Simplify gh action CI tests
Change-Id: I86cdd29ced74d114e1ee506c65d2342c3e77f8c3
diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index eaa02bc..d0c5dd5 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -9,53 +9,81 @@
strategy:
max-parallel: 4
matrix:
- python-version: [3.5, 3.6, 3.7, 3.8]
+ python-version: [3.7, 3.8]
r-version: [3.6, 4.0]
- os: [macOS-latest, ubuntu-latest, windows-latest]
+ os: [windows-latest, macOS-latest, ubuntu-20.04]
exclude:
- # os: windows-latest
- # python-version: 3.8
- - python-version: 3.5
+ - os: macOS-latest
+ python-version: 3.7
- os: windows-latest
+ python-version: 3.7
+ - os: windows-latest
+ r-version: 3.6
+ - os: ubuntu-20.04
+ r-version: 4.0
steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v1
+ uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
+ - name: Cache pip
+ uses: actions/cache@v2
+ with:
+ # This path is specific to Ubuntu
+ path: ~/.cache/pip
+ # Look to see if there is a cache hit for the corresponding requirements file
+ key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+ restore-keys: |
+ ${{ runner.os }}-pip-
+ ${{ runner.os }}-
- name: Set up R ${{ matrix.r-version }}
uses: r-lib/actions/setup-r@master
with:
r-version: ${{ matrix.r-version }}
+ if: runner.os != 'Linux'
+ - name: Set up package maintainers R on Linux
+ run: |
+ sudo apt-get update -y
+ sudo apt-get install -y r-base r-base-dev r-cran-tidyverse r-cran-r.utils r-cran-pixmap r-cran-webshot r-cran-ade4 r-cran-segmented r-cran-purrr r-cran-dygraphs r-cran-cvst r-cran-quantmod r-cran-graphlayouts r-cran-rappdirs r-cran-ggdendro r-cran-seqinr r-cran-heatmaply r-cran-igraph r-cran-plotly libcurl4-gnutls-dev libssl-dev libxml2-dev libsodium-dev python3-pip python3-rpy2 python3-pandas
+ sudo chown $USER /usr/local/lib/R/site-library
+ export R_LIBS_USER=/usr/local/lib/R/site-library
+ if: runner.os == 'Linux'
+ - name: Install R dependencies
+ run: Rscript -e "install.packages('RKorAPClient')"
+ - name: Cache R packages on Linux
+ uses: actions/cache@v1
+ with:
+ path: /usr/local/lib/R/site-library
+ key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('DESCRIPTION') }}
+ if: runner.os == 'Linux'
- name: Cache R packages
uses: actions/cache@v1
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('DESCRIPTION') }}
- - name: Install Linux system dependencies
- if: runner.os == 'Linux'
- run: |
- sudo apt-get update -y
- sudo apt-get install -y libglpk-dev libjq-dev libv8-dev libprotobuf-dev protobuf-compiler libudunits2-dev libgdal-dev libcurl4-gnutls-dev libssl-dev libxml2-dev libsodium-dev python3-rpy2 python3-pandas
+ if: runner.os != 'Linux'
- name: Install dependencies
run: |
python -m pip install --upgrade pip
- - name: Install windows dependencies
- if: runner.os == 'Windows' && matrix.python-version == '3.8'
- run: |
- echo "Bug in setuptools requires update"
- python -m pip install --upgrade setuptools pycparser wheel
+ pip install wheel
- name: Install package
run: |
- python setup.py install
+ pip install .
- name: Test with pytest on POSIX
if: runner.os != 'Windows'
run: |
export LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}
- pip install pytest codecov pytest-cov ipython
- ./scripts/run_tests.sh
+ pip install pytest
+ pytest KorAPClient/tests --junitxml=junit/test-results-${{ matrix.python-version }}.xml
- name: Test with pytest on Windows
if: runner.os == 'Windows'
run: |
- pip install pytest codecov pytest-cov ipython
- ./scripts/run_tests.sh
+ ./scripts/R_run.bat setup.py test
+ - name: Upload check results
+ if: failure()
+ uses: actions/upload-artifact@master
+ with:
+ name: pytest-results-${{ matrix.python-version }}
+ path: junit/test-results-${{ matrix.python-version }}.xml
+
diff --git a/install_r_packages.r b/install_r_packages.r
deleted file mode 100755
index 56f81ce..0000000
--- a/install_r_packages.r
+++ /dev/null
@@ -1,5 +0,0 @@
-args <- commandArgs(trailingOnly = TRUE)
-
-repos <- "https://cran.rstudio.com"
-
-install.packages(args, repos = repos)
diff --git a/scripts/R_run.bat b/scripts/R_run.bat
index 499708e..d10b1da 100755
--- a/scripts/R_run.bat
+++ b/scripts/R_run.bat
@@ -1,6 +1,11 @@
+Rscript -e '.libPaths()'
set R_USER=C:\R
set R_HOME=C:\R
set PATH=%R_HOME%\bin\i386;%PATH%
+set PATH=%R_HOME%\bin;%PATH%
+set PATH=%R_HOME%\bin\x64;%PATH%
+set PATH=%R_HOME%;%PATH%
+echo %PATH%
set
python %1 %2 %3 %4 %5 %6
diff --git a/scripts/run_tests.sh b/scripts/run_tests.sh
index f49f844..15a73d2 100755
--- a/scripts/run_tests.sh
+++ b/scripts/run_tests.sh
@@ -1,7 +1,5 @@
#!/bin/bash
-sudo Rscript ./install_r_packages.r RKorAPClient
-
pytest \
--cov-append \
KorAPClient/tests