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initial commit with updaet

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This commit is contained in:
Deepak Mallubhotla 2024-09-04 14:56:06 -05:00
parent 287e7d174b
commit 3a1db07aa3
Signed by: deepak
GPG Key ID: 976F3357369149AB
17 changed files with 327 additions and 128 deletions
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174
flake.lock generated Normal file
View File

@ -0,0 +1,174 @@
{
"nodes": {
"flake-utils": {
"inputs": {
"systems": "systems"
},
"locked": {
"lastModified": 1710146030,
"narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
"owner": "numtide",
"repo": "flake-utils",
"rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
"type": "github"
},
"original": {
"owner": "numtide",
"repo": "flake-utils",
"type": "github"
}
},
"flake-utils_2": {
"inputs": {
"systems": "systems_2"
},
"locked": {
"lastModified": 1710146030,
"narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
"owner": "numtide",
"repo": "flake-utils",
"rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
"type": "github"
},
"original": {
"owner": "numtide",
"repo": "flake-utils",
"type": "github"
}
},
"nix-github-actions": {
"inputs": {
"nixpkgs": [
"poetry2nixSrc",
"nixpkgs"
]
},
"locked": {
"lastModified": 1703863825,
"narHash": "sha256-rXwqjtwiGKJheXB43ybM8NwWB8rO2dSRrEqes0S7F5Y=",
"owner": "nix-community",
"repo": "nix-github-actions",
"rev": "5163432afc817cf8bd1f031418d1869e4c9d5547",
"type": "github"
},
"original": {
"owner": "nix-community",
"repo": "nix-github-actions",
"type": "github"
}
},
"nixpkgs": {
"locked": {
"lastModified": 1725476236,
"narHash": "sha256-jhtkFFP0v0z0m8oznMJ5szoPA72CGaeJYSv7/uaGpS4=",
"owner": "NixOS",
"repo": "nixpkgs",
"rev": "e9f994aaff25e101d165245dcda1965d7871ff73",
"type": "github"
},
"original": {
"owner": "NixOS",
"repo": "nixpkgs",
"type": "github"
}
},
"poetry2nixSrc": {
"inputs": {
"flake-utils": "flake-utils_2",
"nix-github-actions": "nix-github-actions",
"nixpkgs": [
"nixpkgs"
],
"systems": "systems_3",
"treefmt-nix": "treefmt-nix"
},
"locked": {
"lastModified": 1725322757,
"narHash": "sha256-dgbmWv9ysSAZi27W4DnCdWDG+Q2yCCngVTKApDCN0ms=",
"owner": "nix-community",
"repo": "poetry2nix",
"rev": "184203e05a78f93f3c6329597db4cbec0471984b",
"type": "github"
},
"original": {
"owner": "nix-community",
"repo": "poetry2nix",
"type": "github"
}
},
"root": {
"inputs": {
"flake-utils": "flake-utils",
"nixpkgs": "nixpkgs",
"poetry2nixSrc": "poetry2nixSrc"
}
},
"systems": {
"locked": {
"lastModified": 1681028828,
"narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
"owner": "nix-systems",
"repo": "default",
"rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
"type": "github"
},
"original": {
"owner": "nix-systems",
"repo": "default",
"type": "github"
}
},
"systems_2": {
"locked": {
"lastModified": 1681028828,
"narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
"owner": "nix-systems",
"repo": "default",
"rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
"type": "github"
},
"original": {
"owner": "nix-systems",
"repo": "default",
"type": "github"
}
},
"systems_3": {
"locked": {
"lastModified": 1681028828,
"narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
"owner": "nix-systems",
"repo": "default",
"rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
"type": "github"
},
"original": {
"id": "systems",
"type": "indirect"
}
},
"treefmt-nix": {
"inputs": {
"nixpkgs": [
"poetry2nixSrc",
"nixpkgs"
]
},
"locked": {
"lastModified": 1719749022,
"narHash": "sha256-ddPKHcqaKCIFSFc/cvxS14goUhCOAwsM1PbMr0ZtHMg=",
"owner": "numtide",
"repo": "treefmt-nix",
"rev": "8df5ff62195d4e67e2264df0b7f5e8c9995fd0bd",
"type": "github"
},
"original": {
"owner": "numtide",
"repo": "treefmt-nix",
"type": "github"
}
}
},
"root": "root",
"version": 7
}

