Merge branch 'quantumjot:main' into fix-multichan-error

quantumjot · Jan 23, 2024 · 7b90ba9 · 7b90ba9
2 parents 57dea4e + 8632533
commit 7b90ba9
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diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -79,19 +79,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         os: [ubuntu-latest]
         include:
           - os: macos-11
-            python-version: "3.10"
+            python-version: "3.11"
           - os: macos-latest
-            python-version: "3.10"
+            python-version: "3.11"
           - os: windows-2019
-            python-version: "3.10"
+            python-version: "3.11"
           - os: windows-latest
-            python-version: "3.10"
+            python-version: "3.11"
           - os: ubuntu-20.04
-            python-version: "3.10"
+            python-version: "3.11"
 
     steps:
       - name: Checkout source

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -50,19 +50,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         os: [ubuntu-latest]
         include:
           - os: macos-11
-            python-version: "3.10"
+            python-version: "3.11"
           - os: macos-latest
-            python-version: "3.10"
+            python-version: "3.11"
           - os: windows-2019
-            python-version: "3.10"
+            python-version: "3.11"
           - os: windows-latest
-            python-version: "3.10"
+            python-version: "3.11"
           - os: ubuntu-20.04
-            python-version: "3.10"
+            python-version: "3.11"
 
     steps:
       - uses: actions/checkout@v3
@@ -80,23 +80,16 @@ jobs:
           cache: "pip"
           cache-dependency-path: "pyproject.toml"
 
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-
       # these libraries enable testing on Qt on linux
       - uses: tlambert03/setup-qt-libs@v1
 
-      # note: if you need dependencies from conda, considering using
-      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
-      # and
-      # tox-conda: https://github.com/tox-dev/tox-conda
       - name: Install dependencies
-        run: python -m pip install "tox<4" tox-gh-actions tox-conda
+        run: python -m pip install tox tox-gh-actions
 
       - name: Test with tox
-        run: tox
+        run: tox run
+        env:
+            OS: ${{ matrix.os }}
 
       - name: Coverage
         uses: codecov/codecov-action@v3
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,5 @@
 __pycache__
+_version.py
 .cache
 .coverage
 .coverage.*
@@ -54,14 +55,13 @@ instance
 lib
 lib64
 local_settings.py
-models/MDCK_*
-models/test_config.json
+models
 nosetests.xml
 notebooks
 parts
 pip-delete-this-directory.txt
 pip-log.txt
 sdist
 target
+user_config.json
 var
-_version.py
diff --git a/.napari-hub/DESCRIPTION.md b/.napari-hub/DESCRIPTION.md
@@ -19,15 +19,38 @@ linkages.
 
 We developed `btrack` for cell tracking in time-lapse microscopy data.
 
-![](https://raw.githubusercontent.com/lowe-lab-ucl/arboretum/master/examples/arboretum.gif)
+![tracking2](https://github.com/quantumjot/btrack/assets/8217795/7b16381a-b7e5-4750-98c6-bcdfbe95b908)
 
 <!--
 ## tutorials
 
 * https://napari.org/tutorials/tracking/cell_tracking.html
 -->
 
+## Installation
 
-## associated plugins
+To install the `napari` plugin associated with `btrack` run the command.
+
+```sh
+pip install btrack[napari]
+```
+
+## Example data
+
+You can try out the btrack plugin using sample data:
+
+```sh
+python btrack/napari/examples/show_btrack_widget.py
+```
+
+which will launch `napari` and the `btrack` widget, along with some sample data.
+
+
+## Setting parameters
+
+There are detailed tips and instructions on parameter settings over at the [documentation](https://btrack.readthedocs.io/en/latest/user_guide/index.html).
+
+
+## Associated plugins
 
 * [napari-arboretum](https://www.napari-hub.org/plugins/napari-arboretum) - Napari plugin to enable track graph and lineage tree visualization.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,10 +1,10 @@
 repos:
     - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.262
+      rev: v0.0.278
       hooks:
         - id: ruff
     - repo: https://github.com/Lucas-C/pre-commit-hooks
-      rev: v1.5.1
+      rev: v1.5.3
       hooks:
         - id: remove-tabs
           exclude: Makefile|docs/Makefile|\.bat$
@@ -19,19 +19,18 @@ repos:
           - id: end-of-file-fixer
           - id: mixed-line-ending
             args: [--fix=lf]
-          - id: requirements-txt-fixer
           - id: trailing-whitespace
             args: [--markdown-linebreak-ext=md]
     - repo: https://github.com/psf/black
-      rev: 23.3.0
+      rev: 23.7.0
       hooks:
           - id: black
     - repo: https://github.com/pappasam/toml-sort
-      rev: v0.23.0
+      rev: v0.23.1
       hooks:
         - id: toml-sort-fix
     - repo: https://github.com/pre-commit/mirrors-clang-format
-      rev: v15.0.7
+      rev: v16.0.6
       hooks:
       - id: clang-format
         types_or: [c++, c, cuda]
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.10"
+    python: "3.11"
 
 # Optionally declare the Python requirements required to build your docs
 python:

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1 +1,5 @@
 graft btrack/libs
+prune docs
+prune tests
+prune models
+prune examples
diff --git a/Makefile b/Makefile
@@ -18,15 +18,15 @@ ifeq ($(UNAME), Darwin)
 	# do something OSX
 	CXX = clang++ -arch x86_64 -arch arm64
 	EXT = dylib
-	XLD_FLAGS = -arch x86_64 -arch arm64
+	XLDFLAGS =
 endif
 
 NVCC = nvcc
 
-# If your compiler is a bit older you may need to change -std=c++17 to -std=c++0x
+# If your compiler is a bit older you may need to change -std=c++11 to -std=c++0x
 #-I/usr/include/python2.7 -L/usr/lib/python2.7 # -O3
 LLDBFLAGS =
-CXXFLAGS = -c -std=c++17 -m64 -fPIC -I"./btrack/include" \
+CXXFLAGS = -c -std=c++11 -m64 -fPIC -I"./btrack/include" \
 	       -DDEBUG=false -DBUILD_SHARED_LIB
 OPTFLAGS = -O3
 LDFLAGS = -shared $(XLDFLAGS)

diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 [![PyPI](https://img.shields.io/pypi/v/btrack)](https://pypi.org/project/btrack)
-[![Downloads](https://pepy.tech/badge/btrack/month)](https://pepy.tech/project/btrack)
+[![Downloads](https://static.pepy.tech/badge/btrack/month)](https://pepy.tech/project/btrack)
 [![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Tests](https://github.com/quantumjot/btrack/actions/workflows/test.yml/badge.svg)](https://github.com/quantumjot/btrack/actions/workflows/test.yml)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
@@ -32,22 +32,12 @@ Note that `btrack<=0.5.0` was built against earlier version of
 [Eigen](https://eigen.tuxfamily.org) which used `C++=11`, as of `btrack==0.5.1`
 it is now built against `C++=17`.
 
-#### Installing the latest stable version
+### Installing the latest stable version
 
 ```sh
 pip install btrack
 ```
 
-## Installing on M1 Mac/Apple Silicon/osx-arm64
-
-Best done with [conda](https://github.com/conda-forge/miniforge)
-
-```sh
-conda env create -f environment.yml
-conda activate btrack
-pip install btrack
-```
-
 ## Usage examples
 
 Visit [btrack documentation](https://btrack.readthedocs.io) to learn how to use it and see other examples.