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

Init files #54

Merged
merged 110 commits into from
Jul 24, 2023
Merged

Init files #54

merged 110 commits into from
Jul 24, 2023

Commits on May 4, 2023

  1. adding functionality to add additional seeding on resumes

    @shauntruelove
    shauntruelove committed May 4, 2023
    Configuration menu
    Copy the full SHA
    cd0a2b0 View commit details
    Browse the repository at this point in the history

  2. fix seeding

    @shauntruelove
    shauntruelove committed May 4, 2023
    Configuration menu
    Copy the full SHA
    991a3fd View commit details
    Browse the repository at this point in the history

  3. fix seeding

    @shauntruelove
    shauntruelove committed May 4, 2023
    Configuration menu
    Copy the full SHA
    de2d64c View commit details
    Browse the repository at this point in the history

  4. Merge branch 'seeding_fix' of https://github.com/HopkinsIDD/flepiMoP … 

    …into seeding_fix

# Conflicts:
#	flepimop/main_scripts/create_seeding_added.R
    @shauntruelove
    shauntruelove committed May 4, 2023
    Configuration menu
    Copy the full SHA
    5ad4c54 View commit details
    Browse the repository at this point in the history

Commits on May 5, 2023

  1. fixed dumb seeding error

    @shauntruelove
    shauntruelove committed May 5, 2023
    Configuration menu
    Copy the full SHA
    ed80f86 View commit details
    Browse the repository at this point in the history

  2. fixing seeding

    @shauntruelove
    shauntruelove committed May 5, 2023
    Configuration menu
    Copy the full SHA
    b9ebfa5 View commit details
    Browse the repository at this point in the history

  3. new seeding builder

    @shauntruelove
    shauntruelove committed May 5, 2023
    Configuration menu
    Copy the full SHA
    b8ab6b1 View commit details
    Browse the repository at this point in the history

Commits on May 8, 2023

  1. more resilient to differnt shell (zsh, bash)

    @jcblemai
    jcblemai committed May 8, 2023
    Configuration menu
    Copy the full SHA
    7490b0b View commit details
    Browse the repository at this point in the history

  2. local flag to print all the variables to reproduce failed runs

    @jcblemai
    jcblemai committed May 8, 2023
    Configuration menu
    Copy the full SHA
    2ee20b1 View commit details
    Browse the repository at this point in the history

Commits on May 10, 2023

  1. fix seeding

    @shauntruelove
    shauntruelove committed May 10, 2023
    Configuration menu
    Copy the full SHA
    8cae554 View commit details
    Browse the repository at this point in the history

  2. fix typo in model output directory and limit hosp file

    @saraloo
    saraloo committed May 10, 2023
    Configuration menu
    Copy the full SHA
    5261542 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'seeding_fix' of https://github.com/HopkinsIDD/flepiMoP … 

    …into seeding_fix
    @saraloo
    saraloo committed May 10, 2023
    Configuration menu
    Copy the full SHA
    06c5937 View commit details
    Browse the repository at this point in the history

Commits on May 17, 2023

  1. add options in config to fix either resumed seeding or added seeding

    @shauntruelove
    shauntruelove committed May 17, 2023
    Configuration menu
    Copy the full SHA
    8b3a2ac View commit details
    Browse the repository at this point in the history

  2. Merge branch 'seeding_fix' of https://github.com/HopkinsIDD/flepiMoP … 

    …into seeding_fix
    @shauntruelove
    shauntruelove committed May 17, 2023
    Configuration menu
    Copy the full SHA
    f652db1 View commit details
    Browse the repository at this point in the history

  3. fix parentheses typo added seeding

    @saraloo
    saraloo committed May 17, 2023
    Configuration menu
    Copy the full SHA
    9bd4a56 View commit details
    Browse the repository at this point in the history

  4. fix seeding in config writer

    @shauntruelove
    shauntruelove committed May 17, 2023
    Configuration menu
    Copy the full SHA
    b57ccc8 View commit details
    Browse the repository at this point in the history

  5. Merge branch 'seeding_fix' of https://github.com/HopkinsIDD/flepiMoP … 

    …into seeding_fix
    @shauntruelove
    shauntruelove committed May 17, 2023
    Configuration menu
    Copy the full SHA
    2659f18 View commit details
    Browse the repository at this point in the history

Commits on May 18, 2023

  1. continatation envar

    @jcblemai
    jcblemai committed May 18, 2023
    Configuration menu
    Copy the full SHA
    c9d427e View commit details
    Browse the repository at this point in the history