47
flake.nix Normal file
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@ -0,0 +1,47 @@
{
description = "Application packaged using poetry2nix";
inputs.flake-utils.url = "github:numtide/flake-utils";
inputs.nixpkgs.url = "github:NixOS/nixpkgs";
inputs.poetry2nixSrc = {
url = "github:nix-community/poetry2nix";
inputs.nixpkgs.follows = "nixpkgs";
};
outputs = { self, nixpkgs, flake-utils, poetry2nixSrc }:
flake-utils.lib.eachDefaultSystem (system:
let
pkgs = nixpkgs.legacyPackages.${system};
poetry2nix = poetry2nixSrc.lib.mkPoetry2Nix { inherit pkgs; };
in {
packages = {
kalpaApp = poetry2nix.mkPoetryApplication {
projectDir = self;
python = pkgs.python39;
preferWheels = true;
};
kalpaEnv = poetry2nix.mkPoetryEnv {
projectDir = self;
python = pkgs.python39;
preferWheels = true;
overrides = poetry2nix.overrides.withDefaults (self: super: {
});
};
default = self.packages.${system}.kalpaEnv;
};
devShells.default = pkgs.mkShell {
inputsFrom = [ self.packages.${system}.kalpaEnv ];
buildInputs = [
pkgs.poetry
self.packages.${system}.kalpaEnv
self.packages.${system}.kalpaApp
pkgs.just
pkgs.nodejs
];
shellHook = ''
export DO_NIX_CUSTOM=1
'';
};
}
);
}

2
justfile
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@ -43,7 +43,7 @@ fmt:
else else
poetry run black . poetry run black .
fi fi
find single_dipole_4 -type f -name "*.py" -exec sed -i -e 's/ /\t/g' {} \; find kalpa -type f -name "*.py" -exec sed -i -e 's/ /\t/g' {} \;
find bin -type f -name "*.py" -exec sed -i -e 's/ /\t/g' {} \; find bin -type f -name "*.py" -exec sed -i -e 's/ /\t/g' {} \;
# find tests -type f -name "*.py" -exec sed -i -e 's/ /\t/g' {} \; # find tests -type f -name "*.py" -exec sed -i -e 's/ /\t/g' {} \;

6
kalpa/__init__.py
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@ -1,6 +1,6 @@
from single_dipole_4.read_bin_csv import read_dots_and_binned from kalpa.read_bin_csv import read_dots_and_binned
from single_dipole_4.common import get_model from kalpa.common import get_model
from single_dipole_4.config import ( from kalpa.config import (
Config, Config,
TantriConfig, TantriConfig,
GeneralConfig, GeneralConfig,

6
kalpa/common/__init__.py
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@ -1,6 +1,6 @@
from single_dipole_4.common.model_params import get_model from kalpa.common.model_params import get_model
from single_dipole_4.common.cli_utils import set_up_logging from kalpa.common.cli_utils import set_up_logging
from single_dipole_4.common.runner_utils import ( from kalpa.common.runner_utils import (
new_cd, new_cd,
tantri_binned_output_name, tantri_binned_output_name,
tantri_full_output_name, tantri_full_output_name,

4
kalpa/common/cli_utils.py
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@ -1,11 +1,11 @@
import pathlib import pathlib
import logging import logging
import single_dipole_4.config import kalpa.config
import typing import typing
def set_up_logging( def set_up_logging(
config: single_dipole_4.config.Config, config: kalpa.config.Config,
log_file: typing.Optional[str], log_file: typing.Optional[str],
create_logfile_parents: bool = True, create_logfile_parents: bool = True,
): ):

4
kalpa/common/model_params.py
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@ -2,7 +2,7 @@ import dataclasses
import typing import typing
import logging import logging
from tantri.dipoles.types import Orientation from tantri.dipoles.types import Orientation
import single_dipole_4.config import kalpa.config
_logger = logging.getLogger(__name__) _logger = logging.getLogger(__name__)
@ -51,7 +51,7 @@ def _fixed_z_model_func(
) )
def get_model(params: single_dipole_4.config.ReducedModelParams): def get_model(params: kalpa.config.ReducedModelParams):
model_funcs = { model_funcs = {
Orientation.Z: _fixed_z_model_func, Orientation.Z: _fixed_z_model_func,
Orientation.RANDOM: LogSpacedRandomCountMultipleDipoleFixedMagnitudeModel, Orientation.RANDOM: LogSpacedRandomCountMultipleDipoleFixedMagnitudeModel,

2
kalpa/inference_coalesce/__init__.py
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@ -1,3 +1,3 @@
from single_dipole_4.inference_coalesce.coalescer import Coalescer from kalpa.inference_coalesce.coalescer import Coalescer
__all__ = ["Coalescer"] __all__ = ["Coalescer"]

