brainglobe 0.2.0__tar.gz → 1.5.0__tar.gz

{brainglobe-0.2.0 → brainglobe-1.5.0}/.github/workflows/test_and_deploy.yml

@@ -9,6 +9,9 @@ on:
       - 'v**'
   # Run on all pull-requests
   pull_request:
+  schedule:
+  # Runs at 6:10am UTC on Monday
+    - cron: '10 6 * * 1'
   # Allow workflow dispatch from GitHub
   workflow_dispatch:
 
@@ -38,20 +41,32 @@ jobs:
     strategy:
       matrix:
         # Run all supported Python versions on linux
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.11", "3.12", "3.13"]
         os: [ubuntu-latest]
         # Include one windows and macos run
         include:
         - os: macos-latest
-          python-version: "3.10"
+          python-version: "3.13"
         - os: windows-latest
-          python-version: "3.10"
+          python-version: "3.13"
 
     steps:
       # Run tests
+      - name: install HDF5 libs on ARM Mac
+        if: matrix.os == 'macos-latest'
+        run: brew install hdf5
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
+      # Run tests on napari main if this is a scheduled run
+      - name: Run tests on napari main
+        if: github.event_name == 'schedule'
+        uses: neuroinformatics-unit/actions/test@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
+          tox-args: '-e napari-dev'
 
   build_sdist_wheels:
     name: Build source distribution
@@ -65,13 +80,14 @@ jobs:
   upload_all:
     name: Publish build distributions
     needs: [build_sdist_wheels]
+    if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         name: artifact
         path: dist
-    - uses: pypa/gh-action-pypi-publish@v1.5.0
+    - uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.TWINE_API_KEY }}

brainglobe-1.5.0/CITATION.cff

@@ -0,0 +1,30 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: BrainGlobe
+message: >-
+  You can use the brainglobe.cite() function to generate
+  citations for the BrainGlobe tools you use in your
+  research.
+type: software
+authors:
+  - given-names: BrainGlobe
+    family-names: Developers
+    affiliation: 'Sainsbury Wellcome Centre, University College London'
+    email: hello@brainglobe.info
+  - given-names: Wiliam Michael
+    family-names: Graham
+    email: william.graham@ucl.ac.uk
+    affiliation: 'Advanced Research Computing, University College London'
+    orcid: 'https://orcid.org/0000-0003-0058-263X'
+repository-code: 'https://github.com/brainglobe/brainglobe-meta'
+url: 'https://brainglobe.info/'
+abstract: >-
+  The BrainGlobe Initiative exists to facilitate the
+  development of interoperable Python-based tools for
+  computational neuroanatomy.
+license: BSD-3-Clause
+citation-sentence: >-
+  'This project makes use of the BrainGlobe tool-suite, https://brainglobe.info/'
+year: 2024

{brainglobe-0.2.0 → brainglobe-1.5.0}/MANIFEST.in

@@ -1,3 +1,4 @@
+include CITATION.cff
 include LICENSE
 include README.md
 

brainglobe-1.5.0/PKG-INFO

@@ -0,0 +1,92 @@
+Metadata-Version: 2.4
+Name: brainglobe
+Version: 1.5.0
+Summary: Python-based tools for computational neuroanatomy.
+Author-email: BrainGlobe Developers <hello@brainglobe.info>
+License: BSD-3-Clause
+Project-URL: homepage, https://brainglobe.info
+Project-URL: bug_tracker, https://github.com/brainglobe/brainglobe-meta/issues
+Project-URL: documentation, https://docs.brainglobe.info
+Project-URL: source_code, https://github.com/brainglobe/brainglobe-meta
+Project-URL: user_support, https://forum.image.sc/tag/brainglobe
+Project-URL: twitter, https://twitter.com/brain_globe
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Classifier: License :: OSI Approved :: BSD License
+Requires-Python: >=3.11.0
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: brainglobe-atlasapi<3,>=2.2.0
+Requires-Dist: brainglobe-heatmap<1,>=0.5.5
+Requires-Dist: brainglobe-napari-io<1,>=0.3.4
+Requires-Dist: brainglobe-segmentation<2,>=1.3.1
+Requires-Dist: brainglobe-space<2,>=1.0.3
+Requires-Dist: brainglobe-utils<1,>=0.11.0
+Requires-Dist: brainreg[napari]<2,>=1.0.11
+Requires-Dist: brainrender-napari<1,>=0.0.7
+Requires-Dist: brainrender<3,>=2.1.17
+Requires-Dist: cellfinder[napari]<2,>=1.9.0
+Requires-Dist: napari[all]>=0.6.1
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: setuptools_scm; extra == "dev"
+Dynamic: license-file
+
+[![PyPI version](https://badge.fury.io/py/brainglobe.svg)](https://badge.fury.io/py/brainglobe)
+[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info)
+
+[![Brainglobe logo](https://brainglobe.info/_static/brainglobe.png)](https://brainglobe.info)
+
+# BrainGlobe
+
+This package provides all [BrainGlobe](https://brainglobe.info) tools in one place, installable [in a single command](#installing-and-updating).
+Installing this package will provide you with the complete suite of BrainGlobe tools, without needing to worry about dependency resolution.
+A complete list of the tools provided by this package [is provided on our website](https://brainglobe.info/documentation/index.html#individual-tool-documentation), and you can also read more about these tools there too.
+
+If you are interested in running some of our analysis workflows, you might want to head over to [`brainglobe-workflows`](https://github.com/brainglobe/brainglobe-workflows) and install the analysis pipelines offered by that package too.
+
+## Installing and Updating
+
+See the [installation instructions over on the BrainGlobe website](https://brainglobe.info/documentation/index.html#installing-brainglobe) for full information.
+But the TLDR is;
+
+```bash
+pip install brainglobe
+```
+
+and to update,
+
+```bash
+pip install brainglobe --update
+```
+
+## Seeking help or contributing
+We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).
+
+---
+
+# The Brainglobe Initiative
+
+The BrainGlobe Initiative exists to facilitate the development of interoperable Python-based tools for computational neuroanatomy.
+
+We have three aims:
+
+- Develop specialist software for specific analysis and visualisation needs, such as [cellfinder](https://github.com/brainglobe/cellfinder) and [brainrender](https://github.com/brainglobe/brainrender).
+- Develop core tools to facilitate others to build interoperable tools in Python, e.g. the [BrainGlobe Atlas API](https://github.com/brainglobe/bg-atlasapi).
+- Build a community of neuroscientists and developers to share knowledge, build software and engage with the scientific, and open-source community (e.g. by organising hackathons).
+
+## [Funding](https://brainglobe.info/funders.html#funders) Information
+
+The BrainGlobe project is only possible due to grant funding and the generous support of host institutions, whose information [can be found on this website](https://brainglobe.info/funders.html#funders).

