diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml index f53ad82..7588b55 100644 --- a/.github/workflows/test_and_deploy.yml +++ b/.github/workflows/test_and_deploy.yml @@ -38,7 +38,7 @@ jobs: strategy: matrix: # Run all supported Python versions on linux - python-version: ["3.8", "3.9", "3.10"] + python-version: ["3.9", "3.10"] os: [ubuntu-latest] # Include one windows and macos run include: diff --git a/README.md b/README.md index 491c752..9bd92ca 100644 --- a/README.md +++ b/README.md @@ -36,7 +36,7 @@ Currently included packages, and whether they come with the `pip` and `conda-for | 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) | +| `brainglobe-segmentation` | ☑ | ☑ | `brainglobe_segmentation` | [Site](https://brainglobe.info/documentation/brainglobe-segmentation/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) | diff --git a/brainglobe/__init__.py b/brainglobe/__init__.py index c4fdfa2..5e74c0c 100644 --- a/brainglobe/__init__.py +++ b/brainglobe/__init__.py @@ -12,7 +12,7 @@ import bg_atlasapi import bg_space import brainreg -import brainreg_segment +import brainglobe_segmentation # Expose tools that may not be present # if a conda install was performed diff --git a/docs/brainglobe-interdependencies.md b/docs/brainglobe-interdependencies.md index 4a66fa0..5d5aaea 100644 --- a/docs/brainglobe-interdependencies.md +++ b/docs/brainglobe-interdependencies.md @@ -19,9 +19,8 @@ Packages are listed top to bottom based on the number of brainglobe dependencies | `morphio` | https://github.com/brainglobe/morphapi | https://pypi.org/project/morphio | See notes | | `brainglobe-napari-io` | https://github.com/brainglobe/brainglobe-napari-io | https://pypi.org/project/brainglobe-napari-io | https://github.com/conda-forge/brainglobe-napari-io-feedstock | | `bg-atlasgen` | https://github.com/brainglobe/bg-atlasgen | See notes | See notes | -| `brainreg-segment` | https://github.com/brainglobe/brainreg-segment | https://pypi.org/project/brainreg-segment | https://github.com/conda-forge/brainreg-segment-feedstock | +| `brainglobe-segmentation` | https://github.com/brainglobe/brainglobe-segmentation | https://pypi.org/project/brainglobe-segmentation | https://github.com/conda-forge/brainglobe-segmentation-feedstock | | `cellfinder-napari` | https://github.com/brainglobe/cellfinder-napari | https://pypi.org/project/cellfinder-napari | https://github.com/conda-forge/cellfinder-napari-feedstock | -| `brainreg-napari` | https://github.com/brainglobe/brainreg-napari | https://pypi.org/project/brainreg-napari | https://github.com/conda-forge/brainreg-napari-feedstock | | `cellfinder` | https://github.com/brainglobe/cellfinder | https://pypi.org/project/cellfinder | Not available | @@ -34,5 +33,3 @@ Packages are listed top to bottom based on the number of brainglobe dependencies - [Repository](https://github.com/brainglobe/brainglobe-napari) - Napari plugin for [bg-atlasapi](#bg-atlasapi). Note that repository README uses the name "brainglobe" for "bg-atlasapi" due to a historical renaming. - Dependencies: `bg-atlasapi` -- `brainreg` - - Has optional `[napari]` dependency which just goes away and installs `brainreg-napari` package. diff --git a/pyproject.toml b/pyproject.toml index 6b2141e..6427a5f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ name = "brainglobe" authors = [{ name = "BrainGlobe", email = "code@adamltyson.com" }] description = "Python-based tools for computational neuroanatomy." readme = "README.md" -requires-python = ">=3.8.0" +requires-python = ">=3.9.0" dynamic = ["version"] license = { text = "BSD-3-Clause" } @@ -24,16 +24,15 @@ dependencies = [ "bg-space>=0.5.0", "brainglobe-utils", "bg-atlasapi>=1.0.0", - "brainreg", + "brainreg[napari]>=1.0.0", # 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", + "brainglobe-segmentation>=1.0.0", "cellfinder-napari", - "brainreg-napari", "cellfinder", ] diff --git a/tests/test_unit/test_tool_exposure.py b/tests/test_unit/test_tool_exposure.py index fa49fb6..5e41f7b 100644 --- a/tests/test_unit/test_tool_exposure.py +++ b/tests/test_unit/test_tool_exposure.py @@ -10,7 +10,7 @@ "bg_atlasapi", "bg_space", "brainreg", - "brainreg_segment", + "brainglobe_segmentation", "cellfinder_core", ] OPTIONAL_TOOLS = ["morphapi", "cellfinder"]