Merge pull request #21 from brainglobe/update

Bring package up to date
brainglobe · Dec 13, 2023 · c1ee9bc · c1ee9bc
2 parents 36d42f0 + 214a6a7
commit c1ee9bc
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diff --git a/.github/workflows/test_and_deploy.yml b/.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: ["3.9", "3.10", "3.11"]
+        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/gh-action-pypi-publish@v1.5.0
+      with:
+        user: __token__
+        password: ${{ secrets.TWINE_API_KEY }}
diff --git a/.gitignore b/.gitignore
@@ -1,9 +1,3 @@
-.chache
-workspace.py
-*.mp4
-.vscode
-.vscode/*
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -14,6 +8,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -25,12 +20,9 @@ lib64/
 parts/
 sdist/
 var/
-wheels/
-share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -45,17 +37,13 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
-.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
-*.cover
-*.py,cover
+*,cover
 .hypothesis/
-.pytest_cache/
-cover/
 
 # Translations
 *.mo
@@ -64,83 +52,32 @@ cover/
 # Django stuff:
 *.log
 local_settings.py
-db.sqlite3
-db.sqlite3-journal
 
-# Flask stuff:
+# Flask instance folder
 instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
 
 # Sphinx documentation
 docs/_build/
 
+# MkDocs documentation
+/site/
+
 # PyBuilder
-.pybuilder/
 target/
 
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
+# Pycharm and VSCode
+.idea/
 venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
+.vscode/
 
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
+# IPython Notebook
+.ipynb_checkpoints
 
-# pytype static type analyzer
-.pytype/
+# pyenv
+.python-version
 
-# Cython debug symbols
-cython_debug/
+# OS
+.DS_Store
 
-.idea/*
+# written by setuptools_scm
+**/_version.py
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,17 +1,39 @@
+
+
+# Configuring https://pre-commit.ci/
+ci:
+    autoupdate_schedule: monthly
+
 repos:
--   repo: https://github.com/psf/black
-    rev: 23.11.0
-    hooks:
-    - id: black
-      pass_filenames: true
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
-    hooks:
-    - id: flake8
-      pass_filenames: true
-      # this seems to need to be here in addition to setup.cfg
-      exclude: __init__.py, workspace.py
--   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.0
-    hooks:
-    -   id: mypy
+    - 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]
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,10 @@
+include LICENSE
+include README.md
+exclude .pre-commit-config.yaml
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude docs *
+recursive-exclude tests *
+recursive-exclude examples *
+recursive-exclude images *
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 # BG Heatmaps
-Rendering heatmaps with brainrender.
+Rendering anatomical heatmaps with brainrender and matplotlib.
 
 
 
@@ -20,7 +20,7 @@ Rendering heatmaps with brainrender.
 The starting point for a heatmap visualization is a `dict` assigning scalar values to a set of brain regions (identified by their acronym).
 For example:
 
-```python 
+```python
     regions = dict(  # scalar values for each region
         TH=1,
         RSP=0.2,
@@ -63,7 +63,7 @@ planner = bgh.plan(
         8000,
         5000,
         5000,
-    ),  
+    ),
     orientation="frontal",  # orientation, or 'sagittal', or 'horizontal' or a tuple (x,y,z)
     thickness=2000,  # thickness of the slices used for rendering (in microns)
 )
@@ -109,7 +109,7 @@ bgh.heatmap(
         8000,
         5000,
         5000,
-    ),  
+    ),
     orientation="horizontal",  # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
     title="horizontal view",
     vmin=-5,
@@ -136,14 +136,14 @@ coordinates = bgh.get_plane_coordinates(
         8000,
         5000,
         5000,
-    ),  
+    ),
     orientation="frontal",  # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
 )
 ```
 
 ## Using `bgheatmap` with other atlases.
 
-`bgheatmap` uses `brainrender` which, in turn, uses brainglobe's `Atlas API` under the hood. That means that all of `bgheatmap`'s functionality is compatible with any of the atlases supported by the atlas API. 
+`bgheatmap` uses `brainrender` which, in turn, uses brainglobe's `Atlas API` under the hood. That means that all of `bgheatmap`'s functionality is compatible with any of the atlases supported by the atlas API.
 `bgh.heatmap`, `bgh.planner` and `bgh.get_plane_coordinates` all accept a `atlas_name` argument, pass the name of the atlas name you'd like to use!
 For more information see the API's [https://docs.brainglobe.info/bg-atlasapi/introduction](documentation).
 

diff --git a/bgheatmaps/__init__.py b/bgheatmaps/__init__.py
diff --git a/brainglobe_heatmap/__init__.py b/brainglobe_heatmap/__init__.py
@@ -0,0 +1,11 @@
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("brainglobe-heatmap")
+except PackageNotFoundError:
+    # package is not installed
+    pass
+
+from brainglobe_heatmap.heatmaps import heatmap
+from brainglobe_heatmap.planner import plan
+from brainglobe_heatmap.slicer import get_structures_slice_coords