instruction stringclasses 100
values | code stringlengths 78 193k | response stringlengths 259 170k | file stringlengths 59 203 |
|---|---|---|---|
Create docstrings for API functions |
# Added by C:
# JsException (from jsproxy.c)
import ast
import builtins
import linecache
import tokenize
from collections.abc import Generator
from copy import deepcopy
from importlib import import_module
from io import StringIO
from textwrap import dedent
from types import CodeType
from typing import Any, Literal
... | --- +++ @@ -1,3 +1,6 @@+"""
+A library of helper utilities for connecting Python to the browser environment.
+"""
# Added by C:
# JsException (from jsproxy.c)
@@ -16,6 +19,22 @@
def should_quiet(source: str, /) -> bool:
+ """
+ Should we suppress output?
+
+ Returns
+ -------
+ ``True`` if th... | https://raw.githubusercontent.com/pyodide/pyodide/HEAD/src/py/_pyodide/_base.py |
Please document this code using docstrings | from collections.abc import Callable
from typing import Any, Protocol, cast
from . import (
IN_PYODIDE,
JsCallableDoubleProxy,
JsDomElement,
JsProxy,
JsWeakRef,
create_once_callable,
create_proxy,
)
if IN_PYODIDE:
from js import clearInterval, clearTimeout, setInterval, setTimeout
cl... | --- +++ @@ -16,6 +16,7 @@
class Destroyable(Protocol):
+ """:meta private:"""
def destroy(self):
pass
@@ -43,6 +44,10 @@ def add_event_listener(
elt: JsDomElement, event: str, listener: Callable[[Any], None]
) -> None:
+ """Wrapper for JavaScript's
+ :js:meth:`~EventTarget.addEventLis... | https://raw.githubusercontent.com/pyodide/pyodide/HEAD/src/py/pyodide/ffi/wrappers.py |
Include argument descriptions in docstrings | # Copyright (c) Microsoft Corporation.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wri... | --- +++ @@ -12,6 +12,11 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""
+Python package `playwright` is a Python library to automate Chromium,
+Firefox and WebKit with a single API. Playwright is built to enable cross-browser
+web automation that is ever... | https://raw.githubusercontent.com/microsoft/playwright-python/HEAD/playwright/async_api/__init__.py |
Add structured docstrings to improve clarity | # Copyright (c) Microsoft Corporation.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wri... | --- +++ @@ -12,6 +12,11 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""
+Python package `playwright` is a Python library to automate Chromium,
+Firefox and WebKit with a single API. Playwright is built to enable cross-browser
+web automation that is ever... | https://raw.githubusercontent.com/microsoft/playwright-python/HEAD/playwright/sync_api/__init__.py |
Create structured documentation for my script | # Copyright (c) Microsoft Corporation.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wri... | --- +++ @@ -122,12 +122,17 @@ return handler
def on(self, event: Any, f: Any) -> None:
+ """Registers the function ``f`` to the event name ``event``."""
self._impl_obj.on(event, self._wrap_handler(f))
def once(self, event: Any, f: Any) -> None:
+ """The same as ``self.on``, ... | https://raw.githubusercontent.com/microsoft/playwright-python/HEAD/playwright/_impl/_sync_base.py |
Generate docstrings for script automation | # Copyright (c) Microsoft Corporation.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wri... | --- +++ @@ -76,12 +76,17 @@ return handler
def on(self, event: Any, f: Any) -> None:
+ """Registers the function ``f`` to the event name ``event``."""
self._impl_obj.on(event, self._wrap_handler(f))
def once(self, event: Any, f: Any) -> None:
+ """The same as ``self.on``, ex... | https://raw.githubusercontent.com/microsoft/playwright-python/HEAD/playwright/_impl/_async_base.py |
Add docstrings for utility scripts |
from dataclasses import dataclass, field
from typing import List
from lightrag.utils import get_env_value
@dataclass
class RAGAnythingConfig:
# Directory Configuration
# ---
working_dir: str = field(default=get_env_value("WORKING_DIR", "./rag_storage", str))
"""Directory where RAG storage and cache ... | --- +++ @@ -1,3 +1,8 @@+"""
+Configuration classes for RAGAnything
+
+Contains configuration dataclasses with environment variable support
+"""
from dataclasses import dataclass, field
from typing import List
@@ -6,6 +11,7 @@
@dataclass
class RAGAnythingConfig:
+ """Configuration class for RAGAnything with en... | https://raw.githubusercontent.com/HKUDS/RAG-Anything/HEAD/raganything/config.py |
Add docstrings to my Python code |
import os
from typing import Dict, Any, Optional, Callable
import sys
import asyncio
import atexit
from dataclasses import dataclass, field
from pathlib import Path
from dotenv import load_dotenv
# Add project root directory to Python path
sys.path.insert(0, str(Path(__file__).parent.parent))
# Load environment vari... | --- +++ @@ -1,3 +1,11 @@+"""
+Complete document parsing + multimodal content insertion Pipeline
+
+This script integrates:
+1. Document parsing (using configurable parsers)
+2. Pure text content LightRAG insertion
+3. Specialized processing for multimodal content (using different processors)
+"""
import os
from typ... | https://raw.githubusercontent.com/HKUDS/RAG-Anything/HEAD/raganything/raganything.py |
Fully document this Python code with docstrings | # type: ignore
from __future__ import annotations
import os
import hashlib
import json
import argparse
import base64
import subprocess
import tempfile
import logging
from pathlib import Path
from typing import (
Dict,
List,
Optional,
Union,
Tuple,
Any,
Iterator,
TypeVar,
)
T = TypeVa... | --- +++ @@ -1,4 +1,25 @@ # type: ignore
+"""
+Generic Document Parser Utility
+
+This module provides functionality for parsing documents using the built-in
+MinerU, Docling, and PaddleOCR parsers, and exposes a small registry for
+**in-process** custom parsers (see :func:`register_parser`).