1
kalpa/read_bin_csv.py
View File

@ -202,7 +202,6 @@ class BinnedData:
csv_dict: typing.Dict[str, typing.Any] csv_dict: typing.Dict[str, typing.Any]
measurement_type: str measurement_type: str
# we're ignoring stdevs for the current moment, as in the calculator single_dipole_matches.py script.
def _dot_to_measurement(self, dot_name: str) -> typing.Sequence[Measurement]: def _dot_to_measurement(self, dot_name: str) -> typing.Sequence[Measurement]:
if dot_name not in self.dots_dict: if dot_name not in self.dots_dict:
raise KeyError(f"Could not find {dot_name=} in {self.dots_dict=}") raise KeyError(f"Could not find {dot_name=} in {self.dots_dict=}")

36
kalpa/stages/__init__.py
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@ -1,10 +1,10 @@
import logging import logging
import single_dipole_4.stages.stage01 import kalpa.stages.stage01
import single_dipole_4.stages.stage02 import kalpa.stages.stage02
import single_dipole_4.stages.stage03 import kalpa.stages.stage03
import single_dipole_4.stages.stage04 import kalpa.stages.stage04
import single_dipole_4.common import kalpa.common
import tantri.dipoles.types import tantri.dipoles.types
import argparse import argparse
@ -13,25 +13,25 @@ _logger = logging.getLogger(__name__)
class Runner: class Runner:
def __init__(self, config: single_dipole_4.Config): def __init__(self, config: kalpa.Config):
self.config = config self.config = config
_logger.info(f"Initialising runner with {config=}") _logger.info(f"Initialising runner with {config=}")
def run(self): def run(self):
_logger.info("*** Beginning Stage 01 ***") _logger.info("*** Beginning Stage 01 ***")
stage01 = single_dipole_4.stages.stage01.Stage01Runner(self.config) stage01 = kalpa.stages.stage01.Stage01Runner(self.config)
stage01.run() stage01.run()
_logger.info("*** Beginning Stage 02 ***") _logger.info("*** Beginning Stage 02 ***")
stage02 = single_dipole_4.stages.stage02.Stage02Runner(self.config) stage02 = kalpa.stages.stage02.Stage02Runner(self.config)
stage02.run() stage02.run()
_logger.info("*** Beginning Stage 03 ***") _logger.info("*** Beginning Stage 03 ***")
stage03 = single_dipole_4.stages.stage03.Stage03Runner(self.config) stage03 = kalpa.stages.stage03.Stage03Runner(self.config)
stage03.run() stage03.run()
_logger.info("*** Beginning Stage 04 ***") _logger.info("*** Beginning Stage 04 ***")
stage04 = single_dipole_4.stages.stage04.Stage04Runner(self.config) stage04 = kalpa.stages.stage04.Stage04Runner(self.config)
stage04.run() stage04.run()
@ -55,32 +55,32 @@ def main():
args = parse_args() args = parse_args()
tantri_configs = [ tantri_configs = [
single_dipole_4.TantriConfig(12345, 50, 0.5, 100000), kalpa.TantriConfig(12345, 50, 0.5, 100000),
# single_dipole_4.TantriConfig(1234, 50, 0.0005, 10000), # kalpa.TantriConfig(1234, 50, 0.0005, 10000),
] ]
generation_config = single_dipole_4.GenerationConfig( generation_config = kalpa.GenerationConfig(
tantri_configs=tantri_configs, tantri_configs=tantri_configs,
counts=[1], counts=[1],
num_replicas=3, num_replicas=3,
orientations=[tantri.dipoles.types.Orientation.XY], orientations=[tantri.dipoles.types.Orientation.XY],
num_bin_time_series=25, num_bin_time_series=25,
) )
general_config = single_dipole_4.GeneralConfig( general_config = kalpa.GeneralConfig(
measurement_type=single_dipole_4.MeasurementTypeEnum.POTENTIAL measurement_type=kalpa.MeasurementTypeEnum.POTENTIAL
) )
deepdog_config = single_dipole_4.DeepdogConfig( deepdog_config = kalpa.DeepdogConfig(
costs_to_try=[10, 2, 1, 0.1], costs_to_try=[10, 2, 1, 0.1],
max_monte_carlo_cycles_steps=20, max_monte_carlo_cycles_steps=20,
) )
config = single_dipole_4.Config( config = kalpa.Config(
generation_config=generation_config, generation_config=generation_config,
general_config=general_config, general_config=general_config,
deepdog_config=deepdog_config, deepdog_config=deepdog_config,
) )
single_dipole_4.common.set_up_logging(config, args.log_file) kalpa.common.set_up_logging(config, args.log_file)
_logger.info(f"Got {config=}") _logger.info(f"Got {config=}")
runner = Runner(config) runner = Runner(config)

