From 127ed646b8d616ce70715d31a9239b08936b53a7 Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Tue, 6 Feb 2024 13:51:36 +0000
Subject: [PATCH 1/3] Update CI workflows with manifest

---
 .github/workflows/test_and_deploy.yml | 11 ++++++--
 MANIFEST.in                           |  8 ++++++
 pyproject.toml                        | 39 +++++++++++++++++----------
 tox.ini                               | 15 -----------
 4 files changed, 42 insertions(+), 31 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 368e839..09b211b 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -3,13 +3,20 @@ name: tests
 on: [push, pull_request]
 
 jobs:
-  lint:
+  linting:
+    name: Check Linting
     runs-on: ubuntu-latest
     steps:
       - uses: neuroinformatics-unit/actions/lint@v2
 
+  manifest:
+    name: Check Manifest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/check_manifest@v2
+
   test:
-    needs: lint
+    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..18039b7
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,8 @@
+exclude .pre-commit-config.yaml
+
+include LICENSE
+include README.md
+
+graft imio *.py
+
+prune tests
diff --git a/pyproject.toml b/pyproject.toml
index c400c3e..85b28b9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,7 +3,7 @@ name = "imio"
 description = "Loading and saving of image data."
 readme = "README.md"
 authors = [
-    {name = "Charly Rousseau, Adam Tyson", email = "code@adamltyson.com"},
+    { name = "Charly Rousseau, Adam Tyson", email = "code@adamltyson.com" },
 ]
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -35,19 +35,10 @@ dynamic = ['version']
 Homepage = "https://github.com/brainglobe/imio"
 
 [project.optional-dependencies]
-dev = [
-    "black",
-    "pre-commit",
-    "pytest",
-    "pytest-cov",
-]
+dev = ["black", "pre-commit", "pytest", "pytest-cov"]
 
 [build-system]
-requires = [
-    "setuptools>=45",
-    "wheel",
-    "setuptools_scm[toml]>=6.2",
-]
+requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
@@ -72,7 +63,7 @@ filterwarnings = [
     "ignore:`np.uint0` is a deprecated alias for `np.uintp`",
     "ignore:`np.void0` is a deprecated alias for `np.void`",
     "ignore:`np.bytes0` is a deprecated alias for `np.bytes_`",
-    "ignore:`np.str0` is a deprecated alias for `np.str_`"
+    "ignore:`np.str0` is a deprecated alias for `np.str_`",
 ]
 
 [tool.black]
@@ -82,6 +73,26 @@ line-length = 79
 
 [tool.ruff]
 line-length = 79
-exclude = ["__init__.py","build",".eggs"]
+exclude = ["__init__.py", "build", ".eggs"]
 select = ["I", "E", "F"]
 fix = true
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+envlist = py{38,39,310,311}
+
+[gh-actions]
+python =
+    3.8: py38
+    3.9: py39
+    3.10: py310
+    3.11: py311
+
+[testenv]
+extras =
+    dev
+commands =
+    pytest -v --color=yes --cov=imio --cov-report=xml
+
+"""
diff --git a/tox.ini b/tox.ini
deleted file mode 100644
index 978bb51..0000000
--- a/tox.ini
+++ /dev/null
@@ -1,15 +0,0 @@
-[tox]
-envlist = py{38,39,310,311}
-
-[gh-actions]
-python =
-    3.8: py38
-    3.9: py39
-    3.10: py310
-    3.11: py311
-
-[testenv]
-extras =
-    dev
-commands =
-    pytest -v --color=yes --cov=imio --cov-report=xml

From 7182b5e8372ab1a3e62c8cfdb5e5eb4bcc75337d Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Tue, 6 Feb 2024 13:52:16 +0000
Subject: [PATCH 2/3] Allow workflow to be dispatchable

---
 .github/workflows/test_and_deploy.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 09b211b..0649eb1 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -1,6 +1,13 @@
 name: tests
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - "main"
+    tags:
+      - "v**"
+  pull_request:
+  workflow_dispatch:
 
 jobs:
   linting:

From 64149110898951cf9caddf27bc3560b64a6bdb2a Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Tue, 6 Feb 2024 13:53:01 +0000
Subject: [PATCH 3/3] Add pyarrow dependency to prevent future pandas failures

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 85b28b9..0826dc5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,6 +24,7 @@ dependencies = [
     "nibabel >= 2.1.0",
     "numpy",
     "psutil",
+    "pyarrow",
     "pynrrd",
     "scikit-image",
     "tifffile",