From 01848ea04b80568b2beef51e3b11f38c110ccf7d Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Thu, 4 Apr 2024 14:30:35 +0200
Subject: [PATCH] Implement support for pixi dev installs
---
.gitignore | 4 -
.reuse/dep5 | 1 +
conda/meta.yaml | 2 +-
pixi.lock | 11022 ++++++++++++++++++++++++++++++++++++++++++++++
pyproject.toml | 94 +-
5 files changed, 11095 insertions(+), 28 deletions(-)
create mode 100644 pixi.lock
diff --git a/.gitignore b/.gitignore
index 5ed64156..cd9b0089 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,8 +13,6 @@
coverage.xml
test_results.xml
junit-coverage.xml
-environment.yaml
-environment.yml
html/
build/
doc/api/
@@ -28,5 +26,3 @@ results*/
*_version.py
.venv
.pixi
-pixi.toml
-pixi.lock
diff --git a/.reuse/dep5 b/.reuse/dep5
index fb27b959..29e45b49 100644
--- a/.reuse/dep5
+++ b/.reuse/dep5
@@ -4,6 +4,7 @@ Upstream-Contact: Andre Anjos <andre.anjos@idiap.ch>
Source: https://gitlab.idiap.ch/biosignal/software/mednet
Files:
+ pixi.lock
.gitmodules
doc/_static/style.css
doc/_templates/*
diff --git a/conda/meta.yaml b/conda/meta.yaml
index 1a20d5a4..05cb8ac4 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -78,5 +78,5 @@ test:
about:
home: {{ data['project']['urls']['homepage'] }}
summary: {{ data['project']['description'] }}
- license: {{ data['project']['license']['text'] }}
+ license: {{ data['project']['license'] }}
license_family: GPL
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 00000000..65c9cdb5
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,11022 @@
+version: 4
+environments:
+ default:
+ channels:
+ - url: https://conda.anaconda.org/conda-forge/
+ packages:
+ linux-64:
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/absl-py-2.1.0-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/alabaster-0.7.16-pyhd8ed1ab_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.11-hd590300_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/aom-3.8.2-h59595ed_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/auto-intersphinx-1.0.3-pyhd8ed1ab_0.conda
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diff --git a/pyproject.toml b/pyproject.toml
index 673c956a..bc2fe236 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ dynamic = ["version"]
requires-python = ">=3.10"
description = "Benchmarks for Computer-Aided Disease Detection from Medical Data."
readme = "README.md"
-license = { text = "GNU General Public License v3 (GPLv3)" }
+license = "GPL-3.0-or-later"
authors = [{ name = "Geoffrey Raposo", email = "geoffrey@raposo.ch" }]
maintainers = [
{ name = "Andre Anjos", email = "andre.anjos@idiap.ch" },
@@ -49,6 +49,76 @@ dependencies = [
"versioningit",
]
+[project.urls]
+documentation = "https://www.idiap.ch/software/biosignal/software/docs/biosignal/software/mednet/main/sphinx/"
+homepage = "https://pypi.org/project/mednet"
+repository = "https://gitlab.idiap.ch/biosignal/software/mednet"
+changelog = "https://gitlab.idiap.ch/biosignal/software/mednet/-/releases"
+
+[project.optional-dependencies]
+qa = ["pre-commit"]
+doc = [
+ "sphinx",
+ "furo",
+ "sphinx-autodoc-typehints",
+ "auto-intersphinx",
+ "sphinx-copybutton",
+ "sphinx-inline-tabs",
+ "sphinx-click",
+]
+test = ["pytest", "pytest-cov"]
+
+[project.scripts]
+mednet = "mednet.scripts.cli:cli"
+
+[tool.pixi.project]
+name = "mednet"
+channels = ["conda-forge"]
+platforms = ["linux-64", "osx-arm64"]
+
+[tool.pixi.dependencies]
+clapper = "*"
+click = "*"
+credible = "*"
+numpy = "*"
+scipy = "*"
+scikit-image = "*"
+scikit-learn = "*"
+tqdm = "*"
+psutil = "*"
+tabulate = "*"
+matplotlib = "*"
+pillow = "*"
+pytorch = ">=1.8"
+torchvision = ">=0.10"
+lightning = ">=2.2.0"
+tensorboard = "*"
+grad-cam = ">=1.4.8"
+versioningit = "*"
+
+[tool.pixi.host-dependencies]
+pre-commit = "*"
+ruff = "*"
+reuse = "*"
+sphinx = "*"
+furo = "*"
+sphinx-autodoc-typehints = "*"
+auto-intersphinx = "*"
+sphinx-copybutton = "*"
+sphinx-inline-tabs = "*"
+sphinx-click = "*"
+pytest = "*"
+pytest-cov = "*"
+
+[tool.pixi.pypi-dependencies]
+mednet = { path = ".", editable = true, extras = ["qa", "doc", "test"] }
+
+[tool.pixi.tasks]
+qa-install = "pre-commit install"
+qa = "pre-commit run --all-files"
+doc = "rm -rf doc/api && rm -rf html && sphinx-build -aEW doc html"
+test = "pytest -sv tests/"
+
[tool.hatch.version]
source = "versioningit"
@@ -85,28 +155,6 @@ include = [
[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"
-repository = "https://gitlab.idiap.ch/biosignal/software/mednet"
-changelog = "https://gitlab.idiap.ch/biosignal/software/mednet/-/releases"
-
-[project.optional-dependencies]
-qa = ["pre-commit"]
-doc = [
- "sphinx",
- "furo",
- "sphinx-autodoc-typehints",
- "auto-intersphinx",
- "sphinx-copybutton",
- "sphinx-inline-tabs",
- "sphinx-click",
-]
-test = ["pytest", "pytest-cov", "coverage"]
-
-[project.scripts]
-mednet = "mednet.scripts.cli:cli"
-
[project.entry-points."mednet.config"]
# models
--
GitLab