From 464ed5b0b62ba615cbe4b49af621ace0f53a30b4 Mon Sep 17 00:00:00 2001
From: Daniel CARRON <daniel.carron@idiap.ch>
Date: Mon, 11 Mar 2024 13:36:53 +0000
Subject: [PATCH] Use hatchling and versioningit for versioning
---
.gitignore | 1 +
.gitlab-ci.yml | 6 +++
MANIFEST.in | 7 ----
conda/meta.yaml | 7 +++-
pyproject.toml | 79 +++++++++++++++++++++----------------
setup.py | 7 ----
src/mednet/scripts/utils.py | 25 +++++++++++-
7 files changed, 81 insertions(+), 51 deletions(-)
delete mode 100644 MANIFEST.in
delete mode 100644 setup.py
diff --git a/.gitignore b/.gitignore
index f49b5922..801bf4d0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,3 +27,4 @@ _work/
.pytest_cache/
results*/
trainlog.pdf
+*_version.py
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0ad8ee2d..771c784d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -12,6 +12,12 @@ variables:
GIT_SUBMODULE_DEPTH: 1
XDG_CONFIG_HOME: $CI_PROJECT_DIR/tests/data
+.snippets:
+ setup-metadata:
+ - pip install hatch
+ - PACKAGE_NAME=$(hatch project metadata name)
+ - PACKAGE_VERSION=$(hatch project metadata version)
+
documentation:
before_script:
# for opencv-python dependence
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 5b589c03..00000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,7 +0,0 @@
-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-recursive-include doc *.rst *.png
-recursive-include tests *.py *.png *.csv *.json
-recursive-include src/mednet/config/data *.json *.json.bz2
diff --git a/conda/meta.yaml b/conda/meta.yaml
index 33434fb6..66ef954d 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -6,14 +6,14 @@
package:
name: {{ data['project']['name'] }}
- version: {{ data['project']['version'] }}
+ version: {{ environ.get('PACKAGE_VERSION') }}
source:
path: ..
build:
noarch: python
- number: {{ environ.get('USE_BUILD_NUMBER', 0) }}
+ number: {{ environ.get('NEXT_BUILD_NUMBER', 0) }}
run_exports:
- {{ pin_subpackage(data['project']['name']) }}
script:
@@ -23,6 +23,8 @@ requirements:
host:
- python >=3.10
- pip
+ - hatchling
+ - versioningit
- clapper {{ clapper }}
- click {{ click }}
- credible {{ credible }}
@@ -43,6 +45,7 @@ requirements:
- lightning >=2.2.0
run:
- python >=3.10
+ - versioningit
- {{ pin_compatible('clapper') }}
- {{ pin_compatible('click') }}
- {{ pin_compatible('credible') }}
diff --git a/pyproject.toml b/pyproject.toml
index 11192a1d..f56c58a3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,21 +3,22 @@
# SPDX-License-Identifier: GPL-3.0-or-later
[build-system]
-requires = ["setuptools>=61.0.0", "wheel"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling", "versioningit"]
+build-backend = "hatchling.build"
[project]
name = "mednet"
-version = "1.0.0b0"
+dynamic = ["version"]
requires-python = ">=3.10"
description = "Benchmarks for Computer-Aided Disease Detection from Medical Data."
-dynamic = ["readme"]
+readme = "README.md"
license = { text = "GNU General Public License v3 (GPLv3)" }
authors = [{ name = "Geoffrey Raposo", email = "geoffrey@raposo.ch" }]
maintainers = [
{ name = "Andre Anjos", email = "andre.anjos@idiap.ch" },
{ name = "Daniel Carron", email = "daniel.carron@idiap.ch" },
]
+
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Developers",
@@ -26,6 +27,7 @@ classifiers = [
"Programming Language :: Python :: 3",
"Topic :: Software Development :: Libraries :: Python Modules",
]
+
dependencies = [
"clapper",
"click",
@@ -44,8 +46,29 @@ dependencies = [
"lightning>=2.2.0",
"tensorboard",
"grad-cam>=1.4.8",
+ "versioningit",
+]
+
+[tool.hatch.version]
+source = "versioningit"
+
+[tool.hatch.build.targets.sdist]
+include = [
+ "src/**/*.py",
+ "src/**/*.json",
+ "src/**/*.json.bz2",
+ "tests/**/*.py",
+ "tests/**/*.png",
+ "tests/**/*.csv",
+ "tests/**/*.json",
+ "doc/**/*.rst",
+ "doc/**/*.png",
+ "LICENSES/*.txt",
]
+[tool.hatch.build.targets.wheel]
+packages = ["src/mednet"]
+
[project.urls]
documentation = "https://www.idiap.ch/software/biosignal/software/docs/biosignal/software/mednet/main/sphinx/"
homepage = "https://pypi.org/project/mednet"
@@ -235,16 +258,6 @@ nih-cxr14-padchest = "mednet.config.data.nih_cxr14_padchest.idiap"
# montgomery-shenzhen-indian-padchest aggregated dataset
montgomery-shenzhen-indian-padchest = "mednet.config.data.montgomery_shenzhen_indian_padchest.default"
-[tool.setuptools]
-zip-safe = true
-package-dir = { "" = "src" }
-
-[tool.setuptools.dynamic]
-readme = { file = "README.md" }
-
-[tool.distutils.bdist_wheel]
-universal = true
-
[tool.isort]
profile = "black"
line_length = 80
@@ -261,27 +274,27 @@ junit_log_passing_tests = false
[tool.numpydoc_validation]
checks = [
- "all", # report on all checks, except the below
- "ES01", # Not all functions require extended summaries
- "EX01", # Not all functions require examples
- "GL01", # Expects text to be on the line after the opening quotes but that is in direct opposition of the sphinx recommendations and conflicts with other pre-commit hooks.
