brainglobe · willGraham01 · Feb 23, 2024 · Sep 2, 2020 · Sep 2, 2020 · Sep 2, 2020
diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
@@ -13,7 +13,7 @@ jobs:
   linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: neuroinformatics-unit/actions/lint@v1
+      - uses: neuroinformatics-unit/actions/lint@v2
 
   manifest:
     runs-on: ubuntu-latest
@@ -36,22 +36,17 @@ jobs:
           python-version: "3.9"
 
     steps:
-      - uses: neuroinformatics-unit/actions/test@v1
+      - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
 
   build_sdist_wheels:
     name: Build source distribution and wheel
     needs: [test]
-    if: (
-        github.event_name == 'push' && github.ref_type == 'tag'
-      ) || (
-        github.event_name == 'pull_request' &&
-        contains(github.event.pull_request.labels.*.name, 'Test packaging')
-      )
+    if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
     steps:
-    - uses: neuroinformatics-unit/actions/build_sdist_wheels@v1
+    - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2
 
   upload_all:
     name: Publish build distributions

diff --git a/.gitignore b/.gitignore
@@ -1,9 +1,11 @@
-bg_atlasapi/bg_config.conf
+brainglobe_atlasapi/bg_config.conf
 
 workspace.py
 .vscode/
 
 # Byte-compiled / optimized / DLL files
+__pycache__
+*.__pycache__
 __pycache__/
 *.py[cod]
 *$py.class
@@ -138,6 +140,5 @@ dmypy.json
 .vs/
 *.~lock.*
 
-
 # macOS
 *.DS_Store
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -23,10 +23,3 @@ repos:
       rev: 24.1.1
       hooks:
           - id: black
-    - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.8.0
-      hooks:
-          - id: mypy
-            additional_dependencies:
-                - types-setuptools
-                - types-requests
diff --git a/CITATION.cff b/CITATION.cff
@@ -19,9 +19,9 @@ authors:
     affiliation: 'Sainsbury Wellcome Centre, University College London'
     orcid: 'https://orcid.org/0000-0003-3225-1130'
     email: [email protected]
-repository-code: 'https://github.com/brainglobe/bg-atlasapi'
+repository-code: 'https://github.com/brainglobe/brainglobe-atlasapi'
 url: >-
-  https://brainglobe.info/documentation/bg-atlasapi/index.html
+  https://brainglobe.info/documentation/brainglobe-atlasapi/index.html
 abstract: >-
   A common interface for programmers to download and process
   brain atlas data from multiple sources.

diff --git a/LICENSE b/LICENSE
@@ -1,19 +1,17 @@
 BSD 3-Clause License
 
-Copyright (c) 2020, brainglobe
+Copyright (c) 2020, BrainGlobe
 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
+- 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,
+- 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 the copyright holder nor the names of its
+- Neither the name of the copyright holder nor the names of its
   contributors may be used to endorse or promote products derived from
   this software without specific prior written permission.
 

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -4,4 +4,9 @@ include README.md
 include requirements.txt
 
 exclude .codecov.yml
+exclude .pre-commit-config.yaml
+
+graft brainglobe_atlasapi *.py
+
+prune tests
 prune tutorials
diff --git a/README.md b/README.md
@@ -1,60 +1,61 @@
-# This package has moved!
+# brainglobe-atlasapi
 
