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535 singularity#541

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Lukas113 merged 222 commits intomaini4Ds/Karabo-Pipeline:mainfrom 535_singularityi4Ds/Karabo-Pipeline:535_singularityCopy head branch name to clipboardFeb 13, 2024

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Commits

Commits on Sep 25, 2023

• added sarus doc 🍔

  

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• enhanced doc 🎏

  

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Commits on Sep 26, 2023

• added conda-prefix in dockerfile to have correct set env-var in sarus container 👨

  

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• bugfix gpu-testing 📒

  

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• skip pinocchio-test because it seems not to work properly on each platform 😖

  

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Commits on Oct 2, 2023

• integrated user-build testing in workflow 8️⃣

  

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• updated dockerfile-dev 🎅

  

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• removed test-user-package because testing is now happening before pushing the image 👠

  

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• adapted docker-dev 🍹

  

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• Revert "removed test-user-package because testing is now happening before pushing the image 👠"

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• updated dockerfile-dev 🔌

  

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• changed dev-workflow for testing 💀

  

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• removed workflow-run trigger of dev-image because out of memory 🚈

  

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Commits on Oct 11, 2023

• added mpich std-loc in Dockerfile.user 🍞

  

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• merged main into 512_sarus 🍀

  

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• adapted docker-user ⛎

  

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Commits on Oct 12, 2023

• minor bugfix dockerfile-user 📥

  

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• updated environments-files 🎇

  

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• updated mpi-version in dockerfile 🆎

  

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Commits on Oct 13, 2023

• updated Dockerfile-user structure 👾

  

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Commits on Oct 18, 2023

• added mpi-tests to karabo 🌱

  

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• updated requirements.txt with new versions 🎼

  

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• integrated mpi-tests into github workflow and codecov-report 🆖

  

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• minor fix using pytest-cov instead of coverage in github workflow 🌊

  

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• fixed coverage-files discovery (I think) 🏧

  

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• adapted codecov workflow according to github.com/codecov/codecov-action 🎲

  

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• adapted container-doc 🍗

  

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• bugfix Dockerfile mpi-compilation needs python 🍚

  

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• minor adjustments in Dockerfile.user 😉

  

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Commits on Oct 19, 2023

• added mpi-supported h5py wheel as karabo dependency 🍟

  

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Commits on Oct 26, 2023

• removed pinocchio from environment.yaml 🔘

  

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• updated environment.yaml with mpich-deps 🈴

  

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Commits on Oct 31, 2023

• updated conda-build files 🚟

  

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• replaced np.object0 with according non-deprecated alias 🐳

  

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Commits on Nov 2, 2023

• minor bugfix in pyproject.toml 🙇

  

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• merged main into 512_sarus 🐚

  

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• deleted test-pinocchio (wrongly merged) 🍭

  

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• updated environment files 🐎

  

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• imporved dev-setup 🔉

  

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• removed requirements.txt

  

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• added ipykernel to dev-deps 🚙

  

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• bugfix filter-sources for xarray>2023.2 🔦

  

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• updated build-procedure ⛪

  

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• implemented dynamic versioneering 😔

  

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• removed remaining requirements.txt stuff 👜

  

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• updated Dockerfile-user mpi-installation to be dependent on karabo-user installation version 🛀

  

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Commits on Nov 3, 2023

• refactored dockerfiles 🐭

  

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• added versioneer to meta.yaml build-stage 📚

  

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• added versioneer to meta.yaml build-stage 🚕

  

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• bugfix conda-build meta.yaml for versioneer 💩

  

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• adapted conda-build to custom pkg-version 😤

  

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• adapted Dockerfile.user to a testable (before release) setup 👸

  

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• bugfix build-user-image.yml ➿

  

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• bugfix build-user-image.yml 🚧

  

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Commits on Nov 6, 2023

• updated Dockerfile-user 👏

  

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• bugfix user-dockerfile 🕘

  

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• bugfix Dockerfile-dev 🔖

  

