instance_id stringlengths 10 57 | file_changes listlengths 1 15 | repo stringlengths 7 53 | base_commit stringlengths 40 40 | problem_statement stringlengths 11 52.5k | patch stringlengths 251 7.06M |
|---|---|---|---|---|---|
omni-us__jsonargparse-661 | [
{
"changes": {
"added_entities": null,
"added_modules": [
"jsonargparse/_core.py:ArgumentGroup"
],
"edited_entities": [
"jsonargparse/_core.py:ActionsContainer.add_argument_group",
"jsonargparse/_core.py:ArgumentParser.__init__",
"jsonargparse/_core.py:Arg... | omni-us/jsonargparse | 2285c1a21eb455f0a702da552e84493778ad4d83 | Question: is it possible to make CLI replace parameter dashes with underscores?
I'm curious about replacing argparse with jsonargparse in some of my projects since simply running `CLI(main_fn)` would cover my most common use cases. However, it's not clear to me if there's any hook to change the mapping from Python argu... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index ce19d1a..38345d1 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -12,6 +12,16 @@ The semantic versioning only considers the public API as described in
paths are considered internals and can change in minor and patch releases.
+v4.37.0 (2025-01-??)
+---------------... |
omni-us__jsonargparse-662 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"jsonargparse/_link_arguments.py:DirectedGraph.add_edge",
"jsonargparse/_link_arguments.py:DirectedGraph.topological_sort",
"jsonargparse/_link_arguments.py:ActionLink.instantiation_order... | omni-us/jsonargparse | eee8ea969794e46429637c754e42c4a14892e7b3 | Incorrect instantiation order with nested dependency injection
<!-- If you like this project, please ⭐ star it https://github.com/omni-us/jsonargparse/ -->
## 🐛 Bug report
First of all, this is a really cool project, and I am enjoying it a lot 👍 .
This might be quite niche to be honest, but I encountered unexpec... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 38345d1..19c2a29 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -21,6 +21,11 @@ Added
``add_argument`` (`#661
<https://github.com/omni-us/jsonargparse/pull/661>`__).
+Fixed
+^^^^^
+- Incorrect instantiation order when instantiation targets share a parent (`#66... |
omni-us__jsonargparse-667 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"jsonargparse/_optionals.py:is_annotated_validator"
],
"edited_modules": [
"jsonargparse/_optionals.py:is_annotated_validator"
]
},
"file": "jsonargparse/_optionals.py"
... | omni-us/jsonargparse | 2a4454abfb15172029fba222a69bd3c86164181a | Dot syntax not working correctly for pydantic 2 models
<!-- If you like this project, please ⭐ star it https://github.com/omni-us/jsonargparse/ -->
## 🐛 Bug report
<!-- A clear and concise description of the bug. -->
### To reproduce
```py
from jsonargparse import CLI
from pydantic import BaseModel, Fiel... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 19c2a29..de173b2 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -25,6 +25,8 @@ Fixed
^^^^^
- Incorrect instantiation order when instantiation targets share a parent (`#662
<https://github.com/omni-us/jsonargparse/pull/662>`__).
+- Pydantic discriminated unions ha... |
omni-us__jsonargparse-707 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"jsonargparse/_actions.py:ActionParser._move_parser_actions"
],
"edited_modules": [
"jsonargparse/_actions.py:ActionParser"
]
},
"file": "jsonargparse/_actions.py"
}
] | omni-us/jsonargparse | e90e8e088cfd006ca416dd4ad2df742f63d4fdd8 | instantiate_classes does not instantiate my classes with configured args when classes are added to subparser.
<!-- If you like this project, please ⭐ star it https://github.com/omni-us/jsonargparse/ -->
## 🐛 Bug report
Hey, I am trying to add a subparser to my parser, read in a config specific to that parser and sub... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index feef512..222ae42 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -30,6 +30,11 @@ Changed
``fail_untyped=True`` (`#697
<https://github.com/omni-us/jsonargparse/pull/697>`__).
+Fixed
+^^^^^
+- ``ActionParser`` not updating ``dest`` of groups for instantiation (`#... |
omni-us__jsonargparse-711 | [
{
"changes": {
"added_entities": [
"jsonargparse/_common.py:validate_default"
],
"added_modules": [
"jsonargparse/_common.py:validate_default"
],
"edited_entities": [
"jsonargparse/_common.py:set_parsing_settings"
],
"edited_modules": [
"... | omni-us/jsonargparse | ce4b8aa8f26cc91b0878329b8c14f1b7177f1774 | Path_fr does not use the default value during validation
<!-- If you like this project, please ⭐ star it https://github.com/omni-us/jsonargparse/ -->
## 🐛 Bug report
If I specify a default value for a `Path_fr` parameter, the validation ignores it. This is pretty weird because clearly the value is present and us... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 3ff3e92..35045c4 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -25,6 +25,8 @@ Added
<https://github.com/omni-us/jsonargparse/pull/701>`__).
- Resolve parameters completely from stubs when ``inspect.signature`` fails
(`#698 <https://github.com/omni-us/jsonargpa... |
omni-us__jsonargparse-75 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "jsonargparse/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_mo... | omni-us/jsonargparse | 699ecab03129bfc6e5657269afc1cba03bc61f21 | Argument linking doesn't work for deep-level targets
Example file:
```python
import jsonargparse
from jsonargparse import ActionConfigFile
class D:
pass
class A:
def __init__(self, d: D) -> None:
self.d = d
class BSuper:
pass
class BSub(BSuper):
def __init__(self, a... | diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 078309f..7863e93 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
[bumpversion]
-current_version = 3.19.2
+current_version = 3.19.3
commit = True
tag = True
tag_name = v{new_version}
diff --git a/.sonarcloud.properties b/.sonarcloud.properti... |
omni-us__jsonargparse-77 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"jsonargparse/typehints.py:adapt_typehints"
],
"edited_modules": [
"jsonargparse/typehints.py:adapt_typehints"
]
},
"file": "jsonargparse/typehints.py"
}
] | omni-us/jsonargparse | 989fea756cbeb8a9e30150d56b64520cc1bad0b9 | 'builtins.type' type hint is not parsed properly
### Setup to reproduce the issue:
Within module _**my_module**_:
_**a.py**_:
```
class A:
def __init__(self, a: int = 10):
self.a = a
```
_**b.py**_:
```
from jsonargparse import ArgumentParser
from my_module.a import A
class B:
def _... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 5fae308..e58e0d9 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -17,6 +17,10 @@ Added
- Support for parsing ``Mapping`` and ``MutableMapping`` types.
- Support for parsing ``frozenset``, ``MutableSequence`` and ``MutableSet`` types.
+Changed
+^^^^^^^
+- Docstrings... |
omni-us__jsonargparse-78 | [
{
"changes": {
"added_entities": [
"jsonargparse/actions.py:_ActionSubCommands.get_subcommand"
],
"added_modules": null,
"edited_entities": [
"jsonargparse/actions.py:_ActionSubCommands.handle_subcommands"
],
"edited_modules": [
"jsonargparse/actions.p... | omni-us/jsonargparse | bdc7635685220fa7b108c06626ae1902bad84fc2 | Support for subcommands and `instantiate_classes`
I'm trying to use subcommands and `instantiate_classes` together.
Without subcommand, everything works properly:
```python
from jsonargparse import ArgumentParser
class Foo:
def __init__(self, a: int = 1):
...
parser = ArgumentParser(parse_as_... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 5cfda88..3230abe 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -23,6 +23,7 @@ Fixed
- Don't ignore ``KeyError`` in call to instantiate_classes #81.
- Optional subcommands fail with a KeyError #68.
- Conflicting namespace for subclass key in subcommand.
+- ``instan... |
omni-us__jsonargparse-90 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"jsonargparse/signatures.py:SignatureArguments.add_subclass_arguments"
],
"edited_modules": [
"jsonargparse/signatures.py:SignatureArguments"
]
},
"file": "jsonargparse/... | omni-us/jsonargparse | dde80fb00f48e3a922001542c47f16c986df7fd2 | Config check failed with `add_subclass_arguments(required=False)`
```python
from jsonargparse import ArgumentParser
class A:
...
class B:
...
parser = ArgumentParser()
parser.add_subclass_arguments((A, B), nested_key="foo", required=False)
args = parser.parse_args()
```
produces:
```
scratch_1... | diff --git a/jsonargparse/signatures.py b/jsonargparse/signatures.py
index ba936c6..d0e509a 100644
--- a/jsonargparse/signatures.py
+++ b/jsonargparse/signatures.py
@@ -2,7 +2,7 @@
import inspect
import re
-from argparse import Namespace
+from argparse import Namespace, SUPPRESS
from functools import wraps
from t... |
omry__omegaconf-199 | [
{
"changes": {
"added_entities": [
"omegaconf/_utils.py:_is_union"
],
"added_modules": [
"omegaconf/_utils.py:_is_union"
],
"edited_entities": [
"omegaconf/_utils.py:_resolve_optional",
"omegaconf/_utils.py:get_attr_data",
"omegaconf/_utils.p... | omry/omegaconf | 2f42a758dbf0b515576d59bfcd13a6beda93001b | Add a clear error for Union in structured configs not being supported for now
cc @jrapin
| diff --git a/omegaconf/_utils.py b/omegaconf/_utils.py
index bcd4be3..bec1fe1 100644
--- a/omegaconf/_utils.py
+++ b/omegaconf/_utils.py
@@ -9,6 +9,7 @@ import yaml
from .errors import (
ConfigIndexError,
ConfigTypeError,
+ ConfigValueError,
KeyValidationError,
OmegaConfBaseException,
Valid... |
omry__omegaconf-202 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"omegaconf/_utils.py:format_and_raise"
],
"edited_modules": [
"omegaconf/_utils.py:format_and_raise"
]
},
"file": "omegaconf/_utils.py"
},
{
"changes": {
"... | omry/omegaconf | 9b5f3579b9dbc83cc28b36bc33bf94f341409fde | More helpful stack trace
It would be a good feature to have a bit more helpful stack trace. When using the Structured configurations, and you try to access a non-existent configuration key you basically get a stack trace like this:
```
~/miniconda3/lib/python3.7/site-packages/omegaconf/base.py in _format_and_raise(... | diff --git a/omegaconf/_utils.py b/omegaconf/_utils.py
index bec1fe1..1a5b762 100644
--- a/omegaconf/_utils.py
+++ b/omegaconf/_utils.py
@@ -1,3 +1,4 @@
+import os
import re
import string
import sys
@@ -476,13 +477,21 @@ def format_and_raise(
KEY_TYPE=f"{type(key).__name__}",
)
- s = string.Templa... |
omry__omegaconf-205 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"omegaconf/_utils.py:format_and_raise"
],
"edited_modules": [
"omegaconf/_utils.py:format_and_raise"
]
},
"file": "omegaconf/_utils.py"
},
{
"changes": {
"... | omry/omegaconf | 4c5be9a3b99ad47a1492a2b3481498273ec3a6cd | Variables not resolved when accessing through iterator
When accessing `ListConfig` through the iterator, the variables are not resolved. A similar issue is #21 regarding DictConfig.
config.yaml:
```
var1: 1
var2: 2
var3:
- ${var1}
- ${var2}
```
test.py:
```
import hydra
from omegaconf import DictC... | diff --git a/omegaconf/_utils.py b/omegaconf/_utils.py
index 1a5b762..5879d6d 100644
--- a/omegaconf/_utils.py
+++ b/omegaconf/_utils.py
@@ -477,19 +477,12 @@ def format_and_raise(
KEY_TYPE=f"{type(key).__name__}",
)
- full_backtrace = "OC_CAUSE" in os.environ and os.environ["OC_CAUSE"] == "1"
t... |
omry__omegaconf-211 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"omegaconf/_utils.py:format_and_raise"
],
"edited_modules": [
"omegaconf/_utils.py:format_and_raise"
]
},
"file": "omegaconf/_utils.py"
},
{
"changes": {
"... | omry/omegaconf | 634084fcd6605e74ebc8583f4eb4d33f2ecb2d71 | Double crap in error message
```python
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
from dataclasses import dataclass
import hydra
from hydra.core.config_store import ConfigStore
@dataclass
class MySQLConfig:
driver: str = "mysql"
host: str = "localhost"
port: int ... | diff --git a/omegaconf/_utils.py b/omegaconf/_utils.py
index 5879d6d..b42271e 100644
--- a/omegaconf/_utils.py
+++ b/omegaconf/_utils.py
@@ -1,3 +1,4 @@
+import copy
import os
import re
import string
@@ -438,6 +439,23 @@ def format_and_raise(
from omegaconf import OmegaConf
from omegaconf.base import Node
... |
omry__omegaconf-213 | [
{
"changes": {
"added_entities": [
"omegaconf/_utils.py:_raise_missing_error"
],
"added_modules": [
"omegaconf/_utils.py:_raise_missing_error"
],
"edited_entities": [
"omegaconf/_utils.py:get_attr_data",
"omegaconf/_utils.py:get_dataclass_data"
... | omry/omegaconf | 4cd7f0f49ae3ee56ea8d71335907f33f408032f0 | AssertionError constructued Structured Config with nested MISSING fields
my script ```my_test.py```
```python3
from dataclasses import MISSING, dataclass
from typing import Optional
from omegaconf import OmegaConf
@dataclass
class AConf:
count: Optional[int] = MISSING
@dataclass
class SimpleConf:
... | diff --git a/.coveragerc b/.coveragerc
index 8b322c3..4386da5 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -15,6 +15,7 @@ exclude_lines =
return NotImplemented
assert False
@abstractmethod
+ \.\.\.