+
+Important notes:
+
+- Th... | https://raw.githubusercontent.com/HKUDS/RAG-Anything/HEAD/raganything/parser.py |
Document my Python code with docstrings |
import os
import time
import hashlib
import json
from typing import Dict, List, Any, Tuple, Optional
from pathlib import Path
from raganything.base import DocStatus
from raganything.parser import MineruParser, MineruExecutionError, get_parser
from raganything.utils import (
separate_content,
insert_text_conte... | --- +++ @@ -1,3 +1,8 @@+"""
+Document processing functionality for RAGAnything
+
+Contains methods for parsing documents and processing multimodal content
+"""
import os
import time
@@ -19,8 +24,18 @@
class ProcessorMixin:
+ """ProcessorMixin class containing document processing functionality for RAGAnything... | https://raw.githubusercontent.com/HKUDS/RAG-Anything/HEAD/raganything/processor.py |
Generate consistent documentation across files |
from __future__ import annotations
import logging
import time
from dataclasses import dataclass, field
from typing import Any, Dict, List, Optional
import threading
logger = logging.getLogger(__name__)
@dataclass
class ProcessingEvent:
event_type: str
timestamp: float = field(default_factory=time.time)
... | --- +++ @@ -1,3 +1,24 @@+"""
+Processing callbacks and event system for RAGAnything.
+
+Provides a lightweight publish-subscribe mechanism that lets users hook
+into every stage of the document processing pipeline — parsing, text
+insertion, multimodal processing, and querying.
+
+Usage::
+
+ from raganything.callba... | https://raw.githubusercontent.com/HKUDS/RAG-Anything/HEAD/raganything/callbacks.py |
Improve my code by adding docstrings |
import base64
from typing import Dict, List, Any, Tuple
from pathlib import Path
from lightrag.utils import logger
def separate_content(
content_list: List[Dict[str, Any]],
) -> Tuple[str, List[Dict[str, Any]]]:
text_parts = []
multimodal_items = []
for item in content_list:
content_type = i... | --- +++ @@ -1,3 +1,8 @@+"""
+Utility functions for RAGAnything
+
+Contains helper functions for content separation, text insertion, and other utilities
+"""
import base64
from typing import Dict, List, Any, Tuple
@@ -8,6 +13,15 @@ def separate_content(
content_list: List[Dict[str, Any]],
) -> Tuple[str, List[... | https://raw.githubusercontent.com/HKUDS/RAG-Anything/HEAD/raganything/utils.py |
Annotate my code with docstrings |
import json
import hashlib
import re
import time
from typing import Dict, List, Any
from pathlib import Path
from lightrag import QueryParam
from lightrag.utils import always_get_an_event_loop
from raganything.prompt import PROMPTS
from raganything.utils import (
get_processor_for_type,
encode_image_to_base64,... | --- +++ @@ -1,3 +1,8 @@+"""
+Query functionality for RAGAnything
+
+Contains all query-related methods for both text and multimodal queries
+"""
import json
import hashlib
@@ -16,10 +21,23 @@
class QueryMixin:
+ """QueryMixin class containing query functionality for RAGAnything"""
def _generate_multim... | https://raw.githubusercontent.com/HKUDS/RAG-Anything/HEAD/raganything/query.py |
Help me comply with documentation standards |
import asyncio
import logging
from concurrent.futures import ThreadPoolExecutor, as_completed
from pathlib import Path
from typing import Dict, List, Optional, Tuple
from dataclasses import dataclass
import time
from tqdm import tqdm
from .parser import get_parser
@dataclass
class BatchProcessingResult:
succe... | --- +++ @@ -1,3 +1,9 @@+"""
+Batch and Parallel Document Parsing
+
+This module provides functionality for processing multiple documents in parallel,
+with progress reporting and error handling.
+"""
import asyncio
import logging
@@ -14,6 +20,7 @@
@dataclass
class BatchProcessingResult:
+ """Result of batch p... | https://raw.githubusercontent.com/HKUDS/RAG-Anything/HEAD/raganything/batch_parser.py |
Create documentation for each function signature |
import re
import json
import time
import base64
from typing import Dict, Any, Tuple, List
from pathlib import Path
from dataclasses import dataclass
from lightrag.utils import (
logger,
compute_mdhash_id,
)
from lightrag.lightrag import LightRAG
from dataclasses import asdict
from lightrag.kg.shared_storage i... | --- +++ @@ -1,3 +1,13 @@+"""
+Specialized processors for different modalities
+
+Includes:
+- ContextExtractor: Universal context extraction for multimodal content
+- ImageModalProcessor: Specialized processor for image content
+- TableModalProcessor: Specialized processor for table content
+- EquationModalProcessor: S... | https://raw.githubusercontent.com/HKUDS/RAG-Anything/HEAD/raganything/modalprocessors.py |
Improve documentation using docstrings |
import os
import logging
from pathlib import Path
from typing import Dict, Any, Optional
from dataclasses import dataclass
import tempfile
import subprocess
try:
import markdown
MARKDOWN_AVAILABLE = True
except ImportError:
MARKDOWN_AVAILABLE = False
try:
from weasyprint import HTML
WEASYPRINT_... | --- +++ @@ -1,3 +1,14 @@+"""
+Enhanced Markdown to PDF Conversion
+
+This module provides improved Markdown to PDF conversion with:
+- Better formatting and styling
+- Image support
+- Table support
+- Code syntax highlighting
+- Custom templates
+- Multiple output formats
+"""
import os
import logging
@@ -33,6 +44... | https://raw.githubusercontent.com/HKUDS/RAG-Anything/HEAD/raganything/enhanced_markdown.py |
Insert docstrings into my code |
import asyncio
import logging
from pathlib import Path
from typing import List, Dict, Any, Optional, TYPE_CHECKING
import time
from .batch_parser import BatchParser, BatchProcessingResult
if TYPE_CHECKING:
from .config import RAGAnythingConfig
class BatchMixin:
# Type hints for mixin attributes (will be a... | --- +++ @@ -1,3 +1,8 @@+"""
+Batch processing functionality for RAGAnything
+
+Contains methods for processing multiple documents in batch mode
+"""
import asyncio
import logging
@@ -12,6 +17,7 @@
class BatchMixin:
+ """BatchMixin class containing batch processing functionality for RAGAnything"""
# Ty... | https://raw.githubusercontent.com/HKUDS/RAG-Anything/HEAD/raganything/batch.py |
Create documentation for each function signature | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,24 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Transformations for 3D coordinates.
