From 5431694ec0ea2165e7571e44947cabfd795280aa Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Mon, 2 Oct 2023 15:21:35 +0200
Subject: [PATCH 01/14] ds stats now calculated with the converted inputs and
labels
---
apax/data/statistics.py | 34 +++++++++++-----------
apax/train/eval.py | 12 ++------
apax/train/run.py | 36 +++++++++++++++---------
tests/unit_tests/data/test_statistics.py | 19 ++++++++++++-
4 files changed, 60 insertions(+), 41 deletions(-)
diff --git a/apax/data/statistics.py b/apax/data/statistics.py
index 2a6ffc82..d7f79cd5 100644
--- a/apax/data/statistics.py
+++ b/apax/data/statistics.py
@@ -21,13 +21,13 @@ class PerElementRegressionShift:
dtypes = [float]
@staticmethod
- def compute(atoms_list, shift_options) -> np.ndarray:
+ def compute(inputs, labels, shift_options) -> np.ndarray:
log.info("Computing per element energy regression.")
lambd = shift_options["energy_regularisation"]
- energies = [atoms.get_potential_energy() for atoms in atoms_list]
- numbers = [atoms.numbers for atoms in atoms_list]
- system_sizes = [num.shape[0] for num in numbers]
+ energies = labels["ragged"]["energy"]
+ numbers = inputs["ragged"]["numbers"]
+ system_sizes = inputs["fixed"]["n_atoms"]
energies = np.array(energies)
system_sizes = np.array(system_sizes)
@@ -64,7 +64,7 @@ class IsolatedAtomEnergyShift:
dtypes = [dict[int:float]]
@staticmethod
- def compute(atoms_list, shift_options):
+ def compute(inputs, labels, shift_options):
n_species = 119
elemental_energies_shift = np.zeros(n_species)
for k, v in shift_options.items():
@@ -79,11 +79,11 @@ class MeanEnergyRMSScale:
dtypes = []
@staticmethod
- def compute(atoms_list, scale_options):
+ def compute(inputs, labels, scale_options):
# log.info("Computing per element energy regression.")
- energies = [atoms.get_potential_energy() for atoms in atoms_list]
- numbers = [atoms.numbers for atoms in atoms_list]
- system_sizes = [num.shape[0] for num in numbers]
+ energies = labels["ragged"]["energy"]
+ numbers = inputs["ragged"]["numbers"]
+ system_sizes = inputs["fixed"]["n_atoms"]
energies = np.array(energies)
system_sizes = np.array(system_sizes)
@@ -109,11 +109,11 @@ class PerElementForceRMSScale:
dtypes = []
@staticmethod
- def compute(atoms_list, scale_options):
+ def compute(inputs, labels, scale_options):
n_species = 119
- forces = np.concatenate([atoms.get_forces() for atoms in atoms_list], axis=0)
- numbers = np.concatenate([atoms.numbers for atoms in atoms_list], axis=0)
+ forces = np.concatenate(labels["ragged"]["forces"], axis=0)
+ numbers = np.concatenate(inputs["ragged"]["numbers"], axis=0)
elements = np.unique(numbers)
@@ -133,7 +133,7 @@ class GlobalCustomScale:
dtypes = [float]
@staticmethod
- def compute(atoms_list, scale_options):
+ def compute(inputs, labels, scale_options):
element_scale = scale_options["factor"]
return element_scale
@@ -144,7 +144,7 @@ class PerElementCustomScale:
dtypes = [dict[int, float]]
@staticmethod
- def compute(atoms_list, scale_options):
+ def compute(inputs, labels, scale_options):
n_species = 119
element_scale = np.ones(n_species)
for k, v in scale_options["factors"].items():
@@ -163,7 +163,7 @@ def compute(atoms_list, scale_options):
def compute_scale_shift_parameters(
- train_atoms_list, shift_method, scale_method, shift_options, scale_options
+ inputs, labels, shift_method, scale_method, shift_options, scale_options
):
shift_methods = {method.name: method for method in shift_method_list}
scale_methods = {method.name: method for method in scale_method_list}
@@ -182,8 +182,8 @@ def compute_scale_shift_parameters(
shift_method = shift_methods[shift_method]
scale_method = scale_methods[scale_method]
- shift_parameters = shift_method.compute(train_atoms_list, shift_options)
- scale_parameters = scale_method.compute(train_atoms_list, scale_options)
+ shift_parameters = shift_method.compute(inputs, labels, shift_options)
+ scale_parameters = scale_method.compute(inputs, labels, scale_options)
ds_stats = DatasetStats(shift_parameters, scale_parameters)
return ds_stats
diff --git a/apax/train/eval.py b/apax/train/eval.py
index 747f8f57..e33a18cb 100644
--- a/apax/train/eval.py
+++ b/apax/train/eval.py
@@ -8,7 +8,6 @@
from tqdm import trange
from apax.config import parse_config
-from apax.data.statistics import compute_scale_shift_parameters
from apax.model import ModelBuilder
from apax.train.checkpoints import load_params
from apax.train.metrics import initialize_metrics
@@ -124,16 +123,9 @@ def eval_model(config_path, n_test=-1, log_file="eval.log", log_level="error"):
loss_fn = initialize_loss_fn(config.loss)
Metrics = initialize_metrics(config.metrics)
- test_raw_ds = load_test_data(config, model_version_path, eval_path, n_test)
+ raw_ds = load_test_data(config, model_version_path, eval_path, n_test)
- test_ds = initialize_dataset(config, test_raw_ds)
- ds_stats = compute_scale_shift_parameters(
- test_raw_ds.atoms_list,
- config.data.shift_method,
- config.data.scale_method,
- config.data.shift_options,
- config.data.scale_options,
- )
+ test_ds, ds_stats = initialize_dataset(config, raw_ds)
init_input = test_ds.init_input()
init_box = np.array(init_input["box"][0])
diff --git a/apax/train/run.py b/apax/train/run.py
index e93f50ab..8d66d92a 100644
--- a/apax/train/run.py
+++ b/apax/train/run.py
@@ -72,8 +72,12 @@ def load_data_files(data_config, model_version_path):
return train_raw_ds, val_raw_ds
-def initialize_dataset(config, raw_ds):
+def initialize_dataset(
+ config, raw_ds, calc_stats: bool = True
+): # have to be compatible with eval and only on ds
# Note(Moritz): external labels are actually not read in anywhere
+ # Answer(Nico): external labels are read in the filde utils/data.py in
+ # the load_data() function.
inputs, labels = create_dict_dataset(
raw_ds.atoms_list,
r_max=config.model.r_max,
@@ -82,6 +86,7 @@ def initialize_dataset(config, raw_ds):
pos_unit=config.data.pos_unit,
energy_unit=config.data.energy_unit,
)
+
dataset = TFPipeline(
inputs,
labels,
@@ -89,7 +94,20 @@ def initialize_dataset(config, raw_ds):
config.data.batch_size,
buffer_size=config.data.shuffle_buffer_size,
)
- return dataset
+
+ if calc_stats:
+ ds_stats = compute_scale_shift_parameters(
+ inputs,
+ labels,
+ config.data.shift_method,
+ config.data.scale_method,
+ config.data.shift_options,
+ config.data.scale_options,
+ )
+
+ return dataset, ds_stats
+ else:
+ return dataset
def maximize_l2_cache():
@@ -200,17 +218,9 @@ def run(user_config, log_file="train.log", log_level="error"):
loss_fn = initialize_loss_fn(config.loss)
Metrics = initialize_metrics(config.metrics)
- train_raw_ds, val_raw_ds = load_data_files(config.data, model_version_path)
- train_ds = initialize_dataset(config, train_raw_ds)
- val_ds = initialize_dataset(config, val_raw_ds)
-
- ds_stats = compute_scale_shift_parameters(
- train_raw_ds.atoms_list,
- config.data.shift_method,
- config.data.scale_method,
- config.data.shift_options,
- config.data.scale_options,
- )
+ raw_ds = load_data_files(config.data, model_version_path)
+ train_ds, ds_stats = initialize_dataset(config, raw_ds)
+ val_ds = initialize_dataset(config, raw_ds, calc_stats=False)
log.info("Initializing Model")
init_input = train_ds.init_input()
diff --git a/tests/unit_tests/data/test_statistics.py b/tests/unit_tests/data/test_statistics.py
index a68c0d51..a8d1ae96 100644
--- a/tests/unit_tests/data/test_statistics.py
+++ b/tests/unit_tests/data/test_statistics.py
@@ -15,13 +15,30 @@ def test_energy_per_element():
atoms_list = [atoms1, atoms2, atoms3]
energies = []
+ n_atoms = []
for atoms in atoms_list:
+ n_atoms.append(len(atoms))
+ print(len(atoms))
energy = np.sum(dummy_energies[atoms.numbers])
energies.append(energy)
atoms.calc = SinglePointCalculator(atoms, energy=energy)
+ labels = {
+ "ragged": {
+ "energy": [atoms.get_potential_energy() for atoms in atoms_list],
+ }
+ }
+ inputs = {
+ "ragged": {
+ "numbers": [atoms.numbers for atoms in atoms_list],
+ },
+ "fixed": {
+ "n_atoms": n_atoms,
+ },
+ }
+
elemental_shift = PerElementRegressionShift.compute(
- atoms_list, {"energy_regularisation": 0.0}
+ inputs, labels, {"energy_regularisation": 0.0}
)
regression_energies = []
for atoms in atoms_list:
From e78986852f50e16b6199e52f30958f2fd7618859 Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Mon, 2 Oct 2023 19:53:01 +0200
Subject: [PATCH 02/14] bug fix
---
apax/train/run.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/apax/train/run.py b/apax/train/run.py
index 8d66d92a..ee6f6802 100644
--- a/apax/train/run.py
+++ b/apax/train/run.py
@@ -218,9 +218,9 @@ def run(user_config, log_file="train.log", log_level="error"):
loss_fn = initialize_loss_fn(config.loss)
Metrics = initialize_metrics(config.metrics)
- raw_ds = load_data_files(config.data, model_version_path)
- train_ds, ds_stats = initialize_dataset(config, raw_ds)
- val_ds = initialize_dataset(config, raw_ds, calc_stats=False)
+ train_raw_ds, val_raw_ds = load_data_files(config.data, model_version_path)
+ train_ds, ds_stats = initialize_dataset(config, train_raw_ds)
+ val_ds = initialize_dataset(config, val_raw_ds, calc_stats=False)
log.info("Initializing Model")
init_input = train_ds.init_input()
From d868af44c4982ee53987fbc15571d9e794b18a42 Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Mon, 2 Oct 2023 19:57:42 +0200
Subject: [PATCH 03/14] linting
---
apax/train/run.py | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/apax/train/run.py b/apax/train/run.py
index ee6f6802..bb1974f2 100644
--- a/apax/train/run.py
+++ b/apax/train/run.py
@@ -72,9 +72,7 @@ def load_data_files(data_config, model_version_path):
return train_raw_ds, val_raw_ds
-def initialize_dataset(
- config, raw_ds, calc_stats: bool = True
-): # have to be compatible with eval and only on ds
+def initialize_dataset(config, raw_ds, calc_stats: bool = True):
