Merge pull request #50 from saalfeldlab/build/jdk21

Build/jdk21
saalfeldlab · May 21, 2024 · f3c5e77 · f3c5e77
2 parents d1ae3aa + ea668ef
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diff --git a/.github/workflows/build-installers.yml b/.github/workflows/build-installers.yml
@@ -0,0 +1,69 @@
+# This workflow will build a Java project with Maven
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Build Installers
+
+on:
+  workflow_call:
+  pull_request:
+    branches: [master]
+
+env:
+  DEV_IDENTITY: BXPZTQZ35S # Your Apple Dev identity, something like BXPZTQZ35S
+  PRIMARY_BUNDLE_ID: org.janelia.saalfeldlab.PainteraConvert # Unique to your app, often the launcher class
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [macos-14, ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set Version
+        shell: bash
+        run: |
+          short_version=`git rev-parse --short HEAD`
+          echo "VERSION=$short_version" >> $GITHUB_ENV
+      - name: Download Wix
+        uses: i3h/download-release-asset@v1
+        if: matrix.os == 'windows-latest'
+        with:
+          owner: wixtoolset
+          repo: wix3
+          tag: wix3112rtm
+          file: wix311-binaries.zip
+      - name: Decompress Wix
+        uses: DuckSoft/[email protected]
+        if: matrix.os == 'windows-latest'
+        with:
+          pathSource: wix311-binaries.zip
+          pathTarget: ./target/wix
+      - name: Add Wix to Path
+        run: echo "$HOME/target/wix" >> $GITHUB_PATH
+        if: matrix.os == 'windows-latest'
+      - uses: actions/checkout@v2
+      - name: Set up JDK
+        uses: actions/setup-java@v2
+        with:
+          java-version: 21
+          distribution: 'temurin'
+          cache: 'maven'
+      - name: "Build with Maven"
+        if: matrix.os != 'macos-latest' && matrix.os != 'macos-14'
+        run: mvn -B clean install -Pbuild-installer "-Dmatrix.os=${{ matrix.os }}" --file pom.xml
+      - name: "Build with Maven (macOS No Signing)"
+        env:
+          MACOS_CERTIFICATE: ${{ secrets.MACOS_CERTIFICATE }}
+          MACOS_CERTIFICATE_PWD: ${{ secrets.MACOS_CERTIFICATE_PWD }}
+        if: ${{ env.MACOS_CERTIFICATE == null && (matrix.os == 'macos-latest' || matrix.os == 'macos-14') }}
+        run: mvn -B clean install -Pbuild-installer "-Dmatrix.os=${{ matrix.os }}" --file pom.xml
+
+      - name: Upload Installers
+        uses: actions/upload-artifact@v4
+        with:
+          name: PainteraConvert-${{ matrix.os }}-${{ env.VERSION }}
+          path: |
+            ${{ env.DMG_PATH }}
+            ./target/installer-${{ matrix.os }}/*
diff --git a/.github/workflows/build-main.yml b/.github/workflows/build-main.yml
@@ -16,8 +16,8 @@ jobs:
       - name: Set up Java
         uses: actions/setup-java@v3
         with:
-          java-version: '8'
-          distribution: 'zulu'
+          java-version: '21'
+          distribution: 'temurin'
           cache: 'maven'
       - name: Set up CI environment
         run: .github/setup.sh

diff --git a/.github/workflows/build-pr.yml b/.github/workflows/build-pr.yml
@@ -14,8 +14,8 @@ jobs:
       - name: Set up Java
         uses: actions/setup-java@v3
         with:
-          java-version: '8'
-          distribution: 'zulu'
+          java-version: '21'
+          distribution: 'temurin'
           cache: 'maven'
       - name: Set up CI environment
         run: .github/setup.sh

