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 10, 2024 · 175b677 · 175b677
1 parent ff9e2b6
commit 175b677
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diff --git a/ersilia/serve/standard_api.py b/ersilia/serve/standard_api.py
@@ -64,7 +64,6 @@ def _read_information_file(self):
             with open(os.path.join(self.path, INFORMATION_FILE), "r") as f:
                 info = json.load(f)
                 return info
-
         except FileNotFoundError:
             self.logger.debug(
                 f"Error: File '{INFORMATION_FILE}' not found in the path '{self.path}'"
@@ -295,6 +294,7 @@ def serialize_to_csv(self, input_data, result, output_data):
                     result[idx] = item[list(item.keys())[0]]
 
         assert len(input_data) == len(result)
+
         with open(output_data, "w") as f:
             writer = csv.writer(f)
             writer.writerow(self.header)

diff --git a/test/playground/runner.py b/test/playground/runner.py
@@ -0,0 +1,71 @@
+import subprocess
+import yaml
+from pathlib import Path
+
+
+class NoxSession:
+
+    def __init__(self, name):
+        self.name = name
+
+    def execute(self, noxfile):
+        try:
+            subprocess.run(
+                ["nox","-f", noxfile, "-s", self.name],
+                check=True,
+            )
+            print(f"Session '{self.name}' executed successfully.")
+        except subprocess.CalledProcessError as e:
+            print(f"Error executing session '{self.name}': {e}")
+
+
+class NoxRunner:
+    def __init__(self, config_path="config.yml", noxfile="noxfile.py"):
+        self.original_dir = Path.cwd()
+        self.config_path = Path(config_path)
+        self.noxfile = noxfile
+        self.config = yaml.safe_load(self.config_path.read_text())
+        self.nox_command = "nox"
+        self.queue = []
+
+    def update_yaml_values(self, new_values: dict):
+        existing_config = yaml.safe_load(self.config_path.read_text())
+        existing_config.update(new_values)
+        self.config_path.write_text(yaml.dump(existing_config))
+
+    def get_python_version(self):
+        return self.config.get("python_version", "3.10.10")
+
+    def add_session(self, session_name):
+        self.queue.append(NoxSession(session_name))
+
+    def execute_all(self):
+
+        for session in self.queue:
+            session.execute(self.noxfile)
+        self.queue.clear() 
+
+    def clear_queue(self):
+        self.queue.clear()
+
+    def setup(self):
+        self.add_session("setup")
+
+    def test_from_github(self):
+        self.add_session("test_from_github")
+
+    def test_from_dockerhub(self):
+        self.add_session("test_from_dockerhub")
+
+    def test_auto_fetcher_decider(self):
+        self.add_session("test_auto_fetcher_decider")
+
+    def test_fetch_multiple_models(self):
+        self.add_session("test_fetch_multiple_models")
+
+    def test_serve_multiple_models(self):
+        self.add_session("test_serve_multiple_models")
+
+    def test_conventional_run(self):
+        self.add_session("test_conventional_run")
+