style: use "pyNeuroML" and "pyLEMS" consistently

Related issue: #30

source/NeuroMLOrg/Board.md

@@ -146,7 +146,7 @@ Their main responsibilities are:
 - Preparing the core specification for the NeuroML language.
 - Testing reference implementations of NeuroML compliant applications.
 - Preparing a specification for the LEMS language.
-    This can be a subset of the language supported by the reference implementations in Java (jLEMS) and Python (PyLEMS), but will have to cover all of the LEMS elements required to specify the ComponentType definitions for NeuroML 2.
+    This can be a subset of the language supported by the reference implementations in Java (jLEMS) and Python (pyLEMS), but will have to cover all of the LEMS elements required to specify the ComponentType definitions for NeuroML 2.
 - Responding to community queries about the specification.
 - Establishing a procedure for incorporating major changes into the specification (in cooperation with the {ref}`Scientific Committee <neuromlorg:ScientificCommittee>`).
 

source/Userdocs/Software/NeuroMLlite.md

@@ -36,7 +36,7 @@ pip install neuromllite
 (neuromllite:install_fedora)=
 ### Installation on Fedora Linux
 
-On [Fedora](https://getfedora.org) Linux systems, the [NeuroFedora](https://neuro.fedoraproject.org) community provides PyNeuroML as a package in their [extras repository](https://docs.fedoraproject.org/en-US/neurofedora/copr/) and can be installed using the following commands:
+On [Fedora](https://getfedora.org) Linux systems, the [NeuroFedora](https://neuro.fedoraproject.org) community provides pyNeuroML as a package in their [extras repository](https://docs.fedoraproject.org/en-US/neurofedora/copr/) and can be installed using the following commands:
 
 ```{code-block} console
 sudo dnf copr enable @neurofedora/neurofedora-extra
@@ -132,6 +132,6 @@ You can also use any of the {ref}`communication channels of the NeuroML communit
 (neuromllite:development)=
 ## Development
 
-PyNeuroML is developed on GitHub at [https://github.com/NeuroML/NeuroMLlite](https://github.com/NeuroML/NeuroMLlite) under the [LPGL-3.0 license](https://github.com/NeuroML/NeuroMLlite/blob/master/LICENSE.lesser).
-The repository contains the complete source code along with instructions on building/installing PyNeuroML.
-Please follow the instructions there to build PyNeuroML from source.
+pyNeuroML is developed on GitHub at [https://github.com/NeuroML/NeuroMLlite](https://github.com/NeuroML/NeuroMLlite) under the [LPGL-3.0 license](https://github.com/NeuroML/NeuroMLlite/blob/master/LICENSE.lesser).
+The repository contains the complete source code along with instructions on building/installing pyNeuroML.
+Please follow the instructions there to build pyNeuroML from source.

source/Userdocs/Software/jNeuroML.md

@@ -12,9 +12,9 @@ With jNeuroML you can:
 - **Import** other languages into LEMS (e.g. SBML)
 - **Visualise** NeuroML models and simulations
 
-```{admonition} Use PyNeuroML
+```{admonition} Use pyNeuroML
 :class: dropdown
-{ref}`PyNeuroML <pyneuroml>` builds on jNeuroML and includes additional functions.
+{ref}`pyNeuroML <pyneuroml>` builds on jNeuroML and includes additional functions.
 ```
 (jneuroml:quickstart)=
 ## Quick start

source/Userdocs/Software/libNeuroML.md

@@ -2,9 +2,9 @@
 # libNeuroML
 
 libNeuroML is a Python API package for working with models specified in NeuroML version 2.
-```{admonition} Use PyNeuroML
+```{admonition} Use pyNeuroML
 :class: dropdown
-{ref}`PyNeuroML <pyneuroml>` builds on libNeuroML and includes additional functions.
+{ref}`pyNeuroML <pyneuroml>` builds on libNeuroML and includes additional functions.
 ```
 ```{admonition} Citation
 :class: dropdown