-This package has been renamed to `brainglobe-atlasapi`.
-To continue receiving updates, please switch over to using [the new package](https://github.com/brainglobe/brainglobe-atlasapi).
-
-# BG-atlasAPI
-
-[![Python Version](https://img.shields.io/pypi/pyversions/bg-atlasapi.svg)](https://pypi.org/project/bg-atlasapi)
-[![PyPI](https://img.shields.io/pypi/v/bg-atlasapi.svg)](https://pypi.org/project/bg-atlasapi/)
-[![Wheel](https://img.shields.io/pypi/wheel/bg-atlasapi.svg)](https://pypi.org/project/bg-atlasapi)
+[![Python Version](https://img.shields.io/pypi/pyversions/brainglobe-atlasapi.svg)](https://pypi.org/project/brainglobe-atlasapi)
+[![PyPI](https://img.shields.io/pypi/v/brainglobe-atlasapi.svg)](https://pypi.org/project/brainglobe-atlasapi/)
+[![Wheel](https://img.shields.io/pypi/wheel/brainglobe-atlasapi.svg)](https://pypi.org/project/brainglobe-atlasapi)
 [![Development Status](https://img.shields.io/pypi/status/brainatlas-api.svg)](https://github.com/SainsburyWellcomeCentre/brainatlas-api)
-[![Downloads](https://pepy.tech/badge/bg-atlasapi)](https://pepy.tech/project/bg-atlasapi)
-[![Tests](https://img.shields.io/github/actions/workflow/status/brainglobe/bg-atlasapi/test_and_deploy.yml?branch=main)](
-    https://github.com/brainglobe/bg-atlasapi/actions)
-[![codecov](https://codecov.io/gh/brainglobe/bg-atlasapi/branch/master/graph/badge.svg?token=WTFPFW0TE4)](https://codecov.io/gh/brainglobe/bg-atlasapi)
+[![Downloads](https://pepy.tech/badge/brainglobe-atlasapi)](https://pepy.tech/project/brainglobe-atlasapi)
+[![Tests](https://img.shields.io/github/actions/workflow/status/brainglobe/brainglobe-atlasapi/test_and_deploy.yml?branch=main)](
+    https://github.com/brainglobe/brainglobe-atlasapi/actions)
+[![codecov](https://codecov.io/gh/brainglobe/brainglobe-atlasapi/branch/master/graph/badge.svg?token=WTFPFW0TE4)](https://codecov.io/gh/brainglobe/brainglobe-atlasapi)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.02668/status.svg)](https://doi.org/10.21105/joss.02668)
 [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://docs.brainglobe.info/cellfinder/contributing)
-[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info/documentation/bg-atlasapi/index.html)
+[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info/documentation/brainglobe-atlasapi/index.html)
 [![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
 
-
-The brainglobe atlas API (BG-AtlasAPI) provides a common interface for programmers to download and process brain atlas data from multiple sources.
+The brainglobe atlas API (brainglobe-atlasapi) provides a common interface for programmers to download and process brain atlas data from multiple sources.
 
 ## Atlases available
 
 A number of atlases are in development, but those available currently are:
-* [Allen Mouse Brain Atlas](https://www.brain-map.org) at 10, 25, 50 and 100 micron resolutions
-* [Allen Human Brain Atlas](https://www.brain-map.org) at 100 micron resolution
-* [Max Planck Zebrafish Brain Atlas](http://fishatlas.neuro.mpg.de) at 1 micron resolution
-* [Enhanced and Unified Mouse Brain Atlas](https://kimlab.io/brain-map/atlas/) at 10, 25, 50 and 100 micron resolutions
-* [Smoothed version of the Kim et al. mouse reference atlas](https://doi.org/10.1016/j.celrep.2014.12.014) at 10, 25, 50 and 100 micron resolutions
-* [Gubra's LSFM mouse brain atlas](https://doi.org/10.1007/s12021-020-09490-8) at 20 micron resolution
-* [3D version of the Allen mouse spinal cord atlas](https://doi.org/10.1101/2021.05.06.443008) at 20 x 10 x 10 micron resolution
-* [AZBA: A 3D Adult Zebrafish Brain Atlas](https://doi.org/10.1101/2021.05.04.442625) at 4 micron resolution
-* [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1016/j.neuroimage.2014.04.001) at 39 micron resolution
-* [3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases](https://doi.org/10.7554/eLife.61408) (E13, E15, E18, P4, P14, P28 & P56)
-* [Princeton Mouse Brain Atlas](https://brainmaps.princeton.edu/2020/09/princeton-mouse-brain-atlas-links) at 20 micron resolution
-* [Kim Lab Developmental CCF (P56)](https://data.mendeley.com/datasets/2svx788ddf/1) at 10 micron resolution with 8 reference images - STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2)
+
+- [Allen Mouse Brain Atlas](https://www.brain-map.org) at 10, 25, 50 and 100 micron resolutions
+- [Allen Human Brain Atlas](https://www.brain-map.org) at 100 micron resolution
+- [Max Planck Zebrafish Brain Atlas](http://fishatlas.neuro.mpg.de) at 1 micron resolution
+- [Enhanced and Unified Mouse Brain Atlas](https://kimlab.io/brain-map/atlas/) at 10, 25, 50 and 100 micron resolutions
+- [Smoothed version of the Kim et al. mouse reference atlas](https://doi.org/10.1016/j.celrep.2014.12.014) at 10, 25, 50 and 100 micron resolutions
+- [Gubra's LSFM mouse brain atlas](https://doi.org/10.1007/s12021-020-09490-8) at 20 micron resolution
+- [3D version of the Allen mouse spinal cord atlas](https://doi.org/10.1101/2021.05.06.443008) at 20 x 10 x 10 micron resolution
+- [AZBA: A 3D Adult Zebrafish Brain Atlas](https://doi.org/10.1101/2021.05.04.442625) at 4 micron resolution
+- [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1016/j.neuroimage.2014.04.001) at 39 micron resolution
+- [3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases](https://doi.org/10.7554/eLife.61408) (E13, E15, E18, P4, P14, P28 & P56)
+- [Princeton Mouse Brain Atlas](https://brainmaps.princeton.edu/2020/09/princeton-mouse-brain-atlas-links) at 20 micron resolution
+- [Kim Lab Developmental CCF (P56)](https://data.mendeley.com/datasets/2svx788ddf/1) at 10 micron resolution with 8 reference images - STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2)
 