brainglobe-1.5.0/README.md

@@ -0,0 +1,46 @@
+[![PyPI version](https://badge.fury.io/py/brainglobe.svg)](https://badge.fury.io/py/brainglobe)
+[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info)
+
+[![Brainglobe logo](https://brainglobe.info/_static/brainglobe.png)](https://brainglobe.info)
+
+# BrainGlobe
+
+This package provides all [BrainGlobe](https://brainglobe.info) tools in one place, installable [in a single command](#installing-and-updating).
+Installing this package will provide you with the complete suite of BrainGlobe tools, without needing to worry about dependency resolution.
+A complete list of the tools provided by this package [is provided on our website](https://brainglobe.info/documentation/index.html#individual-tool-documentation), and you can also read more about these tools there too.
+
+If you are interested in running some of our analysis workflows, you might want to head over to [`brainglobe-workflows`](https://github.com/brainglobe/brainglobe-workflows) and install the analysis pipelines offered by that package too.
+
+## Installing and Updating
+
+See the [installation instructions over on the BrainGlobe website](https://brainglobe.info/documentation/index.html#installing-brainglobe) for full information.
+But the TLDR is;
+
+```bash
+pip install brainglobe
+```
+
+and to update,
+
+```bash
+pip install brainglobe --update
+```
+
+## Seeking help or contributing
+We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).
+
+---
+
+# The Brainglobe Initiative
+
+The BrainGlobe Initiative exists to facilitate the development of interoperable Python-based tools for computational neuroanatomy.
+
+We have three aims:
+
+- Develop specialist software for specific analysis and visualisation needs, such as [cellfinder](https://github.com/brainglobe/cellfinder) and [brainrender](https://github.com/brainglobe/brainrender).
+- Develop core tools to facilitate others to build interoperable tools in Python, e.g. the [BrainGlobe Atlas API](https://github.com/brainglobe/bg-atlasapi).
+- Build a community of neuroscientists and developers to share knowledge, build software and engage with the scientific, and open-source community (e.g. by organising hackathons).
+
+## [Funding](https://brainglobe.info/funders.html#funders) Information
+
+The BrainGlobe project is only possible due to grant funding and the generous support of host institutions, whose information [can be found on this website](https://brainglobe.info/funders.html#funders).

