Upgrade Nucleus to support TF 2.5.0.

PiperOrigin-RevId: 381386612

README.md

@@ -80,7 +80,7 @@ Note that install.sh extensively depends on apt-get, so it is unlikely to run
 without extensive modifications on non-Debian-based systems.
 
 Nucleus depends on TensorFlow. By default, install.sh will install a CPU-only
-version of a stable TensorFlow release (currently 2.4). If that isn't what you
+version of a stable TensorFlow release (currently 2.5). If that isn't what you
 want, there are several other options that can be enabled with a simple edit to
 `install.sh`.
 
@@ -94,9 +94,13 @@ bazel test -c opt $BAZEL_FLAGS nucleus/...
 
 ## Version
 
-This is Nucleus 0.5.8. Nucleus follows
+This is Nucleus 0.5.9. Nucleus follows
 [semantic versioning](https://semver.org/).
 
+New in 0.5.9:
+
+*   Upgrade to support TensorFlow 2.5.0 specifically.
+
 New in 0.5.8:
 
 *   Update `util/vis.py` to use updated channel names.

WORKSPACE

@@ -71,7 +71,6 @@ http_archive(
     ],
 )
 
-
 # bazel_skylib is now a required dependency of com_google_protobuf.
 http_archive(
     name = "bazel_skylib",
@@ -93,10 +92,33 @@ http_archive(
     ],
 )
 
-# Import all of the tensorflow dependencies.
-load("@org_tensorflow//tensorflow:workspace.bzl", "tf_workspace")
+http_archive(
+    name = "tf_toolchains",
+    sha256 = "794ec13d2fdbc0a6fd66bcffad63cb967448e93e018151a58bbfac9808883770",
+    strip_prefix = "toolchains-1.1.21",
+    urls = [
+        "http://mirror.tensorflow.org/github.com/tensorflow/toolchains/archive/v1.1.21.tar.gz",
+        "https://github.com/tensorflow/toolchains/archive/v1.1.21.tar.gz",
+    ],
+)
+
+# Import all of the tensorflow dependencies (see TF's WORKSPACE file for how
+# to do this correctly).
+load("@org_tensorflow//tensorflow:workspace3.bzl", "tf_workspace3")
+
+tf_workspace3()
+
+load("@org_tensorflow//tensorflow:workspace2.bzl", "tf_workspace2")
+
+tf_workspace2()
+
+load("@org_tensorflow//tensorflow:workspace1.bzl", "tf_workspace1")
+
+tf_workspace1()
+
+load("@org_tensorflow//tensorflow:workspace0.bzl", "tf_workspace0")
 
-tf_workspace(tf_repo_name = "org_tensorflow")
+tf_workspace0()
 
 new_local_repository(
     name = "clif",

install.sh

@@ -30,8 +30,8 @@
 # Global setting for nucleus builds
 # ------------------------------------------------------------------------------
 
-NUCLEUS_BAZEL_VERSION="3.1.0"
-NUCLEUS_TENSORFLOW_VERSION="2.4.0"
+NUCLEUS_BAZEL_VERSION="3.7.2"
+NUCLEUS_TENSORFLOW_VERSION="2.5.0"
 
 function note_build_stage {
   echo "========== [$(date)] Stage '${1}' starting"
@@ -158,13 +158,6 @@ export PYTHON_BIN_PATH=`which python3`
  echo | ./configure
  )
 
-# We use TensorFlow's .bazelrc as part of Nucleus's. In it they use a java
-# toolchain flag based on a definition in a BUILD file in the TF repo. This
-# causes that flag's usage to raise build errors when building Nucleus unless we
-# also include that BUILD file.
-mkdir -p third_party/toolchains/java
-cp ../tensorflow/third_party/toolchains/java/BUILD third_party/toolchains/java/
-
 echo "Done installing prereqs at $(date)!"
 
 if [[ "$#" -eq 0 ]] || [[ "$1" != "--prereqs_only" ]]; then

nucleus/pip_package/build_pip_package.sh

@@ -28,7 +28,7 @@ set -x
 
 # When changing NUCLEUS_VERSION, be sure to also change it in
 # egg_files/PKG-INFO.
-NUCLEUS_VERSION="0.5.8"
+NUCLEUS_VERSION="0.5.9"
 PACKAGE_NAME="google_nucleus-${NUCLEUS_VERSION}"
 PYTHON_VERSION="3.6"
 

nucleus/pip_package/egg_files/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: google-nucleus
-Version: 0.5.8
+Version: 0.5.9
 Summary: A library for reading and writing genomics data.
 Home-page: https://github.com/google/nucleus
 Author: The Genomics team in Google Brain
@@ -24,7 +24,7 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules