updating

.gitignore

@@ -1,9 +1,22 @@
-*.pyc
-_pycache__/
+# compiled Python files
 *.egg-info/
+__pycache__/
+*.pyc
+dist/
+build/
 
+# test results
 tests/results/
 
+# coverage files
+htmlcov/
+.coverage
+coverage.xml
+
+# compiled documentation
+README.rst
+docs/objects.inv
+docs/.buildinfo
 docs/.doctrees/
 docs/_raw_sources/
 docs/_sources/

CONTRIBUTING.md

@@ -51,15 +51,21 @@ coverage html
 
 ## Documentation convention
 
-BioSimulators-tellurium 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).
+BioSimulators-tellurium 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
+sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
+sphinx-build docs-src docs
+```
 
 ## Submitting changes   
 
 Please use GitHub pull requests to submit changes. Each request should include a brief description of the new and/or modified features.
 
-## Releasing and deploying new versions
+## Releasing new versions
 
-Contact the [BioSimulators Team](mailto:[email protected]) to request release and deployment of new changes. 
+Contact the [BioSimulators Team](mailto:[email protected]) to request release of new changes. 
 
 ## Reporting issues
 

Dockerfile

@@ -33,7 +33,7 @@ LABEL \
     about.summary="Python-based environment for model building, simulation, and analysis that facilitates reproducibility of models in systems and synthetic biology" \
     about.home="http://tellurium.analogmachine.org/" \
     about.documentation="https://tellurium.readthedocs.io/" \
-    about.license_file="https://github.com/sys-bio/tellurium/blob/master/LICENSE.txt" \
+    about.license_file="https://github.com/sys-bio/tellurium/blob/develop/LICENSE.txt" \
     about.license="SPDX:Apache-2.0" \
     about.tags="kinetic modeling,dynamical simulation,systems biology,biochemical networks,SBML,SED-ML,COMBINE,OMEX,BioSimulators" \
     maintainer="BioSimulators Team <[email protected]>"

README.md

@@ -1,9 +1,7 @@
-![Latest version](https://img.shields.io/github/v/tag/biosimulators/Biosimulators_tellurium)
+[![Latest release](https://img.shields.io/github/v/tag/biosimulators/Biosimulators_tellurium)](https://github.com/biosimulations/Biosimulators_tellurium/releases)
 [![PyPI](https://img.shields.io/pypi/v/biosimulators_tellurium)](https://pypi.org/project/biosimulators_tellurium/)
-[![GitHub Workflow Status](https://img.shields.io/github/workflow/status/biosimulators/Biosimulators_tellurium/workflow-id)](https://github.com/biosimulators/Biosimulators_tellurium/actions?query=workflow%3Aworkflow-id)
-[![Documentation](https://img.shields.io/github/license/biosimulators/Biosimulators_tellurium?badges-awesome-green.svg)](https://biosimulators.github.io/Biosimulators_tellurium/)
-[![Issues](https://img.shields.io/github/issues/biosimulators/Biosimulators_tellurium)](https://github.com/biosimulators/Biosimulators_tellurium/issues)
-[![License](https://img.shields.io/github/license/biosimulators/Biosimulators_tellurium?badges-awesome-green.svg)](https://github.com/biosimulators/Biosimulators_tellurium/blob/dev/LICENSE)
+[![CI status](https://img.shields.io/github/workflow/status/biosimulators/Biosimulators_tellurium/workflow-id)](https://github.com/biosimulators/Biosimulators_tellurium/actions?query=workflow%3Aworkflow-id)
+[![Test coverage](https://codecov.io/gh/biosimulators/Biosimulators_tellurium/branch/dev/graph/badge.svg)](https://codecov.io/gh/biosimulators/Biosimulators_tellurium)
 
 # BioSimulators-tellurium
 BioSimulators-compliant command-line interface and Docker image for the [tellurium](http://tellurium.analogmachine.org/) simulation program.

biosimulators_tellurium/__main__.py

@@ -6,47 +6,14 @@
 :License: MIT
 """
 
+from ._version import __version__
 from .core import exec_combine_archive
-import biosimulators_tellurium
-import cement
+from biosimulators_utils.simulator.cli import build_cli
+import tellurium
 
-
-class BaseController(cement.Controller):
-    """ Base controller for command line application """
-
-    class Meta:
-        label = 'base'
-        description = ("BioSimulators-compliant command-line interface to the "
-                       "tellurium simulation program <http://tellurium.analogmachine.org>.")
-        help = "tellurium"
-        arguments = [
-            (['-i', '--archive'], dict(type=str,
-                                       required=True,
-                                       help='Path to OMEX file which contains one or more SED-ML-encoded simulation experiments')),
-            (['-o', '--out-dir'], dict(type=str,
-                                       default='.',
-                                       help='Directory to save outputs')),
-            (['-v', '--version'], dict(action='version',
-                                       version=biosimulators_tellurium.__version__)),
-        ]
-
-    @cement.ex(hide=True)
-    def _default(self):
-        args = self.app.pargs
-        try:
-            exec_combine_archive(args.archive, args.out_dir)
-        except Exception as exception:
-            raise SystemExit(str(exception)) from exception
-
-
-class App(cement.App):
-    """ Command line application """
-    class Meta:
-        label = 'tellurium'
-        base_controller = 'base'
-        handlers = [
-            BaseController,
-        ]
+App = build_cli('tellurium', __version__,
+                'tellurium', tellurium.__version__, 'http://tellurium.analogmachine.org',
+                exec_combine_archive)
 
 
 def main():

docs-src/about.rst

@@ -3,7 +3,7 @@ About BioSimulators-tellurium
 
 License
 -------
-This package is released under the `MIT License <https://github.com/biosimulators/BioSimulators_tellurium/blob/dev/LICENSE>`_. tellurium is released under the `Apache 2.0 License <https://github.com/sys-bio/tellurium/blob/develop/LICENSE.txt>`_.
+This package is released under the `MIT License <https://github.com/biosimulators/Biosimulators_tellurium/blob/dev/LICENSE>`_. tellurium is released under the `Apache 2.0 License <https://github.com/sys-bio/tellurium/blob/develop/LICENSE.txt>`_.
 
 Development team
 ----------------

docs-src/conf.py

@@ -18,7 +18,7 @@
 sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
 
 # -- Project information -----------------------------------------------------
-source_base_url = 'https://github.com/biosimulators/BioSimulators_tellurium/blob/dev/'
+source_base_url = 'https://github.com/biosimulators/Biosimulators_tellurium/blob/dev/'
 project = 'BioSimulators-tellurium'
 copyright = '{}, BioSimulators Team'.format(datetime.datetime.now().year)
 author = 'BioSimulators Team'
@@ -103,7 +103,7 @@ def linkcode_resolve(domain, info):
 
 html_theme_options = {
     'github_user': 'biosimulators',
-    'github_repo': 'BioSimulators_tellurium',
+    'github_repo': 'Biosimulators_tellurium',
     'github_banner': True,
     'github_button': True,
     'description': 'BioSimulators-compliant interface to tellurium',

docs-src/installation.rst

@@ -1,7 +1,7 @@
 Installation instructions
 =========================
 
-BioSimulators-tellurium is available as command-line program and as a command-line program encapsulated into a Docker image.
+BioSimulators-tellurium is available as a command-line program and as a command-line program encapsulated into a Docker image.
 
 Command-line program
 --------------------

docs-src/tutorial.rst

@@ -1,7 +1,7 @@
 Tutorial
 ========
 
-BioSimulators-tellurium is available as command-line program and as a command-line program encapsulated into a Docker image.
+BioSimulators-tellurium is available as a command-line program and as a command-line program encapsulated into a Docker image.
 
 
 Creating COMBINE/OMEX archives and encoding simulation experiments into SED-ML

requirements.optional.txt

@@ -1,3 +1,3 @@
 [test-docker]
 docker
-Biosimulations_utils[docker]
+biosimulations_utils[docker]

requirements.txt

@@ -1,4 +1,3 @@
-cement
 matplotlib
 python_libcombine
 tellurium

tests/test_all.py

@@ -7,7 +7,7 @@
 """
 
 try:
-    from Biosimulations_utils.simulator.testing import SimulatorValidator
+    from biosimulations_utils.simulator.testing import SimulatorValidator
 except ModuleNotFoundError:
     pass
 from biosimulators_tellurium import __main__