[html]
diff --git a/omegaconf/_utils.py b/omegaconf/_utils.py
index b42271e..8c7a6e4 100644
--- a/... |
omry__omegaconf-218 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"omegaconf/dictconfig.py:DictConfig.pop"
],
"edited_modules": [
"omegaconf/dictconfig.py:DictConfig"
]
},
"file": "omegaconf/dictconfig.py"
}
] | omry/omegaconf | 3c187e45be333af5535bff8f7b3a799e4caaa548 | [bug] .pop isn't behaving as standard dict in struct mode
```py
from omegaconf import OmegaConf
c = OmegaConf.create({"a": 1})
OmegaConf.set_struct(c, True)
c.get("b", 1) # Works fine returns 1
c.pop("b", 1) # Throws ConfigAttributeError
```
Expected:
`.pop` should return value 1
Actual:
Throws ConfigAt... | diff --git a/omegaconf/dictconfig.py b/omegaconf/dictconfig.py
index 82a1636..fbac511 100644
--- a/omegaconf/dictconfig.py
+++ b/omegaconf/dictconfig.py
@@ -362,7 +362,7 @@ class DictConfig(BaseContainer, MutableMapping[str, Any]):
if self._get_flag("readonly"):
raise ReadonlyConfigError("... |
omry__omegaconf-220 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"omegaconf/_utils.py:get_value_kind"
],
"edited_modules": [
"omegaconf/_utils.py:get_value_kind"
]
},
"file": "omegaconf/_utils.py"
}
] | omry/omegaconf | fd7846f9300f2e03b57d6dfe976367435b34ba73 | [bug] Env Interpolation doesn't respect paths
```py
from omegaconf import OmegaConf
a = OmegaConf.create({"a": {"b": "${env:DATASET_CONFIG,configs/datasets}"}})
print(a.a.b) # prints '${env:DATASET_CONFIG,configs/datasets}'
```
Should print configs/datasets
Version: 2.0.0.rc24 | diff --git a/omegaconf/_utils.py b/omegaconf/_utils.py
index 8c7a6e4..126fca1 100644
--- a/omegaconf/_utils.py
+++ b/omegaconf/_utils.py
@@ -258,7 +258,7 @@ def get_value_kind(value: Any, return_match_list: bool = False) -> Any:
"""
key_prefix = r"\${(\w+:)?"
- legal_characters = r"([\w\.%_ \\,-]*?)}"
+ ... |
omry__omegaconf-222 | [
{
"changes": {
"added_entities": [
"omegaconf/_utils.py:is_list_annotation",
"omegaconf/_utils.py:get_ref_type"
],
"added_modules": [
"omegaconf/_utils.py:is_list_annotation",
"omegaconf/_utils.py:get_ref_type"
],
"edited_entities": [
"omegac... | omry/omegaconf | 37330820c65e3ae77b17e14d03814714af5315f9 | More informative OmegaConf.get_ref_type
try to return Dict[K, V] and List[T] for DictConfig (unstructured) and ListConfig | diff --git a/.coveragerc b/.coveragerc
index 4386da5..4c9bab1 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -12,7 +12,6 @@ exclude_lines =
raise AssertionError
raise NotImplementedError
raise TypeError
- return NotImplemented
assert False
@abstractmethod
\.\.\.
diff --git a/omegaconf/_u... |
omry__omegaconf-245 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"omegaconf/dictconfig.py:DictConfig._s_validate_and_normalize_key"
],
"edited_modules": [
"omegaconf/dictconfig.py:DictConfig"
]
},
"file": "omegaconf/dictconfig.py"
}... | omry/omegaconf | cac0e1f9fe3f489711cc61808716dfcbc2c2a670 | Invalid error message assigning with an invalid inner Dict key.
```python
from dataclasses import dataclass, field
from typing import List, Any, Dict
from omegaconf import OmegaConf
from enum import Enum
class Color(Enum):
RED = 1
BLUE = 2
GREEN = 3
@dataclass
class Dicts:
d1: Dict[str, A... | diff --git a/omegaconf/dictconfig.py b/omegaconf/dictconfig.py
index 640414a..5499a5b 100644
--- a/omegaconf/dictconfig.py
+++ b/omegaconf/dictconfig.py
@@ -257,9 +257,10 @@ class DictConfig(BaseContainer, MutableMapping[str, Any]):
ret = EnumNode.validate_and_convert_to_enum(key_type, key)
... |
omry__omegaconf-27 | [
{
"changes": {
"added_entities": [
"omegaconf/config.py:Config._dict_conf_eq"
],
"added_modules": null,
"edited_entities": [
"omegaconf/config.py:Config.__init__",
"omegaconf/config.py:Config.get_full_key",
"omegaconf/config.py:Config._to_content",
... | omry/omegaconf | 28182811dcb36ffa25c69839cb94660c140bece4 | Iterating on DictConfig with items returns raw values that does not get resolved.
`family, name = next(iter(default.items()))` | diff --git a/omegaconf/config.py b/omegaconf/config.py
index 25373d8..81461ff 100644
--- a/omegaconf/config.py
+++ b/omegaconf/config.py
@@ -39,10 +39,8 @@ def get_yaml_loader():
class Config(object):
def __init__(self):
- """
- Can't be instantiated
- """
- raise NotImplementedError... |
omry__omegaconf-53 | [
{
"changes": {
"added_entities": [
"omegaconf/config.py:Config._get_node_flag"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"omegaconf/config.py:Config"
]
},
"file": "omegaconf/config.py"
},
{
"changes": {
"added... | omry/omegaconf | db110e3b6effc337fb2dc11fe27b62f24b2f49c2 | open_dict change value to the inherited value
for a nested config:
```yaml
foo:
bar:
baz: 10
```
if foo is struct, and we do
```python
with open_dict(cfg.foo.bar):
bar.baz = 20
```
the struct flag of foo.bar would be changed to True. | diff --git a/omegaconf/config.py b/omegaconf/config.py
index 0a8995d..a1b3f14 100644
--- a/omegaconf/config.py
+++ b/omegaconf/config.py
@@ -83,6 +83,13 @@ class Config(object):
assert value is None or isinstance(value, bool)
self.__dict__['flags'][flag] = value
+ def _get_node_flag(self, flag):
... |
omry__omegaconf-57 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"omegaconf/config.py:Config.merge_with_dotlist"
],
"edited_modules": [
"omegaconf/config.py:Config"
]
},
"file": "omegaconf/config.py"
}
] | omry/omegaconf | db6f59569e541db940b8042e82b97b572138b031 | Handle dotlist override with values containing =
See https://github.com/facebookresearch/hydra/issues/266 (Which is actually one bug in Hydra and one in OmegaConf). | diff --git a/omegaconf/config.py b/omegaconf/config.py
index 6b53109..3c80734 100644
--- a/omegaconf/config.py
+++ b/omegaconf/config.py
@@ -244,12 +244,15 @@ class Config(object):
def merge_with_dotlist(self, dotlist):
for arg in dotlist:
- args = arg.split("=")
- key = args[0]
- ... |
omry__omegaconf-64 | [
{
"changes": {
"added_entities": [
"omegaconf/listconfig.py:ListConfig.__add__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"omegaconf/listconfig.py:ListConfig"
]
},
"file": "omegaconf/listconfig.py"
}
] | omry/omegaconf | 94d59d0090d4503540e92c1da19781fbe1995061 | consider implementing + operator for ListConfig | diff --git a/omegaconf/listconfig.py b/omegaconf/listconfig.py
index 6969aab..d2696b5 100644
--- a/omegaconf/listconfig.py
+++ b/omegaconf/listconfig.py
@@ -207,3 +207,10 @@ class ListConfig(Config):
return v
return MyItems(self.content)
+
+ def __add__(self, o):
+ # res is sharing... |
omry__omegaconf-83 | [
{
"changes": {
"added_entities": [
"omegaconf/dictconfig.py:DictConfig.__copy__",
"omegaconf/dictconfig.py:DictConfig.copy"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"omegaconf/dictconfig.py:DictConfig"
]
},
"file":... | omry/omegaconf | 3c1859c62891924d5f95b266eb8d377b996df276 | OmegaConf object doesn't support a .copy method
A dict is supposed to have a .copy() method (https://docs.python.org/3/library/stdtypes.html#dict.copy). For an OmegaConf object to be compatible with a dict's API, it should also support the copy() method -
```
>>> from omegaconf import OmegaConf
>>> conf = OmegaCon... | diff --git a/omegaconf/dictconfig.py b/omegaconf/dictconfig.py
index 7c180f8..808a687 100644
--- a/omegaconf/dictconfig.py
+++ b/omegaconf/dictconfig.py
@@ -1,4 +1,5 @@
from .config import Config
+import copy
from .errors import (
ReadonlyConfigError,
MissingMandatoryValue,
@@ -21,6 +22,15 @@ class DictConf... |
onesuper__pandasticsearch-30 | [
{
"changes": {
"added_entities": [
"pandasticsearch/dataframe.py:DataFrame.resolve_schema",
"pandasticsearch/dataframe.py:DataFrame.resolve_mappings",
"pandasticsearch/dataframe.py:DataFrame.get_mappings"
],
"added_modules": null,
"edited_entities": [
"pan... | onesuper/pandasticsearch | 13b16ba9d5926438d11fc78b8f0271ec93d9d749 | KeyError: properties in DataFrame.print_schema running against ES 7.x
Hi team,
I installed pandasticsearch version 0.5.1 using
```
pip install pandasticsearch[pandas]
```
and I tried to run this code
```
df = DataFrame.from_es(url='http://localhost:9200', index='my_index')
df.print_schema()
```
I ge... | diff --git a/pandasticsearch/dataframe.py b/pandasticsearch/dataframe.py
index 1f372db..1159dd6 100644
--- a/pandasticsearch/dataframe.py
+++ b/pandasticsearch/dataframe.py
@@ -138,7 +138,7 @@ class DataFrame(object):
raise TypeError('Column does not exist: [{0}]'.format(item))
return Colu... |
onicagroup__runway-1132 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"runway/core/providers/aws/_response.py:ResponseError.__init__",
"runway/core/providers/aws/_response.py:ResponseMetadata.__init__",
"runway/core/providers/aws/_response.py:BaseResponse._... | onicagroup/runway | a3174978c5053ac93d021390ed7990e10864f349 | [TODO] improve `runway.core.providers.aws._response.BaseResponse`
- use pydantic | diff --git a/runway/core/providers/aws/_response.py b/runway/core/providers/aws/_response.py
index 8727a65d..687c7c2f 100644
--- a/runway/core/providers/aws/_response.py
+++ b/runway/core/providers/aws/_response.py
@@ -1,75 +1,64 @@
"""Base class for AWS responses."""