# Note(Moritz): external labels are actually not read in anywhere
# Answer(Nico): external labels are read in the filde utils/data.py in
# the load_data() function.
From 128e5a11fcc20886641b40062cc9422b9cac39ae Mon Sep 17 00:00:00 2001
From: Nico Segreto <segreto@theochem.uni-stuttgart.de>
Date: Tue, 3 Oct 2023 17:42:57 +0200
Subject: [PATCH 04/14] Update statistics.py
bug fix
---
apax/data/statistics.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/apax/data/statistics.py b/apax/data/statistics.py
index d7f79cd5..b30df26e 100644
--- a/apax/data/statistics.py
+++ b/apax/data/statistics.py
@@ -25,7 +25,7 @@ def compute(inputs, labels, shift_options) -> np.ndarray:
log.info("Computing per element energy regression.")
lambd = shift_options["energy_regularisation"]
- energies = labels["ragged"]["energy"]
+ energies = labels["fixed"]["energy"]
numbers = inputs["ragged"]["numbers"]
system_sizes = inputs["fixed"]["n_atoms"]
@@ -81,7 +81,7 @@ class MeanEnergyRMSScale:
@staticmethod
def compute(inputs, labels, scale_options):
# log.info("Computing per element energy regression.")
- energies = labels["ragged"]["energy"]
+ energies = labels["fixed"]["energy"]
numbers = inputs["ragged"]["numbers"]
system_sizes = inputs["fixed"]["n_atoms"]
From 611b3f137d7fffdb2df3822d4775e408f0cbf6fb Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Tue, 3 Oct 2023 18:19:06 +0200
Subject: [PATCH 05/14] ds bug fix
---
apax/train/run.py | 17 +++++++++--------
apax/utils/convert.py | 1 -
tests/unit_tests/data/test_statistics.py | 2 +-
3 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/apax/train/run.py b/apax/train/run.py
index bb1974f2..4d1ea9ad 100644
--- a/apax/train/run.py
+++ b/apax/train/run.py
@@ -85,14 +85,6 @@ def initialize_dataset(config, raw_ds, calc_stats: bool = True):
energy_unit=config.data.energy_unit,
)
- dataset = TFPipeline(
- inputs,
- labels,
- config.n_epochs,
- config.data.batch_size,
- buffer_size=config.data.shuffle_buffer_size,
- )
-
if calc_stats:
ds_stats = compute_scale_shift_parameters(
inputs,
@@ -103,6 +95,15 @@ def initialize_dataset(config, raw_ds, calc_stats: bool = True):
config.data.scale_options,
)
+ dataset = TFPipeline(
+ inputs,
+ labels,
+ config.n_epochs,
+ config.data.batch_size,
+ buffer_size=config.data.shuffle_buffer_size,
+ )
+
+ if calc_stats:
return dataset, ds_stats
else:
return dataset
diff --git a/apax/utils/convert.py b/apax/utils/convert.py
index 046e7689..3c3bd6a3 100644
--- a/apax/utils/convert.py
+++ b/apax/utils/convert.py
@@ -109,7 +109,6 @@ def atoms_to_arrays(
inputs["ragged"]["numbers"].append(atoms.numbers)
inputs["fixed"]["n_atoms"].append(len(atoms))
-
for key, val in atoms.calc.results.items():
if key == "forces":
labels["ragged"][key].append(
diff --git a/tests/unit_tests/data/test_statistics.py b/tests/unit_tests/data/test_statistics.py
index a8d1ae96..de69b4ec 100644
--- a/tests/unit_tests/data/test_statistics.py
+++ b/tests/unit_tests/data/test_statistics.py
@@ -24,7 +24,7 @@ def test_energy_per_element():
atoms.calc = SinglePointCalculator(atoms, energy=energy)
labels = {
- "ragged": {
+ "fixed": {
"energy": [atoms.get_potential_energy() for atoms in atoms_list],
}
}
From 874ffe222ba37d03ee3286346e98b71247b757b3 Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Tue, 3 Oct 2023 18:20:54 +0200
Subject: [PATCH 06/14] implemented pytest.mark.slow
---
.github/workflows/pytest.yaml | 2 +-
pytest.ini | 3 +++
tests/regression_tests/__init__.py | 0
3 files changed, 4 insertions(+), 1 deletion(-)
create mode 100644 pytest.ini
create mode 100644 tests/regression_tests/__init__.py
diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
index 3111eee9..bc45eb79 100644
--- a/.github/workflows/pytest.yaml
+++ b/.github/workflows/pytest.yaml
@@ -28,7 +28,7 @@ jobs:
- name: Unit Tests
run: |
- poetry run coverage run -m pytest tests
+ poetry run coverage run -m pytest -k "not slow"
poetry run coverage report
- name: Coverage Report
diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 00000000..2077a3dd
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,3 @@
+[pytest]
+markers =
+ slow: mark a test as slow and should only run explicitly
\ No newline at end of file
diff --git a/tests/regression_tests/__init__.py b/tests/regression_tests/__init__.py
new file mode 100644
index 00000000..e69de29b
From 4149a5ea72922bcf27afc31971ced4598e42ed5c Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Tue, 3 Oct 2023 18:22:24 +0200
Subject: [PATCH 07/14] first part of regression test
---
tests/regression_tests/apax_config.yaml | 89 ++++++++++++++++++++
tests/regression_tests/test_apax_training.py | 50 +++++++++++
2 files changed, 139 insertions(+)
create mode 100644 tests/regression_tests/apax_config.yaml
create mode 100644 tests/regression_tests/test_apax_training.py
diff --git a/tests/regression_tests/apax_config.yaml b/tests/regression_tests/apax_config.yaml
new file mode 100644
index 00000000..3ed1f789
--- /dev/null
+++ b/tests/regression_tests/apax_config.yaml
@@ -0,0 +1,89 @@
+n_epochs: 1000
+seed: 0
+
+data:
+ directory: models/
+ experiment: apax
+
+ data_path: <PATH>
+
+ n_train: 1000
+ n_valid: 100
+
+ batch_size: 8
+ valid_batch_size: 100
+
+ shift_method: "per_element_regression_shift"
+ shift_options: {"energy_regularisation": 1.0}
+ shuffle_buffer_size: 1000
+
+ pos_unit: Ang
+ energy_unit: eV
+
+model:
+ n_basis: 7
+ n_radial: 5
+ nn: [512, 512]
+
+ r_max: 6.5
+ r_min: 0.5
+
+ calc_stress: false
+ use_zbl: true
+
+ b_init: normal
+ descriptor_dtype: fp32
+ readout_dtype: fp32
+ scale_shift_dtype: fp32
+
+metrics:
+ - name: energy
+ reductions:
+ - mae
+ - name: forces
+ reductions:
+ - mae
+ - mse
+ # - name: stress
+ # reductions:
+ # - mae
+ # - mse
+
+loss:
+ - loss_type: structures
+ name: energy
+ weight: 1.0
+ - loss_type: structures
+ name: forces
+ weight: 8.0
+ - loss_type: cosine_sim
+ name: forces
+ weight: 0.1
+ # - loss_type: structures
+ # name: stress
+ # weight: 1.0
+
+optimizer:
+ opt_name: adam
+ opt_kwargs: {}
+ emb_lr: 0.003
+ nn_lr: 0.002
+ scale_lr: 0.0005
+ shift_lr: 0.025
+ zbl_lr: 0.001
+ transition_begin: 0
+
+callbacks:
+- name: csv
+
+checkpoints:
+ ckpt_interval: 1
+ # The options below are used for transfer learning
+ # base_model_checkpoint: null
+ # reset_layers: []
+
+progress_bar:
+ disable_epoch_pbar: false
+ disable_nl_pbar: false
+
+maximize_l2_cache: false
diff --git a/tests/regression_tests/test_apax_training.py b/tests/regression_tests/test_apax_training.py
new file mode 100644
index 00000000..e1bde72c
--- /dev/null
+++ b/tests/regression_tests/test_apax_training.py
@@ -0,0 +1,50 @@
+import pytest
+import pathlib
+import yaml
+from apax.train.run import run
+import urllib
+import zipfile
+import os
+
+TEST_PATH = pathlib.Path(__file__).parent.resolve()
+MD22_STACHYOSE_URL = "http://www.quantum-machine.org/gdml/repo/static/md22_stachyose.zip"
+
+@pytest.mark.slow
+def test_regression_model_training(get_tmp_path):
+ temp_path = get_tmp_path
+
+ #load dataset and safe it in temp_dir
+ data_path = temp_path / "data"
+ os.makedirs(data_path, exist_ok=True)
+ urllib.request.urlretrieve(MD22_STACHYOSE_URL, data_path / "md22_stachyose.zip")
+
+ with zipfile.ZipFile(data_path / "md22_stachyose.zip", "r") as zip_ref:
+ zip_ref.extractall(data_path)
+
+ input_file_path = (data_path / "md22_stachyose.xyz").as_posix()
+ output_file_path = (data_path / "md22_stachyose_mod.xyz").as_posix()
+ target_string = 'Energy'
+ replacement_string = 'energy'
+
+ replace_string_in_file(input_file_path, output_file_path, target_string, replacement_string)
+
+ #read and adjust config
+ confg_path = TEST_PATH / "apax_config.yaml"
+ with open(confg_path.as_posix(), "r") as stream:
+ config_dict = yaml.safe_load(stream)
+
+ config_dict["data"]["directory"] = temp_path.as_posix()
+ config_dict["data"]["data_path"] = output_file_path
+ config_dict["data"]["energy_unit"] = "kcal/mol"
+
+ run(config_dict)
+
+
+ assert False
+
+def replace_string_in_file(input_file_path, output_file_path, target_string, replacement_string):
+ with open(input_file_path, 'r') as input_file, open(output_file_path, 'w') as output_file:
+ for line in input_file:
+ # Replace all occurrences of the target string with the replacement string
+ modified_line = line.replace(target_string, replacement_string)
+ output_file.write(modified_line)
\ No newline at end of file
From 39c34dcfe848bf9baf7c1e0a66811a426d438019 Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Tue, 3 Oct 2023 18:25:55 +0200
Subject: [PATCH 08/14] tf.tensor conversion after calc of ds_stats
---
apax/train/run.py | 17 +++++++++--------
tests/unit_tests/data/test_statistics.py | 2 +-
2 files changed, 10 insertions(+), 9 deletions(-)
diff --git a/apax/train/run.py b/apax/train/run.py
index bb1974f2..4d1ea9ad 100644
--- a/apax/train/run.py
+++ b/apax/train/run.py
@@ -85,14 +85,6 @@ def initialize_dataset(config, raw_ds, calc_stats: bool = True):
energy_unit=config.data.energy_unit,
)
- dataset = TFPipeline(
- inputs,
- labels,
- config.n_epochs,
- config.data.batch_size,
- buffer_size=config.data.shuffle_buffer_size,
- )
-
if calc_stats:
ds_stats = compute_scale_shift_parameters(
inputs,
@@ -103,6 +95,15 @@ def initialize_dataset(config, raw_ds, calc_stats: bool = True):
config.data.scale_options,
)
+ dataset = TFPipeline(
+ inputs,
+ labels,
+ config.n_epochs,
+ config.data.batch_size,
+ buffer_size=config.data.shuffle_buffer_size,
+ )
+
+ if calc_stats:
return dataset, ds_stats
else:
return dataset
diff --git a/tests/unit_tests/data/test_statistics.py b/tests/unit_tests/data/test_statistics.py
index a8d1ae96..de69b4ec 100644
--- a/tests/unit_tests/data/test_statistics.py
+++ b/tests/unit_tests/data/test_statistics.py
@@ -24,7 +24,7 @@ def test_energy_per_element():
atoms.calc = SinglePointCalculator(atoms, energy=energy)
labels = {
- "ragged": {
+ "fixed": {
"energy": [atoms.get_potential_energy() for atoms in atoms_list],
}
}
From b01a277eb4e1202ddf535d31aa7abedcd83edeff Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Tue, 3 Oct 2023 21:15:16 +0200
Subject: [PATCH 09/14] first model regression test
---
poetry.lock | 3883 +++++++++---------
pyproject.toml | 1 +
tests/regression_tests/apax_config.yaml | 2 +-
tests/regression_tests/test_apax_training.py | 95 +-
4 files changed, 1962 insertions(+), 2019 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index 4e3c6ea2..9c0ea65b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,34 +1,48 @@
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+
[[package]]
name = "absl-py"
version = "1.4.0"
description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py."
