Merge branch 'kilodev' into main

.gitignore

@@ -1,44 +1,133 @@
-gui/userSettings.mat
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-# Windows image file caches
-Thumbs.db
-ehthumbs.db
+# C extensions
+*.so
 
-# Folder config file
-Desktop.ini
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
 
-# Recycle Bin used on file shares
-$RECYCLE.BIN/
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
 
-# Compiled source 
-*.mexa64
-*.mexw64
-*.asv
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
 
-# Windows shortcuts
-*.lnk
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
 
-# =========================
-# Operating System Files
-# =========================
+# Translations
+*.mo
+*.pot
 
-# OSX
-# =========================
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
 
-.DS_Store
-.AppleDouble
-.LSOverride
+# Flask stuff:
+instance/
+.webassets-cache
 
-# Thumbnails
-._*
+# Scrapy stuff:
+.scrapy
 
-# Files that might appear on external disk
-.Spotlight-V100
-.Trashes
+# Sphinx documentation
+docs/_build/
 
-# Directories potentially created on remote AFP share
-.AppleDB
-.AppleDesktop
-Network Trash Folder
-Temporary Items
-.apdisk
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Test data
+tests/.test_data/
+tests/.test_data/*

kilosort_dev/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,54 @@
+name: Bug report
+description: Report a bug.
+title: "BUG: <Please write a comprehensive title after the 'BUG: ' prefix>"
+
+body:
+- type: markdown
+  attributes:
+    value: >
+      Thank you for taking the time to file a bug report. Before creating a new
+      issue, please make sure to take a few minutes to check if this issue has been 
+      brought up before.
+    
+- type: textarea
+  attributes: 
+    label: "Describe the issue:"
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Reproduce the bug:"
+    description: >
+      A short code example that reproduces the problem/missing feature,
+      if applicable.
+    render: python
+
+- type: textarea
+  attributes:
+    label: "Error message:"
+    description: >
+      Please include full error message, if any.
+    render: shell
+
+- type: textarea
+  attributes:
+    label: "Version information:"
+    description: >
+      Version of operating system and python used, as well as any other
+      software versions you think might be relevant to the bug (e.g. CUDA toolkit).
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Context for the issue:"
+    description: |
+      Please explain how this issue affects your work or why it should be prioritized.
+
+- type: textarea
+  attributes:
+    label: "Experiment information:"
+    description: >
+      Type of probe used, species and brain area recorded from, etc, if your bug
+      is related to "strange/unexpected results."

kilosort_dev/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,19 @@
+name: Feature request
+description: Suggest an additional feature you'd like to see in Kilosort.
+title: "FEATURE: <Please write a comprehensive title after the 'FEATURE: ' prefix>"
+
+body:
+- type: textarea
+  attributes: 
+    label: "Feature you'd like to see:"
+    description: >
+        Provide a clear and concise description of the new feature you'd like to
+        see.
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Additional Context"
+    description: >
+        Add any other context or screenshots about the feature request here.

kilosort_dev/.github/ISSUE_TEMPLATE/installation_issue.yml

@@ -0,0 +1,32 @@
+name: Installation issue
+description: Report an issue with installation for Kilosort.
+title: "INSTALLATION: <Please write a comprehensive title.>"
+
+body:
+
+- type: textarea
+  attributes: 
+    label: "Describe the issue:"
+    description: >
+      Let us know what issues you are having with installation.
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Provide environment info:"
+    description: >
+      Please run `conda info` (or the appropriate command for your environment
+      manager) in your Kilosort environment in your terminal/anaconda
+      prompt to let us know the versions of your packages.
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Operating system information:"
+    description: >
+      Operating system and version.
+  validations:
+    required: true
+

kilosort_dev/.github/ISSUE_TEMPLATE/other.yml

@@ -0,0 +1,13 @@
+name: Other issue
+description: Report something about Kilosort.
+title: "<Please write a comprehensive title.>"
+
+body:
+
+- type: textarea
+  attributes: 
+    label: "Describe the issue:"
+    description: >
+      Description.
+  validations:
+    required: true  

kilosort_dev/.github/workflows/test_and_deploy.yml

@@ -0,0 +1,47 @@
+name: tests
+
+on:
+  # NOTE: disabled tests on push because this causes PRs to be tested twice,
+  #       need to figure out how to have both without duplicating tests.
+  # push:
+  #   branches:
+  #     - main
+  #     - "v*x"
+  #   tags:
+  #     - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - main
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+        python: ["3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install setuptools tox tox-gh-actions
+
+      - name: Test with tox
+        run: tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3