From dd6398aace6388ce52f57eec97bdec026068349a Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Tue, 6 Feb 2024 13:38:17 +0000
Subject: [PATCH 1/2] Bring in line with other package CIs

---
 .github/workflows/test_and_deploy.yml | 15 ++++++++----
 MANIFEST.in                           | 11 +++++++++
 pyproject.toml                        | 33 +++++++++++++++++++++++++++
 tox.ini                               | 28 -----------------------
 4 files changed, 55 insertions(+), 32 deletions(-)
 create mode 100644 MANIFEST.in
 delete mode 100644 tox.ini

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 7d3a31d..8bd634c 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -2,11 +2,12 @@ name: tests
 
 on:
   push:
-    branches: [ main ]
+    branches:
+      - "main"
     tags:
-      - '*'
+      - 'v*'
   pull_request:
-    branches: [ '*' ]
+  workflow_dispatch:
 
 jobs:
   linting:
@@ -14,8 +15,14 @@ jobs:
     steps:
       - uses: neuroinformatics-unit/actions/lint@v1
 
+  manifest:
+    name: Check Manifest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/check_manifest@v2
+
   test:
-    needs: [linting]
+    needs: [linting, manifest]
     name: ${{ matrix.os }} py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..fc9d53f
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,11 @@
+include LICENSE
+include README.md
+
+exclude .pre-commit-config.yaml
+exclude codecov.yml
+
+include .napari/config.yml
+
+graft brainglobe_segmentation
+
+prune tests
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 621ddc2..8f0634c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -83,3 +83,36 @@ line-length = 79
 exclude = ["__init__.py", "build", ".eggs"]
 select = ["I", "E", "F"]
 fix = true
+
+[tool.tox]
+legacy_tox_ini = """
+# For more information about tox, see https://tox.readthedocs.io/en/latest/
+[tox]
+envlist = py{38,39,310}
+
+[gh-actions]
+python =
+    3.8: py38
+    3.9: py39
+    3.10: py310
+
+[testenv]
+passenv =
+    CI
+    GITHUB_ACTIONS
+    DISPLAY
+    XAUTHORITY
+    NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
+    PYVISTA_OFF_SCREEN
+deps =
+    pytest  # https://docs.pytest.org/en/latest/contents.html
+    pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
+    pytest-qt  # https://pytest-qt.readthedocs.io/en/latest/
+    coverage
+    napari
+    pyqt5
+    magicgui
+
+commands = pytest -v --color=yes --cov=brainglobe_segmentation --cov-report=xml
+
+"""
diff --git a/tox.ini b/tox.ini
deleted file mode 100644
index 031ceba..0000000
--- a/tox.ini
+++ /dev/null
@@ -1,28 +0,0 @@
-# For more information about tox, see https://tox.readthedocs.io/en/latest/
-[tox]
-envlist = py{38,39,310}
-
-[gh-actions]
-python =
-    3.8: py38
-    3.9: py39
-    3.10: py310
-
-[testenv]
-passenv =
-    CI
-    GITHUB_ACTIONS
-    DISPLAY
-    XAUTHORITY
-    NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
-    PYVISTA_OFF_SCREEN
-deps =
-    pytest  # https://docs.pytest.org/en/latest/contents.html
-    pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
-    pytest-qt  # https://pytest-qt.readthedocs.io/en/latest/
-    coverage
-    napari
-    pyqt5
-    magicgui
-
-commands = pytest -v --color=yes --cov=brainglobe_segmentation --cov-report=xml

From df4bee0e9b75c82dc5e9063f914a28179c17ecbe Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 6 Feb 2024 13:39:42 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 MANIFEST.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index fc9d53f..0d95878 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -8,4 +8,4 @@ include .napari/config.yml
 
 graft brainglobe_segmentation
 
-prune tests
\ No newline at end of file
+prune tests