From f90f3ee9e7b1d504c04599628bbb263187bd0bd3 Mon Sep 17 00:00:00 2001
From: pgleeson
Date: Thu, 25 Apr 2024 08:55:46 +0100
Subject: [PATCH] Format update
---
.github/workflows/ci.yml | 2 +-
docs/sphinx/source/api/Contributors.md | 2 +-
examples/neuroml2/neuroml2_spec.py | 1 -
examples/sbml/sbml32spec.py | 1 -
examples/sbml/sbml_validators.py | 1 -
src/modelspec/base_types.py | 5 -----
src/modelspec/utils.py | 9 ---------
tests/test_utils.py | 1 -
8 files changed, 2 insertions(+), 20 deletions(-)
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e90604ad..bbdc85cf 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -112,7 +112,7 @@ jobs:
python contributors.py
cd sphinx
make clean
- make html
+ make html
- name: Install and test with OMV
if: ${{ matrix.runs-on != 'windows-latest' }}
diff --git a/docs/sphinx/source/api/Contributors.md b/docs/sphinx/source/api/Contributors.md
index 20ab4a5c..ab26a9f3 100644
--- a/docs/sphinx/source/api/Contributors.md
+++ b/docs/sphinx/source/api/Contributors.md
@@ -3,7 +3,7 @@
# Modelspec contributors
This page list names and Github profiles of contributors to Modelspec, listed in no particular order.
-This page is generated periodically, most recently on 2024-04-12.
+This page is generated periodically, most recently on 2024-04-25.
- Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
- Manifest Chakalov ([@mqnifestkelvin](https://github.com/mqnifestkelvin))
diff --git a/examples/neuroml2/neuroml2_spec.py b/examples/neuroml2/neuroml2_spec.py
index 36422ab5..5b9be78c 100644
--- a/examples/neuroml2/neuroml2_spec.py
+++ b/examples/neuroml2/neuroml2_spec.py
@@ -128,7 +128,6 @@ class neuroml(Base):
if __name__ == "__main__":
-
nml_doc = neuroml(id="TestNeuroML")
izh = izhikevich2007Cell(
diff --git a/examples/sbml/sbml32spec.py b/examples/sbml/sbml32spec.py
index c6372a91..6abebf2c 100644
--- a/examples/sbml/sbml32spec.py
+++ b/examples/sbml/sbml32spec.py
@@ -82,7 +82,6 @@ class SBase(Base):
@modelspec.define
class SBaseWithId(SBase):
-
id: str = field(default=None, validator=optional([instance_of(str), valid_sid]))
diff --git a/examples/sbml/sbml_validators.py b/examples/sbml/sbml_validators.py
index 5ab66a5b..b1bb44a5 100644
--- a/examples/sbml/sbml_validators.py
+++ b/examples/sbml/sbml_validators.py
@@ -168,7 +168,6 @@ def validate_sbml(doc, units_consistency: bool = False) -> None:
if __name__ == "__main__":
-
import libsbml
sbml_file = sys.argv[1]
diff --git a/src/modelspec/base_types.py b/src/modelspec/base_types.py
index f9459a37..23f8f2f5 100644
--- a/src/modelspec/base_types.py
+++ b/src/modelspec/base_types.py
@@ -147,7 +147,6 @@ def from_dict(cls, d: Dict[str, Any]) -> "Base":
# If this object has an id attribute, it may have been serialized within a dict with the id as the key, even if
# it is a single object.
if "id" in [f.name for f in attr.fields(cls)] and "id" not in d.keys():
-
keys = list(d.keys())
if len(keys) == 0:
raise ValueError(
@@ -297,7 +296,6 @@ def to_yaml_file(
filename = f"{self.id}.yaml"
with open(filename, "w") as outfile:
-
# We need to setup another
yaml.dump(
yaml_converter.unstructure(self.to_dict()),
@@ -313,7 +311,6 @@ def to_xml_file(
filename: Optional[str] = None,
include_metadata: bool = True,
) -> str:
-
if filename is None:
filename = f"{self.id}.xml"
@@ -636,7 +633,6 @@ def _is_base_type(
can_be_none=False,
can_be_eval_expr=False,
):
-
import numpy
if verbose:
@@ -730,7 +726,6 @@ def _cls_generate_documentation(cls, format: str = MARKDOWN_FORMAT):
rst_url_format = "`%s <%s>`__"
def insert_links(text, format=MARKDOWN_FORMAT):
-
code_ref = ":code:`"
# print(" > Converting: %s" % text)
text2 = text
diff --git a/src/modelspec/utils.py b/src/modelspec/utils.py
index af2ca292..2d4a65c6 100644
--- a/src/modelspec/utils.py
+++ b/src/modelspec/utils.py
@@ -192,14 +192,12 @@ def convert_xml_dict_values(value):
def save_to_json_file(info_dict, filename, indent=4):
-
strj = json.dumps(info_dict, indent=indent)
with open(filename, "w") as fp:
fp.write(strj)
def save_to_yaml_file(info_dict, filename, indent=4):
-
if sys.version_info[0] == 2:
stry = yaml.dump(info_dict, indent=indent, default_flow_style=False)
else:
@@ -251,7 +249,6 @@ def build_xml_element(data, parent=None):
attrs = attr.fields(data.__class__)
for aattr in attrs:
-
print_(" == Looking at: {} ({})".format(aattr, type(aattr)), verbose)
if isinstance(aattr.default, attr.Factory):
children = data.__getattribute__(aattr.name)
@@ -280,7 +277,6 @@ def build_xml_element(data, parent=None):
):
parent.set(attribute_name, str(attribute_value))
elif type(attribute_value) == dict:
-
"""for k, v in attribute_value.items():
child_element = build_xml_element(v)"""
else:
@@ -309,7 +305,6 @@ def ascii_encode_dict(data):
def _parse_element(dict_format, to_build):
-
print_("Parse for element: [%s]" % dict_format, verbose)
for k in dict_format.keys():
print_(
@@ -323,7 +318,6 @@ def _parse_element(dict_format, to_build):
def _parse_attributes(dict_format, to_build):
-
for key in dict_format:
value = dict_format[key]
new_format = True
@@ -489,7 +483,6 @@ def evaluate(
else:
expr = int(expr)
except:
-
try:
if array_format == FORMAT_TENSORFLOW:
expr = tf.constant(float(expr))
@@ -557,7 +550,6 @@ def evaluate(
)
if (type(v) is float or type(v) is str) and int(v) == v:
-
print_(" Returning int: %s" % int(v), verbose)
if array_format == FORMAT_TENSORFLOW:
@@ -576,7 +568,6 @@ def evaluate(
def parse_list_like(list_str):
-
if isinstance(list_str, int):
return [list_str]
elif isinstance(list_str, float):
diff --git a/tests/test_utils.py b/tests/test_utils.py
index f3927865..80fc991d 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -12,7 +12,6 @@
class TestUtils(unittest.TestCase):
def test_evaluate(self):
-
assert evaluate("33") == 33.0
assert evaluate("33") == 33
assert evaluate(33) == 33