# pylint: disable=invalid-name
from http import ... |
onicagroup__runway-1133 | [
{
"changes": {
"added_entities": [
"runway/core/providers/aws/s3/_bucket.py:Bucket.__bool__"
],
"added_modules": null,
"edited_entities": [
"runway/core/providers/aws/s3/_bucket.py:Bucket.exists",
"runway/core/providers/aws/s3/_bucket.py:Bucket.create"
],
... | onicagroup/runway | 35e3fe7c4479d585c9d9a41d8848a22ef1840d68 | [TODO] add `_bool_` to `runway.core.providers.aws.s3._bucket.Bucket`
- `False` if `.forbidden` or `not .exists`
- `True` if `.exists`
- assess if `.exists` should be `False` if `forbidden`
| diff --git a/runway/core/providers/aws/s3/_bucket.py b/runway/core/providers/aws/s3/_bucket.py
index fe0faffa..d0f508b5 100644
--- a/runway/core/providers/aws/s3/_bucket.py
+++ b/runway/core/providers/aws/s3/_bucket.py
@@ -53,14 +53,10 @@ class Bucket(DelCachedPropMixin):
@property
def exists(self) -> bool:... |
onicagroup__runway-1144 | [
{
"changes": {
"added_entities": [
"runway/module/staticsite/handler.py:StaticSite.sanitized_name"
],
"added_modules": null,
"edited_entities": [
"runway/module/staticsite/handler.py:StaticSite._create_dependencies_yaml",
"runway/module/staticsite/handler.py:Stati... | onicagroup/runway | d315e6514fb86c217aa5bc4c3763ca163597f7eb | [TODO] static site: sanitize module name before using it as a stack name
If a module name contains a `.`, it is used in CFN stack names (where it is an invalid character).
regex: `(?=^.{1,128}$)^[a-zA-Z][-a-zA-Z0-9_]+$` | diff --git a/runway/module/staticsite/handler.py b/runway/module/staticsite/handler.py
index 9dca8319..7b869ccd 100644
--- a/runway/module/staticsite/handler.py
+++ b/runway/module/staticsite/handler.py
@@ -12,6 +12,7 @@ from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union, cast
import yaml
from ..._l... |
onicagroup__runway-1219 | [
{
"changes": {
"added_entities": [
"runway/cfngin/hooks/docker/_login.py:LoginArgs._set_ecr",
"runway/cfngin/hooks/docker/_login.py:LoginArgs._set_registry"
],
"added_modules": null,
"edited_entities": [
"runway/cfngin/hooks/docker/_login.py:LoginArgs.__init__",
... | onicagroup/runway | 62cf452c1fe6192ec519a5592d913aa6202d47b4 | use pydantic to parse arguments for all `runway.cfngin.hooks.docker` hooks | diff --git a/Makefile b/Makefile
index da3347c6..b8ad4095 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: build clean help install lint list release test version
+.PHONY: build clean docs help install lint list release test version
SHELL := /bin/bash
diff --git a/runway/cfngin/hooks/docker/_login.py... |
onicagroup__runway-1245 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"runway/cfngin/actions/diff.py:Action._diff_stack"
],
"edited_modules": [
"runway/cfngin/actions/diff.py:Action"
]
},
"file": "runway/cfngin/actions/diff.py"
},
{
... | onicagroup/runway | 2a41ab6982f8d0c927a0b256cf5c58e085fc5b0a | [BUG] runway incorrectly shows parameters to be removed in "plan"
### Bug Description
When running a cloudformation plan on an existing stack, the output states that parameters are to be removed:
```console
phil4079@L4CLYSQ2:~/runway-cloudformation-bug-test$ DEPLOY_ENVIRONMENT=common runway plan
[runway] could... | diff --git a/runway/cfngin/actions/diff.py b/runway/cfngin/actions/diff.py
index 0e68b2f9..8604e9d0 100644
--- a/runway/cfngin/actions/diff.py
+++ b/runway/cfngin/actions/diff.py
@@ -210,9 +210,14 @@ class Action(deploy.Action):
tags = deploy.build_stack_tags(stack)
+ try:
+ provider_stac... |
onicagroup__runway-1249 | [
{
"changes": {
"added_entities": null,
"added_modules": [
"runway/cfngin/hooks/command.py:RunCommandHookArgs"
],
"edited_entities": [
"runway/cfngin/hooks/command.py:run_command"
],
"edited_modules": [
"runway/cfngin/hooks/command.py:run_command"
... | onicagroup/runway | 7070937a9d02b4e4e92435e8f28962196627d0a9 | use pydantic to parse arguments for `runway.cfngin.hooks.command` | diff --git a/runway/cfngin/hooks/command.py b/runway/cfngin/hooks/command.py
index 519294f1..f267e534 100644
--- a/runway/cfngin/hooks/command.py
+++ b/runway/cfngin/hooks/command.py
@@ -1,16 +1,51 @@
"""Command hook."""
import logging
import os
-from subprocess import PIPE, Popen
+import subprocess
from typing imp... |
onicagroup__runway-1302 | [
{
"changes": {
"added_entities": [
"runway/cfngin/lookups/handlers/rxref.py:RxrefLookup.legacy_parse"
],
"added_modules": null,
"edited_entities": [
"runway/cfngin/lookups/handlers/rxref.py:RxrefLookup.handle"
],
"edited_modules": [
"runway/cfngin/look... | onicagroup/runway | 0dbd1469ade292fe1f13817c44fc182b2214e8c6 | update `runway.cfngin.lookups.handlers.rxref` to use the standardized query syntax
Subtask of #1184 | diff --git a/docs/source/cfngin/lookups/rxref.rst b/docs/source/cfngin/lookups/rxref.rst
index 7ce61be0..6434582f 100644
--- a/docs/source/cfngin/lookups/rxref.rst
+++ b/docs/source/cfngin/lookups/rxref.rst
@@ -4,11 +4,11 @@
rxref
#####
-:Query Syntax: ``<stack-name>::<output-name>``
+:Query Syntax: ``<relative-sta... |
onicagroup__runway-1306 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"infrastructure/blueprints/prevent_privilege_escalation.py:AdminPreventPrivilegeEscalation.statement_deny_cost_explorer"
],
"edited_modules": [
"infrastructure/blueprints/prevent_priv... | onicagroup/runway | 1afdae6d38b8c9a3fa79bb3983e80e7a250363b7 | update `runway.cfngin.lookups.handlers.output` to use the standardized query syntax
Subtask of #1184 | diff --git a/docs/source/cfngin/configuration.rst b/docs/source/cfngin/configuration.rst
index 08872f53..0c1791a3 100644
--- a/docs/source/cfngin/configuration.rst
+++ b/docs/source/cfngin/configuration.rst
@@ -823,7 +823,7 @@ To do so, use the :ref:`output lookup` in the :attr:`~cfngin.stack.variables` on
.. code-b... |
onicagroup__runway-1316 | [
{
"changes": {
"added_entities": [
"runway/cfngin/lookups/handlers/kms.py:KmsLookup.legacy_parse"
],
"added_modules": null,
"edited_entities": [
"runway/cfngin/lookups/handlers/kms.py:KmsLookup.handle"
],
"edited_modules": [
"runway/cfngin/lookups/hand... | onicagroup/runway | f23756f0578b15bd5e75479db6f4ee5b28dc8734 | update `runway.cfngin.lookups.handlers.kms` to use the standardized query syntax
Subtask of #1184 | diff --git a/docs/source/cfngin/lookups/kms.rst b/docs/source/cfngin/lookups/kms.rst
index 40684191..88eca43c 100644
--- a/docs/source/cfngin/lookups/kms.rst
+++ b/docs/source/cfngin/lookups/kms.rst
@@ -2,12 +2,27 @@
kms
###
-:Query Syntax: ``[<region>@]<encrypted-blob>``
+:Query Syntax: ``<encrypted-blob>[::region... |
onicagroup__runway-2013 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"runway/core/components/_module_path.py:ModulePath"
]
},
"file": "runway/core/components/_module_path.py"
}
] | onicagroup/runway | 956acd6bd9e25024189622122b70a2730a223653 | [BUG] git repo link not working in path attribute
### Bug Description
I am trying to source terraform module stored in github repo, but when I pass the git link of repo in the "path" attribute of modules section in runway.yml and execute runway plan, it returns error as follows:
$runway plan
return self.__git_... | diff --git a/runway/core/components/_module_path.py b/runway/core/components/_module_path.py
index bdc471fc..60124812 100644
--- a/runway/core/components/_module_path.py
+++ b/runway/core/components/_module_path.py
@@ -37,7 +37,7 @@ class ModulePath:
ARGS_REGEX: ClassVar[str] = r"(\?)(?P<args>.*)$"
REMOTE_SOU... |
onicagroup__runway-2526 | [
{
"changes": {
"added_entities": [
"runway/cfngin/hooks/docker/hook_data.py:DockerHookData.__bool__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"runway/cfngin/hooks/docker/hook_data.py:DockerHookData"
]
},
"file": "runway/cf... | onicagroup/runway | ccb36a6c6730a8e97a032a5252aeb2935317451e | [BUG] Fix docker.hook_data.DockerHookData instance not being truthy.
Description: [BUG] Fix docker.hook_data.DockerHookData instance not being truthy. | diff --git a/runway/cfngin/hooks/docker/hook_data.py b/runway/cfngin/hooks/docker/hook_data.py
index 73e6c8d6..0275f45a 100644
--- a/runway/cfngin/hooks/docker/hook_data.py
+++ b/runway/cfngin/hooks/docker/hook_data.py
@@ -47,3 +47,7 @@ class DockerHookData(MutableMap):
new_obj = cls()
context.hook_da... |
online-judge-tools__api-client-144 | [
{
"changes": {
"added_entities": [
"onlinejudge/service/codechef.py:CodeChefService.get_url_of_login_page",
"onlinejudge/service/codechef.py:CodeChefService.is_logged_in",
"onlinejudge/service/codechef.py:CodeChefProblemData.__init__",
"onlinejudge/service/codechef.py:CodeC... | online-judge-tools/api-client | 78203fe3a71d165674301a8a4718a36867af4f18 | CodeChef parser is broken
``` console
$ oj -v d -n 'https://www.codechef.com/PLIN2020/problems/CNTSET'
[DEBUG] args: Namespace(cookie=PosixPath('/home/ubuntu/.local/share/online-judge-tools/cookie.jar'), directory=None, dry_run=True, format=None, json=False, silent=False, subcommand='d', system=False, u... | diff --git a/README.md b/README.md
index 78b5e52..e1c91fd 100644
--- a/README.md
+++ b/README.md
@@ -27,7 +27,7 @@ $ pip3 install online-judge-api-client
| [Anarchy Golf](http://golf.shinh.org/) | :heavy_check_mark: | :grey_question: (same to samples) | | ... |
online-judge-tools__oj-757 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"onlinejudge_command/download_history.py:DownloadHistory.add"
],
"edited_modules": [
"onlinejudge_command/download_history.py:DownloadHistory"
]
},
"file": "onlinejudge_... | online-judge-tools/oj | 55c801a34d7f7f277b1379c5b77b28626fc9e37e | oj command fails with `ModuleNotFoundError: No module named 'onlinejudge.__about__'` in version 10.0.0
はじめまして、
今朝、online-judge-toolsをインストールしてojコマンドを使用しようとしましたが、うまくいかなかったので報告します。
インストール手順に従ってインストールを行い、README.mdのFAQも読みました。
私の環境が悪かったり、online-judge-toolsの不具合でなければcloseしてください。
よろしくお願いします。
私の環境は以下のとおりです
macOS Mojave 1... | diff --git a/onlinejudge_command/download_history.py b/onlinejudge_command/download_history.py
index fcf4e79..9bfc989 100644
--- a/onlinejudge_command/download_history.py
+++ b/onlinejudge_command/download_history.py
@@ -7,16 +7,14 @@ from typing import *
import onlinejudge_command.logging as log
import onlinejudge... |
online-judge-tools__oj-759 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"onlinejudge_command/utils.py:exec_command"
],
"edited_modules": [
"onlinejudge_command/utils.py:exec_command"
]
},
"file": "onlinejudge_command/utils.py"
}
] | online-judge-tools/oj | 99963a50f30b66ae6ddd6dde3e3fb235c62582e1 | Zombie processes remains when terminate oj test with Ctrl-C | diff --git a/onlinejudge_command/utils.py b/onlinejudge_command/utils.py
index de82639..02e867a 100644
--- a/onlinejudge_command/utils.py
+++ b/onlinejudge_command/utils.py
@@ -77,8 +77,13 @@ def exec_command(command_str: str, *, stdin: Optional[IO[Any]] = None, input: Op
try:
answer, _ = proc.com... |
online-judge-tools__oj-896 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"onlinejudge_command/pretty_printers.py:_make_diff_between_line_and_line_by_comparing_word_by_word"
],
"edited_modules": [
"onlinejudge_command/pretty_printers.py:_make_diff_between_l... | online-judge-tools/oj | d634042e30fe97dfd70301032840c83e60f48dbf | --display-mode=diff で例外が飛ぶことがある
## Summary / 概要
## Steps to reproduce / 再現方法
https://codeforces.com/gym/103081/problem/A のサンプルで以下を使って `$ oj t -c 'python3 main.py' -D`
``` python
#!/usr/bin/env python3
from typing import *
def solve(n: int, k: int, a: List[str]) -> List[str]:
cnt = {}
for a_i... | diff --git a/onlinejudge_command/pretty_printers.py b/onlinejudge_command/pretty_printers.py
index 579645c..1c70780 100644
--- a/onlinejudge_command/pretty_printers.py
+++ b/onlinejudge_command/pretty_printers.py
@@ -270,7 +270,7 @@ def _make_diff_between_line_and_line_by_comparing_word_by_word(a: str, b: str) -
... |
online-judge-tools__oj-900 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"onlinejudge_command/subcommand/generate_input.py:add_subparser",
"onlinejudge_command/subcommand/generate_input.py:check_status",
"onlinejudge_command/subcommand/generate_input.py:genera... | online-judge-tools/oj | e5891655840c0e5dbd6afc8e099a3e1aa6cc0661 | Skip RE on output generator when `oj generate-input --hack`
## Description / 説明
`oj generate-input` コマンドの hack 機能に関して細かな希望(?)です。
`--hack-expected` で指定した出力生成用のプログラムにおいて Runtime error が発生した場合、現状だとそのテストケースはスキップされます。オプションの指定などにより、そのような入力を発見したタイミングで break してその内容を報告させることができると嬉しいです。
## Motivation / 動機
以下が可能になるはずです。
... | diff --git a/onlinejudge_command/subcommand/generate_input.py b/onlinejudge_command/subcommand/generate_input.py
index 4c9f336..2aa4749 100644
--- a/onlinejudge_command/subcommand/generate_input.py
+++ b/onlinejudge_command/subcommand/generate_input.py
@@ -43,7 +43,7 @@ tips:
subparser.add_argument('--width', type... |
online-judge-tools__oj-903 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "onlinejudge_command/__about__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"onl... | online-judge-tools/oj | fa8502e40891b52a436a0fc7b5b23aed9b16bffb | `--display-mode=diff-all` ですべての行が表示されない
## Summary / 概要
`--display-mode=diff-all` ですべての行が表示されません。私の経験上、最終行のみが表示されません。最終行以外は合っていて最終行のみ間違えているときは WA がでるので表示のみの問題だと推測します。
## Steps to reproduce / 再現方法
1. `oj t -M diff-all`
environments:
- version: online-judge-tools 11.5.0 (+ online-judge-api-client 10.10.... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index f0827f0..7e1e212 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,11 +1,5 @@
# Change Log
-## 11.5.0 / 2021-09-09
-
-- [#900](https://github.com/online-judge-tools/oj/pull/900) allow `$ oj g/i --hack-actual ...` without `--hack-expected`
-- [#894](https://github.c... |
oogeso__oogeso-142 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "src/oogeso/core/devices/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"... | oogeso/oogeso | ebb7fa5854021ebedf4294c39f425b1953c441e8 | Update CCS model
Improve CCS model using information from CleanOffHub project | diff --git a/docs/changelog.md b/docs/changelog.md
index 1b85da4..29a8570 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -4,6 +4,10 @@
The format is based on [Keep a Changelog](http://keepachangelog.com/)
and this project adheres to [Semantic Versioning](http://semver.org/).
