anaconda.org/conda-forge
 dependencies:
-  - python>=3.7,<3.8
+  - python>=3.7,<3.9
   - pip>=19.1,<20.3
   - pytorch>=1.0
   - pytorch-scatter>=2.0.9

conda_gpu.yml

@@ -5,7 +5,7 @@ channels:
   - https://conda.anaconda.org/pyg
   - https://conda.anaconda.org/conda-forge
 dependencies:
-  - python>=3.7,<3.8
+  - python>=3.7,<3.9
   - pip>=19.1,<20.3
   - pytorch>=1.0
   - pytorch-scatter>=2.0.9

requirements.txt

@@ -2,11 +2,11 @@
 accelerate>=0.12
 datasets>=1.11.0
 diffusers>=0.2.4
-ipaddress>=1.0.23
-joblib>=1.1.0
 importlib-metadata>=1.7.0,<5.0.0 # temporary: https://github.com/python/importlib_metadata/issues/409
 importlib-resources>=5.10.0
-keras==2.3.1
+ipaddress>=1.0.23
+joblib>=1.1.0
+keras>=2.3.1
 keybert==0.2.0
 minio==7.0.1
 modlamp>=4.0.0
@@ -23,14 +23,15 @@ reinvent-chemistry==0.0.38
 sacremoses>=0.0.41
 scikit-learn>=1.0.0
 scikit-optimize>=0.8.1
+scipy>=1.0.0
 sentencepiece>=0.1.95
 sympy>=1.10.1
 tables>=3.7.0
 tape-proteins>=0.4
 tensorboard!=2.5.0,>=2.2.0
-tensorflow==2.1.0
-torchdrug>=0.1.2
-torchmetrics<0.7
+tensorflow>=2.1.0
+torchdrug>=0.2.0
+torchmetrics>=0.7.0
 torchvision>=0.12.0
 transformers>=4.22.0
 typing_extensions>=3.7.4.3

setup.cfg

@@ -11,15 +11,16 @@ classifiers =
     Operating System :: OS Independent
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
 
 [options]
 install_requires =
     accelerate
     datasets
     diffusers
-    ipaddress
     importlib_metadata
     importlib_resources
+    ipaddress
     joblib
     keras
     keybert

src/gt4sd/algorithms/controlled_sampling/advanced_manufacturing/implementation/core.py

@@ -328,8 +328,11 @@ def __init__(
         self.dimensions = self.define_dimensions(self.representation_order)
 
     def _get_bounds(
-        self, minimum_value: float, maximum_value: float, z_dimension: int
-    ) -> List[Tuple[float, float]]:
+        self,
+        minimum_value: Union[float, np.float32],
+        maximum_value: Union[float, np.float32],
+        z_dimension: int,
+    ) -> List[Tuple[Union[float, np.float32], Union[float, np.float32]]]:
         """
         Define a list of bounds for an hypercube.
 
@@ -366,7 +369,7 @@ def set_bounds(
         for representation_name in self.representations.keys() - self.bounds.keys():
             z_dimension = self.representations[representation_name].z_dimension
             self.bounds[representation_name] = self._get_bounds(
-                MINIMUM_REAL, MAXIMUM_REAL, z_dimension
+                MINIMUM_REAL, MAXIMUM_REAL, z_dimension  # type: ignore
             )
 
     def define_dimensions(self, representation_order: List[str]) -> List[Real]:
@@ -388,8 +391,8 @@ def define_dimensions(self, representation_order: List[str]) -> List[Real]:
             )
             latent_index += representation.z_dimension
             dimensions.extend(
-                [
-                    Real(lower_bound, upper_bound)  # type:ignore
+                [  # type:ignore
+                    Real(lower_bound, upper_bound)
                     for lower_bound, upper_bound in representation_bounds
                 ]
             )

src/gt4sd/frameworks/gflownet/dataloader/data_module.py

@@ -120,12 +120,12 @@ def setup(self, stage: Optional[str]) -> None:  # type:ignore
         self.ix_test = ixs[thresh:]
 
         if stage == "fit" or stage is None:
-            self.train_dataset.set_indexes(self.ix_train)
-            self.val_dataset.set_indexes(self.ix_val)
+            self.train_dataset.set_indexes(self.ix_train)  # type: ignore
+            self.val_dataset.set_indexes(self.ix_val)  # type: ignore
         if stage == "test" or stage is None:
-            self.test_dataset.set_indexes(self.ix_test)
+            self.test_dataset.set_indexes(self.ix_test)  # type: ignore
         if stage == "predict" or stage is None:
-            self.test_dataset.set_indexes(self.ix_test)
+            self.test_dataset.set_indexes(self.ix_test)  # type: ignore
 
         logger.info(
             f"number of data points used for training: {len(self.train_dataset)}"

src/gt4sd/training_pipelines/__init__.py

@@ -22,7 +22,6 @@
 # SOFTWARE.
 #
 """Module initialization for gt4sd traning pipelines."""
-
 import json
 import logging
 from typing import Any, Dict

src/gt4sd/training_pipelines/tests/test_training_moses_organ.py

@@ -22,7 +22,6 @@
 # SOFTWARE.
 #
 """Moses Organ trainer unit tests."""
-
 import os
 import shutil
 import tempfile

src/gt4sd/training_pipelines/tests/test_training_moses_vae.py

@@ -22,7 +22,6 @@
 # SOFTWARE.
 #
 """Moses VAE trainer unit tests."""
-
 import os
 import shutil
 import tempfile

vcs_requirements.txt

@@ -1,6 +1,6 @@
 # version control systems requirements
 guacamol_baselines @ git+https://github.com/GT4SD/[email protected]
-molecule_generation @ git+https://github.com/microsoft/molecule-generation.git@v0.2.0
+molecule_generation @ git+https://github.com/GT4SD/molecule-generation.git@main
 moses @ git+https://github.com/GT4SD/[email protected]
 paccmann_chemistry @ git+https://github.com/PaccMann/[email protected]
 paccmann_generator @ git+https://github.com/PaccMann/[email protected]