Chemprop

New CLI Features
Caching in CLI
`MolGraphs` are now created (by featurizing molecules) and cached at the beginning of training by default in the CLI. If you wish to disable caching, you can use the `--no-cache` flag, which will featurize molecules on the fly instead. (903)
Change the default trial scheduler in HPO
We changed the default trial scheduler for HPO from AsyncHyperBand to FIFO, as it is the default in Ray and was used in version 1. You can switch the trial scheduler back to AsyncHyperBand by using `--raytune-trial-scheduler AsyncHyperBand` if needed. (896)
Support Optuna in HPO
You can use optuna as a HPO search algorithm via `--raytune-search-algorithm optuna`. (888)

CLI Bug Fixes
HPO-related bugs
In 873, we changed the search space for the initial and final learning rate ratios and `max_lr` to avoid very small (~10^-10) learning rates and also ensured that some hyperparameters are saved as integers instead of floating-point numbers (e.g., `batch_size`). In 881, we addressed the bug concerning the incompatibility of the saved config file with the training config. In 836, we shut down Ray processes after HPO completion to avoid zombie processes. For those encountering issues with Ray processes, we suggest you start Ray outside of the Python process.
DDP-related bugs
In 884, we resolved the issue where metrics were not synchronized across processes and disabled the distributed sampler during testing in DDP.
Backwards incompatibility note
In 883, we fixed the bug related to unused parameters in DDP. Models created via the CLI in v2.0.0 without additional atomic descriptors **cannot be used via the CLI** in v2.0.1. You will need to first remove `message_passing.W_d.weight` and `message_passing.W_d.bias` from the model file's state_dict to make it compatible with the current version.

What's Changed
* update v2 installation instructions page in docs by kevingreenman in https://github.com/chemprop/chemprop/pull/831
* Remove Ray zombie processes by shihchengli in https://github.com/chemprop/chemprop/pull/836
* Docker images for v2 by JacksonBurns in https://github.com/chemprop/chemprop/pull/841
* Change Docker sytnax for MyBinder compatibility by JacksonBurns in https://github.com/chemprop/chemprop/pull/872
* [V2] Fix featurizer cli by hwpang in https://github.com/chemprop/chemprop/pull/865
* Fix hyperparameter predictorbase by c-w-feldmann in https://github.com/chemprop/chemprop/pull/832
* V2: Add all notebooks to test by hwpang in https://github.com/chemprop/chemprop/pull/840
* Fix small bugs in hpopt by akshatzalte in https://github.com/chemprop/chemprop/pull/873
* Add pip setup step to environment.yml install instructions by cjmcgill in https://github.com/chemprop/chemprop/pull/889
* Avoid scrambling target column name order by JacksonBurns in https://github.com/chemprop/chemprop/pull/893
* Fix unused parameters issue in DDP by shihchengli in https://github.com/chemprop/chemprop/pull/883
* Fix the inference issue related to the target columns by shihchengli in https://github.com/chemprop/chemprop/pull/895
* Change the default trial scheduler to `FIFOScheduler` by shihchengli in https://github.com/chemprop/chemprop/pull/896
* Add Optuna support for HPO by shihchengli in https://github.com/chemprop/chemprop/pull/888
* Fix Circular Import with `isort` by JacksonBurns in https://github.com/chemprop/chemprop/pull/887
* make LookupAction work with ConfigArgParse by KnathanM in https://github.com/chemprop/chemprop/pull/900
* V2: Fix typo in hpopt installation instruction by hwpang in https://github.com/chemprop/chemprop/pull/897
* V2: Make hpopt config compatible with training config by hwpang in https://github.com/chemprop/chemprop/pull/881
* Fix DDP prediction and checkpoint Issues by shihchengli in https://github.com/chemprop/chemprop/pull/884
* Add simple cache to CLI by KnathanM in https://github.com/chemprop/chemprop/pull/903
* V2: Fix small hpopt bugs and add example notebook by hwpang in https://github.com/chemprop/chemprop/pull/842

New Contributors
* akshatzalte made his first contribution in https://github.com/chemprop/chemprop/pull/873

**Full Changelog**: https://github.com/chemprop/chemprop/compare/v2.0.0...v2.0.1

This is the first stable release of Chemprop v2.0.0, with updates since the v2.0.0-rc.1 release candidate in early March.

