I am trying to run this code using Bazel: https://github.com/google/in-silico-labeling. This is the associated Bazel BUILD file (I have added the appropriate bazel python rules, including a "py_runtime" interpreter path, "default_python_version", and "srcs_version" where applicable):
package(default_visibility = ["//visibility:public"])
py_runtime(
name="python-3.5.2",
files=[],
interpreter_path="/usr/bin/python3.5"
)
py_library(
name = "tensorcheck",
srcs = ["tensorcheck.py"],
srcs_version="PY3",
)
py_library(
name = "util",
srcs = [
"util.py",
],
srcs_version="PY3",
)
py_library(
name = "ops",
srcs = ["ops.py"],
deps = [
":tensorcheck",
],
srcs_version="PY3",
)
py_library(
name = "augment",
srcs = [
"augment.py",
],
deps = [
":ops",
":util",
],
srcs_version="PY3",
)
py_library(
name = "visualize",
srcs = [
"visualize.py",
],
deps = [
":ops",
":util",
],
srcs_version="PY3",
)
py_library(
name = "data_provider",
srcs = [
"data_provider.py",
],
deps = [
":ops",
":tensorcheck",
":util",
],
srcs_version="PY3",
)
py_library(
name = "controller",
srcs = [
"controller.py",
],
deps = [
":augment",
":data_provider",
":ops",
":tensorcheck",
":util",
":visualize",
"//isl/models:model_util",
],
srcs_version="PY3",
)
py_library(
name = "infer",
srcs = [
"infer.py",
],
deps = [
":augment",
":controller",
":data_provider",
":ops",
":tensorcheck",
":util",
":visualize",
"//isl/models:model_util",
],
srcs_version="PY3",
)
py_binary(
name = "launch",
srcs = [
"launch.py",
],
deps = [
":augment",
":controller",
":data_provider",
":infer",
":ops",
":util",
"//isl/models:concordance",
"//isl/models:model_util",
],
default_python_version="PY3",
srcs_version="PY3",
)
filegroup(
name = "testdata",
srcs = glob([
"testdata/**/*.png",
"testdata/*png",
]) + [
"testdata/research_logo.jpg",
],
)
py_library(
name = "test_util",
srcs = ["test_util.py"],
data = [
":testdata",
],
deps = [
":data_provider",
":ops",
":util",
],
srcs_version="PY3",
)
py_test(
name = "tensorcheck_test",
srcs = ["tensorcheck_test.py"],
# Enable the tensorcheck module.
args = ["--tensorcheck_enable_checks"],
deps = [
":tensorcheck",
":test_util",
],
default_python_version="PY3",
srcs_version="PY3",
)
py_test(
name = "util_test",
srcs = [
"util_test.py",
],
deps = [
":test_util",
":util",
],
default_python_version="PY3",
srcs_version="PY3",
)
py_test(
name = "controller_test",
size = "enormous",
srcs = ["controller_test.py"],
deps = [
":augment",
":controller",
":data_provider",
":test_util",
":util",
"//isl/models:fovea",
],
default_python_version="PY3",
srcs_version="PY3",
)
py_test(
name = "ops_test",
size = "large",
srcs = ["ops_test.py"],
deps = [
":ops",
":test_util",
],
default_python_version="PY3",
srcs_version="PY3",
)
py_test(
name = "augment_test",
srcs = ["augment_test.py"],
deps = [
":augment",
":test_util",
":util",
],
default_python_version="PY3",
srcs_version="PY3",
)
py_test(
name = "visualize_test",
size = "large",
srcs = ["visualize_test.py"],
deps = [
":data_provider",
":test_util",
":util",
":visualize",
],
default_python_version="PY3",
srcs_version="PY3",
)
py_test(
name = "data_provider_test",
srcs = ["data_provider_test.py"],
deps = [
":data_provider",
":test_util",
":util",
],
default_python_version="PY3",
srcs_version="PY3",
)
I have also edited a second BUILD file located in the "models" folder of the repository:
package(default_visibility = ["//visibility:public"])
py_runtime(
name="python-3.5.2",
files=[],
interpreter_path="/usr/bin/python3.5"
)
py_library(
name = "model_util",
srcs = ["model_util.py"],
deps = [
"//isl:tensorcheck",
"//isl:util",
],
srcs_version="PY3",
)
py_library(
name = "fovea",
srcs = ["fovea.py"],
deps = [
":model_util",
"//isl:tensorcheck",
"//isl:util",
],
srcs_version="PY3",
)
py_library(
name = "concordance",
srcs = ["concordance.py"],
deps = [
":model_util",
"//isl:tensorcheck",
"//isl:util",
],
srcs_version="PY3",
)
py_test(
name = "model_test",
size = "large",
srcs = ["model_test.py"],
deps = [
":fovea",
":model_util",
"//isl:controller",
"//isl:test_util",
],
default_python_version="PY3",
srcs_version="PY3",
)
However, I get the following error when running the program through Bazel:
bazel run isl:launch -- \ --alsologtostderr \ --base_directory $BASE_DIRECTORY \ --mode EVAL_EVAL \ --metric INFER_FULL \ --stitch_crop_size 150 \ restore_directory $/data1/adamw/insilico_labeling/checkpoints \ read_pngs \ dataset_eval_directory $/data1/adamw/insilico_labeling/data_sample/condition_b_sample \ infer_channel_whitelist DAPI_CONFOCAL,MAP2_CONFOCAL,NFH_CONFOCAL
INFO: Analysed target //isl:launch (1 packages loaded).
INFO: Found 1 target...
Target //isl:launch up-to-date:
bazel-out/k8-py3-fastbuild/bin/isl/launch
INFO: Elapsed time: 0.318s, Critical Path: 0.00s
INFO: 0 processes.
INFO: Build completed successfully, 1 total action
INFO: Running command line: bazel-out/k8-py3-fastbuild/bin/isl/launch ' --alsologtostderr' ' --base_directory' ' --mode' EVAL_EVAL ' --metric' INFER_FULL ' --stitch_crop_size' 150 ' restore_directory' '$/data1/adamw/insilico_labeling/checkpoints' ' read_pngs' ' dataset_eval_directory' '$/data1/adamw/insilico_labeling/data_sample/condition_b_sample' ' infer_cINFO: Build completed successfully, 1 total action
File "/home/adam/.cache/bazel/_bazel_adam/3c24d2105da2efbf30d96eb3fd97126b/execroot/__main__/bazel-out/k8-py3-fastbuild/bin/isl/launch.runfiles/__main__/isl/launch.py", line 199
def get_z_values() -> List[float]:
^
SyntaxError: invalid syntax
Am I missing something in the build file or command line? I have seen that "--force_python" may be deprecated but haven't tried this in combination with the python rules.
