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janoshjanosh
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v0.1.5 (#44)
* bump prettier v3 * more descriptive var names * v0.1.5 * fix ruff PT011 * GH Pages npm install --force
1 parent c03d741 commit 82037a8

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‎.github/workflows/gh-pages.yml‎

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with:
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python-version: "3.11"
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working-directory: site
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install-cmd: npm install --force
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pre-build: |
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pip install lazydocs
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# lazydocs needs package deps to be installed

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.0.275
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rev: v0.0.277
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hooks:
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- id: ruff
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args: [--fix]
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args: [--ignore-words-list, "nd,te,fpr"]
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: v3.0.0-alpha.9-for-vscode
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rev: v3.0.0
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hooks:
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- id: prettier
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args: [--write] # edit files in-place

‎changelog.md‎

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All notable changes to this project will be documented in this file. Dates are displayed in UTC.
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#### [v1.0.0](https://github.com/janosh/matbench-discovery/compare/v0.1.4...v1.0.0)
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#### [v0.1.5](https://github.com/janosh/matbench-discovery/compare/v0.1.4...v0.1.5)
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> 7 July 2023
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- v0.1.5 [`#44`](https://github.com/janosh/matbench-discovery/pull/44)
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- [pre-commit.ci] pre-commit autoupdate [`#42`](https://github.com/janosh/matbench-discovery/pull/42)
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- Update site to show ALIGNN results [`#38`](https://github.com/janosh/matbench-discovery/pull/38)
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- ALIGNN test on WBM data [`#37`](https://github.com/janosh/matbench-discovery/pull/37)
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- Add PDF versions of all SI figures [`#36`](https://github.com/janosh/matbench-discovery/pull/36)
@@ -18,6 +22,7 @@ All notable changes to this project will be documented in this file. Dates are d
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- Add `upload_to_figshare.py` and replace local data-loading with cached Figshare downloads [`#13`](https://github.com/janosh/matbench-discovery/pull/13)
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- DRY workflows [`#8`](https://github.com/janosh/matbench-discovery/pull/8)
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- Add `Files`, `DataFiles` and `PredFiles` classes in `matbench_discovery/data.py` [`#7`](https://github.com/janosh/matbench-discovery/pull/7)
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- fix path issues and using JSON pandas reader for CSV files in train_(cgcnn|wrenformer).py (closes #43) [`#43`](https://github.com/janosh/matbench-discovery/issues/43)
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- Fix KeyError('wyckoff_spglib') in `fetch_process_wbm_dataset.py` (#34) [`#32`](https://github.com/janosh/matbench-discovery/issues/32) [`#33`](https://github.com/janosh/matbench-discovery/issues/33)
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- Fix `compute_struct_fingerprints.py`: cannot insert `material_id`, already exists (#31) [`#30`](https://github.com/janosh/matbench-discovery/issues/30)
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- Fix `fetch_process_wbm_dataset.py` unnecessarily loading WBM initial structures from disk (#29) [`#28`](https://github.com/janosh/matbench-discovery/issues/28)
@@ -38,6 +43,7 @@ All notable changes to this project will be documented in this file. Dates are d
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- add scripts/compute_struct_fingerprints.py to generate matminer SiteStats fingerprints for all MP+WBM structures [`7946b5e`](https://github.com/janosh/matbench-discovery/commit/7946b5e433713ef8f46b839562f09d889331e63b)
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- split model run times into train and test contribs [`b8a18d8`](https://github.com/janosh/matbench-discovery/commit/b8a18d8fd357ea4ec77dae837fdb8317fe978b28)
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- add models/chgnet/{test_chgnet,join_m3gnet_results}.py [`da39074`](https://github.com/janosh/matbench-discovery/commit/da390741b0d0f03fbcca5bcbac725c2211a80427)
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- git surgery purging all large CSV files from repo history [`4a90dee`](https://github.com/janosh/matbench-discovery/commit/4a90dee85965aebbcfcd547353c548eeb19651ce)
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- add scripts/compute_projections.py [`eec1cb4`](https://github.com/janosh/matbench-discovery/commit/eec1cb4073c2db65cd238157f656af963582ffc5)
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- make horizontal versions of roc-models-2x4.pdf and model-run-times-bar.pdf [`551050e`](https://github.com/janosh/matbench-discovery/commit/551050e17cc98cf786707448fd304bb06177a914)
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- add changelog.md [`0621282`](https://github.com/janosh/matbench-discovery/commit/0621282b0ed6ca397b6293e8d6f2bcbaac736468)
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- tweak contributing guide [`b3ea8d3`](https://github.com/janosh/matbench-discovery/commit/b3ea8d3980d62032ed33ae75fb0c7539fafcebe3)
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- upload @pbenner's ALIGNN checkpoint to Figshare and link from models/alignn/readme.md [`da56377`](https://github.com/janosh/matbench-discovery/commit/da5637725e3f785cdf8bd82ff6a3be95858b2eae)
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- start preprint [`fd8355d`](https://github.com/janosh/matbench-discovery/commit/fd8355dca9fe87ef9196980c06907ef377fdcd97)
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- git surgery purging all large CSV files from repo history [`873fa75`](https://github.com/janosh/matbench-discovery/commit/873fa7559fab539f2f1fe8fe6557d5c530b5aabc)
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- rename pages /about-test-test-set to /about-the-data and /how-to-contribute to /contribute [`e41ca32`](https://github.com/janosh/matbench-discovery/commit/e41ca32e768ea06f404b216353521f89e6bee2e2)
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#### v0.1.4
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> 24 February 2023
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> 19 June 2023
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- Add WBM element heatmap to site and data/wbm/readme.md [`#6`](https://github.com/janosh/matbench-discovery/pull/6)
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- doc: remove reference to alignn [`#4`](https://github.com/janosh/matbench-discovery/pull/4)