diff --git a/.github/workflows/publish-installers.yml b/.github/workflows/publish-installers.yml
@@ -0,0 +1,46 @@
+# This workflow will build a Java project with Maven
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Publish Installers
+
+on:
+  push:
+    tags: "paintera-conversion-helper-*.*.*"
+  workflow_dispatch:
+
+
+
+env:
+  DEV_IDENTITY: BXPZTQZ35S # Your Apple Dev identity, something like BXPZTQZ35S
+  PRIMARY_BUNDLE_ID: org.janelia.saalfeldlab.PainteraConvert # Unique to your app, often the launcher class
+
+jobs:
+  build_installers:
+    name: Build Installers
+    uses: ./.github/workflows/build-installers.yml
+
+  create_release:
+    needs: build_installers
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download Artifacts
+        uses: actions/download-artifact@v4
+      - name: Set Version
+        run: |
+          tag_name=$(echo ${{ github.ref }} | grep -oE "[^/]+$")
+          echo "VERSION=$tag_name" >> $GITHUB_ENV
+      - name: Rename Artifacts
+        run: |
+          mv PainteraConvert-ubuntu-latest-*/*.deb PainteraConvert-${{ env.VERSION }}_x86_64.deb
+          mv PainteraConvert-macos-latest-*/*.pkg PainteraConvert-${{ env.VERSION }}-MacOS.pkg
+          mv PainteraConvert-macos-14-*/*.pkg PainteraConvert-${{ env.VERSION }}-MacOS-AppleSilicon.pkg
+      - name: Create Release
+        uses: softprops/action-gh-release@v2
+        with:
+          name: Paintera Convert ${{ env.VERSION }}
+          tag_name: ${{ github.ref }}
+          prerelease: false
+          files: |
+            PainteraConvert-${{ env.VERSION }}_x86_64.deb
+            PainteraConvert-${{ env.VERSION }}-MacOS.pkg
+            PainteraConvert-${{ env.VERSION }}-MacOS-AppleSilicon.pkg
diff --git a/README.md b/README.md
@@ -1,8 +1,32 @@
 [![Build Status](https://github.com/saalfeldlab/paintera-conversion-helper/actions/workflows/build-main.yml/badge.svg)](https://github.com/saalfeldlab/paintera-conversion-helper/actions/workflows/build-main.yml)
+![GitHub Release](https://img.shields.io/github/v/release/saalfeldlab/paintera-conversion-helper)
 
 # Paintera Conversion Helper
 Script to assist conversion of n5 datasets to paintera-friendly formats, as specified [here](https://github.com/saalfeldlab/paintera/issues/61).
 
+## Installation
+Releases can be download for Ubuntu and MacOS from the [Github Releases](https://github.com/saalfeldlab/paintera-conversion-helper/releases)
+
+## Usage
+This conversion tool currently supports any number of datasets (raw or label) with a
+single (global) block size, and will output to a single N5 group in a paintera-compatible
+format.
+
+By default, spark will run locally:
+```
+paintera-convert to-paintera [...]
+```
+
+`paintera-convert` can also convert paintera label sources to scalar label datasets:
+```
+paintera-convert extract-to-scalar [...]
+```
+`extract-to-scalar` will the highest resolution scale level of a Paintera dataset as a scalar `uint64` Dataset. This is useful for using Paintera painted labels (and assignments) in downstream processing, e.g. classifier training. Optionally, the `fragment-segment-assignment` can be considered and additional assignments can be added. See `extract-to-scalar --help` for more details.
+
+
+<details>
+<summary><b>Deprecated</b></summary>
+
 ## Installation
 paintera-conversion-helper is available on conda on the `hanslovsky` channel:
 ```
@@ -35,50 +59,15 @@ To run on the Janelia cluster build a fat jar without Spark:
 mvn -Denforcer.skip=true -Pfat clean package
 ```
 
-## Running
-This conversion tool currently supports any number of datasets (raw or label) with a
-single (global) block size, and will output to a single N5 group in a paintera-compatible
-format. For local spark usage, [install through conda or pip](#installation), and run:
-```
-paintera-convert to-paintera [...]
-```
-
-Introduced in version `0.7.0`, the
-```
-paintera-convert extract-to-scalar [...]
-```
-extracts the highest resolution scale level of a Paintera dataset as a scalar `uint64`. Dataset. This is useful for using Paintera painted labels (and assignments) in downstream processing, e.g. classifier training. Optionally, the `fragment-segment-assignment` can be considered and additional assignments can be added (versions `0.8.0` and later). See `extract-to-scalar --help` for more details.
-
-
-### Janelia cluster
-
-Clone the repository with submodules:
-```
-git clone --recursive https://github.com/saalfeldlab/paintera-conversion-helper.git
-```
-If you have already cloned the repository, run this after cloning to fetch the submodules:
-```
-git submodule update --init --recursive
-```
-
-Then, run the following script to build the package:
-```
-./build-for-cluster.py
-```
-
-For submitting a job to the Janelia cluster you can use the following script:
-```
-startup-scripts/spark-janelia/convert.py  <number of cluster nodes>  <other parameters>
-```
-The first parameter is the number of cluster nodes to use (for example, 5), and the rest is the same parameters as in the `paintera-convert` command.
 
