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Changes for NML v2.3 release #168

Merged
merged 392 commits into from
Sep 20, 2023
Merged

Changes for NML v2.3 release #168

merged 392 commits into from
Sep 20, 2023
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Commits on Sep 27, 2022

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Commits on Sep 28, 2022

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  10. chore: format tests

    [ci skip]
    sanjayankur31 committed Sep 28, 2022
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  15. fix(add_segment): ensure segment groups are included in default groups

    This is required for conversion to NEURON. The members themselves do not
    need to be included.
    sanjayankur31 committed Sep 28, 2022
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Commits on Sep 29, 2022

  1. feat(nml.py): add default name to new segments

    The schema does not require the `name` attribute in `Segment`. However,
    the NEURON code generator seems to require it:
    
    ```
    Exception: java.lang.NullPointerException: Cannot invoke "String.equals(Object)" because the return value of "org.neuroml.model.Segment.getName()" is null
    ```
    sanjayankur31 committed Sep 29, 2022
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  6. feat(nml.py): make get_segment_group* raise ValueError instead of…

    … `Exception`
    
    Specific errors are better than generic ones.
    sanjayankur31 committed Sep 29, 2022
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  7. feat(nml.py): push default segment groups to end

    This is required to ensure that segment groups have already been defined
    before they are included in the default ones.
    sanjayankur31 committed Sep 29, 2022
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  9. feat(nml.py): move cell specific factory code to super class

    No need for it to be limited to the utility function.
    sanjayankur31 committed Sep 29, 2022
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Commits on Sep 30, 2022

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  3. feat(utils): use generateds based validation

    instead of lxml one.
    sanjayankur31 committed Sep 30, 2022
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  4. fix(loaders): use full import to prevent cyclic dependency issues

    loaders <-> utils, and partial imports cause errors.
    sanjayankur31 committed Sep 30, 2022
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  7. feat(version): ensure neuroml.__version__ is still usable

    prevent an API break
    sanjayankur31 committed Sep 30, 2022
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Commits on Oct 4, 2022

  1. feat(generatedssupersuper): make get_members and check_arg_list p…

    …rivate
    
    Users are not expected to use these.
    sanjayankur31 committed Oct 4, 2022
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  2. docs: show inherited members

    So that each component has the necessary members. Users are not expected
    to know that these are inherited from `GeneratedsSuperSuper` and go look
    there.
    sanjayankur31 committed Oct 4, 2022
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  3. fix(generatedssupersuper): make get_members and check_arg_list pr…

    …otected
    
    Not private---they need to be inherited by all the component type classes
    sanjayankur31 committed Oct 4, 2022
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  4. fix: add new methods to create branched and unbranched segment groups

    Before, all segment groups were being created as unbranched with the
    neuro lex ID being set for a section. However, it is not compulsory that
    users will only create unbranched segment groups. For example, a segment
    group for "apical dendrites" would not consist only of unbranched
    segments.
    sanjayankur31 committed Oct 4, 2022
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  5. feat(nml.py)!: group -> group_id for clarity

    BREAKING CHANGE: argument of the cell helper functions has changed from
    `group` to `group_id` to make it clear to users that it is the id of the
    group that is required there, not the object.
    
    The cell builder utilities have not yet been released, so while this is
    a breaking change, this will not affect users unless they've been using
    the development branch.
    sanjayankur31 committed Oct 4, 2022
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  9. docs: show inherited members

    So that all component type classes have the common `add`, `info` etc.
    methods listed directly.
    sanjayankur31 committed Oct 4, 2022
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  14. chore: fix docstring

    TODO: Really have to figure out why this is always wrongly generated
    sanjayankur31 committed Oct 4, 2022
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  15. feat(nml.py): update regeneration scripts

    `get_members` -> `_get_members`
    sanjayankur31 committed Oct 4, 2022
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  18. feat(add_segment): do not add members to the default groups

    It is sufficient to only include the segment groups in the default
    segment groups. This results in shorter NML files.
    sanjayankur31 committed Oct 4, 2022
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  19. feat(cell-builders): allow turning off automatic segment group reorde…

    …ring
    
    When adding lots of segments, one may want to wait until the end of
    the process to reorder the groups, instead of reordering after the
    addition of each segment (which is an unnecessary use of resources).
    sanjayankur31 committed Oct 4, 2022
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Commits on Oct 5, 2022

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Commits on Oct 6, 2022

  1. feat(nml.py)!: uncouple segment type from its group id

    We were inferring the segment type from its group id, but this is not
    appropriate in cases where a user may not be passing a group id at all.
    