+
+This Module contains objects for representing Vectors (Vecs), Rotation Matrices
+(Rots) and proper Rigid transformation (Rigids). These are repr... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/r3.py |
Generate docstrings for exported functions | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Utilities for extracting identifiers from MSA sequence descriptions."""
import dataclasses
import re
@@ -52,6 +53,19 @@
def _parse_sequence_identifier(msa_sequence_identifier: ... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/msa_identifiers.py |
Insert docstrings into my code | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Helper methods for the AlphaFold Colab notebook."""
from typing import AbstractSet, Any, Mapping, Optional, Sequence
from alphafold.common import residue_constants
@@ -23,6 +24,7 @... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/notebooks/notebook_utils.py |
Add inline docstrings for readability | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,26 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Ops for all atom representations.
+
+Generally we employ two different representations for all atom coordinates,
+one is atom37 where each heavy atom corresponds to a given position i... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/all_atom.py |
Fill in missing docstrings in my code | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Code for constructing the model."""
from typing import Any, Mapping, Optional
@@ -30,6 +31,7 @@ def get_confidence_metrics(
prediction_result: Mapping[str, Any], multimer_mod... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/model.py |
Write docstrings for algorithm functions | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Code to generate processed features."""
import copy
from typing import List, Mapping, Tuple
@@ -28,6 +29,7 @@ config: ml_collections.ConfigDict,
num_res: int,
) -> Tuple[... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/features.py |
Add structured docstrings to improve clarity | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Datasets consisting of proteins."""
from typing import Dict, Mapping, Optional, Sequence
from alphafold.model.tf import protein_features
import numpy as np
@@ -21,6 +22,7 @@
def... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/tf/proteins_dataset.py |
Add docstrings explaining edge cases | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""A collection of common Haiku modules for use in protein folding."""
import numbers
from typing import Sequence, Union
@@ -28,6 +29,7 @@
def get_initializer_scale(initializer_na... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/common_modules.py |
Add professional docstrings to my codebase | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""A Python wrapper for hmmsearch - search profile against a sequence db."""
import os
import subprocess
@@ -26,6 +27,7 @@
class Hmmsearch(object):
+ """Python wrapper of the hmm... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/tools/hmmsearch.py |
Document functions with detailed explanations | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -11,6 +11,7 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
+"""Common utilities for data pipeline tools."""
import contextlib
import shutil
import tempfile
@@ -22,6 +23,7... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/tools/utils.py |
Expand my code with proper documentation strings | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Feature pre-processing input pipeline for AlphaFold."""
from alphafold.model.tf import data_transforms
from alphafold.model.tf import shape_placeholders
@@ -31,6 +32,7 @@
def n... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/tf/input_pipeline.py |
Write proper docstrings for these functions | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -11,6 +11,7 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
+"""Model config."""
import copy
import functools
@@ -855,6 +856,7 @@
class EmbeddingsAndEvoformer(base_co... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/config.py |
Document my Python code with docstrings | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Functions for getting templates and calculating template features."""
import abc
import dataclasses
import datetime
@@ -32,43 +33,56 @@
class Error(Exception):
+ """Base class ... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/templates.py |
Write docstrings including parameters and return values | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -11,6 +11,7 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
+"""Vec3Array Class."""
from __future__ import annotations
@@ -30,6 +31,16 @@
@struct_of_array.StructOfArra... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/geometry/vector.py |
Replace inline comments with docstrings | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Functions for building the features for the AlphaFold multimer model."""
import collections
import contextlib
@@ -46,6 +47,7 @@ sequences: Sequence[str],
descriptions: Seq... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/pipeline_multimer.py |
Document all endpoints with docstrings | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Full AlphaFold protein structure prediction script."""
import enum
import json
import os
@@ -275,6 +276,7 @@
def _jnp_to_np(output: Dict[str, Any]) -> Dict[str, Any]:
+ """Recu... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/run_alphafold.py |
Add docstrings including usage examples | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Functions for building the input features for the AlphaFold model."""
import os
from typing import Any, Mapping, MutableMapping, Optional, Sequence, Union
@@ -36,6 +37,7 @@ def mak... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/pipeline.py |
Add standardized docstrings across the file | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Library to run Jackhmmer from Python."""
from concurrent import futures
import glob
@@ -28,6 +29,7 @@
class Jackhmmer:
+ """Python wrapper of the Jackhmmer binary."""
def... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/tools/jackhmmer.py |
Document all public functions with docstrings | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Pairing logic for multimer data pipeline."""
import collections
import dataclasses
@@ -68,6 +69,15 @@
@dataclasses.dataclass(frozen=True, kw_only=True, slots=True)
class MSAStat... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/msa_pairing.py |
Include argument descriptions in docstrings | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""A Python wrapper for hmmbuild - construct HMM profiles from MSA."""
import os
import re
@@ -24,15 +25,50 @@
class Hmmbuild(object):
+ """Python wrapper of the hmmbuild binary.... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/tools/hmmbuild.py |
Help me comply with documentation standards | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Convenience functions for reading data."""
import io
import os
@@ -22,10 +23,11 @@
def get_model_haiku_params(model_name: str, data_dir: str) -> hk.Params:
+ """Get the Haiku ... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/data.py |
Generate descriptive docstrings automatically | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Function to stack repeats of a layer function without shared parameters."""
