Merge branch 'use-pixi' into 'main'

Use pixi

See merge request biosignal/software/mednet!30

.gitignore

@@ -13,8 +13,6 @@
 coverage.xml
 test_results.xml
 junit-coverage.xml
-environment.yaml
-environment.yml
 html/
 build/
 doc/api/
@@ -26,7 +24,5 @@ _work/
 .pytest_cache/
 results*/
 *_version.py
-.pixi
 .venv
-pixi.toml
-pixi.lock
+.pixi

.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/*

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

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