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Refactoring gc_derivatization #1

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Refactoring gc_derivatization #1

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Commits on Jul 7, 2022

  1. testing

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  2. testing

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  3. testing

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  4. move ipynb to example folder

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  5. replace NIST_195_200.txt by NIST_ONSSiMe3.txt

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  6. replace NIST_195_200.txt by NIST_ONSSiMe3.txt

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  7. undo replacement

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  8. cleanning

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  9. Lint

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Commits on Jul 8, 2022

  1. testing

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  2. testing

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  3. testing

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  4. testing

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Commits on Jul 11, 2022

  1. sort

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  2. Sort

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  3. Sort

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  4. copy gc_meox_src.py to example folder (import issues)

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  5. converting ipynb to py

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  6. sorting

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  7. sorting

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Commits on Jul 12, 2022

  1. updates

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Commits on Jul 13, 2022

  1. Refactoring

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  2. Rectoring Py

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Commits on Jul 14, 2022

  1. refac

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Commits on Jul 19, 2022

  1. Add files via upload

    @wverastegui
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  2. Add files via upload

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  3. test

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  4. refact

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  5. Test

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  6. test

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  7. refact

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  8. test

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  9. test

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  10. Refatc

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  11. Update

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  12. update

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  13. Update

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  14. Update

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  15. Update

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  16. Update

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  17. Update

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Commits on Jul 20, 2022

  1. Merge pull request #1 from wverastegui/refact_gc_derivatization 

    Refact gc derivatization
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Commits on Oct 21, 2022

  1. add conda dev environment

    @maximskorik
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  2. fix slicing errors in the notebook

    @maximskorik
    maximskorik committed Oct 21, 2022
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  3. move scripts into gc_derivatization subdir

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Commits on Oct 28, 2022

  1. refactor cli script

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  2. add main func

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  3. move cli to __main__.py

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  4. add pytest to dev requirements

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  5. add input reading and tests with data

    @maximskorik
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  6. move I/O handling to utils.py

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  7. rename directory to reflect the package name

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  8. edit setup.cfg

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  9. move process_one_mol to utils.py; edit input reading

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  10. add pkg dir to setup.cfg

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  11. adjust test for tuples

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  12. add data-writing tests

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  13. add tests for output content

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  14. rename file with IO tests

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  15. omit duplicate func names

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  16. reformat gc_meox_src.py

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  17. remove commented code

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  18. refactor is_derivatized; add tests

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  19. add tests for add_derivatization_groups

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  20. adjust for non-deterministic behaviour

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  21. add pytest plugin to dev env

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  22. use oneliner to unpack tuple

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  23. add docstrings to tests

    @maximskorik
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  24. add test for process_one_mol; rename test script

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  25. make process_one_mol return kekule SMILES

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  26. simplify test since its internals are tested elsewhere

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  27. add test for writing without keep

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  28. add meta.yaml

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  29. move process_one_mol to the main module

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  30. fix imports

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  31. rename module

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  32. fix setup.cfg

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  33. move plotting

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  34. update EDA in notebook

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  35. move process_one_mol test

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  36. remove derivatization.py because it's not used

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  37. add conda build CI workflow

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  38. add python-package-conda CI

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  39. add python-package CI

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  40. update python requirement to >=3.8

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  41. make type hints work with python 3.8

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  42. add sonarcloud code check CI

    @maximskorik
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  43. add CHANGELOG.md

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  44. update README-package.md

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  45. remove docker and bash scripts; move exmaple readme to example dir

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  46. use oneliner for CIs events; use single-quotes for Python versions

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Commits on Oct 31, 2022

  1. sync environment-dev.yaml with setup.cfg

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  2. update installation instructions

    @maximskorik
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  3. correct comment

    @maximskorik
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  4. rename test script

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  5. add tests for cli; add exit code

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  6. add test for ncpu flag

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  7. add test for repeats flag

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  8. move data path into a fixture

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  9. add mock to dev requirements

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  10. remove pytest-cov since its in dev requirements

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  11. add pytest-cov to conda dev

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  12. apply isort; expose functions via __init__.py

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  13. add pytest-cov to requirements-dev.txt

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Commits on Nov 1, 2022

  1. Update conda/meta.yaml

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  2. edit setup.cfg metadata

    @maximskorik
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  3. make conda-dev use requirements.txt

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  4. Merge branch 'prep_package' of https://github.com/maximskorik/gc_deri… 

    …vatization into prep_package
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  5. update example ipynb

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  6. add rdkit to env-dev bc the pkg is called different in conda

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  7. update molecule annotation in ipynb

    @maximskorik
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  8. remove duplicated fixture

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  9. remove horizontal lines in README.md

    @maximskorik
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  10. skip SonarCloud CI step until SONAR_TOKEN secret is set

    @maximskorik
    maximskorik committed Nov 1, 2022
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  11. fix typo in reaction name

    @maximskorik
    maximskorik committed Nov 1, 2022
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Commits on Nov 2, 2022

  1. remove line from ipynb

    @maximskorik
    maximskorik committed Nov 2, 2022
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  2. Merge pull request #9 from maximskorik/prep_package 

    Tidy up the package
    @hechth
    hechth authored Nov 2, 2022
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Commits on Nov 7, 2022

  1. refactor process_one_mol

    @maximskorik
    maximskorik committed Nov 7, 2022
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  2. apply isort

    @maximskorik
    maximskorik committed Nov 7, 2022
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  3. add missing type hints

    @maximskorik
    maximskorik committed Nov 7, 2022
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Commits on Nov 10, 2022