import collections
import contextlib
@@ -67,8 +68,10 @@
class _LayerStack(hk.Module):
+ """Module t... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/layer_stack.py |
Add docstrings to improve readability | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Functions for processing confidence metrics."""
import json
from typing import Dict, Optional, Tuple
@@ -27,6 +28,14 @@
def compute_plddt(logits: np.ndarray) -> np.ndarray:
+ ... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/common/confidence.py |
Add docstrings explaining edge cases | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Specialized mapping functions."""
import functools
import inspect
@@ -33,6 +34,7 @@
def _set_docstring(docstr: str) -> Callable[[T], T]:
+ """Decorator for setting the docstri... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/mapping.py |
Add inline docstrings for readability | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Modules and utilities for the structure module in the multimer system."""
import functools
import numbers
@@ -37,6 +38,7 @@
def squared_difference(x: jnp.ndarray, y: jnp.ndarra... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/folding_multimer.py |
Write docstrings for utility functions | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,11 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Cleans up a PDB file using pdbfixer in preparation for OpenMM simulations.
+
+fix_pdb uses a third-party tool. We also support fixing some additional edge
+cases like removing chains ... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/relax/cleanup.py |
Add inline docstrings for readability | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Library to run HHblits from Python."""
import glob
import os
@@ -29,6 +30,7 @@
class HHBlits:
+ """Python wrapper of the HHblits binary."""
def __init__(
self,
@@ ... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/tools/hhblits.py |
Write docstrings for backend logic | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Library to run HHsearch from Python."""
import glob
import os
@@ -26,6 +27,7 @@
class HHSearch:
+ """Python wrapper of the HHsearch binary."""
def __init__(
self,
... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/tools/hhsearch.py |
Add docstrings that explain purpose and usage | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""A collection of JAX utility functions for use in protein folding."""
import collections
import contextlib
@@ -27,6 +28,7 @@
def stable_softmax(logits: jax.Array) -> jax.Array:
... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/utils.py |
Add docstrings to improve collaboration | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Constants used in AlphaFold."""
import collections
import functools
@@ -414,6 +415,17 @@ Mapping[str, List[Bond]],
Mapping[str, List[BondAngle]],
]:
+ """Load stereo_che... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/common/residue_constants.py |
Create structured documentation for my script | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Parses the mmCIF file format."""
import collections
import dataclasses
import functools
@@ -68,6 +69,21 @@
@dataclasses.dataclass(frozen=True)
class MmcifObject:
+ """Representa... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/mmcif_parsing.py |
Write docstrings that follow conventions | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Data for AlphaFold."""
from alphafold.common import residue_constants
from alphafold.model.tf import shape_helpers
@@ -65,6 +66,7 @@
def curry1(f):
+ """Supply all arguments b... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/tf/data_transforms.py |
Document all public functions with docstrings | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Docker launch script for Alphafold docker image."""
import os
import pathlib
@@ -130,6 +131,7 @@
def _create_mount(mount_name: str, path: str) -> Tuple[types.Mount, str]:
+ ""... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/docker/run_docker.py |
Generate docstrings for script automation | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -11,6 +11,7 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
+"""Rot3Array Matrix Class."""
from __future__ import annotations
@@ -30,6 +31,7 @@
@struct_of_array.Struct... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/geometry/rotation_matrix.py |
Add docstrings to existing functions | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,10 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Modules and code used in the core part of AlphaFold.
+
+The structure generation code is in 'folding.py'.
+"""
import functools
from alphafold.common import residue_constants
from ... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/modules.py |
Add docstrings including usage examples | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Modules and utilities for the structure module."""
import functools
from typing import Dict
@@ -34,6 +35,17 @@
class InvariantPointAttention(hk.Module):
+ """Invariant Point a... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/folding.py |
Write docstrings for this repository | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Functions for parsing various file formats."""
import collections
import dataclasses
import itertools
@@ -27,6 +28,7 @@
@dataclasses.dataclass(frozen=True)
class Msa:
+ """Class... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/parsers.py |
Improve my code by adding docstrings | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Contains descriptions of various protein features."""
import enum
from typing import Dict, Optional, Sequence, Tuple, Union
from alphafold.common import residue_constants
@@ -74,6 +... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/tf/protein_features.py |
Document functions with clear intent | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -11,6 +11,7 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
+"""Rigid3Array Transformations represented by a Matrix and a Vector."""
from __future__ import annotations
@... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/geometry/rigid_matrix_vector.py |
Auto-generate documentation strings for this file | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""A Python wrapper for Kalign."""
import os
import subprocess
from typing import Sequence
@@ -23,6 +24,7 @@
def _to_a3m(sequences: Sequence[str]) -> str:
+ """Converts sequences ... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/tools/kalign.py |
Add docstrings for utility scripts | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,10 +12,23 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Utilities for dealing with shapes of TensorFlow tensors."""
import tensorflow.compat.v1 as tf
def shape_list(x):
+ """Return list of dimensions of a tensor, statically where p... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/tf/shape_helpers.py |
Write docstrings including parameters and return values | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -11,6 +11,7 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
+"""Ops for all atom representations."""
from typing import Dict, Optional
@@ -27,6 +28,14 @@
def _make_c... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/all_atom_multimer.py |
Add professional docstrings to my codebase | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -11,6 +11,7 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
+"""Class decorator to represent (nested) struct of arrays."""
import dataclasses
@@ -30,6 +31,7 @@
@proper... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/geometry/struct_of_array.py |
Write clean docstrings for readability | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Restrained Amber Minimization of a structure."""
import io
import time
@@ -37,6 +38,7 @@
def will_restrain(atom: openmm_app.Atom, rset: str) -> bool:
+ """Returns True if the ... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/relax/amber_minimize.py |
Document my Python code with docstrings | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Utils for minimization."""
import io
from alphafold.common import residue_constants
from Bio import PDB
@@ -19,6 +20,17 @@
def overwrite_b_factors(pdb_str: str, bfactors: np.nda... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/relax/utils.py |
Generate docstrings for exported functions | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Feature processing logic for multimer data pipeline."""
from typing import Iterable, List, MutableMapping
@@ -57,6 +58,7 @@
def _is_homomer_or_monomer(chains: Iterable[pipelin... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/data/feature_processing.py |
Write docstrings for utility functions | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,24 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Quaternion geometry modules.