24
kalpa/stages/stage01.py
View File

@ -4,8 +4,8 @@ import json
import pathlib import pathlib
import argparse import argparse
import logging import logging
import single_dipole_4 import kalpa
import single_dipole_4.common import kalpa.common
import tantri.cli import tantri.cli
import tantri.dipoles.types import tantri.dipoles.types
@ -78,7 +78,7 @@ _logger = logging.getLogger(__name__)
class Stage01Runner: class Stage01Runner:
def __init__(self, config: single_dipole_4.Config): def __init__(self, config: kalpa.Config):
self.config = config self.config = config
_logger.info(f"Initialising Stage01 runner with {config=}") _logger.info(f"Initialising Stage01 runner with {config=}")
@ -100,12 +100,12 @@ class Stage01Runner:
dipoles_json = directory / "dipoles.json" dipoles_json = directory / "dipoles.json"
with open(config_json, "w") as conf_file: with open(config_json, "w") as conf_file:
params = single_dipole_4.ReducedModelParams( params = kalpa.ReducedModelParams(
count=count, orientation=tantri.dipoles.types.Orientation(orientation) count=count, orientation=tantri.dipoles.types.Orientation(orientation)
) )
_logger.debug(f"Got params {params=}") _logger.debug(f"Got params {params=}")
json.dump(params.config_dict(seed), conf_file) json.dump(params.config_dict(seed), conf_file)
# json.dump(single_dipole_4.common.model_config_dict(count, orientation, seed), conf_file) # json.dump(kalpa.common.model_config_dict(count, orientation, seed), conf_file)
tantri.cli._generate_dipoles(config_json, dipoles_json, (seed, replica, 1)) tantri.cli._generate_dipoles(config_json, dipoles_json, (seed, replica, 1))
@ -113,10 +113,10 @@ class Stage01Runner:
for tantri_index, tantri_config in enumerate( for tantri_index, tantri_config in enumerate(
self.config.generation_config.tantri_configs self.config.generation_config.tantri_configs
): ):
output_csv = directory / single_dipole_4.common.tantri_full_output_name( output_csv = directory / kalpa.common.tantri_full_output_name(
tantri_index tantri_index
) )
binned_csv = directory / single_dipole_4.common.tantri_binned_output_name( binned_csv = directory / kalpa.common.tantri_binned_output_name(
tantri_index tantri_index
) )
tantri.cli._write_apsd( tantri.cli._write_apsd(
@ -191,19 +191,19 @@ def main():
args = parse_args() args = parse_args()
tantri_configs = [ tantri_configs = [
single_dipole_4.TantriConfig(31415, 100, 5, 100000), kalpa.TantriConfig(31415, 100, 5, 100000),
single_dipole_4.TantriConfig(314, 100, 0.00005, 100000), kalpa.TantriConfig(314, 100, 0.00005, 100000),
] ]
generation_config = single_dipole_4.GenerationConfig( generation_config = kalpa.GenerationConfig(
tantri_configs=tantri_configs, tantri_configs=tantri_configs,
counts=[1], counts=[1],
num_replicas=3, num_replicas=3,
orientations=[tantri.dipoles.types.Orientation.Z], orientations=[tantri.dipoles.types.Orientation.Z],
) )
config = single_dipole_4.Config(generation_config=generation_config) config = kalpa.Config(generation_config=generation_config)
single_dipole_4.common.set_up_logging(config, args.log_file) kalpa.common.set_up_logging(config, args.log_file)
_logger.info("Generating our data, for the following iterations") _logger.info("Generating our data, for the following iterations")

