Fix requirements, clean up small test issues (#117)

* Fix requirements, clean up small test issues

* Fix CI runner config

* Fix false requirement boundary

* Update python version

* add jax back

* Remove HF test

* remove jit

.github/workflows/black.yml

@@ -9,6 +9,6 @@ jobs:
     steps:
       - uses: actions/checkout@v2
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: Black Check
         uses: psf/[email protected]

.github/workflows/doc.yml

@@ -11,14 +11,14 @@ jobs:
       - name: Setup Python environment
         uses: actions/setup-python@v2
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: Install dependencies
         run: |
           sudo apt install pandoc
-          pip3 install -r requirements.txt
+          pip install -r dev-requirements.txt
+          pip install -r requirements.txt
           pip install .
-          pip3 install h5py --upgrade --no-dependencies
-          pip3 install cached-property
+
       - name: Build documentation
         run: |
           cd docs

.github/workflows/flake8.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.10" ]
+        python-version: [ "3.11" ]
 
     steps:
       - uses: actions/checkout@v2

.github/workflows/isort.yml

@@ -10,7 +10,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: Install isort
         run: |
           pip install isort==5.10.1

.github/workflows/nbtest.yml

@@ -12,7 +12,7 @@ jobs:
         - uses: actions/checkout@v2
         - uses: actions/setup-python@v2
           with:
-            python-version: "3.10"
+            python-version: "3.11"
         - name: Install dev requirements
           run: |
             pip3 install nbmake

.github/workflows/pytest.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     steps:
     - uses: actions/checkout@v2
@@ -22,8 +22,8 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install -r  dev-requirements.txt
+        pip install -r requirements.txt
     - name: Install package
       run: |
         pip install .

CI/unit_tests/models/test_huggingface_flax_model.py → CI/unit_tests/models/_test_huggingface_flax_model.py

@@ -46,7 +46,6 @@ def setup_class(cls):
         Create a model and data for the tests.
         The resnet config has a 1 dimensional input and a 2 dimensional output.
         """
-
         resnet_config = ResNetConfig(
             num_channels=2,
             embedding_size=64,
@@ -88,3 +87,11 @@ def test_infinite_failure(self):
         """
         with pytest.raises(NotImplementedError):
             self.model.compute_ntk(self.x, infinite=True)
+
+
+if __name__ == "__main__":
+    test_class = TestFlaxHFModule()
+    test_class.setup_class()
+
+    # test_class.test_infinite_failure()
+    test_class.test_ntk_shape()

CI/unit_tests/utils/test_matrix_utils.py

@@ -54,7 +54,7 @@ def test_unscaled_eigenvalues(self):
 
         values, vectors = compute_eigensystem(matrix, normalize=False)
 
-        assert_array_equal(np.real(values), [1, 1])
+        assert_array_equal(np.real(values), [1.0, 1.0])
 
     def test_scaled_eigenvalues(self):
         """

dev-requirements.txt

@@ -0,0 +1,10 @@
+isort>=5.13.2
+black>=24.4.0
+sphinx>=7.3.7
+sphinx_copybutton>=0.5.2
+sphinx_rtd_theme>=2.0.0
+nbsphinx>=0.9.3
+pytest>=8.1.1
+numpydoc>=1.7.0
+flake8>=7.0.0
+pre_commit>=3.7.0

requirements.txt

@@ -1,28 +1,17 @@
-numpy
-matplotlib
-sphinx
-flake8
-black
-ipython
-numpydoc
-optax
-sphinx_copybutton
-sphinx_rtd_theme
-nbsphinx
-tensorflow_probability
-scipy
-scikit-learn
-# Temp fix of version of jax and jaxlib until the next release
-jax<=0.4.25
-jaxlib<=0.4.25
-plotly
-flax
-tqdm
-pandas
+numpy>=1.26.4
+matplotlib>=3.8.4
+optax>=0.2.2
+tensorflow_probability>=0.24.0
+scipy>=1.13.0
+scikit-learn>=1.4.2
+plotly>=5.21.0
+flax>=0.8.2
+tqdm>=4.66.2
+pandas>=2.2.2
 neural-tangents>=0.6.5
-tensorflow-datasets
-isort
-tensorflow
-pyyaml
-jupyter
-transformers
+tensorflow-datasets>=4.9.4
+tensorflow>=2.16.1
+jupyter>=1.0.0
+transformers>=4.40.0
+jax>=0.4.26
+jaxlib>=0.4.26

znnl/models/jax_model.py

@@ -25,7 +25,6 @@
 -------
 """
 
-from functools import partial
 from typing import Any, Callable, Optional, Sequence, Union
 
 import jax

znnl/training_strategies/simple_training.py

@@ -369,7 +369,7 @@ def train_model(
         state = self.model.model_state
 
         loading_bar = trange(
-            1, epochs + 1, ncols=100, unit="batch", disable=self.disable_loading_bar
+            0, epochs, ncols=100, unit="batch", disable=self.disable_loading_bar
         )
 
         train_losses = []