+## v1.5.0
+2024-12-05
+- Add... |
oogeso__oogeso-74 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/oogeso/core/devices/compressor.py:CompressorGas._rules",
"src/oogeso/core/devices/compressor.py:CompressorGas.get_flow_var"
],
"edited_modules": [
"src/oogeso/core/device... | oogeso/oogeso | 40a1f94f9c4876c3b8637446f1e4a560e48491f8 | Add unit tests to check that the creation of constraints associated with all devices works as intended | diff --git a/.gitignore b/.gitignore
index 37ed47d..b4da171 100644
--- a/.gitignore
+++ b/.gitignore
@@ -129,4 +129,7 @@ venv.bak/
examples/result/
# Temporary data
-.tmp
\ No newline at end of file
+.tmp
+
+# PyCharm
+.DS_Store
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 9c85f6e.... |
open-contracting__ocdskit-51 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ocdskit/cli/commands/mapping_sheet.py:Command.handle"
],
"edited_modules": [
"ocdskit/cli/commands/mapping_sheet.py:Command"
]
},
"file": "ocdskit/cli/commands/mapping_... | open-contracting/ocdskit | c7aa01345a2d8b7c140faddf06412d34c1c707f6 | mapping-sheet: script omits original description when a reference is used for an object
Currently the flattened schema produced by the mapping-sheet script omits the original description (and other properties) for objects where a reference is used, this means users of the flattened schema may miss out on important cont... | diff --git a/.travis.yml b/.travis.yml
index 7706cb5..e2efa3c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,4 +1,3 @@
-sudo: false
language: python
cache: pip
python:
diff --git a/ocdskit/cli/commands/mapping_sheet.py b/ocdskit/cli/commands/mapping_sheet.py
index 7bb1311..d86108b 100644
--- a/ocdskit/cli/commands... |
open-dicom__dicom_parser-83 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/dicom_parser/image.py:Image.is_mosaic"
],
"edited_modules": [
"src/dicom_parser/image.py:Image"
]
},
"file": "src/dicom_parser/image.py"
}
] | open-dicom/dicom_parser | 759619e39eda56a5eff4dc045baca73da004f429 | "ImageType" not set causes is_mosaic to crash
**Is your feature request related to a problem? Please describe.**
My dicoms don't have any "ImageType" field so I cannot use .data on them I have to work with raw
**Describe the solution you'd like**
To have a more robust check, as the only purpose is to know if it is... | diff --git a/src/dicom_parser/image.py b/src/dicom_parser/image.py
index 2866afb..b62b324 100644
--- a/src/dicom_parser/image.py
+++ b/src/dicom_parser/image.py
@@ -533,7 +533,7 @@ class Image:
bool
Whether the image is a mosaic encoded volume
"""
- return "MOSAIC" in self.header.g... |
open-dicom__dicom_parser-93 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "src/dicom_parser/messages.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/dic... | open-dicom/dicom_parser | ec61d42824b8da34bc3b0feb212df6d65575e46c | Enable instantiating a Series using an iterable of Image instances
Instead of only allowing a path, enable passing an iterable of `Image` instances directly. Images should share the *SeriesInstanceUID* and be sorted by *InstanceNumber*. | diff --git a/src/dicom_parser/messages.py b/src/dicom_parser/messages.py
index 48bd241..604293b 100644
--- a/src/dicom_parser/messages.py
+++ b/src/dicom_parser/messages.py
@@ -16,5 +16,6 @@ UNREGISTERED_MODALITY: str = (
"No sequence identifiers registered for {modality}!"
)
MISSING_HEADER_INFO: str = "No heade... |
open-dynaMIX__raiseorlaunch-44 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raiseorlaunch/raiseorlaunch.py:Raiseorlaunch._log_format_con",
"raiseorlaunch/raiseorlaunch.py:Raiseorlaunch._compare_running",
"raiseorlaunch/raiseorlaunch.py:Raiseorlaunch._is_running"... | open-dynaMIX/raiseorlaunch | 6f4364a598e0612ebe8bdb2516aeeb1080a3219b | crashes when Spotify is closed but not when Spotify is open
This syntax worked to raise Spotify if it was already running, but crashed instead of launching Spotify when it was not running. If I'm doing something invalid, it would be nice if it failed with a more helpful diagnostic message explaining what was invalid.
... | diff --git a/raiseorlaunch/raiseorlaunch.py b/raiseorlaunch/raiseorlaunch.py
index 9ac4338..e164d5d 100644
--- a/raiseorlaunch/raiseorlaunch.py
+++ b/raiseorlaunch/raiseorlaunch.py
@@ -144,8 +144,17 @@ class Raiseorlaunch(object):
Returns:
str: '<Con: class="{}" instance="{}" title="{}" id={}>'
... |
open-mmlab__mmengine-856 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mmengine/config/config.py:Config._get_base_files"
],
"edited_modules": [
"mmengine/config/config.py:Config"
]
},
"file": "mmengine/config/config.py"
}
] | open-mmlab/mmengine | 6af88783fb0c7556cfcdd09c7ad839f9572c3095 | [Bug] File format checking when more than one dot in the path
### Prerequisite
- [X] I have searched [Issues](https://github.com/open-mmlab/mmengine/issues) and [Discussions](https://github.com/open-mmlab/mmengine/discussions) but cannot get the expected help.
- [X] The bug has not been fixed in the latest version(htt... | diff --git a/mmengine/config/config.py b/mmengine/config/config.py
index 6a81797..18560ac 100644
--- a/mmengine/config/config.py
+++ b/mmengine/config/config.py
@@ -550,8 +550,8 @@ class Config:
Returns:
list: A list of base config.
"""
- file_format = filename.partition('.')[-1]
-... |
open-sdg__sdg-build-322 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sdg/inputs/InputBase.py:InputBase.apply_code_map"
],
"edited_modules": [
"sdg/inputs/InputBase.py:InputBase"
]
},
"file": "sdg/inputs/InputBase.py"
},
{
"change... | open-sdg/sdg-build | c78e8bda746c9445737ec9c97785f088b15083fc | Error when using code_map in inputs
Pandas 1.4 introduced a breaking change in the [Series.replace](https://pandas.pydata.org/docs/reference/api/pandas.Series.replace.html) method. If you are using Pandas 1.4 or higher and try to use the code_map parameter, you'll see this error: `ValueError: Series.replace cannot use ... | diff --git a/sdg/inputs/InputBase.py b/sdg/inputs/InputBase.py
index 18f0a9a..8dcf40d 100644
--- a/sdg/inputs/InputBase.py
+++ b/sdg/inputs/InputBase.py
@@ -363,5 +363,8 @@ class InputBase(Loggable):
if row['Dimension'] not in code_dict:
code_dict[row['Dimension']] = {}
... |
open-things__loggingex-14 | [
{
"changes": {
"added_entities": [
"src/loggingex/context/__init__.py:ContextChange.__str__",
"src/loggingex/context/__init__.py:ContextChange.__repr__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/loggingex/context/__init__.py... | open-things/loggingex | 2c84f8745601d62666024edca3e74ebdcfbe685b | Implement __str__ and __repr__ for ContextChange
Currently `ContextChange` looks ugly in the debugger or when printed.
Implement `__str__` and `__repr__` methods to make it pretty and, most importantly, useful. | diff --git a/src/loggingex/context/__init__.py b/src/loggingex/context/__init__.py
index f722f47..23f0337 100644
--- a/src/loggingex/context/__init__.py
+++ b/src/loggingex/context/__init__.py
@@ -128,6 +128,21 @@ class ContextChange:
self.context_restore_token = context_restore_token
+ def __str__(self... |
open2c__bioframe-147 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bioframe/ops.py:select_mask"
],
"edited_modules": [
"bioframe/ops.py:select_mask"
]
},
"file": "bioframe/ops.py"
}
] | open2c/bioframe | 17e766df684ff81e53a63cf8470983ab0711ce1a | select recently changed behavior causing issues in cooltools
as described in https://github.com/open2c/cooltools/issues/435 :
bioframe select became more inclusive and is selecting "more" with v0.4.0 ...
with bioframe 0.3.1
``` python
In [16]: bioframe.select(track, ("chr1",100000000,150000000)).shape
Out[16]: ... | diff --git a/bioframe/ops.py b/bioframe/ops.py
index 2da92b6..4503114 100644
--- a/bioframe/ops.py
+++ b/bioframe/ops.py
@@ -54,12 +54,19 @@ def select_mask(df, region, cols=None):
_verify_columns(df, [ck, sk, ek])
chrom, start, end = parse_region(region)
+
if chrom is None:
raise ValueError("... |
open2c__bioframe-216 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "bioframe/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_module... | open2c/bioframe | 0135c23bb5ed15e86d49f9a97b8dca0d63469b67 | Two tests segfault on s390x
While updating `bioframe` for Fedora to 0.7.1, I noticed two tests, `test_read_sam` and `test_read_bam`, segfaulting when run on `s390x` builders.
