fix end-of-file-fixer

Borda · Borda · commit 0989dd544033 · 2025-03-27T20:27:12.000+01:00
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -30,4 +30,4 @@ If applicable, add screenshots to help explain your problem.
 - Any other relevant information:
 
 **Additional context**
-Add any other context about the problem here.
+Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -14,4 +14,4 @@ A clear and concise description of what the problem is.
 A clear and concise description of what you want to happen. Ideally, with pseudo-code.
 
 **Additional context**
-Add any other context or screenshots about the feature request here.
+Add any other context or screenshots about the feature request here.
diff --git a/.github/ISSUE_TEMPLATE/general-question.md b/.github/ISSUE_TEMPLATE/general-question.md
@@ -9,4 +9,4 @@ assignees: ''
 
 **Describe your question.**
 
-<!-- A clear and concise description of the question. -->
+<!-- A clear and concise description of the question. -->
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ repos:
     rev: v4.0.1
     hooks:
       - id: trailing-whitespace
-#      - id: end-of-file-fixer
+      - id: end-of-file-fixer
 
   - repo: https://github.com/google/yapf
     rev: v0.43.0
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -7,4 +7,4 @@ python:
   version: 3.7
   install:
     - requirements: docs/requirements.txt
-    - requirements: requirements.txt
+    - requirements: requirements.txt
diff --git a/CODE-OF-CONDUCT.md b/CODE-OF-CONDUCT.md
@@ -141,4 +141,4 @@ enforcement ladder](https://github.com/mozilla/diversity).
 
 For answers to common questions about this code of conduct, see the FAQ at
 https://www.contributor-covenant.org/faq. Translations are available at
-https://www.contributor-covenant.org/translations.
+https://www.contributor-covenant.org/translations.
diff --git a/CONTRIBUTE.md b/CONTRIBUTE.md
@@ -121,4 +121,4 @@ The overall naming convention follows this order, although not all items should
 
 Please follow existing examples when in doubt.
 
-Thanks a lot and feel free to reachout if you have any question!
+Thanks a lot and feel free to reachout if you have any question!
diff --git a/docs/install.rst b/docs/install.rst
@@ -24,4 +24,4 @@ Alternatively, you could use **conda** for installation:
 * scikit_learn
 * fuzzywuzzy
 
-To use some of TDC features, you need to install additional packages. Those packages will be automatically installed. Detailed installation instructions will be displayed in the terminal in case automatic installation fails.
+To use some of TDC features, you need to install additional packages. Those packages will be automatically installed. Detailed installation instructions will be displayed in the terminal in case automatic installation fails.
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -6,4 +6,4 @@ DeepPurpose
 rxn4chemistry
 pandas_flavor
 descriptastorus @ git+https://github.com/bp-kelley/descriptastorus.git@2.4.0
-rd_filters @ git+https://github.com/PatWalters/rd_filters.git
+rd_filters @ git+https://github.com/PatWalters/rd_filters.git
diff --git a/docs/tdc.base_dataset.rst b/docs/tdc.base_dataset.rst
@@ -4,4 +4,4 @@ tdc.base\_dataset
 .. automodule:: tdc.base_dataset
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
diff --git a/docs/tdc.chem_utils.rst b/docs/tdc.chem_utils.rst
@@ -39,4 +39,3 @@ tdc.chem\_utils.evaluator module
    :members:
    :undoc-members:
    :show-inheritance:
-
diff --git a/docs/tdc.evaluator.rst b/docs/tdc.evaluator.rst
@@ -4,4 +4,4 @@ tdc.evaluator
 .. automodule:: tdc.evaluator
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
diff --git a/docs/tdc.generation.rst b/docs/tdc.generation.rst
@@ -31,4 +31,4 @@ tdc.generation.retrosyn module
 .. automodule:: tdc.generation.retrosyn
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
diff --git a/docs/tdc.metadata.rst b/docs/tdc.metadata.rst
@@ -4,4 +4,4 @@ tdc.metadata
 .. automodule:: tdc.metadata
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
diff --git a/docs/tdc.multi_pred.rst b/docs/tdc.multi_pred.rst
@@ -104,4 +104,4 @@ tdc.multi\_pred.test\_multi\_pred module
 .. automodule:: tdc.multi_pred.test_multi_pred
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
diff --git a/docs/tdc.oracles.rst b/docs/tdc.oracles.rst
@@ -4,4 +4,4 @@ tdc.oracles
 .. automodule:: tdc.oracles
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
diff --git a/docs/tdc.single_pred.rst b/docs/tdc.single_pred.rst
@@ -88,4 +88,4 @@ tdc.single\_pred.yields module
 .. automodule:: tdc.single_pred.yields
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
diff --git a/examples/generation/docking_generation/GCPN/LICENSE.txt b/examples/generation/docking_generation/GCPN/LICENSE.txt
@@ -10,4 +10,4 @@ Redistribution and use in source and binary forms, with or without modification,
 
