From 76f1dde41601b7e455ec5ea14a1be251c58de9f1 Mon Sep 17 00:00:00 2001
From: Chi Chen <chen08013@gmail.com>
Date: Sat, 3 Dec 2022 17:13:41 -0800
Subject: [PATCH 01/13] Update README.md

Update citation
---
 README.md | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 87938c3..b4580df 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 
 # M3GNet
 
-M3GNet is a new materials graph neural network architecture that incorporates 3-body interactions. A key difference
+[M3GNet](https://www.nature.com/articles/s43588-022-00349-3) is a new materials graph neural network architecture that incorporates 3-body interactions. A key difference
 with prior materials graph implementations such as [MEGNet](https://github.com/materialsvirtuallab/megnet) is the
 addition of the coordinates for atoms and the 3×3 lattice matrix in crystals, which are necessary for obtaining
 tensorial quantities such as forces and stresses via auto-differentiation.
@@ -372,8 +372,7 @@ The training data used to develop the universal M3GNet IAP is `MPF.2021.2.8` and
 Please cite the following work:
 
 ```txt
-Chi Chen, and Shyue Ping Ong. "A Universal Graph Deep Learning Interatomic Potential for the Periodic Table."
-arXiv preprint [arXiv:2202.02450](https://arxiv.org/abs/2202.02450) (2022).
+Chen, C., Ong, S.P. A universal graph deep learning interatomic potential for the periodic table. Nat Comput Sci 2, 718–728 (2022). https://doi.org/10.1038/s43588-022-00349-3.
 ```
 
 # Acknowledgements

From 04e285155cc466f482b13f383bdab6a71cb231ef Mon Sep 17 00:00:00 2001
From: Shyue Ping Ong <sp@ong.ai>
Date: Sat, 3 Dec 2022 18:45:57 -0800
Subject: [PATCH 02/13] Update README.

---
 README.md | 5 +----
 mypy.ini  | 4 ++--
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index b4580df..ff1daad 100644
--- a/README.md
+++ b/README.md
@@ -5,10 +5,7 @@
 
 # M3GNet
 
-[M3GNet](https://www.nature.com/articles/s43588-022-00349-3) is a new materials graph neural network architecture that incorporates 3-body interactions. A key difference
-with prior materials graph implementations such as [MEGNet](https://github.com/materialsvirtuallab/megnet) is the
-addition of the coordinates for atoms and the 3×3 lattice matrix in crystals, which are necessary for obtaining
-tensorial quantities such as forces and stresses via auto-differentiation.
+[M3GNet](https://www.nature.com/articles/s43588-022-00349-3) is a new materials graph neural network architecture that incorporates 3-body interactions. A key difference with prior materials graph implementations such as [MEGNet](https://github.com/materialsvirtuallab/megnet) is the addition of the coordinates for atoms and the 3×3 lattice matrix in crystals, which are necessary for obtaining tensorial quantities such as forces and stresses via auto-differentiation.
 
 As a framework, M3GNet has diverse applications, including:
 
diff --git a/mypy.ini b/mypy.ini
index 7faa1e0..0e4c3cc 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -1,5 +1,5 @@
 [mypy]
 exclude = ["pretrained"]
 ignore_missing_imports = True
-follow_imports = skip
-follow_imports_for_stubs = True
+#follow_imports = skip
+#follow_imports_for_stubs = True

From 708bb7accf615c750654c57406c3da1e528b5824 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 12 Dec 2022 07:27:15 -0800
Subject: [PATCH 03/13] [pre-commit.ci] pre-commit autoupdate (#48)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.3.0 → v4.4.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.3.0...v4.4.0)
- [github.com/PyCQA/flake8: 5.0.4 → 6.0.0](https://github.com/PyCQA/flake8/compare/5.0.4...6.0.0)
- [github.com/asottile/pyupgrade: v3.2.0 → v3.3.0](https://github.com/asottile/pyupgrade/compare/v3.2.0...v3.3.0)
- [github.com/PyCQA/autoflake: v1.7.7 → v2.0.0](https://github.com/PyCQA/autoflake/compare/v1.7.7...v2.0.0)
- [github.com/pre-commit/mirrors-mypy: v0.982 → v0.991](https://github.com/pre-commit/mirrors-mypy/compare/v0.982...v0.991)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f67b663..3f36a3d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,30 +11,30 @@ repos:
       - id: black-jupyter
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+    rev: 6.0.0
     hooks:
       - id: flake8
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.2.0
+    rev: v3.3.0
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
 
   - repo: https://github.com/PyCQA/autoflake
-    rev: v1.7.7
+    rev: v2.0.0
     hooks:
       - id: autoflake
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.982
+    rev: v0.991
     hooks:
       - id: mypy
 

From 1d49cf528eb28956503ef30239537d7594ebff12 Mon Sep 17 00:00:00 2001
From: Shyue Ping Ong <sp@ong.ai>
Date: Tue, 13 Dec 2022 05:23:32 -0800
Subject: [PATCH 04/13] Update notebook since Colab has been upgraded to Python
 3.8.

---
 examples/Cubic Crystal Test.ipynb    | 8 ++------
 examples/Relaxation of LiFePO4.ipynb | 8 ++------
 2 files changed, 4 insertions(+), 12 deletions(-)

diff --git a/examples/Cubic Crystal Test.ipynb b/examples/Cubic Crystal Test.ipynb
index 25f0e29..2a9f025 100644
--- a/examples/Cubic Crystal Test.ipynb	
+++ b/examples/Cubic Crystal Test.ipynb	
@@ -9,9 +9,7 @@
     "\n",
     "This notebook is written to demonstrate the use of M3GNet as a structure relaxer as well as to provide more comprehensive benchmarks for cubic crystals based on exp data on Wikipedia and MP DFT data. This benchmark is limited to cubic crystals for ease of comparison since there is only one lattice parameter. \n",
     "\n",
-    "If you are running this notebook from Google Colab, uncomment the next code box to install m3gnet first.\n",
-    "\n",
-    "> Note: Because Google Colab's python version is sometimes rather old (v3.7 at the time of writing this notebook (Jul 2022), you will need to install m3gnet without dependencies and install the dependencies manually."
+    "If you are running this notebook from Google Colab, uncomment the next code box to install m3gnet first."
    ]
   },
   {
@@ -21,9 +19,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# !pip install --no-deps m3gnet\n",
-    "# !pip install pymatgen ase\n",
-    "# !pip install lxml"
+    "# !pip install m3gnet"
    ]
   },
   {
diff --git a/examples/Relaxation of LiFePO4.ipynb b/examples/Relaxation of LiFePO4.ipynb
index 00fc31d..2d87c7a 100644
--- a/examples/Relaxation of LiFePO4.ipynb	
+++ b/examples/Relaxation of LiFePO4.ipynb	
@@ -9,9 +9,7 @@
     "\n",
     "This notebook shows an example of relaxing the LiFePO4 crystal.\n",
     "\n",
-    "If you are running this notebook from Google Colab, uncomment the next code box to install m3gnet first.\n",
-    "\n",
-    "> Note: Because Google Colab's python version is sometimes rather old (v3.7 at the time of writing this notebook (Jul 2022), you will need to install m3gnet without dependencies and install the dependencies manually."
+    "If you are running this notebook from Google Colab, uncomment the next code box to install m3gnet first."
    ]
   },
   {
@@ -21,9 +19,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# !pip install --no-deps m3gnet\n",
-    "# !pip install pymatgen ase\n",
-    "# !pip install lxml"
+    "# !pip install m3gnet"
    ]
   },
   {

From d436bb082d8523819c625987049b2c6c66c35a7c Mon Sep 17 00:00:00 2001
From: "Sterling G. Baird" <45469701+sgbaird@users.noreply.github.com>
Date: Sat, 17 Dec 2022 04:33:28 -0700
Subject: [PATCH 05/13] fix link not resolving and being hidden (#49)

---
 README.md | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/README.md b/README.md
index ff1daad..77cf995 100644
--- a/README.md
+++ b/README.md
@@ -368,9 +368,7 @@ The training data used to develop the universal M3GNet IAP is `MPF.2021.2.8` and
 
 Please cite the following work:
 
-```txt
-Chen, C., Ong, S.P. A universal graph deep learning interatomic potential for the periodic table. Nat Comput Sci 2, 718–728 (2022). https://doi.org/10.1038/s43588-022-00349-3.
-```
+> Chen, C., Ong, S.P. A universal graph deep learning interatomic potential for the periodic table. Nat Comput Sci 2, 718–728 (2022). https://doi.org/10.1038/s43588-022-00349-3.
 
 # Acknowledgements
 

From 1c94d6c2cd9a5d90ae352b2ced85d551605d9e42 Mon Sep 17 00:00:00 2001
From: Chi Chen <chen08013@gmail.com>
Date: Thu, 23 Feb 2023 10:18:51 -0800
Subject: [PATCH 06/13] Bug/dependency fix (#52)

* new tensorflow is breaking edge cases with only one atom, reverting back

* fix black
---
 m3gnet/models/tests/test_model.py | 7 +++++++
 requirements.txt                  | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/m3gnet/models/tests/test_model.py b/m3gnet/models/tests/test_model.py
index 73cbe84..46484d5 100644
--- a/m3gnet/models/tests/test_model.py
+++ b/m3gnet/models/tests/test_model.py
@@ -17,6 +17,7 @@ def setUpClass(cls) -> None:
         cls.mol = Molecule(["C", "O"], [[0, 0, 0], [1.5, 0, 0]])
         cls.structure = Structure(Lattice.cubic(3.30), ["Mo", "Mo"], [[0, 0, 0], [0.5, 0.5, 0.5]])
         cls.atoms = Atoms(["Mo", "Mo"], [[0, 0, 0], [0.5, 0.5, 0.5]], cell=np.eye(3) * 3.30, pbc=True)
+        cls.single_atoms = Structure(Lattice.cubic(6.0), ["Mo"], [[0, 0, 0]])
 
     def test_m3gnet(self):
 
@@ -46,6 +47,12 @@ def test_potential(self):
             )
         )
 
+    def test_single_atoms(self):
+        self.potential.get_efs(self.structure)
+        e, f, s = self.potential.get_efs(self.single_atoms)
+        shapes = f.numpy().shape
+        self.assertTupleEqual(shapes, (1, 3))
+
     def test_relaxer(self):
         relaxer = Relaxer()  # this loads the default model
 
diff --git a/requirements.txt b/requirements.txt
index 9ca3243..266710d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,3 @@
 pymatgen==2022.11.7
-tensorflow==2.11.0
+tensorflow==2.9.1
 ase==3.22.1

From 9c992b50b10060c596368de4d68909d689a72673 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 23 Feb 2023 10:19:05 -0800
Subject: [PATCH 07/13] [pre-commit.ci] pre-commit autoupdate (#50)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 22.10.0 → 23.1.0](https://github.com/psf/black/compare/22.10.0...23.1.0)
- [github.com/asottile/pyupgrade: v3.3.0 → v3.3.1](https://github.com/asottile/pyupgrade/compare/v3.3.0...v3.3.1)
- [github.com/PyCQA/autoflake: v2.0.0 → v2.0.1](https://github.com/PyCQA/autoflake/compare/v2.0.0...v2.0.1)
- [github.com/nbQA-dev/nbQA: 1.5.3 → 1.6.1](https://github.com/nbQA-dev/nbQA/compare/1.5.3...1.6.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml           | 8 ++++----
 m3gnet/graph/_compute.py          | 1 -
 m3gnet/models/tests/test_model.py | 1 -
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3f36a3d..a2848b2 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ ci:
 
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 23.1.0
     hooks:
       - id: black-jupyter
 
@@ -23,13 +23,13 @@ repos:
       - id: flake8
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.0
+    rev: v3.3.1
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
 
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.0
+    rev: v2.0.1
     hooks:
       - id: autoflake
 