source/Userdocs/Software/PyLEMS.md → source/Userdocs/Software/pyLEMS.md

@@ -1,16 +1,16 @@
 (pylems)=
-# PyLEMS
+# pyLEMS
 
-PyLEMS is a Python package which provides an API, as well as a simulator for the [LEMS](http://lems.github.io/LEMS) language.
+pyLEMS is a Python package which provides an API, as well as a simulator for the [LEMS](http://lems.github.io/LEMS) language.
 It can also be used to run NeuroML2 models.
-```{admonition} Use PyNeuroML
+```{admonition} Use pyNeuroML
 :class: dropdown
-{ref}`PyNeuroML <pyneuroml>` builds on PyLEMS and includes additional functions.
+{ref}`pyNeuroML <pyneuroml>` builds on pyLEMS and includes additional functions.
 ```
 
 ```{admonition} Citation
 :class: dropdown
-Please cite Vella et al. ({cite}`Vella2014`) if you use PyLEMS.
+Please cite Vella et al. ({cite}`Vella2014`) if you use pyLEMS.
 ```
 
 (pylems:quickstart)=
@@ -25,30 +25,30 @@ A number of Free/Open source Integrated Development Environments (IDEs) are also
 An example list is [here](https://opensource.com/resources/python/ides).
 
 (pylems:install_with_pip)=
-### Install PyLEMS with pip
+### Install pyLEMS with pip
 ```{admonition} Tip: Use a virtual environment
 :class: tip dropdown
 
 While using Python packages, it is suggested to use a virtual environment to isolate the software you install from each other.
 Learn more about using virtual environments in Python [here](https://docs.python.org/3/tutorial/venv.html).
 ```
 
-The easiest way to install the latest version of PyLEMS is using the default Python package manager, `pip`:
+The easiest way to install the latest version of pyLEMS is using the default Python package manager, `pip`:
 ```{code-block} console
-pip install PyLEMS
+pip install pyLEMS
 ```
 (pylems:install_fedora)=
 ### Installation on Fedora Linux
 
-On [Fedora](https://getfedora.org) Linux systems, the [NeuroFedora](https://neuro.fedoraproject.org) community provides PyLEMS in the [standard Fedora repos](https://src.fedoraproject.org/rpms/python-PyLEMS) and can be installed using the following commands:
+On [Fedora](https://getfedora.org) Linux systems, the [NeuroFedora](https://neuro.fedoraproject.org) community provides pyLEMS in the [standard Fedora repos](https://src.fedoraproject.org/rpms/python-pyLEMS) and can be installed using the following commands:
 
 ```{code-block} console
-sudo dnf install python3-PyLEMS
+sudo dnf install python3-pyLEMS
 ```
 (pylems:docs)=
 ## Documentation
 
-PyLEMS provides the `pylems` command line utility that can be used to simulate LEMS files.
+pyLEMS provides the `pylems` command line utility that can be used to simulate LEMS files.
 `pylems` is self documented, and you can learn about its usage using the `-h` flag:
 
 ```{code-block} console
@@ -78,16 +78,16 @@ We suggest that you use {ref}`pyNeuroML <pyNeuroML>` where this is not required:
 pylems -I <dir of NeuroML2 install>/NeuroML2CoreTypes/  LEMS_NeuroML2_Model.xml
 ```
 
-For more information on PyLEMS, please see Vella et al. ({cite}`Vella2014`) and Cannon et al. ({cite}`Cannon2014`).
+For more information on pyLEMS, please see Vella et al. ({cite}`Vella2014`) and Cannon et al. ({cite}`Cannon2014`).
 
 (pylems:api_docs)=
 ### API documentation
 ```{admonition} TODO!
 :class: dropdown
-Generate and publish API documentation for PyLEMS.
+Generate and publish API documentation for pyLEMS.
 Issue filed: https://github.com/LEMS/pylems/issues/45
 ```
-The PyLEMS API is also self documented.
+The pyLEMS API is also self documented.
 You can use Python's in-built documentation viewer `pydoc` to view the documentation for any of the package's modules and their functions:
 
 ```{code-block} console
@@ -125,14 +125,14 @@ Most IDEs are able to show you this information as you use them in your Python s
 (pylems:gethelp)=
 ### Getting help
 
-For any questions regarding PyLEMS, please open an issue on the GitHub issue tracker [here](https://github.com/LEMS/pylems/issues).
+For any questions regarding pyLEMS, please open an issue on the GitHub issue tracker [here](https://github.com/LEMS/pylems/issues).
 Any bugs and feature requests can also be filed there.
 