  2. continuation default to resume

    @jcblemai
    jcblemai committed May 18, 2023
    Configuration menu
    Copy the full SHA
    db7d8ac View commit details
    Browse the repository at this point in the history

  3. downloading continuation resume files

    @jcblemai
    jcblemai committed May 18, 2023
    Configuration menu
    Copy the full SHA
    7964f48 View commit details
    Browse the repository at this point in the history

Commits on May 22, 2023

  1. skip initial spaces for hand made csv

    @jcblemai
    jcblemai committed May 22, 2023
    Configuration menu
    Copy the full SHA
    91293a1 View commit details
    Browse the repository at this point in the history

  2. fix

    @jcblemai
    jcblemai committed May 22, 2023
    Configuration menu
    Copy the full SHA
    96d2a22 View commit details
    Browse the repository at this point in the history

Commits on May 23, 2023

  1. single files for initial conditions and seeding

    @jcblemai
    jcblemai committed May 23, 2023
    Configuration menu
    Copy the full SHA
    f4bd654 View commit details
    Browse the repository at this point in the history

  2. black

    @jcblemai
    jcblemai committed May 23, 2023
    Configuration menu
    Copy the full SHA
    7aabf78 View commit details
    Browse the repository at this point in the history

  3. fix

    @jcblemai
    jcblemai committed May 23, 2023
    Configuration menu
    Copy the full SHA
    ace9ff4 View commit details
    Browse the repository at this point in the history

Commits on May 24, 2023

  1. removed deprecated files that use to print the results

    @jcblemai
    jcblemai committed May 24, 2023
    Configuration menu
    Copy the full SHA
    fec65b6 View commit details
    Browse the repository at this point in the history

Commits on May 25, 2023

  1. fix seeding issue if not using seeding

    @shauntruelove
    shauntruelove committed May 25, 2023
    Configuration menu
    Copy the full SHA
    f4e9bd6 View commit details
    Browse the repository at this point in the history

  2. fix seeding requirements in building data

    @shauntruelove
    shauntruelove committed May 25, 2023
    Configuration menu
    Copy the full SHA
    6cfa8de View commit details
    Browse the repository at this point in the history

Commits on May 26, 2023

  1. fix another seeding issue

    @shauntruelove
    shauntruelove committed May 26, 2023
    Configuration menu
    Copy the full SHA
    19c1c25 View commit details
    Browse the repository at this point in the history

  2. remove duplicate section

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    e821873 View commit details
    Browse the repository at this point in the history

  3. detect if seeding is in the config

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    fc66728 View commit details
    Browse the repository at this point in the history

  4. update check

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    bb145d8 View commit details
    Browse the repository at this point in the history

  5. manual merge of seeding_fix

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    980949e View commit details
    Browse the repository at this point in the history

  6. mispushed

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    afc28f2 View commit details
    Browse the repository at this point in the history

  7. still trying to merge

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    64bc7da View commit details
    Browse the repository at this point in the history

  8. fix typos

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    b2def6b View commit details
    Browse the repository at this point in the history

  9. fix bug

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    c95a947 View commit details
    Browse the repository at this point in the history

  10. sane error message

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    2036e75 View commit details
    Browse the repository at this point in the history

  11. inference slots calls the preprocessing of init files

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    9569b1c View commit details
    Browse the repository at this point in the history

  12. addin init building file

    @shauntruelove
    shauntruelove committed May 26, 2023
    Configuration menu
    Copy the full SHA
    ef1ba3b View commit details
    Browse the repository at this point in the history

  13. Merge remote-tracking branch 'origin/seeding_fix' into init_files

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    9be6539 View commit details
    Browse the repository at this point in the history

  14. syncing the init script to bash

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    b423b00 View commit details
    Browse the repository at this point in the history

  15. fix max date issue

    @shauntruelove
    shauntruelove committed May 26, 2023
    Configuration menu
    Copy the full SHA
    cc8692a View commit details
    Browse the repository at this point in the history

  16. Merge remote-tracking branch 'origin/seeding_fix' into init_files

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    be26ef7 View commit details
    Browse the repository at this point in the history

  17. fix so it runs

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    572b5f0 View commit details
    Browse the repository at this point in the history

  18. fix type error, comparing strs to strs

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    7472f2b View commit details
    Browse the repository at this point in the history

  19. initial condition from file now working, with their two flags

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    118aba3 View commit details
    Browse the repository at this point in the history

  20. typo

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    0b25056 View commit details
    Browse the repository at this point in the history