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• minor doc-update in dockerfile-dev 🚸

  

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Commits on Nov 7, 2023

• updated description of build-user-image workflow inputs 🔫

  

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• introduced venv in dockerfile-user to not f*** up base env 😌

  

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• updated dev-img with venv 😓

  

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• updated build-user-image workflow to be able to run on workflow-dispatch 🐬

  

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• added file to build-and-export-docker action 📌

  

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• bugfix build-args in build-user-image workflow 👨

  

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• bugfix get-shallow git-repo from git-rev (not only branches or tags) 📷

  

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• bugfix remote from https and not from ssh 🎮

  

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• updated workflow-dispatch descriptions ‼️

  

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• bugfix build-args passing to docker-build-push action 🆘

  

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• throw exit-code in dockerfile-user if build not set correctly 🎵

  

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• added dev-flag to conda-build 🌹

  

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• added security to dev-builds in conda-build workflow 🛄

  

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• bugfix dev-evaluation in conda-build.yml 🈂️

  

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• outcommented mpich-compilation in Dockerfile 😥

  

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• bugfix conda-build export of env-vars in same step ⛺

  

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Commits on Nov 8, 2023

• added failing tests if PR is draft 🆖

  

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• setup build-user-img, conda-build & test-user-package for dev-testing 🔍

  

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Commits on Nov 17, 2023

• added df-h to build-user-image workflow 🎃

  

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• made docker-build by myself ✂️

  

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• made docker-build by myself entirely 🚥

  

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• ensured to push on ghcr.io ✈️

  

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• bugfix docker-push user-image workflow 💘

  

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• bugfix docker-push user-image workflow 📢

  

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• bugfix added img-name to push image 🚸

  

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• bugfix registry docker push 🍎

  

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• adapted docker-img address accordingly to ghcr.io 🎩

  

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• adapted build-user-image to standard 🐗

  

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• added pytest installation to docker-user image testing workflow 🎢

  

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• bugfix pytest-call in user-image 💴

  

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• added bash shell in docker-run in build-test-user-image 👥

  

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Commits on Nov 20, 2023

• adapted ld-library-path to base-image 2️⃣

  

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• made site-package-location identification in build-user-image more robust 📵

  

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• defined entrypoint to Dockerfile-user ➡️

  

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• bugfix calling tests in build-user-image 🐻

  

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• readded conda-activate-karabo to .bashrc for interactive mode 💓

  

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• bugfix removed unnecessary " at the end of docker-run 🚅

  

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• set env-vars in test-user-image ♓

  

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• minor changes 🎵

  

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• Merge branch 'main' into 512_sarus

  

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• adapted test-workflow to main-setup 💡

  

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• adapted docker-img dev to karabo-venv 📄

  

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• adapted mpi-doc ❇️

  

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• addressed mypy-issues 6️⃣

  

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• added type-ignore to __init__.py because mypy can't handle that 🍥

  

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• adapted exclude-option in setup.cfg to hopefully ignore __init__.py on the runners 🐽

  

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• adapted mypy-exclude-regex to exclude all __init__.py ⏰

  

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• hopefully bugfix to ignore __init__.py by mypy 🍟

  

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• trying editable install to avoid duplicate modules 😓

  

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• added verbose-flag to pytest-testing of docker-image 📫

  

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Commits on Nov 21, 2023

• removed pytest-mpi as dep and added --only-mpi flag handling in conftest.py 👪

  

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• minor changes in pytest test-discovery 🎁

  

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• removed mpi-pytest from codecov because of race-condition issue which doesn't seem to be solvable atm 👬

  

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• bugfix compute filter-mask in filter-sky 👫

  

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• ugly hotfix to initialize dask-mpi inside docker-container 🏯

  

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• added mpi-tests to docker-user tests 💀

  

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• bugfix only enter dask-initialize with mpi if mpirun 🐚

  

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• bugfix conda-build inherited env-vars [skip ci] 👚

  

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• bugfix conda-build inherited env-vars [skip ci] 🚑

