Update igv, build process, python, java (#42)

* Update macos.yml * update igv * update actions * try newer ubuntu * fix java version * update mac actions * use 11 explicitly * Use python 3.10 for nuitka support * Update dependencies for windows * Update path * Update mac java
ResearchIT · Nov 29, 2022 · 63390ce · 63390ce
1 parent ca87465
commit 63390ce
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Showing 6 changed files with 39 additions and 33 deletions.
diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -15,7 +15,7 @@ on:
 jobs:
   build:
 
-    runs-on: macos-10.15
+    runs-on: macos-11
     env:
       MACOSX_DEPLOYMENT_TARGET: 10.12
 
@@ -38,25 +38,30 @@ jobs:
         echo "::set-output name=timestamp::${stamp}"
 
     - name: ccache cache files
-      uses: actions/cache@v1.1.0
+      uses: actions/cache@v3
       with:
          path: ~/.ccache
          key: macos-ccache
 
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         submodules: true
     - name: Set up JDK 1.11
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v2
       with:
-        java-version: 1.11
+        java-version: 11.0
+        distribution: zulu
+    - name: Use python 3.10 for nuitka support
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10' 
     - name: Apply patch
       run: ./scripts/apply_patch.sh
     - name: Bundle macos version
       run: ./macos/bundle_macos.sh
 
     - name: Upload a Build Artifact (non-release)
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       if: ${{ success() && github.event_name != 'release' }}
       # tar file is important
       # https://github.com/actions/upload-artifact#maintaining-file-permissions-and-case-sensitive-files

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -15,16 +15,17 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         submodules: true
     - name: Set up JDK 1.11
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v2
       with:
-        java-version: 1.11
+        java-version: 11.0
+        distribution: zulu
     - name: Install (Windows cross compile)
       run: |
           sudo apt-get update
@@ -35,7 +36,7 @@ jobs:
       run: ./windows/bundle_windows.sh
 
     - name: Upload a Build Artifact (non-release)
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v3
       if: ${{ success() && github.event_name != 'release' }}
       with:
         name: IGV-ScanFold-windows

diff --git a/igv b/igv
diff --git a/macos/bundle_macos.sh b/macos/bundle_macos.sh
@@ -5,14 +5,14 @@ mkdir -p ${BUNDLE_PREFIX}
 
 # build IGV and bundle with JRE
 pushd lib
-curl -L -O https://github.com/adoptium/temurin11-binaries/releases/download/jdk-11.0.12%2B7/OpenJDK11U-jre_x64_mac_hotspot_11.0.12_7.tar.gz
-tar -xzf OpenJDK11U-jre_x64_mac_hotspot_11.0.12_7.tar.gz
-rm  OpenJDK11U-jre_x64_mac_hotspot_11.0.12_7.tar.gz
+curl -L -O https://github.com/adoptium/temurin11-binaries/releases/download/jdk-11.0.17%2B8/OpenJDK11U-jre_x64_mac_hotspot_11.0.17_8.tar.gz
+tar -xzf OpenJDK11U-jre_x64_mac_hotspot_11.0.17_8.tar.gz
+rm  OpenJDK11U-jre_x64_mac_hotspot_11.0.17_8.tar.gz
 popd
 
 pushd igv
 ./gradlew clean
-./gradlew createMacAppWithJavaDistZip -PjdkBundleMac=${TOPLEVEL}/lib/jdk-11.0.12+7-jre/Contents/Home
+./gradlew createMacAppWithJavaDistZip -PjdkBundleMac=${TOPLEVEL}/lib/jdk-11.0.17+8-jre/Contents/Home
 unzip build/distributions/IGV_MacApp_user_WithJava.zip
 mv IGV_User.app ${BUNDLE_PREFIX}/IGV-ScanFold.app
 popd

diff --git a/windows/IGV-ScanFold.bat b/windows/IGV-ScanFold.bat
@@ -1,7 +1,7 @@
 setlocal
 
 SET SCANFOLDRUNDIR=%cd%
-SET SCANFOLDPYTHONINTERPRETER=%SCANFOLDRUNDIR%\scanfold\python-3.9.7-embed-amd64\python
+SET SCANFOLDPYTHONINTERPRETER=%SCANFOLDRUNDIR%\scanfold\python-3.10.8-embed-amd64\python
 SET SCANFOLDRUNSCRIPT=%SCANFOLDRUNDIR%\scanfold\run_scanfold.py
 
 cd %cd%\IGV

diff --git a/windows/bundle_windows.sh b/windows/bundle_windows.sh
@@ -5,14 +5,14 @@ mkdir -p ${BUNDLE_PREFIX}
 
