Merge pull request #80 from matthiaskoenig/develop

Changes for v0.1.13

Author: matthiaskoenig

.github/CONTRIBUTING.rst

@@ -0,0 +1,172 @@
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Report Bugs
+===========
+
+Report bugs at https://github.com/matthiaskoenig/sbmlsim/issues.
+
+If you are reporting a bug, please follow the template guide lines. The more
+detailed your report, the easier and thus faster we can help you.
+
+Fix Bugs
+========
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+==================
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+===================
+
+sbmlsim could always use more documentation, whether as part of the official
+documentation, in docstrings, or even on the web in blog posts, articles, and
+such.
+
+Submit Feedback
+===============
+
+The best way to send feedback is to file an issue at
+https://github.com/matthiaskoenig/sbmlsim/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions are
+  welcome :)
+
+Get Started!
+============
+
+Ready to contribute? Here's how to set up sbmlsim for local development.
+
+1. Fork the https://github.com/matthiaskoenig/sbmlsim repository on GitHub. If you
+   have never done this before, `follow the official guide
+   <https://guides.github.com/activities/forking/>`_
+2. Clone your fork locally as described in the same guide.
+3. Install your local copy into a a Python virtual environment.  You can `read
+   this guide to learn more
+   <https://realpython.com/python-virtual-environments-a-primer/>`_ about them
+   and how to create one. Alternatively, particularly if you are a Windows or
+   Mac user, you can also use `Anaconda <https://docs.anaconda.com/anaconda/>`_.
+   Assuming you have virtualenvwrapper installed, this is how you set up your
+   fork for local development
+
+   .. code-block:: console
+
+       mkvirtualenv sbmlsim
+       cd sbmlsim/
+       pip install -e ".[development]"
+
+4. Create a branch for local development using the ``develop`` branch as a
+   starting point. Use ``fix``, ``refactor``, or ``feat`` as a prefix
+
+   .. code-block:: console
+
+       git checkout devel
+       git checkout -b fix-name-of-your-bugfix
+
+   Now you can make your changes locally.
+
+5. When making changes locally, it is helpful to ``git commit`` your work
+   regularly. On one hand to save your work and on the other hand, the smaller
+   the steps, the easier it is to review your work later. Please use `semantic
+   commit messages
+   <http://karma-runner.github.io/2.0/dev/git-commit-msg.html>`_.
+
+   .. code-block:: console
+
+       git add .
+       git commit -m "fix: Your summary of changes"
+
+6. When you're done making changes, check that your changes pass our test suite (with
+   exception of flake8).
+   This is all included with tox
+
+   .. code-block:: console
+
+       tox
+
+   You can run all tests in parallel using detox. To get detox, just pip install
+   it into your virtualenv.
+
+   To fix the isort and black tests use
+   
+   .. code-block:: console
+
+       isort src/sbmlsim
+       black src/sbmlsim --exclude resources
+
+7. Push your branch to GitHub.
+
+   .. code-block:: console
+
+       git push origin fix-name-of-your-bugfix
+
+8. Open the link displayed in the message when pushing your new branch in order
+   to submit a pull request. Please follow the template presented to you in the
+   web interface to complete your pull request.
+
+For larger features that you want to work on collaboratively with other sbmlsim
+team members, you may consider to first request to join the sbmlsim developers
+team to get write access to the repository so that you can create a branch in
+the main repository (or simply ask the maintainer to create a branch for you).
+Once you have a new branch you can push your changes directly to the main
+repository and when finished, submit a pull request from that branch to
+``develop``.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests in the ``sbmlsim/test``
+   directory. Except in rare circumstances, code coverage must
+   not decrease (as reported by codecov which runs automatically when
+   you submit your pull request)
+2. If the pull request adds functionality, the docs should be
+   updated. Put your new functionality into a function with a
+   docstring.
+3. The pull request will be tested for several different Python versions.
+4. Someone from the @matthiaskoenig/sbmlsim-core team will review your work and guide
+   you to a successful contribution.
+
+Unit tests and benchmarks
+-------------------------
+
+sbmlsim uses `pytest <http://docs.pytest.org/en/latest/>`_ for its
+unit-tests and new features should in general always come with new
+tests that make sure that the code runs as intended. 
+
+To run all tests do::
+
+    (sbmlsim)$ pytest
+
+Branching model
+---------------
+
+``develop``
+    Is the branch all pull-requests should be based on.
+``master``
+    Is only touched by maintainers and is the branch with only tested, reviewed
+    code that is released or ready for the next release.
+``{fix, bugfix, doc, feature}/descriptive-name``
+    Is the recommended naming scheme for smaller improvements, bugfixes,
+    documentation improvement and new features respectively.
+
+Please use concise descriptive commit messages and consider using
+``git pull --rebase`` when you update your own fork to avoid merge commits.
+
+Thank you very much for contributing to sbmlsim!