 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/examples/generation/docking_generation/GCPN/README.md b/examples/generation/docking_generation/GCPN/README.md
@@ -70,9 +70,3 @@ tensorboard --logdir runs
 ```
 
 All the generated molecules along the training process are stored in the `molecule_gen` folder, each run configuration is stored in a different csv file. Molecules are stored using SMILES strings, along with the desired properties scores.
-
-
-
-
-
-
diff --git a/examples/generation/docking_generation/GCPN/gym-molecule/README.md b/examples/generation/docking_generation/GCPN/gym-molecule/README.md
@@ -1 +1 @@
-# Molecule generation environment, compatible with openai gym
+# Molecule generation environment, compatible with openai gym
diff --git a/examples/generation/docking_generation/GCPN/upload.sh b/examples/generation/docking_generation/GCPN/upload.sh
@@ -1,3 +1,2 @@
 
 scp -r $1 tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/GCPN/
-
diff --git a/examples/generation/docking_generation/MARS/README.md b/examples/generation/docking_generation/MARS/README.md
@@ -74,4 +74,4 @@ rm -rf MARS/runs/try4;  python -m MARS.main --run_dir runs/try4
 import pyscreener
 from tdc import Oracle
 oracle2 = Oracle(name = 'Docking_Score', software='vina', pyscreener_path = './', pdbids=['5WIU'], center=(-18.2, 14.4, -16.1), size=(15.4, 13.9, 14.5), buffer=10, path='./', num_worker=1, ncpu=4)
-```
+```
diff --git a/examples/generation/docking_generation/MARS/download.sh b/examples/generation/docking_generation/MARS/download.sh
@@ -1,4 +1 @@
 scp -r tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/MARS/result* .
-
-
-
diff --git a/examples/generation/docking_generation/MARS/upload.sh b/examples/generation/docking_generation/MARS/upload.sh
@@ -1,3 +1,2 @@
 
 scp -r $1 tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/MARS/MARS
-
diff --git a/examples/generation/docking_generation/guacamol_tdc/README.md b/examples/generation/docking_generation/guacamol_tdc/README.md
@@ -106,17 +106,3 @@ python results/analysis.py
 ```
 
 pls see `results/smiles_lstm_hc.png` for results.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/examples/generation/docking_generation/guacamol_tdc/download.sh b/examples/generation/docking_generation/guacamol_tdc/download.sh
@@ -8,5 +8,3 @@ rm -r results/graph_ga_1 results/graph_ga_2 results/graph_ga_3
 scp -r tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/pyscreener/graph_ga/results ./results/graph_ga_1
 scp -r tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/pyscreener/graph_ga/results.2 ./results/graph_ga_2
 scp -r tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/pyscreener/graph_ga/results.3 ./results/graph_ga_3
-
-
diff --git a/examples/generation/docking_generation/guacamol_tdc/guacamol/upload.sh b/examples/generation/docking_generation/guacamol_tdc/guacamol/upload.sh
@@ -1,4 +1,2 @@
 
 scp -r $1 tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/guacamol_tdc/guacamol
-
-
diff --git a/examples/generation/docking_generation/guacamol_tdc/guacamol_baselines/README.md b/examples/generation/docking_generation/guacamol_tdc/guacamol_baselines/README.md
@@ -132,4 +132,3 @@ To execute the goal-directed generation benchmarks:
 ```bash
 python -m smiles_lstm_ppo.goal_directed_generation
 ```
-
diff --git a/examples/generation/docking_generation/guacamol_tdc/guacamol_baselines/fetch_guacamol_dataset.sh b/examples/generation/docking_generation/guacamol_tdc/guacamol_baselines/fetch_guacamol_dataset.sh
@@ -9,4 +9,3 @@ wget https://ndownloader.figshare.com/files/13612760 -O data/guacamol_v1_train.s
 wget https://ndownloader.figshare.com/files/13612766 -O data/guacamol_v1_valid.smiles
 
