From ac1e8b059668f52c2f7366872673272bdda88a76 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 30 Sep 2024 18:33:23 -0400 Subject: [PATCH 1/6] Add github action to codespell main on push and PRs --- .github/workflows/codespell.yml | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 .github/workflows/codespell.yml diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 00000000..c59e0473 --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,25 @@ +# Codespell configuration is within .codespellrc +--- +name: Codespell + +on: + push: + branches: [main] + pull_request: + branches: [main] + +permissions: + contents: read + +jobs: + codespell: + name: Check for spelling errors + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Annotate locations with typos + uses: codespell-project/codespell-problem-matcher@v1 + - name: Codespell + uses: codespell-project/actions-codespell@v2 From 9e7d1d0f83715c428469280055679837506af29f Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 30 Sep 2024 18:33:23 -0400 Subject: [PATCH 2/6] Add rudimentary codespell config --- .codespellrc | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 .codespellrc diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 00000000..cf258894 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,6 @@ +[codespell] +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +skip = .git*,*.pdf,*.svg,*.css,.codespellrc +check-hidden = true +ignore-regex = ^\s*"image/\S+": ".* +# ignore-words-list = From 18e06f54a5c15d0a892ac89b972b62c80f000086 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 30 Sep 2024 18:37:03 -0400 Subject: [PATCH 3/6] Ignore mixed case words --- .codespellrc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.codespellrc b/.codespellrc index cf258894..12d19e31 100644 --- a/.codespellrc +++ b/.codespellrc @@ -2,5 +2,5 @@ # Ref: https://github.com/codespell-project/codespell#using-a-config-file skip = .git*,*.pdf,*.svg,*.css,.codespellrc check-hidden = true -ignore-regex = ^\s*"image/\S+": ".* +ignore-regex = ^\s*"image/\S+": ".*|\b[a-z]*[A-Z][a-zA-Z]*\b # ignore-words-list = From 9cf821b13f36e56390a7ce4d9c1f60f7fb5251fa Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 30 Sep 2024 18:37:11 -0400 Subject: [PATCH 4/6] [DATALAD RUNCMD] run codespell throughout fixing typos automagically (but ignoring overall fail due to ambigous ones) === Do not change lines below === { "chain": [], "cmd": "codespell -w || :", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- scripts/lems/sourceannotations.xml | 14 +++++++------- scripts/lems/xml2md.py | 2 +- scripts/schemas/asttemplates.py | 2 +- scripts/schemas/generate-jupyter-ast.py | 4 ++-- source/Events/2012-Edinburgh.md | 8 ++++---- source/Userdocs/ConvertingModels.md | 2 +- source/Userdocs/ExtendingNeuroMLv2.md | 2 +- source/Userdocs/ImportingMorphologyFiles.md | 2 +- source/Userdocs/LEMSExample4.md | 2 +- source/Userdocs/LEMSExample6.md | 2 +- .../LEMS_elements/Definingcomponenttypes.md | 10 +++++----- .../Userdocs/LEMS_elements/Unitsanddimensions.md | 4 ++-- source/Userdocs/MultiCompartmentOLMexample.md | 4 ++-- source/Userdocs/NML2_examples/NeuroML-DB.ipynb | 4 ++-- .../Walkthroughs/RayEtAl2020/Conversion.md | 2 +- 15 files changed, 32 insertions(+), 32 deletions(-) diff --git a/scripts/lems/sourceannotations.xml b/scripts/lems/sourceannotations.xml index 54c8e9d1..74ab67e4 100644 --- a/scripts/lems/sourceannotations.xml +++ b/scripts/lems/sourceannotations.xml @@ -29,7 +29,7 @@ The value of a constant must be a plain number (no units) giving the SI magnitud - A Dimenson element associated a name with a particular combination of the standards SI base dimensions, mass, lenght, time, current, temperature and amount if substance (moles). Fractional dimensions are not currently supported. + A Dimenson element associated a name with a particular combination of the standards SI base dimensions, mass, length, time, current, temperature and amount if substance (moles). Fractional dimensions are not currently supported. The name to be used when referring to this dimension from variable declaration or units @@ -48,7 +48,7 @@ Amount of substance Luminous intensity - A Unit asociates a symbol with a dimension and a power of ten. For non-metric units a scale can be provided, as in '1 inch = 0.0254 m'. In this case there is a degeneracy between the power and the scale which is best resolved by not using the two together. The offset parameter is available for units which are not zero-offset, such as farenheit. + A Unit associates a symbol with a dimension and a power of ten. For non-metric units a scale can be provided, as in '1 inch = 0.0254 m'. In this case there is a degeneracy between the power and the scale which