correcting capitalization of pyNeuroML

Author: jonrkarr

CONTRIBUTING.md

@@ -1,6 +1,6 @@
-# Contributing to `BioSimulators-PyNeuroML`
+# Contributing to `BioSimulators-pyNeuroML`
 
-We enthusiastically welcome contributions to BioSimulators-PyNeuroML!
+We enthusiastically welcome contributions to BioSimulators-pyNeuroML!
 
 ## Coordinating contributions
 
@@ -11,30 +11,30 @@ Before getting started, please contact the lead developers at [info@biosimulator
 The repository follows standard Python conventions:
 
 * `README.md`: Overview of the repository
-* `biosimulators_pyneuroml/`: Python code for a BioSimulators-compliant command-line interface to PyNeuroML
+* `biosimulators_pyneuroml/`: Python code for a BioSimulators-compliant command-line interface to pyNeuroML
 * `tests/`: unit tests for the command-line interface
 * `setup.py`: installation script for the command-line interface
 * `setup.cfg`: configuration for the installation of the command-line interface
 * `requirements.txt`: dependencies for the command-line interface
 * `requirements.optional.txt`: optional dependencies for the command-line interface
 * `MANIFEST.in`: a list of files to include in the package for the command-line interface
 * `LICENSE`: License
-* `CONTRIBUTING.md`: Guide to contributing to BioSimulators-PyNeuroML (this document)
-* `CODE_OF_CONDUCT.md`: Code of conduct for developers of BioSimulators-PyNeuroML
+* `CONTRIBUTING.md`: Guide to contributing to BioSimulators-pyNeuroML (this document)
+* `CODE_OF_CONDUCT.md`: Code of conduct for developers of BioSimulators-pyNeuroML
 
 ## Coding convention
 
-BioSimulators-PyNeuroML follows standard Python style conventions:
+BioSimulators-pyNeuroML follows standard Python style conventions:
 
 * Class names: `UpperCamelCase`
 * Function names: `lower_snake_case`
 * Variable names: `lower_snake_case`
 
 ## Testing and continuous integration
 
-We strive to have complete test coverage for BioSimulators-PyNeuroML.
+We strive to have complete test coverage for BioSimulators-pyNeuroML.
 
-The unit tests for BioSimulators-PyNeuroML are located in the `tests`  directory. The tests can be executed by running the following command:
+The unit tests for BioSimulators-pyNeuroML are located in the `tests`  directory. The tests can be executed by running the following command:
 ```
 pip install pytest
 python -m pytest tests
@@ -51,7 +51,7 @@ coverage html
 
 ## Documentation convention
 
-BioSimulators-PyNeuroML is documented using [reStructuredText](https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html) and the [napoleon Sphinx plugin](https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html). The documentation can be compiled by running the following commands:
+BioSimulators-pyNeuroML is documented using [reStructuredText](https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html) and the [napoleon Sphinx plugin](https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html). The documentation can be compiled by running the following commands:
 
 ```
 python -m pip install -r docs-src/requirements.txt
@@ -87,8 +87,8 @@ Below are instructions for releasing a new version:
 
 ## Reporting issues
 
-Please use [GitHub issues](https://github.com/biosimulators/Biosimulators_PyNeuroML/issues) to report any issues to the development community.
+Please use [GitHub issues](https://github.com/biosimulators/Biosimulators_pyNeuroML/issues) to report any issues to the development community.
 
 ## Getting help
 
-Please use [GitHub issues](https://github.com/biosimulators/Biosimulators_PyNeuroML/issues) to post questions or contact the lead developers at [[email protected]](mailto:[email protected]).
+Please use [GitHub issues](https://github.com/biosimulators/Biosimulators_pyNeuroML/issues) to post questions or contact the lead developers at [[email protected]](mailto:[email protected]).

