README.qmd

---
format:
  gfm: default
execute:
  echo: false
engine: knitr
---

# severe-CDI

```{python paper_meta}
#| output: asis
import yaml
is_yaml = False
yaml_lines = list()
with open('paper/paper.qmd', 'r') as infile:
    for line in infile:
        if line.startswith('---'):
            is_yaml = not is_yaml
        elif is_yaml:
            yaml_lines.append(line)
yaml_dict = yaml.load(''.join(yaml_lines), Loader = yaml.CLoader)
print('####', ''.join(yaml_dict['title']))
print('\n')
print(', '.join(auth['name'] for auth in yaml_dict['author']))
```

## Abstract

```{python abstract}
#| output: asis
print(yaml_dict['abstract'])
```

## Manuscript

- [Quarto](paper/paper.qmd)
- [PDF](paper/paper.pdf)
- [Markdown](paper/paper-gfm.md)

### Word count

```{python word_count}
#| output: asis
with open('paper/word_count.txt', 'r') as infile:
    for line in infile:
      print('-', line.strip(), end = '\n')
```