brainglobe-1.5.0/brainglobe/__init__.py

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

brainglobe-1.5.0/brainglobe.egg-info/PKG-INFO

@@ -0,0 +1,92 @@
+Metadata-Version: 2.4
+Name: brainglobe
+Version: 1.5.0
+Summary: Python-based tools for computational neuroanatomy.
+Author-email: BrainGlobe Developers <hello@brainglobe.info>
+License: BSD-3-Clause
+Project-URL: homepage, https://brainglobe.info
+Project-URL: bug_tracker, https://github.com/brainglobe/brainglobe-meta/issues
+Project-URL: documentation, https://docs.brainglobe.info
+Project-URL: source_code, https://github.com/brainglobe/brainglobe-meta
+Project-URL: user_support, https://forum.image.sc/tag/brainglobe
+Project-URL: twitter, https://twitter.com/brain_globe
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: OS Independent
+Classifier: License :: OSI Approved :: BSD License
+Requires-Python: >=3.11.0
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: brainglobe-atlasapi<3,>=2.2.0
+Requires-Dist: brainglobe-heatmap<1,>=0.5.5
+Requires-Dist: brainglobe-napari-io<1,>=0.3.4
+Requires-Dist: brainglobe-segmentation<2,>=1.3.1
+Requires-Dist: brainglobe-space<2,>=1.0.3
+Requires-Dist: brainglobe-utils<1,>=0.11.0
+Requires-Dist: brainreg[napari]<2,>=1.0.11
+Requires-Dist: brainrender-napari<1,>=0.0.7
+Requires-Dist: brainrender<3,>=2.1.17
+Requires-Dist: cellfinder[napari]<2,>=1.9.0
+Requires-Dist: napari[all]>=0.6.1
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: setuptools_scm; extra == "dev"
+Dynamic: license-file
+
+[![PyPI version](https://badge.fury.io/py/brainglobe.svg)](https://badge.fury.io/py/brainglobe)
+[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info)
+
+[![Brainglobe logo](https://brainglobe.info/_static/brainglobe.png)](https://brainglobe.info)
+
+# BrainGlobe
+
+This package provides all [BrainGlobe](https://brainglobe.info) tools in one place, installable [in a single command](#installing-and-updating).
+Installing this package will provide you with the complete suite of BrainGlobe tools, without needing to worry about dependency resolution.
+A complete list of the tools provided by this package [is provided on our website](https://brainglobe.info/documentation/index.html#individual-tool-documentation), and you can also read more about these tools there too.
+
+If you are interested in running some of our analysis workflows, you might want to head over to [`brainglobe-workflows`](https://github.com/brainglobe/brainglobe-workflows) and install the analysis pipelines offered by that package too.
+
+## Installing and Updating
+
+See the [installation instructions over on the BrainGlobe website](https://brainglobe.info/documentation/index.html#installing-brainglobe) for full information.
+But the TLDR is;
+
+```bash
+pip install brainglobe
+```
+
+and to update,
+
+```bash
+pip install brainglobe --update
+```
+
+## Seeking help or contributing
+We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).
+
+---
+
+# The Brainglobe Initiative
+
+The BrainGlobe Initiative exists to facilitate the development of interoperable Python-based tools for computational neuroanatomy.
+
+We have three aims:
+
+- Develop specialist software for specific analysis and visualisation needs, such as [cellfinder](https://github.com/brainglobe/cellfinder) and [brainrender](https://github.com/brainglobe/brainrender).
+- Develop core tools to facilitate others to build interoperable tools in Python, e.g. the [BrainGlobe Atlas API](https://github.com/brainglobe/bg-atlasapi).
+- Build a community of neuroscientists and developers to share knowledge, build software and engage with the scientific, and open-source community (e.g. by organising hackathons).
+
+## [Funding](https://brainglobe.info/funders.html#funders) Information
+
+The BrainGlobe project is only possible due to grant funding and the generous support of host institutions, whose information [can be found on this website](https://brainglobe.info/funders.html#funders).

{brainglobe-0.2.0 → brainglobe-1.5.0}/brainglobe.egg-info/SOURCES.txt

@@ -1,12 +1,11 @@
 .gitignore
+CITATION.cff
 LICENSE
 MANIFEST.in
 README.md
 pyproject.toml
-tox.ini
 .github/workflows/test_and_deploy.yml
 brainglobe/__init__.py
-brainglobe/_conda_handles.py
 brainglobe.egg-info/PKG-INFO
 brainglobe.egg-info/SOURCES.txt
 brainglobe.egg-info/dependency_links.txt
@@ -15,5 +14,4 @@ brainglobe.egg-info/top_level.txt
 tests/__init__.py
 tests/test_integration/__init__.py
 tests/test_unit/__init__.py
-tests/test_unit/test__version__.py
-tests/test_unit/test_tool_exposure.py
+tests/test_unit/test__version__.py

brainglobe-1.5.0/brainglobe.egg-info/requires.txt

@@ -0,0 +1,22 @@
+brainglobe-atlasapi<3,>=2.2.0
+brainglobe-heatmap<1,>=0.5.5
+brainglobe-napari-io<1,>=0.3.4
+brainglobe-segmentation<2,>=1.3.1
+brainglobe-space<2,>=1.0.3
+brainglobe-utils<1,>=0.11.0
+brainreg[napari]<2,>=1.0.11
+brainrender-napari<1,>=0.0.7
+brainrender<3,>=2.1.17
+cellfinder[napari]<2,>=1.9.0
+napari[all]>=0.6.1
+
+[dev]
+pytest
+pytest-cov
+coverage
+tox
+black
+mypy
+pre-commit
+ruff
+setuptools_scm