Previously with version 0.6.4 all tests succeeded. It looks like the change introduced in 660ba3f might be the cause. But I haven't analyzed t... | diff --git a/CHANGES.md b/CHANGES.md
index 76709b3..bad6215 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -2,7 +2,9 @@
## [Upcoming release](https://github.com/open2c/bioframe/compare/v0.7.1...HEAD)
-## [v0.7.0](https://github.com/open2c/bioframe/compare/v0.7.0...v0.7.1)
+## v0.7.1
+
+Date: 2024-06-17
Maintenance... |
openatx__uiautomator2-953 | [
{
"changes": {
"added_entities": null,
"added_modules": [
"uiautomator2/abcd.py:AbstractDevice"
],
"edited_entities": null,
"edited_modules": [
"uiautomator2/abcd.py:DeviceInterface"
]
},
"file": "uiautomator2/abcd.py"
},
{
"changes": {
"... | openatx/uiautomator2 | 01effab2d6ad2356af5d9d7b87dd043070e8de9a | (开头的xpath识别错误
使用括号开头的xpath`(//android.widget.ImageView)[2]`用来匹配第n个match的元素时
会被当作自定义的字符串匹配语法处理
- 手机型号：任意
- uiautomator2的版本号：2.16.25
- 手机截图：无
- 相关日志：`uiautomator2.exceptions.XPathElementNotFoundError: ["//*[@text='(//android.widget.ImageView)[2]' or @content-desc='(//android.widget.ImageView)[2]' or @resource-id='... | diff --git a/XPATH.md b/XPATH.md
index 2e80c27..32cef81 100644
--- a/XPATH.md
+++ b/XPATH.md
@@ -146,6 +146,29 @@ el.screenshot()
# 控件滑动
el.swipe("right") # left, right, up, down
el.swipe("right", scale=0.9) # scale默认0.9, 意思是滑动距离为控件宽度的90%, 上滑则为高度的90%
+
+print(el.info)
+# output example
+{'index': '0',
+ 'text': '',
... |
opendatacube__datacube-core-1223 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"datacube/utils/geometry/_base.py:_guess_crs_str"
],
"edited_modules": [
"datacube/utils/geometry/_base.py:_guess_crs_str"
]
},
"file": "datacube/utils/geometry/_base.py... | opendatacube/datacube-core | f19a816f1a8f59041cffe5e53a100c6426e11096 | Non-EPSG WKT projections are slower to create than standard EPSG projections
### Expected behaviour
`CRS` object creation should have near-constant execution times for valid input strings.
### Actual behaviour
`CRS` objects created using a valid WKT string that does not have an equivalent EPSG representation are c... | diff --git a/datacube/utils/geometry/_base.py b/datacube/utils/geometry/_base.py
index 5c2760c7..43454159 100644
--- a/datacube/utils/geometry/_base.py
+++ b/datacube/utils/geometry/_base.py
@@ -141,12 +141,13 @@ def _guess_crs_str(crs_spec: Any) -> Optional[str]:
if isinstance(crs_spec, dict):
crs_spec =... |
opendatacube__datacube-core-1242 | [
{
"changes": {
"added_entities": [
"datacube/utils/geometry/_base.py:_make_crs_key"
],
"added_modules": [
"datacube/utils/geometry/_base.py:_make_crs_key"
],
"edited_entities": [
"datacube/utils/geometry/_base.py:_make_crs",
"datacube/utils/geometry/... | opendatacube/datacube-core | 465c44edd6b50d14d388170805f397561cde3085 | load_ard() task graph creation limited by GeoBox/CRS hash function performance
### Expected behaviour
When I run load_ard() on a large region (the Murray Darling Basin) using distributed dask, I would like to be able to create up to 500,000 tasks for my workflow. That is, fully utilise the dask scheduler’s capacity be... | diff --git a/datacube/utils/geometry/_base.py b/datacube/utils/geometry/_base.py
index 43454159..41b906ef 100644
--- a/datacube/utils/geometry/_base.py
+++ b/datacube/utils/geometry/_base.py
@@ -116,10 +116,25 @@ class BoundingBox(_BoundingBox):
(p1[1], p2[1]))
-@cachetools.cache... |
opendatacube__datacube-core-1281 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"datacube/utils/changes.py:get_doc_changes",
"datacube/utils/changes.py:classify_changes"
],
"edited_modules": [
"datacube/utils/changes.py:get_doc_changes",
"datacube... | opendatacube/datacube-core | 6f96de0b6a876e8bee2b06aea6628f98e754a3e9 | datacube dataset index incorrect comparison of geometry
linked issue: https://github.com/opendatacube/odc-tools/issues/479
### Expected behaviour
when performing `--update-if-exists` `geometry.coordinates` and `grid_spatial.projection.valid_data.coordinates` shouldn't mark `unsafe` when the values are identical bu... | diff --git a/datacube/utils/changes.py b/datacube/utils/changes.py
index 4422ccae..8a226807 100644
--- a/datacube/utils/changes.py
+++ b/datacube/utils/changes.py
@@ -5,6 +5,8 @@
"""
Validation of document/dictionary changes.
"""
+import numpy
+
from itertools import zip_longest
from typing import Any, Callable, L... |
opendatacube__datacube-core-1304 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"datacube/index/eo3.py:prep_eo3"
],
"edited_modules": [
"datacube/index/eo3.py:prep_eo3"
]
},
"file": "datacube/index/eo3.py"
},
{
"changes": {
"added_enti... | opendatacube/datacube-core | c5486c854dc4fe3e1bef670a5ce01010d0caa938 | Doc2Dataset fails if lineage sources are specified as UUIDs rather than strings
Converting an input doc that contains lineage references to a Dataset (using `Doc2Dataset(index, fail_on_missing_lineage=True, verify_lineage=False, skip_lineage=False)`) fails if the lineage references in the input doc are of type `UUID` i... | diff --git a/datacube/index/eo3.py b/datacube/index/eo3.py
index 12aea720..74bb06c6 100644
--- a/datacube/index/eo3.py
+++ b/datacube/index/eo3.py
@@ -9,7 +9,8 @@
"""
from affine import Affine
from functools import reduce
-from typing import Dict, Any, Iterable, Optional, Tuple
+from typing import Dict, Any, Iterabl... |
opendatacube__datacube-core-1402 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"datacube/drivers/postgis/_spatial.py:promote_to_multipolygon"
],
"edited_modules": [
"datacube/drivers/postgis/_spatial.py:promote_to_multipolygon"
]
},
"file": "datacu... | opendatacube/datacube-core | 8b51010635e45ed9f0f6092fd942a5d4e572727f | ShapelyDeprecationWarning: The 'type' attribute is deprecated -> use the 'geom_type' attribute instead.
```
datacube/utils/geometry/_base.py:623: ShapelyDeprecationWarning: The 'type' attribute is deprecated, and will be removed in the future. You can use the 'geom_type' attribute instead.
if geom.type in ['Point... | diff --git a/datacube/drivers/postgis/_spatial.py b/datacube/drivers/postgis/_spatial.py
index c8222f4c..7481745a 100644
--- a/datacube/drivers/postgis/_spatial.py
+++ b/datacube/drivers/postgis/_spatial.py
@@ -147,9 +147,9 @@ def spindexes(engine: Connectable) -> Mapping[CRS, Type[SpatialIndex]]:
def promote_to_mul... |
opendatacube__datacube-core-1443 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"datacube/api/query.py:Query.__init__",
"datacube/api/query.py:_time_to_search_dims",
"datacube/api/query.py:_time_to_open_range"
],
"edited_modules": [
"datacube/api/... | opendatacube/datacube-core | 72ccd88d01ae9f8224a490d89c2b0508233b6d0b | Allow open-ended time ranges
When specifying a time range, be able to have the start or end of the range be open, to indicate all data before or after a date. For example:
`time=('2001', None)`
could indicate all data from 2001 onward.
`time=(None, '2010')`
could indicate all data before 2010.
| diff --git a/datacube/api/core.py b/datacube/api/core.py
index 47a8c179..a07d4500 100644
--- a/datacube/api/core.py
+++ b/datacube/api/core.py
@@ -232,12 +232,17 @@ class Datacube(object):
x=(1516200, 1541300), y=(-3867375, -3867350), crs='EPSG:3577'
- The ``time`` dimension can be speci... |
opendatacube__datacube-core-1457 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"datacube/storage/_read.py:read_time_slice"
],
"edited_modules": [
"datacube/storage/_read.py:read_time_slice"
]
},
"file": "datacube/storage/_read.py"
}
] | opendatacube/datacube-core | c8795e3144fcf6cdabed23eecc9e8cb04626bcef | BUG: Scale in rectilinear reproject produces different results (without dask)
Related:
- #1448
- #1450
### Expected behaviour
reproject behaves similar to GDAL defaults
### Actual behaviour
The behavior has slight differences with GDAL defaults
### Steps to reproduce the behaviour
- Original CRS = EPS... | diff --git a/datacube/storage/_read.py b/datacube/storage/_read.py
index 2c1dd05f..fb5b03b8 100644
--- a/datacube/storage/_read.py
+++ b/datacube/storage/_read.py
@@ -129,7 +129,6 @@ def read_time_slice(rdr,
is_nn = is_resampling_nn(resampling)
scale = pick_read_scale(rr.scale, rdr)
- scale_x, scale_y = ... |
opendatacube__datacube-core-1602 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"datacube/utils/cog.py:_write_cog"
],
"edited_modules": [
"datacube/utils/cog.py:_write_cog"
]
},
"file": "datacube/utils/cog.py"
},
{
"changes": {
"added_... | opendatacube/datacube-core | 8b46c2284e13c74739ca16faba67669af0b9cf74 | Important fix proposal: Implement setting "nan" nodata value for floating point rasters with no nodata attribute
Hi all, as discussed internally within DEA, we have recently encountered an issue where floating point rasters are not displayed correctly in ESRI software due to the lack of an explicitly set nodata attrib... | diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 69235df1..37a245a0 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -76,7 +76,7 @@ jobs:
password: ${{ secrets.DOCKERHUBPASSWD }}
- name: Build Docker
- uses: docker/build-push-action@v5
+ use... |
opendatacube__datacube-core-1673 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"datacube/utils/geometry/tools.py:gbox_boundary",
"datacube/utils/geometry/tools.py:roi_boundary"
],
"edited_modules": [
"datacube/utils/geometry/tools.py:gbox_boundary",
... | opendatacube/datacube-core | cd5f4e99d181718050b8563364f02ee2424e4a72 | Numpy>2.0 causes loss of precision during reproject_and_fuse for inputs with very small resolutions.
### Background
We have some very high resolution rasters (4.2141938e-08 resolution) in EPSG:4326 that were able to be reprojected/resampled/etc. prior to numpy 2.0.
### Expected behaviour
A correct reprojec... | diff --git a/datacube/utils/geometry/tools.py b/datacube/utils/geometry/tools.py
index c4c7018e..8b352245 100644
--- a/datacube/utils/geometry/tools.py
+++ b/datacube/utils/geometry/tools.py
@@ -60,8 +60,8 @@ def gbox_boundary(gbox, pts_per_side=16):
"""
H, W = gbox.shape[:2]
- xx = np.linspace(0, W, pts... |
opendatakosovo__cyrillic-transliteration-28 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cyrtranslit/__init__.py:to_cyrillic"
],
"edited_modules": [
"cyrtranslit/__init__.py:to_cyrillic"
]
},
"file": "cyrtranslit/__init__.py"
},
{
"changes": {
... | opendatakosovo/cyrillic-transliteration | 308ec9fba59f96c5eb8cf74371db8a3c0a3a78d8 | Cyrillic letter Ъ transliterate it to #.
