updating

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+max-line-length = 150
+exclude =
+    tests/*
+    docs/*

.gitignore

@@ -1,11 +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 +51,39 @@ coverage html
 
 ## Documentation convention
 
-BioSimulators-BioNetGen 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-BioNetGen 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
-
-Contact the [BioSimulators Team](mailto:info@biosimulators.org) to request release and deployment of new changes. 
+## Releasing new versions
+
+To release changes, contact the [lead developers](mailto:info@biosimulators.org) to request their release.
+
+Below are instructions for releasing a new version:
+
+1. Make the required changes to the repository.
+  * To update the version of the underyling simulator, update its version numbers in the following files:
+    * `requirements.txt`
+    * `Dockerfile`
+    * `biosimulators.json`
+2. Commit the changes to this repository.
+3. Increment the `__version__` variable in `biosimulators_bionetgen/_version.py`.
+4. Commit this change to `biosimulators_bionetgen/_version.py`.
+5. Add a tag for the new version by running `git tag { version }`. `version` should be equal to the value of the
+   `__version__` variable in `biosimulators_bionetgen/_version.py`.
+6. Push these commits and the new tag to GitHub by running `git push && git push --tags`.
+7. This push will trigger a GitHub action which will execute the following tasks:
+   * Create a GitHub release for the version.
+   * Push the release to PyPI.
+   * Compile the documentation and push the compiled documentation to the repository so that the new documentation is viewable at github.io.
 
 ## Reporting issues
 

Dockerfile

@@ -22,12 +22,13 @@
 
 FROM continuumio/miniconda3:4.8.2
 
-ARG VERSION=2.5.1
+ARG VERSION="0.0.1"
+ARG SIMULATOR_VERSION=2.5.1
 
 # metadata
 LABEL \
     org.opencontainers.image.title="BioNetGen" \
-    org.opencontainers.image.version="${VERSION}" \
+    org.opencontainers.image.version="${SIMULATOR_VERSION}" \
     org.opencontainers.image.description="Open-source software package for rule-based modeling of complex biochemical systems" \
     org.opencontainers.image.url="https://bionetgen.org/" \
     org.opencontainers.image.documentation="https://bionetgen.org/" \
@@ -37,9 +38,9 @@ LABEL \
     org.opencontainers.image.licenses="MIT" \
     \
     base_image="continuumio/miniconda3:4.8.2" \
-    version="0.0.1" \
+    version="${VERSION}" \
     software="BioNetGen" \
-    software.version="${VERSION}" \
+    software.version="${SIMULATOR_VERSION}" \
     about.summary="Open-source software package for rule-based modeling of complex biochemical systems" \
     about.home="https://bionetgen.org/" \
     about.documentation="https://bionetgen.org/" \
@@ -66,7 +67,7 @@ RUN apt-get update -y \
         perl \
         vim \
     \
-    && git clone https://github.com/RuleWorld/bionetgen.git --branch BioNetGen-${VERSION} --depth 1 /root/bionetgen \
+    && git clone https://github.com/RuleWorld/bionetgen.git --branch BioNetGen-${SIMULATOR_VERSION} --depth 1 /root/bionetgen \
     && cd /root/bionetgen \
     && git submodule init \
     && git submodule update \

README.md

@@ -1,9 +1,7 @@
-![Latest version](https://img.shields.io/github/v/tag/biosimulators/Biosimulators_BioNetGen)
+[![Latest release](https://img.shields.io/github/v/tag/biosimulators/Biosimulators_BioNetGen)](https://github.com/biosimulations/Biosimulators_BioNetGen/releases)
 [![PyPI](https://img.shields.io/pypi/v/biosimulators_bionetgen)](https://pypi.org/project/biosimulators_bionetgen/)
-[![GitHub Workflow Status](https://img.shields.io/github/workflow/status/biosimulators/Biosimulators_BioNetGen/workflow-id)](https://github.com/biosimulators/Biosimulators_BioNetGen/actions?query=workflow%3Aworkflow-id)
-[![Documentation](https://img.shields.io/github/license/biosimulators/Biosimulators_BioNetGen?badges-awesome-green.svg)](https://biosimulators.github.io/Biosimulators_BioNetGen/)
-[![Issues](https://img.shields.io/github/issues/biosimulators/Biosimulators_BioNetGen)](https://github.com/biosimulators/Biosimulators_BioNetGen/issues)
-[![License](https://img.shields.io/github/license/biosimulators/Biosimulators_BioNetGen?badges-awesome-green.svg)](https://github.com/biosimulators/Biosimulators_BioNetGen/blob/dev/LICENSE)
+[![CI status](https://github.com/biosimulators/Biosimulators_BioNetGen/workflows/Continuous%20integration/badge.svg)](https://github.com/biosimulators/Biosimulators_BioNetGen/actions?query=workflow%3A%22Continuous+integration%22)
+[![Test coverage](https://codecov.io/gh/biosimulators/Biosimulators_BioNetGen/branch/dev/graph/badge.svg)](https://codecov.io/gh/biosimulators/Biosimulators_BioNetGen)
 
