From ae19fada3c66c7aa60bf05d7f3802b2c6e82f3fa Mon Sep 17 00:00:00 2001
From: Will Graham <32364977+willGraham01@users.noreply.github.com>
Date: Tue, 6 Feb 2024 14:15:11 +0000
Subject: [PATCH] Add manifest to ci (#118)

* Add manifest to CI

* Standardise tox.ini into pyproject
---
 .github/workflows/test_and_deploy.yml | 15 +++++--
 MANIFEST.in                           |  8 ++++
 pyproject.toml                        | 65 ++++++++++++++++-----------
 tox.ini                               | 14 ------
 4 files changed, 59 insertions(+), 43 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 7831c08..774413f 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -2,17 +2,26 @@ name: tests
 
 on:
   push:
-    branches: [ main ]
+    branches:
+      - "main"
   pull_request:
+  workflow_dispatch:
 
 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..c65627f
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,8 @@
+exclude .pre-commit-config.yaml
+
+include LICENSE
+include README.md
+
+graft bg_atlasgen *.py
+
+prune tests
diff --git a/pyproject.toml b/pyproject.toml
index 20d9259..68221d2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,9 +2,9 @@
 name = "bg-atlasgen"
 description = "Scripts generation atlases and utilities for BrainGlobe"
 readme = "README.md"
-license = {file = "LICENSE"}
+license = { file = "LICENSE" }
 authors = [
-    {name = "Luigi Petrucco, Federico Claudi, Adam Tyson", email = "code@adamltyson.com"},
+    { name = "Luigi Petrucco, Federico Claudi, Adam Tyson", email = "code@adamltyson.com" },
 ]
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -41,29 +41,23 @@ dynamic = ["version"]
 Homepage = "https://github.com/brainglobe/bg-atlasgen"
 
 [project.optional-dependencies]
-allenmouse = [
-    "allensdk",
-]
+allenmouse = ["allensdk"]
 
 dev = [
-  "pytest",
-  "pytest-cov",
-  "pytest-mock",
-  "coverage",
-  "tox",
-  "black",
-  "mypy",
-  "pre-commit",
-  "ruff",
-  "setuptools_scm",
+    "pytest",
+    "pytest-cov",
+    "pytest-mock",
+    "coverage",
+    "tox",
+    "black",
+    "mypy",
+    "pre-commit",
+    "ruff",
+    "setuptools_scm",
 ]
 
 [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]
@@ -82,17 +76,36 @@ line-length = 79
 
 [tool.check-manifest]
 ignore = [
-  "*.yaml",
-  "tox.ini",
-  "tests/*",
-  "tests/test_unit/*",
-  "tests/test_integration/*",
+    "*.yaml",
+    "tox.ini",
+    "tests/*",
+    "tests/test_unit/*",
+    "tests/test_integration/*",
 ]
 
 [tool.ruff]
 line-length = 79
-exclude = ["__init__.py","build",".eggs"]
+exclude = ["__init__.py", "build", ".eggs"]
 select = ["I", "E", "F"]
 # E501 Line too long
 ignore = ["E501"]
 fix = true
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+envlist = py{39,310,311}
+
+[gh-actions]
+python =
+    3.9: py39
+    3.10: py310
+    3.11: py311
+
+[testenv]
+extras =
+    dev
+commands =
+    pytest -v --color=yes --cov=bg_atlasgen --cov-report=xml
+
+"""
diff --git a/tox.ini b/tox.ini
deleted file mode 100644
index a53937f..0000000
--- a/tox.ini
+++ /dev/null
@@ -1,14 +0,0 @@
-[tox]
-envlist = py{39,310,311}
-
-[gh-actions]
-python =
-    3.9: py39
-    3.10: py310
-    3.11: py311
-
-[testenv]
-extras =
-    dev
-commands =
-    pytest -v --color=yes --cov=bg_atlasgen --cov-report=xml