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 · 8c04b03 · 8c04b03
1 parent ff9e2b6
commit 8c04b03
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Showing 13 changed files with 124 additions and 43 deletions.
diff --git a/.github/scripts/airtableops.py b/.github/scripts/airtableops.py
@@ -249,7 +249,7 @@ def insert_metadata_to_airtable(model, contributor, api_key):
     if r.status_code == 200:
         text = r.content
         data = yaml.safe_load(text)
-    
+
     airtable_data = {}
     airtable_data["Identifier"] = model
     airtable_data["Slug"] = data["Slug"]
@@ -286,9 +286,15 @@ def update_readme_from_airtable(repo, path):
     subparsers = parser.add_subparsers(dest="command")
 
     # Main commands
-    airtable_insert = subparsers.add_parser("airtable-insert", help="Insert metadata to AirTable")
-    airtable_update = subparsers.add_parser("airtable-update", help="Update metadata to AirTable")
-    readme_update = subparsers.add_parser("readme-update", help="Update README from AirTable")
+    airtable_insert = subparsers.add_parser(
+        "airtable-insert", help="Insert metadata to AirTable"
+    )
+    airtable_update = subparsers.add_parser(
+        "airtable-update", help="Update metadata to AirTable"
+    )
+    readme_update = subparsers.add_parser(
+        "readme-update", help="Update README from AirTable"
+    )
 
     # Options for airtable-insert
     airtable_insert.add_argument("--model", type=str, required=True)
@@ -310,7 +316,7 @@ def update_readme_from_airtable(repo, path):
     if args.command == "airtable-insert":
         print("Inserting metadata to AirTable")
         insert_metadata_to_airtable(args.model, args.contributor, args.api_key)
-    
+
     elif args.command == "airtable-update":
         print("Updating metadata to AirTable")
         # update_metadata_to_airtable(args.user, args.repo, args.branch, args.api_key)
@@ -322,4 +328,4 @@ def update_readme_from_airtable(repo, path):
     else:
         print("Invalid command")
         parser.print_help()
-        exit(1)
+        exit(1)
diff --git a/ersilia/cli/commands/catalog.py b/ersilia/cli/commands/catalog.py
@@ -86,7 +86,7 @@ def catalog(
             except Exception as e:
                 click.echo(click.style(f"Error fetching model metadata: {e}", fg="red"))
             return
-        
+
         # The idea here is to deter the user from running ersilia catalog --local --hub
         if local and hub:
             click.echo(
@@ -96,36 +96,36 @@ def catalog(
                 err=True,
             )
             return
-        
+
         mc = ModelCatalog()
         mc.only_identifier = False if more else True
 
         if hub:
             if browser:
                 mc.airtable()
                 return
-            
+
             catalog_table = mc.hub()
 
-        else: # This will work even if the user doesn't explicitly specify the --local flag
+        else:  # This will work even if the user doesn't explicitly specify the --local flag
             if browser:
                 click.echo(
                     click.style(
                         "Error: Cannot show local models in the browser.\nPlease use the --hub option to see models in the browser.",
-                        fg="red"
+                        fg="red",
                     )
                 )
                 return
             catalog_table = mc.local()
             if not catalog_table.data:
                 click.echo(
-                click.style(
-                    "No local models available. Please fetch a model by running 'ersilia fetch' command",
-                    fg="red",
+                    click.style(
+                        "No local models available. Please fetch a model by running 'ersilia fetch' command",
+                        fg="red",
                     )
                 )
                 return
-        
+
         if file_name is None:
             catalog = catalog_table.as_table() if as_table else catalog_table.as_json()
         else:

diff --git a/ersilia/cli/commands/example.py b/ersilia/cli/commands/example.py
@@ -14,8 +14,8 @@ def example_cmd():
 
     # Example usage: ersilia example {MODEL} -n 10 [--file_name {FILE_NAME} --simple/--complete]
     @ersilia_cli.group(
-            short_help="Generate sample of Ersilia models or model inputs",
-            help="""This command can sample both ersilia models, or inputs for a given or currently running model.\n
+        short_help="Generate sample of Ersilia models or model inputs",
+        help="""This command can sample both ersilia models, or inputs for a given or currently running model.\n
 For the model input, the number of examples can be specified, as well as a file name.\n
 Simple inputs only contain the essential information, while complete inputs contain key and other fields, potentially.\n
 For ersilia models, only model identifiers are returned for a given sample size.
@@ -24,7 +24,6 @@ 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)
@@ -39,7 +38,10 @@ def inputs(model, n_samples, file_name, simple, predefined):
             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"),
+                    click.style(
+                        "Error: No model id given and no model found running in this shell.",
+                        fg="red",
+                    ),
                     err=True,
                 )
                 return
@@ -54,7 +56,6 @@ 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)
@@ -64,4 +65,4 @@ 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/hub/content/catalog.py b/ersilia/hub/content/catalog.py
@@ -236,8 +236,7 @@ def _get_service_class(self, card):
     def airtable(self):
         """List models available in AirTable Ersilia Model Hub base"""
         if webbrowser:
-            webbrowser.open("https://airtable.com/shrUcrUnd7jB9ChZV") #TODO Hardcoded
-
+            webbrowser.open("https://airtable.com/shrUcrUnd7jB9ChZV")  # TODO Hardcoded
 
