Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Run bigscape v2 #251

Merged
merged 57 commits into from
Jul 17, 2024
Merged

Run bigscape v2 #251

merged 57 commits into from
Jul 17, 2024

Commits on May 29, 2024

  1. add BiG-SCAPE 2 to dependencies

    @adraismawur
    adraismawur committed May 29, 2024
    Configuration menu
    Copy the full SHA
    d2dc38b View commit details
    Browse the repository at this point in the history

  2. add example config for bigscape 2

    @adraismawur
    adraismawur committed May 29, 2024
    Configuration menu
    Copy the full SHA
    93848dd View commit details
    Browse the repository at this point in the history

  3. implement running BiG-SCAPE

    @adraismawur
    adraismawur committed May 29, 2024
    Configuration menu
    Copy the full SHA
    9d0a2d0 View commit details
    Browse the repository at this point in the history

Commits on May 31, 2024

  1. fix bigscape2 dependency

    @adraismawur
    adraismawur committed May 31, 2024
    Configuration menu
    Copy the full SHA
    6d40414 View commit details
    Browse the repository at this point in the history

  2. copy db file properly

    @adraismawur
    adraismawur committed May 31, 2024
    Configuration menu
    Copy the full SHA
    02bc843 View commit details
    Browse the repository at this point in the history

  3. remove cluster arg

    @adraismawur
    adraismawur committed May 31, 2024
    Configuration menu
    Copy the full SHA
    2351055 View commit details
    Browse the repository at this point in the history

  4. run ruff formatter

    @adraismawur
    adraismawur committed May 31, 2024
    Configuration menu
    Copy the full SHA
    1b43a31 View commit details
    Browse the repository at this point in the history

  5. fix ruff check issues

    @adraismawur
    adraismawur committed May 31, 2024
    Configuration menu
    Copy the full SHA
    eb28d38 View commit details
    Browse the repository at this point in the history

Commits on Jun 3, 2024

  1. ensure str for mypy static type checking

    @adraismawur
    adraismawur committed Jun 3, 2024
    Configuration menu
    Copy the full SHA
    9293c64 View commit details
    Browse the repository at this point in the history

Commits on Jun 6, 2024

  1. Merge branch 'dev' of github.com:NPLinker/nplinker into run-bigscape-v2

    @adraismawur
    adraismawur committed Jun 6, 2024
    Configuration menu
    Copy the full SHA
    f18ecb5 View commit details
    Browse the repository at this point in the history

Commits on Jun 7, 2024

  1. Move configuration to correct file

    @adraismawur
    adraismawur committed Jun 7, 2024
    Configuration menu
    Copy the full SHA
    4a0e86b View commit details
    Browse the repository at this point in the history

  2. use os.path.join instead of string concat

    @adraismawur
    adraismawur committed Jun 7, 2024
    Configuration menu
    Copy the full SHA
    7361a98 View commit details
    Browse the repository at this point in the history

  3. fix merge mistake

    @adraismawur
    adraismawur committed Jun 7, 2024
    Configuration menu
    Copy the full SHA
    a329e43 View commit details
    Browse the repository at this point in the history

Commits on Jun 14, 2024

  1. remove extra bigscape 2 files

    @adraismawur
    adraismawur committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    caf2711 View commit details
    Browse the repository at this point in the history

  2. add missing library

    @adraismawur
    adraismawur committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    525c707 View commit details
    Browse the repository at this point in the history

  3. add validator for bigscape version

    @adraismawur
    adraismawur committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    2433d76 View commit details
    Browse the repository at this point in the history

  4. add test for bigscape version

    @adraismawur
    adraismawur committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    8447272 View commit details
    Browse the repository at this point in the history

  5. fix typo

    @adraismawur
    adraismawur committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    f6330e9 View commit details
    Browse the repository at this point in the history

Commits on Jun 19, 2024

  1. Merge branch 'dev' of github.com:NPLinker/nplinker into run-bigscape-v2

    @adraismawur
    adraismawur committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    bc096bf View commit details
    Browse the repository at this point in the history

  2. add simple run testing

    @adraismawur
    adraismawur committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    84095b7 View commit details
    Browse the repository at this point in the history

  3. add test to check for nonextent input path

    @adraismawur
    adraismawur committed Jun 19, 2024
    Configuration menu
    Copy the full SHA
    21b4600 View commit details
    Browse the repository at this point in the history

Commits on Jul 15, 2024

  1. add info to docstring

    @adraismawur
    adraismawur committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    a2b6eb8 View commit details
    Browse the repository at this point in the history

