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

To v0.3.3; XML export & sbml, neuroml examples #65

Merged
merged 49 commits into from
Dec 14, 2023
Merged

To v0.3.3; XML export & sbml, neuroml examples #65

merged 49 commits into from
Dec 14, 2023

Commits on Jan 12, 2023

  1. Install hdf5 from source

    @pgleeson
    pgleeson committed Jan 12, 2023
    Configuration menu
    Copy the full SHA
    d3c302e View commit details
    Browse the repository at this point in the history

  2. install libhdf5-dev

    @pgleeson
    pgleeson committed Jan 12, 2023
    Configuration menu
    Copy the full SHA
    f49bb88 View commit details
    Browse the repository at this point in the history

  3. sudo

    @pgleeson
    pgleeson committed Jan 12, 2023
    Configuration menu
    Copy the full SHA
    ad4df19 View commit details
    Browse the repository at this point in the history

Commits on Jan 31, 2023

  1. Update ci.yml

    @pgleeson
    pgleeson authored Jan 31, 2023
    Configuration menu
    Copy the full SHA
    f25194c View commit details
    Browse the repository at this point in the history

Commits on Jun 12, 2023

  1. Merge branch 'development' into experimental

    @pgleeson
    pgleeson committed Jun 12, 2023
    Configuration menu
    Copy the full SHA
    268e72a View commit details
    Browse the repository at this point in the history

Commits on Jul 26, 2023

  1. ci(py311): add to matrix

    @sanjayankur31
    sanjayankur31 committed Jul 26, 2023
    Configuration menu
    Copy the full SHA
    9770a5a View commit details
    Browse the repository at this point in the history

Commits on Jul 27, 2023

  1. Merge branch 'development' into experimental

    @pgleeson
    pgleeson committed Jul 27, 2023
    Configuration menu
    Copy the full SHA
    7573d9e View commit details
    Browse the repository at this point in the history

Commits on Jul 29, 2023

  1. added simple sbml test with example xml showing desired output we sho… 

    …uld be aiming to produce
    @robertvi
    robertvi committed Jul 29, 2023
    Configuration menu
    Copy the full SHA
    2b92351 View commit details
    Browse the repository at this point in the history

Commits on Jul 31, 2023

  1. Merge pull request #53 from robertvi/test_xml3 

    added simple sbml test with example xml
    @pgleeson
    pgleeson authored Jul 31, 2023
    Configuration menu
    Copy the full SHA
    920aef0 View commit details
    Browse the repository at this point in the history

  2. Formatted new sbml files 

    @robertvi It's good to run the test script at:
https://github.com/ModECI/modelspec/blob/development/test_all.sh before
committing as that will run the precommit hooks, including formatting
with black. Tests will fail if the formatting is not done. See
https://mdf.readthedocs.io/en/latest/api/Contributing.html#step-7
    @pgleeson
    pgleeson committed Jul 31, 2023
    Configuration menu
    Copy the full SHA
    f0f8e6c View commit details
    Browse the repository at this point in the history

Commits on Aug 8, 2023

  1. Test 3.11

    @pgleeson
    pgleeson committed Aug 8, 2023
    Configuration menu
    Copy the full SHA
    49d9fc6 View commit details
    Browse the repository at this point in the history

Commits on Aug 15, 2023

  1. Merge pull request #55 from ModECI/test_xml3 

    Latets xml to sbml branch
    @pgleeson
    pgleeson authored Aug 15, 2023
    Configuration menu
    Copy the full SHA
    aede680 View commit details
    Browse the repository at this point in the history

Commits on Aug 23, 2023

  1. Merge branch 'development' into test_sbml

    @pgleeson
    pgleeson committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    e82058b View commit details
    Browse the repository at this point in the history

Commits on Sep 6, 2023

  1. Add comment

    @pgleeson
    pgleeson committed Sep 6, 2023
    Configuration menu
    Copy the full SHA
    c6e70f8 View commit details
    Browse the repository at this point in the history