  21. fixed init file to include all compartments at 0 if missing

    @shauntruelove
    shauntruelove committed May 26, 2023
    Configuration menu
    Copy the full SHA
    129413d View commit details
    Browse the repository at this point in the history

  22. more fixes

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    962cf59 View commit details
    Browse the repository at this point in the history

  23. Merge remote-tracking branch 'origin/seeding_fix' into init_files

    @jcblemai
    jcblemai committed May 26, 2023
    Configuration menu
    Copy the full SHA
    f6dcb82 View commit details
    Browse the repository at this point in the history

Commits on May 27, 2023

  1. glue code

    @jcblemai
    jcblemai committed May 27, 2023
    Configuration menu
    Copy the full SHA
    5486c32 View commit details
    Browse the repository at this point in the history

  2. made the immune ladder use envar

    @jcblemai
    jcblemai committed May 27, 2023
    Configuration menu
    Copy the full SHA
    63341e6 View commit details
    Browse the repository at this point in the history

  3. hopefully not too badly done: init files moving (this is a mess)

    @jcblemai
    jcblemai committed May 27, 2023
    Configuration menu
    Copy the full SHA
    551eb67 View commit details
    Browse the repository at this point in the history

  4. ⚠️ hack to get R17 going

    @jcblemai
    jcblemai committed May 27, 2023
    Configuration menu
    Copy the full SHA
    b92cab7 View commit details
    Browse the repository at this point in the history

  5. message for continaution

    @jcblemai
    jcblemai committed May 27, 2023
    Configuration menu
    Copy the full SHA
    1a5d6f9 View commit details
    Browse the repository at this point in the history

Commits on May 30, 2023

  1. making initial condiiton folder draw safer: loads from each mc instea… 

    …d of only mc_name
    @jcblemai
    jcblemai committed May 30, 2023
    Configuration menu
    Copy the full SHA
    749c7ef View commit details
    Browse the repository at this point in the history

  2. a better check philosophy

    @jcblemai
    jcblemai committed May 30, 2023
    Configuration menu
    Copy the full SHA
    797cb0d View commit details
    Browse the repository at this point in the history

  3. fixed init script

    @shauntruelove
    shauntruelove committed May 30, 2023
    Configuration menu
    Copy the full SHA
    10fb91e View commit details
    Browse the repository at this point in the history

  4. popnode check

    @jcblemai
    jcblemai committed May 30, 2023
    Configuration menu
    Copy the full SHA
    884f031 View commit details
    Browse the repository at this point in the history

  5. Merge remote-tracking branch 'origin/seeding_fix' into init_files

    @jcblemai
    jcblemai committed May 30, 2023
    Configuration menu
    Copy the full SHA
    1ff19d0 View commit details
    Browse the repository at this point in the history

  6. fix vacc in init

    @shauntruelove
    shauntruelove committed May 30, 2023
    Configuration menu
    Copy the full SHA
    0f74180 View commit details
    Browse the repository at this point in the history

  7. merge

    @jcblemai
    jcblemai committed May 30, 2023
    Configuration menu
    Copy the full SHA
    f0f69a8 View commit details
    Browse the repository at this point in the history

  8. zsh safe

    @jcblemai
    jcblemai committed May 30, 2023
    Configuration menu
    Copy the full SHA
    665e833 View commit details
    Browse the repository at this point in the history

  9. disabling population check for R17

    @jcblemai
    jcblemai committed May 30, 2023
    Configuration menu
    Copy the full SHA
    53dcabc View commit details
    Browse the repository at this point in the history

  10. new message

    @jcblemai
    jcblemai committed May 30, 2023
    Configuration menu
    Copy the full SHA
    3b07d62 View commit details
    Browse the repository at this point in the history

Commits on May 31, 2023

  1. fix deprecation warning (and actual error in the docker

    @jcblemai
    jcblemai committed May 31, 2023
    Configuration menu
    Copy the full SHA
    6bd5e4f View commit details
    Browse the repository at this point in the history

  2. Merge branch 'init_files' of https://github.com/HopkinsIDD/flepiMoP i… 

    …nto init_files
    @jcblemai
    jcblemai committed May 31, 2023
    Configuration menu
    Copy the full SHA
    da0b34d View commit details
    Browse the repository at this point in the history

  3. prune by llik

    @jcblemai
    jcblemai committed May 31, 2023
    Configuration menu
    Copy the full SHA
    6b4e63e View commit details
    Browse the repository at this point in the history

Commits on Jun 2, 2023

  1. fix

    @jcblemai
    jcblemai committed Jun 2, 2023
    Configuration menu
    Copy the full SHA
    f83f1be View commit details
    Browse the repository at this point in the history

