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Convert StructureMatcher inline code to HTML for partial link #59

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Aug 24, 2022
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Convert StructureMatcher inline code to HTML for partial link #59

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auto format readme
janosh Aug 19, 2022
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StructureMatcher readme inline code to HTML
janosh Aug 19, 2022
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Merge branch 'main' into readme-structurematcher-link
janosh Aug 20, 2022
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24 changes: 15 additions & 9 deletions README.md
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Expand Up @@ -24,6 +24,7 @@ of best (i.e. metric) associated with it.
## Getting Started

Installation, a dummy example, output metrics for the example, and descriptions of the benchmark metrics.

### Installation

Create a conda environment with the `matbench-genmetrics` package installed from the
Expand Down Expand Up @@ -101,15 +102,16 @@ print(mptm.recorded_metrics)

### Metrics

| Metric | Description |
|---|---|
| Validity | One minus (Wasserstein distance between distribution of space group numbers for train and generated structures divided by distance of dummy case between train and `space_group_number == 1`). See also https://github.com/sparks-baird/matbench-genmetrics/issues/44 |
| Coverage | Match counts between held-out test structures and generated structures divided by number of test structures ("predict the future"). |
| Novelty | One minus (match counts between train structures and generated structures divided by number of generated structures). |
| Uniqueness | One minus (non-self-comparing match counts within generated structures divided by total possible non-self-comparing matches). |
| Metric | Description |
| ---------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Validity | One minus (Wasserstein distance between distribution of space group numbers for train and generated structures divided by distance of dummy case between train and `space_group_number == 1`). See also <https://github.com/sparks-baird/matbench-genmetrics/issues/44> |
| Coverage | Match counts between held-out test structures and generated structures divided by number of test structures ("predict the future"). |
| Novelty | One minus (match counts between train structures and generated structures divided by number of generated structures). |
| Uniqueness | One minus (non-self-comparing match counts within generated structures divided by total possible non-self-comparing matches). |

A match is when <code><a href="https://pymatgen.org/pymatgen.analysis.structure_matcher.html#pymatgen.analysis.structure_matcher.StructureMatcher">StructureMatcher</a>(stol=0.5, ltol=0.3, angle_tol=10.0).fit(s1, s2)</code> evaluates to `True`.


A match is when [`StructureMatcher`](https://pymatgen.org/pymatgen.analysis.structure_matcher.html#pymatgen.analysis.structure_matcher.StructureMatcher)`(stol=0.5, ltol=0.3, angle_tol=10.0).fit(s1, s2)`
evaluates to `True`.

## Advanced Installation

Expand Down Expand Up @@ -197,17 +199,21 @@ Then take a look into the `scripts` and `notebooks` folders.
in `setup.cfg` if you want to ship and install your package via `pip` later on.
2. Create concrete dependencies as `environment.lock.yml` for the exact reproduction of your
environment with:

```bash
conda env export -n matbench-genmetrics -f environment.lock.yml
```

For multi-OS development, consider using `--no-builds` during the export.
3. Update your current environment with respect to a new `environment.lock.yml` using:

```bash
conda env update -f environment.lock.yml --prune
```

## Project Organization

```
```txt
├── AUTHORS.md <- List of developers and maintainers.
├── CHANGELOG.md <- Changelog to keep track of new features and fixes.
├── CONTRIBUTING.md <- Guidelines for contributing to this project.
Expand Down