  1. Merge pull request #14 from maximskorik/refactor_proc_one_mol 

    Refactor process_one_mol
    @maximskorik
    maximskorik authored Nov 10, 2022
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  2. Move SonarCloud scan to an individual job (#15) 

    * move SonarCloud to a separate job

* add check for secret

* update sonarcloud args
    @maximskorik
    maximskorik authored Nov 10, 2022
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Commits on Nov 22, 2022

  1. Create MIT LICENSE

    @maximskorik
    maximskorik committed Nov 22, 2022
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Commits on Nov 23, 2022

  1. bump version to 1.0.0

    @maximskorik
    maximskorik committed Nov 23, 2022
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  2. change pkg name to gc-meox-tms

    @maximskorik
    maximskorik committed Nov 23, 2022
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  3. change pkg name and references to GH repo to gc-meox-tms

    @maximskorik
    maximskorik committed Nov 23, 2022
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  4. unify setup config in pyproject.toml

    @maximskorik
    maximskorik committed Nov 23, 2022
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  5. update README.md

    @maximskorik
    maximskorik committed Nov 23, 2022
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Commits on Nov 24, 2022

  1. add Conda to the installation guide

    @maximskorik
    maximskorik authored Nov 24, 2022
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Commits on Dec 13, 2022

  1. document is_derivatized

    @maximskorik
    maximskorik committed Dec 13, 2022
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  2. document remove_derivatization_groups

    @maximskorik
    maximskorik committed Dec 13, 2022
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  3. document add_derivatization_groups

    @maximskorik
    maximskorik committed Dec 13, 2022
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  4. document process_one_mol

    @maximskorik
    maximskorik committed Dec 13, 2022
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  5. document read_input_txt

    @maximskorik
    maximskorik committed Dec 13, 2022
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  6. document write_tab_separated

    @maximskorik
    maximskorik committed Dec 13, 2022
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  7. document write_flat

    @maximskorik
    maximskorik committed Dec 13, 2022
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  8. add developer documentation and isort package to dev env

    @maximskorik
    maximskorik committed Dec 13, 2022
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  9. correct typo

    @maximskorik
    maximskorik committed Dec 13, 2022
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  10. add newline

    @maximskorik
    maximskorik committed Dec 13, 2022
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  11. correct typo

    @maximskorik
    maximskorik committed Dec 13, 2022
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  12. add cloning step to dev installation

    @maximskorik
    maximskorik committed Dec 13, 2022
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  13. update installation instructions for users

    @maximskorik
    maximskorik committed Dec 13, 2022
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  14. add "Publish to PyPi" workflow

    @maximskorik
    maximskorik committed Dec 13, 2022
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  15. Merge pull request #23 from maximskorik/add_docs 

    Document functions with docstrings and add developer documentation
    @hechth
    hechth authored Dec 13, 2022
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  16. Merge pull request #24 from maximskorik/pypi_action 

    add "Publish to PyPi" GH workflow
    @hechth
    hechth authored Dec 13, 2022
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Commits on Dec 14, 2022

  1. fix publish_pypi workflow

    @maximskorik
    maximskorik committed Dec 14, 2022
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  2. bump package version for pypi release

    @maximskorik
    maximskorik committed Dec 14, 2022
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  3. update CHANGELOG.md

    @maximskorik
    maximskorik committed Dec 14, 2022
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  4. add pip installation to README.md

    @maximskorik
    maximskorik authored Dec 14, 2022
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Commits on Jun 23, 2023

  1. Create project_automation.yml

    @hechth
    hechth authored Jun 23, 2023
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Commits on Jun 26, 2023

  1. updated python-package.yaml

    @zargham-ahmad
    zargham-ahmad committed Jun 26, 2023
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Commits on Oct 23, 2023

  1. Merge pull request #27 from zargham-ahmad/sonar-ci 

    updated sonarcloud ci
    @hechth
    hechth authored Oct 23, 2023
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Commits on Mar 13, 2024

  1. Fixed test failure & lint

    @wverastegui
    wverastegui committed Mar 13, 2024
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  2. Corrected typos

    @wverastegui
    wverastegui committed Mar 13, 2024
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Commits on Apr 18, 2024

  1. Update pyproject.toml

    @hechth
    hechth authored Apr 18, 2024
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  2. Update requirements.txt

    @hechth
    hechth authored Apr 18, 2024
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Commits on Apr 19, 2024

  1. Merge pull request #32 from RECETOX/hechth-patch-1 

    Update pyproject.toml
    @hechth
    hechth authored Apr 19, 2024
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  2. Merge branch 'master' into wverastegui/issue28

    @hechth
    hechth authored Apr 19, 2024
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  3. Merge pull request #31 from RECETOX/wverastegui/issue28 

    Fixed test units failure
    @hechth
    hechth authored Apr 19, 2024
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Commits on Jun 4, 2024

  1. Fix wrongly named file upload to Sonar

    @MarcHagen
    MarcHagen authored Jun 4, 2024
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Commits on Jun 7, 2024

  1. updated ci pipelines

    @hechth
    hechth committed Jun 7, 2024
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  2. updated python versions

    @hechth
    hechth committed Jun 7, 2024
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  3. python versions as string

    @hechth
    hechth committed Jun 7, 2024
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  4. added conda update conda to list

    @hechth
    hechth committed Jun 7, 2024
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  5. Merge pull request #34 from RECETOX/ci_update 

    updated ci pipelines
    @hechth
    hechth authored Jun 7, 2024
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  6. Merge branch 'master' into patch-1

    @hechth
    hechth authored Jun 7, 2024
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  7. Merge pull request #33 from MarcHagen/patch-1 

    Fix wrongly named file upload to Sonar
    @hechth
    hechth authored Jun 7, 2024
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