brainglobe-1.5.0/pyproject.toml

@@ -0,0 +1,112 @@
+[project]
+name = "brainglobe"
+authors = [{ name = "BrainGlobe Developers", email = "hello@brainglobe.info" }]
+description = "Python-based tools for computational neuroanatomy."
+readme = "README.md"
+requires-python = ">=3.11.0"
+dynamic = ["version"]
+
+license = { text = "BSD-3-Clause" }
+
+classifiers = [
+  "Development Status :: 2 - Pre-Alpha",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Operating System :: OS Independent",
+  "License :: OSI Approved :: BSD License",
+]
+
+dependencies = [
+  "brainglobe-atlasapi>=2.2.0,<3",
+  "brainglobe-heatmap>=0.5.5,<1",
+  "brainglobe-napari-io>=0.3.4,<1",
+  "brainglobe-segmentation>=1.3.1,<2",
+  "brainglobe-space>=1.0.3,<2",
+  "brainglobe-utils>=0.11.0,<1",
+  "brainreg[napari]>=1.0.11,<2",
+  "brainrender-napari>=0.0.7,<1",
+  "brainrender>=2.1.17,<3",
+  "cellfinder[napari]>=1.9.0,<2",
+  "napari[all]>=0.6.1",
+]
+
+[project.optional-dependencies]
+dev = [
+  "pytest",
+  "pytest-cov",
+  "coverage",
+  "tox",
+  "black",
+  "mypy",
+  "pre-commit",
+  "ruff",
+  "setuptools_scm",
+]
+
+[project.urls]
+homepage = "https://brainglobe.info"
+bug_tracker = "https://github.com/brainglobe/brainglobe-meta/issues"
+documentation = "https://docs.brainglobe.info"
+source_code = "https://github.com/brainglobe/brainglobe-meta"
+user_support = "https://forum.image.sc/tag/brainglobe"
+twitter = "https://twitter.com/brain_globe"
+
+[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*"]
+exclude = ["tests*"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=brainglobe"
+
+[tool.black]
+target-version = ['py311', 'py312', 'py313']
+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.tox]
+legacy_tox_ini = """
+[tox]
+envlist = py{311,312,313}, napari-dev
+isolated_build = True
+
+[gh-actions]
+python =
+    3.11: py311
+    3.12: py312
+    3.13: py313
+
+[testenv]
+extras =
+    dev
+commands =
+    pytest -v --color=yes --cov=brainglobe --cov-report=xml
+deps =
+    napari-dev: git+https://github.com/napari/napari
+"""

