Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add new default feature preset and updates for new matminer & pymatgen versions #101

Merged
merged 11 commits into from
Dec 21, 2022
Merged

Add new default feature preset and updates for new matminer & pymatgen versions #101

merged 11 commits into from
Dec 21, 2022

Conversation

ml-evs
Copy link
Collaborator

@ml-evs ml-evs commented Oct 17, 2022 •
edited
Loading

This PR updates most of the core dependencies of MODNet to the latest versions, plus a few associated changes:

  • Disable slow tests in CI and uses a pip cache to accelerate install time (closes CI tests are very slow #102)
  • Add a new Matminer2023Featurizer/CompositionOnlyMatminer2023Featurizer that mimics the old DeBreuck2020Featurizer but uses the latest matminer featurizer definitions (same featurizers, but potentially different values and different representations required).
  • Makes Matminer2023 the new default preset.
  • Adds a warning when loading DeBreuck2020Featurizer with an incompatible matminer version (i.e. >0.6).

@ml-evs
Copy link
Collaborator Author

ml-evs commented Dec 16, 2022 •
edited
Loading

This is currently held up by hackingmaterials/matminer#896 and hackingmaterials/matminer#864, but I've done the appropriate plumbing, defined a new featurizer for 2023 and updated the tests.

EDIT: tweaked the code to add my patch from the above PR.

@ml-evs ml-evs force-pushed the ml-evs/update_deps branch 3 times, most recently from 45a9836 to e7851fd Compare December 16, 2022 18:17
@ml-evs ml-evs changed the title Update dependencies Changes required to latest pymatgen and matminer Dec 16, 2022
@ml-evs ml-evs force-pushed the ml-evs/update_deps branch 5 times, most recently from 5ea310d to a17d41f Compare December 18, 2022 22:54
@ml-evs ml-evs changed the title Changes required to latest pymatgen and matminer Add new default feature preset and updates for new matminer & pymatgen versions Dec 18, 2022
@ml-evs ml-evs marked this pull request as ready for review December 18, 2022 23:01
This was referenced Dec 20, 2022
Closed
Merged
ppdebreuck
ppdebreuck reviewed Dec 20, 2022
View reviewed changes
README.md Outdated Show resolved Hide resolved
ppdebreuck
ppdebreuck approved these changes Dec 20, 2022
View reviewed changes
Copy link
Owner

@ppdebreuck ppdebreuck left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks @ml-evs !

@ml-evs ml-evs force-pushed the ml-evs/update_deps branch 2 times, most recently from 68e0574 to 2ba4fed Compare December 21, 2022 10:43
dependabot bot and others added 8 commits December 21, 2022 11:46
@dependabot @ml-evs
Update many dependencies
36ec3e0 
Bump pymatgen from 2020.8.13 to 2022.9.21

Bumps [pymatgen](https://github.com/materialsproject/pymatgen) from 2020.8.13 to 2022.9.21.
- [Release notes](https://github.com/materialsproject/pymatgen/releases)
- [Changelog](https://github.com/materialsproject/pymatgen/blob/master/CHANGES.rst)
- [Commits](materialsproject/pymatgen@v2020.8.13...v2022.9.21)

---
updated-dependencies:
- dependency-name: pymatgen
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

Bump matminer from 0.6.5 to 0.7.8

Bumps [matminer](https://github.com/hackingmaterials/matminer) from 0.6.5 to 0.7.8.
- [Release notes](https://github.com/hackingmaterials/matminer/releases)
- [Changelog](https://github.com/hackingmaterials/matminer/blob/main/docs/changelog.html)
- [Commits](hackingmaterials/matminer@v0.6.5...v0.7.8)

---
updated-dependencies:
- dependency-name: matminer
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Update sphinx requirement from ~=4.4 to ~=5.3

Updates the requirements on [sphinx](https://github.com/sphinx-doc/sphinx) to permit the latest version.
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES)
- [Commits](sphinx-doc/sphinx@v4.4.0...v5.3.0)

---
updated-dependencies:
- dependency-name: sphinx
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

Bump scikit-learn from 0.23.2 to 1.1.2

Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 0.23.2 to 1.1.2.
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@0.23.2...1.1.2)

---
updated-dependencies:
- dependency-name: scikit-learn
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

Bump scikit-learn from 0.23.2 to 1.2.0

Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 0.23.2 to 1.2.0.
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@0.23.2...1.2.0)

---
updated-dependencies:
- dependency-name: scikit-learn
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

Bump numpy from 1.23.4 to 1.23.5

Bumps [numpy](https://github.com/numpy/numpy) from 1.23.4 to 1.23.5.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.23.4...v1.23.5)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

Bump pandas from 1.5.0 to 1.5.2

Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.5.0 to 1.5.2.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Changelog](https://github.com/pandas-dev/pandas/blob/main/RELEASE.md)
- [Commits](pandas-dev/pandas@v1.5.0...v1.5.2)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

Unpin deps in setup.py

Bump matminer to 0.8

Update pre-commit hooks
@ml-evs
Update outdated pymatgen imports and associated tweaks
0cafb24
@ml-evs
Add warning to DeBreuck2020Featurizer when used with newer matminer
7e51577
@ml-evs
Add and make default a Matminer2023 featurizer preset
f1ae91f 
- Rename old test moddatas to 2020 and add 2023 versions and update tests

- Add same alias to new moddata
@ml-evs
Add pip dependency cache
57ad6b7
@ml-evs
Bump modnet version to 0.2.0~develop
cdd92ea
@ml-evs
Fix CI pip install process
e8a528d
@ml-evs
Simplify CI pip cache
f80ffe3
@ml-evs
Slow dependabot down and also configure gh actions updates
31c8491
@ml-evs
Remove specific pymatgen clause in README
96da75e
@ml-evs
Fix some typos and format changes
4e96424 
- Fix spelling 'mistake'

- Fix another typo

- Fix shields.io badge using new format

- Fix hopefully final typo
@ml-evs ml-evs merged commit baec48a into master Dec 21, 2022
@ml-evs ml-evs deleted the ml-evs/update_deps branch December 21, 2022 10:52
@ml-evs ml-evs mentioned this pull request Jan 10, 2023
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ppdebreuck ppdebreuck ppdebreuck approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

CI tests are very slow
2 participants
@ml-evs @ppdebreuck