Commits on Sep 13, 2023

  1. Merge branch 'main' into test_neuroml

    @pgleeson
    pgleeson committed Sep 13, 2023
    Configuration menu
    Copy the full SHA
    57615ec View commit details
    Browse the repository at this point in the history

  2. Update gha version

    @pgleeson
    pgleeson committed Sep 13, 2023
    Configuration menu
    Copy the full SHA
    9d3ffa9 View commit details
    Browse the repository at this point in the history

  3. Bump version to v0.3.3

    @pgleeson
    pgleeson committed Sep 13, 2023
    Configuration menu
    Copy the full SHA
    d03ffb2 View commit details
    Browse the repository at this point in the history

  4. Merge branch 'test_neuroml' into test_sbml

    @pgleeson
    pgleeson committed Sep 13, 2023
    Configuration menu
    Copy the full SHA
    c304185 View commit details
    Browse the repository at this point in the history

  5. Some doc updates

    @pgleeson
    pgleeson committed Sep 13, 2023
    Configuration menu
    Copy the full SHA
    2964ff4 View commit details
    Browse the repository at this point in the history

  6. Merge branch 'test_neuroml' into test_sbml

    @pgleeson
    pgleeson committed Sep 13, 2023
    Configuration menu
    Copy the full SHA
    035c405 View commit details
    Browse the repository at this point in the history

Commits on Sep 15, 2023

  1. Merge pull request #61 from ModECI/test_neuroml 

    To v0.3.3 & some updates to docs
    @pgleeson
    pgleeson authored Sep 15, 2023
    Configuration menu
    Copy the full SHA
    c20f2f2 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'development' into test_sbml

    @pgleeson
    pgleeson committed Sep 15, 2023
    Configuration menu
    Copy the full SHA
    b865e16 View commit details
    Browse the repository at this point in the history

Commits on Sep 18, 2023

  1. Update testing on save/load json/yaml

    @pgleeson
    pgleeson committed Sep 18, 2023
    Configuration menu
    Copy the full SHA
    18ea90b View commit details
    Browse the repository at this point in the history

  2. Minimal working sbml example 

    Update a number of print statements
    @pgleeson
    pgleeson committed Sep 18, 2023
    Configuration menu
    Copy the full SHA
    d65bc18 View commit details
    Browse the repository at this point in the history

  3. Updates to core sbml model definition

    @pgleeson
    pgleeson committed Sep 18, 2023
    Configuration menu
    Copy the full SHA
    af43a93 View commit details
    Browse the repository at this point in the history

  4. Don't test xml examples on py3.7

    @pgleeson
    pgleeson committed Sep 18, 2023
    Configuration menu
    Copy the full SHA
    5c1eba6 View commit details
    Browse the repository at this point in the history

  5. Update ci.yml

    @pgleeson
    pgleeson authored Sep 18, 2023
    Configuration menu
    Copy the full SHA
    53c86e9 View commit details
    Browse the repository at this point in the history

  6. Add sbml requirements

    @pgleeson
    pgleeson committed Sep 18, 2023
    Configuration menu
    Copy the full SHA
    f5c7445 View commit details
    Browse the repository at this point in the history

  7. Merge branch 'test_sbml' of github.com:ModECI/modelspec into test_sbml

    @pgleeson
    pgleeson committed Sep 18, 2023
    Configuration menu
    Copy the full SHA
    5b2a2f7 View commit details
    Browse the repository at this point in the history

  8. Merge pull request #51 from sanjayankur31/feat/3.11 

    ci(py311): add to matrix
    @pgleeson
    pgleeson authored Sep 18, 2023
    Configuration menu
    Copy the full SHA
    fe6b3ae View commit details
    Browse the repository at this point in the history