-category = "main"
optional = false
python-versions = ">=3.6"
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+]
[[package]]
name = "alabaster"
version = "0.7.13"
description = "A configurable sidebar-enabled Sphinx theme"
-category = "dev"
optional = false
python-versions = ">=3.6"
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[[package]]
name = "annotated-types"
version = "0.5.0"
description = "Reusable constraint types to use with typing.Annotated"
-category = "main"
optional = false
python-versions = ">=3.7"
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[[package]]
name = "array-record"
version = "0.4.1"
description = "A file format that achieves a new frontier of IO efficiency"
-category = "main"
optional = false
python-versions = ">=3.9"
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[package.dependencies]
absl-py = "*"
@@ -38,9 +52,12 @@ etils = {version = "*", extras = ["epath"]}
name = "ase"
version = "3.22.1"
description = "Atomic Simulation Environment"
-category = "main"
optional = false
python-versions = ">=3.6"
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matplotlib = ">=3.1.0"
@@ -55,9 +72,12 @@ test = ["pytest (>=5.0.0)", "pytest-mock (>=3.3.0)", "pytest-xdist (>=1.30.0)"]
name = "astunparse"
version = "1.6.3"
description = "An AST unparser for Python"
-category = "main"
optional = false
python-versions = "*"
+files = [
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+ {file = "astunparse-1.6.3.tar.gz", hash = "sha256:5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872"},
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[package.dependencies]
six = ">=1.6.1,<2.0"
@@ -67,9 +87,12 @@ wheel = ">=0.23.0,<1.0"
name = "attrs"
version = "23.1.0"
description = "Classes Without Boilerplate"
-category = "main"
optional = false
python-versions = ">=3.7"
+files = [
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[package.extras]
cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
@@ -82,17 +105,33 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
name = "babel"
version = "2.12.1"
description = "Internationalization utilities"
-category = "dev"
optional = false
python-versions = ">=3.7"
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name = "black"
version = "22.12.0"
description = "The uncompromising code formatter."
-category = "dev"
optional = false
python-versions = ">=3.7"
+files = [
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click = ">=8.0.0"
@@ -111,49 +150,144 @@ uvloop = ["uvloop (>=0.15.2)"]
name = "cached-property"
version = "1.5.2"
description = "A decorator for caching properties in classes."
-category = "main"
optional = false
python-versions = "*"
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name = "cachetools"
version = "5.3.1"
description = "Extensible memoizing collections and decorators"
-category = "main"
optional = false
python-versions = ">=3.7"
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name = "certifi"
version = "2023.7.22"
description = "Python package for providing Mozilla's CA Bundle."
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optional = false
python-versions = ">=3.6"
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name = "cfgv"
version = "3.4.0"
description = "Validate configuration and produce human readable error messages."
-category = "dev"
optional = false
python-versions = ">=3.8"
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description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
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python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
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description = "Equivariant convolutional neural networks for the group E(3) of 3 dimensional rotations, translations, and mirrors."
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optional = false
python-versions = ">=3.7"
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attrs = "*"
@@ -349,24 +650,28 @@ tqdm = "*"
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version = "0.6.1"
description = "A new flavour of deep learning operations"
-category = "main"
optional = false
python-versions = ">=3.7"
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version = "1.4.1"
description = "Collection of common python utils"
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optional = false
python-versions = ">=3.9"
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importlib_resources = {version = "*", optional = true, markers = "extra == \"epath\""}
numpy = {version = "*", optional = true, markers = "extra == \"enp\""}
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zipp = {version = "*", optional = true, markers = "extra == \"epath\""}
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version = "1.1.3"
description = "Backport of PEP 654 (exception groups)"
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python-versions = ">=3.7"
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version = "2.0.2"
description = "execnet: rapid multi-Python deployment"
-category = "dev"
optional = false
python-versions = ">=3.7"
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name = "filelock"
version = "3.12.3"
description = "A platform independent file lock."
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optional = false
python-versions = ">=3.8"
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description = "the modular source code checker: pep8 pyflakes and co"
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optional = false
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name = "flatbuffers"
version = "23.5.26"
description = "The FlatBuffers serialization format for Python"
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optional = false
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description = "Flax: A neural network library for JAX designed for flexibility"
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description = "Python AST that abstracts the underlying Python version"
-category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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version = "2.1.0"
description = "Copy your docs directly to the gh-pages branch."
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optional = false
python-versions = "*"
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@@ -516,9 +880,12 @@ dev = ["flake8", "markdown", "twine", "wheel"]
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version = "2.17.3"
description = "Google Authentication Library"
-category = "main"
optional = false
python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*"
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cachetools = ">=2.0.0,<6.0"
@@ -537,9 +904,12 @@ requests = ["requests (>=2.20.0,<3.0.0dev)"]
name = "google-auth-oauthlib"
version = "1.0.0"
description = "Google Authentication Library"
-category = "main"
optional = false
python-versions = ">=3.6"
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google-auth = ">=2.15.0"
@@ -552,9 +922,13 @@ tool = ["click (>=6.0.0)"]
name = "google-pasta"
version = "0.2.0"
description = "pasta is an AST-based Python refactoring library"
-category = "main"
optional = false
python-versions = "*"
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-category = "main"
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description = "Read and write HDF5 files from Python"
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optional = false
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@@ -599,9 +1044,12 @@ numpy = ">=1.17.3"
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version = "2.5.27"
description = "File identification library for Python"
-category = "dev"
optional = false
python-versions = ">=3.8"
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@@ -610,25 +1058,34 @@ license = ["ukkonen"]
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version = "3.4"
description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
optional = false
python-versions = ">=3.5"
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@@ -660,9 +1123,11 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"]
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@@ -687,9 +1152,9 @@ tpu = ["jaxlib (==0.4.14)", "libtpu-nightly (==0.1.dev20230727)"]
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version = "0.2.8"
description = ""
-category = "main"
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@@ -716,9 +1181,22 @@ resolved_reference = "e107c26d877f1d5cfb5de2ff880213e7670c6e9a"
name = "jaxlib"
version = "0.4.14"
description = "XLA library for JAX"
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optional = false
python-versions = ">=3.9"
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ml-dtypes = ">=0.2.0"
@@ -733,9 +1211,12 @@ cuda12-pip = ["nvidia-cublas-cu12", "nvidia-cuda-cupti-cu12", "nvidia-cuda-nvcc-
name = "jaxtyping"
version = "0.2.21"
description = "Type annotations and runtime checking for shape and dtype of JAX arrays, and PyTrees."
-category = "main"
optional = false
python-versions = "~=3.9"
+files = [
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+]
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numpy = ">=1.20.0"
@@ -746,9 +1227,12 @@ typing-extensions = ">=3.7.4.1"
name = "jinja2"
version = "3.1.2"
description = "A very fast and expressive template engine."
-category = "dev"
optional = false
python-versions = ">=3.7"
+files = [
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+]
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MarkupSafe = ">=2.0"
@@ -760,9 +1244,12 @@ i18n = ["Babel (>=2.7)"]
name = "jmp"
version = "0.0.4"
description = "JMP is a Mixed Precision library for JAX."