 You can also use any of the {ref}`communication channels of the NeuroML community <contact>`.
 
 (pylems:development)=
 ## Development
 
-PyLEMS is developed on GitHub at [https://github.com/LEMS/pylems](https://github.com/LEMS/pylems) under the [LGPL-3.0 license](https://github.com/LEMS/pylems/blob/master/LICENSE.lesser).
-The repository contains the complete source code along with instructions on building/installing PyLEMS.
-Please follow the instructions there to build PyLEMS from source.
+pyLEMS is developed on GitHub at [https://github.com/LEMS/pylems](https://github.com/LEMS/pylems) under the [LGPL-3.0 license](https://github.com/LEMS/pylems/blob/master/LICENSE.lesser).
+The repository contains the complete source code along with instructions on building/installing pyLEMS.
+Please follow the instructions there to build pyLEMS from source.

source/Userdocs/Software/PyNeuroML.md → source/Userdocs/Software/pyNeuroML.md

@@ -1,20 +1,20 @@
 (pyneuroml)=
-# PyNeuroML
+# pyNeuroML
 
 ```{admonition} Suggested NeuroML tool
 :class: dropdown
-PyNeuroML is the suggested software tool for working with NeuroML.
-It builds on {ref}`jNeuroML <jneuroml>`, {ref}`libNeuroML <libneuroml>`, and {ref}`PyLEMS <pylems>`.
+pyNeuroML is the suggested software tool for working with NeuroML.
+It builds on {ref}`jNeuroML <jneuroml>`, {ref}`libNeuroML <libneuroml>`, and {ref}`pyLEMS <pylems>`.
 ```
 ```{admonition} Citation
 :class: dropdown
-Please cite Vella et al. ({cite}`Vella2014`) if you use PyNeuroML.
+Please cite Vella et al. ({cite}`Vella2014`) if you use pyNeuroML.
 ```
 
-PyNeuroML is a Python package that allows you to work with NeuroML models using the Python programming language.
+pyNeuroML is a Python package that allows you to work with NeuroML models using the Python programming language.
 It includes all the API functions provided by {ref}`libNeuroML <libNeuroML>` and {ref}`pyLEMS <pylems>`, and also wraps all the functions that {ref}`jNeuroML <jNeuroML>` provides, which can therefore be used from within Python itself.
 
-With PyNeuroML you can:
+With pyNeuroML you can:
 
 - **Create** NeuroML models and simulations
 - **Validate** NeuroML v1.8.1 and v2.x files
@@ -34,13 +34,13 @@ However, if you do not have Python installed on your system, please follow the o
 A number of Free/Open source Integrated Development Environments (IDEs) are also available that make working with Python (even) easier.
 An example list is [here](https://opensource.com/resources/python/ides).
 
-Since PyNeuroML wraps around jNeuroML which is written in Java, you will need a Java Runtime Environment (JRE) installed on your system.
+Since pyNeuroML wraps around jNeuroML which is written in Java, you will need a Java Runtime Environment (JRE) installed on your system.
 On most Linux systems [Free/Open source OpenJDK runtime environment](https://openjdk.java.net/) is already pre-installed.
 You can also install Oracle's proprietary Java platform from their [download page](https://www.oracle.com/java/technologies/javase-downloads.html) if you prefer.
 Please refer to your operating system's documentation to install a JRE.
 