is best resolved by not using the two together. The offset parameter is available for units which are not zero-offset, such as fahrenheit. As with constants, units are only referred to within expressions using their symbols, so the name is just for readability. @@ -89,13 +89,13 @@ The component type that this type inherits field definitions for, if any - + - + @@ -117,7 +117,7 @@ The dimension, or 'none'. This should be the name of an already defined dimensio An optional description of the parameter - A parameter of which the value is a path expression. When a ComponentType declares a PathParameter, a corresponding Component definition should have an attibute with that name whose value is a path expression that evaluates within the instance tree of the built model. This is used, for example, in the definition of a group component class, where the coresponding component specifies a path over the instance tree which selectesthe items that should go in the group. + A parameter of which the value is a path expression. When a ComponentType declares a PathParameter, a corresponding Component definition should have an attribute with that name whose value is a path expression that evaluates within the instance tree of the built model. This is used, for example, in the definition of a group component class, where the corresponding component specifies a path over the instance tree which selectesthe items that should go in the group. Name of the parameter @@ -213,7 +213,7 @@ An optional description of the ComponentReference - Specifies that instances of components based on this class can containe a named collection of other instances. This provides for containers for oprating on groups of instances with path and filter expressions defined in components to operate over the instance tree. + Specifies that instances of components based on this class can containe a named collection of other instances. This provides for containers for operating on groups of instances with path and filter expressions defined in components to operate over the instance tree. @@ -241,7 +241,7 @@ An optional description of the element - Specifies that a component can accept attached components of a particular class. Attached components can be added at build time dependent on other events. For scoping and access purposes they are like child components. The cannonical use of attachments is in adding synapses to a cell when a network connection is made. + Specifies that a component can accept attached components of a particular class. Attached components can be added at build time dependent on other events. For scoping and access purposes they are like child components. The canonical use of attachments is in adding synapses to a cell when a network connection is made. A name for the Attachments diff --git a/scripts/lems/xml2md.py b/scripts/lems/xml2md.py index 30ebb2a9..1c8085ac 100644 --- a/scripts/lems/xml2md.py +++ b/scripts/lems/xml2md.py @@ -56,7 +56,7 @@ def get_lems_examples(srcdirs, examples_max=5): """Get examples for component types - :param srcdirs: directores where examples are + :param srcdirs: directories where examples are :type srcdir: list(str) :param examples_max: maximum number of examples to store :type examples_max: int diff --git a/scripts/schemas/asttemplates.py b/scripts/schemas/asttemplates.py index c538dda9..8d7e6f89 100644 --- a/scripts/schemas/asttemplates.py +++ b/scripts/schemas/asttemplates.py @@ -55,7 +55,7 @@ def get_lems_type(variable): def format_math(expr): - """Replace math symbols with HTML conterparts + """Replace math symbols with HTML counterparts :param expr: expression to format :type expr: str diff --git a/scripts/schemas/generate-jupyter-ast.py b/scripts/schemas/generate-jupyter-ast.py index 8baaefcc..4f12e7e1 100644 --- a/scripts/schemas/generate-jupyter-ast.py +++ b/scripts/schemas/generate-jupyter-ast.py @@ -181,7 +181,7 @@ def get_libneuroml_signatures(): def get_comp_examples(srcdirs, examples_max=3): """Get examples for component types - :param srcdirs: directores where examples are + :param srcdirs: directories where examples are :type srcdir: list(str) :param examples_max: maximum number of examples to store :type examples_max: int @@ -474,7 +474,7 @@ def main(srcdir, destdir): units = model.units units = sorted(units, key=lambda unit: unit.symbol) - # lables are translated as lowercase in jupyter, so we append two + # labels are translated as lowercase in jupyter, so we append two # consecutive underscores to differentiate same ones, like M and m. symbols = [] for unit in units: diff --git a/source/Events/2012-Edinburgh.md b/source/Events/2012-Edinburgh.md index 0042916d..12d07971 100644 --- a/source/Events/2012-Edinburgh.md +++ b/source/Events/2012-Edinburgh.md @@ -79,7 +79,7 @@ Chair: Andrew Davison * - 11:30 - **Collaborative Modelling Repository update** - Padraig presented the initial work towards an open source, collaborative repository for NeuroML models, the Open Source Brain project. A preliminary version of this is avaliable here. It will be based on a version control repository (initially Mercurial) storing the model files. It will have automatic generation of online documentation of the models from ChannelML, MorphML, etc. Connectivity matrices for network connections, etc. can be generated for models which are stored in neuroConstruct format. NeuroLex IDs can be used to identify cells and channels to other resources. Feedback on the initial implementation was welcomed. + Padraig presented the initial work towards an open source, collaborative repository for NeuroML models, the Open Source Brain project. A preliminary version of this is available here. It will be based on a version control repository (initially Mercurial) storing the model files. It will have automatic generation of online documentation of the models from ChannelML, MorphML, etc. Connectivity matrices for network connections, etc. can be generated for models which are stored in neuroConstruct format. NeuroLex IDs can be used to identify cells and channels to other resources. Feedback on the initial implementation was welcomed. - Padraig Gleeson @@ -148,7 +148,7 @@ Chair: Sharon Crook - * - 17:30 - - **Reconvene and presentated discussions** + - **Reconvene and presented discussions** - * - 18:00 @@ -263,7 +263,7 @@ Chair: Avrama Blackwell Sarah gave a brief overview of libSBML and SBML Level 3. libSBML, which provides an API for creating, editing and saving SBML in many languages (e.g. C++, Python, Java, Ruby, Perl) has been instrumental in the growth of the number of applications supporting SBML. - SBML Level 3 has a modular architecture, featuring a core specification (roughly in line with previous SBML releases) and a number of specialist packages, which applications can choose to support or not. Examples of these packages incluse layout for storing the spatial topology of a model's network diagram, comp for defining how a model is composed from other models and spatial for describing models that involve a spatial component. libSBML already has a generic framework to support extensions for generic packages. + SBML Level 3 has a modular architecture, featuring a core specification (roughly in line with previous SBML releases) and a number of specialist packages, which applications can choose to support or not. Examples of these packages include layout for storing the spatial topology of a model's network diagram, comp for defining how a model is composed from other models and spatial for describing models that involve a spatial component. libSBML already has a generic framework to support extensions for generic packages. - Sarah Keating @@ -281,7 +281,7 @@ Chair: Avrama Blackwell - * - 17:30 - - **Reconvene and presentated discussions** + - **Reconvene and presented discussions** - * - 18:00 diff --git a/source/Userdocs/ConvertingModels.md b/source/Userdocs/ConvertingModels.md index bfbef02f..a2b1722f 100644 --- a/source/Userdocs/ConvertingModels.md +++ b/source/Userdocs/ConvertingModels.md @@ -116,7 +116,7 @@ Create a script to load the output of mod analysis and nml analysis and compare (userdocs:creating_models:converting_conductance:compare_single_comp)= ### 4c) Compare single compartment cell with channels -Ensure you have a passive soma example in NeuroML which reproduces the behaviour of an equivalent passibe version inthe original format (from steps 3a and 4a above). +Ensure you have a passive soma example in NeuroML which reproduces the behaviour of an equivalent passibe version in the original format (from steps 3a and 4a above). Gradually test the cell with passive conductance and *each channel individually*. Plot v along with rate variables for each channel & compare how they look during current pulse ([example in NEURON](https://github.com/OpenSourceBrain/BlueBrainProjectShowcase/blob/master/NMC/NEURON/Test_Soma.hoc) vs [example in NeuroML](https://github.com/OpenSourceBrain/BlueBrainProjectShowcase/blob/master/NMC/NeuroML2/Soma_AllNML2.cell.nml) and [LEMS](https://github.com/OpenSourceBrain/BlueBrainProjectShowcase/blob/master/NMC/NeuroML2/LEMS_Soma_AllNML2.xml)) diff --git a/source/Userdocs/ExtendingNeuroMLv2.md b/source/Userdocs/ExtendingNeuroMLv2.md index ed049e0a..3394670b 100644 --- a/source/Userdocs/ExtendingNeuroMLv2.md +++ b/source/Userdocs/ExtendingNeuroMLv2.md @@ -10,7 +10,7 @@ They define the membership structure of the type, but they do not specify values Once