* Consolidate MinimalLib Dockerfiles to avoid code duplication
Remove Dockerfile_legacy_browsers since IE11 is not used anymore
* add project name to docker-compose YAML files
* add projectName to azure pipelines DockerCompose section
* updated scripts/build_rdkit.js and Dockerfiles to enable end-to-end
builds
* changes in response to review
* - remove unused docker-compose file
- update azure-pipelines.yml
* fix service dependency
* CI build should copy_from_local
* docs update, make it work for local builds, minimize git clone
* - changes in response to review
- added an option to build from the local source tree to
scripts/build_rdkitjs.sh
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* c++20 builds working
* get MolStandardize building with clang19
* get FMCS building with clang-19
* set cxx version to c++20
* remove a few more compiler warnings
* bump min boost version, CI cleanup
* boost 1.81 is not available from conda-forge
* remove unused constants
* bump linux version for CI
* remove another unused variable
* fix (hopefully) cartridge CI builds
* simplify cartridge environment
* try postgresql14 in CI
* start the postgresql service
* change the columns used in the pandastools nbtest
* remove missed merge conflict artifact
* get github4823 test to pass with numpy 2.2
* remove a compiler warning/error with g++13
* bump min linux runtime in CI to ubuntu 22.04
bump min boost version
some other minor cleanup
* boost version -> 1.82
* change postgresql install
* Update linux_build_cartridge.yml
* Update linux_build.yml
* Update linux_build.yml
* Update linux_build_cartridge.yml
* Update linux_build.yml
* Update linux_build.yml
* Update azure-pipelines.yml
* trigger CI run
* please build
---------
Co-authored-by: = <=>
* try adding a CI job to build the minimallib docker image
* update
* try simplification
* path
* path
* re-enable the other ci builds
remove the obsolete .yml file
* temporarily be explicit about using the macos-12 image
This is driven by the changes suggested here: https://github.com/actions/runner-images/issues/9262
We need to update the mac build scripts to install miniforge ourselves.
<sigh>
* lock the compiler version too
19.1 seems to cause problems with the libcffi code
* cmake modernization
- get rid of some warnings
- switch to what I hope is the correct way of doing things
- bump min cmake version to 3.16
- bump min boost version to 1.70
This builds on linux
* remove some usages of PYTHON_EXECUTABLE
* remove old-school python usage from coverage tests
* remove unused CI file
* bump boost version for windows builds to 1.84
* still trying to get the ci builds working
* typo
* eventually the CI will work
* robustify some tests
* Compile time and runtime deprecation warnings
* Used [[deprecated]] attribute to mark deprecation on cpp side
* Used RDLog to escalate deprecation warnings to python
* deprecated non fingerprint generator fingerprint generation functions
* Address build errors
* suppress deprecation warnings in cpps and tests
* experiment with new SWIG versions in the mac azure pipeline
* More deprecation suppression
* revert mac java experiment
* Fix SWIG syntax errors
* Attempt to fix windows unit test
* Remove test because of logging behavior
* Change linux java build to SWIG 4.1
- removes the need for preprocessor interaction
* Change mac java build to SWIG 4.1
* try updating the CI buid
* lock cmake version
needed to find JNI correctly
* update compiler versions
needed for the boost
* Fix typo and unavailable version
* Fix version conflict
* update mac build
* get linux build working?
---------
Co-authored-by: Patrick Penner <patrick@ppenner.com>
* ci updates
* forgotten update
* inch by inch
* remove unused variable
* try a gcc bump
* get rid of a bunch of unused-but-set errors in clang16
* be more selective
* disable a test in an obsolete module which is mysteriously failing
* switch from boost::any to std::any
* changes in response to review
* handle the slightly different error messages from different compilers
* document changed error message
* try to use g++10 for the linux builds
* remove those CXX defns
* another spelling
* stupid typo
* bump all linux builds to g++-10
* some day this will be done
* small steps
* increase mac ci builds runtime
* get the config of the windows DLL builds to match the main windows builds
* bump boost version
* Update vs_build_dll.yml
* sigh...