‎data/mp/get_mp_energies.py‎

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# %%
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df_cse = pd.read_json(DATA_FILES.mp_computed_structure_entries).set_index("material_id")
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df_cse["structure"] = [
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Structure.from_dict(cse["structure"]) for cse in tqdm(df_cse.entry)
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struct_col = "structure"
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df_cse[struct_col] = [
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Structure.from_dict(cse[struct_col]) for cse in tqdm(df_cse.entry)
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]
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wyk_col = "wyckoff_spglib"
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df_cse[wyk_col] = [
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wyckoff_col = "wyckoff_spglib"
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df_cse[wyckoff_col] = [
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get_aflow_label_from_spglib(struct, errors="ignore")
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for struct in tqdm(df_cse.structure)
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]
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# make sure symmetry detection succeeded for all structures
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assert df_cse[wyk_col].str.startswith("invalid").sum() == 0
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df[wyk_col] = df_cse[wyk_col]
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assert df_cse[wyckoff_col].str.startswith("invalid").sum() == 0
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df[wyckoff_col] = df_cse[wyckoff_col]
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spg_nums = df[wyk_col].str.split("_").str[2].astype(int)
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spg_nums = df[wyckoff_col].str.split("_").str[2].astype(int)
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# make sure all our spacegroup numbers match MP's
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assert (spg_nums.sort_index() == df_spg["number"].sort_index()).all()
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‎data/wbm/eda.py‎

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# %%
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wyk_col, spg_col = "wyckoff_spglib", "spacegroup"
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df_wbm[spg_col] = df_wbm[wyk_col].str.split("_").str[2].astype(int)
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df_mp[spg_col] = df_mp[wyk_col].str.split("_").str[2].astype(int)
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wyckoff_col, spg_col = "wyckoff_spglib", "spacegroup"
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df_wbm[spg_col] = df_wbm[wyckoff_col].str.split("_").str[2].astype(int)
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df_mp[spg_col] = df_mp[wyckoff_col].str.split("_").str[2].astype(int)
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# %%

‎models/cgcnn/train_cgcnn.py‎

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df_in = pd.read_csv(data_path).set_index(id_col)
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df_cse = pd.read_json(DATA_FILES.mp_computed_structure_entries).set_index(id_col)
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df_in[input_col] = [Structure.from_dict(cse["structure"]) for cse in tqdm(df_cse.entry)]
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df_in[input_col] = [Structure.from_dict(cse[input_col]) for cse in tqdm(df_cse.entry)]
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assert target_col in df_in
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‎models/wrenformer/analyze_wrenformer.py‎

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).index
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spg_col = "spacegroup"
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wyk_col = "wyckoff_spglib"
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df_wbm[spg_col] = df_wbm[wyk_col].str.split("_").str[2].astype(int)
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wyckoff_col = "wyckoff_spglib"
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df_wbm[spg_col] = df_wbm[wyckoff_col].str.split("_").str[2].astype(int)
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df_bad = df_wbm.loc[bad_ids]
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title = f"{len(df_bad)} {model} preds<br>with {max_each_true=}, {min_each_pred=}"
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# %%
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df_mp = pd.read_csv(DATA_FILES.mp_energies).set_index("material_id")
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df_mp[spg_col] = df_mp[wyk_col].str.split("_").str[2].astype(int)
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df_mp["isopointal_proto_from_aflow"] = df_mp[wyk_col].map(
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df_mp[spg_col] = df_mp[wyckoff_col].str.split("_").str[2].astype(int)
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df_mp["isopointal_proto_from_aflow"] = df_mp[wyckoff_col].map(
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get_isopointal_proto_from_aflow
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)
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df_mp.isopointal_proto_from_aflow.value_counts().head(12)
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# %%
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proto_col = "Isopointal Prototypes"
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df_proto_counts = (
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df_bad[wyk_col].map(get_isopointal_proto_from_aflow).value_counts().to_frame()
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df_bad[wyckoff_col].map(get_isopointal_proto_from_aflow).value_counts().to_frame()
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‎pyproject.toml‎

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[project]
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name = "matbench-discovery"
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version = "0.1.4"
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version = "0.1.5"
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description = "A benchmark for machine learning energy models on inorganic crystal stability prediction from unrelaxed structures"
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authors = [{ name = "Janosh Riebesell", email = "janosh@lbl.gov" }]
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readme = "readme.md"
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"PLR", # pylint refactor
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"PLW2901", # redefined-loop-name
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"PT006", # pytest-parametrize-names-wrong-type
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"PT011", # pytest-raises-too-broad
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"PT013", # pytest-incorrect-pytest-import
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]
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pydocstyle.convention = "google"

‎site/package.json‎

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"@iconify/svelte": "^3.1.4",
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"@rollup/plugin-yaml": "^4.1.1",
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"@sveltejs/adapter-static": "^2.0.2",
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"@sveltejs/kit": "^1.21.0",
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"@sveltejs/kit": "^1.22.1",
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"@sveltejs/vite-plugin-svelte": "^2.4.2",
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"@typescript-eslint/eslint-plugin": "^5.61.0",
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"@typescript-eslint/parser": "^5.61.0",
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"js-yaml": "^4.1.0",
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"katex": "^0.16.8",
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"mdsvex": "^0.11.0",
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"prettier": "^2.8.8",
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"prettier": "^3.0.0",
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"prettier-plugin-svelte": "^2.10.1",
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"rehype-autolink-headings": "^6.1.1",
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"rehype-katex-svelte": "^1.2.0",
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"rehype-slug": "^5.1.0",
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"remark-math": "3.0.0",
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"svelte": "^4.0.3",
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"svelte-check": "^3.4.4",
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"svelte": "^4.0.5",
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"svelte-check": "^3.4.5",
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"svelte-multiselect": "^10.0.0",
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"svelte-preprocess": "^5.0.4",
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"svelte-toc": "^0.5.5",
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"svelte-zoo": "^0.4.8",
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"svelte2tsx": "^0.6.16",
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"svelte2tsx": "^0.6.19",
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"tslib": "^2.6.0",
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"typescript": "5.1.6",
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"vite": "^4.3.9"
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"vite": "^4.4.2"
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},
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"prettier": {
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"semi": false,

‎site/src/app.html‎

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<!DOCTYPE html>
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<!doctype html>
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<html lang="en">
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<head>
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<meta name="author" content="Janosh Riebesell" />

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