-category = "main"
optional = false
python-versions = "*"
+files = [
+ {file = "jmp-0.0.4-py3-none-any.whl", hash = "sha256:6aa7adbddf2bd574b28c7faf6e81a735eb11f53386447896909c6968dc36807d"},
+ {file = "jmp-0.0.4.tar.gz", hash = "sha256:5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730"},
+]
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numpy = ">=1.19.5"
@@ -774,9 +1261,12 @@ jax = ["jax (>=0.2.20)", "jaxlib (>=0.1.71)"]
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version = "0.0.6.dev0"
description = "Jraph: A library for Graph Neural Networks in Jax"
-category = "main"
optional = false
python-versions = ">=3.6"
+files = [
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+ {file = "jraph-0.0.6.dev0.tar.gz", hash = "sha256:c3ac3a0b224b344eb6d367e8bc312d95ea41bf825d01ea31b80dd8c22c0dd8b8"},
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jax = ">=0.1.55"
@@ -791,1841 +1281,19 @@ ogb-examples = ["absl-py (>=0.9)", "dm-haiku (>=0.0.2)", "dm-tree (>=0.1.5)", "o
name = "keras"
version = "2.12.0"
description = "Deep learning for humans."
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optional = false
python-versions = ">=3.8"
+files = [
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+]
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]
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+
+[[package]]
+name = "markdown"
+version = "3.4.4"
+description = "Python implementation of John Gruber's Markdown."
+optional = false
+python-versions = ">=3.7"
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]
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+
+[package.extras]
+docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.0)", "mkdocs-nature (>=0.4)"]
+testing = ["coverage", "pyyaml"]
+
+[[package]]
+name = "markupsafe"
+version = "2.1.3"
+description = "Safely add untrusted strings to HTML/XML markup."
+optional = false
+python-versions = ">=3.7"
+files = [
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@@ -2804,7 +1506,14 @@ markupsafe = [
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]
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+
+[[package]]
+name = "matplotlib"
+version = "3.7.2"
+description = "Python plotting package"
+optional = false
+python-versions = ">=3.8"
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@@ -2847,7 +1556,25 @@ matplotlib = [
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]
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+kiwisolver = ">=1.0.1"
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+pillow = ">=6.2.0"
+pyparsing = ">=2.3.1,<3.1"
+python-dateutil = ">=2.7"
+
+[[package]]
+name = "matscipy"
+version = "0.8.0"
+description = "Generic Python Materials Science tools"
+optional = false
+python-versions = ">=3.7.0"
+files = [
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@@ -2874,22 +1601,91 @@ matscipy = [
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]
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+scipy = ">=1.2.3"
+
+[package.extras]
+docs = ["sphinx", "sphinx-rtd-theme"]
+test = ["pytest", "sympy"]
+
+[[package]]
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+version = "0.7.0"
+description = "McCabe checker, plugin for flake8"
+optional = false
+python-versions = ">=3.6"
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]
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+description = "A deep merge function for 🐍."
+optional = false
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+
+[[package]]
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+version = "0.1.1"
+description = "ML Collections is a library of Python collections designed for ML usecases."
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+six = "*"
+
+[[package]]
+name = "ml-dtypes"
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+description = ""
+optional = false
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@@ -2908,11 +1704,40 @@ ml-dtypes = [
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]
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+ {version = ">=1.21.2", markers = "python_version > \"3.9\" and python_version <= \"3.10\""},
+]
+
+[package.extras]
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+
+[[package]]
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+version = "1.3.0"
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]
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+develop = ["codecov", "pycodestyle", "pytest (>=4.6)", "pytest-cov", "wheel"]
+docs = ["sphinx"]
+gmpy = ["gmpy2 (>=2.1.0a4)"]
+tests = ["pytest (>=4.6)"]
+
+[[package]]
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+description = "MessagePack serializer"
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+python-versions = "*"
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@@ -2977,19 +1802,50 @@ msgpack = [
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]
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]
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+optional = false
+python-versions = ">=3.5"
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]
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+[package.dependencies]
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+
+[[package]]
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+version = "1.23.5"
+description = "NumPy is the fundamental package for array computing with Python."
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@@ -3019,31 +1875,188 @@ numpy = [
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]
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+[package.extras]
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@@ -3524,10 +3204,36 @@ tensorflow-io-gcs-filesystem = [
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@@ -3546,47 +3252,184 @@ tensorstore = [
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-toml = [
+
+[package.extras]
+tests = ["pytest", "pytest-cov"]
+
+[[package]]
+name = "toml"
+version = "0.10.2"
+description = "Python Library for Tom's Obvious, Minimal Language"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+files = [
{file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"},
{file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"},
]
-tomli = [
+
+[[package]]
+name = "tomli"
+version = "2.0.1"
+description = "A lil' TOML parser"
+optional = false
+python-versions = ">=3.7"
+files = [
{file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
{file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
]
-toolz = [
+
+[[package]]
+name = "toolz"
+version = "0.12.0"
+description = "List processing tools and functional utilities"
+optional = false
+python-versions = ">=3.5"
+files = [
{file = "toolz-0.12.0-py3-none-any.whl", hash = "sha256:2059bd4148deb1884bb0eb770a3cde70e7f954cfbbdc2285f1f2de01fd21eb6f"},
{file = "toolz-0.12.0.tar.gz", hash = "sha256:88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194"},
]
-tqdm = [
+
+[[package]]
+name = "tqdm"
+version = "4.66.1"
+description = "Fast, Extensible Progress Meter"
+optional = false
+python-versions = ">=3.7"
+files = [
{file = "tqdm-4.66.1-py3-none-any.whl", hash = "sha256:d302b3c5b53d47bce91fea46679d9c3c6508cf6332229aa1e7d8653723793386"},
{file = "tqdm-4.66.1.tar.gz", hash = "sha256:d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7"},
]
-typeguard = [
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+
+[package.extras]
+dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+notebook = ["ipywidgets (>=6)"]
+slack = ["slack-sdk"]
+telegram = ["requests"]
+
+[[package]]
+name = "typeguard"
+version = "4.1.3"
+description = "Run-time type checker for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
{file = "typeguard-4.1.3-py3-none-any.whl", hash = "sha256:5b7453b1e3b35fcfe2d62fa4ec500d05e6f2f2eb46f4126ae964677fcc384fff"},
{file = "typeguard-4.1.3.tar.gz", hash = "sha256:7d4264cd631ac1157c5bb5ec992281b4f1e2ba7a35db91bc15f442235e244803"},
]
-typer = [
+
+[package.dependencies]
+typing-extensions = {version = ">=4.7.0", markers = "python_version < \"3.12\""}
+
+[package.extras]
+doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"]
+test = ["coverage[toml] (>=7)", "mypy (>=1.2.0)", "pytest (>=7)"]
+
+[[package]]
+name = "typer"
+version = "0.7.0"
+description = "Typer, build great CLIs. Easy to code. Based on Python type hints."
+optional = false
+python-versions = ">=3.6"
+files = [
{file = "typer-0.7.0-py3-none-any.whl", hash = "sha256:b5e704f4e48ec263de1c0b3a2387cd405a13767d2f907f44c1a08cbad96f606d"},
{file = "typer-0.7.0.tar.gz", hash = "sha256:ff797846578a9f2a201b53442aedeb543319466870fbe1c701eab66dd7681165"},
]
-typing-extensions = [
+
+[package.dependencies]
+click = ">=7.1.1,<9.0.0"
+colorama = {version = ">=0.4.3,<0.5.0", optional = true, markers = "extra == \"all\""}
+rich = {version = ">=10.11.0,<13.0.0", optional = true, markers = "extra == \"all\""}
+shellingham = {version = ">=1.3.0,<2.0.0", optional = true, markers = "extra == \"all\""}
+
+[package.extras]
+all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
+dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"]
+doc = ["cairosvg (>=2.5.2,<3.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pillow (>=9.3.0,<10.0.0)"]
+test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<8.0.0)", "pytest-cov (>=2.10.0,<5.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<4.0.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"]
+
+[[package]]
+name = "typing-extensions"
+version = "4.7.1"
+description = "Backported and Experimental Type Hints for Python 3.7+"
+optional = false
+python-versions = ">=3.7"
+files = [
{file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
{file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
]
-urllib3 = [
+
+[[package]]
+name = "tzdata"
+version = "2023.3"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+files = [
+ {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
+ {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
+]
+
+[[package]]
+name = "urllib3"
+version = "2.0.4"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+optional = false
+python-versions = ">=3.7"
+files = [
{file = "urllib3-2.0.4-py3-none-any.whl", hash = "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4"},
{file = "urllib3-2.0.4.tar.gz", hash = "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11"},
]
-virtualenv = [
+
+[package.extras]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
+[[package]]
+name = "virtualenv"
+version = "20.24.5"
+description = "Virtual Python Environment builder"
+optional = false
+python-versions = ">=3.7"
+files = [
{file = "virtualenv-20.24.5-py3-none-any.whl", hash = "sha256:b80039f280f4919c77b30f1c23294ae357c4c8701042086e3fc005963e4e537b"},
{file = "virtualenv-20.24.5.tar.gz", hash = "sha256:e8361967f6da6fbdf1426483bfe9fca8287c242ac0bc30429905721cefbff752"},
]
-watchdog = [
+
+[package.dependencies]
+distlib = ">=0.3.7,<1"
+filelock = ">=3.12.2,<4"
+platformdirs = ">=3.9.1,<4"
+
+[package.extras]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
+
+[[package]]
+name = "watchdog"
+version = "3.0.0"
+description = "Filesystem events monitoring"
+optional = false
+python-versions = ">=3.7"
+files = [
{file = "watchdog-3.0.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:336adfc6f5cc4e037d52db31194f7581ff744b67382eb6021c868322e32eef41"},
{file = "watchdog-3.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a70a8dcde91be523c35b2bf96196edc5730edb347e374c7de7cd20c43ed95397"},
{file = "watchdog-3.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:adfdeab2da79ea2f76f87eb42a3ab1966a5313e5a69a0213a3cc06ef692b0e96"},
@@ -3615,15 +3458,48 @@ watchdog = [
{file = "watchdog-3.0.0-py3-none-win_ia64.whl", hash = "sha256:5d9f3a10e02d7371cd929b5d8f11e87d4bad890212ed3901f9b4d68767bee759"},
{file = "watchdog-3.0.0.tar.gz", hash = "sha256:4d98a320595da7a7c5a18fc48cb633c2e73cda78f93cac2ef42d42bf609a33f9"},
]
-werkzeug = [
+
+[package.extras]
+watchmedo = ["PyYAML (>=3.10)"]
+
+[[package]]
+name = "werkzeug"
+version = "2.3.7"
+description = "The comprehensive WSGI web application library."
