Releases | Open Source Science

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v1.0.4

Minor release to simply fix an error where debug logs were still included. Whoops :)

Scientific Software - Peer-reviewed - Python
Published by blaiszik over 1 year ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v1.0.3

Fixes minor bug that was preventing publishing Foundry datasets through the Python SDK. This was caused by a str-int issue on the publicationYear field.
Fixed a bug that allowed users to set a local and Globus source for data to be published

Scientific Software - Peer-reviewed - Python
Published by blaiszik over 1 year ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v1.0.2

Fixed a bug that did not bundle the full schema files with the PyPI release.

Scientific Software - Peer-reviewed - Python
Published by blaiszik over 1 year ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v1.0.1

Add openpyxl and bump mdfconnectclient to latest

Scientific Software - Peer-reviewed - Python
Published by blaiszik over 1 year ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v1.0.0

What's Changed

Add https upload by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/281
https upload bugfix by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/322
add static badge with link to gitbook by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/333
Update publishing notebook and minor bugfixes by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/336
Merging main into dev to reflect updates to logos and some README by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/300
Split specification by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/344
Implementing new search() function (and refactor) by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/408
Download dataset by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/413
Publishing rework by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/451
Publishing rework by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/455
Fix https download method by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/458
Fix https download method by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/460
Add repr_htmls and remove DLHub by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/461
Pydantic v2 updates. Minor updates to Foundry API to enable simple da… by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/462
Update examples by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/463

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/v0.5.1...v1.0.0

Scientific Software - Peer-reviewed - Python
Published by blaiszik over 1 year ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.7.7

What's Changed

Load fix by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/454
Minor fixes to allow organization or organizations in metadata for Fo… by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/453

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/v0.7.6...v0.7.7

Scientific Software - Peer-reviewed - Python
Published by blaiszik almost 2 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.7.6

Minor patch to change config MDF organization name from foundry to Foundry

Scientific Software - Peer-reviewed - Python
Published by blaiszik almost 2 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.7.5

What's Changed

Updated notebooks by @kjschmidt913 in https://github.com/MLMI2-CSSI/foundry/pull/421
Updating the way Colab env sets various global variables by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/427
Create data_publish issue template by @kjschmidt913 in https://github.com/MLMI2-CSSI/foundry/pull/431
Minor fixes to work with MDF Connect Client v0.5.0 by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/432

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/v0.7.4...v0.7.5

Scientific Software - Peer-reviewed - Python
Published by blaiszik almost 2 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.7.4

Minor release

Removes DLHub functionality and requirements (this is migrated to Garden)
Adds more robust support for https downloading. Deeper paths are supported and download progress is updated live
Minimize requirements (removed dlhub-sdk, scikit-learn)
Pins pydantic to avoid some validation errors in the newest releases (to address later)

Scientific Software - Peer-reviewed - Python
Published by blaiszik almost 2 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.7.3 -- Establish Zenodo integration

Integrate with Zenodo to have a persistent DOI that thinks to the sourcecode.

The DOI will be continuously updated to the latest release via Zenodo.

Scientific Software - Peer-reviewed - Python
Published by ascourtas almost 2 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.7.2 -- Download using HTTPS by default

Summary

Updated dataset download functionality to use HTTPS as the default; this means a user does not have to set up a Globus Endpoint in order to download or load a dataset. This should cut down on the barrier to entry for using Foundry Datasets and improve overall user experience. Documentation was updated accordingly.

Added minor updates to fix broken links in documentation and improve/standardize docstrings.

Fixed a broken GitBook integration such that changes made in our documentation are now reflected in the GitHub repo.

Changes made in line with JOSS paper submission review.

What's Changed

docstring updates by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/415
Add a Dependabot config to autoupdate GitHub action versions by @kurtmckee in https://github.com/MLMI2-CSSI/foundry/pull/393
Joss https default by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/416

New Contributors

@kurtmckee made their first contribution in https://github.com/MLMI2-CSSI/foundry/pull/393

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/v0.7.1...v0.7.2

Scientific Software - Peer-reviewed - Python
Published by ascourtas almost 2 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.7.1 - Code fixes, splits specification, and metadata validation and handling

This release addresses some previous bugs with loading datasets on init(); that functionality has been removed for the time being, in favor of a more robust refactor in future releases.

In addition to code fixes, we've added the following functionality and improvements:

Users can now specify to download specific splits when they load_data(); this reduces the time and RAM required for people to use datasets when they may only need part of it.

Ex: tr = f.load_data(split="train")

Also, dataset metadata are now validated with appropriate error handling, so a user publishing a new dataset is instantly notified if any part of their specification is incompatible with the metadata schema. This will improve the user experience for both dataset publishers and consumers.

Additionally, this release includes code cleanup, docs improvements, and new applied AI examples.