 wget https://ndownloader.figshare.com/files/13612757 -O data/guacamol_v1_test.smiles
-
diff --git a/examples/generation/docking_generation/guacamol_tdc/guacamol_baselines/upload.sh b/examples/generation/docking_generation/guacamol_tdc/guacamol_baselines/upload.sh
@@ -1,4 +1,2 @@
 
 scp -r $1 tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/guacamol_tdc/guacamol_baselines
-
-
diff --git a/examples/generation/docking_generation/guacamol_tdc/results0/graph_ga/goal_directed_params.json b/examples/generation/docking_generation/guacamol_tdc/results0/graph_ga/goal_directed_params.json
@@ -10,4 +10,4 @@
     "seed": 0,
     "smiles_file": "data/guacamol_v1_all.smiles",
     "suite": "v3"
-}
+}
diff --git a/examples/generation/docking_generation/guacamol_tdc/results0/random_smiles_sampler/goal_directed_results.json b/examples/generation/docking_generation/guacamol_tdc/results0/random_smiles_sampler/goal_directed_results.json
@@ -1776,4 +1776,4 @@
             }
         }
     ]
-}
+}
diff --git a/examples/generation/docking_generation/guacamol_tdc/results0/smiles_ga/goal_directed_params.json b/examples/generation/docking_generation/guacamol_tdc/results0/smiles_ga/goal_directed_params.json
@@ -10,4 +10,4 @@
     "seed": 42,
     "smiles_file": "data/guacamol_v1_all.smiles",
     "suite": "v3"
-}
+}
diff --git a/examples/generation/docking_generation/guacamol_tdc/results0/smiles_lstm_ppo/goal_directed_params.json b/examples/generation/docking_generation/guacamol_tdc/results0/smiles_lstm_ppo/goal_directed_params.json
@@ -10,4 +10,4 @@
     "output_dir": "/net/sunlab/psunlab1/molecular_data/graphnn/guacamol_tdc/guacamol_baselines/smiles_lstm_ppo",
     "seed": 42,
     "suite": "v3"
-}
+}
diff --git a/examples/generation/docking_generation/guacamol_tdc/results0/smiles_lstm_ppo/pretrained_model/model_final_0.473.json b/examples/generation/docking_generation/guacamol_tdc/results0/smiles_lstm_ppo/pretrained_model/model_final_0.473.json
@@ -1 +1 @@
-{"input_size": 47, "hidden_size": 1024, "output_size": 47, "n_layers": 3, "rnn_dropout": 0.2}
+{"input_size": 47, "hidden_size": 1024, "output_size": 47, "n_layers": 3, "rnn_dropout": 0.2}
diff --git a/examples/generation/docking_generation/guacamol_tdc/results_limit_oracle/best_from_chembl.json b/examples/generation/docking_generation/guacamol_tdc/results_limit_oracle/best_from_chembl.json
@@ -1336,4 +1336,4 @@
             }
         }
     ]
-}
+}
diff --git a/examples/generation/docking_generation/guacamol_tdc/results_limit_oracle/graph_ga.json b/examples/generation/docking_generation/guacamol_tdc/results_limit_oracle/graph_ga.json
@@ -1336,4 +1336,4 @@
             }
         }
     ]
-}
+}
diff --git a/examples/generation/docking_generation/guacamol_tdc/results_limit_oracle/random_smiles_sampler.json b/examples/generation/docking_generation/guacamol_tdc/results_limit_oracle/random_smiles_sampler.json
@@ -1336,4 +1336,4 @@
             }
         }
     ]
-}
+}
diff --git a/examples/generation/docking_generation/guacamol_tdc/results_limit_oracle/smiles_ga.json b/examples/generation/docking_generation/guacamol_tdc/results_limit_oracle/smiles_ga.json
@@ -1336,4 +1336,4 @@
             }
         }
     ]
-}
+}
diff --git a/examples/generation/docking_generation/guacamol_tdc/upload.sh b/examples/generation/docking_generation/guacamol_tdc/upload.sh
@@ -10,7 +10,3 @@ scp guacamol_baselines/graph_ga/graph_ga_run.py  tfu42@orcus1.cc.gatech.edu:/pro
 scp guacamol_baselines/smiles_lstm_hc/run_smiles_lstm_hc.py  tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/pyscreener/run_smiles_lstm_hc.py
 