    So, we uncouple the segment type from the group id and ask users to
    include it explicitly.
    sanjayankur31 committed Oct 6, 2022
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  7. perf(add_segment): do not use _add

    It will run the checks again, which we don't need.
    sanjayankur31 committed Oct 6, 2022
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Commits on Oct 7, 2022

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  2. feat(nml.py): do not run membership checks when adding segments

    Checking for membership is not performant for segment groups with larger
    numbers of segments. Instead, we will add a function to optimise segment
    groups that will de-duplicate them etc.
    sanjayankur31 committed Oct 7, 2022
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  11. perf(nml.py): use low level methods for performance

    There's no need to use `add` here since we're constructing the various
    object and can be quite sure that they are correct.
    
    Not using `add` here gives a huge performance boost because `add` gets
    members each time, and then goes through them to see where the component
    should fit.
    sanjayankur31 committed Oct 7, 2022
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Commits on Oct 10, 2022

  1. perf(nml.py): cache _get_members to improve performance

    very very useful when repeated calls are being made to methods that use
    `_get_members` like `_add` and so on.
    sanjayankur31 committed Oct 10, 2022
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Commits on Oct 11, 2022

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  5. chore(nml.py): remove some type hints

    We can't import `typing` in nml.py at the top level, so adding hints
    that require the `typing` module causes trouble. Just remove them.
    sanjayankur31 committed Oct 11, 2022
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  7. chore(nml.py): correct docstring formatting

    This particular docstring is always formatted wrongly by black. Not sure
    what's going on.
    sanjayankur31 committed Oct 11, 2022
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  8. Merge pull request #150 from NeuralEnsemble/feat/add-sectionise-method

    Feat/add sectionise method
    sanjayankur31 committed Oct 11, 2022
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Commits on Nov 7, 2022

  1. Slightly less verbose

    pgleeson committed Nov 7, 2022
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Commits on Nov 10, 2022

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Commits on Nov 24, 2022

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  2. feat(cell-builders): improve default group creation

    - only create all and soma default groups
    - dendrite/axon groups created whenever a segment of their respective
      type is added for the first time.
    sanjayankur31 committed Nov 24, 2022
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  3. feat(cell-builder): allow reordering/optimisation after segment addit…

    …ions
    
    - adds options to allow disabling when required
    sanjayankur31 committed Nov 24, 2022
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Commits on Nov 25, 2022

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Commits on Nov 28, 2022

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  3. Revert "improvement(info): make list/dict return same values as print…

    …ed text"
    
    This reverts commit 94b9068.
    sanjayankur31 committed Nov 28, 2022
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  4. feat(cell): improve summary to also show biophysical props.

    - also adds `morphinfo` and `biophysinfo` methods.
    sanjayankur31 committed Nov 28, 2022
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  5. chore(nml): regenerate

    sanjayankur31 committed Nov 28, 2022
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  7. Merge pull request #154 from NeuralEnsemble/feat/cell-util-improvemen…

    …ts-153
    
    Improvements noted in #153
    sanjayankur31 committed Nov 28, 2022
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Commits on Nov 29, 2022

  1. feat!(loaders): remove deprecated SWCLoader class

    It was marked as defunct long ago but remained in the sources. Removing
    this now to prevent users from using it
    
    BREAKING CHANGE: removes defunct SWCLoader class.
    sanjayankur31 committed Nov 29, 2022
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Commits on Nov 30, 2022

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  3. chore: update changelog

    sanjayankur31 committed Nov 30, 2022
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  5. Merge pull request #155 from NeuralEnsemble/feat/deprecate-swcloader

    feat!(loaders): remove deprecated SWCLoader class
    pgleeson committed Nov 30, 2022
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Commits on Dec 2, 2022