brainglobe-0.2.0/PKG-INFO

@@ -1,109 +0,0 @@
-Metadata-Version: 2.1
-Name: brainglobe
-Version: 0.2.0
-Summary: Python-based tools for computational neuroanatomy.
-Author-email: BrainGlobe <code@adamltyson.com>
-License: BSD-3-Clause
-Classifier: Development Status :: 2 - Pre-Alpha
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Operating System :: OS Independent
-Classifier: License :: OSI Approved :: BSD License
-Requires-Python: >=3.8.0
-Description-Content-Type: text/markdown
-Provides-Extra: dev
-License-File: LICENSE
-
-[![PyPI version](https://badge.fury.io/py/brainglobe.svg)](https://badge.fury.io/py/brainglobe)
-[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info)
-[![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
-
-# brainglobe
-
-The BrainGlobe Initiative exists to facilitate the development of interoperable
-Python-based tools for computational neuroanatomy.
-
-We have three aims:
-
-- Develop specialist software for specific analysis and visualisation needs,
-  such as [cellfinder](https://github.com/brainglobe/cellfinder) and
-  [brainrender](https://github.com/brainglobe/brainrender).
-
-- Develop core tools to facilitate others to build interoperable tools in Python, e.g. the
-  [BrainGlobe Atlas API](https://github.com/brainglobe/bg-atlasapi).
-
-- Build a community of neuroscientists and developers to share knowledge, build software and engage
-  with the scientific, and open-source community (e.g. by organising hackathons).
-
-### [**Funding**](https://brainglobe.info/funders.html#funders) Information
-
-The BrainGlobe project is only possible due to grant funding and the generous support of host institutions, whose information [can be found on this website](https://brainglobe.info/funders.html#funders).
-
----
-
-## BrainGlobe tools
-
-This package provides all BrainGlobe tools in one place, requested [through a single command](#installation).
-
-You can read more about the individual tools on the [documentation website](https://brainglobe.info/documentation/index.html).
-Currently included packages, and whether they come with the `pip` and `conda-forge` installs are listed below:
-|       Package        |  `pip`   | `conda`  | `from brainglobe import` |                               Documentation                               |
-| :------------------: | :------: | :------: | :----------------------: | :-----------------------------------------------------------------------: |
-| BrainGlobe Atlas API | &#x2611; | &#x2611; |      `bg_atlasapi`       |   [Site](https://brainglobe.info/documentation/bg-atlasapi/index.html)    |
-|      `bg-space`      | &#x2611; | &#x2611; |        `bg-space`        |     [Site](https://brainglobe.info/documentation/bg-space/index.html)     |
-|      `brainreg`      | &#x2611; | &#x2611; |        `brainreg`        |     [Site](https://brainglobe.info/documentation/brainreg/index.html)     |
-|  `brainreg-segment`  | &#x2611; | &#x2611; |    `brainreg_segment`    | [Site](https://brainglobe.info/documentation/brainreg-segment/index.html) |
-|    `brainrender`     |          |          |                          |   [Site](https://brainglobe.info/documentation/brainrender/index.html)    |
-|     `cellfinder`     | &#x2611; | Pending  |    `cellfinder_core`     |    [Site](https://brainglobe.info/documentation/cellfinder/index.html)    |
-|      `morphapi`      | &#x2611; | Pending  |        `morphapi`        |     [Site](https://brainglobe.info/documentation/morphapi/index.html)     |
-
----
-
-## Installation
-
-We recommend users install into a fresh virtual environment using `pip`; since this will resolve all complex dependencies (like `tensorflow`) automatically, across all operating systems and (compatible) Python versions.
-
-### **Recommended**: via `pip`
-The `brainglobe` package can be installed from [PyPI](https://pypi.org/project/brainglobe/) into a Python environment by running
-```sh
-pip install brainglobe
-```
-This will fetch and install all `brainglobe` packages and tools into your current environment.
-Alternatively, you can download the source from [PyPI here](https://pypi.org/project/brainglobe/#files).
-
-### **Alternatives**: via `conda`
-We are currently in the process of making BrainGlobe's tools available from `conda-forge` as an alternative to `PyPI`.
-However certain tools are currently not available on `conda-forge`, specifically:
-- `brainrender` (in progress)
-- `morphapi` (in progress)
-- `cellfinder` ([see below](#cellfinder-and-conda-forge))
-
-In your desired virtual environment, run
-```sh
-conda install -c conda-forge brainglobe
-```
-to install the compatible BrainGlobe tools.
-This will install all BrainGlobe tools that are compatible with your platform and which are currently available via `conda-forge`.
-
-#### **`cellfinder` and `conda-forge`**
-
-Choosing to install via `conda` will provide the (source code for the) `cellfinder` tool.
-However due to an ongoing issue with `tensorflow`'s availability on `conda-forge`, the install _will not_ provide `tensorflow` itself.
-This is because `tensorflow` versions newer than `1.14.0` are not provided via `conda` channels, and `cellfinder-core` (one of the brainglobe tools) requires a version between `2.5.0` and `2.11.1`.
-See [this issue on GitHub for more details](https://github.com/conda-forge/cellfinder-core-feedstock/issues/13).
-Users that want to run `cellfinder` will need to manually install a compatible version of `tensorflow` into their environment, before running the `conda install` command above.
-- Windows users will _have_ to manually install their own version of `tensorflow` if they want to use the `conda-forge` install and the `cellfinder` tools.
-- `conda-forge` _may_ be able to resolve the dependencies automatically for Linux and MacOS users, however we do not guarantee this. In such a case, a manual install of `tensorflow` will be required first.
-
-If using the `conda-forge` install; attempting to `import` any of `cellfinder`, `cellfinder-napari`, or `cellfinder-core` in your Python scripts may throw an error if the issues above cannot be resolved on your platform.
-Similarly, attempting to use `cellfinder`'s CLI functionality will also raise an error.
-
----
-
-## Contributing
-
-**Contributors to BrainGlobe are absolutely encouraged**, whether to fix a bug, develop a new feature, or add a new atlas.
-If you would like to contribute, please take a look at our [developer documentation](https://brainglobe.info/developers/index.html).

