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

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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

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ml-evs
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@ml-evs ml-evs commented Oct 17, 2022 •
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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).

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ml-evs commented Dec 16, 2022 •
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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
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ppdebreuck reviewed Dec 20, 2022
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ppdebreuck approved these changes Dec 20, 2022
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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] <[email protected]>

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] <[email protected]>

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] <[email protected]>

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] <[email protected]>

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] <[email protected]>

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] <[email protected]>

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] <[email protected]>

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
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CI tests are very slow
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