.github/ISSUE_TEMPLATE/01-bug-report.md

@@ -0,0 +1,49 @@
+---
+name: Bug report
+about: Report a bug to help improve this project
+---
+
+<!--
+
+Before you create a new problem report, please look through the list of existing open
+ and closed issues to see if there are similar ones.
+ 
+https://github.com/matthiaskoenig/sbmlsim/issues
+
+-->
+
+#### Problem description
+
+Please explain:
+* **what** you tried to achieve,
+* **how** you went about it (referring to the code sample), and
+* **why** the current behaviour is a problem and what output
+  you expected instead.
+
+#### Code Sample
+
+Create a [minimal, complete, verifiable example](https://stackoverflow.com/help/mcve).
+
+<!-- Paste your code between the ``` tickmarks below or link to a gist. -->
+```python
+```
+
+<!-- If there was a crash, please include the traceback between the ``` tickmarks below. -->
+```
+```
+
+### Context
+
+<!-- Run the following code and paste the output between the ``` tickmarks below
+inside the details block.
+
+python -c "import sbmlsim;sbmlsim.show_versions()"
+
+-->
+
+<details>
+
+```
+```
+
+</details>

.github/ISSUE_TEMPLATE/02-question.md

@@ -0,0 +1,16 @@
+---
+name: Question
+about: Ask a question
+---
+
+### Checklist
+
+<!-- To help keep this issue tracker clean and focused, please make sure that you have
+ tried *all* of the following resources before submitting your question. -->
+
+- [ ] I searched the [documentation](https://sbmlutils.readthedocs.io).
+- [ ] I looked through [similar issues on GitHub](https://github.com/matthiaskoenig/sbmlutils/issues).
+
+### Question
+
+<!-- Please ask your question here. -->

.github/ISSUE_TEMPLATE/03-feature-request.md

@@ -0,0 +1,36 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+---
+
+### Checklist
+
+<!-- Please make sure you check all these items before submitting your feature request. -->
+
+- [ ] There are [no similar issues or pull requests](https://github.com/matthiaskoenig/sbmlutils/issues) for this yet.
+
+### Is your feature related to a problem? Please describe it.
+
+<!--
+A clear and concise description of what you are trying to achieve.
+"I want to be able to [...] but I can't because [...]".
+-->
+
+## Describe the solution you would like.
+
+<!--
+A clear and concise description of what you would want to happen.
+For API changes, try to provide a code snippet of what you would like the new API to
+look like.
+-->
+
+## Describe alternatives you considered
+
+<!--
+Please describe any alternative solutions or features you've considered to solve
+your problem and why they wouldn't solve it.
+-->
+
+## Additional context
+
+<!-- Provide any additional context, screenshots, tracebacks, etc. about the feature here. -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,2 @@
+# Ref: https://help.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository#configuring-the-template-chooser
+blank_issues_enabled: true

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,4 @@
+* [ ] fix #(issue number)
+* [ ] description of feature/fix
+* [ ] tests added/passed
+* [ ] add an entry to the [next release](../release-notes/next-release.md)

.github/SUPPORT.rst

@@ -0,0 +1,6 @@
+=======
+Support
+=======
+
+* You can post questions in `GitHub issues
+  <https://github.com/matthiaskoenig/sbmlsim/issues>`_.

.github/workflows/main.yml

@@ -81,9 +81,3 @@ jobs:
         body_path: "release-notes/${{ steps.tag.outputs.version }}.md"
         draft: false
         prerelease: false
-    - name: Pull request to master
-      uses: vsoch/pull-request-action@1.0.6
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        PULL_REQUEST_FROM_BRANCH: "develop"
-        PULL_REQUEST_BRANCH: "master"

.gitignore

@@ -23,7 +23,7 @@ __pycache__
 # documentation
 docs_builder/_build/
 
-
+src/sbmlsim/examples/experiments/glucose/results/DoseResponseExperiment/DoseResponseExperiment_fig1.svg
 src/sbmlsim/examples/experiments/repressilator/RepressilatorExperiment/RepressilatorExperiment_task_tc.h5
 src/sbmlsim/examples/experiments/midazolam/results/
 src/sbmlsim/examples/experiments/midazolam/results_fit/

MANIFEST.in

@@ -3,4 +3,3 @@ include README.rst
 
 recursive-include src/sbmlsim/test/data *
 recursive-include src/sbmlsim/resources/ *
-recursive-include src/sbmlsim/report/templates *