  

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• bugfix conda-build set output-vars [skip ci] 🌈

  

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• removed notebook-test from user-img test because data-dirs are not part of package and therefore would cause an error [skip ci] 🕠

  

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• bugfix casting to str-to-boolean for reproducable github-workflows 🔩

  

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Commits on Nov 22, 2023

• added debugging logs to github workflows [skip ci] ☎️

  

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Commits on Nov 29, 2023

• adapted meta.yaml to pin compatible numpy ❓

  

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Commits on Dec 1, 2023

• updated conda-build to be closer to a best-practise build 😿

  

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Commits on Dec 4, 2023

• fixed bluebild-version 🌅

  

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• removed echos and improved build-user-image workflow 🔻

  

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• removed build-string default to ensure that workflow-user knows what he/she does 🐟

  

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• minor update in container.md ⏩

  

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• bugfix check leading v in tag in conda-build workflow 🍙

  

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• bugfix set dev-string check correclty in conda-build.yml 🚷

  

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• merged main into 512_sarus

  

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• added versioneer to dev-dep ⚪

  

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• improved version definition security for conda-build workflows ♒

  

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• minor imporvements in conda-build ⤵️

  

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• hopefully bugfix of github boolean passing in reusable workflow see #1483 of github runners 🎈

  

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Commits on Dec 5, 2023

• improved version definition security for conda-build workflows ↪️

  

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• added little verbosity to conda-build workflow 📍

  

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• hopefully bugfix to trigger build-docker by taking boolean values directly from input 👂

  

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Commits on Dec 6, 2023

• bugfix build-user-image.yml 🛅

  

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• minor improvements in build-user-image.yml 🎫

  

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• replaced exit 2 with exit 1 in all bash scripts 3️⃣

  

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• bugfix install environment in user Dockerfile correctly 💙

  

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• removed weird leading v to github-workflows version-args 🍚

  

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• updated codecov.yml to not fail if below target 🎰

  

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• bugfix: added python interpreter and versioneer through conda for checking conda-build worklow inputs 🇷🇺

  

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• added conda-prefix to python interpreter to hopefully get viable binary Ⓜ️

  

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• added conda-prefix to python interpreter to hopefully get viable binary

  

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Commits on Dec 7, 2023

• removed dev-deps in environment.yaml and meta.yaml ⌛

  

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• bugfix: removed bdsf dev-dep 💒

  

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• addressed mypy-issues 🚝

  

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• updated mypy-complaints chunks-dict issue in sky-model 🚞

  

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• fixed build-nr of feedstock-deps 🐹

  

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• addresses mypy attr-defined for matplotlib BLUE 😾

  

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Commits on Dec 8, 2023

• renamed build-user-image do build-docker-image 🐚

  

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• adapted readme-badges 🍰

  

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Commits on Dec 12, 2023

• addressed pr-request to install mpich via apt 🐒

  

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• adapted documentation and dockerfile-steps 🍶

  

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• bugfix added -y to apt install in Dockerfile [skip ci] ↩️

  

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• improved docs ♈

  

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Commits on Dec 13, 2023

• changed Dockerfile setup to use andromeda user instead of root 😉

  

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• minor update in dockerfile 🔛

  

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• changed run-stages of dockerfile 🍲

  

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• removed user-changeing because of singularity uid issues 🔫

  

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• moved Dockerfile to root & removed docker-dir 🚌

  

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• added bash-env to env-vars for singularity noninteractive-shell [skip ci] 🕣

  

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Commits on Dec 14, 2023

• bugfix: correctly activate venv in docker & singularity container for interactive and non-interactive shells 💛

  

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• fixed conda activate functionality for docker & singularity interactive and non-interactive shells 💉

  

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• removed unnecessary sourcing in dockerfile [skip ci] 🔣

  

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• added ldconfig after mpich-installation in dockerfile 👤

  

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• minor changes in dockerfile [skip ci] 🐟

  