+
+This introduces a representation of coordinate frames that is based around a
+‘QuatAffine’ object. This object describes an array of coordinate frames.... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/quat_affine.py |
Document functions with detailed explanations | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Amber relaxation."""
from typing import Any, Dict, Sequence, Tuple
from alphafold.common import protein
from alphafold.relax import amber_minimize
@@ -20,6 +21,7 @@
class AmberR... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/relax/relax.py |
Create documentation for each function signature | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Config for the protein folding model and experiment."""
from collections.abc import Mapping
import contextlib
@@ -27,6 +28,7 @@
def _strip_optional(t: type[Any]) -> type[Any]:
... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/base_config.py |
Add docstrings with type hints explained | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Protein data type."""
import collections
import dataclasses
@@ -62,6 +63,7 @@
@dataclasses.dataclass(frozen=True)
class Protein:
+ """Protein structure representation."""
... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/common/protein.py |
Create docstrings for each class method | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | --- +++ @@ -12,6 +12,13 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Core modules, which have been refactored in AlphaFold-Multimer.
+
+The main difference is that MSA sampling pipeline is moved inside the JAX model
+for easier implementation of recycl... | https://raw.githubusercontent.com/google-deepmind/alphafold/HEAD/alphafold/model/modules_multimer.py |
Insert docstrings into my code | # Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | --- +++ @@ -13,6 +13,11 @@ # limitations under the License.
# ==============================================================================
+"""Simple, end-to-end, LeNet-5-like convolutional MNIST model example.
+This should achieve a test error of 0.7%. Please keep this model as simple and
+linear as possible, it ... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/tmp/mnist_center_loss.py |
Add docstrings that explain logic | # MIT License
#
# Copyright (c) 2016 David Sandberg
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, me... | --- +++ @@ -1,3 +1,5 @@+"""Functions for building the face recognition network.
+"""
# MIT License
#
# Copyright (c) 2016 David Sandberg
@@ -58,6 +60,14 @@ return affine1
def l2_loss(tensor, weight=1.0, scope=None):
+ """Define a L2Loss, useful for regularize, i.e. weight decay.
+ Args:
+ tensor: ... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/tmp/network.py |
Add docstrings explaining edge cases | # MIT License
#
# Copyright (c) 2016 David Sandberg
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, me... | --- +++ @@ -1,3 +1,6 @@+"""Training a face recognizer with TensorFlow based on the FaceNet paper
+FaceNet: A Unified Embedding for Face Recognition and Clustering: http://arxiv.org/abs/1503.03832
+"""
# MIT License
#
# Copyright (c) 2016 David Sandberg
@@ -266,6 +269,8 @@ return step
def select_triplets(em... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/src/train_tripletloss.py |
Include argument descriptions in docstrings | # MIT License
#
# Copyright (c) 2016 David Sandberg
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, me... | --- +++ @@ -1,3 +1,6 @@+"""Visualize individual feature channels and their combinations to explore the space of patterns learned by the neural network
+Based on http://nbviewer.jupyter.org/github/tensorflow/tensorflow/blob/master/tensorflow/examples/tutorials/deepdream/deepdream.ipynb
+"""
# MIT License
#
# Copyrig... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/tmp/visualize.py |
Create documentation strings for testing functions | # Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... | --- +++ @@ -13,6 +13,12 @@ # limitations under the License.
# ==============================================================================
+"""Contains the definition of the Inception Resnet V1 architecture.
+As described in http://arxiv.org/abs/1602.07261.
+ Inception-v4, Inception-ResNet and the Impact of Resid... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/src/models/inception_resnet_v1.py |
Generate descriptive docstrings automatically | # MIT License
#
# Copyright (c) 2016 David Sandberg
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, me... | --- +++ @@ -1,3 +1,6 @@+""" Tensorflow implementation of the face detection / alignment algorithm found at
+https://github.com/kpzhang93/MTCNN_face_detection_alignment
+"""
# MIT License
#
# Copyright (c) 2016 David Sandberg
@@ -32,6 +35,7 @@ import os
def layer(op):
+ """Decorator for composable network laye... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/src/align/detect_face.py |
Add docstrings to incomplete code | # Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | --- +++ @@ -13,6 +13,11 @@ # limitations under the License.
# ==============================================================================
+"""Simple, end-to-end, LeNet-5-like convolutional MNIST model example.
+This should achieve a test error of 0.7%. Please keep this model as simple and
+linear as possible, it ... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/tmp/mnist_noise_labels.py |
Create docstrings for each class method | # Copyright 2015-2016 Carnegie Mellon University
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ag... | --- +++ @@ -12,6 +12,7 @@ # See the License for the specific language governing permissions and
# limitations under the License.
+"""Module for dlib-based alignment."""
# NOTE: This file has been copied from the openface project.
# https://github.com/cmusatyalab/openface/blob/master/openface/align_dlib.py
@@ -6... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/tmp/align_dlib.py |
Add docstrings for better understanding | import tensorflow as tf
import numpy as np
import importlib
import argparse
import facenet
import os
import math
def face_distance(face_encodings, face_to_compare):
import numpy as np
if len(face_encodings) == 0:
return np.empty((0))
#return 1/np.linalg.norm(face_encodings - face_to_compare, axis=1... | --- +++ @@ -1,3 +1,4 @@+""" Face Cluster """
import tensorflow as tf
import numpy as np
import importlib
@@ -6,6 +7,13 @@ import os
import math
def face_distance(face_encodings, face_to_compare):
+ """
+ Given a list of face encodings, compare them to a known face encoding and get a euclidean distance
+ f... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/contributed/clustering.py |
Add docstrings for internal functions | # MIT License
#
# Copyright (c) 2016 David Sandberg
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, me... | --- +++ @@ -1,3 +1,5 @@+"""Functions for building the face recognition network.