* disable python on that build
* add back cairo
* more windmills
* no boost cmake
disable other builds for now
* re-enable the doctests...
* we do need jupyter if we want to do the doctests
* add a blank line?
* hrm
* try moving the install command
* add jupyter sooner
re-enable other builds
* remove some more deprecated numpy stuff
* workaround for changes to random.shuffle in python 3.11
* fix pickling of rdkit mols in python 3.11
* add py311 build to CI
* update py311 CI
* remove qt for py311 for the moment
* only use the new code with pyversion >=3.11
* use the new logic for all pickle_suites
* need to work with older py too
* version bump, update c++ standard
* update docs version
* switch back to windows-2019 for windows CI builds
windows-latest is now windows-2022, which include Visual Studio 2022 and I'd like to keep building with Visual Studio 2019 for a while
* try win2022 and vs2022 for the moment
* Back to 2019, back to C++14
we get rid of the C++17 stuff for now until we can remove the
binary_function usage... that's for a separate PR
* update CI VMs to latest versions
* update win build parms
* sigh...
* if at first you don\'t succeed
* iterating
* be explicit about which test config to use
* add back sphinx
* update some expected results that changed with previous fixes
* Fixes#4386
* try to actually generate an error when the cartridge tests fail
* update azure pipelines cartridge builds
* ensure psql dev env is there
temporarily disable other azure pipelines builds
* psql version
* gather info
* gather info
* gather info
* gather info
* gather info
* more descriptors
* try forcing psql12
* remove the package correctly
* remove the package correctly
* remove the package correctly
* sooo much fun
* sooooo much fun
* seems to be working now, enable the others
* support v3k output in cartridge
* tests do not pass
* docs
* update expected tests
* linux CI modernization
- remove 16.04 python builds
- switch 16.04 java build to 20.04
* update
* update
* use dynamic libs
-fPIC never ceases to amuse
* specify swig version
* force swig3
* force swig3
* re-enable the other tests
These are failing and I'm not convinced that there's value in continuing to do them here anyway.
Autofuzz is still running against the code base, so we still have fuzzer coverage
* Fixes#3648
Code now builds without either MAEParser or coordgen integration enabled.
* add CI build with minimal dependencies
* remove doctests from the new CI build
they need the cairo support
* Fixes#2757
Note that fix here really means changing the way the doctest uses the code
* add py38 to build matrix
* adjust to more modern boost
* update another set of expected results
* re-enable the other CI configs
* Add initial fuzz target
* Polish
Integrated the existing targets from @Google-Autofuzz.
Added a dictionary for smiles and a little corpora too.
Cleanup cmake.
* Fix Typo
* Remove debugging oversight
* Fail, when not building fuzzers statically
* Don't build fuzzers by default
* Add azure pipeline for fuzzing
* Format files; catch all exceptions
* Debugging pipeline
* Fix format of corpora files
* Add corpora for mol strings
* Add dictionary for mol strings
* Add README.md
* Remove very similar fuzz target
* Add mol pickle/deserialization fuzzer
* Improve fuzz readme
Co-authored-by: intrigus <abc123zeus@live.de>
* first pass at getting an azure devops build of the cartridge working
* typo
* rename, disable other builds for testing
* tweaking
* tweaking
* use system boost
* sudo for install
* re-enable the other tests
* add linux_java build
* trigger azure pipelines builds on dev/ branches
* make sure boost::iostreams gets linked in the SWIG wrappers
* updates to get static boost builds working on mac
* update linux a bit and add mac build
* forgot to save the mac file
* install version of boost with -fPIC
* try to force use of the boost installed in /usr
* typo
* add library hint
* diagnosing a failing build
* be explicit about CXX version
* try to force use of the system compilers
instead of the ones from conda
* stop using conda
* typp
* re-enable full build
* disable the appveyor builds