+</details>
 
 ### Usage Example
 To convert the `raw` and `neuron_ids` datasets of [sample A of the cremi challenge](https://cremi.org/data/) into Paintera format with mipmaps on Linux, assuming that you downloaded the data into `$HOME/Downloads`, run:
 ```sh
 paintera-convert to-paintera \
   --scale 2,2,1 2,2,1 2,2,1 2 2 \
-  --revert-array-attributes \
+  --reverse-array-attributes \
   --output-container=paintera-converted.n5 \
   --container=sample_A_20160501.hdf \
     -d volumes/raw \
@@ -88,18 +77,12 @@ paintera-convert to-paintera \
     -d volumes/labels/neuron_ids
 ```
 
-or for a locally compiled fat jar:
-```
-java -Dspark.master=local[*] -jar target/paintera-conversion-helper-0.4.1-SNAPSHOT-shaded.jar [...]
-```
-with any desired command line arguments.
-
 ### Usage Help
 ```
 $ paintera-convert to-paintera --help
 Usage: paintera-convert to-paintera [[--block-size=X,Y,Z|U] [--scale=X,Y,Z|U...] [--scale=X,Y,Z|U...]...
                                     [--downsample-block-sizes=X,Y,Z|U...] [--downsample-block-sizes=X,Y,Z|U...]...
-                                    [--revert-array-attributes] [--resolution=X,Y,Z|U] [--offset=X,Y,Z|U] [-m=N...]
+                                    [--reverse-array-attributes] [--resolution=X,Y,Z|U] [--offset=X,Y,Z|U] [-m=N...]
                                     [-m=N...]... [--label-block-lookup-n5-block-size=N]
                                     [--winner-takes-all-downsampling]] ([--container=CONTAINER] [] (-d=DATASET
                                     [--target-dataset=TARGET_DATASET] [[--type=TYPE]   ])...)... [--overwrite-existing]
@@ -117,9 +100,9 @@ Options:
       --downsample-block-sizes=X,Y,Z|U...
                              Use --container-downsample-block-sizes and --dataset-downsample-block-sizes for container
                                and dataset specific block sizes, respectively.
-      --revert-array-attributes
-                             Revert array attributes like resolution and offset, i.e. [x, y, z] -> [z, y, x].
-                             Use --container-revert-array-attributes and --dataset-revert-array-attributes for
+      --reverse-array-attributes
+                             Reverse array attributes like resolution and offset, i.e. [x, y, z] -> [z, y, x].
+                             Use --container-reverse-array-attributes and --dataset-reverse-array-attributes for
                                container and dataset specific setting, respectively.
       --resolution=X,Y,Z|U   Specify resolution (overrides attributes of input datasets, if any).
                              Use --container-resolution and --dataset-resolution for container and dataset specific
@@ -155,3 +138,27 @@ Options:
       --help
 ```
 
+### Janelia cluster
+
+Clone the repository with submodules:
+```
+git clone --recursive https://github.com/saalfeldlab/paintera-conversion-helper.git
+```
+If you have already cloned the repository, run this after cloning to fetch the submodules:
+```
+git submodule update --init --recursive
+```
+
+Then, run the following script to build the package:
+```
+./build-for-cluster.py
+```
+
+For submitting a job to the Janelia cluster you can use the following script:
+```
+startup-scripts/spark-janelia/convert.py  <number of cluster nodes>  <other parameters>
+```
+The first parameter is the number of cluster nodes to use (for example, 5), and the rest is the same parameters as in the `paintera-convert` command.
+
+
+