brainglobe-0.2.0/README.md

@@ -1,90 +0,0 @@
-[![PyPI version](https://badge.fury.io/py/brainglobe.svg)](https://badge.fury.io/py/brainglobe)
-[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info)
-[![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
-
-# brainglobe
-
-The BrainGlobe Initiative exists to facilitate the development of interoperable
-Python-based tools for computational neuroanatomy.
-
-We have three aims:
-
-- Develop specialist software for specific analysis and visualisation needs,
-  such as [cellfinder](https://github.com/brainglobe/cellfinder) and
-  [brainrender](https://github.com/brainglobe/brainrender).
-
-- Develop core tools to facilitate others to build interoperable tools in Python, e.g. the
-  [BrainGlobe Atlas API](https://github.com/brainglobe/bg-atlasapi).
-
-- Build a community of neuroscientists and developers to share knowledge, build software and engage
-  with the scientific, and open-source community (e.g. by organising hackathons).
-
-### [**Funding**](https://brainglobe.info/funders.html#funders) Information
-
-The BrainGlobe project is only possible due to grant funding and the generous support of host institutions, whose information [can be found on this website](https://brainglobe.info/funders.html#funders).
-
----
-
-## BrainGlobe tools
-
-This package provides all BrainGlobe tools in one place, requested [through a single command](#installation).
-
-You can read more about the individual tools on the [documentation website](https://brainglobe.info/documentation/index.html).
-Currently included packages, and whether they come with the `pip` and `conda-forge` installs are listed below:
-|       Package        |  `pip`   | `conda`  | `from brainglobe import` |                               Documentation                               |
-| :------------------: | :------: | :------: | :----------------------: | :-----------------------------------------------------------------------: |
-| BrainGlobe Atlas API | ☑ | ☑ |      `bg_atlasapi`       |   [Site](https://brainglobe.info/documentation/bg-atlasapi/index.html)    |
-|      `bg-space`      | ☑ | ☑ |        `bg-space`        |     [Site](https://brainglobe.info/documentation/bg-space/index.html)     |
-|      `brainreg`      | ☑ | ☑ |        `brainreg`        |     [Site](https://brainglobe.info/documentation/brainreg/index.html)     |
-|  `brainreg-segment`  | ☑ | ☑ |    `brainreg_segment`    | [Site](https://brainglobe.info/documentation/brainreg-segment/index.html) |
-|    `brainrender`     |          |          |                          |   [Site](https://brainglobe.info/documentation/brainrender/index.html)    |
-|     `cellfinder`     | ☑ | Pending  |    `cellfinder_core`     |    [Site](https://brainglobe.info/documentation/cellfinder/index.html)    |
-|      `morphapi`      | ☑ | Pending  |        `morphapi`        |     [Site](https://brainglobe.info/documentation/morphapi/index.html)     |
-
----
-
-## Installation
-
-We recommend users install into a fresh virtual environment using `pip`; since this will resolve all complex dependencies (like `tensorflow`) automatically, across all operating systems and (compatible) Python versions.
-
-### **Recommended**: via `pip`
-The `brainglobe` package can be installed from [PyPI](https://pypi.org/project/brainglobe/) into a Python environment by running
-```sh
-pip install brainglobe
-```
-This will fetch and install all `brainglobe` packages and tools into your current environment.
-Alternatively, you can download the source from [PyPI here](https://pypi.org/project/brainglobe/#files).
-
-### **Alternatives**: via `conda`
-We are currently in the process of making BrainGlobe's tools available from `conda-forge` as an alternative to `PyPI`.
-However certain tools are currently not available on `conda-forge`, specifically:
-- `brainrender` (in progress)
-- `morphapi` (in progress)
-- `cellfinder` ([see below](#cellfinder-and-conda-forge))
-
-In your desired virtual environment, run
-```sh
-conda install -c conda-forge brainglobe
-```
-to install the compatible BrainGlobe tools.
-This will install all BrainGlobe tools that are compatible with your platform and which are currently available via `conda-forge`.
-
-#### **`cellfinder` and `conda-forge`**
-
-Choosing to install via `conda` will provide the (source code for the) `cellfinder` tool.
-However due to an ongoing issue with `tensorflow`'s availability on `conda-forge`, the install _will not_ provide `tensorflow` itself.
-This is because `tensorflow` versions newer than `1.14.0` are not provided via `conda` channels, and `cellfinder-core` (one of the brainglobe tools) requires a version between `2.5.0` and `2.11.1`.
-See [this issue on GitHub for more details](https://github.com/conda-forge/cellfinder-core-feedstock/issues/13).
-Users that want to run `cellfinder` will need to manually install a compatible version of `tensorflow` into their environment, before running the `conda install` command above.
-- Windows users will _have_ to manually install their own version of `tensorflow` if they want to use the `conda-forge` install and the `cellfinder` tools.
-- `conda-forge` _may_ be able to resolve the dependencies automatically for Linux and MacOS users, however we do not guarantee this. In such a case, a manual install of `tensorflow` will be required first.
-
-If using the `conda-forge` install; attempting to `import` any of `cellfinder`, `cellfinder-napari`, or `cellfinder-core` in your Python scripts may throw an error if the issues above cannot be resolved on your platform.
-Similarly, attempting to use `cellfinder`'s CLI functionality will also raise an error.
-
----
-
-## Contributing
-
-**Contributors to BrainGlobe are absolutely encouraged**, whether to fix a bug, develop a new feature, or add a new atlas.
-If you would like to contribute, please take a look at our [developer documentation](https://brainglobe.info/developers/index.html).

brainglobe-0.2.0/brainglobe/__init__.py

@@ -1,25 +0,0 @@
-from importlib.metadata import PackageNotFoundError, version
-
-from ._conda_handles import _CELLFINDER_INSTALLED, _MORPHAPI_INSTALLED
-
-try:
-    __version__ = version("brainglobe")
-except PackageNotFoundError:
-    # package is not installed
-    pass
-
-# Expose tools under the brainglobe namespace
-import bg_atlasapi
-import bg_space
-import brainreg
-import brainreg_segment
-
-# Expose tools that may not be present
-# if a conda install was performed
-if _MORPHAPI_INSTALLED:
-    # Import morphapi
-    import morphapi
-
-# cellfinder and associated packages
-if _CELLFINDER_INSTALLED:
-    import cellfinder_core

brainglobe-0.2.0/brainglobe/_conda_handles.py

@@ -1,16 +0,0 @@
-from importlib.metadata import PackageNotFoundError, version
-from warnings import warn
-
-_CELLFINDER_INSTALLED = True
-try:
-    version("cellfinder_core")
-except PackageNotFoundError as e:
-    _CELLFINDER_INSTALLED = False
-    warn(f"BrainGlobe: cellfinder-core unavailable. Caught {str(e)}")
-
-_MORPHAPI_INSTALLED = True
-try:
-    version("morphapi")
-except PackageNotFoundError as e:
-    _MORPHAPI_INSTALLED = False
-    warn(f"BrainGlobe: morphapi unavailable. Caught {str(e)}")

