Fix compile scripts

alejoe91 · alejoe91 · commit 6bb034f043bc · 2023-06-05T17:23:43.000+02:00
diff --git a/.github/workflows/test_containers_singularity.yml b/.github/workflows/test_containers_singularity.yml
@@ -17,13 +17,19 @@ jobs:
         os: ["ubuntu-latest", ]
     steps:
       - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.9'
 
       - uses: eWaterCycle/setup-singularity@v7
         with:
           singularity-version: 3.8.3
 
+      - name: Python version
+        run: |
+          python --version
+
       - name: Install dependencies
         run: |
           pip install tridesclous
diff --git a/kilosort-compiled/kilosort-compiled/compile.sh b/kilosort-compiled/kilosort-compiled/compile.sh
@@ -33,7 +33,7 @@ mkdir -p $TMP_DIR
 
 echo "Compiling kilosort_master..."
 cd $TMP_DIR
-matlab -batch "mcc -m $SI_PATH/spikeinterface/sorters/external/kilosort_master.m -a $SI_PATH/spikeinterface/sorters/utils -a $KS_PATH -o ${KS_COMPILED_NAME}"
+matlab -batch "mcc -m ${SI_PATH}/src/spikeinterface/sorters/external/kilosort_master.m -a ${SI_PATH}/src/spikeinterface/sorters/utils -a $KS_PATH -o ${KS_COMPILED_NAME}"
 
 echo "Creating base docker image..."
 matlab -batch "compiler.package.docker('${KS_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'ks-matlab-base')"
diff --git a/kilosort-compiled/kilosort2-compiled/compile.sh b/kilosort-compiled/kilosort2-compiled/compile.sh
@@ -33,7 +33,7 @@ mkdir -p $TMP_DIR
 
 echo "Compiling kilosort_master..."
 cd $TMP_DIR
-matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/external/kilosort2_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH} -o ${KS2_COMPILED_NAME}"
+matlab -batch "mcc -m ${SI_PATH}/src/spikeinterface/sorters/external/kilosort2_master.m -a ${SI_PATH}/src/spikeinterface/sorters/utils -a ${KS_PATH} -o ${KS2_COMPILED_NAME}"
 
 echo "Creating base docker image..."
 matlab -batch "compiler.package.docker('${KS2_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'ks2-matlab-base')"
diff --git a/kilosort-compiled/kilosort2_5-compiled/compile.sh b/kilosort-compiled/kilosort2_5-compiled/compile.sh
@@ -33,7 +33,7 @@ mkdir -p $TMP_DIR
 
 echo "Compiling kilosort_master..."
 cd $TMP_DIR
-matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/external/kilosort2_5_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH} -o ${KS2_5_COMPILED_NAME}"
+matlab -batch "mcc -m ${SI_PATH}/src/spikeinterface/sorters/external/kilosort2_5_master.m -a ${SI_PATH}/src/spikeinterface/sorters/utils -a ${KS_PATH} -o ${KS2_5_COMPILED_NAME}"
 
 echo "Creating base docker image..."
 matlab -batch "compiler.package.docker('${KS2_5_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'ks2_5-matlab-base')"
diff --git a/kilosort-compiled/kilosort3-compiled/compile.sh b/kilosort-compiled/kilosort3-compiled/compile.sh
@@ -33,7 +33,7 @@ mkdir -p $TMP_DIR
 
 echo "Compiling kilosort_master..."
 cd $TMP_DIR
-matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/external/kilosort3_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH} -o ${KS3_COMPILED_NAME}"
+matlab -batch "mcc -m ${SI_PATH}/src/spikeinterface/sorters/external/kilosort3_master.m -a ${SI_PATH}/src/spikeinterface/sorters/utils -a ${KS_PATH} -o ${KS3_COMPILED_NAME}"
 
 echo "Creating base docker image..."
 matlab -batch "compiler.package.docker('${KS3_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'ks3-matlab-base')"
diff --git a/mountainsort4/Dockerfile b/mountainsort4/Dockerfile
@@ -7,4 +7,4 @@ RUN pip install numpy
 
 RUN pip install requests
 # Install MountainSort4
-RUN pip install mountainsort4==1.0.3
+RUN pip install mountainsort4==1.0.4
diff --git a/mountainsort4/build.sh b/mountainsort4/build.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker build -t spikeinterface/mountainsort4-base:latest -t spikeinterface/mountainsort4-base:1.0.3 .
+docker build -t spikeinterface/mountainsort4-base:latest -t spikeinterface/mountainsort4-base:1.0.4 .
diff --git a/mountainsort5/Dockerfile b/mountainsort5/Dockerfile
@@ -0,0 +1,8 @@
+FROM python:3.8
+
+# downgrade pip version to avoid dependency issues during installations
+RUN pip install --no-input pip==21.2.4
+
+RUN pip install numpy
+
+RUN pip install mountainsort5==0.3.0
diff --git a/mountainsort5/build.sh b/mountainsort5/build.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker build -t spikeinterface/mountainsort5-base:latest -t spikeinterface/mountainsort5-base:0.3.0 .
diff --git a/mountainsort5/push.sh b/mountainsort5/push.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+docker push --all-tags spikeinterface/mountainsort5-base
diff --git a/requirements_test.txt b/requirements_test.txt
@@ -1,3 +1,3 @@
-git+https://github.com/SpikeInterface/spikeinterface.git#egg=spikeinterface[full]
+spikeinterface[full] @ git+https://github.com/SpikeInterface/spikeinterface.git
 spython==0.2.1
 pytest==7.1.2

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,3 @@`
`1`	`1`	`#!/bin/bash`
`2`	`2`
`3`		`-docker build -t spikeinterface/mountainsort4-base:latest -t spikeinterface/mountainsort4-base:1.0.3 .`
	`3`	`+docker build -t spikeinterface/mountainsort4-base:latest -t spikeinterface/mountainsort4-base:1.0.4 .`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+#!/bin/bash`
	`2`	`+`
	`3`	`+docker build -t spikeinterface/mountainsort5-base:latest -t spikeinterface/mountainsort5-base:0.3.0 .`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+#!/bin/bash`
	`2`	`+`
	`3`	`+docker push --all-tags spikeinterface/mountainsort5-base`