 # BioSimulators-BioNetGen
 BioSimulators-compliant command-line interface and Docker image for the [BioNetGen](https://bionetgen.org/) simulation program.

biosimulators_bionetgen/__init__.py

@@ -1,4 +1,4 @@
 from ._version import __version__  # noqa: F401
 # :obj:`str`: version
 
-from .core import exec_combine_archive  # noqa: F401
+from .core import exec_sedml_docs_in_combine_archive  # noqa: F401

biosimulators_bionetgen/__main__.py

@@ -6,46 +6,14 @@
 :License: MIT
 """
 
-from .core import exec_combine_archive
-import biosimulators_bionetgen
-import cement
-
-
-class BaseController(cement.Controller):
-    """ Base controller for command line application """
-
-    class Meta:
-        label = 'base'
-        description = "BioSimulators-compliant command-line interface to the BioNetGen simulation program <https://bionetgen.org>."
-        help = "bionetgen"
-        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_bionetgen.__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 = 'bionetgen'
-        base_controller = 'base'
-        handlers = [
-            BaseController,
-        ]
+from ._version import __version__
+from .core import get_bionetgen_version, exec_sedml_docs_in_combine_archive
+from biosimulators_utils.simulator.cli import build_cli
+import subprocess
+
+App = build_cli('bionetgen', __version__,
+                'BioNetGen', get_bionetgen_version(), 'https://bionetgen.org',
+                exec_sedml_docs_in_combine_archive)
 
 
 def main():

biosimulators_bionetgen/core.py

@@ -7,31 +7,42 @@
 :License: MIT
 """
 
-from Biosimulations_utils.biomodel.data_model import BiomodelVariable  # noqa: F401
-from Biosimulations_utils.simulation.data_model import TimecourseSimulation, SimulationResultsFormat
-from Biosimulations_utils.simulator.utils import exec_simulations_in_archive
+from biosimulations_utils.biomodel.data_model import BiomodelVariable  # noqa: F401
+from biosimulators_utils import TimecourseSimulation, TimecourseSimulationexec_sed_tasks_in_combine_archive
 import os
 import pandas
 import re
 import shutil
 import subprocess
 import tempfile
 
-__all__ = ['exec_combine_archive', 'BioNetGenSimulationRunner']
+__all__ = ['get_bionetgen_version', 'exec_sedml_docs_in_combine_archive', 'BioNetGenSimulationRunner']
 
 
-def exec_combine_archive(archive_file, out_dir):
+BIONETGEN_PATH = os.getenv(BIONETGEN_PATH, 'BNG2.pl')
+
+
+def get_bionetgen_version():
+    """ Get the version of BioNetGen 
+
+    Returns:
+        :obj:`str`: version
+    """
+    return subprocess.check_output([BIONETGEN_PATH, '--version']).decode().strip().split(' ')[2]
+
+
+def exec_sedml_docs_in_combine_archive(archive_file, out_dir):
     """ Execute the SED tasks defined in a COMBINE archive and save the outputs
 
     Args:
         archive_file (:obj:`str`): path to COMBINE archive
         out_dir (:obj:`str`): directory to store the outputs of the tasks
     """
-    exec_simulations_in_archive(archive_file, BioNetGenSimulationRunner().run, out_dir)
+    exec_sed_tasks_in_combine_archive(archive_file, BioNetGenSimulationRunner().run, out_dir)
 
 
 class BioNetGenSimulationRunner(object):
-    def run(self, model_filename, model_sed_urn, simulation, working_dir, out_filename, out_format):
+    def run(self, model_filename, model_sed_urn, simulation, working_dir, out_filename):
         """ Execute a simulation and save its results
 
         Args:
@@ -40,7 +51,6 @@ def run(self, model_filename, model_sed_urn, simulation, working_dir, out_filena
            simulation (:obj:`TimecourseSimulation`): simulation
            working_dir (:obj:`str`): directory of the SED-ML file
            out_filename (:obj:`str`): path to save the results of the simulation
-           out_format (:obj:`SimulationResultsFormat`): format to save the results of the simulation (e.g., `HDF5`)
         """
         # check that model is encoded in BGNL
         if model_sed_urn != "urn:sedml:language:bngl":
@@ -50,10 +60,6 @@ def run(self, model_filename, model_sed_urn, simulation, working_dir, out_filena
         if not isinstance(simulation, TimecourseSimulation):
             raise NotImplementedError('{} is not supported'.format(simulation.__class__.__name__))
 