This was raised in #12 by @097115. To reproduce this issue:
```bash
python cyrtranslit.py -l RU -i tests/ru.txt
``` | diff --git a/cyrtranslit/__init__.py b/cyrtranslit/__init__.py
index 39eed72..34d47e6 100644
--- a/cyrtranslit/__init__.py
+++ b/cyrtranslit/__init__.py
@@ -99,6 +99,10 @@ def to_cyrillic(string_to_transliterate, lang_code='sr'):
if index != length_of_string_to_transliterate - 1:
c_plus_1 ... |
openfoodfacts__openfoodfacts-python-191 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openfoodfacts/api.py:ProductResource.text_search"
],
"edited_modules": [
"openfoodfacts/api.py:ProductResource"
]
},
"file": "openfoodfacts/api.py"
}
] | openfoodfacts/openfoodfacts-python | 506f7a8b57918e0caff49747ded699d8176d599f | Problem with product search, something is certainly hardcoded
### What
The App always return the result for "eau mineral" (I guess it's for this because it's always starting with cristaline)
which is basically making the API useless
### Steps to reproduce the behavior:
import openfoodfacts
api = openfoodfacts.AP... | diff --git a/README.md b/README.md
index 0294826..181e6dc 100644
--- a/README.md
+++ b/README.md
@@ -112,4 +112,4 @@ Contributors:
Copyright 2016-2022 Open Food Facts
-The Open Food Facts Python SDK is licensed under the [MIT License](https://github.com/openfoodfacts/openfoodfacts-python/blob/develop/LICENSE).... |
openfoodfacts__openfoodfacts-python-26 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openfoodfacts/__init__.py:add_by_facet_fetch_function"
],
"edited_modules": [
"openfoodfacts/__init__.py:add_by_facet_fetch_function"
]
},
"file": "openfoodfacts/__init... | openfoodfacts/openfoodfacts-python | 0858f6688ca51c0064aa1891b342a441680bf5c9 | Travis build failing
@frankrousseau : Travis notifications are now available on Slack, shortly after you commit. The build is currently broken (looks like an encoding issue)
writing manifest file 'openfoodfacts.egg-info/SOURCES.txt'
running build_ext
Traceback (most recent call last):
File "setup.py", line 63, ... | diff --git a/README.md b/README.md
index 20ee03d..218f642 100644
--- a/README.md
+++ b/README.md
@@ -137,6 +137,8 @@ states = openfoodfacts.facets.get_states()
*Get all products for given facets.*
+Page access (pagination) is available through parameters.
+
```python
products = openfoodfacts.products.get_by_face... |
openforcefield__openff-evaluator-606 | [
{
"changes": {
"added_entities": [
"openff/evaluator/attributes/attributes.py:AttributeClass.__init__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"openff/evaluator/attributes/attributes.py:AttributeClass"
]
},
"file": "openf... | openforcefield/openff-evaluator | 3b386557f9185a4d27d3a92cc913802766bbe97a | Allow AttributeClasses to be initialized with values
Currently all subclasses of AttributeClasses need their attributes to be set separately to instantiation, e.g.:
```
batch = Batch()
batch.id = ...
batch.force_field_id = ...
```
It'd be quite handy to be able to initialize attributes e.g. `Batch(id=..., force_field... | diff --git a/openff/evaluator/attributes/attributes.py b/openff/evaluator/attributes/attributes.py
index b03dc1a..5fcbfb4 100644
--- a/openff/evaluator/attributes/attributes.py
+++ b/openff/evaluator/attributes/attributes.py
@@ -53,6 +53,11 @@ class AttributeClass(TypedBaseModel):
attributes with additional metada... |
openforcefield__openff-evaluator-611 | [
{
"changes": {
"added_entities": [
"openff/evaluator/substances/substances.py:Substance.to_substance_n_molecules"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"openff/evaluator/substances/substances.py:Substance"
]
},
"file": ... | openforcefield/openff-evaluator | 3b386557f9185a4d27d3a92cc913802766bbe97a | Add easy way to create new substance for specific number of molecules
A Substance may be created with mole fractions of 0.5098 for one component and 0.4902 for another, but when actually creating a box of 100 molecules, this gets turned into actual mole fractions of 0.51 and 0.49 respectively. This will pose an issue w... | diff --git a/openff/evaluator/substances/substances.py b/openff/evaluator/substances/substances.py
index 44afb8b..fc4bb80 100644
--- a/openff/evaluator/substances/substances.py
+++ b/openff/evaluator/substances/substances.py
@@ -220,6 +220,107 @@ class Substance(AttributeClass):
return self.amounts[identifie... |
openforcefield__openff-interchange-1186 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/interchange/interop/gromacs/_import/_import.py:from_files"
],
"edited_modules": [
"openff/interchange/interop/gromacs/_import/_import.py:from_files"
]
},
"file":... | openforcefield/openff-interchange | a9d1128df7c8878850bd73ddf857db983731d146 | GROMACS writer assumes unique molecules are sorted
**Description**
Working with a data source which is not sorted by chemically uniques molecule, i.e.
```
ATOM 194 Cl- Cl- A 2 37.846 20.981 12.009 1.00 0.00 Cl
ATOM 195 Na+ Na+ A 3 12.107 6.695 0.364 1.00 0.00 Na
... | diff --git a/docs/releasehistory.md b/docs/releasehistory.md
index 3e62319f..d51da967 100644
--- a/docs/releasehistory.md
+++ b/docs/releasehistory.md
@@ -16,6 +16,11 @@ Please note that all releases prior to a version 1.0.0 are considered pre-releas
### Behavior changes
* #1137 Internally use `openmm.LangevinMiddl... |
openforcefield__openff-nagl-165 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/nagl/lookups.py:AtomPropertiesLookupTable.lookup"
],
"edited_modules": [
"openff/nagl/lookups.py:AtomPropertiesLookupTable"
]
},
"file": "openff/nagl/lookups.py"... | openforcefield/openff-nagl | 92d3302570664bec4b4719d49bfa8f68ef4090df | Cannot assign partial charges to molecules with 1024+ atoms
## Expected behavior ##
<!-- A clear and concise description of what you want to do and what you think should happen. (Code to reproduce the behavior can be added below). -->
I'm not sure exactly what I expected for a maximum molecule size, but I would g... | diff --git a/openff/nagl/lookups.py b/openff/nagl/lookups.py
index 229a35e..9c7412b 100644
--- a/openff/nagl/lookups.py
+++ b/openff/nagl/lookups.py
@@ -137,8 +137,12 @@ class AtomPropertiesLookupTable(BaseLookupTable):
If the property value cannot be found for this molecule
"""
from open... |
openforcefield__openff-nagl-65 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/nagl/label/_label.py:LabelConformers.apply"
],
"edited_modules": [
"openff/nagl/label/_label.py:LabelConformers"
]
},
"file": "openff/nagl/label/_label.py"
},
... | openforcefield/openff-nagl | 3a7acc180399232d93eaaa233e5301995e829c43 | NAGL charge assignment applying global warnings filter
## Expected behavior ##
A global warnings filter shouldn't be inherited from library calls.
## Actual behavior ##
Getting charges through NAGL appears to be adding a `('ignore', None, <class 'Warning'>, None, 0)` warnings filter.
As far as I'm aware thi... | diff --git a/openff/nagl/label/_label.py b/openff/nagl/label/_label.py
index 0569331..8351949 100644
--- a/openff/nagl/label/_label.py
+++ b/openff/nagl/label/_label.py
@@ -105,25 +105,24 @@ class LabelConformers(_BaseLabel):
self.n_conformer_column: [],
}
- with capture_toolkit_warnings(... |
openforcefield__openff-nagl-71 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/nagl/toolkits/openeye.py:NAGLOpenEyeToolkitWrapper._run_normalization_reactions",
"openff/nagl/toolkits/openeye.py:NAGLOpenEyeToolkitWrapper.get_molecule_hybridizations",
"openff/... | openforcefield/openff-nagl | caa91d4c4a822cd312fc3d27f4ecb79096862a46 | Explicit exclusion of OpenEyeToolkitWrapper from global registry still leads to `to_openeye` attempt.
## Expected behavior ##
Assuming my understanding of `toolkit_registry_manager` is correct, specifically excluding OpenEyeToolkitWrapper would be expected to default to using NAGLRDKitToolkitWrapper when generating... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 08053bf..5b48d87 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,25 @@ The rules for this file:
* accompany each entry with github issue/PR number (Issue #xyz)
-->
+## [Unreleased]
+
+### Authors
+<!-- GitHub usernames of contributors to this release -->
+-... |
openforcefield__openff-qcsubmit-317 | [
{
"changes": {
"added_entities": null,
"added_modules": [
"openff/qcsubmit/exceptions.py:InvalidConvergeSettingsError",
"openff/qcsubmit/exceptions.py:ConflictingConvergeSettingsError"
],
"edited_entities": null,
"edited_modules": null
},
"file": "openff/qcs... | openforcefield/openff-qcsubmit | 637c82384d2811d2addd427d9b06a1130ceab890 | `PortalClient` no longer accepts `memory_cache_key` keyword, leading to failing tests
**Problem**
The newest version of QCSubmit removed the `memory_cache_key` keyword from the `PortalClient` (seen at this [commit](https://github.com/MolSSI/QCFractal/commit/bb032490ded34a410f3b93b34409038a9ff30d10)), which is causing i... | diff --git a/devtools/conda-envs/basic.yaml b/devtools/conda-envs/basic.yaml
index 0bf1483..7ffa66f 100644
--- a/devtools/conda-envs/basic.yaml
+++ b/devtools/conda-envs/basic.yaml
@@ -25,7 +25,7 @@ dependencies:
- qcengine >=0.25
- qcelemental >=0.25.1
- - qcfractal >=0.56,<0.58
+ - qcfractal >=0.56
- qca... |
openforcefield__openff-toolkit-1001 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/toolkit/topology/molecule.py:Molecule.visualize"
],
"edited_modules": [
"openff/toolkit/topology/molecule.py:Molecule"
]
},
"file": "openff/toolkit/topology/mole... | openforcefield/openff-toolkit | f5b5558f2142b36cff5c036c2600cb225f086871 | Add optional argument to Molecule.visualize() to suppress hydrogens
**Is your feature request related to a problem? Please describe.**
Frequently, `Molecule.visualize()` makes 2D diagrams that are too cluttered because explicit hydrogens are shown.
![image](https://user-images.githubusercontent.com/3656088/97918206-9... | diff --git a/docs/releasehistory.md b/docs/releasehistory.md
index 6e52d1c0..0b030490 100644
--- a/docs/releasehistory.md
+++ b/docs/releasehistory.md
@@ -14,6 +14,10 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
logic for library charges was updated to use only one unique match... |
openforcefield__openff-toolkit-1003 | [
{
"changes": {
"added_entities": null,
"added_modules": [
"openff/toolkit/utils/exceptions.py:ParseError"
],
"edited_entities": null,
"edited_modules": null
},
"file": "openff/toolkit/utils/exceptions.py"
},
{
"changes": {
"added_entities": [
"... | openforcefield/openff-toolkit | 317180da3a1b2437a7411a008da468b452faa1d1 | `Molecule.from_pdb_with_smiles()` warns about the pdb having unspecified stereochemistry
**Describe the bug**
`Molecule.from_pdb_and_smiles` gives a spurious warning about the PDB file having unspecified stereochemistry. This is spurious because the whole purpose of the method is to work around this limitation of th... | diff --git a/docs/releasehistory.md b/docs/releasehistory.md
index a3e0c974..c73b643d 100644
--- a/docs/releasehistory.md
+++ b/docs/releasehistory.md
@@ -46,10 +46,21 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
set to 0 with appropriate units, rather than `None`
- [PR #956... |
openforcefield__openff-toolkit-1171 | [
{
"changes": {
"added_entities": [
"openff/toolkit/topology/molecule.py:FrozenMolecule._make_carboxylic_acids_cis"
],
"added_modules": null,
"edited_entities": [
"openff/toolkit/topology/molecule.py:FrozenMolecule.generate_conformers",
"openff/toolkit/topology/mol... | openforcefield/openff-toolkit | 9362b714c5ab064700d24a32095c42d5d79292aa | OpenEye charging for trans-carboxylic acids will fail; incorporate workaround
Currently, OpenEye charging for (neutral) trans carboxylic acids will fail for reasons I'll explain below. OpenEye has come up with a fix/workaround which we should likely propagate into our charging code, see https://github.com/oess/openmm_o... | diff --git a/docs/releasehistory.md b/docs/releasehistory.md
index f363d422..1e16afec 100644
--- a/docs/releasehistory.md
+++ b/docs/releasehistory.md
@@ -8,6 +8,21 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
## Current development
+### Behaviors changed and bugfixes
+
+- [P... |
openforcefield__openff-toolkit-1184 | [
{
"changes": {
"added_entities": [
"openff/toolkit/utils/rdkit_wrapper.py:RDKitToolkitWrapper._constrain_end_directions",
"openff/toolkit/utils/rdkit_wrapper.py:RDKitToolkitWrapper._constrain_rank"
],
"added_modules": null,
"edited_entities": [
"openff/toolkit/uti... | openforcefield/openff-toolkit | de6e1dde50f165009e8ee36606b8d16528547dba | Conflicting single bond directions around double bond
**Describe the bug**
If I create a molecule from the following CMILES with `from_mapped_smiles`
```
mol = Molecule.from_mapped_smiles(
"[H:37][c:14]1[c:13]([c:12]([c:11]([c:16]([c:15]1[H:38])[H:39])/[N+:10](=[C:9](\[N:17]2[C:18]([C:19]([C:20]([C:21]2([H:... | diff --git a/devtools/conda-envs/openeye.yaml b/devtools/conda-envs/openeye.yaml
index 30e164da..8e9b4107 100644
--- a/devtools/conda-envs/openeye.yaml
+++ b/devtools/conda-envs/openeye.yaml
@@ -35,3 +35,4 @@ dependencies:
- qcengine
- mdtraj
- openff-interchange
+ - python-constraint
diff --git a/devtools/co... |
openforcefield__openff-toolkit-1417 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/toolkit/topology/molecule.py:FrozenMolecule.to_dict",
"openff/toolkit/topology/molecule.py:FrozenMolecule._initialize_from_dict",
"openff/toolkit/topology/molecule.py:FrozenMolecu... | openforcefield/openff-toolkit | 0182a57388ca86d751f8ac5c0457f0374e6fe714 | `deepcopy`ing a `Molecule` re-uses the properties dict
**Describe the bug**
`mol.properties` is not copied when calling `copy.deepcopy(mol)`, so that modifying the copy's properties modifies the original.