a ComponentType has been defined, an instance of it can be created by setting values for its members. This object is referred to as a **Component** in LEMS. -Having definitions in LEMS allows their re-use, and all new ComponentTypes can be submitted for inclusion to the NeuroMLv2 specification to be made accessible to other users. +Having definitions in LEMS allows their reuse, and all new ComponentTypes can be submitted for inclusion to the NeuroMLv2 specification to be made accessible to other users. - Like NeuroML, LEMS also has a [well defined schema](https://github.com/LEMS/LEMS/tree/master/Schemas/LEMS) (XSD) that is used to validate LEMS XML files. - Also similar to NeuroML, you can use the {ref}`LEMS Python tools ` to work with LEMS and do not need to work directly with the XML files. diff --git a/source/Userdocs/ImportingMorphologyFiles.md b/source/Userdocs/ImportingMorphologyFiles.md index 88300345..6305b9cf 100644 --- a/source/Userdocs/ImportingMorphologyFiles.md +++ b/source/Userdocs/ImportingMorphologyFiles.md @@ -104,7 +104,7 @@ Usually, morphologies are embedded in NeuroML cell definition files, {ref}`for e However, morphologies (and {ref}`biophysical properties `) can also be stored as "standalone" entities outside the cell definition and referred to. Further, they can also be stored in external files that may be "included" in the cell definition file (using the [IncludeType](https://libneuroml.readthedocs.io/en/latest/userdocs/coreclasses.html#includetype) model element). -This allows the re-use of morphology and biophysical properties in multiple cell models: +This allows the reuse of morphology and biophysical properties in multiple cell models: ```{code-block} xml diff --git a/source/Userdocs/LEMSExample4.md b/source/Userdocs/LEMSExample4.md index 1362ee36..11a85f10 100644 --- a/source/Userdocs/LEMSExample4.md +++ b/source/Userdocs/LEMSExample4.md @@ -46,7 +46,7 @@ First then, the following definitions can be used to express ion channel models This says that a gate can contain any number of states and transitions. A state has an occupancy variable, and a transition has links to two states giving the source and target states for the transition. -The transition element here is an abstract element because it doesn't provide a Dynamics block but just specifies what quantities transitions should privide via the two exposures. +The transition element here is an abstract element because it doesn't provide a Dynamics block but just specifies what quantities transitions should provide via the two exposures. One of the most useful forms of transition is a damped Boltzman equation which can be parameterizd as follows: ```{code-block} xml diff --git a/source/Userdocs/LEMSExample6.md b/source/Userdocs/LEMSExample6.md index 64e13b85..ea72bf77 100644 --- a/source/Userdocs/LEMSExample6.md +++ b/source/Userdocs/LEMSExample6.md @@ -27,7 +27,7 @@ The 'variable' attribute is for future use - at present, the independent variabl A Run element can be added to the Dynamics block in any type definition to make it independently runnable. -Running a simulation without any output is rarely much use, so there are two futher elements that can be included in the Dynamics block: Show and Record. +Running a simulation without any output is rarely much use, so there are two further elements that can be included in the Dynamics block: Show and Record. The 'src' attribute of the Show element points to the components that should be shown. These in turn can contain other Show elements but eventually everything pointed to by a Show element should contain one or more Record elements. These specify what will actually be sent as output. diff --git a/source/Userdocs/LEMS_elements/Definingcomponenttypes.md b/source/Userdocs/LEMS_elements/Definingcomponenttypes.md index c44f48fc..ebb19577 100644 --- a/source/Userdocs/LEMS_elements/Definingcomponenttypes.md +++ b/source/Userdocs/LEMS_elements/Definingcomponenttypes.md @@ -48,13 +48,13 @@ Please file any issues or questions at the [issue tracker here](https://github.c **componentReferences**$ {ref}`lemsschema:componentreference_` **componentTypeReferences**$ {ref}`lemsschema:componenttypereference_` **locations**$ {ref}`lemsschema:location_` -**propertys**$ {ref}`lemsschema:property_` +**properties**$ {ref}`lemsschema:property_` **dynamicses**$ {ref}`lemsschema:dynamics_` **structures**$ {ref}`lemsschema:structure_` **simulations**$ {ref}`lemsschema:simulation_` **equilibriums**$ {ref}`lemsschema:equilibrium_` **procedures**$ {ref}`lemsschema:procedure_` -**geometrys**$ {ref}`lemsschema:geometry_` +**geometries**$ {ref}`lemsschema:geometry_` **fixeds**$ {ref}`lemsschema:fixed_` **constants**$ {ref}`lemsschema:constant_` **attachmentses**$ {ref}`lemsschema:attachments_` @@ -195,7 +195,7 @@ Please file any issues or questions at the [issue tracker here](https://github.c (lemsschema:pathparameter_)= ## PathParameter -A parameter of which the value is a path expression. When a ComponentType declares a PathParameter, a corresponding Component definition should have an attibute with that name whose value is a path expression that evaluates within the instance tree of the built model. This is used, for example, in the definition of a group component class, where the coresponding component specifies a path over the instance tree which selectesthe items that should go in the group. +A parameter of which the value is a path expression. When a ComponentType declares a PathParameter, a corresponding Component definition should have an attribute with that name whose value is a path expression that evaluates within the instance tree of the built model. This is used, for example, in the definition of a group component class, where the corresponding component specifies a path over the instance tree which selectesthe items that should go in the group. `````{tab-set} ````{tab-item} Properties @@ -697,7 +697,7 @@ Please file any issues or questions at the [issue tracker here](https://github.c (lemsschema:collection_)= ## Collection -Specifies that instances of components based on this class can containe a named collection of other instances. This provides for containers for oprating on groups of instances with path and filter expressions defined in components to operate over the instance tree. +Specifies that instances of components based on this class can containe a named collection of other instances. This provides for containers for operating on groups of instances with path and filter expressions defined in components to operate over the instance tree. `````{tab-set} ````{tab-item} Properties @@ -873,7 +873,7 @@ Please file any issues or questions at the [issue tracker here](https://github.c (lemsschema:attachments_)= ## Attachments -Specifies that a component can accept attached components of a particular class. Attached components can be added at build time dependent on other events. For scoping and access purposes they are like child components. The cannonical use of attachments is in adding synapses to a cell when a network connection is made. +Specifies that a component can accept attached components of a particular class. Attached components can be added at build time dependent on other events. For scoping and access purposes they are like child components. The canonical use of attachments is in adding synapses to a cell when a network connection is made. `````{tab-set} ````{tab-item} Properties diff --git a/source/Userdocs/LEMS_elements/Unitsanddimensions.md b/source/Userdocs/LEMS_elements/Unitsanddimensions.md index d2f11289..491962e9 100644 --- a/source/Userdocs/LEMS_elements/Unitsanddimensions.md +++ b/source/Userdocs/LEMS_elements/Unitsanddimensions.md @@ -13,7 +13,7 @@ Please file any issues or questions at the [issue tracker here](https://github.c (lemsschema:dimension_)= ## Dimension -A Dimenson element associated a name with a particular combination of the standards SI base dimensions, mass, lenght, time, current, temperature and amount if substance (moles). Fractional dimensions are not currently supported. +A Dimenson element associated a name with a particular combination of the standards SI base dimensions, mass, length, time, current, temperature and amount if substance (moles). Fractional dimensions are not currently supported. `````{tab-set} ````{tab-item} Properties @@ -71,7 +71,7 @@ Please file any issues or questions at the [issue tracker here](https://github.c (lemsschema:unit_)= ## Unit -A Unit asociates a symbol with a dimension and a power of ten. For non-metric units a scale can be provided, as in '1 inch = 0.0254 m'. In this case there is a degeneracy between the power and the scale which is best resolved by not using the two together. The offset parameter is available for units which are not zero-offset, such as farenheit. +A Unit associates a symbol with a dimension and a power of ten. For non-metric units a scale can be provided, as in '1 inch = 0.0254 m'. In this case there is a degeneracy between the power and the scale which is best resolved by not using the two together. The offset parameter is available for units which are not zero-offset, such as fahrenheit. `````{tab-set} ````{tab-item} Properties diff --git a/source/Userdocs/MultiCompartmentOLMexample.md b/source/Userdocs/MultiCompartmentOLMexample.md index a26c72b7..56d37e56 100644 --- a/source/Userdocs/MultiCompartmentOLMexample.md +++ b/source/Userdocs/MultiCompartmentOLMexample.md @@ -139,7 +139,7 @@ language: python lines: 123-142 ---- ``` -The utility function takes the dimensions of the segment---it's {ref}`proximal ` and {ref}`distal ` co-ordinates and the diameter to create a segment of the provided name. +The utility function takes the dimensions of the segment---it's {ref}`proximal ` and {ref}`distal ` coordinates and the diameter to create a segment of the provided name. Additionally, since segments need to be contiguous, it makes the first segment the *parent* of the second, to build a chain. Finally, it places the segment into the specified segment group and the default groups that we also have and adds the segment to the cell's morphology. @@ -179,7 +179,7 @@ Next, we proceed to our {ref}`biophysical properties ` - {ref}`initial membrane potential ` - {ref}`channel densities ` - - {ref}`specifc capacitances ` + - {ref}`specific capacitances ` - the {ref}`intracellular properties ` - {ref}`resistivity ` diff --git a/source/Userdocs/NML2_examples/NeuroML-DB.ipynb b/source/Userdocs/NML2_examples/NeuroML-DB.ipynb index efe4212b..0eb62336 100644 --- a/source/Userdocs/NML2_examples/NeuroML-DB.ipynb +++ b/source/Userdocs/NML2_examples/NeuroML-DB.ipynb @@ -567,7 +567,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### 2.2) Generate a plot of the actvity of the cell under current clamp input" + "### 2.2) Generate a plot of the activity of the cell under current clamp input" ] }, { @@ -1182,7 +1182,7 @@ "\n", "for i in range(0, size_exc):\n", " for j in range(0, size_inh):\n", - " if random.random() <= prob_connection: # probablistic connection...\n", + " if random.random() <= prob_connection: # probabilistic connection...\n", " connection = ConnectionWD(\n", " id=proj_count,\n", " pre_cell_id=\"%s[%i]\" % (pop_exc.id, i),\n", diff --git a/source/Userdocs/Walkthroughs/RayEtAl2020/Conversion.md b/source/Userdocs/Walkthroughs/RayEtAl2020/Conversion.md index e7a92de1..45bfb1b1 100644 --- a/source/Userdocs/Walkthroughs/RayEtAl2020/Conversion.md +++ b/source/Userdocs/Walkthroughs/RayEtAl2020/Conversion.md @@ -543,7 +543,7 @@ We have two cases here: The nas channel is now done. If we look at the other channels---naf, kv, and kst---they follow similar formalisms. -So, we can re-use our newly created component types, `Ray_inf` and `Ray_tau`. +So, we can reuse our newly created component types, `Ray_inf` and `Ray_tau`. In fact, we consolidate them in a single file, `RaySigmoid.nml`, and "include" this in the channel definition files. For example, here is `kv.channel.nml`: From 3b7a0e241e1c987e0681a018d1dfdef2b9ce4c41 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 30 Sep 2024 21:10:53 -0400 Subject: [PATCH 5/6] [DATALAD RUNCMD] Do interactive fixing of some ambigous typos === Do not change lines below === { "chain": [], "cmd": "codespell -w -i 3 -C 2", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- scripts/lems/sourceannotations.xml | 6 +++--- scripts/schemas/asttemplates.py | 4 ++-- source/Events/2012-Edinburgh.md | 2 +- source/Userdocs/ConvertingModels.md | 2 +- source/Userdocs/LEMSExample1.md | 2 +- source/Userdocs/LEMS_elements/Definingcomponenttypes.md | 2 +- source/Userdocs/LEMS_elements/Dynamics.md | 4 ++-- 7 files changed, 11 insertions(+), 11 deletions(-) diff --git a/scripts/lems/sourceannotations.xml b/scripts/lems/sourceannotations.xml index 74ab67e4..a3e12537 100644 --- a/scripts/lems/sourceannotations.xml +++ b/scripts/lems/sourceannotations.xml @@ -213,7 +213,7 @@ An optional description of the ComponentReference - Specifies that instances of components based on this class can containe a named collection of other instances. This provides for containers for operating on groups of instances with path and filter expressions defined in components to operate over the instance tree. + Specifies that instances of components based on this class can contain a named collection of other instances. This provides for containers for operating on groups of instances with path and filter expressions defined in components to operate over the instance tree. @@ -319,7 +319,7 @@ The dimension, or 'none'. This should be the name of an already defined dimensio An optional description of the derived variable -Either 'add' or 'multiply'. This applies if ther are multiple matches to the path or if 'required' is false. In the latter case, for multiply mode, multiplicative expressions in this variable behave as if the term was absent. Additive expressions generate an error. Conversely, if set to 'add' then additive expressions behave as if it was not there and multiplicative ones generateand error. +Either 'add' or 'multiply'. This applies if there are multiple matches to the path or if 'required' is false. In the