Add one master CI which builds, tests and deploys (#231)

* Add one master CI which builds, tests and deploys

* Change needs order

* Fix matrix syntax

* Change flag to 17 from 11

* Don't error if can't find

* Change wilcard pattern

* Download store output

* v3

* Check working directory

* Run ls on right section

* Switch to lowercase

* Run uname to see output

* Check OS output

* Change back the extension

* Remove the test step

* Remove ls step

* Don't specify path to library

* Don't fail fast

* Use add_dll_directory

* Fix fail fast

* Revert "Use add_dll_directory"

This reverts commit caf8cbb.

* Revert "Revert "Use add_dll_directory""

This reverts commit 1b2569d.

* Adjust DLL directory and specify path manually

* Fix DLL path

* Hardcode the path 😢

* Build windows binary

* Test adding windows binary to CI

* Fix job

* Don't download

* Fix CI tabs

* Removed needs

* Use old binary

* Undo comments

* Remove the DLL

* Remove the flags

* Check cross-compiling on Windows

* Install dependencies

* Compile on windows too

* Remove apt install

* Cross compile Windows on Linux

* Reduce jobs from 10 to 5

* Set environment variable

* Selectively install dependency

* SImplify if

* Bump codecov

* Only install mingw on certain item

* Forgot matrix.

* Add windows cross compile to name

* Wrap the if statements

* Try `if: true`

* Fix whitespace

* Update first

* Try templating the name

* Revert "Try templating the name"

This reverts commit 21b8662.

* Fail fast == true

* Remove whitespace

* Change indent

.github/workflows/build_wheels_test_and_deploy.yml

@@ -0,0 +1,135 @@
+name: Build Wheels, Test & Deploy
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    paths-ignore:
+      - "**.md"
+      - "**.rst"
+
+jobs:
+  build_wheels:
+    name: |
+      Build wheels on ${{ matrix.os }} with
+      windows_cross_compile=${{ matrix.windows_cross_compile }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest]
+        windows_cross_compile: [false, true]
+        exclude:
+          - os: macos-latest
+            windows_cross_compile: true
+
+    steps:
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y mingw-w64
+        if: matrix.windows_cross_compile
+
+      - uses: actions/checkout@v3
+
+      - name: Build wheels
+        run: bash build.sh
+        env:
+          WINDOWS_CROSS_COMPILE: ${{ matrix.windows_cross_compile }}
+
+      - name: Upload artefacts
+        uses: actions/upload-artifact@v3
+        with:
+            name: artefacts
+            path: |
+              btrack/libs/*
+            if-no-files-found: error
+
+  test:
+    needs: build_wheels
+    name: ${{ matrix.os }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+        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:
+      - uses: actions/checkout@v3
+
+      - name: Download artefacts
+        uses: actions/download-artifact@v3
+        with:
+            name: artefacts
+            path: btrack/libs
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: "pyproject.toml"
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: "3.10"
+
+      # 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 --upgrade pip
+          python -m pip install "tox<4" tox-gh-actions tox-conda
+
+      - name: Test with tox
+        run: tox
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+
+  deploy:
+    needs: test
+    runs-on: "ubuntu-latest"
+    if: |
+      github.repository == 'quantumjot/btrack'
+      && github.event_name == 'push'
+      && startsWith(github.ref, 'refs/tags')
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v3
+
+      - name: Download artefacts
+        uses: actions/download-artifact@v3
+        with:
+            name: artefacts
+            path: btrack/libs
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: "pyproject.toml"
+
+      - name: Install build dependencies
+        run: python -m pip install build wheel
+
+      - name: Build distributions
+        shell: bash -l {0}
+        run: python -m build
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/checks.yml → .github/workflows/linting.yml

@@ -1,4 +1,4 @@
-name: checks
+name: Linting
 
 on: [push, pull_request]
 

.gitignore

@@ -1,11 +1,10 @@
 btrack/include/eigen
-btrack/__pycache__
-btrack/optimise/__pycache__
+__pycache__
 btrack/agents.py
 btrack/render_movie.py
 models/MDCK_*
 examples/napari.png
-examples/.ipynb_checkpoints
+*.ipynb_checkpoints
 models/test_config.json
 notebooks
 deprecated
@@ -25,3 +24,6 @@ docs/api/*
 coverage.xml
 .envrc
 .hypothesis
+*.DLL
+*.dylib
+*.so

Makefile

@@ -1,24 +1,25 @@
 UNAME := $(shell uname)
 
 ifeq ($(UNAME), Linux)
-	# do something Linux #-fopenmp -static
-	CXX = g++
-	EXT = so
-	XLDFLAGS = -Wl,--no-undefined -Wl,--no-allow-shlib-undefined
-	#-L/usr/local/cuda/lib64 -lcuda -lcudart
+	ifeq ($(WINDOWS_CROSS_COMPILE),true)
+		# do something Windowsy
+		CXX = x86_64-w64-mingw32-g++
+		EXT	= DLL
+		XLDFLAGS = -static-libgcc -static-libstdc++
+	else
+		# do something Linux #-fopenmp -static
+		CXX = g++
+		EXT = so
+		XLDFLAGS = -Wl,--no-undefined -Wl,--no-allow-shlib-undefined
+		#-L/usr/local/cuda/lib64 -lcuda -lcudart
+	endif
 endif
 ifeq ($(UNAME), Darwin)
 	# do something OSX
 	CXX = clang++ -arch x86_64 -arch arm64
 	EXT = dylib
 	XLD_FLAGS = -arch x86_64 -arch arm64
 endif
-ifeq ($(UNAME), Windows)
-	# do something Windowsy
-	CXX = x86_64-w64-mingw32-g++
-	EXT = DLL
-	XLDFLAGS = -static-libgcc -static-libstdc++
-endif
 
 NVCC = nvcc
 
@@ -29,13 +30,13 @@ VERSION_MAJOR = $(shell cat $(VERSION_FILE) | cut -f1 -d.)
 VERSION_MINOR = $(shell cat $(VERSION_FILE) | cut -f2 -d.)
 VERSION_BUILD = $(shell cat $(VERSION_FILE) | cut -f3 -d.)
 
-# If your compiler is a bit older you may need to change -std=c++11 to -std=c++0x
+# If your compiler is a bit older you may need to change -std=c++17 to -std=c++0x
 #-I/usr/include/python2.7 -L/usr/lib/python2.7 # -O3
 LLDBFLAGS =
-CXXFLAGS = -c -std=c++11 -m64 -fPIC -I"./btrack/include" \
-					 -DDEBUG=false -DVERSION_MAJOR=$(VERSION_MAJOR) \
-					 -DVERSION_MINOR=$(VERSION_MINOR) -DVERSION_BUILD=$(VERSION_BUILD) \
-					 -DBUILD_SHARED_LIB
+CXXFLAGS = -c -std=c++17 -m64 -fPIC -I"./btrack/include" \
+		   -DDEBUG=false -DVERSION_MAJOR=$(VERSION_MAJOR) \
+		   -DVERSION_MINOR=$(VERSION_MINOR) -DVERSION_BUILD=$(VERSION_BUILD) \
+		   -DBUILD_SHARED_LIB
 OPTFLAGS = -O3
 LDFLAGS = -shared $(XLDFLAGS)
 

build.sh

@@ -14,7 +14,3 @@ fi
 echo "Compiling btrack from source..."
 make clean
 make
-
-# run the installation
-echo "Installing btrack python package..."
-pip install -e .