**To Reproduce**
```python
from copy import deepcopy
from openff.toolkit import Molecule
mol = Molecule... | diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 7bae40b5..2495269b 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -49,7 +49,7 @@ jobs:
PYTEST_ARGS: -r fE --tb=short -nauto --cov=openff --cov-config=setup.cfg --cov-append --cov-report=xml
steps:
- - uses... |
openforcefield__openff-toolkit-1567 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/toolkit/topology/molecule.py:Bond.from_dict",
"openff/toolkit/topology/molecule.py:Bond.molecule",
"openff/toolkit/topology/molecule.py:FrozenMolecule.to_dict",
"openff/to... | openforcefield/openff-toolkit | 37dd378d107d1bb52c062e2067ddf89f884a438b | Allow setting `Molecule.name` in constructor and some methods
**Is your feature request related to a problem? Please describe.**
<!-- A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] -->
`Molecule.name` is not relevant in all use cases but critical in some, i.e. exporting... | diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
index 26a8c402..ee228b5c 100644
--- a/.github/workflows/examples.yml
+++ b/.github/workflows/examples.yml
@@ -139,6 +139,7 @@ jobs:
NB_ARGS+=" --ignore=examples/check_dataset_parameter_coverage"
NB_ARGS+=" --ignore=ex... |
openforcefield__openff-toolkit-1581 | [
{
"changes": {
"added_entities": [
"openff/toolkit/topology/_mm_molecule.py:_SimpleMolecule.is_isomorphic_with",
"openff/toolkit/topology/_mm_molecule.py:_SimpleMolecule.are_isomorphic"
],
"added_modules": null,
"edited_entities": [
"openff/toolkit/topology/_mm_mo... | openforcefield/openff-toolkit | beb55797479e67396e138753d6c790be6d869013 | Add isomorphism checks for `_SimpleMolecule`
**Is your feature request related to a problem? Please describe.**
<!-- A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] -->
When I do something like `Interchange.from_openmm`, I end up with a topology of `_SimpleMolecule`. Exp... | diff --git a/openff/toolkit/topology/_mm_molecule.py b/openff/toolkit/topology/_mm_molecule.py
index 3b272927..8e5fac62 100644
--- a/openff/toolkit/topology/_mm_molecule.py
+++ b/openff/toolkit/topology/_mm_molecule.py
@@ -9,7 +9,7 @@ TypedMolecule TODOs
deserialize a Molecule or a TypedMolecule.
"""
-from typing... |
openforcefield__openff-toolkit-1609 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/toolkit/topology/molecule.py:FrozenMolecule.are_isomorphic"
],
"edited_modules": [
"openff/toolkit/topology/molecule.py:FrozenMolecule"
]
},
"file": "openff/tool... | openforcefield/openff-toolkit | e4a3b2ab6acc529c6138617045baab9332d9dab4 | isIsomorphic function behaves oddly
I tested the isomorphic function on a simple molecule and found that while it is isomorphic to itself (duh...) I do not get the atom correspondence printed if I copy the molecule by converting it to smiles first. This does not match the API description where the function should retur... | diff --git a/openff/toolkit/topology/molecule.py b/openff/toolkit/topology/molecule.py
index ce0c6972..13536058 100644
--- a/openff/toolkit/topology/molecule.py
+++ b/openff/toolkit/topology/molecule.py
@@ -1941,8 +1941,9 @@ class FrozenMolecule(Serializable):
The second molecule to test for isomorphism.
... |
openforcefield__openff-toolkit-1622 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/toolkit/topology/molecule.py:FrozenMolecule.__init__",
"openff/toolkit/topology/molecule.py:FrozenMolecule.from_file",
"openff/toolkit/topology/molecule.py:FrozenMolecule.from_pol... | openforcefield/openff-toolkit | 96fbfd5b647421617f309abc48642a931d5fca48 | `Topology.from_pdb` does not accept `pathlib.Path`
**Describe the bug**
<!-- A clear and concise description of what the bug is. -->
The toolkit sometimes handles `pathlib.Path` inputs, but `Topology.from_pdb` is [not one of those cases](https://github.com/openforcefield/openff-toolkit/blob/0.13.0/openff/toolkit/to... | diff --git a/docs/releasehistory.md b/docs/releasehistory.md
index 7d24bb4e..e1658e88 100644
--- a/docs/releasehistory.md
+++ b/docs/releasehistory.md
@@ -18,6 +18,7 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
### Bugfixes
- [PR #1617](https://github.com/openforcefield/openff... |
openforcefield__openff-toolkit-1652 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/toolkit/utils/ambertools_wrapper.py:AmberToolsToolkitWrapper.assign_partial_charges",
"openff/toolkit/utils/ambertools_wrapper.py:AmberToolsToolkitWrapper.assign_fractional_bond_orders"
... | openforcefield/openff-toolkit | 13817ba9222fa89abba79e3babf387c9aa2bcbdf | Assigning partial charges is not thread safe
**Describe the bug**
If I create an OpenFF Molecule object from a RDKit Molecule object, I get an error when trying to parametrize it. In the following code, if I instead create the Molecule from SMILES with
```python
mol = Molecule.from_smiles('[H][O][C]([H])([H])[S... | diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
index cd22488c..ad61078c 100644
--- a/.github/workflows/examples.yml
+++ b/.github/workflows/examples.yml
@@ -141,6 +141,7 @@ jobs:
NB_ARGS+=" --ignore=examples/using_smirnoff_in_amber_or_gromacs"
NB_ARGS+=" --ignore=... |
openforcefield__openff-toolkit-2026 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/toolkit/topology/molecule.py:FrozenMolecule.__repr__"
],
"edited_modules": [
"openff/toolkit/topology/molecule.py:FrozenMolecule"
]
},
"file": "openff/toolkit/to... | openforcefield/openff-toolkit | 459a73340d3ca43a40d03911927802bb147cfe16 | `Molecule.__repr__` effectively hangs for large molecules
**Describe the bug**
<!-- A clear and concise description of what the bug is. -->
The [implementation](https://github.com/openforcefield/openff-toolkit/blob/74cfe94e8cda29e933866b8d895849073ba00689/openff/toolkit/topology/molecule.py#L1319-L1328) of `repr` for ... | diff --git a/docs/releasehistory.md b/docs/releasehistory.md
index 2c7a6ac8..30c1a123 100644
--- a/docs/releasehistory.md
+++ b/docs/releasehistory.md
@@ -12,6 +12,8 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
### Behavior changes
+- [PR #2026](https://github.com/openforcefi... |
openforcefield__openff-toolkit-762 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/toolkit/topology/molecule.py:FrozenMolecule.from_rdkit"
],
"edited_modules": [
"openff/toolkit/topology/molecule.py:FrozenMolecule"
]
},
"file": "openff/toolkit/... | openforcefield/openff-toolkit | ae2a812a4be4184d9b5db71e370341346a3c0343 | Molecule.from_rdkit() allows input of implicit-hydrogen molecules
**Describe the bug**
The `Molecule.from_rdkit(rdmol)` method will allow implicit-hydrogen molecules to be imported without converting them to explicit-hydrogen molecules.
**To Reproduce**
```python
from rdkit import Chem
molOrig = Chem.MolFromSmil... | diff --git a/docs/environment.yml b/docs/environment.yml
index 3c2ef1d9..470cc184 100644
--- a/docs/environment.yml
+++ b/docs/environment.yml
@@ -9,6 +9,7 @@ dependencies:
- sphinx_bootstrap_theme
- myst-parser
- testpath ==0.3.1
+ - docutils ==0.16 # Temporary https://github.com/executablebooks/MyST... |
openforcefield__openff-toolkit-799 | [
{
"changes": {
"added_entities": [
"openff/toolkit/topology/molecule.py:FrozenMolecule.smirnoff_impropers",
"openff/toolkit/topology/molecule.py:FrozenMolecule.amber_impropers"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"openff/to... | openforcefield/openff-toolkit | d0b768a6d2cd0297b34aab3618197604b81d6e03 | Make `offmol.smirnoff_impropers` and `offmol.single_impropers`
**Describe the bug**
Not really a bug, possibly naive question about intended behavior in enumerating indices for improper torsions.
I was surprised at the large number of torsions included in `offmol.impropers` for some molecules (e.g. `len(methane.imp... | diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
index 72b6c9d5..5d77ab43 100644
--- a/docs/releasehistory.rst
+++ b/docs/releasehistory.rst
@@ -16,6 +16,14 @@ New features
OpenEye wrapper.
- `PR #793 <https://github.com/openforcefield/openforcefield/pull/793>`_: Add an initial ELF conformer selection... |
openforcefield__openff-toolkit-816 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openff/toolkit/typing/engines/smirnoff/forcefield.py:ForceField.parse_smirnoff_from_source"
],
"edited_modules": [
"openff/toolkit/typing/engines/smirnoff/forcefield.py:ForceField"
... | openforcefield/openff-toolkit | 61eaadb312ecb396ac94610fd0a45223426da8e4 | Allow Smirnoff99Frosst force fields with lower case names
**Is your feature request related to a problem? Please describe.**
When trying to run the smirnoff99Frosst forcefields via QCArchive the name is lowered somewhere within the internals of QCFractal/QCEngine which means the force field can not be loaded on Linux... | diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
index 9b561182..e196dcfa 100644
--- a/docs/releasehistory.rst
+++ b/docs/releasehistory.rst
@@ -45,6 +45,8 @@ Behavior changed
slightly different energies as a result of this change.
- `PR #839 <https://github.com/openforcefield/openforcefield/pull/839>... |
openlawlibrary__pygls-150 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygls/exceptions.py:JsonRpcException.__init__"
],
"edited_modules": [
"pygls/exceptions.py:JsonRpcException"
]
},
"file": "pygls/exceptions.py"
},
{
"changes": ... | openlawlibrary/pygls | 6cb9af98e67f4e71620c4ba1f0d0cd15757e8312 | If the request handler throws an exception, respond with Error
An endpoint request handler may throw an exception, e.g.
```
:: --> anakin textDocument/hover(3): {'position': {'character': 30, 'line': 37}, 'textDocument': {'uri': 'file:///home/raoul/.config/sublime-text-3/Packages/LSP/plugin/core/session_view.py'}}
... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index efc4a7c..945aeed 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,9 +21,11 @@ and this project adheres to [Semantic Versioning][semver].
