From 9b71836faa06e254e8399744e0a852115e303676 Mon Sep 17 00:00:00 2001 From: Brian Drawert Date: Wed, 9 Mar 2022 10:20:22 -0800 Subject: [PATCH 1/2] more readme cleanup --- README.md | 7 +++++-- RELEASE_NOTES | 17 ----------------- 2 files changed, 5 insertions(+), 19 deletions(-) delete mode 100644 RELEASE_NOTES 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 From 39cb7f634f3950dfdcbdd20b6034a47389ac4811 Mon Sep 17 00:00:00 2001 From: Brian Drawert Date: Wed, 9 Mar 2022 10:26:15 -0800 Subject: [PATCH 2/2] Trying to re-enable the Docker environment, image does not work --- Dockerfile | 23 +++++++++++++++++++++++ README.md | 30 +++++++++++++----------------- 2 files changed, 36 insertions(+), 17 deletions(-) create mode 100644 Dockerfile diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 00000000..993f4c1d --- /dev/null +++ b/Dockerfile @@ -0,0 +1,23 @@ +FROM jupyter/minimal-notebook:latest + +USER root + +RUN apt-get update && apt-get install -y libgl1-mesa-glx gdb + +RUN apt-get install -y libtiff5-dev libjpeg8-dev libopenjp2-7-dev zlib1g-dev \ + libfreetype6-dev liblcms2-dev libwebp-dev tcl8.6-dev tk8.6-dev python3-tk \ + libharfbuzz-dev libfribidi-dev libxcb1-dev + +RUN apt-get -o Dpkg::Options::="--force-confmiss" install --reinstall netbase + +USER jovyan + +RUN python3 -m pip install gdbgui matplotlib coverage + +WORKDIR /home/jovyan + +COPY --chown=jovyan:users ./requirements.txt ./requirements.txt + +RUN pip install -r ./requirements.txt + +CMD start-notebook.sh diff --git a/README.md b/README.md index 2e6a4d93..67fce685 100644 --- a/README.md +++ b/README.md @@ -25,13 +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) + - [_Debugging_](#debugging) + - [_Profiling_](#profiling) - [License](#license) - [Authors and history](#authors-and-history) - [Acknowledgments](#acknowledgments) @@ -74,7 +72,6 @@ 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. - Getting help ------------ @@ -124,6 +110,16 @@ New developments happen primarily in the [`develop`](https://github.com/StochSS/ |:---------------:|:--------------:| | [![Build Status](https://github.com/StochSS/SpatialPy/actions/workflows/run-tests.yml/badge.svg)](https://github.com/StochSS/SpatialPy/actions/workflows/run-tests.yml) | [![Build Status](https://github.com/StochSS/SpatialPy/actions/workflows/run-tests.yml/badge.svg?branch=develop)](https://github.com/StochSS/SpatialPy/actions/workflows/run-tests.yml) +### Debugging + +In order to compile the solver binary for use by the debugger, run `solver.compile()` with `debug=True`. This will inject the `-g` flag into the `gcc` command that compiles the solver, enabling gdb debug information. + +You can invoke `solver.run_debugger()` anytime after you instantiate a solver in Python to start up a new session of gdbgui. The debugger will be available at http://127.0.0.1:5000. + + +### Profiling + +To enable profiling, both `solver.compile()` and `solver.run()` need to be invoked with `profile=True`. If you don't run `solver.compile()` explicitly, invoking `solver.run()` with `profile=True` will run `compile()` correctly for you. License -------