 # build IGV and bundle with JRE
 pushd lib
-curl -L -O https://github.com/adoptium/temurin11-binaries/releases/download/jdk-11.0.12%2B7/OpenJDK11U-jre_x64_windows_hotspot_11.0.12_7.zip
-unzip OpenJDK11U-jre_x64_windows_hotspot_11.0.12_7.zip
-rm  OpenJDK11U-jre_x64_windows_hotspot_11.0.12_7.zip
+curl -L -O https://github.com/adoptium/temurin11-binaries/releases/download/jdk-11.0.17%2B8/OpenJDK11U-jre_x64_windows_hotspot_11.0.17_8.zip
+unzip OpenJDK11U-jre_x64_windows_hotspot_11.0.17_8.zip
+rm  OpenJDK11U-jre_x64_windows_hotspot_11.0.17_8.zip
 popd
 
 pushd igv
 ./gradlew clean
-./gradlew createWinWithJavaDist -PjdkBundleWindows=${TOPLEVEL}/lib/jdk-11.0.12+7-jre
+./gradlew createWinWithJavaDist -PjdkBundleWindows=${TOPLEVEL}/lib/jdk-11.0.17+8-jre
 mv build/IGV-WinExe-WithJava-dist/IGV_user ${BUNDLE_PREFIX}/IGV
 popd
 
@@ -21,29 +21,29 @@ popd
 mkdir -p ${BUNDLE_PREFIX}/scanfold/
 
 pushd lib
-curl -L -O https://www.python.org/ftp/python/3.9.7/python-3.9.7-embed-amd64.zip
-unzip -d ${BUNDLE_PREFIX}/scanfold/python-3.9.7-embed-amd64 python-3.9.7-embed-amd64.zip
-rm python-3.9.7-embed-amd64.zip
+curl -L -O https://www.python.org/ftp/python/3.10.8/python-3.10.8-embed-amd64.zip
+unzip -d ${BUNDLE_PREFIX}/scanfold/python-3.10.8-embed-amd64 python-3.10.8-embed-amd64.zip
+rm python-3.10.8-embed-amd64.zip
 popd
 
-pushd ${BUNDLE_PREFIX}/scanfold/python-3.9.7-embed-amd64
+pushd ${BUNDLE_PREFIX}/scanfold/python-3.10.8-embed-amd64
 echo '
-python39.zip
+python310.zip
 .
 ..
 site-packages
-' >> python39._pth
+' >> python310._pth
 mkdir -p site-packages
 
 # biopython
-curl -L -O https://files.pythonhosted.org/packages/60/da/c67fef644a92c2e44743ad8c3f0321b140e226f2b55112f066a9415c9d91/biopython-1.79-cp39-cp39-win_amd64.whl
-unzip -d site-packages biopython-1.79-cp39-cp39-win_amd64.whl
-rm biopython-1.79-cp39-cp39-win_amd64.whl
+curl -L -O https://files.pythonhosted.org/packages/06/ed/6fbab8be0b4868f5105d76f3ab8b202c1bffd23d43cd422ba485af374b71/biopython-1.80-cp310-cp310-win_amd64.whl
+unzip -d site-packages biopython-1.80-cp310-cp310-win_amd64.whl
+rm biopython-1.80-cp310-cp310-win_amd64.whl
 
 # numpy
-curl -L -O https://files.pythonhosted.org/packages/01/d9/6e5f6cbd9d1fc90c6c8d96e70754700ed6f93f90f321f887a3f26bf65715/numpy-1.21.2-cp39-cp39-win_amd64.whl
-unzip -d site-packages numpy-1.21.2-cp39-cp39-win_amd64.whl
-rm numpy-1.21.2-cp39-cp39-win_amd64.whl
+curl -L -O https://files.pythonhosted.org/packages/6a/03/ae6c3c307f9c5c7516de3df3e764ebb1de33e54e197f0370992138433ef4/numpy-1.23.5-cp310-cp310-win_amd64.whl
+unzip -d site-packages numpy-1.23.5-cp310-cp310-win_amd64.whl
+rm numpy-1.23.5-cp310-cp310-win_amd64.whl
 popd
 
 # scanfold