The primary objectives of v2.0.0 are making Chemprop more usable from within Python scripts, more modular, easier to maintain and develop, more compute/memory efficient, and usable with PyTorch Lightning. Some features will not be migrated from v1 to v2 (e.g. web, sklearn). Some v1 features will be added in later versions of v2 (v2.1+) (e.g. uncertainty, interpret, atom- and bond-targets); see milestones [here](https://github.com/chemprop/chemprop/milestones). The new version also has substantially faster featurization speeds and much higher unit test coverage, enables training on multiple GPUs, and works on Windows (in addition to Linux and Mac). Finally, the incorporation of a batch normalization layer is expected to result in smoother training and improved predictions. We encourage all Chemprop users to try using v2.0.0 to see how it can improve their workflows.

v2 documentation can be found [here](https://chemprop.readthedocs.io/en/main/).

There are v2 tutorial notebooks in the [`examples/`](https://github.com/chemprop/chemprop/tree/main/examples) directory.

A helpful transition guide from Chemprop v1 to v2 can be found [here](https://docs.google.com/spreadsheets/u/3/d/e/2PACX-1vRshySIknVBBsTs5P18jL4WeqisxDAnDE5VRnzxqYEhYrMe4GLS17w5KeKPw9sged6TmmPZ4eEZSTIy/pubhtml). This includes a side-by-side comparison of CLI argument options, a list of which arguments will be implemented in later versions of v2, and a list of changes to default hyperparameters.

Note that if you install from source, the primary branch of our repository has been renamed from `master` to `main`.

Due to development team bandwidth, Chemprop v1 will no longer be actively developed, so that we can focus our efforts on v2. Bug reports and questions about v1 are still welcome to benefit users who haven't yet made the switch to v2, but bug reports will not be fixed by the development team.

Please let us know of any bugs you find, questions you have, or enhancements you want in Chemprop v2 by opening an issue.

This is a release candidate for Chemprop v2.0.0, to be released in April 2024.

The primary objectives of v2.0.0 are making Chemprop more usable from within Python scripts, more modular, easier to maintain and develop, more compute/memory efficient, and usable with PyTorch Lightning. Some features will not be migrated from v1 to v2 (e.g. web, sklearn). Some v1 features will be added in later versions of v2 (v2.1+) (e.g. uncertainty, interpret, atom- and bond-targets); see milestones [here](https://github.com/chemprop/chemprop/milestones). The new version also has substantially faster featurization speeds and much higher unit test coverage, enables training on multiple GPUs, and works on Windows (in addition to Linux and Mac). Finally, the incorporation of a batch normalization layer is expected to result in smoother training and improved predictions. The label as a “release candidate” reflects its availability to be downloaded via PyPI and that only minor changes are expected for the Python API before the final release. We expect most remaining changes before the release of v2.0.0 in April to be focused on additional improvements to the command line interface (CLI), which does not yet have feature parity with v1. We encourage all Chemprop users to try using v2.0.0-rc.1 to see how it can improve their workflows.

The v2 documentation can be found [here](https://chemprop.readthedocs.io/en/v2-dev/index.html).

There are tutorial notebooks for v2 in the [examples/](https://github.com/chemprop/chemprop/tree/v2/dev/examples) directory.

A helpful transition guide from v1 to v2 can be found [here](https://docs.google.com/spreadsheets/u/3/d/e/2PACX-1vRshySIknVBBsTs5P18jL4WeqisxDAnDE5VRnzxqYEhYrMe4GLS17w5KeKPw9sged6TmmPZ4eEZSTIy/pubhtml). This includes a side-by-side comparison of CLI argument options, a list of which arguments will be implemented in later versions of v2, and a list of changes to default hyperparameters.

You can subscribe to our development status and notes for this version: https://github.com/chemprop/chemprop/issues/517.

Ongoing work for this version is available on the `v2/dev` [branch](https://github.com/chemprop/chemprop/tree/v2/dev).

Please let us know of any bugs you find by opening an issue.

This is the final release of chemprop v1. All future development will be done on [chemprop v2](https://github.com/chemprop/chemprop/issues/517). The development team is still happy to answer questions about v1, but no new feature requests or PRs for v1 will be accepted. Users who identify bugs in v1 are still encouraged to open issues to report them - they will be tagged as [`v1-wontfix`](https://github.com/chemprop/chemprop/labels/v1-wontfix) to signify that we won't be publishing fixes for them in official chemprop releases, but the bugs can still be open to community discussion.

We encourage all users to try migrating their workflows over to chemprop v2 (available now as a release candidate, stable version planned to be released within the next week) and let us know of any issues you encounter. All v1 releases will remain available on PyPI, and the v1 source code will remain available in this GitHub organization.