+"""
# MIT License
#
# Copyright (c) 2016 David Sandberg
@@ -40,6 +42,16 @@ from six import iteritems
def triplet_loss(anchor, positive, negative, alpha):
+ """Calculate the triplet loss according to the FaceNet paper
+
+ A... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/src/facenet.py |
Add docstrings to clarify complex logic | # boilerplate code
import numpy as np
from functools import partial
import PIL.Image
import tensorflow as tf
import matplotlib.pyplot as plt
import urllib2
import os
import zipfile
def main():
# download pre-trained model by running the command below in a shell
# wget https://storage.googleapis.com/download.... | --- +++ @@ -51,6 +51,7 @@ # Helper functions for TF Graph visualization
#pylint: disable=unused-variable
def strip_consts(graph_def, max_const_size=32):
+ """Strip large constant values from graph_def."""
strip_def = tf.GraphDef()
for n0 in graph_def.node:
n = strip_d... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/tmp/deepdream.py |
Generate documentation strings for clarity | # Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... | --- +++ @@ -13,6 +13,12 @@ # limitations under the License.
# ==============================================================================
+"""Contains the definition of the Inception Resnet V2 architecture.
+As described in http://arxiv.org/abs/1602.07261.
+ Inception-v4, Inception-ResNet and the Impact of Resid... | https://raw.githubusercontent.com/davidsandberg/facenet/HEAD/src/models/inception_resnet_v2.py |
Write docstrings for data processing functions | #from __future__ import print_function, division
import torch
import numpy as np
from sklearn.preprocessing import StandardScaler
import random
from PIL import Image
import torch.utils.data as data
import os
import os.path
def make_dataset(image_list, labels):
if labels:
len_ = len(image_list)
images... | --- +++ @@ -47,6 +47,25 @@
class ImageList(object):
+ """A generic data loader where the images are arranged in this way: ::
+ root/dog/xxx.png
+ root/dog/xxy.png
+ root/dog/xxz.png
+ root/cat/123.png
+ root/cat/nsdf3.png
+ root/cat/asd932_.png
+ Args:
+ root (... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/CSG/utils/preprocess/data_list.py |
Generate missing documentation strings | #!/usr/bin/env python3.6
__author__ = "Chang Liu"
__email__ = "changliu@microsoft.com"
import sys, os
from warnings import warn
import torch as tc
import torch.nn as nn
import torchvision as tv
from . import backbone
from . import mlp
sys.path.append('..')
from distr import tensorify, is_same_tensor, wrap4_multi_batch... | --- +++ @@ -1,4 +1,11 @@ #!/usr/bin/env python3.6
+''' CNN Architecture
+
+Based on the architecture in MDD <https://github.com/thuml/MDD>,
+and leverage the repositories of `domainbed` <https://github.com/facebookresearch/DomainBed>
+and `pytorch_GAN_zoo` <https://github.com/facebookresearch/pytorch_GAN_zoo>.
+Archite... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/CSG/arch/cnn.py |
Generate docstrings with examples | import torch
import logging
from espnet.asr.asr_utils import add_results_to_json
import argparse
import numpy as np
import collections
import json
def str2bool(str):
return True if str.lower() == 'true' else False
def setup_logging(verbose=1):
if verbose > 0:
logging.basicConfig(
level=lo... | --- +++ @@ -35,6 +35,10 @@
# Load and save
def load_pretrained_model(model, model_path, modules_to_load=None, exclude_modules=None):
+ '''
+ load_pretrained_model(model=model, model_path="",
+ modules_to_load=None, exclude_modules="")
+ '''
model_dict = torch.load(model_... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/ASR/CMatch/utils.py |
Add detailed documentation for each class | #!/usr/bin/env python3.6
import math
import torch as tc
from .utils import edic
from .base import Distr
__author__ = "Chang Liu"
__version__ = "1.0.1"
__email__ = "changliu@microsoft.com"
def elbo(p_joint: Distr, q_cond: Distr, obs: edic, n_mc: int=10, repar: bool=True) -> tc.Tensor: # [shape_bat] -> [shape_bat]
... | --- +++ @@ -1,4 +1,11 @@ #!/usr/bin/env python3.6
+'''Probabilistic Programming Package.
+
+The prototype is distributions, which can be a conditional one with
+functions for parameters to define the dependency. Distribution
+multiplication is implemented, as well as the mean, expectation,
+sampling with backprop capab... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/CSG/distr/tools.py |
Create structured documentation for my script | import collections
from espnet.nets.pytorch_backend.e2e_asr_transformer import *
from espnet.nets.pytorch_backend.e2e_asr_transformer import E2E as SpeechTransformer
from espnet.nets.pytorch_backend.transformer.encoder import *
from espnet.nets.pytorch_backend.transformer.decoder import *
from espnet.nets.pytorch_backe... | --- +++ @@ -150,6 +150,14 @@ ),
)
def forward(self, xs, masks, return_repr=False):
+ """Encode input sequence.
+ Args:
+ xs (torch.Tensor): Input tensor (#batch, time, idim).
+ masks (torch.Tensor): Mask tensor (#batch, time).
