Entry point

pyproject.toml

@@ -14,6 +14,7 @@ pandas = "^2.1.4"
 pyarrow = "^14.0.1"
 scipy = "^1.11.4"
 jinja2 = "^3.1.2"
+typer = "^0.9.0"
 
 [tool.poetry.group.dev.dependencies]
 rich = "^13.6.0"
@@ -28,6 +29,9 @@ enable = true
 vcs = "git"
 style = "semver"
 
+[tool.poetry.scripts]
+deemian = "deemian.deemian:app"
+
 [build-system]
 requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
 build-backend = "poetry_dynamic_versioning.backend"

src/deemian/deemian.py

@@ -0,0 +1,32 @@
+import typer
+from rich.console import Console
+
+from deemian.engine.builder import DeemianData
+from deemian.engine.processor import parser, InstructionTransformer
+from deemian.engine.director import director
+
+
+console = Console()
+app = typer.Typer()
+
+
+@app.command(short_help="run deemian script")
+def run(script_name: str):
+    console.print(f"[bold magenta]Running {script_name}[/bold magenta]")
+    with open(script_name) as f:
+        text = f.read()
+
+    command_tree = parser(text)
+    transformer = InstructionTransformer()
+    command_tree = transformer.transform(command_tree)
+
+    deemian_data = DeemianData()
+    director(command_tree, deemian_data)
+
+
+# one command one callback, just a temporary helper command
+# delete this when there are multiple commands
+# https://typer.tiangolo.com/tutorial/commands/one-or-multiple/
+@app.callback()
+def callback():
+    pass

src/deemian/writer/templates/01_detailed_conf_first.txt

@@ -4,6 +4,9 @@ interaction for "{{ pair_name }}":
 
 {%- set subject_1, subject_2 = interacting_subjects[pair_name] -%}
 {%- set df = interaction_data.dataframe -%}
+{%- if len(df) == 0 %}
+    No interaction detected
+{%- else -%}
 {%- set confs = df.conformation.unique() -%}
 {%- set groupbyconf = df.groupby('conformation') -%}
 
@@ -52,4 +55,5 @@ conf {{ "{}".format(conf).rjust(10) }}
 {% endfor -%}
 {% endif %}
 {% endfor %}
+{% endif %}
 {% endfor %}

src/deemian/writer/templates/02_detailed_type_first.txt

@@ -4,6 +4,9 @@ interaction for "{{ pair_name }}":
 
 {%- set subject_1, subject_2 = interacting_subjects[pair_name] -%}
 {%- set df = interaction_data.dataframe -%}
+{%- if len(df) == 0 %}
+    No interaction detected
+{%- else -%}
 {%- set unique_interaction = df.interaction_type.unique() %}
 {%- set groupbytype = df.groupby('interaction_type') %}
 
@@ -55,4 +58,5 @@ interaction for "{{ pair_name }}":
 {% endfor -%}
 {% endfor -%}
 {%- endif %}
+{% endif %}
 {% endfor %}

src/deemian/writer/templates/03_clustered_conf_first.txt

@@ -4,6 +4,9 @@ interaction for "{{ pair_name }}":
 
 {%- set subject_1, subject_2 = interacting_subjects[pair_name] -%}
 {%- set df = interaction_data.dataframe -%}
+{%- if len(df) == 0 %}
+    No interaction detected
+{%- else -%}
 {%- set confs = df.conformation.unique() -%}
 {%- set groupbyconf = df.groupby('conformation') -%}
 
@@ -54,4 +57,5 @@ conf {{ "{}".format(conf).rjust(10) }}
 {% endfor -%}
 {%- endif %}
 {% endfor %}
+{% endif %}
 {% endfor %}

src/deemian/writer/templates/04_clustered_type_first.txt

@@ -4,7 +4,9 @@ interaction for "{{ pair_name }}":
 
 {%- set subject_1, subject_2 = interacting_subjects[pair_name] -%}
 {%- set df = interaction_data.dataframe -%}
-
+{%- if len(df) == 0 %}
+    No interaction detected
+{%- else -%}
 {%- set unique_interaction = df.interaction_type.unique() %}
 {%- set groupbytype = df.groupby('interaction_type') %}
 {%- if 'electrostatic_cation' in unique_interaction %}
@@ -59,4 +61,5 @@ interaction for "{{ pair_name }}":
 {% endfor -%}
 {% endfor %}
 {%- endif %}
+{% endif %}
 {% endfor %}

src/deemian/writer/templates/05_summarized_conf_first.txt

@@ -4,6 +4,9 @@ interaction for "{{ pair_name }}":
 
 {%- set subjects = interacting_subjects[pair_name] -%}
 {%- set df = interaction_data.dataframe -%}
+{%- if len(df) == 0 %}
+    No interaction detected
+{%- else -%}
 {%- set confs = df.conformation.unique() -%}
 {%- set groupbyconf = df.groupby('conformation') -%}
 
@@ -63,4 +66,5 @@ conf {{ "{}".format(conf).rjust(10) }}
 {% endfor -%}
 {%- endif %}
 {% endfor %}
+{% endif %}
 {% endfor %}

src/deemian/writer/templates/06_summarized_type_first.txt

@@ -4,7 +4,9 @@ interaction for "{{ pair_name }}":
 
 {%- set subjects = interacting_subjects[pair_name] -%}
 {%- set df = interaction_data.dataframe -%}
-
+{%- if len(df) == 0 %}
+    No interaction detected
+{%- else -%}
 {%- set unique_interaction = df.interaction_type.unique() %}
 {%- set groupbytype = df.groupby('interaction_type') %}
 {%- if 'electrostatic_cation' in unique_interaction %}
@@ -69,4 +71,5 @@ interaction for "{{ pair_name }}":
 {% endfor -%}
 {% endfor -%}
 {%- endif %}
+{% endif %}
 {% endfor %}

tests/test_deemian.py

@@ -1 +1,14 @@
-# from deemian import deemian
+from unittest.mock import patch
+
+from typer.testing import CliRunner
+
+from deemian.deemian import app
+
+
+runner = CliRunner()
+
+
+def test_app():
+    with patch("deemian.deemian.director"):
+        result = runner.invoke(app, ["run", "tests/data/n1-oseltamivir-5nzn.txt"])
+        assert result.exit_code == 0