Dockerfile

@@ -6,12 +6,12 @@ ARG SIMULATOR_VERSION="0.5.11"
 
 # metadata
 LABEL \
-    org.opencontainers.image.title="PyNeuroML" \
+    org.opencontainers.image.title="pyNeuroML" \
     org.opencontainers.image.version="${SIMULATOR_VERSION}" \
     org.opencontainers.image.description="Python package for reading, writing, simulating and analysing NeuroML2/LEMS models" \
     org.opencontainers.image.url="https://github.com/NeuroML/pyNeuroML" \
     org.opencontainers.image.documentation="https://github.com/NeuroML/pyNeuroML/" \
-    org.opencontainers.image.source="https://github.com/biosimulators/Biosimulators_PyNeuroML" \
+    org.opencontainers.image.source="https://github.com/biosimulators/Biosimulators_pyNeuroML" \
     org.opencontainers.image.authors="BioSimulators Team <[email protected]>" \
     org.opencontainers.image.vendor="BioSimulators Team" \
     org.opencontainers.image.licenses="LGPL-3.0-only" \
@@ -36,9 +36,9 @@ RUN apt-get update -y \
     && rm -rf /var/lib/apt/lists/*
 
 # Copy code for command-line interface into image and install it
-COPY . /root/Biosimulators_PyNeuroML
-RUN pip install /root/Biosimulators_PyNeuroML \
-    && rm -rf /root/Biosimulators_PyNeuroML
+COPY . /root/Biosimulators_pyNeuroML
+RUN pip install /root/Biosimulators_pyNeuroML \
+    && rm -rf /root/Biosimulators_pyNeuroML
 RUN pip install "pyneuroml==${SIMULATOR_VERSION}"
 ENV VERBOSE=0 \
     MPLBACKEND=PDF

README.md

@@ -1,16 +1,16 @@
-[![Latest release](https://img.shields.io/github/v/tag/biosimulators/Biosimulators_PyNeuroML)](https://github.com/biosimulations/Biosimulators_PyNeuroML/releases)
+[![Latest release](https://img.shields.io/github/v/tag/biosimulators/Biosimulators_pyNeuroML)](https://github.com/biosimulations/Biosimulators_pyNeuroML/releases)
 [![PyPI](https://img.shields.io/pypi/v/biosimulators_pyneuroml)](https://pypi.org/project/biosimulators_pyneuroml/)
-[![CI status](https://github.com/biosimulators/Biosimulators_PyNeuroML/workflows/Continuous%20integration/badge.svg)](https://github.com/biosimulators/Biosimulators_PyNeuroML/actions?query=workflow%3A%22Continuous+integration%22)
-[![Test coverage](https://codecov.io/gh/biosimulators/Biosimulators_PyNeuroML/branch/dev/graph/badge.svg)](https://codecov.io/gh/biosimulators/Biosimulators_PyNeuroML)
+[![CI status](https://github.com/biosimulators/Biosimulators_pyNeuroML/workflows/Continuous%20integration/badge.svg)](https://github.com/biosimulators/Biosimulators_pyNeuroML/actions?query=workflow%3A%22Continuous+integration%22)
+[![Test coverage](https://codecov.io/gh/biosimulators/Biosimulators_pyNeuroML/branch/dev/graph/badge.svg)](https://codecov.io/gh/biosimulators/Biosimulators_pyNeuroML)
 
-# BioSimulators-PyNeuroML
-BioSimulators-compliant command-line interface and Docker image for the [PyNeuroML](https://github.com/NeuroML/pyNeuroML) simulation program.
+# BioSimulators-pyNeuroML
+BioSimulators-compliant command-line interface and Docker image for the [pyNeuroML](https://github.com/NeuroML/pyNeuroML) simulation program.
 
-This command-line interface and Docker image enable users to use PyNeuroML to execute [COMBINE/OMEX archives](https://combinearchive.org/) that describe one or more simulation experiments (in [SED-ML format](https://sed-ml.org)) of one or more models (in [NeuroML format](https://neuroml.org/])).
+This command-line interface and Docker image enable users to use pyNeuroML to execute [COMBINE/OMEX archives](https://combinearchive.org/) that describe one or more simulation experiments (in [SED-ML format](https://sed-ml.org)) of one or more models (in [NeuroML format](https://neuroml.org/])).
 