+ Returns:
+ ... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/ASR/CMatch/e2e_asr_udatransformer.py |
Fully document this Python code with docstrings | #!/usr/bin/env python3.6
import math
import torch as tc
from .utils import edic, edicify, expand_front, fargnames, fedic, swap_dim_ranges, tcsizeify, tcsize_broadcast, tcsize_div, tensorify
__author__ = "Chang Liu"
__version__ = "1.0.1"
__email__ = "changliu@microsoft.com"
class Distr:
default_device = None
... | --- +++ @@ -1,4 +1,11 @@ #!/usr/bin/env python3.6
+'''Probabilistic Programming Package.
+
+The prototype is distributions, which can be a conditional one with
+functions for parameters to define the dependency. Distribution
+multiplication is implemented, as well as the mean, expectation,
+sampling with backprop capab... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/CSG/distr/base.py |
Generate missing documentation strings | import torch
import numpy as np
'''
Borrowed and modified from neural_sp:
https://github.com/hirofumi0810/neural_sp/blob/154d9248b54e3888797fd81f93adc4700a75509a/neural_sp/models/seq2seq/decoders/ctc.py#L625
'''
LOG_0 = -1e10
LOG_1 = 0
def np2tensor(array, device=None):
tensor = torch.from_numpy(array).to(devi... | --- +++ @@ -10,9 +10,23 @@ LOG_1 = 0
def np2tensor(array, device=None):
+ """Convert form np.ndarray to torch.Tensor.
+ Args:
+ array (np.ndarray): A tensor of any sizes
+ Returns:
+ tensor (torch.Tensor):
+ """
tensor = torch.from_numpy(array).to(device)
return tensor
def pad_li... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/ASR/CMatch/ctc_aligner.py |
Document this script properly | # Copyright 2019 Shigeki Karita
# Apache 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
from argparse import Namespace
from distutils.util import strtobool
import logging
import math
import numpy
import torch
from espnet.nets.pytorch_backend.e2e_asr_transformer import *
from espnet.nets.pytorch_backend.transfo... | --- +++ @@ -1,6 +1,7 @@ # Copyright 2019 Shigeki Karita
# Apache 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
+"""Transformer speech recognition model (pytorch)."""
from argparse import Namespace
from distutils.util import strtobool
@@ -36,6 +37,7 @@
class SimAdapter(MultiHeadedAttention):
def __ini... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/ASR/Adapter/e2e_asr_adaptertransformer.py |
Add docstrings to my Python code | #!/usr/bin/env python3.6
import sys
import math
import torch as tc
sys.path.append('..')
from distr import Distr, edic
__author__ = "Chang Liu"
__email__ = "changliu@microsoft.com"
def elbo_z2xy(p_zx: Distr, p_y1z: Distr, q_z1x: Distr, obs_xy: edic, n_mc: int=0, wlogpi: float=1., repar: bool=True) -> tc.Tensor:
i... | --- +++ @@ -1,4 +1,7 @@ #!/usr/bin/env python3.6
+""" Modification to the `distr` package for the structure of the
+ Causal Semantic Generative model.
+"""
import sys
import math
import torch as tc
@@ -9,6 +12,9 @@ __email__ = "changliu@microsoft.com"
def elbo_z2xy(p_zx: Distr, p_y1z: Distr, q_z1x: Distr, obs_... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/CSG/methods/xdistr.py |
Add missing documentation to my Python functions | import torch
import logging
from espnet.asr.asr_utils import add_results_to_json
import argparse
import numpy as np
import collections
import json
def load_head_from_pretrained_model(model, model_path):
model_dict = torch.load(model_path, map_location=lambda storage, loc: storage)
if "model" in model_dict.key... | --- +++ @@ -20,6 +20,9 @@ model.load_state_dict(dst_state)
def load_adapter_from_pretrained_model(model, model_path, src_adapter, tgt_adapter):
+ '''
+ src_adapter, tgt_adapter: str, names of the source and target adapters to load parameters
+ '''
model_dict = torch.load(model_path, map_location=la... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/ASR/Adapter/utils.py |
Write docstrings for backend logic | #!/usr/bin/env python3.6
import torch as tc
from functools import partial, wraps
from inspect import signature
__author__ = "Chang Liu"
__version__ = "1.0.1"
__email__ = "changliu@microsoft.com"
# enhanced dictionary
class edic(dict):
def __and__(self, other): return edic({k:other[k] for k in set(self) & set(oth... | --- +++ @@ -1,4 +1,11 @@ #!/usr/bin/env python3.6
+'''Probabilistic Programming Package.
+
+The prototype is distributions, which can be a conditional one with
+functions for parameters to define the dependency. Distribution
+multiplication is implemented, as well as the mean, expectation,
+sampling with backprop capab... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/CSG/distr/utils.py |
Write docstrings describing each step | #!/usr/bin/env python3.6
import sys, os
import json
import torch as tc
import torch.nn as nn
sys.path.append('..')
from distr import tensorify, is_same_tensor, wrap4_multi_batchdims
__author__ = "Chang Liu"
__email__ = "changliu@microsoft.com"
def init_linear(nnseq, wmean, wstd, bval):
for mod in nnseq:
i... | --- +++ @@ -1,4 +1,8 @@ #!/usr/bin/env python3.6
+'''Multi-Layer Perceptron Architecture.
+
+For causal discriminative model and the corresponding generative model.
+'''
import sys, os
import json
import torch as tc
@@ -45,6 +49,11 @@ class MLPsvy1x(MLPBase):
def __init__(self, dim_x, dims_postx2prev, dim_v, di... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/CSG/arch/mlp.py |
Add documentation for all methods | import numpy as np
from sklearn import svm
def proxy_a_distance(source_X, target_X, verbose=False):
nb_source = np.shape(source_X)[0]
nb_target = np.shape(target_X)[0]
if verbose:
print('PAD on', (nb_source, nb_target), 'examples')
C_list = np.logspace(-5, 4, 10)
half_source, half_target... | --- +++ @@ -2,6 +2,9 @@ from sklearn import svm
def proxy_a_distance(source_X, target_X, verbose=False):
+ """
+ Compute the Proxy-A-Distance of a source/target representation
+ """
nb_source = np.shape(source_X)[0]
nb_target = np.shape(target_X)[0]
@@ -37,6 +40,9 @@
def estimate_mu(_X1, _Y1... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/DeepMEDA/dynamic_factor.py |
Generate docstrings for exported functions |
from __future__ import absolute_import
import random
import cv2
import keras
import numpy as np
from evaldnn.utils import common
class ImageNetValData():
class ImageNetValDataX():
def __init__(self, dir, filenames, fashion, size, transform):
self._dir = dir
self._filenames = ... | --- +++ @@ -1,3 +1,6 @@+"""
+Provides some useful utils for keras model evaluation.
