Rename to brainglobe-space

.github/workflows/test_and_deploy.yml

@@ -2,33 +2,62 @@ name: Run tests
 
 on:
   push:
-    branches: [ main ]
+    branches:
+      - "main"
+    tags:
+      - "v**"
   pull_request:
+  workflow_dispatch:
+
+concurrency:
+  # Cancel this workflow if it is running,
+  # and then changes are applied on top of the HEAD of the branch,
+  # triggering another run of the workflow
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
-  lint:
+  linting:
+    name: Check Linting
     runs-on: ubuntu-latest
     steps:
-      - uses: neuroinformatics-unit/actions/lint@v1
+      - uses: neuroinformatics-unit/actions/lint@v2
+
+  manifest:
+    name: Check Manifest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: neuroinformatics-unit/actions/lint@v2
 
   test:
-    needs: lint
-    name: ${{ matrix.os }} py${{ matrix.python-version }}
+    name: Run package tests
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # Run across a mixture of Python versions and operating systems
         include:
         - os: ubuntu-latest
           python-version: "3.11"
         - os: macos-latest
           python-version: "3.10"
         - os: windows-latest
           python-version: "3.9"
-        - os: ubuntu-latest
-          python-version: "3.8"
 
     steps:
       - uses: neuroinformatics-unit/actions/test@v1
         with:
           python-version: ${{ matrix.python-version }}
+
+  build_sdist_wheel:
+    name: Build source distribution and wheel
+    needs: [test, linting, manifest]
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    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 }}

MANIFEST.in

@@ -1,2 +1,10 @@
 include LICENSE
 include README.md
+
+exclude .pre-commit-config.yaml
+exclude .codecov.yml
+
+graft brainglobe_space
+
+prune tests
+prune docs

README.md

@@ -1,34 +1,27 @@
-# `bg-space` has become `brainglobe-space`
-
-To continue receiving updates, please switch to using [`brainglobe-space`](https://github.com/brainglobe/brainglobe-space) instead of this package.
-`bg-space` will no longer be receiving updates, and has been replaced by `brainglobe-space` in all other aspects of the BrainGlobe tool suite.
-
-Old README.md contents are below.
-
-# BG-Space
-
-Anatomical space conventions made easy.
-
-[![Python Version](https://img.shields.io/pypi/pyversions/bg-space.svg)](https://pypi.org/project/bg-space)
-[![PyPI](https://img.shields.io/pypi/v/bg-space.svg)](https://pypi.org/project/bg-space)
-[![Build Status](https://travis-ci.com/brainglobe/bg-space.svg?branch=master)](https://travis-ci.com/brainglobe/bg-space)
+[![Python Version](https://img.shields.io/pypi/pyversions/brainglobe-space.svg)](https://pypi.org/project/brainglobe-space)
+[![PyPI](https://img.shields.io/pypi/v/brainglobe-space.svg)](https://pypi.org/project/brainglobe-space)
+[![Build Status](https://travis-ci.com/brainglobe/brainglobe-space.svg?branch=master)](https://travis-ci.com/brainglobe/brainglobe-space)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
-[![Coverage Status](https://coveralls.io/repos/github/brainglobe/bg-space/badge.svg)](https://coveralls.io/github/brainglobe/bg-space)
+[![Coverage Status](https://coveralls.io/repos/github/brainglobe/brainglobe-space/badge.svg)](https://coveralls.io/github/brainglobe/brainglobe-space)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4552537.svg)](https://doi.org/10.5281/zenodo.4552537)
 
+# brainglobe-space
+
+Anatomical space conventions made easy.
+
 Working with anatomical images, one often encounters the problem of matching the orientation of stacks with different conventions about axes orientation and order. Moreover, when multiple swaps and flips are involved, it can be annoying to map the same transformations to volumes and points (e.g., coordinates or meshes).
 
-`bg-space` provides a neat way of defining an anatomical space, and of operating stacks and point transformations between spaces.
+`brainglobe-space` provides a neat way of defining an anatomical space, and of operating stacks and point transformations between spaces.
 
-If you use `bg-space` for your analyses, please cite its Zenodo DOI https://zenodo.org/record/4552537#.YDAFzi1Q2Rs!
+If you use `brainglobe-space` for your analyses, please cite its [Zenodo DOI](https://zenodo.org/record/4552537#.YDAFzi1Q2Rs!) <https://zenodo.org/record/4552537#.YDAFzi1Q2Rs!>
 
 ## Installation
 
-You can install `bg-space` with:
+You can install `brainglobe-space` with:
 
 ```bash
-pip install bg-space
+pip install brainglobe-space
 ```
 
 ## Usage
@@ -43,7 +36,7 @@ target_origin = ("Inferior", "Posterior", "Right")
 A stack can be then easily transformed from the source to the target space:
 
 ```python
-import bg_space as bg
+import brainglobe_space as bg
 import numpy as np
 stack = np.random.rand(3, 2, 4)
 
@@ -60,7 +53,8 @@ mapped_stack = bg.map_stack_to("lsa", "ipr", stack)
 ```
 
 ---
-**NOTE**
+
+## NOTE
 
 When you work with a stack, the origin is the upper left corner when you show the first element `stack[0, :, :]` with matplotlib or when you open the stack with ImageJ. First dimension is the one that you are slicing, the second the height of the image, and the third the width of the image.
 