latter case, for multiply mode, multiplicative expressions in this variable behave as if the term was absent. Additive expressions generate an error. Conversely, if set to 'add' then additive expressions behave as if it was not there and multiplicative ones generateand error. Set to true if it OK for this variable to be absent. See 'reduce' for what happens in this case @@ -358,7 +358,7 @@ Name of state variable in state elements The name of the attribute in the rate element that defines the source of the transition -Attribute tha defines the target +Attribute that defines the target Name of forward rate exposure diff --git a/scripts/schemas/asttemplates.py b/scripts/schemas/asttemplates.py index 8d7e6f89..c434bfb4 100644 --- a/scripts/schemas/asttemplates.py +++ b/scripts/schemas/asttemplates.py @@ -387,12 +387,12 @@ def format_math(expr): dynamics = env.from_string(textwrap.dedent( """ ````{tab-item} {{ title }} - {% if comp_type.structure and (comp_type.structure.withs|length + + {% if comp_type.structure and (comp_type.structure.widths|length + comp_type.structure.child_instances|length + comp_type.structure.multi_instantiates|length + comp_type.structure.event_connections|length) > 0 %} **Structure** - {%- for w in comp_type.structure.withs %} + {%- for w in comp_type.structure.widths %} : WITH **{{ w.instance }}** AS **{{ w.as_ }}** {%- endfor -%} {% for ci in comp_type.structure.child_instances %} diff --git a/source/Events/2012-Edinburgh.md b/source/Events/2012-Edinburgh.md index 12d07971..8b1fa318 100644 --- a/source/Events/2012-Edinburgh.md +++ b/source/Events/2012-Edinburgh.md @@ -207,7 +207,7 @@ Chair: Michael Hines * - 11:00 - **The OpenWorm project: Using NeuroML in a highly detailed model of C. elegans ([PPT](https://docs.neuroml.org/_static/NeuroML2012/Open_Worm_03-13-12.ppt))** - Stephen presented the OpenWorm project. This ambitious project aims to build an in silico model of C. elegans. This well studied system with ~1000 cells and 302 identified neurons is an ideal system with which to attempt a full simulation of a living organism down to cellular scale. Many different approaches are being take in the project at the moment, including investigatin Smoothed Particle Hydrodynamics (SHP) to allow simulation of the interaction of the worm with its environment, and creating a new parallel (GPU based) simulator in Java which will support physical and electrical simulations. Full reconstructions of all of the cells are available in 3D and those of the neurons have been converted to NeuroML, which will form the basis of a simulation of the worm's nervous system. + Stephen presented the OpenWorm project. This ambitious project aims to build an in silico model of C. elegans. This well studied system with ~1000 cells and 302 identified neurons is an ideal system with which to attempt a full simulation of a living organism down to cellular scale. Many different approaches are being take in the project at the moment, including investigating Smoothed Particle Hydrodynamics (SHP) to allow simulation of the interaction of the worm with its environment, and creating a new parallel (GPU based) simulator in Java which will support physical and electrical simulations. Full reconstructions of all of the cells are available in 3D and those of the neurons have been converted to NeuroML, which will form the basis of a simulation of the worm's nervous system. One of the concrete outcomes of code sprinting work on the fringes of the NeuroML/CodeJam meeting was the updated OpenWorm Browser, where the full cellular structure of the worm can be browsed in 3D. diff --git a/source/Userdocs/ConvertingModels.md b/source/Userdocs/ConvertingModels.md index a2b1722f..e7fa3062 100644 --- a/source/Userdocs/ConvertingModels.md +++ b/source/Userdocs/ConvertingModels.md @@ -138,7 +138,7 @@ export_to_neuroml2("test.hoc", "test.morphonly.cell.nml", includeBiophysicalProp Alternatively manually add the `` elements to the cell file (as [here](https://github.com/OpenSourceBrain/SmithEtAl2013-L23DendriticSpikes/blob/master/NeuroML2/L23_NoHotSpot.cell.nml#L16711)). -You can use the tools for {ref}`visualising NeuroML Models ` to compare how these versions look agains the originals. +You can use the tools for {ref}`visualising NeuroML Models ` to compare how these versions look against the originals. As with the single compartment example, it's best to **start off with the passive case**, i.e no active channels on the soma or dendrites, and compare that to the original code (for membrane potential at multiple locations!), and gradually add channels. diff --git a/source/Userdocs/LEMSExample1.md b/source/Userdocs/LEMSExample1.md index f5f0a541..7b4970fc 100644 --- a/source/Userdocs/LEMSExample1.md +++ b/source/Userdocs/LEMSExample1.md @@ -294,7 +294,7 @@ Although the channel models have now been defined, they still need to be used in For this we'll just define a basic channel population type. There is one new construct here: the ComponentRef element which in this case says that a channel population needs a reference to a component of type HHChannel. This is much like a Child element, but instead of the component being defined then and there inside the channel population, there is just a reference to it. -The Dynamics block for a cannel population just computes the total conductance and then the current, in this case using Ohm's law. +The Dynamics block for a channel population just computes the total conductance and then the current, in this case using Ohm's law. ```{code-block} xml diff --git a/source/Userdocs/LEMS_elements/Definingcomponenttypes.md b/source/Userdocs/LEMS_elements/Definingcomponenttypes.md index ebb19577..1554c863 100644 --- a/source/Userdocs/LEMS_elements/Definingcomponenttypes.md +++ b/source/Userdocs/LEMS_elements/Definingcomponenttypes.md @@ -697,7 +697,7 @@ Please file any issues or questions at the [issue tracker here](https://github.c (lemsschema:collection_)= ## Collection -Specifies that instances of components based on this class can containe a named collection of other instances. This provides for containers for operating on groups of instances with path and filter expressions defined in components to operate over the instance tree. +Specifies that instances of components based on this class can contain a named collection of other instances. This provides for containers for operating on groups of instances with path and filter expressions defined in components to operate over the instance tree. `````{tab-set} ````{tab-item} Properties diff --git a/source/Userdocs/LEMS_elements/Dynamics.md b/source/Userdocs/LEMS_elements/Dynamics.md index b449cc64..e2d7cf59 100644 --- a/source/Userdocs/LEMS_elements/Dynamics.md +++ b/source/Userdocs/LEMS_elements/Dynamics.md @@ -267,7 +267,7 @@ Please file any issues or questions at the [issue tracker here](https://github.c **select**$ String$ A path to the variable that supplies the value. Note that to select a variable from another component, the variable must be marked as an Exposure. Exactly one of 'select' and 'value' is required **dimension**$ String$ The dimension, or 'none'. This should be the name of an already defined dimension element **description**$ String$ An optional description of the derived variable -**reduce**$ String$ Either 'add' or 'multiply'. This applies if ther are multiple matches to the path or if 'required' is false. In the latter case, for multiply mode, multiplicative expressions in this variable behave as if the term was absent. Additive expressions generate an error. Conversely, if set to 'add' then additive expressions behave as if it was not there and multiplicative ones generateand error. +**reduce**$ String$ Either 'add' or 'multiply'. This applies if there are multiple matches to the path or if 'required' is false. In the latter case, for multiply mode, multiplicative expressions in this variable behave as if the term was absent. Additive expressions generate an error. Conversely, if set to 'add' then additive expressions behave as if it was not there and multiplicative ones generateand error. **exposure**$ String$ **required**$ boolean$ Set to true if it OK for this variable to be absent. See 'reduce' for what happens in this case **value**$ String$ A string defining the value of the element @@ -553,7 +553,7 @@ Please file any issues or questions at the [issue tracker here](https://github.c **edges**$ String$ The element that provides the transitions for the scheme **stateVariable**$ String$ Name of state variable in state elements **edgeSource**$ String$ The name of the attribute in the rate element that defines the source of the transition -**edgeTarget**$ String$ Attribute tha defines the target +**edgeTarget**$ String$ Attribute that defines the target **forwardRate**$ String$ Name of forward rate exposure **reverseRate**$ String$ Name of reverse rate exposure From a23aae2fc3215f54fb0339a72d4da9016fe342a0 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 30 Sep 2024 21:11:33 -0400 Subject: [PATCH 6/6] Just ignore those few childs and childrens --- .codespellrc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.codespellrc b/.codespellrc index 12d19e31..29eaffbb 100644 --- a/.codespellrc +++ b/.codespellrc @@ -3,4 +3,4 @@ skip = .git*,*.pdf,*.svg,*.css,.codespellrc check-hidden = true ignore-regex = ^\s*"image/\S+": ".*|\b[a-z]*[A-Z][a-zA-Z]*\b -# ignore-words-list = +ignore-words-list = childrens,childs