+"""
from __future__ import absolute_import
@@ -11,6 +14,31 @@
class ImageNetValData():
+ """ Class for loading and preprocessing imagenet validation set.
+
+ One can download the imagenet validation set at http://image-n... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/ReMoS/CV_adv/nc_prune/coverage/utils/keras.py |
Create documentation strings for testing functions |
from __future__ import absolute_import
import random
import warnings
import numpy as np
import tensorflow as tf
from tensorflow.contrib.slim.nets import inception
from tensorflow.contrib.slim.nets import nasnet
from tensorflow.contrib.slim.nets import pnasnet
from tensorflow.contrib.slim.nets import resnet_v1
from t... | --- +++ @@ -1,3 +1,6 @@+"""
+Provides some useful utils for tensorflow model evaluation.
+"""
from __future__ import absolute_import
@@ -17,6 +20,36 @@
class ImageNetValData():
+ """ Class for loading and preprocessing imagenet validation set.
+
+ One can download the imagenet validation set at http://im... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/ReMoS/CV_adv/nc_prune/coverage/utils/tensorflow.py |
Write docstrings for backend logic |
from __future__ import absolute_import
import random
import PIL
import numpy as np
import torch
import torchvision
from evaldnn.utils import common
class ImageNetValDataset(torch.utils.data.Dataset):
mean = (0.485, 0.456, 0.406)
std = (0.229, 0.224, 0.225)
def __init__(self, resize_size, center_crop... | --- +++ @@ -1,3 +1,6 @@+"""
+Provides some useful utils for torch model evaluation.
+"""
from __future__ import absolute_import
@@ -12,6 +15,30 @@
class ImageNetValDataset(torch.utils.data.Dataset):
+ """ Class for loading and preprocessing imagenet validation set.
+
+ One can download the imagenet valid... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/ReMoS/CV_adv/nc_prune/coverage/utils/pytorch.py |
Add docstrings with type hints explained | import torch
import torch.nn as nn
from torch.utils.model_zoo import load_url as load_state_dict_from_url
from pdb import set_trace as st
__all__ = ['ResNet', 'resnet18', 'resnet34', 'resnet50', 'resnet101',
'resnet152', 'resnext50_32x4d', 'resnext101_32x8d',
'wide_resnet50_2', 'wide_resnet101_2'... | --- +++ @@ -22,11 +22,13 @@
def conv3x3(in_planes, out_planes, stride=1, groups=1, dilation=1):
+ """3x3 convolution with padding"""
return nn.Conv2d(in_planes, out_planes, kernel_size=3, stride=stride,
padding=dilation, groups=groups, bias=False, dilation=dilation)
def conv1x1(in... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/ReMoS/CV_adv/model/fe_resnet.py |
Add return value explanations in docstrings |
from __future__ import absolute_import
import numpy as np
from numba import njit, prange
import copy
from .utils import common
from pdb import set_trace as st
class MyNeuronCoverage:
def __init__(self, threshold=0.5):
self._threshold = threshold
self._layer_neuron_id_to_global_neuron_id = {}
... | --- +++ @@ -1,3 +1,6 @@+"""
+Provides a class for model neuron coverage evaluation.
+"""
from __future__ import absolute_import
@@ -9,6 +12,18 @@ from pdb import set_trace as st
class MyNeuronCoverage:
+ """ Class for model neuron coverage evaluation.
+
+ Based on the outputs of the intermediate layers, u... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/ReMoS/CV_backdoor/remos/coverage/my_neuron_coverage.py |
Improve documentation using docstrings |
from __future__ import absolute_import
import numpy as np
from numba import njit, prange
from .utils import common
from .my_neuron_coverage import MyNeuronCoverage
from pdb import set_trace as st
class TopKNeuronCoverage(MyNeuronCoverage):
def __init__(self, k=5):
super(TopKNeuronCoverage, self).__init_... | --- +++ @@ -1,3 +1,6 @@+"""
+Provides a class for model neuron coverage evaluation.
+"""
from __future__ import absolute_import
@@ -19,6 +22,29 @@ @staticmethod
@njit(parallel=True)
def _calc_1(intermediate_layer_output, features_index, threshold):
+ """Calculate the mean of each output from e... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/ReMoS/CV_adv/nc_prune/coverage/top_k_coverage.py |
Provide docstrings following PEP 257 |
from __future__ import absolute_import
import numpy as np
from numba import njit, prange
import copy
from .utils import common
from pdb import set_trace as st
class MyNeuronCoverage:
def __init__(self, threshold=0.5):
self._threshold = threshold
self._layer_neuron_id_to_global_neuron_id = {}
... | --- +++ @@ -1,3 +1,6 @@+"""
+Provides a class for model neuron coverage evaluation.
+"""
from __future__ import absolute_import
@@ -9,6 +12,18 @@ from pdb import set_trace as st
class MyNeuronCoverage:
+ """ Class for model neuron coverage evaluation.
+
+ Based on the outputs of the intermediate layers, u... | https://raw.githubusercontent.com/jindongwang/transferlearning/HEAD/code/deep/ReMoS/CV_adv/nc_prune/coverage/my_neuron_coverage.py |
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