Update and standardise tooling

.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 }}

.gitignore

@@ -1,45 +1,3 @@
-# Ignored file types
-*.ckpt
-*.vscode
-*.json
-*.xml
-*.idea
-*.pyc
-*.vtk
-*.obj
-*.stl
-*.nrrd
-*.svg
-*.tdms
-
-# These file formats are tracked
-# *.avi
-# *.png
-# *.mp4
-# *.jpg
-
-
-# User folder where they can save stuff without it being tracked by git
-User/*
-
-# Visual studio stuff
-*/tempCodeRunnerFile.py
-*/.ipynb_checkpoints
-.ipynb_checkpoints
-*/__pycache__
-__pycache__
-.DS_Store
-Users/
-
-# Test scripts and hidden files
-workspace.py
-workspace.ipynb
-playground.py
-secrets
-
-# Custom config files
-*.conf.custom
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -50,6 +8,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -61,11 +20,9 @@ lib64/
 parts/
 sdist/
 var/
-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -85,9 +42,8 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
-*.cover
+*,cover
 .hypothesis/
-.pytest_cache/
 
 # Translations
 *.mo
@@ -96,59 +52,32 @@ coverage.xml
 # Django stuff:
 *.log
 local_settings.py
-db.sqlite3
 
-# Flask stuff:
+# Flask instance folder
 instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
 
 # Sphinx documentation
-doc/build/
+docs/_build/
 
-# pydocmd
-_build/
-mkdocs.yml
+# MkDocs documentation
+/site/
 
 # PyBuilder
 target/
 
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# 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/
+# IPython Notebook
+.ipynb_checkpoints
 
-.idea/
+# pyenv
+.python-version
 
-*.~lock.*
+# OS
+.DS_Store
 
-# Test reports
-reports
+# written by setuptools_scm
+**/_version.py

.pre-commit-config.yaml

@@ -1,17 +1,42 @@
+
+
 # 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
+    - 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
+                - types-requests
+                - types-PyYAML
+                - types-retry
+    - repo: https://github.com/mgedmin/check-manifest
+      rev: "0.49"
+      hooks:
+          - id: check-manifest
+            args: [--no-build-isolation]
+            additional_dependencies: [setuptools-scm]

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 BrancoLab
+Copyright (c) 2023 University College London
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -0,0 +1,9 @@
+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 *

README.md

@@ -2,7 +2,7 @@
 
 ## Overview
 Morphapi is a lightweight python package for downloading neurons
-morphological reconstructions from publicly available datasets. 
+morphological reconstructions from publicly available datasets.
 
 Please see the [documentation](https://brainglobe.info/documentation/morphapi/index.html)
 

examples/download/allen_morphology_api.py

@@ -15,7 +15,7 @@
 # Download some neurons
 neurons = am.download_neurons(neurons[:5].id.values)
 
-# ------------------------------- Visualisation ------------------------------ #
+# ----------------------- Visualisation --------------------- #
 print("creating meshes")
 neurons = [neuron.create_mesh()[1] for neuron in neurons]