30
kalpa/stages/stage02.py
View File

@ -30,8 +30,8 @@ import json
# #
# #
# folder in curr dir # folder in curr dir
import single_dipole_4 import kalpa
import single_dipole_4.common import kalpa.common
_logger = logging.getLogger(__name__) _logger = logging.getLogger(__name__)
@ -74,7 +74,7 @@ def enumify_orientation_string(
class Stage02Runner: class Stage02Runner:
def __init__(self, config: single_dipole_4.Config): def __init__(self, config: kalpa.Config):
self.config = config self.config = config
_logger.info(f"Initialising Stage02 runner with {config=}") _logger.info(f"Initialising Stage02 runner with {config=}")
@ -106,7 +106,7 @@ class Stage02Runner:
return ["dot1", "dot2", current_dot] return ["dot1", "dot2", current_dot]
def run_in_subdir(self, subdir: pathlib.Path): def run_in_subdir(self, subdir: pathlib.Path):
with single_dipole_4.common.new_cd(subdir): with kalpa.common.new_cd(subdir):
_logger.debug(f"Running inside {subdir=}") _logger.debug(f"Running inside {subdir=}")
# TODO hardcoding that we're executing every job index. # TODO hardcoding that we're executing every job index.
@ -140,7 +140,7 @@ class Stage02Runner:
seed_index: int, seed_index: int,
): ):
# _logger.info(f"Got job index {job_index}") # _logger.info(f"Got job index {job_index}")
# NOTE This guy runs inside subdirs, obviously. In something like <single_dipole_4>/out/z-10-2/dipoles # NOTE This guy runs inside subdirs, obviously. In something like <kalpa>/out/z-10-2/dipoles
# we had job_index, trial_name, args let's see what we need # we had job_index, trial_name, args let's see what we need
@ -153,10 +153,10 @@ class Stage02Runner:
) )
num_tantri_configs = len(self.config.generation_config.tantri_configs) num_tantri_configs = len(self.config.generation_config.tantri_configs)
binned_datas = [ binned_datas = [
single_dipole_4.read_dots_and_binned( kalpa.read_dots_and_binned(
self.config.get_dots_json_path(), self.config.get_dots_json_path(),
pathlib.Path("..") pathlib.Path("..")
/ single_dipole_4.common.tantri_binned_output_name(tantri_index), / kalpa.common.tantri_binned_output_name(tantri_index),
) )
for tantri_index in range(num_tantri_configs) for tantri_index in range(num_tantri_configs)
] ]
@ -188,11 +188,11 @@ class Stage02Runner:
mccount, mccountcycles = occupancies_dict[avg_filled] mccount, mccountcycles = occupancies_dict[avg_filled]
model_params = single_dipole_4.ReducedModelParams( model_params = kalpa.ReducedModelParams(
count=avg_filled, log_magnitude=log_magnitude, orientation=orientation count=avg_filled, log_magnitude=log_magnitude, orientation=orientation
) )
models.append(single_dipole_4.get_model(model_params)) models.append(kalpa.get_model(model_params))
_logger.info(f"have {len(models)} models to look at") _logger.info(f"have {len(models)} models to look at")
if len(models) == 1: if len(models) == 1:
@ -229,7 +229,7 @@ class Stage02Runner:
_logger.info(results) _logger.info(results)
def run(self): def run(self):
"""Going to iterate over every folder in out_dir, and execute the subdir stuff inside dirs like <single_dipole_4>/out/z-10-2/dipoles""" """Going to iterate over every folder in out_dir, and execute the subdir stuff inside dirs like <kalpa>/out/z-10-2/dipoles"""
out_dir_path = self.config.get_out_dir_path() out_dir_path = self.config.get_out_dir_path()
subdirs = [child for child in out_dir_path.iterdir() if child.is_dir] subdirs = [child for child in out_dir_path.iterdir() if child.is_dir]
# _logger.info(f"Going to execute within each of the directories in {subdirs=}") # _logger.info(f"Going to execute within each of the directories in {subdirs=}")
@ -261,14 +261,14 @@ def main():
args = parse_args() args = parse_args()
tantri_configs = [ tantri_configs = [
single_dipole_4.TantriConfig(31415, 100, 5, 100000), kalpa.TantriConfig(31415, 100, 5, 100000),
single_dipole_4.TantriConfig(314, 100, 0.00005, 100000), kalpa.TantriConfig(314, 100, 0.00005, 100000),
] ]
generation_config = single_dipole_4.GenerationConfig(tantri_configs=tantri_configs) generation_config = kalpa.GenerationConfig(tantri_configs=tantri_configs)
config = single_dipole_4.Config(generation_config=generation_config) config = kalpa.Config(generation_config=generation_config)
single_dipole_4.common.set_up_logging(config, args.log_file) kalpa.common.set_up_logging(config, args.log_file)
_logger.info("Generating our data, for the following iterations") _logger.info("Generating our data, for the following iterations")

