Adding new/updated io.github.betaseg_cellsketch-add-labelmap_0.2.1

solutions/io.github.betaseg/cellsketch-add-labelmap/CHANGELOG.md

@@ -4,6 +4,9 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.2.1] - 2024-03-06
+Fix executable issue with gradlew
+
 ## [0.2.0] - 2024-01-03
 Update CellSketch version
 

solutions/io.github.betaseg/cellsketch-add-labelmap/gradlew.bat

@@ -1,89 +1,89 @@
-@rem
-@rem Copyright 2015 the original author or authors.
-@rem
-@rem Licensed under the Apache License, Version 2.0 (the "License");
-@rem you may not use this file except in compliance with the License.
-@rem You may obtain a copy of the License at
-@rem
-@rem      https://www.apache.org/licenses/LICENSE-2.0
-@rem
-@rem Unless required by applicable law or agreed to in writing, software
-@rem distributed under the License is distributed on an "AS IS" BASIS,
-@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-@rem See the License for the specific language governing permissions and
-@rem limitations under the License.
-@rem
-
-@if "%DEBUG%" == "" @echo off
-@rem ##########################################################################
-@rem
-@rem  Gradle startup script for Windows
-@rem
-@rem ##########################################################################
-
-@rem Set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" setlocal
-
-set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
-set APP_BASE_NAME=%~n0
-set APP_HOME=%DIRNAME%
-
-@rem Resolve any "." and ".." in APP_HOME to make it shorter.
-for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
-
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
-
-@rem Find java.exe
-if defined JAVA_HOME goto findJavaFromJavaHome
-
-set JAVA_EXE=java.exe
-%JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto execute
-
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:findJavaFromJavaHome
-set JAVA_HOME=%JAVA_HOME:"=%
-set JAVA_EXE=%JAVA_HOME%/bin/java.exe
-
-if exist "%JAVA_EXE%" goto execute
-
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
-
-goto fail
-
-:execute
-@rem Setup the command line
-
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
-
-
-@rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
-
-:end
-@rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
-
-:fail
-rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
-rem the _cmd.exe /c_ return code!
-if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
-
-:mainEnd
-if "%OS%"=="Windows_NT" endlocal
-
-:omega
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto execute
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto execute
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

solutions/io.github.betaseg/cellsketch-add-labelmap/solution.py

@@ -21,10 +21,13 @@ def install():
 
 def get_gradle_executable():
     from sys import platform
+    import os
     from album.runner.api import get_app_path
     if platform == "win32":
         return str(get_app_path().joinpath('gradlew.bat').absolute())
-    return str(get_app_path().joinpath('gradlew').absolute())
+    gradle_executable = str(get_app_path().joinpath('gradlew').absolute())
+    os.chmod(gradle_executable, 0o755)
+    return gradle_executable
 
 
 def run():
@@ -60,7 +63,7 @@ def is_file_arg(arg_name):
 setup(
     group="io.github.betaseg",
     name="cellsketch-add-labelmap",
-    version="0.2.0",
+    version="0.2.1",
     solution_creators=["Deborah Schmidt"],
     title="CellSketch: Add labelmap",
     description="This solution adds a labelmap to an existing CellSketch project.",

solutions/io.github.betaseg/cellsketch-add-labelmap/solution.yml

@@ -38,15 +38,13 @@ args:
   name: thresholdConnectionFilamentEnds
   required: false
   type: float
-changelog: 'Update CellSketch version
-
-  '
+changelog: Fix executable issue with gradlew
 cite:
 - doi: https://doi.org/10.1083/jcb.202010039
-  text: "A. M\xC3\xBCller, D. Schmidt, C. S. Xu, S. Pang, J. V. D'Costa, S. Kretschmar,\
-    \ C. M\xC3\xBCnster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D\
-    \ FIB-SEM reconstruction of microtubule-organelle interaction in whole primary\
-    \ mouse \xCE\xB2 cells. J Cell Biol 1 February 2021; 220 (2): e202010039."
+  text: "A. M\xFCller, D. Schmidt, C. S. Xu, S. Pang, J. V. D'Costa, S. Kretschmar,\
+    \ C. M\xFCnster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D FIB-SEM\
+    \ reconstruction of microtubule-organelle interaction in whole primary mouse \u03B2\
+    \ cells. J Cell Biol 1 February 2021; 220 (2): e202010039."
 description: This solution adds a labelmap to an existing CellSketch project.
 group: io.github.betaseg
 name: cellsketch-add-labelmap
@@ -56,6 +54,6 @@ tags:
 - cellsketch
 - segmentation
 - annotation
-timestamp: '2024-01-03T19:16:00.579534'
+timestamp: '2024-03-06T16:33:42.882948'
 title: 'CellSketch: Add labelmap'
-version: 0.2.0
+version: 0.2.1