-A list of the algorithms and algorithm parameters supported by PyNeuroML is available at [BioSimulators](https://biosimulators.org/simulators/pyneuroml).
+A list of the algorithms and algorithm parameters supported by pyNeuroML is available at [BioSimulators](https://biosimulators.org/simulators/pyneuroml).
 
-A simple web application and web service for using PyNeuroML to execute COMBINE/OMEX archives is also available at [runBioSimulations](https://run.biosimulations.org).
+A simple web application and web service for using pyNeuroML to execute COMBINE/OMEX archives is also available at [runBioSimulations](https://run.biosimulations.org).
 
 ## Installation
 
@@ -33,7 +33,7 @@ docker pull ghcr.io/biosimulators/pyneuroml
 ```
 usage: pyneuroml [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
 
-BioSimulators-compliant command-line interface to the PyNeuroML <https://github.com/NeuroML/pyNeuroML> simulation program.
+BioSimulators-compliant command-line interface to the pyNeuroML <https://github.com/NeuroML/pyNeuroML> simulation program.
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -64,7 +64,7 @@ docker run \
 ```
 
 ## Documentation
-Documentation is available at https://biosimulators.github.io/Biosimulators_PyNeuroML/.
+Documentation is available at https://biosimulators.github.io/Biosimulators_pyNeuroML/.
 
 ## License
 This package is released under the [MIT](LICENSE).

biosimulators_pyneuroml/__main__.py

@@ -1,4 +1,4 @@
-""" BioSimulators-compliant command-line interface to the `PyNeuroML <https://github.com/NeuroML/pyNeuroML>`_ simulation program.
+""" BioSimulators-compliant command-line interface to the `pyNeuroML <https://github.com/NeuroML/pyNeuroML>`_ simulation program.
 
 :Author: Jonathan Karr <[email protected]>
 :Date: 2021-05-28
@@ -12,7 +12,7 @@
 import pyneuroml
 
 App = build_cli('pyneuroml', __version__,
-                'PyNeuroML', pyneuroml.__version__, 'https://github.com/NeuroML/pyNeuroML',
+                'pyNeuroML', pyneuroml.__version__, 'https://github.com/NeuroML/pyNeuroML',
                 exec_sedml_docs_in_combine_archive)
 
 

biosimulators_pyneuroml/core.py

@@ -1,4 +1,4 @@
-""" Methods for using PyNeuroML to execute SED tasks in COMBINE archives and save their outputs
+""" Methods for using pyNeuroML to execute SED tasks in COMBINE archives and save their outputs
 
 :Author: Jonathan Karr <[email protected]>
 :Date: 2021-05-28
@@ -157,7 +157,7 @@ def exec_sed_task(task, variables, log=None):
                     ])
                     warn(msg, BioSimulatorsWarning)
 
-    # Validate that start time is 0 because this is the only option that PyNeuroML supports
+    # Validate that start time is 0 because this is the only option that pyNeuroML supports
     if simulation.initial_time != 0:
         raise NotImplementedError('Initial simulation time {} is not supported. Initial time must be 0.'.format(simulation.initial_time))
 

biosimulators_pyneuroml/data_model.py

@@ -1,4 +1,4 @@
-""" Data model for PyNeuroML algorithms and their parameters
+""" Data model for pyNeuroML algorithms and their parameters
 
 :Author: Jonathan Karr <[email protected]>
 :Date: 2021-05-28

setup.py

@@ -26,10 +26,10 @@
     name=name,
     version=md.version,
     description=("BioSimulators-compliant command-line interface to "
-                 "the PyNeuroML simulation program."),
+                 "the pyNeuroML simulation program."),
     long_description=md.long_description,
-    url="https://github.com/biosimulators/Biosimulators_PyNeuroML",
-    download_url="https://github.com/biosimulators/Biosimulators_PyNeuroML",
+    url="https://github.com/biosimulators/Biosimulators_pyNeuroML",
+    download_url="https://github.com/biosimulators/Biosimulators_pyNeuroML",
     author='BioSimulators Team',
     author_email="[email protected]",
     license="MIT",