From 80507f26d57fda0b4c8898aeb007575072b8af78 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 1 May 2023 21:57:05 +0000
Subject: [PATCH 01/15] Bump pandas from 1.5.2 to 2.2.3

Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.5.2 to 2.2.3.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](https://github.com/pandas-dev/pandas/compare/v1.5.2...v2.2.3)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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

diff --git a/requirements.txt b/requirements.txt
index 81c0afa6..bd822828 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 tensorflow==2.11.0
-pandas==1.5.2
+pandas==2.2.3
 scikit-learn==1.3.2
 matminer==0.9.2
 numpy>=1.25

From af34c8ebff1a19998c861af02c9f4f2c04b1bfb7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 1 Jan 2024 21:02:47 +0000
Subject: [PATCH 02/15] Bump actions/setup-python from 4 to 5

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 18db3e03..b194fa5b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -20,7 +20,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
 
@@ -48,7 +48,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'

From ed81ca039cdb9017036b7afcc20e7f9d409e6dfa Mon Sep 17 00:00:00 2001
From: Matthew Evans <git@ml-evs.science>
Date: Sat, 26 Oct 2024 15:17:36 +0200
Subject: [PATCH 03/15] Use `pip` cache for linting step

---
 .github/workflows/ci.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b194fa5b..53f7e3a3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -23,6 +23,9 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: '3.10'
+        cache: pip
+        cache-dependency-path: |
+          **/requirements*.txt
 
     - name: Install pre-commit
       run: |

From aa1e0a437c9c89d07625e1e341acec08145cb3e5 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 1 Oct 2023 21:37:16 +0000
Subject: [PATCH 04/15] Bump actions/checkout from 3 to 4

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v3...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 53f7e3a3..1cbec06e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -17,7 +17,7 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python 3.10
       uses: actions/setup-python@v5
@@ -48,7 +48,7 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5

From 80ad9e9668ff325319ed3a3c655ee75f1409b04c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 2 Apr 2024 15:38:59 +0000
Subject: [PATCH 05/15] Bump tensorflow from 2.11.0 to 2.16.1

Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.11.0 to 2.16.1.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/v2.16.1/RELEASE.md)
- [Commits](https://github.com/tensorflow/tensorflow/compare/v2.11.0...v2.16.1)

---
updated-dependencies:
- dependency-name: tensorflow
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt |  2 +-
 setup.py         | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index bd822828..158bf22a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-tensorflow==2.11.0
+tensorflow==2.16.1
 pandas==2.2.3
 scikit-learn==1.3.2
 matminer==0.9.2
diff --git a/setup.py b/setup.py
index 28781da1..6e4f6700 100644
--- a/setup.py
+++ b/setup.py
@@ -32,12 +32,12 @@
     include_package_data=True,
     packages=setuptools.find_packages(),
     install_requires=[
-        "pandas~=1.5",
-        "tensorflow~=2.10,<2.12",
-        "pymatgen>=2023",
-        "matminer~=0.9",
-        "numpy>=1.24",
-        "scikit-learn~=1.3",
+        "pandas <= 1.5, < 3",
+        "tensorflow ~= 2.10, < 2.17",
+        "pymatgen >= 2023",
+        "matminer ~= 0.9",
+        "numpy >= 1.24",
+        "scikit-learn ~= 1.3",
     ],
     tests_require=tests_require,
     test_suite="modnet.tests",

From c0af72cd4923403478b7feb58b793fe4b29f76e6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sat, 1 Jun 2024 21:39:16 +0000
Subject: [PATCH 06/15] Bump scikit-learn from 1.3.2 to 1.5.2

Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 1.3.2 to 1.5.2.
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](https://github.com/scikit-learn/scikit-learn/compare/1.3.2...1.5.2)

---
updated-dependencies:
- dependency-name: scikit-learn
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 158bf22a..fb507172 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,8 @@
 tensorflow==2.16.1
 pandas==2.2.3
-scikit-learn==1.3.2
+tensorflow==2.11.0
+pandas==1.5.2
+scikit-learn==1.5.0
 matminer==0.9.2
 numpy>=1.25
 pymatgen==2024.3.1
-scikit-learn==1.3.2

From fe8918510fdf7bfbf5d0e94668438f293d52cfe6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sat, 1 Jun 2024 21:39:07 +0000
Subject: [PATCH 07/15] Bump pymatgen from 2024.3.1 to 2024.5.31