  2. fix so flepi send even when the llik fails + fix timezone for filter

    @jcblemai
    jcblemai committed Jun 2, 2023
    Configuration menu
    Copy the full SHA
    23373a7 View commit details
    Browse the repository at this point in the history

Commits on Jun 3, 2023

  1. allow init script

    @shauntruelove
    shauntruelove committed Jun 3, 2023
    Configuration menu
    Copy the full SHA
    a23296e View commit details
    Browse the repository at this point in the history

Commits on Jun 5, 2023

  1. try fix for FCH : resume works without init

    @jcblemai
    jcblemai committed Jun 5, 2023
    Configuration menu
    Copy the full SHA
    22eac07 View commit details
    Browse the repository at this point in the history

  2. more fixes

    @jcblemai
    jcblemai committed Jun 5, 2023
    Configuration menu
    Copy the full SHA
    dda251f View commit details
    Browse the repository at this point in the history

  3. build conda env for rockfish

    @jcblemai
    jcblemai committed Jun 5, 2023
    Configuration menu
    Copy the full SHA
    9694b8a View commit details
    Browse the repository at this point in the history

  4. fix env

    @jcblemai
    jcblemai committed Jun 5, 2023
    Configuration menu
    Copy the full SHA
    50cca31 View commit details
    Browse the repository at this point in the history

Commits on Jun 6, 2023

  1. fix: proposal were rejected on the basis of the probability density >… 

    … updated to rejected if the value is outside the theoretical bounds of the distribution
    @jcblemai
    jcblemai committed Jun 6, 2023
    Configuration menu
    Copy the full SHA
    a9dab13 View commit details
    Browse the repository at this point in the history

  2. logfiles: better naming convention and making sure it also contains f… 

    …ilter mc
    @jcblemai
    jcblemai committed Jun 6, 2023
    Configuration menu
    Copy the full SHA
    182c902 View commit details
    Browse the repository at this point in the history

  3. fix: folder creation

    @jcblemai
    jcblemai committed Jun 6, 2023
    Configuration menu
    Copy the full SHA
    ff7dd23 View commit details
    Browse the repository at this point in the history

  4. fix: forgot namespace

    @jcblemai
    jcblemai committed Jun 6, 2023
    Configuration menu
    Copy the full SHA
    e44590a View commit details
    Browse the repository at this point in the history

  5. Adding pre-processing and init scripts

    @shauntruelove
    shauntruelove committed Jun 6, 2023
    Configuration menu
    Copy the full SHA
    192ee0d View commit details
    Browse the repository at this point in the history

  6. temporarily turned on init script and updated path

    @shauntruelove
    shauntruelove committed Jun 6, 2023
    Configuration menu
    Copy the full SHA
    3b4895a View commit details
    Browse the repository at this point in the history

Commits on Jun 7, 2023

  1. fix post-processing scripts

    @jcblemai
    jcblemai committed Jun 7, 2023
    Configuration menu
    Copy the full SHA
    3559e98 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'init_files' of https://github.com/HopkinsIDD/flepiMoP i… 

    …nto init_files
    @jcblemai
    jcblemai committed Jun 7, 2023
    Configuration menu
    Copy the full SHA
    1a3fbe2 View commit details
    Browse the repository at this point in the history

  3. made postprocessing call explicit so it can be redone from logs

    @jcblemai
    jcblemai committed Jun 7, 2023
    Configuration menu
    Copy the full SHA
    7777de6 View commit details
    Browse the repository at this point in the history

  4. send postprocessing plots to s3 and fs_results path

    @jcblemai
    jcblemai committed Jun 7, 2023
    Configuration menu
    Copy the full SHA
    9b5c1c6 View commit details
    Browse the repository at this point in the history

Commits on Jun 8, 2023

  1. add top and bottom 5 llik plots and cumulatives to snapshot

    @saraloo
    saraloo committed Jun 8, 2023
    Configuration menu
    Copy the full SHA
    696781b View commit details
    Browse the repository at this point in the history

  2. add preOm no delta init

    @shauntruelove
    shauntruelove committed Jun 8, 2023
    Configuration menu
    Copy the full SHA
    2594444 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'init_files' of https://github.com/HopkinsIDD/flepiMoP i… 

    …nto init_files
    @shauntruelove
    shauntruelove committed Jun 8, 2023
    Configuration menu
    Copy the full SHA
    d48d42c View commit details
    Browse the repository at this point in the history

  4. cleaned for sara

    @jcblemai
    jcblemai committed Jun 8, 2023
    Configuration menu
    Copy the full SHA
    61d5c16 View commit details
    Browse the repository at this point in the history