@@ -39,7 +39,7 @@ repos:
       - id: mypy
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.5.3
+    rev: 1.6.1
     hooks:
       - id: nbqa-flake8
         args: [--ignore=E402]
diff --git a/m3gnet/graph/_compute.py b/m3gnet/graph/_compute.py
index e206dae..8f335b3 100644
--- a/m3gnet/graph/_compute.py
+++ b/m3gnet/graph/_compute.py
@@ -156,7 +156,6 @@ def _list_include_threebody_indices(graph: list, threebody_cutoff: float | None
         ij_reverse_map = None
         original_index = np.arange(n_bond)
     if bond_atom_indices.shape[0] > 0:
-
         bond_indices, n_triple_ij, n_triple_i, n_triple_s = _compute_3body(
             bond_atom_indices,
             graph[Index.N_ATOMS],
diff --git a/m3gnet/models/tests/test_model.py b/m3gnet/models/tests/test_model.py
index 46484d5..0fd380c 100644
--- a/m3gnet/models/tests/test_model.py
+++ b/m3gnet/models/tests/test_model.py
@@ -20,7 +20,6 @@ def setUpClass(cls) -> None:
         cls.single_atoms = Structure(Lattice.cubic(6.0), ["Mo"], [[0, 0, 0]])
 
     def test_m3gnet(self):
-
         g = self.model.graph_converter(self.mol)
 
         val = self.model.predict_structure(self.mol).numpy().ravel()

From b2a92f7c82731fe23800aaca665b8dc093756de4 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 23 Feb 2023 10:21:02 -0800
Subject: [PATCH 08/13] Bump tensorflow from 2.9.1 to 2.9.3 (#59)

Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.9.1 to 2.9.3.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md)
- [Commits](https://github.com/tensorflow/tensorflow/compare/v2.9.1...v2.9.3)

---
updated-dependencies:
- dependency-name: tensorflow
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 266710d..c4c232c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,3 @@
 pymatgen==2022.11.7
-tensorflow==2.9.1
+tensorflow==2.9.3
 ase==3.22.1

From 70e7cd86b5ecd9eaf6174e1da2f843b16450b1a5 Mon Sep 17 00:00:00 2001
From: "K. YAN" <38057488+YKQ98@users.noreply.github.com>
Date: Tue, 4 Apr 2023 18:57:48 -0500
Subject: [PATCH 09/13] update a concrete example to load the MPF dataset (#69)

load MPF dataset from shared block_0 and block_1 files
---
 README.md | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/README.md b/README.md
index 77cf995..f4ad7fa 100644
--- a/README.md
+++ b/README.md
@@ -317,6 +317,56 @@ VASP calculations (default unit is kBar) should be multiplied by -0.1 to work di
 
 We use validation dataset to select the stopping epoch number. The dataset has similar format as the training dataset.
 
