new commit with work from temporary repo

decided to keep everything here instead of in `brainglobe-scripts`
`brainglobe-scripts` is now obsolete.

.github/workflows/test_and_deploy.yml

@@ -0,0 +1,66 @@
+name: tests
+
+on:
+  push:
+    branches:
+      - '*'
+    tags:
+      - '*'
+  pull_request:
+
+jobs:
+  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: [linting, manifest]
+    name: ${{ matrix.os }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # Run all supported Python versions on linux
+        python-version: ["3.8", "3.9", "3.10"]
+        os: [ubuntu-latest]
+        # Include one windows and macos run
+        include:
+        - os: macos-latest
+          python-version: "3.10"
+        - os: windows-latest
+          python-version: "3.10"
+
+    steps:
+      # Run tests
+      - uses: neuroinformatics-unit/actions/test@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+  build_sdist_wheels:
+    name: Build source distribution
+    needs: [test]
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    runs-on: ubuntu-latest
+    steps:
+    - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
+
+
+  upload_all:
+    name: Publish build distributions
+    needs: [build_sdist_wheels]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v3
+      with:
+        name: artifact
+        path: dist
+    - uses: pypa/[email protected]
+      with:
+        user: __token__
+        password: ${{ secrets.TWINE_API_KEY }}

.gitignore

@@ -0,0 +1,83 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+**/_version.py

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: check-docstring-first
+          - id: check-executables-have-shebangs
+          - id: check-merge-conflict
+          - id: check-toml
+          - id: end-of-file-fixer
+          - id: mixed-line-ending
+            args: [--fix=lf]
+          - id: requirements-txt-fixer
+          - id: trailing-whitespace
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.272
+      hooks:
+        - id: ruff
+    - repo: https://github.com/psf/black
+      rev: 23.3.0
+      hooks:
+          - id: black
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v1.3.0
+      hooks:
+          - id: mypy
+            additional_dependencies:
+                - types-setuptools
+    - repo: https://github.com/mgedmin/check-manifest
+      rev: "0.49"
+      hooks:
+          - id: check-manifest
+            args: [--no-build-isolation]
+            additional_dependencies: [setuptools-scm]

LICENSE

@@ -0,0 +1,28 @@
+
+Copyright (c) 2023, BrainGlobe developers
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of brainglobe-scripts nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -0,0 +1,8 @@
+include LICENSE
+include README.md
+exclude .pre-commit-config.yaml
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude docs *
+recursive-exclude tests *

README.md

@@ -0,0 +1 @@
+# brainglobe-workflows

brainglobe_workflows/__init__.py

@@ -0,0 +1,7 @@
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("brainglobe-scripts")
+except PackageNotFoundError:
+    # package is not installed
+    pass

pyproject.toml

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+[project]
+name = "brainglobe-workflows"
+authors = [{name = "BrainGlobe developers", email= "[email protected]"}]
+description = "A place to keep scripts to use as benchmarks, user-examples end-to-end tests and for tutorials"
+readme = "README.md"
+requires-python = ">=3.8.0"
+dynamic = ["version"]
+
+license = {text = "BSD-3-Clause"}
+
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Operating System :: OS Independent",
+    "License :: OSI Approved :: BSD License",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/brainglobe/brainglobe-scripts"
+"Bug Tracker" = "https://github.com/brainglobe/brainglobe-scripts/issues"
+"Documentation" = "https://github.com/brainglobe/brainglobe-scripts"
+"Source Code" = "https://github.com/brainglobe/brainglobe-scripts"
+"User Support" = "https://github.com/brainglobe/brainglobe-scripts/issues"
+
+[project.optional-dependencies]
+dev = [
+  "pytest",
+  "pytest-cov",
+  "coverage",
+  "tox",
+  "black",
+  "mypy",
+  "pre-commit",
+  "ruff",
+  "setuptools_scm",
+]
+
+[build-system]
+requires = [
+    "setuptools>=45",
+    "wheel",
+    "setuptools_scm[toml]>=6.2",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+include = ["brainglobe_scripts*"]
+exclude = ["tests*"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=brainglobe_scripts"
+
+[tool.black]
+target-version = ['py38', 'py39', 'py310']
+skip-string-normalization = false
+line-length = 79
+
+[tool.setuptools_scm]
+
+[tool.check-manifest]
+ignore = [
+  ".yaml",
+  "tox.ini",
+  "tests/",
+  "tests/test_unit/",
+  "tests/test_integration/",
+]
+
+[tool.ruff]
+line-length = 79
+exclude = ["__init__.py","build",".eggs"]
+select = ["I", "E", "F"]
+fix = true
+
+[tool.cibuildwheel]
+build = "cp38-* cp39-* cp310-*"
+
+[tool.cibuildwheel.macos]
+archs = ["x86_64", "arm64"]
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+envlist = py{38,39,310}
+isolated_build = True
+
+[gh-actions]
+python =
+    3.8: py38
+    3.9: py39
+    3.10: py310
+
+[testenv]
+extras =
+    dev
+commands =
+    pytest -v --color=yes --cov=brainglobe_scripts --cov-report=xml
+"""

tests/test_unit/test_placeholder.py

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+def test_placeholder():
+    assert True