physics/deepdog
2
0
Fork 0
Code Issues 2 Pull Requests 9 Projects Releases Wiki Activity

feat: better management of cli wrapper

Browse Source
This commit is contained in:
Deepak Mallubhotla 2024-04-27 23:04:33 -05:00
parent 4b2e573715
commit b0ad4bead0
Signed by: deepak
GPG Key ID: BEBAEBF28083E022
6 changed files with 110 additions and 46 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
deepdog/cli/probs/__init__.py
View File

@ -1,5 +1,5 @@
from deepdog.cli.probs.main import main
from deepdog.cli.probs.main import wrapped_main
__all__ = [
"main",
"wrapped_main",
]

4
deepdog/cli/probs/args.py
View File

@ -27,8 +27,8 @@ def parse_args() -> argparse.Namespace:
)
parser.add_argument(
"--indexify-json",
help="A json file with the indexify config for parsing job indexes",
default="indexes.json",
help="A json file with the indexify config for parsing job indexes. Will skip if not present",
default="",
)
parser.add_argument(
"--seed-index",

47
deepdog/cli/probs/dicts.py
View File

@ -2,6 +2,7 @@ import typing
from deepdog.results import BayesrunOutput
import logging
import csv
import tqdm
_logger = logging.getLogger(__name__)
@ -21,7 +22,8 @@ def build_model_dict(
typing.Tuple, typing.Dict[typing.Tuple, typing.Dict["str", typing.Any]]
] = {}
for out in bayes_outputs:
_logger.info("building model dict")
for out in tqdm.tqdm(bayes_outputs, desc="reading outputs", leave=False):
for model_result in out.results:
model_key = tuple(v for v in model_result.parsed_model_keys.values())
if model_key not in model_dict:
@ -88,10 +90,21 @@ def write_uncoalesced_dict(
def coalesced_dict(
uncoalesced_model_dict: typing.Dict[
typing.Tuple, typing.Dict[typing.Tuple, typing.Dict["str", typing.Any]]
]
],
minimum_count: float = 0.1,
):
"""
pass in uncoalesced dict
the minimum_count field is what we use to make sure our probs are never zero
"""
coalesced_dict = {}
# we are already iterating so for no reason because performance really doesn't matter let's count the keys ourselves
num_keys = 0
# first pass coalesce
for model_key, model_dict in uncoalesced_model_dict.items():
num_keys += 1
for calculation in model_dict.values():
if model_key not in coalesced_dict:
coalesced_dict[model_key] = {
@ -104,6 +117,33 @@ def coalesced_dict(
sub_dict["calculations_coalesced"] += 1
sub_dict["count"] += calculation["count"]
sub_dict["success"] += calculation["success"]
# second pass do probability calculation
prior = 1 / num_keys
_logger.info(f"Got {num_keys} model keys, so our prior will be {prior}")
total_weight = 0
for coalesced_model_dict in coalesced_dict.values():
model_weight = (
max(minimum_count, coalesced_model_dict["success"])
/ coalesced_model_dict["count"]
) * prior
total_weight += model_weight
total_prob = 0
for coalesced_model_dict in coalesced_dict.values():
model_weight = (
max(minimum_count, coalesced_model_dict["success"])
/ coalesced_model_dict["count"]
)
prob = model_weight * prior / total_weight
coalesced_model_dict["prob"] = prob
total_prob += prob
_logger.debug(
f"Got a total probability of {total_prob}, which should be close to 1 up to float/rounding error"
)
return coalesced_dict
@ -120,7 +160,7 @@ def write_coalesced_dict(
_logger.info(f"Detected model field names {model_field_names}")
collected_fieldnames = list(model_field_names)
collected_fieldnames.extend(["calculations_coalesced", "success", "count"])
collected_fieldnames.extend(["calculations_coalesced", "success", "count", "prob"])
with open(coalesced_output_filename, "w", newline="") as coalesced_output_file:
writer = csv.DictWriter(coalesced_output_file, fieldnames=collected_fieldnames)
writer.writeheader()
@ -132,6 +172,7 @@ def write_coalesced_dict(
"calculations_coalesced": model_dict["calculations_coalesced"],
"success": model_dict["success"],
"count": model_dict["count"],
"prob": model_dict["prob"],
}
)
writer.writerow(row)

