📦 Compile ST_BarcodeMap Using GitHub Actions

.github/workflows/release.yml

@@ -0,0 +1,51 @@
+name: Build and Release ST_BarcodeMap
+
+on:
+  push:
+    tags:
+      - 'v*'  # Triggers on version tags like v0.0.1
+
+jobs:
+  build-and-release:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          environment-file: environment.yml
+          activate-environment: barcodeenv
+          python-version: 3.9
+
+      - name: Install C++ dependencies
+        shell: bash -l {0}
+        run: |
+          mamba install -c conda-forge gcc_linux-64 gxx_linux-64
+          export CC=$(which x86_64-conda-linux-gnu-gcc)
+          export CXX=$(which x86_64-conda-linux-gnu-g++)
+          echo "Using CC=$CC"
+          echo "Using CXX=$CXX"
+          make
+
+      - name: Rename binary with version
+        run: |
+          mkdir -p dist
+          cp ST_BarcodeMap dist/ST_BarcodeMap-${{ github.ref_name }}-linux
+          chmod +x dist/ST_BarcodeMap-${{ github.ref_name }}-linux
+
+      - name: Upload binary to GitHub Release
+        uses: softprops/action-gh-release@v1
+        with:
+          name: Release ${{ github.ref_name }}
+          tag_name: ${{ github.ref_name }}
+          files: dist/ST_BarcodeMap-${{ github.ref_name }}-linux
+          body: |
+            🔁 Automated release for **${{ github.ref_name }}**
+            🐧 Platform: **Linux**
+            📦 Binary: `ST_BarcodeMap-${{ github.ref_name }}-linux`
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

Makefile

@@ -4,39 +4,35 @@ DIR_OBJ := ./obj
 
 PREFIX ?= /usr/local
 BINDIR ?= $(PREFIX)/bin
-INCLUDE_DIRS ?=
-LIBRARY_DIRS ?=
+
+# Use Conda’s Boost, but system GCC
+INCLUDE_DIRS = -I$(DIR_INC) -I$(CONDA_PREFIX)/include -I/usr/include/hdf5/serial
+LIBRARY_DIRS = -L$(CONDA_PREFIX)/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial
 
 SRC := $(wildcard ${DIR_SRC}/*.cpp)
 OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
 
-TARGET := ST_BarcodeMap-0.0.1
-
+TARGET := ST_BarcodeMap
 BIN_TARGET := ${TARGET}
 
-CXX ?= g++
-CXXFLAGS := -std=c++11 -g -O3 -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
-LIBS := -lz -lpthread
-LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(LIBS) $(LD_FLAGS)
-
+CXX := g++
+CXXFLAGS := -std=c++11 -g -O3 $(INCLUDE_DIRS)
+LD_FLAGS := $(LIBRARY_DIRS) -lboost_serialization -lhdf5 -lz -lpthread
 
-${BIN_TARGET}:${OBJ}
+${BIN_TARGET}: ${OBJ}
 	$(CXX) $(OBJ) -o $@ $(LD_FLAGS)
 
-${DIR_OBJ}/%.o:${DIR_SRC}/%.cpp make_obj_dir
+${DIR_OBJ}/%.o: ${DIR_SRC}/%.cpp make_obj_dir
 	$(CXX) -c $< -o $@ $(CXXFLAGS)
 
-.PHONY:clean
+.PHONY: clean
 clean:
-	rm obj/*.o
-	rm $(TARGET)
+	rm -f ${DIR_OBJ}/*.o
+	rm -f ${TARGET}
 
 make_obj_dir:
-	@if test ! -d $(DIR_OBJ) ; \
-	then \
-		mkdir $(DIR_OBJ) ; \
-	fi
+	@if [ ! -d ${DIR_OBJ} ]; then mkdir -p ${DIR_OBJ}; fi
 
 install:
-	install $(TARGET) $(BINDIR)/$(TARGET)
+	install ${TARGET} ${BINDIR}/${TARGET}
 	@echo "Installed."

README.md

@@ -13,9 +13,24 @@ This program can map barcode of stereomics-seq to stereomics-chip
 | zlib          | >=1.2.11 | file compressing and decompressing                         |
 | hdf5          | >=1.10.7 | hdf5 format mask file read                                 |
 
+## Using conda
+If the conda is not set up yet, please install conda first, following the link below:
+[https://www.anaconda.com/docs/getting-started/miniconda/install#macos-linux-installation](https://www.anaconda.com/docs/getting-started/miniconda/install#macos-linux-installation)
+
+To meet the above prerequisites, a conda environment can be created as shown below:
+```bash
+conda install mamba -n base -c conda-forge
+mamba create -n barcodeenv boost=1.73 hdf5=1.10.7 zlib=1.2.11 -c conda-forge
+conda activate barcodeenv
+mamba install -c conda-forge gcc_linux-64 gxx_linux-64
+mamba install -c conda-forge boost=1.73
+```
+
 ## make the runnable program
 ```
 ##add the requested packages in your environment value or specify their path in Makefile by INCLUDE_DIRS and LIBRARY_DIRS
+conda activate barcodeenv
+export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
 
 cd ST_BarcodeMap
 make

environment.yml

@@ -0,0 +1,11 @@
+name: barcodeenv
+channels:
+  - conda-forge
+dependencies:
+  - boost=1.73
+  - hdf5=1.10.7
+  - zlib=1.2.11
+  - gcc_linux-64
+  - gxx_linux-64
+  - make
+  - mamba