  2. add exception on invalid version number

    @adraismawur
    adraismawur committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    c03f64a View commit details
    Browse the repository at this point in the history

  3. move log to after validation

    @adraismawur
    adraismawur committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    9e9758e View commit details
    Browse the repository at this point in the history

  4. add version info to log

    @adraismawur
    adraismawur committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    9e8c767 View commit details
    Browse the repository at this point in the history

  5. use specific exception

    @adraismawur
    adraismawur committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    e9f7345 View commit details
    Browse the repository at this point in the history

  6. rework return codes and exceptions

    @adraismawur
    adraismawur committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    775cbf5 View commit details
    Browse the repository at this point in the history

Commits on Jul 16, 2024

  1. add wrong version test

    @adraismawur
    adraismawur committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    874ea3a View commit details
    Browse the repository at this point in the history

  2. add invalid path test for v2

    @adraismawur
    adraismawur committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    bd699de View commit details
    Browse the repository at this point in the history

  3. specify exception

    @adraismawur
    adraismawur committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    3189999 View commit details
    Browse the repository at this point in the history

  4. fix tests not correctly running

    @adraismawur
    adraismawur committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    19e72f2 View commit details
    Browse the repository at this point in the history

  5. change imports to reflect style in other tests

    @adraismawur
    adraismawur committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    a9c9cec View commit details
    Browse the repository at this point in the history

  6. specify exception type

    @adraismawur
    adraismawur committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    2164f6c View commit details
    Browse the repository at this point in the history

  7. add minimal test data

    @adraismawur
    adraismawur committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    92578fd View commit details
    Browse the repository at this point in the history

  8. add real data tests

    @adraismawur
    adraismawur committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    3ac3e91 View commit details
    Browse the repository at this point in the history

  9. remove class

    @adraismawur
    adraismawur committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    0db25d8 View commit details
    Browse the repository at this point in the history

  10. force string for mypy

    @adraismawur
    adraismawur committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    65fa549 View commit details
    Browse the repository at this point in the history

Commits on Jul 17, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Cunliang Geng <[email protected]>
    @adraismawur @CunliangGeng
    adraismawur and CunliangGeng authored Jul 17, 2024
    Configuration menu
    Copy the full SHA
    3096bcc View commit details
    Browse the repository at this point in the history

  2. add exceptions to docstring

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    d4cf769 View commit details
    Browse the repository at this point in the history

  3. add docstring to tests

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    c00d59c View commit details
    Browse the repository at this point in the history

  4. use tmp path instead of data path

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    18b2317 View commit details
    Browse the repository at this point in the history

  5. add missing typing

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    8a356a5 View commit details
    Browse the repository at this point in the history

  6. add explanation of cluster mode

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    5726f22 View commit details
    Browse the repository at this point in the history

  7. parameterize tests

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    aab5e69 View commit details
    Browse the repository at this point in the history

  8. remove two gbks

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    1d6da60 View commit details
    Browse the repository at this point in the history

  9. better documentation

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    7914f3a View commit details
    Browse the repository at this point in the history

  10. skip tests with dataset

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    88c1f19 View commit details
    Browse the repository at this point in the history

  11. do not check output code within run

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    195c791 View commit details
    Browse the repository at this point in the history

  12. move log

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    6cc45d1 View commit details
    Browse the repository at this point in the history

  13. add test with incorrect parameters for runtime exception

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    4a288a9 View commit details
    Browse the repository at this point in the history

  14. remove temporary nplinker.toml

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    a24454c View commit details
    Browse the repository at this point in the history

  15. add stderr to error log

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    a4b3a46 View commit details
    Browse the repository at this point in the history

  16. add import needed for skipping test on CI

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    84eb933 View commit details
    Browse the repository at this point in the history

  17. Apply suggestions from code review 

    Co-authored-by: Cunliang Geng <[email protected]>
    @adraismawur @CunliangGeng
    adraismawur and CunliangGeng authored Jul 17, 2024
    Configuration menu
    Copy the full SHA
    69f7674 View commit details
    Browse the repository at this point in the history

  18. expand docstring

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    5cadd45 View commit details
    Browse the repository at this point in the history

  19. Apply suggestions from code review 

    Co-authored-by: Cunliang Geng <[email protected]>
    @adraismawur @CunliangGeng
    adraismawur and CunliangGeng authored Jul 17, 2024
    Configuration menu
    Copy the full SHA
    1efc8fd View commit details
    Browse the repository at this point in the history

  20. fix ruff complaints

    @adraismawur
    adraismawur committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    bdd1f8e View commit details
    Browse the repository at this point in the history