89
deepdog/cli/probs/main.py
View File

@ -6,6 +6,9 @@ import deepdog.cli.probs.dicts
import deepdog.results
import deepdog.indexify
import pathlib
import tqdm
import tqdm.contrib.logging
_logger = logging.getLogger(__name__)
@ -28,53 +31,65 @@ def set_up_logging(log_file: str):
logging.captureWarnings(True)
def wrapped_main(args: argparse.Namespace):
def main(args: argparse.Namespace):
"""
Main function with passed in arguments and no additional logging setup in case we want to extract out later
"""
_logger.info(f"args: {args}")
if args.coalesced_keys:
raise NotImplementedError(
"Currently not supporting coalesced keys, but maybe in future"
with tqdm.contrib.logging.logging_redirect_tqdm():
_logger.info(f"args: {args}")
try:
if args.coalesced_keys:
raise NotImplementedError(
"Currently not supporting coalesced keys, but maybe in future"
)
except AttributeError:
# we don't care if this is missing because we don't actually want it to be there
pass
indexifier = None
if args.indexify_json:
with open(args.indexify_json, "r") as indexify_json_file:
indexify_data = json.load(indexify_json_file)
if args.seed_index > 0:
indexify_data[args.seed_fieldname] = list(range(args.seed_index))
# _logger.debug(f"Indexifier data looks like {indexify_data}")
indexifier = deepdog.indexify.Indexifier(indexify_data)
bayes_dir = pathlib.Path(args.bayesrun_directory)
out_files = [f for f in bayes_dir.iterdir() if f.name.endswith("bayesrun.csv")]
_logger.info(
f"Reading {len(out_files)} bayesrun.csv files in directory {args.bayesrun_directory}"
)
with open(args.indexify_json, "r") as indexify_json_file:
indexify_data = json.load(indexify_json_file)
if args.seed_index > 0:
indexify_data[args.seed_fieldname] = list(range(args.seed_index))
# _logger.debug(f"Indexifier data looks like {indexify_data}")
indexifier = deepdog.indexify.Indexifier(indexify_data)
# _logger.info(out_files)
parsed_output_files = [
deepdog.results.read_output_file(f, indexifier)
for f in tqdm.tqdm(out_files, desc="reading files", leave=False)
]
bayes_dir = pathlib.Path(args.bayesrun_directory)
out_files = [f for f in bayes_dir.iterdir() if f.name.endswith("bayesrun.csv")]
_logger.info(
f"Found {len(out_files)} bayesrun.csv files in directory {args.bayesrun_directory}"
)
# _logger.info(out_files)
parsed_output_files = [
deepdog.results.read_output_file(f, indexifier) for f in out_files
]
_logger.info("building uncoalesced dict")
uncoalesced_dict = deepdog.cli.probs.dicts.build_model_dict(parsed_output_files)
_logger.info("building uncoalesced dict")
uncoalesced_dict = deepdog.cli.probs.dicts.build_model_dict(parsed_output_files)
if "uncoalesced_outfile" in args and args.uncoalesced_outfile:
deepdog.cli.probs.dicts.write_uncoalesced_dict(
args.uncoalesced_outfile, uncoalesced_dict
)
else:
_logger.info("Skipping writing uncoalesced")
if args.uncoalesced_outfile:
deepdog.cli.probs.dicts.write_uncoalesced_dict(
args.uncoalesced_outfile, uncoalesced_dict
)
else:
_logger.info("Skipping writing uncoalesced")
_logger.info("building coalesced dict")
coalesced = deepdog.cli.probs.dicts.coalesced_dict(uncoalesced_dict)
_logger.info("building coalesced dict")
coalesced = deepdog.cli.probs.dicts.coalesced_dict(uncoalesced_dict)
if args.coalesced_outfile:
deepdog.cli.probs.dicts.write_coalesced_dict(args.coalesced_outfile, coalesced)
else:
_logger.info("Skipping writing coalesced")
if "coalesced_outfile" in args and args.coalesced_outfile:
deepdog.cli.probs.dicts.write_coalesced_dict(
args.coalesced_outfile, coalesced
)
else:
_logger.info("Skipping writing coalesced")
def main():
def wrapped_main():
args = deepdog.cli.probs.args.parse_args()
set_up_logging(args.log_file)
wrapped_main(args)
main(args)

2
poetry.lock generated
View File

@ -1220,4 +1220,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
[metadata]
lock-version = "2.0"
python-versions = ">=3.8.1,<3.10"
content-hash = "b7f33da5b5a2af6bcb2a4c95cf391d04a76047d4f7e5c105b7cc38c73563fa51"
content-hash = "828610d9447294e707a6df2affb6ee7947e2be3b567371217265a8b94a9768f6"

10
pyproject.toml
View File

@ -9,6 +9,7 @@ python = ">=3.8.1,<3.10"
pdme = "^0.9.3"
numpy = "1.22.3"
scipy = "1.10"
tqdm = "^4.66.2"
[tool.poetry.dev-dependencies]
pytest = ">=6"
@ -20,7 +21,7 @@ black = "^22.3.0"
syrupy = "^4.0.8"
[tool.poetry.scripts]
probs = "deepdog.cli.probs:main"
probs = "deepdog.cli.probs:wrapped_main"
[build-system]
requires = ["poetry-core>=1.0.0"]
@ -41,6 +42,13 @@ module = [
]
ignore_missing_imports = true
[[tool.mypy.overrides]]
module = [
"tqdm",
"tqdm.*"
]
ignore_missing_imports = true
[tool.semantic_release]
version_toml = "pyproject.toml:tool.poetry.version"
tag_format = "{version}"