 ## Installation
-BG-AtlasAPI works with Python >3.6, and can be installed from PyPI with:
+
+brainglobe-atlasapi works with Python >3.6, and can be installed from PyPI with:
+
 ```bash
-pip install bg-atlasapi
+pip install brainglobe-atlasapi
 ```
 
 ## Usage
-Full information can be found in the [documentation](https://brainglobe.info/documentation/bg-atlasapi/index.html)
+
+Full information can be found in the [documentation](https://brainglobe.info/documentation/brainglobe-atlasapi/index.html)
+
 ### Python API
-**List of atlases**
 
-To see a list of atlases use `bg_atlasapi.show_atlases`
+#### List of atlases
+
+To see a list of atlases use `brainglobe_atlasapi.show_atlases`
+
 ```python
-from bg_atlasapi import show_atlases
+from brainglobe_atlasapi import show_atlases
 show_atlases()
 #                                Brainglobe Atlases
 # ╭──────────────────────────────────┬────────────┬───────────────┬──────────────╮
@@ -71,19 +72,19 @@ show_atlases()
 # ╰──────────────────────────────────┴────────────┴───────────────┴──────────────╯
 ```
 
-**Using the atlases**
+#### Using the atlases
 
 All the features of each atlas can be accessed via the `BrainGlobeAtlas` class.
 
-
 e.g. for the 25um Allen Mouse Brain Atlas:
 
 ```python
-from bg_atlasapi.bg_atlas import BrainGlobeAtlas
+from brainglobe_atlasapi.bg_atlas import BrainGlobeAtlas
 atlas = BrainGlobeAtlas("allen_mouse_25um")
 ```
 
 The various files associated with the atlas can then be accessed as attributes of the class:
+
 ```python
 # reference image
 reference_image = atlas.reference
@@ -101,9 +102,10 @@ print(hemispheres_image.shape)
 # (528, 320, 456)
 ```
 
-**Brain regions**
+#### Brain regions
 
 There are multiple ways to work with individual brain regions. To see a dataframe of each brain region, with it's unique ID, acronym and full name, use `atlas.lookup_df`:
+
 ```python
 atlas.lookup_df.head(8)
 #      acronym         id                           name
@@ -118,6 +120,7 @@ atlas.lookup_df.head(8)
 ```
 
 Each brain region can also be access by the acronym, e.g. for primary visual cortex (VISp):
+
 ```python
 from pprint import pprint
 VISp = atlas.structures["VISp"]
@@ -131,20 +134,55 @@ pprint(VISp)
 #  'structure_id_path': [997, 8, 567, 688, 695, 315, 669, 385]}
 ```
 
-### Note on coordinates in `bg-atlasapi`
-Working with both image coordinates and cartesian coordinates in the same space can be confusing! In `bg-atlasapi`, the origin is always assumed to be in the upper left corner of the image (sectioning along the first dimension), the "ij" convention. This means that when plotting meshes and points using cartesian systems, you might encounter confusing behaviors coming from the fact that in cartesian plots one axis is inverted with respect to  ij coordinates (vertical axis increases going up, image row indexes increase going down). To make things as consistent as possible, in `bg-atlasapi` the 0 of the meshes coordinates is assumed to coincide with the 0 index of the images stack, and meshes coordinates increase following the direction stack indexes increase.
-To deal with transformations between your data space and `bg-atlasapi`, you might find the [brainglobe-space](https://github.com/brainglobe/brainglobe-space) package helpful.
+### Note on coordinates in `brainglobe-atlasapi`
+
+Working with both image coordinates and cartesian coordinates in the same space can be confusing!
+In `brainglobe-atlasapi`, the origin is always assumed to be in the upper left corner of the image (sectioning along the first dimension), the "ij" convention.
+This means that when plotting meshes and points using cartesian systems, you might encounter confusing behaviors coming from the fact that in cartesian plots one axis is inverted with respect to  ij coordinates (vertical axis increases going up, image row indexes increase going down).
+To make things as consistent as possible, in `brainglobe-atlasapi` the 0 of the meshes coordinates is assumed to coincide with the 0 index of the images stack, and meshes coordinates increase following the direction stack indexes increase.
+To deal with transformations between your data space and `brainglobe-atlasapi`, you might find the [brainglobe-space](https://github.com/brainglobe/brainglobe-space) package helpful.
+
+## Contributing to brainglobe-atlasapi
 