@@ -84,7 +78,6 @@ mapped_stack = source_space.map_stack_to("ipr", stack)  # transform the stack
 mapped_annotations = source_space.map_points_to("ipr", annotations)  # transform the points
 ```
 
-
 The points are transformed through the generation of a transformation matrix.
 Finally, if we want to log this matrix (e.g., to reconstruct the full transformations sequence of a registration), we can get it:
 
@@ -98,6 +91,7 @@ transformation_matrix = source_space.transformation_matrix_to("ipr", stack.shape
 The target get always be defined as a `bg.AnatomicalSpace` object, or a valid origin specification plus a shape (the shape is required only if axes flips are required).
 
 ## Matching space resolutions and offsets
+
 The `AnatomicalSpace` class can deal also with stack resampling/padding/cropping. This requires simply specifying values for resolutions and offsets when instantiating a `AnatomicalSpace` object. Once that is done, using `AnatomicalSpace.transformation_matrix_to` creating affine transformation matrices from one space to the other will be a piece of cake!
 
 ```python
@@ -114,7 +108,6 @@ target_space = bgs.AnatomicalSpace("asl", resolution=(1, 1, 1), shape=(5, 4, 2))
 source_space.transformation_matrix_to(target_space, stack, to_target_shape=True)
 ```
 
-
 ## Easy iteration over projections
 
 Finally, another convenient feature of BGSpace is the possibility of iterating easily through the projections of the stack and generate section names and axes labels:
@@ -130,7 +123,8 @@ for i, (plane, labels) in enumerate(zip(sc.sections, sc.axis_labels)):
     axs[i].set_xlabel(labels[1])
 ```
 
-![](/docs/img/projections.png)
+![Projection illustrations](/docs/img/projections.png)
 
 ## Contributing
+
 Contributions are very welcome. Please see the [developers guide](https://brainglobe.info/developers/index.html).

brainglobe_space/__init__.py

@@ -0,0 +1,10 @@
+__author__ = """Luigi Petrucco @brainglobe"""
+__version__ = "0.6.0"
+
+from brainglobe_space.core import AnatomicalSpace, SpaceConvention
+from brainglobe_space.functions import (
+    map_to,
+    map_stack_to,
+    transformation_matrix_to,
+    transform_points_to,
+)

bg_space/core.py → brainglobe_space/core.py

@@ -4,7 +4,7 @@
 import numpy as np
 from scipy import ndimage as nd
 
-from bg_space.utils import deprecated, ordered_list_from_set
+from brainglobe_space.utils import deprecated, ordered_list_from_set
 
 
 def to_target(method):
@@ -486,7 +486,7 @@ def __eq__(self, other):
 
 @deprecated(
     "SpaceConvention will be removed from v0.6. "
-    "Use bg_space.AnatomicalSpace instead"
+    "Use brainglobe_space.AnatomicalSpace instead"
 )
 class SpaceConvention(AnatomicalSpace):
     pass

bg_space/functions.py → brainglobe_space/functions.py

@@ -1,4 +1,4 @@
-from bg_space.core import AnatomicalSpace
+from brainglobe_space.core import AnatomicalSpace
 
 
 # TODO convert to a smarter way to generate those parsing class' methods:

pyproject.toml

@@ -1,66 +1,67 @@
 [project]
-name = "bg_space"
+name = "brainglobe_space"
 description = "Anatomical space conventions made easy"
 readme = "README.md"
-authors = [
-    {name = "Luigi Petrucco", email = "[email protected]"},
-]
+authors = [{ name = "Luigi Petrucco", email = "[email protected]" }]
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
     "Operating System :: OS Independent",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
 ]
-requires-python = ">=3.8"
-dependencies = [
-    "numpy",
-    "scipy",
-]
+requires-python = ">=3.9"
+dependencies = ["numpy", "scipy"]
 dynamic = ["version"]
 
 [project.urls]
-Homepage = "https://github.com/brainglobe/bg-space"
+Homepage = "https://github.com/brainglobe/brainglobe-space"
 
 [project.optional-dependencies]
-dev = [
-    "gitpython",
-    "pre-commit",
-    "pytest",
-    "pytest-cov",
-]
+dev = ["gitpython", "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]
 include-package-data = true
 
 [tool.setuptools.packages.find]
-include = ["bg_space*"]
+include = ["brainglobe_space*"]
 
 [tool.setuptools_scm]
 
 [tool.pytest.ini_options]
-filterwarnings = [
-    "error",
-]
+filterwarnings = ["error"]
 
 [tool.black]
-target-version = ['py38', 'py39', 'py310', 'py311']
+target-version = ['py39', 'py310', 'py311']
 skip-string-normalization = false
 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{39,310,311}
+
+[gh-actions]
+python =
+    3.9: py39
+    3.10: py310
+    3.11: py311
+
+[testenv]
+extras =
+    dev
+commands =
+    pytest -v --color=yes --cov=brainglobe_space --cov-report=xml
+"""

tests/test_core.py

@@ -4,7 +4,7 @@
 import numpy as np
 import pytest
 
-from bg_space import AnatomicalSpace, SpaceConvention
+from brainglobe_space import AnatomicalSpace, SpaceConvention
 
 from .utils import create_label_array
 

tests/test_functions.py

@@ -1,8 +1,8 @@
 import numpy as np
 import pytest
 
-from bg_space.core import AnatomicalSpace
-from bg_space.functions import (
+from brainglobe_space.core import AnatomicalSpace
+from brainglobe_space.functions import (
     map_stack_to,
     map_to,
     transform_points_to,

tests/utils.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from bg_space import AnatomicalSpace
+from brainglobe_space import AnatomicalSpace
 
 char_add = np.core.defchararray.add