Merge pull request #29 from tillahoffmann/yaml

Change from json to yaml for readability.

.gitignore

@@ -154,6 +154,7 @@ figures/
 publications/*/*
 # ... except the summary and data
 !publications/*/*.json
+!publications/*/*.yaml
 !publications/*/*.rst
 
 shedding/*.c

README.rst

@@ -15,7 +15,7 @@ Uncertainties surrounding the concentration of viral RNA fragments in the faeces
 📊 Datasets
 -----------
 
-Datasets can be found in the ``publications`` directory as JSON files following a common schema (see ``schema.json`` for details). All RNA loads are reported as log10 gene copies per mL. The results from individual samples are linked to patients wherever possible to provide longitudional information.
+Datasets can be found in the ``publications`` directory as YAML files following a common schema (see ``schema.yaml`` for details). All RNA loads are reported as log10 gene copies per mL. The results from individual samples are linked to patients wherever possible to provide longitudional information.
 
 .. jinja::
 

conf.py

@@ -12,10 +12,10 @@
 from glob import glob
 import inspect
 from jinja2 import Template
-import json
 import os
 import shedding
 import sphinx
+import yaml
 
 
 def _parse_key(argument):
@@ -74,12 +74,12 @@ def setup(app):
 
 
 # -- Datasets for jinja templates --------------------------------------------
-filenames = glob("publications/*/*.json")
+filenames = glob("publications/*/*.yaml")
 jinja_context = {}
 for filename in sorted(filenames):
     with open(filename) as fp:
         key, _ = os.path.splitext(os.path.basename(filename))
-        jinja_context.setdefault("publications", {})[key] = json.load(fp)
+        jinja_context.setdefault("publications", {})[key] = yaml.safe_load(fp)
 
 # Get all modules for the documentation
 modules = set()
@@ -130,7 +130,11 @@ def setup(app):
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = [
+    ".eggs",
+    "build",
     "PolyChordLite",
+    "README.rst",
+    "venv",
 ]
 
 # -- Options for HTML output -------------------------------------------------

convert_cycle_threshold.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 import argparse
-import json
 import numpy as np
+import yaml
 
 
 LOOKUP = {
@@ -27,7 +27,7 @@ def parse_values(values):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     parser.add_argument(
-        "--format", choices=["plain", "json"], default="json", help="output format"
+        "--format", choices=["plain", "yaml"], default="yaml", help="output format"
     )
     parser.add_argument(
         "--log10",
@@ -46,9 +46,9 @@ def parse_values(values):
     poly = np.polynomial.Polynomial.fit(args.reference, args.target, 1)
     results = poly(np.log10(args.values) if args.log10 else args.values)
 
-    if args.format == "json":
+    if args.format == "yaml":
         results = [{"reference": x, "target": y} for x, y in zip(args.values, results)]
-        print(json.dumps(results, indent=4))
+        print(yaml.dumps(results, indent=4))
     elif args.format == "plain":
         print("\n".join(map(str, results)))
     else:

plot_datasets.py

@@ -1,7 +1,7 @@
 from glob import glob
-import json
 from matplotlib import pyplot as plt
 import numpy as np
+import yaml
 
 
 def to_float(x):
@@ -15,15 +15,15 @@ def to_float(x):
     "head_width": 0.1,
 }
 lim_length = 0.25
-filenames = glob("publications/*/*.json")
+filenames = glob("publications/*/*.yaml")
 
 fig, ax = plt.subplots()
 ylabels = []
 for i, filename in enumerate(sorted(filenames, reverse=True)):
     color = f"C{i}"
 
     with open(filename) as fp:
-        publication = json.load(fp)
+        publication = yaml.safe_load(fp)
     ylabels.append(publication["key"])
 
     # Plot the level of quantification

publications/Cheung2020/Cheung2020.yaml

@@ -0,0 +1,16 @@
+# yaml-language-server: $schema=../../schema.yaml
+assay: '?'
+doi: 10.1053/j.gastro.2020.03.065
+key: Cheung et al. 2020
+load_summaries:
+  max: 7.6
+  median: 4.7
+  min: 3.4
+loq: null
+patients:
+  n: 59
+  negative: 50
+  positive: 9
+samples: {}
+title: 'Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in
+  Fecal Samples From a Hong Kong Cohort: Systematic Review and Meta-analysis'

publications/Han2020/Han2020.yaml

@@ -0,0 +1,48 @@
+# yaml-language-server: $schema=../../schema.yaml
+assay: PowerChek-E
+doi: 10.1093/cid/ciaa447
+key: Han et al. 2020
+loads:
+- day: 9
+  patient: 0
+  value: 4.616479
+- day: 15
+  patient: 0
+  value: null
+- day: 6
+  patient: 1
+  value: 6.792
+- day: 8
+  patient: 1
+  value: 6.593
+- day: 10
+  patient: 1
+  value: 7.219
+- day: 13
+  patient: 1
+  value: 6.383
+- day: 15
+  patient: 1
+  value: 7.618
+- day: 17
+  patient: 1
+  value: 6.23
+- day: 18
+  patient: 1
+  value: 5.855
+loq: 3.7558748557
+patients:
+  details:
+  - description: mother
+  - age: 0
+    description: neonate
+  n: 2
+  negative: 0
+  positive: 2
+samples:
+  n: 9
+  negative: 1
+  positive: 8
+temporal: symptoms
+title: Sequential Analysis of Viral Load in a Neonate and Her Mother Infected With
+  Severe Acute Respiratory Syndrome Coronavirus 2

publications/Jeong2020/Jeong2020.yaml

@@ -0,0 +1,41 @@
+# yaml-language-server: $schema=../../schema.yaml
+assay: S
+doi: 10.1016/j.cmi.2020.07.020
+key: Jeong et al. 2020
+loads:
+- day: 8
+  err: null
+  patient: 1
+  stage: recovery
+  value: null
+- day: 13
+  err: 0.19
+  patient: 2
+  stage: recovery
+  value: 1.51
+- day: 11
+  err: null
+  patient: 3
+  stage: recovery
+  value: null
+- day: 15
+  err: 0.11
+  patient: 4
+  stage: acute
+  value: 2.18
+- day: 30
+  err: 0.28
+  patient: 5
+  stage: recovery
+  value: 2.01
+loq: 0.3
+patients:
+  n: 5
+  negative: 2
+  positive: 3
+samples:
+  n: 5
+  negative: 2
+  positive: 3
+temporal: symptoms
+title: Viable SARS-CoV-2 in various specimens from COVID-19 patients