+If you want to use the offical MPF dataset shared above, here are some code examples that you can follow to load the dataset smoothly and train your own model.
+
+First, load the MPF dataset consisting of block_0 and block_1
+
+```python
+import pickle as pk
+import pandas as pd
+import pymatgen
+
+print('loading the MPF dataset 2021')
+with open('/yourpath/block_0.p', 'rb') as f:
+    data = pk.load(f)
+
+with open('/yourpath/block_1.p', 'rb') as f:
+    data2 = pk.load(f)
+print('MPF dataset 2021 loaded')
+data.update(data2)
+df = pd.DataFrame.from_dict(data)
+```
+
+Then, split the data based on material id and map the energy to formation energy with unit eV/atom
+
+```python
+id_train, id_val, id_test = get_id_train_val_test(
+    total_size=len(data),
+    split_seed=42,
+    train_ratio=0.90,
+    val_ratio=0.05,
+    test_ratio=0.05,
+    keep_data_order=False,
+)
+
+cnt = 0
+for idx, item in df.items():
+    # import pdb; pdb.set_trace()
+    if cnt in id_train:
+        for iid in range(len(item['energy'])):
+            dataset_train.append({"atoms":item['structure'][iid], "energy":item['energy'][iid] / len(item['force'][iid]), "force": np.array(item['force'][iid])})
+    elif cnt in id_val:
+        for iid in range(len(item['energy'])):
+            dataset_val.append({"atoms":item['structure'][iid], "energy":item['energy'][iid] / len(item['force'][iid]), "force": np.array(item['force'][iid])})
+    elif cnt in id_test:
+        for iid in range(len(item['energy'])):
+            dataset_test.append({"atoms":item['structure'][iid], "energy":item['energy'][iid] / len(item['force'][iid]), "force": np.array(item['force'][iid])})
+    cnt += 1
+
+print('using %d samples to train, %d samples to evaluate, and %d samples to test'%(len(dataset_train), len(dataset_val), len(dataset_test)))
+```
+After this, you can use the dataset_train to train, dataset_val to evaluate, and dataset_test to test.
+
 A minimal example of model training is shown below.
 
 ```python

From 924a46f8b80801efcfe44e4d5fb0f78c562f6ba9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 4 Apr 2023 16:58:02 -0700
Subject: [PATCH 10/13] [pre-commit.ci] pre-commit autoupdate (#62)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 23.1.0 → 23.3.0](https://github.com/psf/black/compare/23.1.0...23.3.0)
- [github.com/PyCQA/autoflake: v2.0.1 → v2.0.2](https://github.com/PyCQA/autoflake/compare/v2.0.1...v2.0.2)
- [github.com/pre-commit/mirrors-mypy: v0.991 → v1.1.1](https://github.com/pre-commit/mirrors-mypy/compare/v0.991...v1.1.1)
- [github.com/nbQA-dev/nbQA: 1.6.1 → 1.7.0](https://github.com/nbQA-dev/nbQA/compare/1.6.1...1.7.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a2848b2..23c08b0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ ci:
 
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
       - id: black-jupyter
 
@@ -29,17 +29,17 @@ repos:
         args: [--py38-plus]
 
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.1
+    rev: v2.0.2
     hooks:
       - id: autoflake
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.991
+    rev: v1.1.1
     hooks:
       - id: mypy
 
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.6.1
+    rev: 1.7.0
     hooks:
       - id: nbqa-flake8
         args: [--ignore=E402]

From d4ea965150bbbf2edb5239ee9dffe90635cffc5c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 2 May 2023 10:08:05 -0700
Subject: [PATCH 11/13] [pre-commit.ci] pre-commit autoupdate (#72)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/asottile/pyupgrade: v3.3.1 → v3.3.2](https://github.com/asottile/pyupgrade/compare/v3.3.1...v3.3.2)
- [github.com/PyCQA/autoflake: v2.0.2 → v2.1.1](https://github.com/PyCQA/autoflake/compare/v2.0.2...v2.1.1)
- [github.com/pre-commit/mirrors-mypy: v1.1.1 → v1.2.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.1.1...v1.2.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 23c08b0..cd1eaaa 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -23,18 +23,18 @@ repos:
       - id: flake8
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
+    rev: v3.3.2
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
 
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.0.2
+    rev: v2.1.1
     hooks:
       - id: autoflake
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.1.1
+    rev: v1.2.0
     hooks:
       - id: mypy
 

From 06560e3021a80c9bc0aa0d1bf909a30cd551fcf9 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 6 Jun 2023 16:54:23 -0700
Subject: [PATCH 12/13] [pre-commit.ci] pre-commit autoupdate (#74)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/asottile/pyupgrade: v3.3.2 → v3.4.0](https://github.com/asottile/pyupgrade/compare/v3.3.2...v3.4.0)
- [github.com/pre-commit/mirrors-mypy: v1.2.0 → v1.3.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.2.0...v1.3.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index cd1eaaa..1ec5b0d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -23,7 +23,7 @@ repos:
       - id: flake8
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.2
+    rev: v3.4.0
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
@@ -34,7 +34,7 @@ repos:
       - id: autoflake
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.2.0
+    rev: v1.3.0
     hooks:
       - id: mypy
 

From 101625a5f71d2230050bbdb7441f7a08ee91b938 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 6 Jun 2023 16:54:34 -0700
Subject: [PATCH 13/13] Bump tensorflow from 2.9.3 to 2.11.1 (#65)

Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.9.3 to 2.11.1.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md)
- [Commits](https://github.com/tensorflow/tensorflow/compare/v2.9.3...v2.11.1)

---
updated-dependencies:
- dependency-name: tensorflow
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index c4c232c..03cfa84 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,3 @@
 pymatgen==2022.11.7
-tensorflow==2.9.3
+tensorflow==2.11.1
 ase==3.22.1