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Commits on Dec 21, 2023

• outcommented mpi-hook from dockerfile because it's still error-prone 📢

  

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• adapted container-doc ↩️

  

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Commits on Jan 9, 2024

• bugfix: in test docker-image to enable --only-mpi custom flag for pytest 📓

  

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• added karabo shared lib to ldconfig cache to enable native cscs-mpi-hook 🕡

  

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• replaced weird file-handler root-dir setup with /tmp with honor of TMP, TMPDIR & TEMP 🌐

  

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Commits on Jan 11, 2024

• changed tmp-dir-name setup to avoid collisions 🐂

  

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• loosened mpich-version constraints because we no longer rely on apt to install mpich ◻️

  

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• updated mpi-doc 😡

  

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• minor bugfix for mpi-tests in ci

  

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Commits on Jan 12, 2024

• added scratch as a possible tmpdir in FileHandler ⏰

  

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• bugfix get-tmp-dir 🐲

  

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Commits on Jan 17, 2024

• Merge branch 'main' into 512_sarus

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• added cachetools as dep 😇

  

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• redesigned FileHandler for short- and long-term-memory caching 😡

  

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• improved file-handler by getting unique tmp-dir per unique object 💥

  

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• refactored image and imager to new filehandler-setup 😔

  

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• adapted interferometer.py and telescope.py to new FileHandler setup ↪️

  

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• adapted visibility and sourcedetection to new FileHandler setup 🙌

  

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Commits on Jan 22, 2024

• enhanced FileHandler get-tmp-dir with subdir & mkdir option 🚘

  

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• adapted Karabo to new FileHandler setup 🐍

  

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• bugfix accessing .ltm and .stm through FileHandler 👅

  

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• bugfixes FileHandler & according tests 📝

  

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• changed Downloadobject-storage cache from site-packages to tmp 🌁

  

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Commits on Jan 23, 2024

• removed weird KaraboResource pseudo-interface from repo ♥️

  

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• removed FileHandler get-tmp-dir subdir option because seems unnecessary ⛽

  

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• implemented seed-option to FileHandler.get-tmp-dir 🍢

  

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• changed ltm & stm of FileHandler from static functions to lazy class-attributes 📄

  

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• intermediate commit separating Dask & Slurm concerns in dask.py 🕔

  

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Commits on Jan 24, 2024

• adapted other karabo-files to new DaskHandler setup 🚨

  

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• readded accidentally removed plotting-util.py 👡

  

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• bugfix dask-usage 🍀

  

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• minor bugfix in test-dask 🚬

  

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Commits on Jan 25, 2024

• Merge branch 'main' into 512_sarus

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• Merge branch '512_sarus' into 535_singularity

  

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Commits on Jan 29, 2024

• merged main into 512_sarus 👚

  

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• Merge branch '512_sarus' into 535_singularity

  

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• refactored create_baseline_cut_telelescope to improved disk-caching & be less error-prone 😷

  

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• bugfixes in Telescope.create-baseline-cut-telescope 🔑

  

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• addressed mypy-issues 😐

  

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• updated singularity-doc 🍓

  

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Commits on Jan 30, 2024

• addressed PR-requests 🎍

  

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• merged 512-saus into 535-singularity 🔉

  

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Commits on Feb 1, 2024

• addressed PR526 requests 🍀

  

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• resolved merge-conflict from 512-sarus

  

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• bugfix removed set libmamba-solver globally in installation-user.md 📦

  

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• Merge branch '512_sarus' into 535_singularity

  

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• made plot-function api more consistent 😰

  

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• resolved merge-conflict from main 🐒

  

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Commits on Feb 5, 2024

• refactored DaskHandler to use just a single DaskHandler class for function-calling purpose 🎼

  

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• bugfix removed fetch-dask-handler function from karabo 🎁

  

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Commits on Feb 8, 2024

• addressed PR540 requests 🐻

  

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Commits on Feb 13, 2024

• bugfix seeding ltm-memory 🎵

  

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• Merge branch 'main' into 535_singularity

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