30
kalpa/stages/stage03.py
View File

@ -15,8 +15,8 @@ import logging
# # import itertools # # import itertools
import pdme import pdme
import single_dipole_4.stages import kalpa.stages
import single_dipole_4.stages.stage03_1 import kalpa.stages.stage03_1
import tantri.cli import tantri.cli
import tantri.cli.file_importer import tantri.cli.file_importer
import tantri.dipoles.types import tantri.dipoles.types
@ -25,8 +25,8 @@ import tantri.dipoles.types
# #
# #
# folder in curr dir # folder in curr dir
import single_dipole_4 import kalpa
import single_dipole_4.common import kalpa.common
_logger = logging.getLogger(__name__) _logger = logging.getLogger(__name__)
@ -70,7 +70,7 @@ def read_coalesced_csv(parent_path: pathlib.Path, dot_name: str, target_cost):
class Stage03Runner: class Stage03Runner:
def __init__(self, config: single_dipole_4.Config): def __init__(self, config: kalpa.Config):
self.config = config self.config = config
_logger.info(f"Initialising Stage03 runner with {config=}") _logger.info(f"Initialising Stage03 runner with {config=}")
@ -85,7 +85,7 @@ class Stage03Runner:
_logger.info(f"Got dots {self.dots=}") _logger.info(f"Got dots {self.dots=}")
def merge_coalesceds(self, sorted_dir: pathlib.Path): def merge_coalesceds(self, sorted_dir: pathlib.Path):
out_path = sorted_dir / single_dipole_4.common.merged_coalesced_name() out_path = sorted_dir / kalpa.common.merged_coalesced_name()
with out_path.open("w", newline="") as outfile: with out_path.open("w", newline="") as outfile:
writer = csv.DictWriter(outfile, OUT_FIELDNAMES) writer = csv.DictWriter(outfile, OUT_FIELDNAMES)
writer.writeheader() writer.writeheader()
@ -100,15 +100,15 @@ class Stage03Runner:
""" """
Subdir passed in should be e.g. <>/out/z-10-1/ Subdir passed in should be e.g. <>/out/z-10-1/
""" """
with single_dipole_4.common.new_cd(subdir): with kalpa.common.new_cd(subdir):
_logger.debug(f"Running inside {subdir=}") _logger.debug(f"Running inside {subdir=}")
single_dipole_4.stages.stage03_1.move_all_in_dipoles(subdir / "dipoles") kalpa.stages.stage03_1.move_all_in_dipoles(subdir / "dipoles")
seed_index = 0 seed_index = 0
sorted_dir = pathlib.Path(single_dipole_4.common.sorted_bayesruns_name()) sorted_dir = pathlib.Path(kalpa.common.sorted_bayesruns_name())
_logger.info(f"{sorted_dir.resolve()}") _logger.info(f"{sorted_dir.resolve()}")
for cost in self.config.deepdog_config.costs_to_try: for cost in self.config.deepdog_config.costs_to_try:
@ -138,7 +138,7 @@ class Stage03Runner:
# #
def run(self): def run(self):
"""Going to iterate over every folder in out_dir, and execute the subdir stuff inside dirs like <single_dipole_4>/out/z-10-2/dipoles""" """Going to iterate over every folder in out_dir, and execute the subdir stuff inside dirs like <kalpa>/out/z-10-2/dipoles"""
out_dir_path = self.config.get_out_dir_path() out_dir_path = self.config.get_out_dir_path()
subdirs = [child for child in out_dir_path.iterdir() if child.is_dir] subdirs = [child for child in out_dir_path.iterdir() if child.is_dir]
# _logger.info(f"Going to execute within each of the directories in {subdirs=}") # _logger.info(f"Going to execute within each of the directories in {subdirs=}")
@ -170,19 +170,19 @@ def main():
args = parse_args() args = parse_args()
tantri_configs = [ tantri_configs = [
single_dipole_4.TantriConfig(31415, 100, 5, 100000), kalpa.TantriConfig(31415, 100, 5, 100000),
single_dipole_4.TantriConfig(314, 100, 0.00005, 100000), kalpa.TantriConfig(314, 100, 0.00005, 100000),
] ]
generation_config = single_dipole_4.GenerationConfig( generation_config = kalpa.GenerationConfig(
tantri_configs=tantri_configs, tantri_configs=tantri_configs,
counts=[1], counts=[1],
num_replicas=3, num_replicas=3,
orientations=[tantri.dipoles.types.Orientation.Z], orientations=[tantri.dipoles.types.Orientation.Z],
) )
config = single_dipole_4.Config(generation_config=generation_config) config = kalpa.Config(generation_config=generation_config)
single_dipole_4.common.set_up_logging(config, args.log_file) kalpa.common.set_up_logging(config, args.log_file)
_logger.info("Generating our data, for the following iterations") _logger.info("Generating our data, for the following iterations")

