cherry-pick h5py issue fix (mlflow#3671)

* cherry-pick h5py issue Signed-off-by: harupy <17039389+harupy@users.noreply.github.com> * empty Signed-off-by: harupy <17039389+harupy@users.noreply.github.com>
simonvanbernem · Nov 11, 2020 · 4582e46 · 4582e46
1 parent 93e505b
commit 4582e46
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Showing 4 changed files with 13 additions and 5 deletions.
diff --git a/dev/extra-ml-requirements.txt b/dev/extra-ml-requirements.txt
@@ -5,7 +5,8 @@
 azureml-sdk==1.2.0
 # Required by mlflow.keras
 keras==2.3.1
-# Pin h5py < 3.0.0 to avoid this issue: https://github.com/h5py/h5py/issues/1732
+# Pin h5py < 3.0.0 to avoid this issue: https://github.com/tensorflow/tensorflow/issues/44467
+# TODO: unpin after we use tensorflow >= 2.4
 h5py<3.0.0
 # Required by mlflow.sklearn
 scikit-learn

diff --git a/mlflow/R/mlflow/.create-test-env.R b/mlflow/R/mlflow/.create-test-env.R
@@ -7,7 +7,8 @@ library(reticulate)
 use_condaenv(mlflow:::mlflow_conda_env_name())
 # pinning tensorflow version to 1.14 until test_keras_model.R is fixed
 keras::install_keras(method = "conda", envname = mlflow:::mlflow_conda_env_name(), tensorflow="1.15.2")
-# pinning h5py < 3.0.0 to avoid this issue: https://github.com/h5py/h5py/issues/1732
+# pinning h5py < 3.0.0 to avoid this issue:  https://github.com/tensorflow/tensorflow/issues/44467
+# TODO: unpin after we use tensorflow >= 2.4
 reticulate::conda_install("'h5py<3.0.0'", envname = mlflow:::mlflow_conda_env_name(), pip = TRUE)
 reticulate::conda_install(Sys.getenv("MLFLOW_HOME", "../../../../."), envname = mlflow:::mlflow_conda_env_name(), pip = TRUE)
 reticulate::conda_install("xgboost", envname = mlflow:::mlflow_conda_env_name())

diff --git a/mlflow/keras.py b/mlflow/keras.py
@@ -74,6 +74,11 @@ def get_default_conda_env(include_cloudpickle=False, keras_module=None):
     else:
         pip_deps.append("tensorflow=={}".format(tf.__version__))
 
+    # Tensorflow<2.4 does not work with h5py>=3.0.0
+    # see https://github.com/tensorflow/tensorflow/issues/44467
+    if LooseVersion(tf.__version__) < LooseVersion("2.4"):
+        pip_deps.append("h5py<3.0.0")
+
     return _mlflow_conda_env(
         additional_conda_deps=conda_deps,
         additional_pip_deps=pip_deps,

diff --git a/tests/keras/test_keras_model_export.py b/tests/keras/test_keras_model_export.py
@@ -210,8 +210,10 @@ def _import_module(name, **kwargs):
             assert x == b
 
 
-@pytest.mark.skip("Unskip this test once https://github.com/h5py/h5py/issues/1732 is fixed")
-@pytest.mark.parametrize("build_model", [model, tf_keras_model])
+@pytest.mark.parametrize(
+    "build_model,save_format",
+    [(model, None), (tf_keras_model, None), (tf_keras_model, "h5"), (tf_keras_model, "tf")],
+)
 @pytest.mark.large
 def test_model_save_load(build_model, model_path, data):
     x, _ = data
@@ -269,7 +271,6 @@ def test_signature_and_examples_are_saved_correctly(model, data):
                     assert all((_read_example(mlflow_model, path) == example).all())
 
 
-@pytest.mark.skip("Unskip this test once https://github.com/h5py/h5py/issues/1732 is fixed")
 @pytest.mark.large
 def test_custom_model_save_load(custom_model, custom_layer, data, custom_predicted, model_path):
     x, _ = data