+optional = false
+python-versions = ">=3.8"
+files = [
{file = "werkzeug-2.3.7-py3-none-any.whl", hash = "sha256:effc12dba7f3bd72e605ce49807bbe692bd729c3bb122a3b91747a6ae77df528"},
{file = "werkzeug-2.3.7.tar.gz", hash = "sha256:2b8c0e447b4b9dbcc85dd97b6eeb4dcbaf6c8b6c3be0bd654e25553e0a2157d8"},
]
-wheel = [
+
+[package.dependencies]
+MarkupSafe = ">=2.1.1"
+
+[package.extras]
+watchdog = ["watchdog (>=2.3)"]
+
+[[package]]
+name = "wheel"
+version = "0.41.2"
+description = "A built-package format for Python"
+optional = false
+python-versions = ">=3.7"
+files = [
{file = "wheel-0.41.2-py3-none-any.whl", hash = "sha256:75909db2664838d015e3d9139004ee16711748a52c8f336b52882266540215d8"},
{file = "wheel-0.41.2.tar.gz", hash = "sha256:0c5ac5ff2afb79ac23ab82bab027a0be7b5dbcf2e54dc50efe4bf507de1f7985"},
]
-wrapt = [
+
+[package.extras]
+test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
+
+[[package]]
+name = "wrapt"
+version = "1.14.1"
+description = "Module for decorators, wrappers and monkey patching."
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+files = [
{file = "wrapt-1.14.1-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:1b376b3f4896e7930f1f772ac4b064ac12598d1c38d04907e696cc4d794b43d3"},
{file = "wrapt-1.14.1-cp27-cp27m-manylinux1_i686.whl", hash = "sha256:903500616422a40a98a5a3c4ff4ed9d0066f3b4c951fa286018ecdf0750194ef"},
{file = "wrapt-1.14.1-cp27-cp27m-manylinux1_x86_64.whl", hash = "sha256:5a9a0d155deafd9448baff28c08e150d9b24ff010e899311ddd63c45c2445e28"},
@@ -3689,11 +3565,44 @@ wrapt = [
{file = "wrapt-1.14.1-cp39-cp39-win_amd64.whl", hash = "sha256:dee60e1de1898bde3b238f18340eec6148986da0455d8ba7848d50470a7a32fb"},
{file = "wrapt-1.14.1.tar.gz", hash = "sha256:380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d"},
]
-zipp = [
+
+[[package]]
+name = "zipp"
+version = "3.16.2"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.8"
+files = [
{file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
{file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
]
-znh5md = [
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+
+[[package]]
+name = "znh5md"
+version = "0.1.7"
+description = "High Performance Interface for H5MD Trajectories"
+optional = false
+python-versions = ">=3.9,<4.0"
+files = [
{file = "znh5md-0.1.7-py3-none-any.whl", hash = "sha256:2d5505738c92c79e2de907acf89956662c94472a350f1ddfd55c509c0cc44960"},
{file = "znh5md-0.1.7.tar.gz", hash = "sha256:fa437c805da4a7a24d6265f632ebbc36863fd15c952e2ce1a3b2d35c6241e00d"},
]
+
+[package.dependencies]
+ase = ">=3.22.1,<4.0.0"
+chemfiles = ">=0.10.3,<0.11.0"
+h5py = ">=3.7.0,<4.0.0"
+tqdm = ">=4.65.0,<5.0.0"
+typer = {version = ">=0.7.0,<0.8.0", extras = ["all"]}
+
+[package.extras]
+dask = ["dask[array] (>=2022.11.1,<2023.0.0)"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = ">=3.10,<3.12"
+content-hash = "afe5299a8eb49bf6e749c4f9f3ad895199be032f372247dfe8b7d44c33dba1c8"
diff --git a/pyproject.toml b/pyproject.toml
index 50061f18..4f34cbee 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,6 +43,7 @@ pre-commit = "^2.20.0"
isort = "^5.10.1"
flake8 = "^5.0.4"
sphinx-autodoc-typehints = "^1.21.8"
+pandas = "^2.1.1"
[build-system]
requires = ["poetry-core"]
diff --git a/tests/regression_tests/apax_config.yaml b/tests/regression_tests/apax_config.yaml
index 3ed1f789..436dd94b 100644
--- a/tests/regression_tests/apax_config.yaml
+++ b/tests/regression_tests/apax_config.yaml
@@ -3,7 +3,7 @@ seed: 0
data:
directory: models/
- experiment: apax
+ experiment: test
data_path: <PATH>
diff --git a/tests/regression_tests/test_apax_training.py b/tests/regression_tests/test_apax_training.py
index e1bde72c..801a32fc 100644
--- a/tests/regression_tests/test_apax_training.py
+++ b/tests/regression_tests/test_apax_training.py
@@ -1,50 +1,83 @@
-import pytest
+import os
import pathlib
-import yaml
-from apax.train.run import run
import urllib
import zipfile
-import os
+
+import numpy as np
+import pandas as pd
+import pytest
+import yaml
+
+from apax.train.run import run
TEST_PATH = pathlib.Path(__file__).parent.resolve()
MD22_STACHYOSE_URL = "http://www.quantum-machine.org/gdml/repo/static/md22_stachyose.zip"
-@pytest.mark.slow
-def test_regression_model_training(get_tmp_path):
- temp_path = get_tmp_path
- #load dataset and safe it in temp_dir
- data_path = temp_path / "data"
+def download_and_extract_data(data_path, filename, url, file_format):
+ file_path = data_path / filename
+
os.makedirs(data_path, exist_ok=True)
- urllib.request.urlretrieve(MD22_STACHYOSE_URL, data_path / "md22_stachyose.zip")
+ urllib.request.urlretrieve(url, file_path)
- with zipfile.ZipFile(data_path / "md22_stachyose.zip", "r") as zip_ref:
+ with zipfile.ZipFile(file_path, "r") as zip_ref:
zip_ref.extractall(data_path)
- input_file_path = (data_path / "md22_stachyose.xyz").as_posix()
- output_file_path = (data_path / "md22_stachyose_mod.xyz").as_posix()
- target_string = 'Energy'
- replacement_string = 'energy'
-
- replace_string_in_file(input_file_path, output_file_path, target_string, replacement_string)
+ return file_path.with_suffix(f".{file_format}")
+
+
+def modify_xyz_file(file_path, target_string, replacement_string):
+ new_file_path = file_path.with_name(file_path.stem + "_mod" + file_path.suffix)
+
+ with open(file_path, "r") as input_file, open(new_file_path, "w") as output_file:
+ for line in input_file:
+ # Replace all occurrences of the target string with the replacement string
+ modified_line = line.replace(target_string, replacement_string)
+ output_file.write(modified_line)
+ return new_file_path
+
- #read and adjust config
- confg_path = TEST_PATH / "apax_config.yaml"
- with open(confg_path.as_posix(), "r") as stream:
+def load_config_and_run_training(
+ config_path, file_path, working_dir, energy_unit="eV", pos_unit="Ang"
+):
+ with open(config_path.as_posix(), "r") as stream:
config_dict = yaml.safe_load(stream)
- config_dict["data"]["directory"] = temp_path.as_posix()
- config_dict["data"]["data_path"] = output_file_path
- config_dict["data"]["energy_unit"] = "kcal/mol"
+ config_dict["data"]["directory"] = working_dir.as_posix()
+ config_dict["data"]["data_path"] = file_path.as_posix()
+ config_dict["data"]["energy_unit"] = energy_unit
+ config_dict["data"]["pos_unit"] = pos_unit
run(config_dict)
-
- assert False
+ return
-def replace_string_in_file(input_file_path, output_file_path, target_string, replacement_string):
- with open(input_file_path, 'r') as input_file, open(output_file_path, 'w') as output_file:
- for line in input_file:
- # Replace all occurrences of the target string with the replacement string
- modified_line = line.replace(target_string, replacement_string)
- output_file.write(modified_line)
\ No newline at end of file
+
+@pytest.mark.slow
+def test_regression_model_training(get_tmp_path):
+ config_path = TEST_PATH / "apax_config.yaml"
+ working_dir = get_tmp_path
+ data_path = working_dir / "data"
+ filename = "md22_stachyose.zip"
+
+ file_path = download_and_extract_data(data_path, filename, MD22_STACHYOSE_URL, "xyz")
+
+ file_path = modify_xyz_file(
+ file_path, target_string="Energy", replacement_string="energy"
+ )
+
+ load_config_and_run_training(config_path, file_path, working_dir, "kcal/mol")
+
+ current_metrics = pd.read_csv(working_dir / "test/log.csv")
+
+ comparison_metrics = {
+ "val_energy_mae": 0.2048215700433502,
+ "val_forces_mae": 0.054957914591049,
+ "val_forces_mse": 0.0056583952479869,
+ "val_loss": 0.1395589689994847,
+ }
+
+ for key in comparison_metrics.keys():
+ assert (
+ abs((np.array(current_metrics[key])[-1] / comparison_metrics[key]) - 1) < 1e-4
+ )
From dbaa12bbc174e36e32a058946b8f2e6a7c3a38ba Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Thu, 5 Oct 2023 20:35:29 +0200
Subject: [PATCH 10/14] removed note
---
apax/train/run.py | 3 ---
1 file changed, 3 deletions(-)
diff --git a/apax/train/run.py b/apax/train/run.py
index 4d1ea9ad..c182dbde 100644
--- a/apax/train/run.py
+++ b/apax/train/run.py
@@ -73,9 +73,6 @@ def load_data_files(data_config, model_version_path):
def initialize_dataset(config, raw_ds, calc_stats: bool = True):
- # Note(Moritz): external labels are actually not read in anywhere
- # Answer(Nico): external labels are read in the filde utils/data.py in
- # the load_data() function.
inputs, labels = create_dict_dataset(
raw_ds.atoms_list,
r_max=config.model.r_max,
From db70e3a53901cab23c964b9c2ef43fb60e458ebf Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Thu, 5 Oct 2023 20:43:40 +0200
Subject: [PATCH 11/14] using coonvert function in statistics test
---
tests/unit_tests/data/test_statistics.py | 18 +++++-------------
1 file changed, 5 insertions(+), 13 deletions(-)
diff --git a/tests/unit_tests/data/test_statistics.py b/tests/unit_tests/data/test_statistics.py
index de69b4ec..6b3d4243 100644
--- a/tests/unit_tests/data/test_statistics.py
+++ b/tests/unit_tests/data/test_statistics.py
@@ -3,6 +3,7 @@
from ase.calculators.singlepoint import SinglePointCalculator
from apax.data.statistics import PerElementRegressionShift
+from apax.data.input_pipeline import create_dict_dataset
def test_energy_per_element():
@@ -23,19 +24,10 @@ def test_energy_per_element():
energies.append(energy)
atoms.calc = SinglePointCalculator(atoms, energy=energy)
- labels = {
- "fixed": {
- "energy": [atoms.get_potential_energy() for atoms in atoms_list],
- }
- }
- inputs = {
- "ragged": {
- "numbers": [atoms.numbers for atoms in atoms_list],
- },
- "fixed": {
- "n_atoms": n_atoms,
- },
- }
+ inputs, labels = create_dict_dataset(
+ atoms_list,
+ r_max=6.5,
+ )
elemental_shift = PerElementRegressionShift.compute(
inputs, labels, {"energy_regularisation": 0.0}
From 5519d7cf946b4761a96cfff7651d20e0a688a2a8 Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Thu, 5 Oct 2023 20:47:25 +0200
Subject: [PATCH 12/14] got rid of pandas dep
---
poetry.lock | 3613 +++++++++++++++++++++++++-----------------------
pyproject.toml | 1 -
2 files changed, 1852 insertions(+), 1762 deletions(-)
diff --git a/poetry.lock b/poetry.lock
index 9c0ea65b..1b79baa4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,48 +1,34 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
-
[[package]]
name = "absl-py"
version = "1.4.0"
description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py."