brainglobe-0.2.0/brainglobe.egg-info/PKG-INFO

@@ -1,109 +0,0 @@
-Metadata-Version: 2.1
-Name: brainglobe
-Version: 0.2.0
-Summary: Python-based tools for computational neuroanatomy.
-Author-email: BrainGlobe <code@adamltyson.com>
-License: BSD-3-Clause
-Classifier: Development Status :: 2 - Pre-Alpha
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Operating System :: OS Independent
-Classifier: License :: OSI Approved :: BSD License
-Requires-Python: >=3.8.0
-Description-Content-Type: text/markdown
-Provides-Extra: dev
-License-File: LICENSE
-
-[![PyPI version](https://badge.fury.io/py/brainglobe.svg)](https://badge.fury.io/py/brainglobe)
-[![Website](https://img.shields.io/website?up_message=online&url=https%3A%2F%2Fbrainglobe.info)](https://brainglobe.info)
-[![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
-
-# brainglobe
-
-The BrainGlobe Initiative exists to facilitate the development of interoperable
-Python-based tools for computational neuroanatomy.
-
-We have three aims:
-
-- Develop specialist software for specific analysis and visualisation needs,
-  such as [cellfinder](https://github.com/brainglobe/cellfinder) and
-  [brainrender](https://github.com/brainglobe/brainrender).
-
-- Develop core tools to facilitate others to build interoperable tools in Python, e.g. the
-  [BrainGlobe Atlas API](https://github.com/brainglobe/bg-atlasapi).
-
-- Build a community of neuroscientists and developers to share knowledge, build software and engage
-  with the scientific, and open-source community (e.g. by organising hackathons).
-
-### [**Funding**](https://brainglobe.info/funders.html#funders) Information
-
-The BrainGlobe project is only possible due to grant funding and the generous support of host institutions, whose information [can be found on this website](https://brainglobe.info/funders.html#funders).
-
----
-
-## BrainGlobe tools
-
-This package provides all BrainGlobe tools in one place, requested [through a single command](#installation).
-
-You can read more about the individual tools on the [documentation website](https://brainglobe.info/documentation/index.html).
-Currently included packages, and whether they come with the `pip` and `conda-forge` installs are listed below:
-|       Package        |  `pip`   | `conda`  | `from brainglobe import` |                               Documentation                               |
-| :------------------: | :------: | :------: | :----------------------: | :-----------------------------------------------------------------------: |
-| BrainGlobe Atlas API | &#x2611; | &#x2611; |      `bg_atlasapi`       |   [Site](https://brainglobe.info/documentation/bg-atlasapi/index.html)    |
-|      `bg-space`      | &#x2611; | &#x2611; |        `bg-space`        |     [Site](https://brainglobe.info/documentation/bg-space/index.html)     |
-|      `brainreg`      | &#x2611; | &#x2611; |        `brainreg`        |     [Site](https://brainglobe.info/documentation/brainreg/index.html)     |
-|  `brainreg-segment`  | &#x2611; | &#x2611; |    `brainreg_segment`    | [Site](https://brainglobe.info/documentation/brainreg-segment/index.html) |
-|    `brainrender`     |          |          |                          |   [Site](https://brainglobe.info/documentation/brainrender/index.html)    |
-|     `cellfinder`     | &#x2611; | Pending  |    `cellfinder_core`     |    [Site](https://brainglobe.info/documentation/cellfinder/index.html)    |
-|      `morphapi`      | &#x2611; | Pending  |        `morphapi`        |     [Site](https://brainglobe.info/documentation/morphapi/index.html)     |
-
----
-
-## Installation
-
-We recommend users install into a fresh virtual environment using `pip`; since this will resolve all complex dependencies (like `tensorflow`) automatically, across all operating systems and (compatible) Python versions.
-
-### **Recommended**: via `pip`
-The `brainglobe` package can be installed from [PyPI](https://pypi.org/project/brainglobe/) into a Python environment by running
-```sh
-pip install brainglobe
-```
-This will fetch and install all `brainglobe` packages and tools into your current environment.
-Alternatively, you can download the source from [PyPI here](https://pypi.org/project/brainglobe/#files).
-
-### **Alternatives**: via `conda`
-We are currently in the process of making BrainGlobe's tools available from `conda-forge` as an alternative to `PyPI`.
-However certain tools are currently not available on `conda-forge`, specifically:
-- `brainrender` (in progress)
-- `morphapi` (in progress)
-- `cellfinder` ([see below](#cellfinder-and-conda-forge))
-
-In your desired virtual environment, run
-```sh
-conda install -c conda-forge brainglobe
-```
-to install the compatible BrainGlobe tools.
-This will install all BrainGlobe tools that are compatible with your platform and which are currently available via `conda-forge`.
-
-#### **`cellfinder` and `conda-forge`**
-
-Choosing to install via `conda` will provide the (source code for the) `cellfinder` tool.
-However due to an ongoing issue with `tensorflow`'s availability on `conda-forge`, the install _will not_ provide `tensorflow` itself.
-This is because `tensorflow` versions newer than `1.14.0` are not provided via `conda` channels, and `cellfinder-core` (one of the brainglobe tools) requires a version between `2.5.0` and `2.11.1`.
-See [this issue on GitHub for more details](https://github.com/conda-forge/cellfinder-core-feedstock/issues/13).
-Users that want to run `cellfinder` will need to manually install a compatible version of `tensorflow` into their environment, before running the `conda install` command above.
-- Windows users will _have_ to manually install their own version of `tensorflow` if they want to use the `conda-forge` install and the `cellfinder` tools.
-- `conda-forge` _may_ be able to resolve the dependencies automatically for Linux and MacOS users, however we do not guarantee this. In such a case, a manual install of `tensorflow` will be required first.
-
-If using the `conda-forge` install; attempting to `import` any of `cellfinder`, `cellfinder-napari`, or `cellfinder-core` in your Python scripts may throw an error if the issues above cannot be resolved on your platform.
-Similarly, attempting to use `cellfinder`'s CLI functionality will also raise an error.
-
----
-
-## Contributing
-
-**Contributors to BrainGlobe are absolutely encouraged**, whether to fix a bug, develop a new feature, or add a new atlas.
-If you would like to contribute, please take a look at our [developer documentation](https://brainglobe.info/developers/index.html).