6
kalpa/stages/stage03_1.py
View File

@ -1,4 +1,4 @@
import single_dipole_4.common import kalpa.common
import os import os
import logging import logging
import argparse import argparse
@ -27,7 +27,7 @@ def target_dir(filename) -> BFile:
raise ValueError(f"Could not parse {filename=}") raise ValueError(f"Could not parse {filename=}")
tag = parsed_slug["tag"] tag = parsed_slug["tag"]
cost = parsed_slug["target_cost"] cost = parsed_slug["target_cost"]
target_dirname = f"{single_dipole_4.common.sorted_bayesruns_name()}/{tag}-{cost}" target_dirname = f"{kalpa.common.sorted_bayesruns_name()}/{tag}-{cost}"
file = fileresult.path file = fileresult.path
bfile = BFile(file=file, target_dirname=target_dirname) bfile = BFile(file=file, target_dirname=target_dirname)
@ -49,7 +49,7 @@ def move_all_in_dipoles(dipoles_path: pathlib.Path):
_logger.info(f"Going to try to move files in {dipoles_path=}") _logger.info(f"Going to try to move files in {dipoles_path=}")
sorted_dir = pathlib.Path(single_dipole_4.common.sorted_bayesruns_name()) sorted_dir = pathlib.Path(kalpa.common.sorted_bayesruns_name())
sorted_dir.mkdir(exist_ok=True, parents=True) sorted_dir.mkdir(exist_ok=True, parents=True)
bayesruns = [ bayesruns = [

24
kalpa/stages/stage04.py
View File

@ -2,9 +2,9 @@ import typing
import logging import logging
import argparse import argparse
import csv import csv
import single_dipole_4 import kalpa
import single_dipole_4.common import kalpa.common
import single_dipole_4.inference_coalesce import kalpa.inference_coalesce
import tantri.dipoles.types import tantri.dipoles.types
_logger = logging.getLogger(__name__) _logger = logging.getLogger(__name__)
@ -93,7 +93,7 @@ def is_actual(row, actual_normal_orientation, actual_count):
class Stage04Runner: class Stage04Runner:
def __init__(self, config: single_dipole_4.Config): def __init__(self, config: kalpa.Config):
self.config = config self.config = config
_logger.info(f"Initialising Stage04 runner with {config=}") _logger.info(f"Initialising Stage04 runner with {config=}")
@ -104,8 +104,8 @@ class Stage04Runner:
subdir_path = self.config.get_out_dir_path() / subdir_name subdir_path = self.config.get_out_dir_path() / subdir_name
csv_path = ( csv_path = (
subdir_path subdir_path
/ single_dipole_4.common.sorted_bayesruns_name() / kalpa.common.sorted_bayesruns_name()
/ single_dipole_4.common.merged_coalesced_name() / kalpa.common.merged_coalesced_name()
) )
_logger.debug(f"Reading {csv_path=}") _logger.debug(f"Reading {csv_path=}")
with csv_path.open(mode="r", newline="") as csvfile: with csv_path.open(mode="r", newline="") as csvfile:
@ -148,7 +148,7 @@ class Stage04Runner:
megamerged_reader = csv.DictReader(infile) megamerged_reader = csv.DictReader(infile)
rows = [row for row in megamerged_reader] rows = [row for row in megamerged_reader]
_logger.debug(rows[0]) _logger.debug(rows[0])
coalescer = single_dipole_4.inference_coalesce.Coalescer( coalescer = kalpa.inference_coalesce.Coalescer(
rows, num_replicas=self.config.generation_config.num_replicas rows, num_replicas=self.config.generation_config.num_replicas
) )
_logger.info(coalescer.actual_dict.keys()) _logger.info(coalescer.actual_dict.keys())
@ -191,19 +191,19 @@ def main():
args = parse_args() args = parse_args()
tantri_configs = [ tantri_configs = [
single_dipole_4.TantriConfig(31415, 100, 5, 100000), kalpa.TantriConfig(31415, 100, 5, 100000),
single_dipole_4.TantriConfig(314, 100, 0.00005, 100000), kalpa.TantriConfig(314, 100, 0.00005, 100000),
] ]
generation_config = single_dipole_4.GenerationConfig( generation_config = kalpa.GenerationConfig(
tantri_configs=tantri_configs, tantri_configs=tantri_configs,
counts=[1], counts=[1],
num_replicas=3, num_replicas=3,
orientations=[tantri.dipoles.types.Orientation.Z], orientations=[tantri.dipoles.types.Orientation.Z],
) )
config = single_dipole_4.Config(generation_config=generation_config) config = kalpa.Config(generation_config=generation_config)
single_dipole_4.common.set_up_logging(config, args.log_file) kalpa.common.set_up_logging(config, args.log_file)
_logger.info("Generating our data, for the following iterations") _logger.info("Generating our data, for the following iterations")

