Creating python API for Nox sessions (#1414)

* Update config.yml - fix Circle CI pipeline * Playground Implementation * Playground Implementation * Support CLI batching, and more * Update CLI test * Update CLI test * Update CLI test * CLI test Update * A few fix on the playground test * A few fix on the playground test * A few fix on the playground test * Playground with all command at #1368 * Playground with all command at #1368 * Playground with all command at #1368 * Playground with all command at #1368 * Playground with all command at #1368 * Playground with all command at #1368 * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground * Session Parallelization on CLI test playground with pytest dependency * Rich lib integration pyproject config * Make the serializer use the fields from the header (#1406) * Generalize Standard Run (#1411) * Modify header calculation to choose from predefined example output file or standard example output file * Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function * Remove unused method * Make csv serialization work for any kind of model api response * Remove the standard flag from the CLI since it is now the default run * Update tests * Creating python for Nox sessions * Creating python for Nox sessions * Generalize Standard Run (#1411) * Modify header calculation to choose from predefined example output file or standard example output file * Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function * Remove unused method * Make csv serialization work for any kind of model api response * Remove the standard flag from the CLI since it is now the default run * Update tests * Generalize Standard Run (#1411) * Modify header calculation to choose from predefined example output file or standard example output file * Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function * Remove unused method * Make csv serialization work for any kind of model api response * Remove the standard flag from the CLI since it is now the default run * Update tests * Make the serializer use the fields from the header (#1406) * Merge sample command with the example command (#1422) * Merge sample command with the example command * Fix example command usage * Generalize Standard Run (#1411) * Modify header calculation to choose from predefined example output file or standard example output file * Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function * Remove unused method * Make csv serialization work for any kind of model api response * Remove the standard flag from the CLI since it is now the default run * Update tests * Conflict resolved with upstream * Conflict resolved with upstream * Generalize Standard Run (#1411) * Modify header calculation to choose from predefined example output file or standard example output file * Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function * Remove unused method * Make csv serialization work for any kind of model api response * Remove the standard flag from the CLI since it is now the default run * Update tests * Make the serializer use the fields from the header (#1406) * Generalize Standard Run (#1411) * Modify header calculation to choose from predefined example output file or standard example output file * Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function * Remove unused method * Make csv serialization work for any kind of model api response * Remove the standard flag from the CLI since it is now the default run * Update tests * Conflict resolved with upstream * Conflict resolved with upstream * Unnecessary files removed * Generalize Standard Run (#1411) * Modify header calculation to choose from predefined example output file or standard example output file * Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function * Remove unused method * Make csv serialization work for any kind of model api response * Remove the standard flag from the CLI since it is now the default run * Update tests * Unnecessary files removed * Generalize Standard Run (#1411) * Modify header calculation to choose from predefined example output file or standard example output file * Remove the readiness function from SCRA because it is redundant, since those checks are also performed by the amenable function * Remove unused method * Make csv serialization work for any kind of model api response * Remove the standard flag from the CLI since it is now the default run * Update tests * Make the serializer use the fields from the header (#1406) * Unnecessary files removed * Unnecessary files removed * Unnecessary files removed * Unnecessary files removed * Fix: Unnecessary files removed --------- Co-authored-by: Dhanshree Arora <[email protected]>
ersilia-os · Dec 12, 2024 · a16e320 · a16e320
1 parent 82e8200
commit a16e320
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 5 deletions.
diff --git a/ersilia/cli/commands/example.py b/ersilia/cli/commands/example.py
@@ -37,7 +37,6 @@ def example_cmd():
     def example():
         pass
 
-
     @example.command()
     @click.argument("model", required=False, default=None, type=click.STRING)
     @click.option("--n_samples", "-n", default=5, type=click.INT)
@@ -50,6 +49,15 @@ def inputs(model, n_samples, file_name, simple, predefined):
         else:
             session = Session(config_json=None)
             model_id = session.current_model_id()
+            if model_id is None:
+                click.echo(
+                    click.style(
+                        "Error: No model id given and no model found running in this shell.",
+                        fg="red",
+                    ),
+                    err=True,
+                )
+                return
         eg = ExampleGenerator(model_id=model_id)
         if file_name is None:
             echo(
@@ -61,7 +69,6 @@ def inputs(model, n_samples, file_name, simple, predefined):
         else:
             eg.example(n_samples, file_name, simple, try_predefined=predefined)
 
-
     @example.command()
     @click.option("--n_samples", "-n", default=5, type=click.INT)
     @click.option("--file_name", "-f", default=None, type=click.STRING)
@@ -71,4 +78,4 @@ def models(n_samples, file_name):
         if file_name is None:
             echo(json.dumps(sampler.sample(n_samples), indent=4))
         else:
-            sampler.sample(n_samples, file_name)
+            sampler.sample(n_samples, file_name)
diff --git a/ersilia/io/input.py b/ersilia/io/input.py
@@ -271,7 +271,7 @@ def example(self, n_samples, file_name, simple, try_predefined):
         if try_predefined is True and file_name is not None:
             self.logger.debug("Trying with predefined input")
             predefined_available = self.predefined_example(file_name)
-        
+
         if predefined_available:
             with open(file_name, "r") as f:
                 return f.read()

diff --git a/ersilia/utils/exceptions_utils/exceptions.py b/ersilia/utils/exceptions_utils/exceptions.py
@@ -93,7 +93,9 @@ def run_from_terminal(self):
         output_file = os.path.join(framework_dir, "example_output.csv")
         tmp_folder = make_temp_dir(prefix="ersilia-")
         log_file = os.path.join(tmp_folder, "terminal.log")
-        run_command("ersilia example inputs {0} -n 3 -f {1}".format(self.model_id, input_file))
+        run_command(
+            "ersilia example inputs {0} -n 3 -f {1}".format(self.model_id, input_file)
+        )
         cmd = "bash {0} {1} {2} {3} 2>&1 | tee -a {4}".format(
             exec_file, framework_dir, input_file, output_file, log_file
         )