fix before new release

.gitlab-ci.yml

 stages:
     - style
     - test_code
-    - update_docs
+    - release
 
 
 check_style:
     stage: style
-    image: sissource.ethz.ch:5005/sispub/emzed/linux_base_images/ubuntu_19_10_for_emzed
+    image:
+      name: registry.gitlab.com/emzed3/linux-base-images:ubuntu-23_04
+      entrypoint: [ '/bin/bash', '-c', 'ln -snf /bin/bash /bin/sh && /bin/bash -c $0' ]
     tags:
         - docker-executor
     script:
@@ -18,24 +20,38 @@ windows_tests:
     stage: test_code
     tags:
         - windows
+    before_script:
+        - $VENV = [System.IO.Path]::GetRandomFileName()
+        - Set-Content -Path venv.txt -Value $VENV
+    parallel:
+      matrix:
+        - PYTHON_VERSION: [ '3.9.13', '3.10.11', '3.11.3' ]
     script:
+        - Import-Module Pscx
+        - Import-VisualStudioVars 2017 x86
         - set "CI_TMP=%temp%\%time::=.%.emzed.tmp"
-        - if (Test-Path venv) { Remove-Item venv -Recurse; }
-        - python -m venv venv
-        - venv/Scripts/python -m pip install -U pip setuptools
-        - venv/Scripts/pip install --extra-index-url https://pypi-sissource.ethz.ch/simple emzed3
-        - venv/Scripts/pip install -e .
-        - venv/Scripts/pip install -r requirements_dev.txt
-        - venv/Scripts/python -c 'import emzed_ext_mzmine2 as e; e.init()'
-        - venv/Scripts/pytest -s tests
+        - Invoke-Expression "C:/home/Administrator/.pyenv/pyenv-win/versions/${Env:PYTHON_VERSION}/python.exe -m venv $VENV"
+        - Invoke-Expression "${VENV}/Scripts/activate.ps1"
+        - python -m pip install -U pip setuptools
+        - pip install -e .
+        - pip install -r requirements_dev.txt
+        - python -c 'import emzed_ext_mzmine2 as e; e.init()'
+        - pytest -s tests
+    after_script:
+        - $VENV = Get-Content -Path venv.txt
+        - Remove-Item $VENV -Recurse
 
 
 .ubuntu: &ubuntu
     stage: test_code
     tags:
         - docker-executor
-    script: &ubuntu-script
-        - pip install --extra-index-url https://pypi-sissource.ethz.ch/simple emzed3
+    parallel:
+      matrix:
+        - PYTHON_VERSION: [ '3.9.17', '3.10.12', '3.11.4' ]
+    script:
+        - /.pyenv/versions/${PYTHON_VERSION}/bin/python -m venv venv
+        - source venv/bin/activate
         - pip install -e .
         - pip install -r requirements_dev.txt
         - sleep ${SLEEP:-0}
@@ -46,31 +62,27 @@ windows_tests:
             - htmlcov/
 
 
-ubuntu_19_10:
+ubuntu_22_04:
     <<: *ubuntu
-    image: sissource.ethz.ch:5005/sispub/emzed/linux_base_images/ubuntu_19_10_for_emzed
+    image: registry.gitlab.com/emzed3/linux-base-images:ubuntu-22_04
 
-
-ubuntu_20_04:
+ubuntu_23_04:
     <<: *ubuntu
-    image: sissource.ethz.ch:5005/sispub/emzed/linux_base_images/ubuntu_20_04_for_emzed
-    script:
-      - *ubuntu-script
-      - make build_docs
-    artifacts:
-      paths:
-        - docs/_build/html
-
+    image: registry.gitlab.com/emzed3/linux-base-images:ubuntu-23_04
 