Bumps [pymatgen](https://github.com/materialsproject/pymatgen) from 2024.3.1 to 2024.5.31.
- [Release notes](https://github.com/materialsproject/pymatgen/releases)
- [Changelog](https://github.com/materialsproject/pymatgen/blob/master/docs/CHANGES.md)
- [Commits](https://github.com/materialsproject/pymatgen/compare/v2024.3.1...v2024.5.31)

---
updated-dependencies:
- dependency-name: pymatgen
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index fb507172..a7c636ba 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,8 +1,6 @@
 tensorflow==2.16.1
 pandas==2.2.3
-tensorflow==2.11.0
-pandas==1.5.2
 scikit-learn==1.5.0
 matminer==0.9.2
 numpy>=1.25
-pymatgen==2024.3.1
+pymatgen==2024.5.31

From f33ee6b37d1f1673a84410886d25cd433931ee07 Mon Sep 17 00:00:00 2001
From: Matthew Evans <git@ml-evs.science>
Date: Sat, 26 Oct 2024 15:51:40 +0200
Subject: [PATCH 08/15] Remove deprecated Bayesian model tests from CI run

---
 .github/workflows/ci.yml   | 6 +++---
 modnet/tests/test_model.py | 3 +++
 pytest.ini                 | 1 +
 setup.py                   | 2 +-
 4 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1cbec06e..37b62ee1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -31,7 +31,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -U setuptools wheel
-        pip install .[dev,bayesian]
+        pip install .[dev]
 
     - name: Run pre-commit
       run: |
@@ -62,9 +62,9 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
-        pip install .[test,dev,bayesian]
+        pip install .[test,dev]
 
     - name: Run tests with pytest
       run: |
         # run tests with pytest, reporting coverage and timings
-        pytest -m "not slow" -rs -vvv  --durations=0 --cov=./modnet/
+        pytest -m "not slow" -m "not deprecated" -rs -vvv  --durations=0 --cov=./modnet/
diff --git a/modnet/tests/test_model.py b/modnet/tests/test_model.py
index c4853e07..1742b466 100644
--- a/modnet/tests/test_model.py
+++ b/modnet/tests/test_model.py
@@ -142,6 +142,7 @@ def test_model_integration(subset_moddata, tf_session):
     assert not np.isnan(model.evaluate(data))
 
 
+@pytest.mark.deprecated
 def test_train_small_bayesian_single_target(subset_moddata, tf_session):
     """Tests the single target training."""
     from modnet.models import BayesianMODNetModel
@@ -165,6 +166,7 @@ def test_train_small_bayesian_single_target(subset_moddata, tf_session):
     assert not np.isnan(model.evaluate(data))
 
 
+@pytest.mark.deprecated
 def test_train_small_bayesian_single_target_classif(subset_moddata, tf_session):
     """Tests the single target training."""
     from modnet.models import BayesianMODNetModel
@@ -196,6 +198,7 @@ def is_metal(egap):
     assert not np.isnan(model.evaluate(data))
 
 
+@pytest.mark.deprecated
 def test_train_small_bayesian_multi_target(subset_moddata, tf_session):
     """Tests the multi-target training."""
     from modnet.models import BayesianMODNetModel
diff --git a/pytest.ini b/pytest.ini
index 76178536..c382c881 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,3 +1,4 @@
 [pytest]
 markers =
     slow: marks tests as slow (deselect with '-m "not slow"')
+    deprecated: mark tests as deprecated (deselect with -m "not deprecated")
diff --git a/setup.py b/setup.py
index 6e4f6700..9ed48722 100644
--- a/setup.py
+++ b/setup.py
@@ -42,7 +42,7 @@
     tests_require=tests_require,
     test_suite="modnet.tests",
     extras_require={
-        "bayesian": ["tensorflow-probability==0.18"],
+        "bayesian": ["tensorflow-probability==0.18", "tensorflow == 2.11.*"],
         "test": tests_require,
         "dev": dev_require,
     },

From 4b31560dde2a342f26728fddabbf1ead13d72314 Mon Sep 17 00:00:00 2001
From: Matthew Evans <git@ml-evs.science>
Date: Sat, 26 Oct 2024 16:34:05 +0200
Subject: [PATCH 09/15] Add CI debug print of installed versions

---
 .github/workflows/ci.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 37b62ee1..dbbd67a9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -64,6 +64,10 @@ jobs:
         pip install -r requirements.txt
         pip install .[test,dev]
 
+    - name: List installed versions
+      run: |
+        pip list
+
     - name: Run tests with pytest
       run: |
         # run tests with pytest, reporting coverage and timings

From ed08b698786d00ee9ba4d7712980418faa1fc615 Mon Sep 17 00:00:00 2001
From: Matthew Evans <git@ml-evs.science>
Date: Sat, 26 Oct 2024 16:40:01 +0200
Subject: [PATCH 10/15] Downgrade tensorflow to avoid needing keras downgrade

---
 requirements.txt | 2 +-
 setup.py         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index a7c636ba..24046bcd 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-tensorflow==2.16.1
+tensorflow==2.15.1
 pandas==2.2.3
 scikit-learn==1.5.0
 matminer==0.9.2
diff --git a/setup.py b/setup.py
index 9ed48722..849a3396 100644
--- a/setup.py
+++ b/setup.py
@@ -33,7 +33,7 @@
     packages=setuptools.find_packages(),
     install_requires=[
         "pandas <= 1.5, < 3",
-        "tensorflow ~= 2.10, < 2.17",
+        "tensorflow ~= 2.10, < 2.16",
         "pymatgen >= 2023",
         "matminer ~= 0.9",
         "numpy >= 1.24",

From c63084237c0cfd49aaff76c3a78fc95970e379f9 Mon Sep 17 00:00:00 2001
From: Matthew Evans <git@ml-evs.science>
Date: Sat, 26 Oct 2024 17:00:16 +0200
Subject: [PATCH 11/15] Try to deprecate 'learning_rate' again

---
 modnet/models/vanilla.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/modnet/models/vanilla.py b/modnet/models/vanilla.py
index 56ebd7f6..6eb8b4ff 100644
--- a/modnet/models/vanilla.py
+++ b/modnet/models/vanilla.py
@@ -1343,6 +1343,9 @@ def fit(
         }
 
         fit_params.update(fit_params_kw)
+        if "learning_rate" in fit_params:
+            fit_params.pop("learning_rate")
+            warnings.warn("learning_rate is deprecated, use lr instead.")
 
         if loss is None:
             loss = "mse"

From 96fb84d4d5a25be62e2efec6e660a4ee52b882df Mon Sep 17 00:00:00 2001
From: Matthew Evans <git@ml-evs.science>
Date: Sun, 17 Nov 2024 13:06:23 +0000
Subject: [PATCH 12/15] Take all models from ensemble when refitting in
 `fit_preset`

No idea how this wasn't triggered in the tests previously...
---
 modnet/models/ensemble.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modnet/models/ensemble.py b/modnet/models/ensemble.py
index 880d09e9..dc2fce8e 100644
--- a/modnet/models/ensemble.py
+++ b/modnet/models/ensemble.py
@@ -438,7 +438,7 @@ def fit_preset(
             for i in range(n_splits):
                 best_5_idx = np.argsort(val_losses[:, i])[:5]
                 for idx in best_5_idx:
-                    final_models += models[idx][i].model
+                    final_models.extend(models[idx][i].models)
             self.__init__(modnet_models=final_models)
 
         os.environ["TF_CPP_MIN_LOG_LEVEL"] = "0"  # reset

From 0d09c57d5ccb3b1170fff9301aece2ee2c441601 Mon Sep 17 00:00:00 2001
From: Matthew Evans <git@ml-evs.science>
Date: Mon, 25 Nov 2024 10:55:31 +0000
Subject: [PATCH 13/15] Add test for ensemble multi-target with custom loss

---
 modnet/tests/test_model.py | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/modnet/tests/test_model.py b/modnet/tests/test_model.py
index 1742b466..646b94d4 100644
--- a/modnet/tests/test_model.py
+++ b/modnet/tests/test_model.py
@@ -303,6 +303,41 @@ def test_train_small_bootstrap_multi_target(small_moddata, tf_session):
     model.predict(data, return_unc=True)
 
 
+def test_train_small_bootstrap_custom_loss_multi_target(small_moddata, tf_session):
+    """Tests a multi-target ensemble model with a custom loss per target,
+    modified from Hao Wu's example.
+
+    """
+    from modnet.models import EnsembleMODNetModel
+    import tensorflow as tf
+
+    def custom_loss(y_true, y_pred):
+        loss1 = y_pred - y_true
+        return tf.reduce_mean(
+            tf.math.abs(
+                tf.boolean_mask(loss1, tf.reduce_all(~tf.math.is_nan(loss1), axis=1))
+            )
+        )
+
+    data = small_moddata
+    # set 'optimal' features manually
+    data.optimal_features = [
+        col for col in data.df_featurized.columns if col.startswith("ElementProperty")
+    ]
+
+    model = EnsembleMODNetModel(
+        [[["eform", "egap"]]],
+        weights={"eform": 1, "egap": 1},
+        num_neurons=[[16], [8], [8], [4]],
+        n_feat=10,
+        n_models=3,
+        bootstrap=True,
+    )
+
+    model.fit(data, loss=[custom_loss, custom_loss], epochs=2)
+    model.predict(data, return_unc=True)
+
+
 @pytest.mark.slow
 def test_train_small_bootstrap_presets(small_moddata, tf_session):
     """Tests the `fit_preset()` method."""