 scp -r guacamol_baselines/smiles_lstm_hc tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/pyscreener/
-
-
-
-
diff --git a/examples/generation/docking_generation/moldqn/README.md b/examples/generation/docking_generation/moldqn/README.md
@@ -132,4 +132,3 @@ python multi_obj_opt.py --model_dir=${OUTPUT_DIR} --hparams="./configs/multi_obj
 ```
 python target_sas.py --model_dir="${OUTPUT_DIR}" --hparams="./configs/target_sas.json" --start_molecule="CCN1c2ccccc2Cc3c(O)ncnc13" --loss_type="l2" --target_sas=2.5
 ```
-
diff --git a/examples/generation/docking_generation/moldqn/chemgraph/download.sh b/examples/generation/docking_generation/moldqn/chemgraph/download.sh
@@ -1,3 +1,2 @@
 
 scp -r tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/mol_dqn_docking/chemgraph/docking_smilesvaluelst_* .
-
diff --git a/examples/generation/docking_generation/moldqn/chemgraph/dqn/py/SA_Score/README b/examples/generation/docking_generation/moldqn/chemgraph/dqn/py/SA_Score/README
@@ -6,4 +6,3 @@ Journal of Cheminformatics 1:8 (2009)
 http://www.jcheminf.com/content/1/1/8
 
 Contribution from Peter Ertl and Greg Landrum
-
diff --git a/examples/generation/docking_generation/moldqn/mol_dqn.yml b/examples/generation/docking_generation/moldqn/mol_dqn.yml
@@ -167,4 +167,3 @@ dependencies:
     - zipp==3.1.0
     - zmq==0.0.0
 prefix: /nethome/tfu42/.conda/envs/openai-rl
-
diff --git a/examples/generation/docking_generation/moldqn/upload.sh b/examples/generation/docking_generation/moldqn/upload.sh
@@ -1,3 +1,2 @@
 
 scp -r $1 tfu42@orcus1.cc.gatech.edu:/project/molecular_data/graphnn/mol_dqn_docking/
-
diff --git a/examples/huggingface_examples/herg/.gitignore b/examples/huggingface_examples/herg/.gitignore
@@ -1,3 +1,3 @@
 tutorial_model
 result
-mlruns
+mlruns
diff --git a/examples/multi_pred/drugcombo/README.md b/examples/multi_pred/drugcombo/README.md
@@ -12,4 +12,3 @@ python train_MLP.py --epochs 10 --batch_size 128 --cuda True
 '''
 
 ```
-
diff --git a/examples/multi_pred/dti_dg/README.md b/examples/multi_pred/dti_dg/README.md
@@ -18,4 +18,4 @@ python train.py --algorithm GroupDRO --seed 0
 
 ### Add your own domain generalization algorithm
 
-Go to `domainbed/algorithm.py` script to add your algorithm.
+Go to `domainbed/algorithm.py` script to add your algorithm.
diff --git a/setup.cfg b/setup.cfg
@@ -1,2 +1,2 @@
 [metadata]
-description-file = README.md
+description-file = README.md
diff --git a/tdc/__init__.py b/tdc/__init__.py
@@ -2,4 +2,4 @@
 from .oracles import Oracle
 from .benchmark_deprecated import BenchmarkGroup
 from .model_server.tdc_hf import tdc_hf_interface
-from tdc.utils.knowledge_graph import KnowledgeGraph
+from tdc.utils.knowledge_graph import KnowledgeGraph
diff --git a/tdc/dataset_configs/__init__.py b/tdc/dataset_configs/__init__.py
@@ -1,2 +1,2 @@
 from .config import DatasetConfig
-from .brown_mdm2_ace2_12ca5_config import BrownProteinPeptideConfig
+from .brown_mdm2_ace2_12ca5_config import BrownProteinPeptideConfig
diff --git a/tdc/feature_generators/base.py b/tdc/feature_generators/base.py
@@ -1,2 +1,2 @@
 class FeatureGenerator(object):
-    pass
+    pass
diff --git a/tdc/multi_pred/dti.py b/tdc/multi_pred/dti.py
@@ -84,4 +84,4 @@ def harmonize_affinities(self, mode=None):
         self.entity2 = df.Target.values
         self.y = df.Y.values
         print_sys("The original data has been updated!")
-        return df
+        return df
diff --git a/tutorials/User_Group/opt_drd3_5000.json b/tutorials/User_Group/opt_drd3_5000.json
