From 1c5061b961c4d8bca7e4174f1347a86adae3dba5 Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Sat, 16 Mar 2024 18:38:00 +0100
Subject: [PATCH] Simplify toolchain to use ruff instead of
black/isort/docformatter; Update all files to match setup rules
---
.pre-commit-config.yaml | 9 +--
.../tbx11k_make_splits.py | 0
src/mednet/utils/summary.py | 61 -------------------
3 files changed, 2 insertions(+), 68 deletions(-)
rename src/mednet/config/data/tbx11k/make_splits_from_database.py => helpers/tbx11k_make_splits.py (100%)
delete mode 100644 src/mednet/utils/summary.py
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4e949b9a..079c8eae 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,22 +7,17 @@
# See https://pre-commit.com/hooks.html for more hooks
repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.3.2
+ rev: v0.3.3
hooks:
- id: ruff
args: [ --fix ]
- id: ruff-format
- - repo: https://github.com/pycqa/docformatter
- rev: v1.7.5
- hooks:
- - id: docformatter
- args: [ --wrap-summaries=0 ]
- repo: https://github.com/numpy/numpydoc
rev: v1.6.0
hooks:
- id: numpydoc-validation
- repo: https://github.com/pre-commit/mirrors-mypy
- rev: v1.8.0
+ rev: v1.9.0
hooks:
- id: mypy
args: [ --install-types, --non-interactive, --no-strict-optional, --ignore-missing-imports ]
diff --git a/src/mednet/config/data/tbx11k/make_splits_from_database.py b/helpers/tbx11k_make_splits.py
similarity index 100%
rename from src/mednet/config/data/tbx11k/make_splits_from_database.py
rename to helpers/tbx11k_make_splits.py
diff --git a/src/mednet/utils/summary.py b/src/mednet/utils/summary.py
deleted file mode 100644
index bff705e3..00000000
--- a/src/mednet/utils/summary.py
+++ /dev/null
@@ -1,61 +0,0 @@
-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-# Adapted from https://github.com/pytorch/pytorch/issues/2001#issuecomment-405675488
-
-from functools import reduce
-
-import torch
-
-from torch.nn.modules.module import _addindent
-
-
-# ignore this space!
-def _repr(model: torch.nn.Module) -> tuple[str, int]:
- # We treat the extra repr like the sub-module, one item per line
- extra_lines = []
- extra_repr = model.extra_repr()
- # empty string will be split into list ['']
- if extra_repr:
- extra_lines = extra_repr.split("\n")
- child_lines = []
- total_params = 0
- for key, module in model._modules.items():
- mod_str, num_params = _repr(module)
- mod_str = _addindent(mod_str, 2)
- child_lines.append("(" + key + "): " + mod_str)
- total_params += num_params
- lines = extra_lines + child_lines
-
- for _, p in model._parameters.items():
- if hasattr(p, "dtype"):
- total_params += reduce(lambda x, y: x * y, p.shape)
-
- main_str = model._get_name() + "("
- if lines:
- # simple one-liner info, which most builtin Modules will use
- if len(extra_lines) == 1 and not child_lines:
- main_str += extra_lines[0]
- else:
- main_str += "\n " + "\n ".join(lines) + "\n"
-
- main_str += ")"
- main_str += f", {total_params:,} params"
- return main_str, total_params
-
-
-def summary(model: torch.nn.Module) -> tuple[str, int]:
- """Count the number of parameters in each model layer.
-
- Parameters
- ----------
- model
- Model to summarize.
-
- Returns
- -------
- tuple[int, str]
- A tuple containing a multiline string representation of the network and the number of parameters.
- """
- return _repr(model)
--
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