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* fix isort & black & toml-sort & sphinx error

* fix ci error

* fix ci error

* add comments

* Update Makefile

* change sphinx build command

* add auto-lint

* add black args

* format with black

* Auto Linting document

* fix ci error

---------

Co-authored-by: you-n-g <you-n-g@users.noreply.github.com>
Co-authored-by: Young <afe.young@gmail.com>
This commit is contained in:
Linlang
2024-07-26 12:12:16 +08:00
committed by GitHub
parent 45b7a169fe
commit c7cfd397ca
56 changed files with 604 additions and 475 deletions
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rdagent/utils/env.py
+14 -7
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@@ -144,16 +144,21 @@ class QlibDockerConf(DockerConf):
class DMDockerConf(DockerConf):
class Config:
env_prefix = "DM_DOCKER_"
env_prefix = "DM_DOCKER_"
build_from_dockerfile: bool = True
dockerfile_folder_path: Path = Path(__file__).parent.parent / "scenarios" / "data_mining" / "docker"
image: str = "local_dm:latest"
mount_path: str = "/workspace/dm_workspace/"
default_entry: str = "python train.py"
extra_volumes: dict = {Path("~/.rdagent/.data/physionet.org/files/mimic-eicu-fiddle-feature/1.0.0/FIDDLE_mimic3/").expanduser().resolve(): "/root/.data/"}
extra_volumes: dict = {
Path("~/.rdagent/.data/physionet.org/files/mimic-eicu-fiddle-feature/1.0.0/FIDDLE_mimic3/")
.expanduser()
.resolve(): "/root/.data/"
}
shm_size: str | None = "16g"
# physionet.org/files/mimic-eicu-fiddle-feature/1.0.0/FIDDLE_mimic3
class DockerEnv(Env[DockerConf]):
# TODO: Save the output into a specific file
@@ -181,9 +186,9 @@ class DockerEnv(Env[DockerConf]):
if not self.conf.enable_gpu:
return {}
gpu_kwargs = {
"device_requests": [
docker.types.DeviceRequest(count=-1, capabilities=[['gpu']])
] if self.conf.enable_gpu else None,
"device_requests": [docker.types.DeviceRequest(count=-1, capabilities=[["gpu"]])]
if self.conf.enable_gpu
else None,
}
try:
client.containers.run(self.conf.image, "nvidia-smi", **gpu_kwargs)
@@ -220,7 +225,7 @@ class DockerEnv(Env[DockerConf]):
# auto_remove=True, # remove too fast might cause the logs not to be get
network=self.conf.network,
shm_size=self.conf.shm_size,
**self._gpu_kwargs(client)
**self._gpu_kwargs(client),
)
logs = container.logs(stream=True)
for log in logs:
@@ -273,7 +278,9 @@ class DMDockerEnv(DockerEnv):
data_path = next(iter(self.conf.extra_volumes.keys()))
if not (Path(data_path)).exists():
logger.info("We are downloading!")
cmd = 'wget -r -N -c -np --user={} --password={} -P ~/.rdagent/.data/ https://physionet.org/files/mimic-eicu-fiddle-feature/1.0.0/'.format(username, password)
cmd = "wget -r -N -c -np --user={} --password={} -P ~/.rdagent/.data/ https://physionet.org/files/mimic-eicu-fiddle-feature/1.0.0/".format(
username, password
)
os.system(cmd)
else:
logger.info("Data already exists. Download skipped.")