-        # check that the desired output format is supported
-        if out_format != SimulationResultsFormat.HDF5:
-            raise NotImplementedError("Simulation results format '{}' is not supported".format(out_format))
-
         # read the model from the BNGL file
         model_lines = self.read_model(model_filename, model_sed_urn)
 
@@ -70,11 +76,11 @@ def run(self, model_filename, model_sed_urn, simulation, working_dir, out_filena
         out_dir = tempfile.mkdtemp()
 
         # simulate the modified model
-        subprocess.check_call(['BNG2.pl', modified_model_filename, '--outdir', out_dir])
+        subprocess.check_call([BIONETGEN_PATH, modified_model_filename, '--outdir', out_dir])
 
         # put files into output path
         gdat_results_filename = os.path.join(out_dir, os.path.splitext(os.path.basename(modified_model_filename))[0] + '.gdat')
-        self.convert_simulation_results(gdat_results_filename, out_filename, out_format)
+        self.convert_simulation_results(gdat_results_filename, out_filename)
 
         # cleanup temporary files
         os.remove(modified_model_filename)
@@ -348,24 +354,17 @@ def replace_model_block(self, model_lines, i_old_block_start, i_old_block_end, n
             + new_block_lines \
             + model_lines[i_old_block_end:]
 
-    def convert_simulation_results(self, gdat_filename, out_filename, out_format):
+    def convert_simulation_results(self, gdat_filename, out_filename):
         """ Convert simulation results from gdat to the desired output format
 
         Args:
             gdat_filename (:obj:`str`): path to simulation results in gdat format
             out_filename (:obj:`str`): path to save the results of the simulation
-            out_format (:obj:`str`): format to save the results of the simulation (e.g., `csv`)
 
         Raises:
             :obj:`NotImplementedError`: if the desired output format is not supported
         """
         data = self.read_simulation_results(gdat_filename)
-        if out_format == 'csv':
-            data.to_csv(out_filename)
-        elif out_format == 'tsv':
-            data.to_csv(out_filename, sep='\t')
-        else:
-            raise NotImplementedError('Unsupported output format {}'.format(out_format))
 
     def read_simulation_results(self, gdat_filename):
         """ Read the results of a simulation

docs-src/about.rst

@@ -3,7 +3,7 @@ About BioSimulators-BioNetGen
 
 License
 -------
-This package is released under the `MIT License <https://github.com/biosimulators/BioSimulators_BioNetGen/blob/dev/LICENSE>`_. BioNetGen is released under the `MIT License <https://github.com/RuleWorld/bionetgen/blob/master/LICENSE>`_.
+This package is released under the `MIT License <https://github.com/biosimulators/Biosimulators_BioNetGen/blob/dev/LICENSE>`_. BioNetGen is released under the `MIT License <https://github.com/RuleWorld/bionetgen/blob/master/LICENSE>`_.
 
 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_BioNetGen/blob/dev/'
+source_base_url = 'https://github.com/biosimulators/Biosimulators_BioNetGen/blob/dev/'
 project = 'BioSimulators-BioNetGen'
 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_BioNetGen',
+    'github_repo': 'Biosimulators_BioNetGen',
     'github_banner': True,
     'github_button': True,
     'description': 'BioSimulators-compliant interface to BioNetGen',

docs-src/installation.rst

@@ -1,7 +1,7 @@
 Installation instructions
 =========================
 
-BioSimulators-BioNetGen is available as command-line program and as a command-line program encapsulated into a Docker image.
+BioSimulators-BioNetGen 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-BioNetGen is available as command-line program and as a command-line program encapsulated into a Docker image.
+BioSimulators-BioNetGen 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]
-Biosimulations_utils[docker]
+biosimulations_utils[docker]
 docker

requirements.txt

@@ -1,3 +1,2 @@
-Biosimulations_utils
-cement
+biosimulations_utils
 pandas

tests/test_all.py

@@ -10,7 +10,7 @@
 from biosimulators_bionetgen import __main__
 from unittest import mock
 try:
-    from Biosimulations_utils.simulator.testing import SimulatorValidator
+    from biosimulations_utils.simulator.testing import SimulatorValidator
 except ModuleNotFoundError:
     pass
 import biosimulators_bionetgen