What's Changed

Metadata error handling by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/377
remove breaking changes that load on init by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/406
Split specification by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/344
automating api documentation using github action by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/342
Removing remnants of XTract by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/355
Merge Split specification from dev into main (https://github.com/MLMI2-CSSI/foundry/pull/344) by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/356
Update README.md with contributing instructions by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/357
add jingrui examples by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/363
Adds note for quickstart globus set to false by @marshallmcdonnell in https://github.com/MLMI2-CSSI/foundry/pull/374

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/v0.7.0...v0.7.1

Scientific Software - Peer-reviewed - Python
Published by ascourtas about 2 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - [YANKED] v0.7.0 -- New feature: loading split specifications

Yanked due to mistakenly deploying "Load on init" changes before they were ready

Overview

Users can now specify to download specific splits when they load_data(); this reduces the time and RAM required for people to use datasets when they may only need part of it.

Ex: tr = f.load_data(split="train")

Additionally, this release includes code cleanup, docs improvements, and new applied AI examples.

What's Changed

Split specification by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/344
automating api documentation using github action by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/342
Removing remnants of XTract by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/355
Merege Split specification from dev into main (#344) by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/356
Update README.md with contributing instructions by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/357
add jingrui examples by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/363
Load on init by @blue442 in https://github.com/MLMI2-CSSI/foundry/pull/358
Adds note for quickstart globus set to false by @marshallmcdonnell in https://github.com/MLMI2-CSSI/foundry/pull/374

New Contributors

@marshallmcdonnell made their first contribution in https://github.com/MLMI2-CSSI/foundry/pull/374

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/v0.6.3...v0.7.0

Scientific Software - Peer-reviewed - Python
Published by ascourtas over 2 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.6.3 -- Patch for requirements

Patch to update the base requirements for DLHub SDK to 2.0.3

Scientific Software - Peer-reviewed - Python
Published by ascourtas over 2 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.6.2 -- Swap default download method to HTTPS

This release changes the default download path to HTTPS from Globus. Users can still download using Globus by setting the flag globus=True in the Foundry load() function.

Scientific Software - Peer-reviewed - Python
Published by blaiszik over 2 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.6.0 -- Add ability to upload via HTTPS

Users now have the option to upload datasets via HTTPS instead of using Globus Connect Personal; this saves users time and energy.

Includes function name changes as well as updates for compatibility with DLHub SDK >= 2.0.x (container-service compat release).

Other changes include: - minor bugfixes - data publishing notebook updates

Scientific Software - Peer-reviewed - Python
Published by ascourtas over 2 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.5.1 -- Fix PyPI installation, improve docmentation

What's Changed

Improve HTTPS downloads by @WardLT in https://github.com/MLMI2-CSSI/foundry/pull/277
Update README.md by @Aadit-Ambadkar in https://github.com/MLMI2-CSSI/foundry/pull/275
updated model pub notebook by @kjschmidt913 in https://github.com/MLMI2-CSSI/foundry/pull/284
Set Header Images to an absolute URL via raw.githubusercontent by @cyschneck in https://github.com/MLMI2-CSSI/foundry/pull/283
remove extraneous "no" by @sgbaird in https://github.com/MLMI2-CSSI/foundry/pull/299
Add website link by @WardLT in https://github.com/MLMI2-CSSI/foundry/pull/301

New Contributors

@WardLT made their first contribution in https://github.com/MLMI2-CSSI/foundry/pull/277
@cyschneck made their first contribution in https://github.com/MLMI2-CSSI/foundry/pull/283
@sgbaird made their first contribution in https://github.com/MLMI2-CSSI/foundry/pull/299

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/v0.5.0...v0.5.1

Scientific Software - Peer-reviewed - Python
Published by blaiszik almost 3 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.5.0 -- Publish models to DLHub and improved dataset functionality

Overview

New functionality includes: - publish models to DLHub using publish_model() - search() capability for datasets - generate a BibTex citation using get_citation()

We also improved info logging, added testing for Python 3.10, parallelized HTTPS downloads for faster dataset loading, and added buttons in our example notebooks to open them in Google Colab.

Also includes code cleanup, minor bug fixes, and improved testing capabilities.

What's Changed

Fix Logging and Remove unnecessary code by @Aadit-Ambadkar in https://github.com/MLMI2-CSSI/foundry/pull/228
address code style (Issue #245) by @isaac-darling in https://github.com/MLMI2-CSSI/foundry/pull/246
Blaiszik patch 1 by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/238
add Python 3.10 tests and flake8 error checking by @isaac-darling in https://github.com/MLMI2-CSSI/foundry/pull/231
Add search by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/256
Create README.md by @kjschmidt913 in https://github.com/MLMI2-CSSI/foundry/pull/261
Open in Colab Buttons by @Aadit-Ambadkar in https://github.com/MLMI2-CSSI/foundry/pull/253
Moving some functions to utils by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/262
added the publish wrapper by @isaac-darling in https://github.com/MLMI2-CSSI/foundry/pull/235
Update README.md by @kjschmidt913 in https://github.com/MLMI2-CSSI/foundry/pull/269
Update README.md by @kjschmidt913 in https://github.com/MLMI2-CSSI/foundry/pull/270
Update read logic by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/271
Added new search test. Removed some stray commented-out code. by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/272
Paralellize HTTPS downloads. Remove joblib and six requirements by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/273
Get citation function by @blaiszik in https://github.com/MLMI2-CSSI/foundry/pull/274
Dev by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/265