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  2. chore: regenerate

    sanjayankur31 committed Dec 2, 2022
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  5. chore: fix f-string

    sanjayankur31 committed Dec 2, 2022
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Commits on Dec 6, 2022

  1. fix(loaders): do not empty list of includes even if `include_includes…

    …` is False
    
    They are not processed, but they are still listed as files that are to
    be included. This ensures that the model description accurately matches
    the XML file.
    sanjayankur31 committed Dec 6, 2022
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Commits on Dec 7, 2022

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Commits on Jan 19, 2023

  1. Print version info

    pgleeson committed Jan 19, 2023
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  3. Update github actions

    pgleeson committed Jan 19, 2023
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Commits on Jan 25, 2023

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Commits on Jan 31, 2023

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  2. Merge pull request #159 from NeuralEnsemble/feat/py3.11

    ci(py311): add py311 to matrix/setup.py
    sanjayankur31 committed Jan 31, 2023
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Commits on Feb 15, 2023

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Commits on Mar 1, 2023

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  2. wip

    sanjayankur31 committed Mar 1, 2023
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  9. ci: add libgraphviz-dev

    required for pygraphviz
    sanjayankur31 committed Mar 2, 2023
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  10. ci: add libgraphviz-dev

    required for pygraphviz
    sanjayankur31 committed Mar 2, 2023
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Commits on Mar 7, 2023

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Commits on Mar 9, 2023

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Commits on Mar 10, 2023

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  3. fix(nml.py): handle case of zero length segments

    TODO: add validation tests for zero length segments?
    sanjayankur31 committed Mar 10, 2023
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Commits on Mar 13, 2023

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Commits on Mar 14, 2023

  1. feat(cell-helpers): check conventional morph root first

    ... if convention is followed, there's no need to create a graph.
    sanjayankur31 committed Mar 14, 2023
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  5. improvement: use get_segment_length method

    .. instead of re-implementing it
    sanjayankur31 committed Mar 14, 2023
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Commits on Mar 16, 2023

  1. feat(nml.py): split out helper imports into separate file

    using the generateDS `--custom-imports-template` option.
    
    This required tweaking of some code to prevent cyclic imports:
    `neuroml.__init__` imports all `nml.py` classes, but the helper methods
    import some utils from other `neuroml.*` modules
    sanjayankur31 committed Mar 16, 2023
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Commits on Apr 19, 2023

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Commits on Apr 20, 2023

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  3. Merge pull request #161 from NeuralEnsemble/feat/format-black

    chore: format with black
    sanjayankur31 committed Apr 20, 2023
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Commits on Apr 24, 2023

  1. Merge pull request #162 from NeuralEnsemble/development

    Development -> exp
    pgleeson committed Apr 24, 2023
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  2. Merge pull request #163 from NeuralEnsemble/feat/lengths

    Feat/lengths -> exp
    pgleeson committed Apr 24, 2023
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  3. Test miltiple os

    pgleeson committed Apr 24, 2023
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  4. test(lengths): remove dot exporter method and pygraphviz dev dep

    this is functionality provided by networkx, so folks can install the
    optional networkx deps if they need to.
    sanjayankur31 committed Apr 24, 2023
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Commits on Apr 25, 2023

  1. Merge pull request #164 from NeuralEnsemble/feat/lengths

    test(lengths): remove dot exporter method and pygraphviz dev dep
    pgleeson committed Apr 25, 2023
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Commits on Apr 26, 2023

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  2. chore: correct docstring

    Really not sure why this happens each time..
    sanjayankur31 committed Apr 26, 2023
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  3. Merge pull request #166 from NeuralEnsemble/fix/165

    fix: refactor `print_` to remove circular imports
    pgleeson committed Apr 26, 2023
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Commits on May 2, 2023

  1. Merge pull request #160 from NeuralEnsemble/feat/lengths

    Add graph representation for morphology, and some methods to fetch shortest lengths between segments
    pgleeson committed May 2, 2023
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  4. Merge pull request #167 from NeuralEnsemble/experimental

    Minor update on ci script
    pgleeson committed May 2, 2023
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Commits on May 3, 2023

