Merge pull request #407 from ICB-DCM/develop

Release 0.10.13

.github/workflows/ci_pr.yml

@@ -4,7 +4,7 @@ name: CI
 on: [pull_request]
 
 jobs:
-  notebooks:
+  notebooks1:
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -23,18 +23,50 @@ jobs:
       uses: actions/cache@v1
       with:
         path: ~/.cache
-        key: ${{ runner.os }}-ci-notebooks
+        key: ${{ runner.os }}-ci-notebooks1
 
     - name: Install dependencies
       run: |
-        .github/workflows/ci_dependencies.sh R petab
+        .github/workflows/ci_dependencies.sh
         pip install jupyter
-        pip install -e .[petab,R]
+        pip install -e .
 
     - name: Run notebooks
       timeout-minutes: 10
       run: |
-        test/run_notebooks.sh
+        test/run_notebooks.sh 1
+
+  notebooks2:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v2
+
+    - name: Prepare python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache
+      uses: actions/cache@v1
+      with:
+        path: ~/.cache
+        key: ${{ runner.os }}-ci-notebooks2
+
+    - name: Install dependencies
+      run: |
+        .github/workflows/ci_dependencies.sh R
+        pip install jupyter
+        pip install -e .[R]
+
+    - name: Run notebooks
+      timeout-minutes: 10
+      run: |
+        test/run_notebooks.sh 2
 
   docs:
     runs-on: ubuntu-latest

.github/workflows/ci_push.yml

@@ -85,7 +85,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.7]
+        python-version: [3.8]
 
     steps:
     - name: Check out repository

doc/contribute.rst

@@ -22,11 +22,11 @@ Contribute tests
 
 We're committed to testing our code. Tests that are required to pass are located in the
 ``test`` folder. All files starting with ``test_`` contain tests and are automatically run
-on Travis CI. To run them manually, type::
+on GitHub Actions. They can be run manually via::
 
     python3 -m pytest test
 
-You can also run specific tests only.
+You can also run only specific tests.
 
 We encourage to test whatever possible. However, it might not always be easy to
 test code which is based on random sampling. We still encourage to provide general sanity
@@ -59,7 +59,7 @@ Create an own branch or fork, on which you can implement your changes. To
 get your work merged, please:
 
 1. create a pull request to the develop branch,
-2. check that all tests on travis pass,
+2. check that all tests pass,
 3. check that the documentation is up-to-date,
 4. request a code review from the main developers.
 

doc/deploy.rst

@@ -4,9 +4,10 @@
 Deploy
 ======
 
-New featuers and bug fixes are continually added to the develop branch. On
-every merge to master, the version number in ``pyabc/version.py`` should
-be incremented as described below.
+The develop branch contains the working version of the package with
+new features and bug fixes. Regularly, also new production versions
+of the package should be released. The latest release is represented
+in the main branch.
 
 Versioning scheme
 -----------------
@@ -24,28 +25,28 @@ Create a new release
 --------------------
 
 After new commits have been added via pull requests to the develop branch,
-changes can be merged to master and a new version of pyABC can be released.
-Every merge to master should coincide with an incremented version number
+changes can be merged to main and a new version of pyABC can be released.
+Every merge to main should coincide with an incremented version number
 and a git tag on the respective merge commit.
 
-Merge into master
-~~~~~~~~~~~~~~~~~
+Merge into main
+~~~~~~~~~~~~~~~
 
-1. create a pull request from develop to master,
-2. check that all tests on travis pass,
+1. create a pull request from develop to main,
+2. check that all tests pass,
 3. check that the documentation is up-to-date,
 4. adapt the version number in ``pyabc/version.py`` (see above),
 5. update the release notes in ``doc/releasenotes.rst``,
 6. request a code review,
-7. merge into the origin master branch.
+7. merge into the origin main branch.
 
 To be able to actually perform the merge, sufficient rights may be required.
 Also, at least one review is required.
 
-Create a release on github
+Create a release on GitHub
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-After merging into master, create a new release on GitHub. This can be done
+After merging into main, create a new release on GitHub. This can be done
 either directly on the project GitHub website, or via the CLI as described
 in
 `Git Basics - Tagging <https://git-scm.com/book/en/v2/Git-Basics-Tagging>`_.
@@ -55,16 +56,14 @@ In the release form,
 * include the latest additions to ``doc/releasenotes.rst`` in the release
   description.
 
-Upload to the Python package index PyPI
----------------------------------------
+Upload to PyPI
+--------------
 
-The upload to pypi has been automatized via travis since pyabc version 0.9.11,
-and is triggered whenever a new release tag is created on the github master
-branch.
+The upload to the python package index PyPI has been automatized via GitHub
+Actions and is triggered whenever a new release tag is created.
 
-To manually upload a new version to pypi, proceed as follows:
-
-First, a so called "wheel" is created via::
+Should it be necessary to manually upload a new version to PyPI,
+proceed as follows: First, a so called "wheel" is created via::
 
     python setup.py bdist_wheel
 
@@ -75,9 +74,9 @@ This archive is uploaded using twine::
 
     twine upload dist/pyabc-x.y.z-py3-non-any.wheel
 
-replacing x.y.z by the appropriate version number.
+replacing x.y.z by the respective version number.
 
 For a more in-depth discussion see also the
 `section on distributing packages 
 <https://packaging.python.org/tutorials/distributing-packages>`_
-of the Python packaging guide
+of the Python packaging guide.

doc/examples.rst

@@ -8,8 +8,8 @@ The following examples should help to get a better idea of how to use pyABC.
 .. toctree::
    :maxdepth: 1
 
-   examples/quickstart.ipynb
    examples/parameter_inference.ipynb
+   examples/model_selection.ipynb
    examples/early_stopping.ipynb
    examples/resuming.ipynb
    examples/using_R.ipynb
@@ -29,9 +29,8 @@ The following examples should help to get a better idea of how to use pyABC.
 Download the examples as notebooks
 ----------------------------------
 
-* :download:`Quickstart <examples/quickstart.ipynb>`
 * :download:`Parameter inference <examples/parameter_inference.ipynb>`
-* :download:`Model selection (Quickstart) <examples/quickstart.ipynb>`
+* :download:`Model selection <examples/model_selection.ipynb>`
 * :download:`Early stopping of model simulations <examples/early_stopping.ipynb>`
 * :download:`Resuming stored ABC runs <examples/resuming.ipynb>`
 * :download:`Using R with pyABC <examples/using_R.ipynb>`