diff --git a/naglmbis/models/__pycache__/base_model.cpython-311.pyc b/naglmbis/models/__pycache__/base_model.cpython-311.pyc index e62da21..92a203e 100644 Binary files a/naglmbis/models/__pycache__/base_model.cpython-311.pyc and b/naglmbis/models/__pycache__/base_model.cpython-311.pyc differ diff --git a/scripts/data/nagl_datasets/out.txt b/scripts/data/nagl_datasets/out.txt deleted file mode 100644 index e69de29..0000000 diff --git a/scripts/data/nagl_datasets/slurm-22500079.out b/scripts/data/nagl_datasets/slurm-22500079.out deleted file mode 100644 index 0caf749..0000000 --- a/scripts/data/nagl_datasets/slurm-22500079.out +++ /dev/null @@ -1,34 +0,0 @@ -Traceback (most recent call last): - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/blocks.py", line 1429, in setitem - values[indexer] = casted - ~~~~~~^^^^^^^^^ -ValueError: NumPy boolean array indexing assignment cannot assign 2406 input values to the 1 output values where the mask is true - -The above exception was the direct cause of the following exception: - -Traceback (most recent call last): - File "/mnt/storage/nobackup/nca121/nagl-mbis/scripts/data/nagl_datasets/append_parquets.py", line 40, in - pandas_parquet.loc[pandas_parquet['smiles'] == tagged_smiles, 'esp_column'] = record[0].esp - ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 911, in __setitem__ - iloc._setitem_with_indexer(indexer, value, self.name) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 1942, in _setitem_with_indexer - self._setitem_with_indexer_split_path(indexer, value, name) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 1982, in _setitem_with_indexer_split_path - self._setitem_with_indexer_2d_value(indexer, value) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 2057, in _setitem_with_indexer_2d_value - self._setitem_single_column(loc, value_col, pi) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 2175, in _setitem_single_column - self.obj._mgr.column_setitem(loc, plane_indexer, value) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 1337, in column_setitem - new_mgr = col_mgr.setitem((idx,), value) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 415, in setitem - return self.apply("setitem", indexer=indexer, value=value) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 363, in apply - applied = getattr(b, f)(**kwargs) - ^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/blocks.py", line 1432, in setitem - raise ValueError( -ValueError: setting an array element with a sequence. diff --git a/scripts/data/nagl_datasets/slurm-22500872.out b/scripts/data/nagl_datasets/slurm-22500872.out deleted file mode 100644 index 10d0bbe..0000000 --- a/scripts/data/nagl_datasets/slurm-22500872.out +++ /dev/null @@ -1,34 +0,0 @@ -Traceback (most recent call last): - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/blocks.py", line 1429, in setitem - values[indexer] = casted - ~~~~~~^^^^^^^^^ -ValueError: NumPy boolean array indexing assignment cannot assign 2406 input values to the 1 output values where the mask is true - -The above exception was the direct cause of the following exception: - -Traceback (most recent call last): - File "/mnt/storage/nobackup/nca121/nagl-mbis/scripts/data/nagl_datasets/append_parquets.py", line 40, in - pandas_parquet.loc[pandas_parquet['smiles'] == tagged_smiles, 'esp_column'] = record[0].esp.tolist() - ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 911, in __setitem__ - iloc._setitem_with_indexer(indexer, value, self.name) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 1942, in _setitem_with_indexer - self._setitem_with_indexer_split_path(indexer, value, name) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 1982, in _setitem_with_indexer_split_path - self._setitem_with_indexer_2d_value(indexer, value) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 2057, in _setitem_with_indexer_2d_value - self._setitem_single_column(loc, value_col, pi) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 2175, in _setitem_single_column - self.obj._mgr.column_setitem(loc, plane_indexer, value) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 1337, in column_setitem - new_mgr = col_mgr.setitem((idx,), value) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 415, in setitem - return self.apply("setitem", indexer=indexer, value=value) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 363, in apply - applied = getattr(b, f)(**kwargs) - ^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/blocks.py", line 1432, in setitem - raise ValueError( -ValueError: setting an array element with a sequence. diff --git a/scripts/data/nagl_datasets/slurm-22501266.out b/scripts/data/nagl_datasets/slurm-22501266.out deleted file mode 100644 index 38fca63..0000000 --- a/scripts/data/nagl_datasets/slurm-22501266.out +++ /dev/null @@ -1,34 +0,0 @@ -Traceback (most recent call last): - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/blocks.py", line 1429, in setitem - values[indexer] = casted - ~~~~~~^^^^^^^^^ -ValueError: NumPy boolean array indexing assignment cannot assign 2406 input values to the 1 output values where the mask is true - -The above exception was the direct cause of the following exception: - -Traceback (most recent call last): - File "/mnt/storage/nobackup/nca121/nagl-mbis/scripts/data/nagl_datasets/append_parquets.py", line 42, in - pandas_parquet.loc[pandas_parquet['smiles'] == tagged_smiles, 'esp_column'] = record[0].esp.tolist() - ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 911, in __setitem__ - iloc._setitem_with_indexer(indexer, value, self.name) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 1942, in _setitem_with_indexer - self._setitem_with_indexer_split_path(indexer, value, name) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 1982, in _setitem_with_indexer_split_path - self._setitem_with_indexer_2d_value(indexer, value) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 2057, in _setitem_with_indexer_2d_value - self._setitem_single_column(loc, value_col, pi) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/indexing.py", line 2175, in _setitem_single_column - self.obj._mgr.column_setitem(loc, plane_indexer, value) - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 1337, in column_setitem - new_mgr = col_mgr.setitem((idx,), value) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 415, in setitem - return self.apply("setitem", indexer=indexer, value=value) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/managers.py", line 363, in apply - applied = getattr(b, f)(**kwargs) - ^^^^^^^^^^^^^^^^^^^^^^^ - File "/mnt/nfs/home/nca121/mambaforge/envs/naglmbis/lib/python3.12/site-packages/pandas/core/internals/blocks.py", line 1432, in setitem - raise ValueError( -ValueError: setting an array element with a sequence. diff --git a/scripts/training/train_model.py b/scripts/training/train_model.py index 07034ab..6a5e781 100644 --- a/scripts/training/train_model.py +++ b/scripts/training/train_model.py @@ -87,11 +87,7 @@ def configure_model( def configure_data() -> DataConfig: return DataConfig( training=Dataset( -<<<<<<< HEAD - sources=["../datasets/training.parquet"], -======= - sources=["/home/localadmin/projects/nagl-mbis-release-for-training/nagl-mbis/scripts/datasets/testing.parquet"], ->>>>>>> 2469f10361fc24ac1bf64a5da1aa84db5e853498 + sources=["./testing.parquet"], # The 'column' must match one of the label columns in the parquet # table that was create during stage 000. # The 'readout' column should correspond to one our or model readout @@ -115,11 +111,7 @@ def configure_data() -> DataConfig: batch_size=250, ), validation=Dataset( -<<<<<<< HEAD - sources=["../datasets/validation.parquet"], -======= - sources=["/home/localadmin/projects/nagl-mbis-release-for-training/nagl-mbis/scripts/datasets/validation.parquet"], ->>>>>>> 2469f10361fc24ac1bf64a5da1aa84db5e853498 + sources=["./validation.parquet"], targets=[ ReadoutTarget( column="mbis-charges", @@ -137,11 +129,7 @@ def configure_data() -> DataConfig: ], ), test=Dataset( -<<<<<<< HEAD - sources=["../datasets/testing.parquet"], -======= - sources=["/home/localadmin/projects/nagl-mbis-release-for-training/nagl-mbis/scripts/datasets/testing.parquet"], ->>>>>>> 2469f10361fc24ac1bf64a5da1aa84db5e853498 + sources=["./testing.parquet"], targets=[ ReadoutTarget( column="mbis-charges",