     def hub(self):
         """List models available in Ersilia model hub from the S3 JSON"""
@@ -249,7 +248,7 @@ def hub(self):
             status = self._get_status(model)
             if status == "In Progress":
                 continue
-            
+
             identifier = self._get_item(model, "identifier")
             if self.only_identifier:
                 R += [[identifier]]
@@ -258,9 +257,11 @@ def hub(self):
                 title = self._get_title(model)
                 R += [[identifier, slug, title]]
 
-        columns = ["Identifier"] if self.only_identifier else ["Identifier", "Slug", "Title"]
+        columns = (
+            ["Identifier"] if self.only_identifier else ["Identifier", "Slug", "Title"]
+        )
         return CatalogTable(R, columns=columns)
-                
+
     def local(self):
         """List models available locally"""
         mc = ModelCard()

diff --git a/ersilia/io/input.py b/ersilia/io/input.py
@@ -273,7 +273,7 @@ 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/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/ersilia/utils/exceptions_utils/card_exceptions.py b/ersilia/utils/exceptions_utils/card_exceptions.py
@@ -21,6 +21,7 @@ def __init__(self):
         self.hints = ""
         ErsiliaError.__init__(self, self.message, self.hints)
 
+
 # TODO Unused - remove
 class BaseInformationError(ErsiliaError):
     def __init__(self):

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
         )

diff --git a/ersilia/utils/exceptions_utils/hubdata_exceptions.py b/ersilia/utils/exceptions_utils/hubdata_exceptions.py
@@ -1,5 +1,6 @@
 from .exceptions import ErsiliaError
 
+
 # Note: Not really used anywhere right now except in the sanitize class
 class InvalidUrlInAirtableError(ErsiliaError):
     def __init__(self, url):

diff --git a/test/cli/test_close.py b/test/cli/test_close.py
@@ -17,10 +17,11 @@ def mock_close():
 
 @pytest.fixture
 def mock_session():
-    with patch.object(Session, "current_model_id", return_value=MODEL_ID), patch.object(
-        Session, "current_service_class", return_value="pulled_docker"
-    ), patch.object(Session, "tracking_status", return_value=False), patch.object(
-        Session, "current_output_source", return_value="LOCAL_ONLY"
+    with (
+        patch.object(Session, "current_model_id", return_value=MODEL_ID),
+        patch.object(Session, "current_service_class", return_value="pulled_docker"),
+        patch.object(Session, "tracking_status", return_value=False),
+        patch.object(Session, "current_output_source", return_value="LOCAL_ONLY"),
     ):
         yield
 

diff --git a/test/cli/test_run.py b/test/cli/test_run.py
@@ -118,10 +118,11 @@ def mock_post_side_effect(input, output, output_source):
 
 @pytest.fixture
 def mock_session(compound_csv):
-    with patch.object(Session, "current_model_id", return_value=MODEL_ID), patch.object(
-        Session, "current_service_class", return_value="pulled_docker"
-    ), patch.object(Session, "tracking_status", return_value=False), patch.object(
-        Session, "current_output_source", return_value="LOCAL_ONLY"
+    with (
+        patch.object(Session, "current_model_id", return_value=MODEL_ID),
+        patch.object(Session, "current_service_class", return_value="pulled_docker"),
+        patch.object(Session, "tracking_status", return_value=False),
+        patch.object(Session, "current_output_source", return_value="LOCAL_ONLY"),
     ):
         yield
 

diff --git a/test/playground/runner.py b/test/playground/runner.py
@@ -0,0 +1,68 @@
+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")
diff --git a/test/test_models.py b/test/test_models.py
@@ -29,12 +29,11 @@ def mock_set_apis():
 
 @pytest.fixture
 def mock_session():
-    with patch.object(
-        Session, "current_model_id", return_value=MODELS[1]
-    ), patch.object(
-        Session, "current_service_class", return_value="docker"
-    ), patch.object(Session, "tracking_status", return_value=False), patch.object(
-        Session, "current_output_source", return_value="LOCAL_ONLY"
+    with (
+        patch.object(Session, "current_model_id", return_value=MODELS[1]),
+        patch.object(Session, "current_service_class", return_value="docker"),
+        patch.object(Session, "tracking_status", return_value=False),
+        patch.object(Session, "current_output_source", return_value="LOCAL_ONLY"),
     ):
         yield