  1. chore: sync schema

    sanjayankur31 committed May 3, 2023
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  3. chore: sync schema

    sanjayankur31 committed May 3, 2023
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  5. chore: sync schema

    sanjayankur31 committed May 3, 2023
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  7. Merge pull request #169 from NeuralEnsemble/feat/sync-nml2-205

    Regenerate for NeuroML2#205
    pgleeson committed May 3, 2023
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Commits on May 4, 2023

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Commits on May 10, 2023

  1. Add python-publish

    pgleeson committed May 10, 2023
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  2. Update python-publish.yml

    pgleeson committed May 10, 2023
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  3. To v0.5.1

    pgleeson committed May 10, 2023
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Commits on May 11, 2023

  1. feat(schema): link to schema documentation index

    The format is:
    
    ```
    https://docs.neuroml.org/Userdocs/Schemas/Index.html?highlight={lowerCamelCase name of component type}#{lower case name of component type}
    ```
    sanjayankur31 committed May 11, 2023
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Commits on May 19, 2023

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  2. Merge pull request #170 from NeuralEnsemble/feat/link-to-index

    feat(schema): link to schema documentation index (cosmetic change)
    pgleeson committed May 19, 2023
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  3. Merge pull request #171 from NeuralEnsemble/experimental

    numpy should be an explicit requirement
    pgleeson committed May 19, 2023
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Commits on Jun 14, 2023

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  4. Test on mac, win

    pgleeson committed Jun 14, 2023
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Commits on Jun 22, 2023

  1. Remove travis file

    pgleeson committed Jun 22, 2023
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  2. Remove mongodb setup step

    pgleeson committed Jun 22, 2023
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  3. Remove deps

    pgleeson committed Jun 22, 2023
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  5. Just run pytest on linux

    pgleeson committed Jun 22, 2023
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  7. To v0.5.3

    pgleeson committed Jun 22, 2023
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  8. Merge pull request #174 from NeuralEnsemble/experimental

    To v0.5.3; uses setup.cfg; tested on mac & win too
    pgleeson committed Jun 22, 2023
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Commits on Jul 26, 2023

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  2. Minor formatting

    pgleeson committed Jul 26, 2023
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Commits on Aug 16, 2023

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Commits on Aug 17, 2023

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  3. chore(loaders): fix type hinting for doc generation

    otherwise sphinx fails with:
    
    ```
      File
      "/home/asinha/Documents/02_Code/00_mine/NeuroML/software/libNeuroML/neuroml/loaders.py",
      line 191, in <module>
          ) -> neuroml.nml.nml.NeuroMLDocument:
          AttributeError: module 'neuroml' has no attribute 'nml'
    
    ```
    
    Not sure what the root cause is, but this tweak fixes it.
    sanjayankur31 committed Aug 17, 2023
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  4. Merge pull request #177 from NeuralEnsemble/feat/cell-optimise-natsort

    Feat/cell optimise natsort -> exp
    pgleeson committed Aug 17, 2023
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Commits on Sep 8, 2023

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  5. feat(utils): add utils to generate relative paths between components

    Given that we have a well defined structure, we should ideally be able
    to generate all paths automatically. The information is present, we just
    need to figure out how to use it.
    sanjayankur31 committed Sep 8, 2023
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Commits on Sep 11, 2023

  1. Merge pull request #178 from NeuralEnsemble/feat/path-util

    Towards semi-automated path generation
    pgleeson committed Sep 11, 2023
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Commits on Sep 19, 2023

  1. Merge pull request #179 from NeuralEnsemble/experimental

    Use natsort to properly sort segments/groups when optimising
    pgleeson committed Sep 19, 2023
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  2. To v0.5.4

    pgleeson committed Sep 19, 2023
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Commits on Sep 20, 2023

  1. Update to latest schema

    pgleeson committed Sep 20, 2023
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  2. Regenerated nml.py

    pgleeson committed Sep 20, 2023
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  3. To v0.5.5

    pgleeson committed Sep 20, 2023
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  4. Merge pull request #181 from NeuralEnsemble/experimental

    To v0.5.5; updated schema (with hindmarsh rose) and regenerated nml.py
    pgleeson committed Sep 20, 2023
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