  9. Merge pull request #63 from ModECI/test_neuroml 

    Tests on Python 3.11
    @pgleeson
    pgleeson authored Sep 18, 2023
    Configuration menu
    Copy the full SHA
    c2317e5 View commit details
    Browse the repository at this point in the history

  10. Generates same example sbml; restructured handling of listOf... classes 

    Can certainly be made more succinct, but generating valid SBML
    @pgleeson
    pgleeson committed Sep 18, 2023
    Configuration menu
    Copy the full SHA
    1064af3 View commit details
    Browse the repository at this point in the history

  11. Merge branch 'development' into test_sbml

    @pgleeson
    pgleeson committed Sep 18, 2023
    Configuration menu
    Copy the full SHA
    c77b629 View commit details
    Browse the repository at this point in the history

Commits on Sep 19, 2023

  1. Generate spec docs for sbml

    @pgleeson
    pgleeson committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    757a450 View commit details
    Browse the repository at this point in the history

  2. Update COMBINE specs docs

    @pgleeson
    pgleeson committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    37a9da1 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #64 from ModECI/test_sbml 

    Adds SBML API generation example
    @pgleeson
    pgleeson authored Sep 19, 2023
    Configuration menu
    Copy the full SHA
    02de41a View commit details
    Browse the repository at this point in the history

Commits on Nov 8, 2023

  1. Regenerated

    @pgleeson
    pgleeson committed Nov 8, 2023
    Configuration menu
    Copy the full SHA
    c3000df View commit details
    Browse the repository at this point in the history

  2. Add isbn to doc

    @pgleeson
    pgleeson committed Nov 8, 2023
    Configuration menu
    Copy the full SHA
    5f6b50d View commit details
    Browse the repository at this point in the history

  3. Add pandas requirement for docs

    @pgleeson
    pgleeson committed Nov 8, 2023
    Configuration menu
    Copy the full SHA
    309eecb View commit details
    Browse the repository at this point in the history

Commits on Nov 22, 2023

  1. Tweak

    @pgleeson
    pgleeson committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    5b96714 View commit details
    Browse the repository at this point in the history

  2. Pin cattrs to test if that's the issue...

    @pgleeson
    pgleeson committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    dbb3222 View commit details
    Browse the repository at this point in the history

Commits on Nov 23, 2023

  1. Update setup.cfg

    @pgleeson
    pgleeson authored Nov 23, 2023
    Configuration menu
    Copy the full SHA
    b8b1f66 View commit details
    Browse the repository at this point in the history

Commits on Dec 13, 2023

  1. Add 3.11 as supported env

    @pgleeson
    pgleeson committed Dec 13, 2023
    Configuration menu
    Copy the full SHA
    50c54c5 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'development' into experimental

    @pgleeson
    pgleeson committed Dec 13, 2023
    Configuration menu
    Copy the full SHA
    3386d4a View commit details
    Browse the repository at this point in the history

  3. Test unpin cattrs

    @pgleeson
    pgleeson committed Dec 13, 2023
    Configuration menu
    Copy the full SHA
    6216251 View commit details
    Browse the repository at this point in the history

  4. More specific version...

    @pgleeson
    pgleeson committed Dec 13, 2023
    Configuration menu
    Copy the full SHA
    8e93394 View commit details
    Browse the repository at this point in the history

  5. Remove 3.7 support...

    @pgleeson
    pgleeson committed Dec 13, 2023
    Configuration menu
    Copy the full SHA
    1f6db92 View commit details
    Browse the repository at this point in the history

  6. h5py install not required

    @pgleeson
    pgleeson committed Dec 13, 2023
    Configuration menu
    Copy the full SHA
    386fa23 View commit details
    Browse the repository at this point in the history

  7. Merge pull request #69 from ModECI/experimental 

    Fix cattrs issue
    @pgleeson
    pgleeson authored Dec 13, 2023
    Configuration menu
    Copy the full SHA
    490505e View commit details
    Browse the repository at this point in the history