Merge pull request #300 from ICB-DCM/develop

Release 0.10.2
ICB-DCM · May 10, 2020 · db0e807 · db0e807
2 parents ad222b4 + 3a755bd
commit db0e807
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diff --git a/.travis_pip_reqs.txt → .ci_pip_reqs.txt b/.travis_pip_reqs.txt → .ci_pip_reqs.txt
@@ -1,3 +1,4 @@
+wheel
 cloudpickle
 gitpython
 sqlalchemy
@@ -24,8 +25,6 @@ ipython
 feather-format
 bkcharts
 tzlocal
-rpy2>=3.2.0
-cffi>=1.13.1
 flake8
 pytest
 codecov

diff --git a/.github/workflows/ci_dependencies.sh b/.github/workflows/ci_dependencies.sh
@@ -0,0 +1,48 @@
+#!/bin/sh
+
+# apt
+sudo apt-get update
+sudo apt-get install redis-server
+
+# pip
+python -m pip install --upgrade pip
+pip install -r .ci_pip_reqs.txt
+
+# install package
+pip install -e .
+
+# optional dependencies
+for par in "$@"
+do
+    case $par in
+
+        R)
+	    # R environment
+            sudo apt-key adv \
+                --keyserver keyserver.ubuntu.com \
+                --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+            sudo add-apt-repository \
+                'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
+            sudo apt-get update
+            sudo apt-get install r-base
+            pip install rpy2>=3.2.0 cffi>=1.13.1
+        ;;
+
+        petab)
+	    # PEtab
+            sudo apt-get install swig3.0 libatlas-base-dev libhdf5-serial-dev
+            sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
+            pip install https://github.com/icb-dcm/petab/archive/develop.zip
+            pip install -e \
+                'git+https://github.com/icb-dcm/amici.git@develop#egg=amici&subdirectory=python/sdist'
+            git clone --depth 1 \
+                https://github.com/petab-dev/petab_test_suite .tmp/petab_test_suite
+            pip install -e .tmp/petab_test_suite
+        ;;
+
+        *)
+            echo "Unknown argument" >&2
+	    exit 1
+        ;;
+    esac
+done
diff --git a/.github/workflows/ci_pr.yml b/.github/workflows/ci_pr.yml
@@ -0,0 +1,64 @@
+name: CI
+
+# trigger
+on: [pull_request]
+
+jobs:
+  notebooks:
+    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-notebooks
+
+    - name: Install dependencies
+      run: .github/workflows/ci_dependencies.sh R petab
+
+    - name: Run notebooks
+      run: |
+        test/run_notebooks.sh
+
+  docs:
+    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-docs
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get install pandoc
+        python -m pip install --upgrade pip
+        pip install -e .
+        pip install sphinx nbsphinx nbconvert sphinx-rtd-theme
+
+    - name: Build docs
+      run: sphinx-build -W -b html doc/ doc/_build/html
diff --git a/.github/workflows/ci_push.yml b/.github/workflows/ci_push.yml
@@ -0,0 +1,113 @@
+name: CI
+
+# trigger
+on: [push]
+
+jobs:
+  base:
+    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-base
+        restore-keys: ${{ runner.os }}-
+
+    - name: Install dependencies
+      run: .github/workflows/ci_dependencies.sh R
+
+    - name: Run tests
+      run: |
+        python -m pytest --cov=pyabc --cov-report=xml \
+          test/test_* test/visualization/test_*
+
+    - name: Coverage
+      uses: codecov/codecov-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
+
+  external:
+    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-external
+        restore-keys: ${{ runner.os }}-
+
+    - name: Install dependencies
+      run: .github/workflows/ci_dependencies.sh R
+
+    - name: Run tests
+      run: |
+        python -m pytest --cov=pyabc --cov-report=xml \
+          test/external/test_*
+
+    - name: Coverage
+      uses: codecov/codecov-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
+
+  petab:
+    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-petab
+        restore-keys: ${{ runner.os }}-
+
+    - name: Install dependencies
+      run: .github/workflows/ci_dependencies.sh petab
+
+    - name: Run tests
+      run: |
+        python -m pytest --cov=pyabc --cov-report=xml \
+          test/petab/test_*
+
+    - name: Coverage
+      uses: codecov/codecov-action@v1
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -0,0 +1,35 @@
+name: Deploy
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+    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: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+     
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*
+
diff --git a/.travis.yml b/.travis.yml
diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 <img src="https://raw.githubusercontent.com/ICB-DCM/pyABC/master/doc/logo/logo.png" alt="pyABC logo" width="30%"/>
 
-[![build Status](https://travis-ci.org/ICB-DCM/pyABC.svg?branch=master)](https://travis-ci.org/ICB-DCM/pyABC)
+[![CI](https://github.com/ICB-DCM/pyABC/workflows/CI/badge.svg)](https://github.com/ICB-DCM/pyABC/actions)
 [![docs](https://readthedocs.org/projects/pyabc/badge/?version=latest)](http://pyabc.readthedocs.io/en/latest/)
 [![codacy](https://api.codacy.com/project/badge/Grade/923a9ab160e6420b9fc468701be60a98)](https://www.codacy.com/app/yannikschaelte/pyABC?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=ICB-DCM/pyABC&amp;utm_campaign=Badge_Grade)
 [![codecov](https://codecov.io/gh/ICB-DCM/pyABC/branch/master/graph/badge.svg)](https://codecov.io/gh/ICB-DCM/pyABC)

diff --git a/doc/api_sge.rst b/doc/api_sge.rst
@@ -1,9 +1,6 @@
 .. _api_sge:
 
 .. automodule:: pyabc.sge
-   :members:
-   :special-members: __init__, __call__
-   :show-inheritance:
 
 .. autoclass:: pyabc.sge.SGE
    :members:

diff --git a/doc/index.rst b/doc/index.rst
@@ -1,8 +1,8 @@
 Welcome to pyABC's documentation!
 =================================
 
-.. image:: https://travis-ci.org/ICB-DCM/pyABC.svg?branch=master
-   :target: https://travis-ci.org/ICB-DCM/pyABC
+.. image:: https://github.com/ICB-DCM/pyABC/workflows/CI/badge.svg
+   :target: https://github.com/ICB-DCM/pyABC/actions
 .. image:: https://readthedocs.org/projects/pyabc/badge/?version=latest
    :target: https://pyabc.readthedocs.io/en/latest
 .. image:: https://api.codacy.com/project/badge/Grade/923a9ab160e6420b9fc468701be60a98

diff --git a/doc/releasenotes.rst b/doc/releasenotes.rst
@@ -8,6 +8,15 @@ Release Notes
 ...........
 
 
+0.10.2 (2020-05-09)
+-------------------
+
+* Update CI test system: latest Ubuntu, python 3.8, simplify R build (#296).
+* Add weights logging to adaptive distances (#295).
+* Migrate CI tests to GitHub Actions for speed-up, reliability and
+  maintainability (#297, #298).
+
+
 0.10.1 (2020-03-17)
 -------------------
 

diff --git a/doc/sampler.rst b/doc/sampler.rst
@@ -368,7 +368,7 @@ Pickling
 
 .. note::
 
-   This section is of interest to developers, of if you encounter memory
+   This section is of interest to developers, or if you encounter memory
    problems.
 
 For most of the samplers, pyABC uses

diff --git a/flake8_exclude.txt b/flake8_exclude.txt