+category = "main"
optional = false
python-versions = ">=3.6"
-files = [
- {file = "absl-py-1.4.0.tar.gz", hash = "sha256:d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d"},
- {file = "absl_py-1.4.0-py3-none-any.whl", hash = "sha256:0d3fe606adfa4f7db64792dd4c7aee4ee0c38ab75dfd353b7a83ed3e957fcb47"},
-]
[[package]]
name = "alabaster"
version = "0.7.13"
description = "A configurable sidebar-enabled Sphinx theme"
+category = "dev"
optional = false
python-versions = ">=3.6"
-files = [
- {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"},
- {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
-]
[[package]]
name = "annotated-types"
version = "0.5.0"
description = "Reusable constraint types to use with typing.Annotated"
+category = "main"
optional = false
python-versions = ">=3.7"
-files = [
- {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"},
- {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"},
-]
[[package]]
name = "array-record"
version = "0.4.1"
description = "A file format that achieves a new frontier of IO efficiency"
+category = "main"
optional = false
python-versions = ">=3.9"
-files = [
- {file = "array_record-0.4.1-py310-none-any.whl", hash = "sha256:6a0c8ed6fdfaaf2cecd3d5c6b9c13e116ad3299649611c8fd184d64557fbaba8"},
- {file = "array_record-0.4.1-py39-none-any.whl", hash = "sha256:a74e9c0075860777b79e4b3ac278f67add270acf78520d3b9cf8c325aef42951"},
-]
[package.dependencies]
absl-py = "*"
@@ -52,12 +38,9 @@ etils = {version = "*", extras = ["epath"]}
name = "ase"
version = "3.22.1"
description = "Atomic Simulation Environment"
+category = "main"
optional = false
python-versions = ">=3.6"
-files = [
- {file = "ase-3.22.1-py3-none-any.whl", hash = "sha256:66cc481e3d82bea8931d5fe677119932ea0bd1bc08b901fd84f36b37fa681c9e"},
- {file = "ase-3.22.1.tar.gz", hash = "sha256:004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432"},
-]
[package.dependencies]
matplotlib = ">=3.1.0"
@@ -72,12 +55,9 @@ test = ["pytest (>=5.0.0)", "pytest-mock (>=3.3.0)", "pytest-xdist (>=1.30.0)"]
name = "astunparse"
version = "1.6.3"
description = "An AST unparser for Python"
+category = "main"
optional = false
python-versions = "*"
-files = [
- {file = "astunparse-1.6.3-py2.py3-none-any.whl", hash = "sha256:c2652417f2c8b5bb325c885ae329bdf3f86424075c4fd1a128674bc6fba4b8e8"},
- {file = "astunparse-1.6.3.tar.gz", hash = "sha256:5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872"},
-]
[package.dependencies]
six = ">=1.6.1,<2.0"
@@ -87,12 +67,9 @@ wheel = ">=0.23.0,<1.0"
name = "attrs"
version = "23.1.0"
description = "Classes Without Boilerplate"
+category = "main"
optional = false
python-versions = ">=3.7"
-files = [
- {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
- {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
-]
[package.extras]
cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
@@ -105,33 +82,17 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte
name = "babel"
version = "2.12.1"
description = "Internationalization utilities"
+category = "dev"
optional = false
python-versions = ">=3.7"
-files = [
- {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
- {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
-]
[[package]]
name = "black"
version = "22.12.0"
description = "The uncompromising code formatter."
+category = "dev"
optional = false
python-versions = ">=3.7"
-files = [
- {file = "black-22.12.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9eedd20838bd5d75b80c9f5487dbcb06836a43833a37846cf1d8c1cc01cef59d"},
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- {file = "black-22.12.0-cp39-cp39-win_amd64.whl", hash = "sha256:559c7a1ba9a006226f09e4916060982fd27334ae1998e7a38b3f33a37f7a2148"},
- {file = "black-22.12.0-py3-none-any.whl", hash = "sha256:436cc9167dd28040ad90d3b404aec22cedf24a6e4d7de221bec2730ec0c97bcf"},
- {file = "black-22.12.0.tar.gz", hash = "sha256:229351e5a18ca30f447bf724d007f890f97e13af070bb6ad4c0a441cd7596a2f"},
-]
[package.dependencies]
click = ">=8.0.0"
@@ -150,144 +111,49 @@ uvloop = ["uvloop (>=0.15.2)"]
name = "cached-property"
version = "1.5.2"
description = "A decorator for caching properties in classes."
+category = "main"
optional = false
python-versions = "*"
-files = [
- {file = "cached-property-1.5.2.tar.gz", hash = "sha256:9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130"},
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-]
[[package]]
name = "cachetools"
version = "5.3.1"
description = "Extensible memoizing collections and decorators"
+category = "main"
optional = false
python-versions = ">=3.7"
-files = [
- {file = "cachetools-5.3.1-py3-none-any.whl", hash = "sha256:95ef631eeaea14ba2e36f06437f36463aac3a096799e876ee55e5cdccb102590"},
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-]
[[package]]
name = "certifi"
version = "2023.7.22"
description = "Python package for providing Mozilla's CA Bundle."
+category = "main"
optional = false
python-versions = ">=3.6"
-files = [
- {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
- {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
-]
[[package]]
name = "cfgv"
version = "3.4.0"
description = "Validate configuration and produce human readable error messages."
+category = "dev"
optional = false
python-versions = ">=3.8"
-files = [
- {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
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-]
[[package]]
name = "charset-normalizer"
version = "3.2.0"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+category = "main"
optional = false
python-versions = ">=3.7.0"
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name = "docutils"
version = "0.18.1"
description = "Docutils -- Python Documentation Utilities"
+category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
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[[package]]
name = "e3nn-jax"
version = "0.19.3"
description = "Equivariant convolutional neural networks for the group E(3) of 3 dimensional rotations, translations, and mirrors."
+category = "main"
optional = false
python-versions = ">=3.7"
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attrs = "*"
@@ -650,28 +349,24 @@ tqdm = "*"
name = "einops"
version = "0.6.1"
description = "A new flavour of deep learning operations"
+category = "main"
optional = false
python-versions = ">=3.7"
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name = "etils"
version = "1.4.1"
description = "Collection of common python utils"
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optional = false
python-versions = ">=3.9"
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importlib_resources = {version = "*", optional = true, markers = "extra == \"epath\""}
numpy = {version = "*", optional = true, markers = "extra == \"enp\""}
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+typing_extensions = {version = "*", optional = true, markers = "extra == \"epath\""}
zipp = {version = "*", optional = true, markers = "extra == \"epath\""}
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@@ -696,12 +391,9 @@ lazy-imports = ["etils[ecolab]"]
name = "exceptiongroup"
version = "1.1.3"
description = "Backport of PEP 654 (exception groups)"
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optional = false
python-versions = ">=3.7"
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@@ -710,12 +402,9 @@ test = ["pytest (>=6)"]
name = "execnet"
version = "2.0.2"
description = "execnet: rapid multi-Python deployment"
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optional = false
python-versions = ">=3.7"
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testing = ["hatch", "pre-commit", "pytest", "tox"]
@@ -724,12 +413,9 @@ testing = ["hatch", "pre-commit", "pytest", "tox"]
name = "filelock"
version = "3.12.3"
description = "A platform independent file lock."
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optional = false
python-versions = ">=3.8"
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@@ -742,12 +428,9 @@ testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pyt
name = "flake8"
version = "5.0.4"
description = "the modular source code checker: pep8 pyflakes and co"
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optional = false
python-versions = ">=3.6.1"
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name = "flatbuffers"
version = "23.5.26"
description = "The FlatBuffers serialization format for Python"
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optional = false
python-versions = "*"
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name = "flax"
version = "0.7.2"
description = "Flax: A neural network library for JAX designed for flexibility"
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optional = false
python-versions = "*"
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name = "fonttools"
version = "4.42.1"
description = "Tools to manipulate font files"
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python-versions = ">=3.8"
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name = "gast"
version = "0.4.0"
description = "Python AST that abstracts the underlying Python version"
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optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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name = "ghp-import"
version = "2.1.0"
description = "Copy your docs directly to the gh-pages branch."
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optional = false
python-versions = "*"
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@@ -880,12 +516,9 @@ dev = ["flake8", "markdown", "twine", "wheel"]
name = "google-auth"
version = "2.17.3"
description = "Google Authentication Library"
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version = "1.0.0"
description = "Google Authentication Library"
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description = "A deep merge function for 🐍."
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version = "1.5.2"
description = "Project documentation with Markdown."
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version = "0.1.1"
description = "ML Collections is a library of Python collections designed for ML usecases."
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version = "0.1"
description = "A custom YAML tag for referencing environment variables in YAML files. "
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optional = false
python-versions = ">=3.6"
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pyyaml = "*"
@@ -2595,12 +1354,9 @@ pyyaml = "*"
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version = "2.31.0"
description = "Python HTTP for Humans."