From f602fb37a2ef496f6b4ede7b8c2308e01d4e2553 Mon Sep 17 00:00:00 2001
From: Matthew Evans <git@ml-evs.science>
Date: Mon, 25 Nov 2024 10:55:45 +0000
Subject: [PATCH 14/15] Add test for GA with mulit-target + custom loss

---
 modnet/tests/test_hyper_opt.py | 38 ++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/modnet/tests/test_hyper_opt.py b/modnet/tests/test_hyper_opt.py
index dc117b74..7c4ed851 100644
--- a/modnet/tests/test_hyper_opt.py
+++ b/modnet/tests/test_hyper_opt.py
@@ -29,3 +29,41 @@ def test_ga(small_moddata, tf_session):
 
     assert type(model) is EnsembleMODNetModel
     assert len(model.models) == 1
+
+
+def test_ga_multi_target(small_moddata, tf_session):
+    """Tests the modnet.hyper_opt.FitGenetic algorithm."""
+    from modnet.hyper_opt import FitGenetic
+
+    data = small_moddata
+    # set 'optimal' features manually
+    data.optimal_features = [
+        col for col in data.df_featurized.columns if col.startswith("ElementProperty")
+    ]
+
+    def custom_loss(y_true, y_pred):
+        import tensorflow as tf
+        loss1 = y_pred - y_true
+        return tf.reduce_mean(
+            tf.math.abs(
+                tf.boolean_mask(loss1, tf.reduce_all(~tf.math.is_nan(loss1), axis=1))
+            )
+        )
+
+    ga = FitGenetic(data)
+    model = ga.run(
+        size_pop=2,
+        num_generations=2,
+        prob_mut=0.5,
+        nested=2,
+        n_jobs=2,
+        early_stopping=2,
+        refit=1,
+        loss=[custom_loss, custom_loss],
+        fast=True,
+    )
+
+    from modnet.models import EnsembleMODNetModel
+
+    assert type(model) is EnsembleMODNetModel
+    assert len(model.models) == 1

From 32868505a9720dee928288b7ae72365c66f6df00 Mon Sep 17 00:00:00 2001
From: Matthew Evans <git@ml-evs.science>
Date: Mon, 25 Nov 2024 12:41:57 +0000
Subject: [PATCH 15/15] Add test case for simple model with custom loss

---
 modnet/tests/test_model.py | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/modnet/tests/test_model.py b/modnet/tests/test_model.py
index 646b94d4..1bcd4464 100644
--- a/modnet/tests/test_model.py
+++ b/modnet/tests/test_model.py
@@ -75,6 +75,38 @@ def test_train_small_model_multi_target(subset_moddata, tf_session):
     model.predict(data)
     assert not np.isnan(model.evaluate(data))
 
+def test_train_small_model_multi_target_custom_loss(subset_moddata, tf_session):
+    """Tests the multi-target training."""
+    from modnet.models import MODNetModel
+    from functools import partial
+    import tensorflow as tf
+
+    data = subset_moddata
+    # set 'optimal' features manually
+    data.optimal_features = [
+        col for col in data.df_featurized.columns if col.startswith("ElementProperty")
+    ]
+
+    def custom_loss(y_true, y_pred, rescale=1):
+        loss1 = y_pred - y_true
+        return rescale * tf.reduce_mean(
+            tf.math.abs(
+                tf.boolean_mask(loss1, tf.reduce_all(~tf.math.is_nan(loss1), axis=1))
+            )
+        )
+
+    model = MODNetModel(
+        [[["eform", "egap"]]],
+        weights={"eform": 1, "egap": 1},
+        num_neurons=[[16], [8], [8], [4]],
+        n_feat=10,
+    )
+
+    model.fit(data, loss=[partial(custom_loss, rescale=10), custom_loss], epochs=2)
+    model.predict(data)
+    breakpoint()
+    assert not np.isnan(model.evaluate(data))
+
 
 def test_train_small_model_presets(subset_moddata, tf_session):
     """Tests the `fit_preset()` method."""