40
poetry.lock generated
View File

@ -1,4 +1,4 @@
# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. # This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
[[package]] [[package]]
name = "black" name = "black"
@ -73,22 +73,20 @@ files = [
[[package]] [[package]]
name = "deepdog" name = "deepdog"
version = "1.3.0" version = "1.4.0"
description = "" description = ""
optional = false optional = false
python-versions = ">=3.8.1,<3.10" python-versions = "<3.10,>=3.8.1"
files = [] files = [
develop = true {file = "deepdog-1.4.0-py3-none-any.whl", hash = "sha256:aabaae5f1dad01ff52ea1475448800af0494c250432cff3f8ebe5f41580e830e"},
{file = "deepdog-1.4.0.tar.gz", hash = "sha256:60e952c13d601985caf445522ee6232d6d089a373a48b83b05732324df6c2dc7"},
]
[package.dependencies] [package.dependencies]
numpy = "1.22.3" numpy = "1.22.3"
pdme = "^1.5.0" pdme = ">=1.5.0,<2.0.0"
scipy = "1.10" scipy = "1.10"
tqdm = "^4.66.2" tqdm = ">=4.66.2,<5.0.0"
[package.source]
type = "directory"
url = "../deepdog"
[[package]] [[package]]
name = "mypy-extensions" name = "mypy-extensions"
@ -221,24 +219,6 @@ dev = ["click", "doit (>=0.36.0)", "flake8", "mypy", "pycodestyle", "pydevtool",
doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"] doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"]
test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
[[package]]
name = "tantri"
version = "1.1.0"
description = "Python dipole model evaluator"
optional = false
python-versions = ">=3.8.1,<3.10"
files = []
develop = true
[package.dependencies]
click = "^8.1.7"
numpy = "^1.22.3"
scipy = "~1.10"
[package.source]
type = "directory"
url = "../tantri"
[[package]] [[package]]
name = "tomli" name = "tomli"
version = "2.0.1" version = "2.0.1"
@ -284,4 +264,4 @@ files = [
[metadata] [metadata]
lock-version = "2.0" lock-version = "2.0"
python-versions = ">=3.8.1,<3.10" python-versions = ">=3.8.1,<3.10"
content-hash = "3c0c0391fcd01dabcbc7add8d92f0dac5c218e78aa375df1e9845c514a26dd83" content-hash = "ea6ff51c2e1b8a65a98c932f38e2f360076a90ee7706676cbf83e306bf6565e7"

19
pyproject.toml
View File

@ -1,17 +1,16 @@
[tool.poetry] [tool.poetry]
name = "single-dipole-4" name = "kalpa"
version = "0.0.0" version = "0.0.1"
description = "running single dipole 4 test" description = "Groups up and runs full run."
authors = ["Deepak Mallubhotla <dmallubhotla+github@gmail.com>"] authors = ["Deepak Mallubhotla <dmallubhotla+github@gmail.com>"]
readme = "README.md" readme = "README.md"
[tool.poetry.dependencies] [tool.poetry.dependencies]
python = ">=3.8.1,<3.10" python = ">=3.8.1,<3.10"
deepdog = {path = "../deepdog", develop = true}
tantri = {path = "../tantri", develop = true}
pdme = "^1.5.0" pdme = "^1.5.0"
deepdog = "^1.4.0"
[tool.poetry.group.dev.dependencies] [tool.poetry.group.dev.dependencies]
black = "^24.8.0" black = "^24.8.0"
@ -20,8 +19,8 @@ requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api" build-backend = "poetry.core.masonry.api"
[tool.poetry.scripts] [tool.poetry.scripts]
stage01 = "single_dipole_4.stages.stage01:main" stage01 = "kalpa.stages.stage01:main"
stage02 = "single_dipole_4.stages.stage02:main" stage02 = "kalpa.stages.stage02:main"
stage03 = "single_dipole_4.stages.stage03:main" stage03 = "kalpa.stages.stage03:main"
stage04 = "single_dipole_4.stages.stage04:main" stage04 = "kalpa.stages.stage04:main"
sd4 = "single_dipole_4.stages:main" sd4 = "kalpa.stages:main"