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optional = false
python-versions = ">=3.7"
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version = "1.3.1"
description = "OAuthlib authentication support for Requests."
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python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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@@ -2634,12 +1387,9 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"]
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version = "12.6.0"
description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
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@@ -2652,12 +1402,9 @@ jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"]
name = "rsa"
version = "4.9"
description = "Pure-Python RSA implementation"
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optional = false
python-versions = ">=3.6,<4"
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@@ -2666,35 +1413,9 @@ pyasn1 = ">=0.1.3"
name = "scipy"
version = "1.11.2"
description = "Fundamental algorithms for scientific computing in Python"
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python-versions = "<3.13,>=3.9"
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@@ -2708,61 +1429,64 @@ test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeo
name = "setuptools"
version = "68.2.0"
description = "Easily download, build, install, upgrade, and uninstall Python packages"
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optional = false
python-versions = ">=3.8"
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+version = "7.1.0"
+description = "the blessed package to manage your versions by scm tags"
+category = "main"
+optional = false
+python-versions = ">=3.7"
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+setuptools = "*"
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+typing-extensions = "*"
+
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+toml = ["setuptools (>=42)"]
+
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name = "shellingham"
version = "1.5.3"
description = "Tool to Detect Surrounding Shell"
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optional = false
python-versions = ">=3.7"
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name = "six"
version = "1.16.0"
description = "Python 2 and 3 compatibility utilities"
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optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
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name = "snowballstemmer"
version = "2.2.0"
description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+category = "dev"
optional = false
python-versions = "*"
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name = "sphinx"
version = "5.3.0"
description = "Python documentation generator"
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optional = false
python-versions = ">=3.6"
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@@ -2791,12 +1515,9 @@ test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
name = "sphinx-autodoc-typehints"
version = "1.23.0"
description = "Type hints (PEP 484) support for the Sphinx autodoc extension"
+category = "dev"
optional = false
python-versions = ">=3.7"
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@@ -2810,12 +1531,9 @@ type-comment = ["typed-ast (>=1.5.4)"]
name = "sphinx-rtd-theme"
version = "1.3.0"
description = "Read the Docs theme for Sphinx"
+category = "dev"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
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@@ -2829,12 +1547,9 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
name = "sphinxcontrib-applehelp"
version = "1.0.7"
description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
+category = "dev"
optional = false
python-versions = ">=3.9"
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@@ -2847,12 +1562,9 @@ test = ["pytest"]
name = "sphinxcontrib-devhelp"
version = "1.0.5"
description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
+category = "dev"
optional = false
python-versions = ">=3.9"
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@@ -2865,12 +1577,9 @@ test = ["pytest"]
name = "sphinxcontrib-htmlhelp"
version = "2.0.4"
description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+category = "dev"
optional = false
python-versions = ">=3.9"
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@@ -2883,12 +1592,9 @@ test = ["html5lib", "pytest"]
name = "sphinxcontrib-jquery"
version = "4.1"
description = "Extension to include jQuery on newer Sphinx releases"
+category = "dev"
optional = false
python-versions = ">=2.7"
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@@ -2897,12 +1603,9 @@ Sphinx = ">=1.8"
name = "sphinxcontrib-jsmath"
version = "1.0.1"
description = "A sphinx extension which renders display math in HTML via JavaScript"
+category = "dev"
optional = false
python-versions = ">=3.5"
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@@ -2911,12 +1614,9 @@ test = ["flake8", "mypy", "pytest"]
name = "sphinxcontrib-qthelp"
version = "1.0.6"
description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
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optional = false
python-versions = ">=3.9"
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description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
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Sphinx = ">=5"
@@ -2947,12 +1644,9 @@ test = ["pytest"]
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description = "Computer algebra system (CAS) in Python"
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optional = false
python-versions = ">=3.8"
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description = "Pretty-print tabular data"
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python-versions = ">=3.7"
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widechars = ["wcwidth"]
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description = "Fast data loading for TensorBoard"
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description = "TensorFlow is an open source machine learning framework for everyone."
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python-versions = ">=3.8"
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description = "TensorFlow is an open source machine learning framework for everyone."
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@@ -3105,12 +1760,9 @@ wrapt = ">=1.11.0,<1.15"
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version = "4.9.3"
description = "tensorflow/datasets is a library of datasets ready to use with TensorFlow."
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@@ -3171,19 +1823,1687 @@ youtube-vis = ["pycocotools"]
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description = "TensorFlow Estimator."
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-files = [
+werkzeug = [
{file = "werkzeug-2.3.7-py3-none-any.whl", hash = "sha256:effc12dba7f3bd72e605ce49807bbe692bd729c3bb122a3b91747a6ae77df528"},
{file = "werkzeug-2.3.7.tar.gz", hash = "sha256:2b8c0e447b4b9dbcc85dd97b6eeb4dcbaf6c8b6c3be0bd654e25553e0a2157d8"},
]
-
-[package.dependencies]
-MarkupSafe = ">=2.1.1"
-
-[package.extras]
-watchdog = ["watchdog (>=2.3)"]
-
-[[package]]
-name = "wheel"
-version = "0.41.2"
-description = "A built-package format for Python"
-optional = false
-python-versions = ">=3.7"
-files = [
+wheel = [
{file = "wheel-0.41.2-py3-none-any.whl", hash = "sha256:75909db2664838d015e3d9139004ee16711748a52c8f336b52882266540215d8"},
{file = "wheel-0.41.2.tar.gz", hash = "sha256:0c5ac5ff2afb79ac23ab82bab027a0be7b5dbcf2e54dc50efe4bf507de1f7985"},
]
-
-[package.extras]
-test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
-
-[[package]]
-name = "wrapt"
-version = "1.14.1"
-description = "Module for decorators, wrappers and monkey patching."
-optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
-files = [
+wrapt = [
{file = "wrapt-1.14.1-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:1b376b3f4896e7930f1f772ac4b064ac12598d1c38d04907e696cc4d794b43d3"},
{file = "wrapt-1.14.1-cp27-cp27m-manylinux1_i686.whl", hash = "sha256:903500616422a40a98a5a3c4ff4ed9d0066f3b4c951fa286018ecdf0750194ef"},
{file = "wrapt-1.14.1-cp27-cp27m-manylinux1_x86_64.whl", hash = "sha256:5a9a0d155deafd9448baff28c08e150d9b24ff010e899311ddd63c45c2445e28"},
@@ -3565,44 +3689,11 @@ files = [
{file = "wrapt-1.14.1-cp39-cp39-win_amd64.whl", hash = "sha256:dee60e1de1898bde3b238f18340eec6148986da0455d8ba7848d50470a7a32fb"},
{file = "wrapt-1.14.1.tar.gz", hash = "sha256:380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d"},
]
-
-[[package]]
-name = "zipp"
-version = "3.16.2"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-optional = false
-python-versions = ">=3.8"
-files = [
+zipp = [
{file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
{file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
]
-
-[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
-
-[[package]]
-name = "znh5md"
-version = "0.1.7"
-description = "High Performance Interface for H5MD Trajectories"
-optional = false
-python-versions = ">=3.9,<4.0"
-files = [
+znh5md = [
{file = "znh5md-0.1.7-py3-none-any.whl", hash = "sha256:2d5505738c92c79e2de907acf89956662c94472a350f1ddfd55c509c0cc44960"},
{file = "znh5md-0.1.7.tar.gz", hash = "sha256:fa437c805da4a7a24d6265f632ebbc36863fd15c952e2ce1a3b2d35c6241e00d"},
-]
-
-[package.dependencies]
-ase = ">=3.22.1,<4.0.0"
-chemfiles = ">=0.10.3,<0.11.0"
-h5py = ">=3.7.0,<4.0.0"
-tqdm = ">=4.65.0,<5.0.0"
-typer = {version = ">=0.7.0,<0.8.0", extras = ["all"]}
-
-[package.extras]
-dask = ["dask[array] (>=2022.11.1,<2023.0.0)"]
-
-[metadata]
-lock-version = "2.0"
-python-versions = ">=3.10,<3.12"
-content-hash = "afe5299a8eb49bf6e749c4f9f3ad895199be032f372247dfe8b7d44c33dba1c8"
+]
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 4f34cbee..50061f18 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,6 @@ pre-commit = "^2.20.0"
isort = "^5.10.1"
flake8 = "^5.0.4"
sphinx-autodoc-typehints = "^1.21.8"
-pandas = "^2.1.1"
[build-system]
requires = ["poetry-core"]
From ade74a5836e15f1b3f42c5937afed77012d706a8 Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Thu, 5 Oct 2023 21:03:18 +0200
Subject: [PATCH 13/14] regression test overhaul
---
tests/conftest.py | 34 +++++++-
tests/regression_tests/apax_config.yaml | 16 ++--
