New CI system (#123)

* Drone CI -> Woodpecker CI

.ci/run_ci.sh

@@ -1,6 +1,6 @@
-#!/bin/bash -xe
+#!/bin/bash
 
-set -u
+set -eux
 export PKG_NAME=$1
 SUNDBASE=$2
 set +u
@@ -10,19 +10,20 @@ if [ ! -e "$SUNDBASE/include/sundials/sundials_config.h" ]; then
     exit 1
 fi
 
+# REPO_TEMP_DIR="$(mktemp -d)"
+# trap 'rm -rf -- "$REPO_TEMP_DIR"' EXIT
+# cp -ra . "$REPO_TEMP_DIR/."
+# cd "$REPO_TEMP_DIR"
+
 mkdir -p $HOME/.config/pip/
-echo -e "[global]\nno-cache-dir = false\ndownload-cache = $(pwd)/ci_cache/pip_cache" >$HOME/.config/pip/pip.conf
+echo -e "[global]\nno-cache-dir = false\ndownload-cache = $CI_WORKSPACE/cache-ci/pip_cache" >$HOME/.config/pip/pip.conf
 python3 -m pip install symcxx pysym  # unofficial backends, symengine is tested in the conda build
 
 # (cd ./tmp/pycvodes;
 SUND_CFLAGS="-isystem $SUNDBASE/include $CFLAGS"
 SUND_LDFLAGS="-Wl,--disable-new-dtags -Wl,-rpath,$SUNDBASE/lib -L$SUNDBASE/lib $LDFLAGS"
 CFLAGS=$SUND_CFLAGS LDFLAGS=$SUND_LDFLAGS python3 -m pip install pycvodes
-git clean -xfd # -e tmp/
 
-# export CPATH=$SUNDBASE/include
-# export LIBRARY_PATH=$SUNDBASE/lib
-# export LD_LIBRARY_PATH=$SUNDBASE/lib
 
 python3 setup.py sdist
 PKG_VERSION=$(python3 setup.py --version)

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "external/anyode"]
 	path = external/anyode
-	url = git://github.com/bjodah/anyode
+	url = https://github.com/bjodah/anyode

.woodpecker.yaml

@@ -0,0 +1,76 @@
+when:
+  - event: [push]
+
+steps:
+
+  - name: restore-cache
+    image: bjodah/bjodahimg20dot:21.8.a
+    commands:
+      - curl ftp://${CI_REPO_NAME}:$${ARTIFACTS_PASS}@$${FTP_SERVER}/cache/cache-ci.tar | tar -C / x || mkdir -p $CI_WORKSPACE/cache-ci/pip_cache
+    secrets: [ ARTIFACTS_PASS, FTP_SERVER ]
+    when:
+     - event: push
+       repo: bjodah/pyodesys
+
+  - name: test-sund-5.7.0-rel
+    depends_on: restore-cache
+    image: bjodah/bjodahimg20dot:21.8.a
+    environment:
+      - CC=gcc-11
+      - CXX=g++-11
+      - OMP_NUM_THREADS=1
+      - ANYODE_NUM_THREADS=2
+      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost-1.77.0/include
+      - LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
+      - LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
+      - SUNDBASE=/opt/sundials-5.7.0-release
+    commands:
+      - cp -ra $CI_WORKSPACE /tmp/test-sund-5.7.0-rel
+      - cd /tmp/test-sund-5.7.0-rel
+      - python3 -m pip install --cache-dir $CI_WORKSPACE/cache-ci/pip_cache --upgrade-strategy=eager --upgrade cython https://github.com/bjodah/pycompilation/archive/master.tar.gz
+      - bash -c "ulimit -v 2048000; .ci/run_ci.sh pyodesys $SUNDBASE"
+      - ./scripts/prepare_deploy.sh
+      - bash -c '[[ $(python3 setup.py --version) =~ ^[0-9]+.* ]]'
+      - cp -ra /tmp/test-sund-5.7.0-rel/deploy $CI_WORKSPACE/
+
+  - name: test-sund-5.7.0-extended
+    depends_on: restore-cache
+    image: bjodah/bjodahimg20dot:21.8.a
+    environment:
+      - CC=gcc-11
+      - CXX=g++-11
+      - OMP_NUM_THREADS=1
+      - ANYODE_NUM_THREADS=2
+      - CPLUS_INCLUDE_PATH=/usr/include/suitesparse:/opt/boost-1.77.0/include
+      - LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
+      - LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu
+      - SUNDBASE=/opt/sundials-5.7.0-extended
+      - PYCVODES_NO_LAPACK=1
+      - PYCVODES_NO_KLU=1
+    commands:
+      - cp -ra $CI_WORKSPACE/ /tmp/test-sund-5.7.0-extended
+      - cd /tmp/test-sund-5.7.0-extended
+      - python3 -m pip install --cache-dir $CI_WORKSPACE/cache-ci/pip_cache --upgrade-strategy=eager --upgrade cython
+      - bash -c "ulimit -v 2048000; .ci/run_ci.sh pyodesys $SUNDBASE"
+      - ./scripts/grep-for-merge-blocking-token.sh
+      - ./scripts/grep-for-binary-data.sh
+
+  - name: rebuild-cache
+    image: bjodah/bjodahimg20dot:21.8.a
+    commands:
+      - find $CI_WORKSPACE/cache-ci/ -type f -mtime +90 -exec rm {} \;
+      - tar cf cache-ci.tar $CI_WORKSPACE/cache-ci/
+      - curl -T cache-ci.tar ftp://${CI_REPO_NAME}:$${ARTIFACTS_PASS}@$${FTP_SERVER}/cache/
+    secrets: [ ARTIFACTS_PASS, FTP_SERVER ]
+    depends_on:
+      - test-sund-5.7.0-rel
+
+  - name: deploy-public-html
+    image: bjodah/bjodahimg20dot:21.8.a
+    commands:
+      - tar -C deploy/public_html -czf ${CI_REPO_NAME}-${CI_COMMIT_BRANCH}.tar.gz .
+      - curl -T ${CI_REPO_NAME}-${CI_COMMIT_BRANCH}.tar.gz ftp://${CI_REPO_NAME}:$${ARTIFACTS_PASS}@$${FTP_SERVER}/public_html/
+    secrets: [ ARTIFACTS_PASS, FTP_SERVER ]
+    depends_on:
+      - test-sund-5.7.0-rel
+

