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**Breaking**: data_kind: Now 'matrix' represents a 2-D numpy array and unrecognized data types fall back to 'vectors' #4649

**Breaking**: data_kind: Now 'matrix' represents a 2-D numpy array and unrecognized data types fall back to 'vectors'

**Breaking**: data_kind: Now 'matrix' represents a 2-D numpy array and unrecognized data types fall back to 'vectors' #4649

Workflow file for this run

# Test PyGMT with GMT dev version on Linux/macOS/Windows
#
# This workflow runs regular PyGMT tests with the GMT dev version, and also pre-release
# versions of several dependencies like NumPy, Pandas, Xarray, etc. If any tests fail,
# it also uploads the diff images as workflow artifacts. The GMT dev version is
# installed by fetching the latest source codes from the GMT master branch and
# compiling.
#
# It is triggered in a pull request if labeled with 'run/test-gmt-dev'.
# It is also scheduled to run on Monday, Wednesday, and Friday on the main branch.
#
name: GMT Dev Tests
on:
# push:
# branches: [ main ]
pull_request:
types: [ opened, reopened, labeled, synchronize ]
paths:
- 'pygmt/**'
- '.github/workflows/ci_tests_dev.yaml'
workflow_dispatch:
# Schedule tests on Monday/Wednesday/Friday
schedule:
- cron: '0 0 * * 1,3,5'
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
jobs:
test_gmt_dev:
name: ${{ matrix.os }} - GMT ${{ matrix.gmt_git_ref }}
runs-on: ${{ matrix.os }}
if: github.event_name != 'pull_request' || contains(github.event.pull_request.labels.*.name, 'run/test-gmt-dev')
strategy:
fail-fast: false
matrix:
os: [ubuntu-24.04, macos-15, windows-2022]
gmt_git_ref: [master]
timeout-minutes: 30
defaults:
run:
shell: bash -l {0}
steps:
# Checkout current git repository
- name: Checkout
uses: actions/[email protected]
with:
# fetch all history so that setuptools-scm works
fetch-depth: 0
- name: Get current week number of year
id: date
run: echo "date=$(date +%Y-W%W)" >> $GITHUB_OUTPUT # e.g., 2024-W19
# Install Micromamba with conda-forge dependencies
- name: Setup Micromamba
uses: mamba-org/[email protected]
with:
environment-name: pygmt
condarc: |
channels:
- conda-forge
- nodefaults
cache-downloads: false
cache-environment: true
# environment cache is persistent for one week.
cache-environment-key: micromamba-environment-${{ steps.date.outputs.date }}
create-args: >-
python=3.12
cmake
make
ninja
curl
fftw
ghostscript=10.04.0
glib
hdf5
libblas
libcblas
libgdal
liblapack
libnetcdf
pcre
zlib
# Checkout current GMT repository
- name: Checkout the GMT source from ${{ matrix.gmt_git_ref }} branch
uses: actions/[email protected]
with:
repository: 'GenericMappingTools/gmt'
ref: ${{ matrix.gmt_git_ref }}
path: 'gmt'
# Build GMT from source on Linux/macOS, script is adapted from
# https://github.com/GenericMappingTools/gmt/blob/6.5.0/ci/build-gmt.sh
- name: Build GMT on Linux/macOS
run: |
cd gmt/
mkdir build
cd build
cmake -G Ninja .. \
-DCMAKE_INSTALL_PREFIX=${{ env.GMT_INSTALL_DIR }} \
-DCMAKE_BUILD_TYPE=Release \
-DGMT_ENABLE_OPENMP=TRUE \
-DGMT_USE_THREADS=TRUE
cmake --build .
cmake --build . --target install
cd ..
rm -rf gmt/
env:
GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir
if: runner.os != 'Windows'
- name: Build GMT on Windows
shell: cmd
run: |
cd gmt/
mkdir build
cd build
call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
cmake -G Ninja .. ^
-DCMAKE_INSTALL_PREFIX=${{ env.GMT_INSTALL_DIR }} ^
-DCMAKE_BUILD_TYPE=Release ^
-DCMAKE_PREFIX_PATH=${{ env.MAMBA_ROOT_PREFIX }}\envs\pygmt\Library ^
-DGMT_ENABLE_OPENMP=TRUE ^
-DGMT_USE_THREADS=TRUE
cmake --build .
cmake --build . --target install
cd ..
rm -rf gmt/
env:
GMT_INSTALL_DIR: ${{ runner.temp }}/gmt-install-dir
if: runner.os == 'Windows'
- name: Add GMT's bin to PATH
run: echo '${{ runner.temp }}/gmt-install-dir/bin' >> $GITHUB_PATH
# Install dependencies from PyPI
- name: Install dependencies
run: |
python -m pip install --pre --prefer-binary \
--extra-index https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
numpy pandas xarray netCDF4 packaging \
build contextily dvc geopandas ipython pyarrow rioxarray \
pytest pytest-cov pytest-doctestplus pytest-mpl pytest-rerunfailures pytest-xdist\
sphinx-gallery
# Show installed pkg information for postmortem diagnostic
- name: List installed packages
run: micromamba list
# Pull baseline image data from dvc remote (DAGsHub)
- name: Pull baseline image data from dvc remote
run: dvc pull --no-run-cache --verbose && ls -lhR pygmt/tests/baseline/
# Download cached remote files (artifacts) from GitHub
- name: Download remote data from GitHub
run: |
# Download cached files to ~/.gmt directory and list them
gh run download --name gmt-cache --dir ~/.gmt/
# Change modification times of the two files, so GMT won't refresh it
touch ~/.gmt/gmt_data_server.txt ~/.gmt/gmt_hash_server.txt
ls -lhR ~/.gmt
env:
GH_TOKEN: ${{ github.token }}
# Install the package that we want to test
- name: Install the package
run: make install
# Run the tests
- name: Test with pytest
run: make test PYTEST_EXTRA="-r P -n auto --reruns 2"
env:
GMT_LIBRARY_PATH: ${{ runner.temp }}/gmt-install-dir/lib
# Upload diff images on test failure
- name: Upload diff images if any test fails
uses: actions/[email protected]
if: ${{ failure() }}
with:
name: artifact-GMT-${{ matrix.gmt_git_ref }}-${{ runner.os }}
path: tmp-test-dir-with-unique-name