-# Contributing to bg-atlasapi
 **Contributors to bg-atlaspi are absolutely encouraged**, whether you want to fix bugs, add/request new features or simply ask questions.
 
-If you would like to contribute to `bg-atlasapi` (or any of the downstream tools like [brainrender](https://github.com/brainglobe/brainrender) etc.) please get in touch by opening a new issue or pull request on [GitHub](https://github.com/brainglobe/bg-atlasapi). Please also see the [developers guide](https://brainglobe.info/developers/index.html).
+If you would like to contribute to `brainglobe-atlasapi` (or any of the downstream tools like [brainrender](https://github.com/brainglobe/brainrender) etc.) please get in touch by opening a new issue or pull request on [GitHub](https://github.com/brainglobe/brainglobe-atlasapi).
+Please also see the [developers guide](https://brainglobe.info/developers/index.html).
 
-Someone might have already asked a question you might have, so if you're not sure where to start, check out the [issues](https://github.com/brainglobe/bg-atlasapi/issues) (and the issues of the other repositories).
+Someone might have already asked a question you might have, so if you're not sure where to start, check out the [issues](https://github.com/brainglobe/brainglobe-atlasapi/issues) (and the issues of the other repositories).
 
 ## Citation
+
 If you find the BrainGlobe Atlas API useful, please cite the paper in your work:
 
 >Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W. and Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668, https://doi.org/10.21105/joss.02668
 
 **Don't forget to cite the developers of the atlas that you used!**
+
+---
+
+# Atlas Generation and Adding a New Atlas
+
+For full instructions to add a new BrainGlobe atlas, please see [here](https://brainglobe.info/documentation/brainglobe_atlasapi/adding-a-new-atlas.html).
+
+The `brainglobe_atlasapi.atlas_generation` submodule contains code for the generation of cleaned-up data, for the main `brainglobe_atlasapi` module.
+This code was previously the `bg-atlasgen` module.
+
+## To contribute
+
+1. Fork this repo
+2. Clone your repo
+3. Run `git clone https://github.com/brainglobe/brainglobe-atlasapi`
+4. Install an editable version of the package; by running `pip install -e .` within the cloned directory
+5. Create a script to package your atlas, and place into `brainglobe_atlasapi/atlas_generation/atlas_scripts`. Please see other scripts for examples.
+
+Your script should contain everything required to run.
+The raw data should be hosted on a publicly accessible repository so that anyone can run the script to recreate the atlas.
+
+If you need to add any dependencies, please add them as an extra in the `pyproject.toml` file, e.g.:
+
+```python
+[project.optional-dependencies]
+allenmouse = ["allensdk"]
+newatlas = ["dependency_1", "dependency_2"]
+```
diff --git a/bg_atlasapi/__init__.py b/bg_atlasapi/__init__.py
diff --git a/brainglobe_atlasapi/__init__.py b/brainglobe_atlasapi/__init__.py
@@ -0,0 +1,13 @@
+from importlib.metadata import PackageNotFoundError, metadata
+
+try:
+    __version__ = metadata("brainglobe-atlasapi")["Version"]
+    __author__ = metadata("brainglobe-atlasapi")["Author"]
+    del metadata
+except PackageNotFoundError:
+    # package is not installed
+    pass
+
+
+from brainglobe_atlasapi.bg_atlas import BrainGlobeAtlas
+from brainglobe_atlasapi.list_atlases import show_atlases
diff --git a/brainglobe_atlasapi/atlas_generation/__init__.py b/brainglobe_atlasapi/atlas_generation/__init__.py
@@ -0,0 +1,5 @@
+__version__ = "1"  # will set major version of all atlases
+
+from rich.traceback import install
+
+install()
diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/__init__.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/__init__.py