brainglobe-0.2.0/brainglobe.egg-info/requires.txt

@@ -1,24 +0,0 @@
-napari[all]
-bg-space>=0.5.0
-brainglobe-utils
-bg-atlasapi>=1.0.0
-brainreg
-imio
-cellfinder-core>=0.3
-morphapi>=0.1.3.0
-brainglobe-napari-io
-brainreg-segment>=0.0.2
-cellfinder-napari
-brainreg-napari
-cellfinder
-
-[dev]
-pytest
-pytest-cov
-coverage
-tox
-black
-mypy
-pre-commit
-ruff
-setuptools_scm

brainglobe-0.2.0/pyproject.toml

@@ -1,93 +0,0 @@
-[project]
-name = "brainglobe"
-authors = [{ name = "BrainGlobe", email = "code@adamltyson.com" }]
-description = "Python-based tools for computational neuroanatomy."
-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",
-]
-
-dependencies = [
-  "napari[all]",
-  "bg-space>=0.5.0",
-  "brainglobe-utils",
-  "bg-atlasapi>=1.0.0",
-  "brainreg",
-  # brainglobe-napari [WIP],
-  "imio",
-  "cellfinder-core>=0.3",
-  "morphapi>=0.1.3.0",
-  "brainglobe-napari-io",
-  # bg-atlasgen [LOCAL ONLY],
-  "brainreg-segment>=0.0.2",
-  "cellfinder-napari",
-  "brainreg-napari",
-  "cellfinder",
-]
-
-[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*"]
-exclude = ["tests*"]
-
-[tool.pytest.ini_options]
-addopts = "--cov=brainglobe"
-
-[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"]

brainglobe-0.2.0/tests/test_unit/test_tool_exposure.py

@@ -1,57 +0,0 @@
-import inspect
-
-import pytest
-from importlib_metadata import PackageNotFoundError
-
-import brainglobe as bg
-
-# Tools that will be exposed in the brainglobe module/namespace
-EXPOSED_TOOLS = [
-    "bg_atlasapi",
-    "bg_space",
-    "brainreg",
-    "brainreg_segment",
-    "cellfinder_core",
-]
-OPTIONAL_TOOLS = ["morphapi", "cellfinder"]
-
-
-def test_tool_exposure() -> None:
-    """Assert that each of the user-facing tool sub-modules can be imported."""
-
-    for exposed_tool in EXPOSED_TOOLS:
-        assert hasattr(
-            bg, exposed_tool
-        ), f"brainglobe has no (exposed) tool {exposed_tool}"
-        assert inspect.ismodule(
-            getattr(bg, exposed_tool)
-        ), f"brainglobe.{exposed_tool} is not a submodule"
-
-    # Determine if optional dependencies were installed,
-    # and exposed if necessary
-
-    # morphapi - should be exposed if installed
-    if bg._MORPHAPI_INSTALLED:
-        assert hasattr(
-            bg, "morphapi"
-        ), "morphapi is installed but not exposed."
-        assert inspect.ismodule(
-            bg.morphapi
-        ), "brainglobe.morphapi is not a module"
-    else:
-        assert not hasattr(bg, "morphapi")
-
-    # cellfinder - should not be exposed if installed
-    # cellfinder_core - should be exposed if installed
-    if bg._CELLFINDER_INSTALLED:
-        assert not hasattr(
-            bg, "cellfinder"
-        ), "brainglobe.cellfinder is exposed"
-        assert hasattr(
-            bg, "cellfinder_core"
-        ), "brainglobe.cellfinder_core is not exposed"
-    else:
-        # cellfinder_core should be aliased to a function
-        # that throws an error when invoked
-        with pytest.raises(PackageNotFoundError):
-            bg.cellfinder_core()

brainglobe-0.2.0/tox.ini

@@ -1,15 +0,0 @@
-[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 --cov-report=xml