tests/regression_tests/test_apax_training.py | 82 ++++++++------------
3 files changed, 75 insertions(+), 57 deletions(-)
diff --git a/tests/conftest.py b/tests/conftest.py
index 8018bc4b..4356acd7 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,5 +1,7 @@
from typing import List
-
+import os
+import urllib
+import zipfile
import numpy as np
import pytest
from ase import Atoms
@@ -74,3 +76,33 @@ def example_atoms(num_data: int, pbc: bool, calc_results: List[str]) -> Atoms:
def get_tmp_path(tmp_path_factory):
test_path = tmp_path_factory.mktemp("apax_tests")
return test_path
+
+
+@pytest.fixture(scope="session")
+def get_md22_stachyose(get_tmp_path):
+ url = "http://www.quantum-machine.org/gdml/repo/static/md22_stachyose.zip"
+ data_path = get_tmp_path / "data"
+ file_path = data_path / "md22_stachyose.zip"
+
+ os.makedirs(data_path, exist_ok=True)
+ urllib.request.urlretrieve(url, file_path)
+
+ with zipfile.ZipFile(file_path, "r") as zip_ref:
+ zip_ref.extractall(data_path)
+
+ file_path = modify_xyz_file(
+ file_path.with_suffix(".xyz"), target_string="Energy", replacement_string="energy"
+ )
+
+ return file_path
+
+
+def modify_xyz_file(file_path, target_string, replacement_string):
+ new_file_path = file_path.with_name(file_path.stem + "_mod" + file_path.suffix)
+
+ with open(file_path, "r") as input_file, open(new_file_path, "w") as output_file:
+ for line in input_file:
+ # Replace all occurrences of the target string with the replacement string
+ modified_line = line.replace(target_string, replacement_string)
+ output_file.write(modified_line)
+ return new_file_path
\ No newline at end of file
diff --git a/tests/regression_tests/apax_config.yaml b/tests/regression_tests/apax_config.yaml
index 436dd94b..0a098ff6 100644
--- a/tests/regression_tests/apax_config.yaml
+++ b/tests/regression_tests/apax_config.yaml
@@ -1,4 +1,4 @@
-n_epochs: 1000
+n_epochs: 200
seed: 0
data:
@@ -10,7 +10,7 @@ data:
n_train: 1000
n_valid: 100
- batch_size: 8
+ batch_size: 32
valid_batch_size: 100
shift_method: "per_element_regression_shift"
@@ -66,10 +66,10 @@ loss:
optimizer:
opt_name: adam
opt_kwargs: {}
- emb_lr: 0.003
- nn_lr: 0.002
- scale_lr: 0.0005
- shift_lr: 0.025
+ emb_lr: 0.02
+ nn_lr: 0.03
+ scale_lr: 0.001
+ shift_lr: 0.05
zbl_lr: 0.001
transition_begin: 0
@@ -83,7 +83,7 @@ checkpoints:
# reset_layers: []
progress_bar:
- disable_epoch_pbar: false
- disable_nl_pbar: false
+ disable_epoch_pbar: true
+ disable_nl_pbar: true
maximize_l2_cache: false
diff --git a/tests/regression_tests/test_apax_training.py b/tests/regression_tests/test_apax_training.py
index 801a32fc..7091b600 100644
--- a/tests/regression_tests/test_apax_training.py
+++ b/tests/regression_tests/test_apax_training.py
@@ -2,6 +2,7 @@
import pathlib
import urllib
import zipfile
+import uuid
import numpy as np
import pandas as pd
@@ -9,75 +10,60 @@
import yaml
from apax.train.run import run
+from apax.data.statistics import scale_method_list, shift_method_list
TEST_PATH = pathlib.Path(__file__).parent.resolve()
-MD22_STACHYOSE_URL = "http://www.quantum-machine.org/gdml/repo/static/md22_stachyose.zip"
-
-
-def download_and_extract_data(data_path, filename, url, file_format):
- file_path = data_path / filename
-
- os.makedirs(data_path, exist_ok=True)
- urllib.request.urlretrieve(url, file_path)
-
- with zipfile.ZipFile(file_path, "r") as zip_ref:
- zip_ref.extractall(data_path)
-
- return file_path.with_suffix(f".{file_format}")
-
-
-def modify_xyz_file(file_path, target_string, replacement_string):
- new_file_path = file_path.with_name(file_path.stem + "_mod" + file_path.suffix)
-
- with open(file_path, "r") as input_file, open(new_file_path, "w") as output_file:
- for line in input_file:
- # Replace all occurrences of the target string with the replacement string
- modified_line = line.replace(target_string, replacement_string)
- output_file.write(modified_line)
- return new_file_path
-
def load_config_and_run_training(
- config_path, file_path, working_dir, energy_unit="eV", pos_unit="Ang"
+ config_path, **config_kwargs
):
with open(config_path.as_posix(), "r") as stream:
config_dict = yaml.safe_load(stream)
- config_dict["data"]["directory"] = working_dir.as_posix()
- config_dict["data"]["data_path"] = file_path.as_posix()
- config_dict["data"]["energy_unit"] = energy_unit
- config_dict["data"]["pos_unit"] = pos_unit
+ for pydentic_model_key, config_mods in config_kwargs.items():
+ for h_param_key, value in config_mods.items():
+ config_dict[pydentic_model_key][h_param_key] = value
run(config_dict)
+
+
+def load_csv(filename):
+ data = np.loadtxt(filename, delimiter=',', skiprows=1) # Skip the header row
+
+ with open(filename, 'r') as file:
+ header = file.readline().strip().split(',')
- return
+ data_dict = {header[i]: data[:, i].tolist() for i in range(len(header))}
+ return data_dict
+
@pytest.mark.slow
-def test_regression_model_training(get_tmp_path):
+def test_regression_model_training(get_md22_stachyose, get_tmp_path):
config_path = TEST_PATH / "apax_config.yaml"
- working_dir = get_tmp_path
- data_path = working_dir / "data"
- filename = "md22_stachyose.zip"
+ working_dir = get_tmp_path / str(uuid.uuid4())
+ file_path = get_md22_stachyose
- file_path = download_and_extract_data(data_path, filename, MD22_STACHYOSE_URL, "xyz")
-
- file_path = modify_xyz_file(
- file_path, target_string="Energy", replacement_string="energy"
- )
+ data_config_mods = {
+ "directory": working_dir.as_posix(),
+ "data_path": file_path.as_posix(),
+ "energy_unit": "kcal/mol",
+ }
- load_config_and_run_training(config_path, file_path, working_dir, "kcal/mol")
+ load_config_and_run_training(config_path, data=data_config_mods)
- current_metrics = pd.read_csv(working_dir / "test/log.csv")
+ current_metrics = load_csv(working_dir / "test/log.csv")
comparison_metrics = {
- "val_energy_mae": 0.2048215700433502,
- "val_forces_mae": 0.054957914591049,
- "val_forces_mse": 0.0056583952479869,
- "val_loss": 0.1395589689994847,
+ "val_energy_mae": 0.24696787788040334,
+ "val_forces_mae": 0.09672525137916232,
+ "val_forces_mse": 0.017160819058234304,
+ "val_loss": 0.45499257304743396,
}
+ for key in comparison_metrics.keys():
+ print(np.array(current_metrics[key])[-1])
for key in comparison_metrics.keys():
assert (
- abs((np.array(current_metrics[key])[-1] / comparison_metrics[key]) - 1) < 1e-4
- )
+ abs((np.array(current_metrics[key])[-1] / comparison_metrics[key]) - 1) < 1e-3
+ )
\ No newline at end of file
From ee0b36eb3cfeed2e7feb63eacb63433b09608411 Mon Sep 17 00:00:00 2001
From: Tetracarbonylnickel <segreto@theochem.uni-stuttgart.de>
Date: Thu, 5 Oct 2023 21:06:02 +0200
Subject: [PATCH 14/14] linting
---
tests/conftest.py | 17 +++++++-------
tests/regression_tests/test_apax_training.py | 24 +++++++-------------
tests/unit_tests/data/test_statistics.py | 2 +-
3 files changed, 18 insertions(+), 25 deletions(-)
diff --git a/tests/conftest.py b/tests/conftest.py
index 4356acd7..0d5a08bc 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,7 +1,8 @@
-from typing import List
import os
import urllib
import zipfile
+from typing import List
+
import numpy as np
import pytest
from ase import Atoms
@@ -89,14 +90,14 @@ def get_md22_stachyose(get_tmp_path):
with zipfile.ZipFile(file_path, "r") as zip_ref:
zip_ref.extractall(data_path)
-
+
file_path = modify_xyz_file(
- file_path.with_suffix(".xyz"), target_string="Energy", replacement_string="energy"
- )
-
+ file_path.with_suffix(".xyz"), target_string="Energy", replacement_string="energy"
+ )
+
return file_path
-
-
+
+
def modify_xyz_file(file_path, target_string, replacement_string):
new_file_path = file_path.with_name(file_path.stem + "_mod" + file_path.suffix)
@@ -105,4 +106,4 @@ def modify_xyz_file(file_path, target_string, replacement_string):
# Replace all occurrences of the target string with the replacement string
modified_line = line.replace(target_string, replacement_string)
output_file.write(modified_line)
- return new_file_path
\ No newline at end of file
+ return new_file_path
diff --git a/tests/regression_tests/test_apax_training.py b/tests/regression_tests/test_apax_training.py
index 7091b600..339cb28a 100644
--- a/tests/regression_tests/test_apax_training.py
+++ b/tests/regression_tests/test_apax_training.py
@@ -1,22 +1,16 @@
-import os
import pathlib
-import urllib
-import zipfile
import uuid
import numpy as np
-import pandas as pd
import pytest
import yaml
from apax.train.run import run
-from apax.data.statistics import scale_method_list, shift_method_list
TEST_PATH = pathlib.Path(__file__).parent.resolve()
-def load_config_and_run_training(
- config_path, **config_kwargs
-):
+
+def load_config_and_run_training(config_path, **config_kwargs):
with open(config_path.as_posix(), "r") as stream:
config_dict = yaml.safe_load(stream)
@@ -25,19 +19,19 @@ def load_config_and_run_training(
config_dict[pydentic_model_key][h_param_key] = value
run(config_dict)
-
+
def load_csv(filename):
- data = np.loadtxt(filename, delimiter=',', skiprows=1) # Skip the header row
+ data = np.loadtxt(filename, delimiter=",", skiprows=1) # Skip the header row
- with open(filename, 'r') as file:
- header = file.readline().strip().split(',')
+ with open(filename, "r") as file:
+ header = file.readline().strip().split(",")
data_dict = {header[i]: data[:, i].tolist() for i in range(len(header))}
return data_dict
-
+
@pytest.mark.slow
def test_regression_model_training(get_md22_stachyose, get_tmp_path):
config_path = TEST_PATH / "apax_config.yaml"
@@ -60,10 +54,8 @@ def test_regression_model_training(get_md22_stachyose, get_tmp_path):
"val_forces_mse": 0.017160819058234304,
"val_loss": 0.45499257304743396,
}
- for key in comparison_metrics.keys():
- print(np.array(current_metrics[key])[-1])
for key in comparison_metrics.keys():
assert (
abs((np.array(current_metrics[key])[-1] / comparison_metrics[key]) - 1) < 1e-3
- )
\ No newline at end of file
+ )
diff --git a/tests/unit_tests/data/test_statistics.py b/tests/unit_tests/data/test_statistics.py
index 6b3d4243..e2e698ee 100644
--- a/tests/unit_tests/data/test_statistics.py
+++ b/tests/unit_tests/data/test_statistics.py
@@ -2,8 +2,8 @@
from ase import Atoms
from ase.calculators.singlepoint import SinglePointCalculator
-from apax.data.statistics import PerElementRegressionShift
from apax.data.input_pipeline import create_dict_dataset
+from apax.data.statistics import PerElementRegressionShift
def test_energy_per_element():