- "GL08", # Causes issues if we don't have a docstring at the top of the file. Disabling this might fail to catch actual missing docstrings.
- "PR04", # numpydoc does not currently support PEP484 typehints, which we are using
- "RT03", # Since sphinx is unable to understand type annotations we need to remove some types from 'Returns', which breaks this check.
- "SA01", # We do not use Also sections
- "SS06", # Summary will span multiple lines if too long because of reformatting by other hooks.
+ "all", # report on all checks, except the below
+ "ES01", # Not all functions require extended summaries
+ "EX01", # Not all functions require examples
+ "GL01", # Expects text to be on the line after the opening quotes but that is in direct opposition of the sphinx recommendations and conflicts with other pre-commit hooks.
+ "GL08", # Causes issues if we don't have a docstring at the top of the file. Disabling this might fail to catch actual missing docstrings.
+ "PR04", # numpydoc does not currently support PEP484 typehints, which we are using
+ "RT03", # Since sphinx is unable to understand type annotations we need to remove some types from 'Returns', which breaks this check.
+ "SA01", # We do not use Also sections
+ "SS06", # Summary will span multiple lines if too long because of reformatting by other hooks.
]
-exclude = [ # don't report on objects that match any of these regex
- '\.__len__$',
- '\.__getitem__$',
- '\.__iter__$',
- '\.__exit__$',
+exclude = [ # don't report on objects that match any of these regex
+ '\.__len__$',
+ '\.__getitem__$',
+ '\.__iter__$',
+ '\.__exit__$',
]
-override_SS05 = [ # override SS05 to allow docstrings starting with these words
- '^Process ',
- '^Assess ',
- '^Access ',
- '^This',
+override_SS05 = [ # override SS05 to allow docstrings starting with these words
+ '^Process ',
+ '^Assess ',
+ '^Access ',
+ '^This',
]
diff --git a/setup.py b/setup.py
deleted file mode 100644
index f13f857e..00000000
--- a/setup.py
+++ /dev/null
@@ -1,7 +0,0 @@
-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-from setuptools import setup
-
-setup()
diff --git a/src/mednet/scripts/utils.py b/src/mednet/scripts/utils.py
index 6524ed9d..d05973d3 100644
--- a/src/mednet/scripts/utils.py
+++ b/src/mednet/scripts/utils.py
@@ -6,6 +6,7 @@
import json
import logging
import pathlib
+import re
import shutil
import lightning.pytorch
@@ -120,17 +121,37 @@ def execution_metadata() -> dict[str, int | float | str]:
# collects dependence information
package_name = __package__.split(".")[0]
requires = importlib.metadata.requires(package_name) or []
- dependence_names = [k.split()[0] for k in requires]
+ dependence_names = [re.split(r"(\=|~|!|>|<|;|\s)+", k)[0] for k in requires]
dependencies = {
k: importlib.metadata.version(k) # version number as str
for k in dependence_names
if importlib.util.find_spec(k) is not None # if is installed
}
+ # checks if the current version corresponds to a dirty (uncommitted) change
+ # set, issues a warning to the user
+ current_version = importlib.metadata.version(package_name)
+ try:
+ import versioningit
+
+ actual_version = versioningit.get_version(".", config={})
+ if current_version != actual_version:
+ logger.warning(
+ f"Version mismatch between current version set "
+ f"({current_version}) and actual version returned by "
+ f"versioningit ({actual_version}). This typically happens "
+ f"when you commit changes locally and do not re-install the "
+ f"package. Run `pip install -e .` or equivalent to fix this."
+ )
+ except Exception as e:
+ # not in a git repo?
+ logger.debug(f"Error {e}")
+ pass
+
data = {
"datetime": datetime,
"package-name": __package__.split(".")[0],
- "package-version": importlib.metadata.version(package_name),
+ "package-version": current_version,
"dependencies": dependencies,
"user": __import__("getpass").getuser(),
"conda-env": os.environ.get("CONDA_DEFAULT_ENV", ""),
--
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