example of api usage

examples/.gitignore

+*.dot
+*.png

examples/api_basics.py

+"""Basic example of API usage"""
+
+import biseau as bs
+
+# straightforward way : just use default options for all scripts
+bs.single_image_from_filenames(
+    fnames=('scripts/raw_data.lp', 'scripts/compute_score.py', 'scripts/render_interactions.json'),
+    outfile='interactions.png',
+    dotfile='interactions.dot',
+)
+
+
+# We can also load all scripts in a given dir
+scripts = list(bs.build_scripts_from_dir('scripts/'))
+
+# Or from a single filename
+scripts.extend(bs.build_scripts_from_file('myscripts/hello-world.json'))
+
+# Now, we can choose any subset of these scripts to make a context describing a graph
+final_context = bs.run(scripts[:3])
+# this context (which is pure ASP) can be compiled to dot
+print(final_context)
+bs.compile_to_single_image(final_context, outfile='example.png')
+
+# note that scripts are complex objects, that have options :
+a_script = next(bs.build_scripts_from_file('scripts/compute_score.py'))
+print(f"Script {a_script.name} have options:", a_script.options)
+print("  Current values are:", a_script.options_values)
+print("  Changing values… ")
+a_script.options_values['multiplier'] = 3
+print("  Now values are:", a_script.options_values)

examples/myscripts/hello-world.json

+[{
+    "name": "JSON Example 1",
+    "description": "example of JSON module",
+    "ASP": "color(A,B,C) :- triplet(A,B,C,_).",
+    "tags": ["json example"],
+    "inputs": ["triplet/4"],
+    "outputs": ["color/3"]
+},{
+    "name": "JSON Example 2",
+    "description": "example of JSON module",
+    "ASP": "p(X) :- q(X,Y). yolande(C) :- michel(C).",
+    "tags": ["json example"],
+    "inputs": ["q/2", "michel/1"],
+    "outputs": ["p/1", "yolande/1"]
+}]

examples/scripts/compute_score.py

+
+from itertools import combinations
+
+NAME = "Ranker"
+OUTPUTS = "score/3"
+
+def run_on(models, *, multiplier:float=2):
+    for model in models:
+        for (geneA, valA), (geneB, valB) in combinations(model.get('gene', ()), r=2):
+            score = abs(float(valA) - float(valB)) * float(multiplier)
+            yield f'score({geneA},{geneB},"{score}").'

examples/scripts/raw_data.lp

+% raw data
+gene(a,2).
+gene(b,3).
+gene(c,1).

examples/scripts/render_interactions.json

+{
+    "name": "Interactions renderer",
+    "description": "Render score/3 as a graph",
+    "ASP": "link(A,B) :- score(A,B,_).\nlabel(A,B,L) :- score(A,B,L).",
+    "inputs": ["score/3"],
+    "outputs": ["link/2", "label/3"]
+}