 (pyneuroml:install_with_pip)=
-### Install PyNeuroML with pip
+### Install pyNeuroML with pip
 
 ```{admonition} Tip: Use a virtual environment
 :class: tip dropdown
@@ -49,15 +49,15 @@ While using Python packages, it is suggested to use a virtual environment to iso
 Learn more about using virtual environments in Python [here](https://docs.python.org/3/tutorial/venv.html).
 ```
 
-The easiest way to install the latest version of PyNeuroML is using the default Python package manager, `pip`:
+The easiest way to install the latest version of pyNeuroML is using the default Python package manager, `pip`:
 
 ```{code-block} console
 pip install pyneuroml
 ```
 (pyneuroml:install_fedora)=
 ### Installation on Fedora Linux
 
-On [Fedora](https://getfedora.org) Linux systems, the [NeuroFedora](https://neuro.fedoraproject.org) community provides PyNeuroML as a package in their [extras repository](https://docs.fedoraproject.org/en-US/neurofedora/copr/) and can be installed using the following commands:
+On [Fedora](https://getfedora.org) Linux systems, the [NeuroFedora](https://neuro.fedoraproject.org) community provides pyNeuroML as a package in their [extras repository](https://docs.fedoraproject.org/en-US/neurofedora/copr/) and can be installed using the following commands:
 
 ```{code-block} console
 sudo dnf copr enable @neurofedora/neurofedora-extra
@@ -66,7 +66,7 @@ sudo dnf install python3-pyneuroml
 (pyneuroml:docs)=
 ## Documentation
 
-PyNeuroML provides a set of command line utilities along with an API to use from within Python scripts:
+pyNeuroML provides a set of command line utilities along with an API to use from within Python scripts:
 
 ```{admonition} TODO!
 :class: dropdown
@@ -116,10 +116,10 @@ Shared options:
 
 ```{admonition} TODO!
 :class: dropdown
-Generate and publish API documentation for PyNeuroML.
+Generate and publish API documentation for pyNeuroML.
 Issue filed: https://github.com/NeuroML/pyNeuroML/issues/86
 ```
-The PyNeuroML API is also self documented.
+The pyNeuroML API is also self documented.
 You can use Python's in-built documentation viewer `pydoc` to view the documentation for any of the package's modules and their functions:
 ```{code-block} console
 
@@ -176,14 +176,14 @@ Most IDEs are able to show you this information as you use them in your Python s
 (pyneuroml:gethelp)=
 ### Getting help
 
-For any questions regarding PyNeuroML, please open an issue on the GitHub issue tracker [here](https://github.com/NeuroML/pyNeuroML/issues).
+For any questions regarding pyNeuroML, please open an issue on the GitHub issue tracker [here](https://github.com/NeuroML/pyNeuroML/issues).
 Any bugs and feature requests can also be filed there.
 
 You can also use any of the {ref}`communication channels of the NeuroML community <contact>`.
 
 (pyneuroml:development)=
 ## Development
 
-PyNeuroML is developed on GitHub at [https://github.com/NeuroML/pyNeuroML](https://github.com/NeuroML/pyNeuroML) under the [LPGL-3.0 license](https://github.com/NeuroML/pyNeuroML/blob/master/LICENSE.lesser).
-The repository contains the complete source code along with instructions on building/installing PyNeuroML.
-Please follow the instructions there to build PyNeuroML from source.
+pyNeuroML is developed on GitHub at [https://github.com/NeuroML/pyNeuroML](https://github.com/NeuroML/pyNeuroML) under the [LPGL-3.0 license](https://github.com/NeuroML/pyNeuroML/blob/master/LICENSE.lesser).
+The repository contains the complete source code along with instructions on building/installing pyNeuroML.
+Please follow the instructions there to build pyNeuroML from source.

source/_toc.yml

@@ -44,9 +44,9 @@
         - file: ./Userdocs/v1tov2.md
     - file: ./Userdocs/Software/Software
       sections:
-        - file: ./Userdocs/Software/PyNeuroML
+        - file: ./Userdocs/Software/pyNeuroML
         - file: ./Userdocs/Software/libNeuroML
-        - file: ./Userdocs/Software/PyLEMS
+        - file: ./Userdocs/Software/pyLEMS
         - file: ./Userdocs/Software/NeuroMLlite
         - file: ./Userdocs/Software/jNeuroML
         - file: ./Userdocs/Software/jLEMS