  5. merge

    @jcblemai
    jcblemai committed Jun 8, 2023
    Configuration menu
    Copy the full SHA
    256b6b5 View commit details
    Browse the repository at this point in the history

  6. remove dependency

    @jcblemai
    jcblemai committed Jun 8, 2023
    Configuration menu
    Copy the full SHA
    8b8af8f View commit details
    Browse the repository at this point in the history

Commits on Jun 9, 2023

  1. make snpi plots bigger in snapshot

    @saraloo
    saraloo committed Jun 9, 2023
    Configuration menu
    Copy the full SHA
    f60a5dd View commit details
    Browse the repository at this point in the history

  2. Merge branch 'init_files' of https://github.com/HopkinsIDD/flepiMoP i… 

    …nto init_files
    @saraloo
    saraloo committed Jun 9, 2023
    Configuration menu
    Copy the full SHA
    babaf3c View commit details
    Browse the repository at this point in the history

  3. TO CHECK: does not perturb the first iteration as to not loose good r… 

    …un on seeding
    @jcblemai
    jcblemai committed Jun 9, 2023
    Configuration menu
    Copy the full SHA
    3c8e999 View commit details
    Browse the repository at this point in the history

  4. merge

    @jcblemai
    jcblemai committed Jun 9, 2023
    Configuration menu
    Copy the full SHA
    624e8db View commit details
    Browse the repository at this point in the history

  5. fix post-processing uploaded

    @jcblemai
    jcblemai committed Jun 9, 2023
    Configuration menu
    Copy the full SHA
    b97516d View commit details
    Browse the repository at this point in the history

  6. add back hpar to snapshot

    @saraloo
    saraloo committed Jun 9, 2023
    Configuration menu
    Copy the full SHA
    174e6b4 View commit details
    Browse the repository at this point in the history

  7. Merge branch 'init_files' of https://github.com/HopkinsIDD/flepiMoP i… 

    …nto init_files
    @saraloo
    saraloo committed Jun 9, 2023
    Configuration menu
    Copy the full SHA
    0c9477c View commit details
    Browse the repository at this point in the history

  8. removed the init file script

    @jcblemai
    jcblemai committed Jun 9, 2023
    Configuration menu
    Copy the full SHA
    45ea23f View commit details
    Browse the repository at this point in the history

Commits on Jun 13, 2023

  1. comment out extra data pull

    @shauntruelove
    shauntruelove committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    51b18d5 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'init_files' of https://github.com/HopkinsIDD/flepiMoP i… 

    …nto init_files
    @shauntruelove
    shauntruelove committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    6d9e18b View commit details
    Browse the repository at this point in the history

Commits on Jun 21, 2023

  1. fix config.writer::seir_chunk glue::collapse back to paste

    @saraloo
    saraloo committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    8c3ba6b View commit details
    Browse the repository at this point in the history

Commits on Jun 27, 2023

  1. better functions for debug

    @jcblemai
    jcblemai committed Jun 27, 2023
    Configuration menu
    Copy the full SHA
    a528c5c View commit details
    Browse the repository at this point in the history

Commits on Jul 10, 2023

  1. fix variant error in buildcoviddata

    @shauntruelove
    shauntruelove committed Jul 10, 2023
    Configuration menu
    Copy the full SHA
    dc84998 View commit details
    Browse the repository at this point in the history

Commits on Jul 13, 2023

  1. fixing Delphi API key. adding input options

    @shauntruelove
    shauntruelove committed Jul 13, 2023
    Configuration menu
    Copy the full SHA
    f981cef View commit details
    Browse the repository at this point in the history

  2. add Delphi messages

    @shauntruelove
    shauntruelove committed Jul 13, 2023
    Configuration menu
    Copy the full SHA
    5b8aec1 View commit details
    Browse the repository at this point in the history

  3. deleting problem line

    @shauntruelove
    shauntruelove committed Jul 13, 2023
    Configuration menu
    Copy the full SHA
    7884e2d View commit details
    Browse the repository at this point in the history

  4. remove error line

    @shauntruelove
    shauntruelove committed Jul 13, 2023
    Configuration menu
    Copy the full SHA
    74ed274 View commit details
    Browse the repository at this point in the history

Commits on Jul 17, 2023

  1. Merge branch 'main-fixvarerr' into init_files

    @shauntruelove
    shauntruelove committed Jul 17, 2023
    Configuration menu
    Copy the full SHA
    514ef1d View commit details
    Browse the repository at this point in the history