diff --git a/.github/workflows/run-unit-tests.yml b/.github/workflows/run-unit-tests.yml index cabdc656..6f6c939d 100644 --- a/.github/workflows/run-unit-tests.yml +++ b/.github/workflows/run-unit-tests.yml @@ -23,6 +23,8 @@ jobs: python3 -m pip install --upgrade pip python3 -m pip install -r requirements.txt python3 -m pip install coverage + python3 -m pip install nbformat + python3 -m pip install nbconvert - name: Run tests run: coverage run test/run_unit_tests.py diff --git a/README.md b/README.md index 2cf28137..2e6a4d93 100644 --- a/README.md +++ b/README.md @@ -25,9 +25,11 @@ Table of contents - [_Using the source code repository_](#using-the-source-code-repository) - [Usage](#usage) - [_Simple example to illustrate the use of SpatialPy_](#simple-example-to-illustrate-the-use-of-spatialpy) + - [Getting help](#getting-help) - [Contributing](#contributing) - [License](#license) @@ -72,8 +74,8 @@ SpatialPy provides simple object-oriented abstractions for defining a model of a The `run()` method can be customized using keyword arguments to select different solvers, random seed, data return type and more. For more detailed examples on how to use SpatialPy, please see the Jupyter notebooks contained in the [examples](https://github.com/StochSS/SpatialPy/tree/main/examples) subdirectory. - -### Docker environment + Getting help ------------ diff --git a/RELEASE_NOTES b/RELEASE_NOTES deleted file mode 100644 index 718c22b1..00000000 --- a/RELEASE_NOTES +++ /dev/null @@ -1,17 +0,0 @@ - RELEASE NOTES - SpatialPy - -These are release notes for SpatialPy. ----------------------------------------- -Date: 2/25/2021 -Version: 0.5.0+beta ----------------------------------------- -- Initial beta release ----------------------------------------- -Date: 3/9/2021 -Version: 0.5.1+beta ----------------------------------------- -- Added pickling Results -- Added add_mesh() function -- timespan() now includes option to set timestep size -- Added ability to read StochSS domains diff --git a/spatialpy/__version__.py b/spatialpy/__version__.py index 22fc6782..46a5efd9 100644 --- a/spatialpy/__version__.py +++ b/spatialpy/__version__.py @@ -23,7 +23,7 @@ # @website https://github.com/StochSS/SpatialPy # ============================================================================= -__version__ = '1.0' +__version__ = '1.0.2' __title__ = 'SpatialPy' __description__ = 'Python Interface for Spatial Stochastic Biochemical Simulations' __url__ = 'https://spatialpy.github.io/SpatialPy/' diff --git a/test/run_unit_tests.py b/test/run_unit_tests.py index b35fb3f3..a99aca7a 100755 --- a/test/run_unit_tests.py +++ b/test/run_unit_tests.py @@ -33,11 +33,13 @@ import test_species import test_parameter import test_reaction + import test_notebooks modules = [ test_species, test_parameter, - test_reaction + test_reaction, + test_notebooks ] for module in modules: