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Changes for NML v2.3 release #168
Commits on Sep 27, 2022
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Commits on Sep 28, 2022
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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.
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Commits on Sep 29, 2022
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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 ```
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feat(nml.py): make
get_segment_group*
raiseValueError
instead of…… `Exception` Specific errors are better than generic ones.
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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.
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feat(nml.py): move cell specific factory code to super class
No need for it to be limited to the utility function.
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Commits on Sep 30, 2022
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feat(utils): use generateds based validation
instead of lxml one.
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fix(loaders): use full import to prevent cyclic dependency issues
loaders <-> utils, and partial imports cause errors.
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feat(version): ensure
neuroml.__version__
is still usableprevent an API break
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Commits on Oct 4, 2022
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feat(generatedssupersuper): make
get_members
andcheck_arg_list
p……rivate Users are not expected to use these.
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So that each component has the necessary members. Users are not expected to know that these are inherited from `GeneratedsSuperSuper` and go look there.
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fix(generatedssupersuper): make
get_members
andcheck_arg_list
pr……otected Not private---they need to be inherited by all the component type classes
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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.
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feat(nml.py)!:
group
->group_id
for clarityBREAKING 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.
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So that all component type classes have the common `add`, `info` etc. methods listed directly.
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Merge pull request #149 from NeuralEnsemble/feat/doc-tweaks
Feat/doc tweaks
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TODO: Really have to figure out why this is always wrongly generated
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feat(nml.py): update regeneration scripts
`get_members` -> `_get_members`
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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.
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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).
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Commits on Oct 5, 2022
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Commits on Oct 6, 2022
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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.
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perf(add_segment): do not use
_add
It will run the checks again, which we don't need.
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Commits on Oct 7, 2022
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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.
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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.
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Commits on Oct 10, 2022
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perf(nml.py): cache
_get_members
to improve performancevery very useful when repeated calls are being made to methods that use `_get_members` like `_add` and so on.
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Commits on Oct 11, 2022
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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.
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chore(nml.py): correct docstring formatting
This particular docstring is always formatted wrongly by black. Not sure what's going on.
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Merge pull request #150 from NeuralEnsemble/feat/add-sectionise-method
Feat/add sectionise method
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Commits on 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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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.
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feat(cell-builder): allow reordering/optimisation after segment addit…
…ions - adds options to allow disabling when required
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Commits on Nov 25, 2022
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improvement(nml.py): ensure
membrane_properties
exists before child…… elements are set
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Commits on Nov 28, 2022
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Revert "improvement(info): make list/dict return same values as print…
…ed text" This reverts commit 94b9068.
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feat(cell): improve summary to also show biophysical props.
- also adds `morphinfo` and `biophysinfo` methods.
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Merge pull request #154 from NeuralEnsemble/feat/cell-util-improvemen…
…ts-153 Improvements noted in #153
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Commits on Nov 29, 2022
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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.
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Revert "feat!(loaders): remove deprecated SWCLoader class"
This reverts commit b4721d1.
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Merge pull request #155 from NeuralEnsemble/feat/deprecate-swcloader
feat!(loaders): remove deprecated SWCLoader class
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Commits on Dec 6, 2022
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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.
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Merge pull request #159 from NeuralEnsemble/feat/py3.11
ci(py311): add py311 to matrix/setup.py
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Commits on Feb 15, 2023
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fix(nml.py): handle case of zero length segments
TODO: add validation tests for zero length segments?
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Commits on Mar 13, 2023
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feat(cell-helpers): check conventional morph root first
... if convention is followed, there's no need to create a graph.
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improvement: use
get_segment_length
method.. instead of re-implementing it
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Commits on Mar 16, 2023
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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
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Commits on Apr 19, 2023
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Merge pull request #161 from NeuralEnsemble/feat/format-black
chore: format with black
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Commits on Apr 24, 2023
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Merge pull request #162 from NeuralEnsemble/development
Development -> exp
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Merge pull request #163 from NeuralEnsemble/feat/lengths
Feat/lengths -> exp
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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.
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Merge pull request #164 from NeuralEnsemble/feat/lengths
test(lengths): remove dot exporter method and pygraphviz dev dep
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Really not sure why this happens each time..
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Merge pull request #166 from NeuralEnsemble/fix/165
fix: refactor `print_` to remove circular imports
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Merge pull request #160 from NeuralEnsemble/feat/lengths
Add graph representation for morphology, and some methods to fetch shortest lengths between segments
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Merge pull request #167 from NeuralEnsemble/experimental
Minor update on ci script
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Commits on May 3, 2023
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Merge pull request #169 from NeuralEnsemble/feat/sync-nml2-205
Regenerate for NeuroML2#205
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Commits on May 4, 2023
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docs: add
lxml
to requirementsNot included already: see https://readthedocs.org/api/v2/build/20585279.txt
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Commits on May 11, 2023
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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} ```
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Merge pull request #170 from NeuralEnsemble/feat/link-to-index
feat(schema): link to schema documentation index (cosmetic change)
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Merge pull request #171 from NeuralEnsemble/experimental
numpy should be an explicit requirement
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Commits on Jun 14, 2023
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Commits on Jun 22, 2023
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Merge pull request #174 from NeuralEnsemble/experimental
To v0.5.3; uses setup.cfg; tested on mac & win too
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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.
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Merge pull request #177 from NeuralEnsemble/feat/cell-optimise-natsort
Feat/cell optimise natsort -> exp
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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.
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Merge pull request #178 from NeuralEnsemble/feat/path-util
Towards semi-automated path generation
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Merge pull request #179 from NeuralEnsemble/experimental
Use natsort to properly sort segments/groups when optimising
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Commits on Sep 20, 2023
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Merge pull request #181 from NeuralEnsemble/experimental
To v0.5.5; updated schema (with hindmarsh rose) and regenerated nml.py
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