 update_docs:
-    stage: update_docs
-    image: sissource.ethz.ch:5005/sispub/emzed/linux_base_images/ubuntu_20_04_for_emzed
+
+    stage: release
+    image: registry.gitlab.com/emzed3/linux-base-images:ubuntu-23_04
     tags:
         - docker-executor
-    script:
-        - chmod 0600 ${SSH_PRIVATE_KEY}
-        - scp -r -i ${SSH_PRIVATE_KEY} -o 'StrictHostKeyChecking no' docs/_build/html/* w3_emzed2@emzed.ethz.ch:htdocs/3/emzed.ext.mzmine2
-    dependencies:
-        - ubuntu_20_04
     rules:
-      - if: '$CI_COMMIT_MESSAGE =~ /(\[VERSION\])|\[DOCS\]/'
+      - if: '$CI_PIPELINE_SOURCE == "schedule"'
+        when: never
+      - if: '$CI_COMMIT_MESSAGE =~ /\[VERSION\]/ && $CI_COMMIT_REF_NAME == "main"'
+    script:
+        - pip install -e .
+        - pip install -r requirements_dev.txt
+        - make build_docs
+        - chmod 0600 ${SSH_PRIVATE_KEY_EMZED_WEBSITE}
+        - rsync -e "ssh -o StrictHostKeyChecking=no -i ${SSH_PRIVATE_KEY_EMZED_WEBSITE}" -v docs/_build/html/* "w3_emzed2@emzed.ethz.ch:3/emzed.ext.mzmine2"

compile_java_code.sh

@@ -9,15 +9,11 @@
 set -x
 set -e
 
-#JDK_HOME=/Users/uweschmitt/Downloads/jdk-11.0.2.jdk/Contents/Home/
-#JDK_HOME=/Library/Java/JavaVirtualMachines/openjdk-12.0.2.jdk/Contents/Home/
 JDK_HOME=/Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Home
 
 JAVAC=${JDK_HOME}/bin/javac
 JAR=${JDK_HOME}/bin/jar
 
-#MZMINE_JARS=~/Downloads/MZmine-2.51-macOS/lib
-#MZMINE_JARS=~/Projects/mzmine2/build/MZmine-2.52-macOS/lib  # /mzmine2-2.52.jar
 MZMINE_JARS=$(cat ~/.emzed3/emzed.ext.mzmine2/mzmine2/mzmine2_home)/lib
 echo ${MZMINE_JARS}
 cd src/emzed_ext_mzmine2/java
@@ -28,4 +24,10 @@ mkdir -p ${BUILD_ROOT}
 cp *.java ${BUILD_ROOT}
 
 ${JAVAC} -Xlint:unchecked -cp "${MZMINE_JARS}/*" ${BUILD_ROOT}/*.java
+echo
 ${JAR} cf extensions.jar ${BUILD_ROOT}/../../../../../ch
+set +x
+
+echo
+echo
+echo DONE

reformat_code.sh

@@ -6,7 +6,7 @@
 # Distributed under terms of the MIT license.
 #
 
-isort -y --multi-line 3 -rc src tests benchmarks
+isort src tests benchmarks
 black src tests benchmarks
 
 java -jar development_tools/google-java-format-1.7-all-deps.jar --replace src/emzed_ext_mzmine2/java/*.java

setup.py

 from setuptools import find_packages, setup
 
-install_requires = ("requests", "emzed3>=0.0.45")
+install_requires = ("requests", "emzed>=3.0.0a1")
 
 setup(
     name="emzed_ext_mzmine2",

src/emzed_ext_mzmine2/remove_shoulder_peaks.py

@@ -61,8 +61,9 @@ def remove_shoulder_peaks(peakmap, parameters):
     peakmap_back = PeakMap.load(temp_file_out)
 
     # the mzXML parser of mzmine2 rounds rt values, we fix this here:
-    for s, s_back in zip(pm_ms_1, peakmap_back):
-        s_back._set_rt(s.rt)
+    with peakmap_back.spectra_for_modification() as spectra_back:
+        for s, s_back in zip(pm_ms_1, spectra_back):
+            s_back._set_rt(s.rt)
 
     peakmap_back.merge(pm_ms_else)
 

start_linux_ci_container.sh

@@ -10,3 +10,4 @@ done
 
 ID=$(docker ps | grep runner | grep concurrent | grep build | cut -d " " -f 1)
 docker exec -it ${ID} bash
+docker stop ${ID}