README.rst

@@ -1,26 +1,17 @@
 pyodesys
 ========
 
-.. image:: http://hera.physchem.kth.se:8090/api/badges/bjodah/pyodesys/status.svg
-   :target: http://hera.physchem.kth.se:8090/bjodah/pyodesys
-   :alt: Build status on Drone
-.. image:: https://circleci.com/gh/bjodah/pyodesys.svg?style=svg
-   :target: https://circleci.com/gh/bjodah/pyodesys
-   :alt: Build status on CircleCI
+.. image:: http://hackspett.bjodah.se/api/badges/8/status.svg
+   :target: http://hackspett.bjodah.se/repos/8
+   :alt: Build status on Woodpecker CI
 .. image:: https://img.shields.io/pypi/v/pyodesys.svg
    :target: https://pypi.python.org/pypi/pyodesys
    :alt: PyPI version
-.. image:: https://img.shields.io/badge/python-3.7,3.8-blue.svg
-   :target: https://www.python.org/
-   :alt: Python version
 .. image:: https://img.shields.io/pypi/l/pyodesys.svg
    :target: https://github.com/bjodah/pyodesys/blob/master/LICENSE
    :alt: License
-.. image:: http://img.shields.io/badge/benchmarked%20by-asv-green.svg?style=flat
-   :target: http://hera.physchem.kth.se/~pyodesys/benchmarks
-   :alt: airspeedvelocity
-.. image:: http://hera.physchem.kth.se/~pyodesys/branches/master/htmlcov/coverage.svg
-   :target: http://hera.physchem.kth.se/~pyodesys/branches/master/htmlcov
+.. image:: http://artifacts.bjodah.se/pyodesys/branches/master/htmlcov/coverage.svg
+   :target: http://artifacts.bjodah.se/pyodesys/branches/master/htmlcov
    :alt: coverage
 .. image:: http://joss.theoj.org/papers/10.21105/joss.00490/status.svg
    :target: https://doi.org/10.21105/joss.00490
@@ -63,7 +54,7 @@ Documentation
 Auto-generated API documentation for latest stable release is found here:
 `<https://bjodah.github.io/pyodesys/latest>`_
 (and the development version for the current master branch is found here:
-`<http://hera.physchem.kth.se/~pyodesys/branches/master/html>`_).
+`<http://artifacts.bjodah.se/pyodesys/branches/master/html>`_).
 
 
 Installation
@@ -227,7 +218,7 @@ further reduced by a factor equal to the number of cores of your CPU (number of
 the environment variable ``ANYODE_NUM_THREADS``).
 
 For further examples, see `examples/ <https://github.com/bjodah/pyodesys/tree/master/examples>`_, and rendered
-jupyter notebooks here: `<http://hera.physchem.kth.se/~pyodesys/branches/master/examples>`_
+jupyter notebooks here: `<http://artifacts.bjodah.se/pyodesys/branches/master/examples>`_
 
 Run notebooks using binder
 ~~~~~~~~~~~~~~~~~~~~~~~~~~

pyodesys/symbolic.py

@@ -67,7 +67,7 @@ def _get_ny_nparams_from_kw(ny, nparams, kwargs):
 
 
 def _get_lin_invar_mtx(lin_invar, be, ny, names=None):
-    if lin_invar is None or lin_invar == []:
+    if lin_invar is None or len(lin_invar) == 0:
         return None
     else:
         if isinstance(lin_invar[0], dict) and names: