3.0.0 release

CHANGELOG.rst

@@ -4,14 +4,6 @@ Changelog
 Version v3.0.0
 --------------
 
-Breaking Changes
-~~~~~~~~~~~~~~~~
-- Edge populations' ``iter_connections`` returns ``CircuitNodeId`` instead of ``int``
-
-
-Version v2.1.0
---------------
-
 New Features
 ~~~~~~~~~~~~
 - Added simulation config validation
@@ -20,10 +12,10 @@ New Features
 
   - deprecated ``validate``
 
-
 Breaking Changes
 ~~~~~~~~~~~~~~~~
-- Deprecated the commandline subcommand ``validate`` in favor of new ``validate-circuit`` command
+- Edge populations' ``iter_connections`` returns ``CircuitNodeId`` instead of ``int``
+- Removed the commandline subcommand ``validate`` in favor of new ``validate-circuit`` command
 
 
 Version v2.0.2

bluepysnap/circuit_validation.py

@@ -2,6 +2,7 @@
 
 The idea here is to not depend on libsonata if possible, so we can use this in all situations
 """
+
 import logging
 from pathlib import Path
 

bluepysnap/cli.py

@@ -1,12 +1,11 @@
 """The project's command line launcher."""
+
 import functools
 import logging
-import warnings
 
 import click
 
 from bluepysnap import circuit_validation, simulation_validation
-from bluepysnap.utils import Deprecate
 
 CLICK_EXISTING_FILE = click.Path(exists=True, file_okay=True, dir_okay=False)
 
@@ -43,27 +42,6 @@ def wrapper(*args, **kwargs):
     return wrapper
 
 
-@cli.command()
-@circuit_validation_params
-def validate(config_file, skip_slow, only_errors):
-    """[DEPRECATED] Validate Sonata circuit based on config file.
-
-    Args:
-        config_file (str): path to Sonata circuit config file
-        skip_slow (bool): skip slow tests
-        only_errors (bool): only print fatal errors
-    """
-    with warnings.catch_warnings():
-        # Making sure the warning is shown
-        warnings.simplefilter("always", DeprecationWarning)
-        Deprecate.warn(
-            "Calling circuit validation with 'validate' is deprecated. "
-            "Please use 'validate-circuit' instead."
-        )
-
-    circuit_validation.validate(config_file, skip_slow, only_errors)
-
-
 @cli.command()
 @circuit_validation_params
 def validate_circuit(config_file, skip_slow, only_errors):

bluepysnap/query.py

@@ -1,4 +1,5 @@
 """Module to process search queries of nodes/edges."""
+
 import operator
 from collections.abc import Mapping
 from copy import deepcopy

bluepysnap/schemas/__init__.py

@@ -1,4 +1,5 @@
 """Schemas and schema parser."""
+
 from bluepysnap.schemas.schemas import (
     validate_circuit_schema,
     validate_edges_schema,

bluepysnap/schemas/schemas.py

@@ -1,4 +1,5 @@
 """Functions for schema based validation of circuit files."""
+
 from pathlib import Path
 
 import h5py

bluepysnap/simulation_validation.py

@@ -1,4 +1,5 @@
 """Standalone module that validates Sonata simulation. See ``validate-simulation`` function."""
+
 import contextlib
 import io
 import os

tests/data/reporting/create_reports.py

@@ -1,4 +1,5 @@
 """Taken from the libsonata lib."""
+
 import h5py
 import numpy as np
 

tests/test_cli.py

@@ -14,40 +14,31 @@
 @patch("bluepysnap.schemas.validate_nodes_schema", Mock(return_value=[]))
 @patch("bluepysnap.schemas.validate_edges_schema", Mock(return_value=[]))
 @patch("bluepysnap.schemas.validate_circuit_schema", Mock(return_value=[]))
-def test_cli_correct():
+def test_cli_validate_circuit_correct():
     runner = CliRunner()
-
-    with pytest.warns(
-        BluepySnapDeprecationWarning,
-        match="Calling circuit validation with 'validate' is deprecated",
-    ):
-        result = runner.invoke(cli, ["validate", str(TEST_DATA_DIR / "circuit_config.json")])
-
+    result = runner.invoke(cli, ["validate-circuit", str(TEST_DATA_DIR / "circuit_config.json")])
     assert result.exit_code == 0
     assert click.style("No Error: Success.", fg="green") in result.stdout
 
 
-def test_cli_no_config():
+def test_cli_validate_circuit_no_config():
     runner = CliRunner()
-    result = runner.invoke(cli, ["validate"])
+    result = runner.invoke(cli, ["validate-circuit"])
     assert result.exit_code == 2
     assert "Missing argument 'CONFIG_FILE'" in result.stdout
 
 
-@patch("bluepysnap.schemas.validate_nodes_schema", Mock(return_value=[]))
-@patch("bluepysnap.schemas.validate_edges_schema", Mock(return_value=[]))
-@patch("bluepysnap.schemas.validate_circuit_schema", Mock(return_value=[]))
-def test_cli_validate_circuit_correct():
-    runner = CliRunner()
-    result = runner.invoke(cli, ["validate-circuit", str(TEST_DATA_DIR / "circuit_config.json")])
-    assert result.exit_code == 0
-    assert click.style("No Error: Success.", fg="green") in result.stdout
-
-
 def test_cli_validate_simulation_correct():
     runner = CliRunner()
     result = runner.invoke(
         cli, ["validate-simulation", str(TEST_DATA_DIR / "simulation_config.json")]
     )
     assert result.exit_code == 0
     assert click.style("No Error: Success.", fg="green") in result.stdout
+
+
+def test_cli_validate_simulation_no_config():
+    runner = CliRunner()
+    result = runner.invoke(cli, ["validate-simulation"])
+    assert result.exit_code == 2
+    assert "Missing argument 'CONFIG_FILE'" in result.stdout

tests/test_schemas.py

@@ -187,8 +187,8 @@ def test_validate_config_ok_missing_optional_fields(to_remove):
             [["networks", "edges", 0, "populations"]],
             "networks.edges[0]: 'populations' is a required property",
         ),
-        ([["networks", "nodes", 0]], "networks.nodes: [] is too short"),
-        ([["networks", "edges", 0]], "networks.edges: [] is too short"),
+        ([["networks", "nodes", 0]], "networks.nodes: [] should be non-empty"),
+        ([["networks", "edges", 0]], "networks.edges: [] should be non-empty"),
         ([["networks", "nodes"]], "networks: 'nodes' is a required property"),
         ([["networks", "edges"]], "networks: 'edges' is a required property"),
         ([["networks"]], "'networks' is a required property"),