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/v0.4.0...v0.5.0

Scientific Software - Peer-reviewed - Python
Published by ascourtas about 3 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.4.0 - Search functionality, plus updates to logging and testing

What's Changed

Added search() functionality to search through datsets, in addition to listing them all with list()
Improved logging capabilities and error messages
Added flake8 linting as mandatory
Made style changes per flake8 feedback
Added additional testing functionality

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/v0.3.0...v0.4.0

Scientific Software - Peer-reviewed - Python
Published by ascourtas over 3 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.3.0 - Minor release for compatibility with newest FuncX and DLHub

Overview

Compatibility with FuncX 1.0.x and DLHub SDK 1.0.0. Also includes testing clean up and improvements, the ability for a user to pass the funcX endpoint ID into run(), initial PyTorch Dataset support, and minor changes.

What's Changed

test python package dependency caching optimization by @BraedenCu in https://github.com/MLMI2-CSSI/foundry/pull/191
add option to pass in funcx_endpoint in run() by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/194
Add Convert to Pytorch Dataset Functionality by @Aadit-Ambadkar in https://github.com/MLMI2-CSSI/foundry/pull/200
Replace PNG with SVG by @Aadit-Ambadkar in https://github.com/MLMI2-CSSI/foundry/pull/202
Fix .load function by @Aadit-Ambadkar in https://github.com/MLMI2-CSSI/foundry/pull/227
fix unused imports, code style, and update syntax by @isaac-darling in https://github.com/MLMI2-CSSI/foundry/pull/229
merge tests into single file by @isaac-darling in https://github.com/MLMI2-CSSI/foundry/pull/233
To tf dataset by @Aadit-Ambadkar in https://github.com/MLMI2-CSSI/foundry/pull/201
Funcx 1.0.x compat by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/249
Dev - funcx and dlhub 1.0.0 compatibility by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/250

New Contributors

@BraedenCu made their first contribution in https://github.com/MLMI2-CSSI/foundry/pull/191
@isaac-darling made their first contribution in https://github.com/MLMI2-CSSI/foundry/pull/229

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/0.2.2...v0.3.0

Scientific Software - Peer-reviewed - Python
Published by ascourtas over 3 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - v0.2.2

The main goal of this release is to remove a dependency on the deprecated XTract service for https downloading of datasets.

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/0.2.1...0.2.2

Scientific Software - Peer-reviewed - Python
Published by blaiszik over 3 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - 0.2.0 -- Minor release for compatibility with Globus SDK 3

Add compatibility with Globus SDK 3. Additionally, add back in the f.run() functionality so users can run their DLHub models with the Foundry interface. Add visibility of DOIs to dataset summaries.

What's Changed

Adding doi to list by @kjschmidt913 in https://github.com/MLMI2-CSSI/foundry/pull/171
Fix init auth by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/176
update reqs for Globus SDK 3, and version to 0.2.0 by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/177
Dev by @ascourtas in https://github.com/MLMI2-CSSI/foundry/pull/178

Full Changelog: https://github.com/MLMI2-CSSI/foundry/compare/0.1.2...0.2.0

Scientific Software - Peer-reviewed - Python
Published by ascourtas over 3 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - (Yanked) 0.1.2 -- Patch to expose `f.run()` functionality

Re-added the f.run() functionality so that Foundry users can run DLHub servables using the Foundry SDK. Requires Globus SDK v2 and DLHub SDK version 0.10.0

EDIT: After release we discovered a bug where instantiating Foundry without providing authorizers resulted in an error; this was fixed in release 0.2.0, and this release was yanked

Scientific Software - Peer-reviewed - Python
Published by ascourtas over 3 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - 0.1.1 (minor patch)

Add joblib to setup.py and requirements.txt

Scientific Software - Peer-reviewed - Python
Published by ascourtas almost 4 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - 0.1.0 - Minor release for robust dataset functionality

Overview

includes updates from 2021 summer students
test coverage and GHA support
Foundry SDK fixes
improved example notebooks
OOP refactoring
README updates and improvements

Breaking Changes

Loading datasets has changed. Users will specify index=mdf when instantiating Foundry: f = Foundry(index="mdf") and will load data like this: f.load('dataset_name_or_DOI') data = f.load_data()["split_name"]

Previously, users did not specify an index and loaded data as f = f.load("dataset_name").

Scientific Software - Peer-reviewed - Python
Published by ascourtas about 4 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - 0.0.17

Patch to make Foundry compatible with Globus SDK>=3.0, as well as MDF. Currently incompatible with DLHub.

Scientific Software - Peer-reviewed - Python
Published by ascourtas about 4 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - 0.0.16

Bumping version in setup.py - previous conflicted with PyPI.
Updating funcX requirements

Scientific Software - Peer-reviewed - Python
Published by blaiszik over 4 years ago

Foundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Science - 0.0.15

Fixes issue with loading HDF5 files from the wrong path
Updates funcX requirement to be in line with the version needed.
Reduces testing on main deployment to PR only

Scientific Software - Peer-reviewed - Python
Published by blaiszik over 4 years ago