What's Changed
* fix the `uncal_vars` for atom/bond property prediction by shihchengli in https://github.com/chemprop/chemprop/pull/712
* [v1]: Add Docker Image Building Action and Official Images to DockerHub by JacksonBurns in https://github.com/chemprop/chemprop/pull/718
* remove macos and windows from v1 ci by JacksonBurns in https://github.com/chemprop/chemprop/pull/720
* update docker build `if` to use correct upstream branch name by JacksonBurns in https://github.com/chemprop/chemprop/pull/723
* fix the task names by shihchengli in https://github.com/chemprop/chemprop/pull/725
* Fixed typo in README.md by willspag in https://github.com/chemprop/chemprop/pull/745

New Contributors
* willspag made their first contribution in https://github.com/chemprop/chemprop/pull/745

**Full Changelog**: https://github.com/chemprop/chemprop/compare/v1.7.0...v1.7.1

What's Changed
* new split per molecular weight by soulios in https://github.com/chemprop/chemprop/pull/456
* Specify license for Chemprop logos by mliu49 in https://github.com/chemprop/chemprop/pull/461
* Add `todo.md` by davidegraff in https://github.com/chemprop/chemprop/pull/492
* Update authors list in license file and alphabetically sort by cjmcgill in https://github.com/chemprop/chemprop/pull/532
* update authors in LICENSE and setup files for v1 by kevingreenman in https://github.com/chemprop/chemprop/pull/533
* Fix Transpose bug in Inequality Regression by cjmcgill in https://github.com/chemprop/chemprop/pull/308
* Add Dirichlet Evidential Uncertainty Quantification by cjmcgill in https://github.com/chemprop/chemprop/pull/423
* New metrics by soulios in https://github.com/chemprop/chemprop/pull/542
* Updating README with ADMET-AI details by swansonk14 in https://github.com/chemprop/chemprop/pull/554
* Improve error message when gilbrat is needed. by KnathanM in https://github.com/chemprop/chemprop/pull/569
* limit chempropv1 python version to 3.7, 3.8 only by JacksonBurns in https://github.com/chemprop/chemprop/pull/618
* Add a `CITATIONS.bib` by JacksonBurns in https://github.com/chemprop/chemprop/pull/627
* Limit Maximum Allowed `flask` Version in v1 by JacksonBurns in https://github.com/chemprop/chemprop/pull/628
* move num_unc_tasks definition to ensure always defined by kevingreenman in https://github.com/chemprop/chemprop/pull/632
* Switching np.mean to np.nanmean to handle NaN metrics by swansonk14 in https://github.com/chemprop/chemprop/pull/453
* Fix the dtype for targets of different sizes by shihchengli in https://github.com/chemprop/chemprop/pull/638
* Add setters for atom and bond constraints by shihchengli in https://github.com/chemprop/chemprop/pull/637
* switch v1 readthedocs build from conda to mamba by kevingreenman in https://github.com/chemprop/chemprop/pull/660
* Fix v1 docs theme by kevingreenman in https://github.com/chemprop/chemprop/pull/669
* Conformal Calibration by danielxu9393 in https://github.com/chemprop/chemprop/pull/304
* add note on feature releases and instructions for ssl+ddp by JacksonBurns in https://github.com/chemprop/chemprop/pull/685
* remove unnecessary argument for reshape function by shihchengli in https://github.com/chemprop/chemprop/pull/671
* Fix atom/bond property prediction with atom-mapped SMILES and target classification by shihchengli in https://github.com/chemprop/chemprop/pull/673
* Pass num_workers to MoleculeDataLoader during interpretation by kevingreenman in https://github.com/chemprop/chemprop/pull/691
* conformal quantile prediction bug fix by shihchengli in https://github.com/chemprop/chemprop/pull/693

New Contributors
* soulios made their first contribution in https://github.com/chemprop/chemprop/pull/456
* danielxu9393 made their first contribution in https://github.com/chemprop/chemprop/pull/304

**Full Changelog**: https://github.com/chemprop/chemprop/compare/v1.6.1...v1.7.0

Bug fix
PR 383 unexpectedly broke the atom mapping for reaction mode. The issue is described in Issue 426 and fixed by PR 427.

What's Changed
* Fix versioning issues - metadata and dependencies by kevingreenman in https://github.com/chemprop/chemprop/pull/420
* add job to tests action for PyPI package by JacksonBurns in https://github.com/chemprop/chemprop/pull/422
* added chemprop manuscript to readme by hesther in https://github.com/chemprop/chemprop/pull/425
* Keep Support for Python 3.7 and 3.8 when fixing `gilbrat` Issue by JacksonBurns in https://github.com/chemprop/chemprop/pull/431
* Fix reaction atom mapping by shihchengli in https://github.com/chemprop/chemprop/pull/427


**Full Changelog**: https://github.com/chemprop/chemprop/compare/v1.6.0...v1.6.1