### Fixed
- Periodically check client pid and exit server ([#149])
+- Fix server handling of client errors ([#141])
-[#139]: ht... |
openlawlibrary__pygls-160 | [
{
"changes": {
"added_entities": [
"pygls/lsp/types/basic_structures.py:JsonRPCRequestMessage.check_result_or_error",
"pygls/lsp/types/basic_structures.py:WorkspaceEdit.check_result_or_error"
],
"added_modules": null,
"edited_entities": [
"pygls/lsp/types/basic_st... | openlawlibrary/pygls | 4d8d8e25fbedd3d41b75e8bfe041c99fe3611b1d | Type of the id field in response message
The type of the `id` field in server response message is always `str` [now](https://github.com/openlawlibrary/pygls/blob/4d8d8e25fbedd3d41b75e8bfe041c99fe3611b1d/pygls/lsp/types/basic_structures.py#L72).
The LSP client can't get response for `{"id": 1, "method": "initialize}`... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index dcba8a6..348262e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,8 +13,10 @@ and this project adheres to [Semantic Versioning][semver].
### Fixed
+- Fix `pydantic` Unions type conversion ([#160])
- Fix change_notifications type (pydantic bug) ([#158])
+[#160]: ... |
openlawlibrary__pygls-177 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"pygls/lsp/types/basic_structures.py:ResourceOperationKind",
"pygls/lsp/types/basic_structures.py:CreateFile",
"pygls/lsp/types/basic_structures.py:RenameFil... | openlawlibrary/pygls | 78eef2615e5d89615f566169ffd4faa0a1ede8b2 | CreateFile, RenameFile, and DeleteFile missing required kind field
According to spec, `CreateFile`, `RenameFile`, and `DeleteFile` requires the `kind` field: https://microsoft.github.io/language-server-protocol/specifications/specification-current/#resourceChanges
CreateFile: https://github.com/openlawlibrary/pygl... | diff --git a/pygls/lsp/types/basic_structures.py b/pygls/lsp/types/basic_structures.py
index 5ed2092..e628a4a 100644
--- a/pygls/lsp/types/basic_structures.py
+++ b/pygls/lsp/types/basic_structures.py
@@ -244,12 +244,19 @@ class TextEdit(Model):
new_text: str
+class ResourceOperationKind(str, enum.Enum):
+ ... |
openlawlibrary__pygls-247 | [
{
"changes": {
"added_entities": [
"pygls/lsp/types/basic_structures.py:Model.__init__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"pygls/lsp/types/basic_structures.py:Model"
]
},
"file": "pygls/lsp/types/basic_structures.py... | openlawlibrary/pygls | 96bc69df9c963979ce76f386e83fa059093bc284 | `exclude_none = True` breaks `shutdown` requests
Unfortunately, it looks like #236 breaks [`shutdown`](https://microsoft.github.io/language-server-protocol/specifications/lsp/3.17/specification/#shutdown) requests.
I have a [command](https://github.com/swyddfa/esbonio/blob/ea8311a2b79ab8ef74157e9d5b2635e6b7b6a9e9/c... | diff --git a/pygls/lsp/types/basic_structures.py b/pygls/lsp/types/basic_structures.py
index 879c15b..2b28b59 100644
--- a/pygls/lsp/types/basic_structures.py
+++ b/pygls/lsp/types/basic_structures.py
@@ -54,6 +54,14 @@ class Model(BaseModel):
'from_': 'from'
}
+ def __init__(self, **data: An... |
openlawlibrary__pygls-252 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygls/workspace.py:Document.__init__",
"pygls/workspace.py:Workspace._create_document",
"pygls/workspace.py:Workspace.put_document"
],
"edited_modules": [
"pygls/work... | openlawlibrary/pygls | e99a07e741e8aed9c146209daf2271adaf826c7a | Missing language_id in "class Document"
I need to get language_id to identify source's kind. And there are so many LS need this too, such as [efm](https://github.com/mattn/efm-langserver).
pygls declared "TextDocumentItem" with lanuage_id in "pygls/lsp/types/basic_structures.py", but never use /store language_id.
... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 148cefb..d26b9ce 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning][semver].
### Fixed
+- `Document` objects now expose a text document's `language_id`
+
## [0.12] - 04/07/2022
### Added
diff --git a/py... |
openlawlibrary__pygls-303 | [
{
"changes": {
"added_entities": [
"pygls/protocol.py:LanguageServerProtocol._publish_diagnostics_deprecator",
"pygls/protocol.py:LanguageServerProtocol._construct_publish_diagnostic_type"
],
"added_modules": null,
"edited_entities": [
"pygls/protocol.py:LanguageS... | openlawlibrary/pygls | feff213f7484d2f15ed70da3eb2128f01a987916 | Add an optional version parameter to LanguageServerProtocol publish_diagnostics
- The LSP v15 added an optional version parameter to the publishDiagnostics notification.
- PublishDiagnosticsParams includes version but,
- LanguageServerProtocol.publish_diagnostics is not using version
Please make version an option... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index d49b73c..363a4c0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,11 +13,12 @@ and this project adheres to [Semantic Versioning][semver].
- Fix progress example in json extension. ([#230])
- Fix `AttributeErrors` in `get_configuration_async`, `get_configuration_call... |
openlawlibrary__pygls-304 | [
{
"changes": {
"added_entities": [
"pygls/workspace.py:is_char_beyond_multilingual_plane"
],
"added_modules": [
"pygls/workspace.py:is_char_beyond_multilingual_plane"
],
"edited_entities": [
"pygls/workspace.py:utf16_unit_offset",
"pygls/workspace.py... | openlawlibrary/pygls | 6139c71bb5b050a9be49ddcfdee356b54cbd55e6 | position_from_utf16 in workspace.py may return incorrect result.
The following code that mimics the way position_from_utf16 calculates the result, demonstrates the issue:
```python
def utf16_unit_offset(chars: str):
"""Calculate the number of characters which need two utf-16 code units.
Arguments:
... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 95ed61e..a1a037d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning][semver].
### Changed
### Fixed
+[#304]: https://github.com/openlawlibrary/pygls/issues/304
- `pygls` no longer overrides the event loop ... |
openlawlibrary__pygls-396 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygls/workspace/workspace.py:Workspace.__init__"
],
"edited_modules": [
"pygls/workspace/workspace.py:Workspace"
]
},
"file": "pygls/workspace/workspace.py"
}
] | openlawlibrary/pygls | 571fd1c569603475475883c118b56ba4680ca023 | Bug: Workspace._root_path attribute not set if if self._root_uri is None
I believe this is incorrect behavior. Relevant code:
https://github.com/openlawlibrary/pygls/blob/571fd1c569603475475883c118b56ba4680ca023/pygls/workspace/workspace.py#L49C1-L49C1
`if self._root_uri is None`, then `self._root_path` is never ... | diff --git a/pygls/workspace/workspace.py b/pygls/workspace/workspace.py
index 746c1ba..405a798 100644
--- a/pygls/workspace/workspace.py
+++ b/pygls/workspace/workspace.py
@@ -52,6 +52,8 @@ class Workspace(object):
if root_path is None:
raise Exception("Couldn't get `root_path` from `root... |
openlawlibrary__pygls-51 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygls/exceptions.py:JsonRpcException.to_dict"
],
"edited_modules": [
"pygls/exceptions.py:JsonRpcException"
]
},
"file": "pygls/exceptions.py"
},
{
"changes": {... | openlawlibrary/pygls | 3c5433648d278cc72b3b5ecf50ca0b73c57b2f75 | Message: TypeError: 'NoneType' object is not iterable
I'd like to use this to build an LSP for a small language called OpenSCAD, so I started investigating this project (excellent code and docs by the way!). I'm normally a Neovim user, but for sake of better understanding pygls, I installed VS code (in other words, mig... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index a1d2aa1..7a894cc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning][semver].
## [Unreleased]
+### Changed
+
+- Fix initialization failure when no workspace is open
+
## [0.7.3] - 01/30/2019
### Added
dif... |
openlawlibrary__pygls-64 | [
{
"changes": {
"added_entities": [
"pygls/protocol.py:JsonRPCResponseMessage.without_none_fields"
],
"added_modules": null,
"edited_entities": [
"pygls/protocol.py:JsonRPCProtocol._send_response"
],
"edited_modules": [
"pygls/protocol.py:JsonRPCProtoco... | openlawlibrary/pygls | 488c5f271865aedd8314edd0206024430adc466e | Response object should contain result OR error field
**Current behavior:**
Both _result_ and _error_ fields are serialized and returned as part of response object to the client.
**Expected behavior:**
From json RPC [specification](https://www.jsonrpc.org/specification):
```
jsonrpc
A String specifying the... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9a31d44..4667dd6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,10 +13,12 @@ and this project adheres to [Semantic Versioning][semver].
### Changed
+- Response object should contain result OR error field ([#64])
- Fix handling parameters whose names are reserved... |
openlawlibrary__pygls-65 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygls/protocol.py:LanguageServerProtocol.bf_initialize"
],
"edited_modules": [
"pygls/protocol.py:LanguageServerProtocol"
]
},
"file": "pygls/protocol.py"
},
{
... | openlawlibrary/pygls | f830a3778a145a4d366a5c5781f4e19170cb229f | Support multiple text document synchronization options
Currently we support just incremental updates. The goal is to support all synchronization options specified by the [protocol](https://microsoft.github.io/language-server-protocol/specification):
```
/**
* Defines how the host (editor) should sync document cha... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4667dd6..f5b2be6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning][semver].
### Added
+- Full text document synchronization support ([#65])
- Add more tests for `deserialize_message` function ([#61])
###... |
openmc-dev__openmc-1380 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openmc/cell.py:Cell.rotation",
"openmc/cell.py:Cell.create_xml_subelement"
],
"edited_modules": [
"openmc/cell.py:Cell"
]
},
"file": "openmc/cell.py"
},
{
... | openmc-dev/openmc | 6799da13f1af3ca4e468c58df5f70a9c057092dd | Allow explicit instanciation of rotation matrix
Using the Tait-Bryan angles we cannot represent reflection of universes, this is needed to represent some geometries, therefore allow explicit instanciation through overloading the read of the rotation element to allow full spec i.e. ```<rotation="1 0 0 0 -1 0 0 0 1"/>``` | diff --git a/include/openmc/cell.h b/include/openmc/cell.h
index 7206938c4..8a330060c 100644
--- a/include/openmc/cell.h
+++ b/include/openmc/cell.h
@@ -179,10 +179,10 @@ public:
//! \brief Rotational tranfsormation of the filled universe.
//
- //! The vector is empty if there is no rotation. Otherwise, the f... |
openmc-dev__openmc-2074 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openmc/cell.py:Cell.from_xml_element"
],
"edited_modules": [
"openmc/cell.py:Cell"
]
},
"file": "openmc/cell.py"
},
{
"changes": {
"added_entities": null,... | openmc-dev/openmc | 7752afb554aa05103ed8f62a3c26b12632bbac2c | Plot.from_xml_element doesn't grab colors from XML file
Code to reproduce below. We really should set something up to avoid having to write all this XML I/O boilerplate, maybe something similar to the dataclass functionality introduced recently to python.
```
gpad% cat plots.xml
<?xml version='1.0' encoding='utf-8... | diff --git a/openmc/cell.py b/openmc/cell.py
index feba18da5..103a34fe6 100644
--- a/openmc/cell.py
+++ b/openmc/cell.py
@@ -690,7 +690,10 @@ class Cell(IDManagerMixin):
for key in ('temperature', 'rotation', 'translation'):
value = get_text(elem, key)
if value is not None:
- ... |
openmc-dev__openmc-2217 | [
{
"changes": {
"added_entities": [
"openmc/mesh.py:RegularMesh.from_domain"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"openmc/mesh.py:RegularMesh"
]
},
"file": "openmc/mesh.py"
}
] | openmc-dev/openmc | aea56288198bb53ed753c6b3b48a7b767f4806ee | feature request: RegularMesh from universe class method
I find myself making RegularMesh that encompass the entire geometry quite often. When making weight windows, flux maps or dose maps.
We have ```Universe.bounding_box``` property and I was wondering if anyone else would like a new class method on the ```RegularM... | diff --git a/openmc/mesh.py b/openmc/mesh.py
index 8ac4b1594..a4c50a608 100644
--- a/openmc/mesh.py
+++ b/openmc/mesh.py
@@ -279,6 +279,7 @@ class StructuredMesh(MeshBase):
return vtk_grid
+
class RegularMesh(StructuredMesh):
"""A regular Cartesian mesh in one, two, or three dimensions
@@ -509,6 +5... |
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