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 |
|---|---|---|---|---|---|
bimpression__sosw-96 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sosw/app.py:Processor.__init__",
"sosw/app.py:Processor._account",
"sosw/app.py:Processor._region"
],
"edited_modules": [
"sosw/app.py:Processor"
]
},
"... | bimpression/sosw | 0b84a348f05bbc2a8d306bbf2b32b990fde02620 | Implement global context
Research the best practices of making the Context object from the Lambda handler accessible by core Processor. He should implement internal interfaces for some of the Context object method. | diff --git a/sosw/app.py b/sosw/app.py
index 4aa6713..3858b40 100644
--- a/sosw/app.py
+++ b/sosw/app.py
@@ -32,9 +32,10 @@ class Processor:
"""
DEFAULT_CONFIG = {}
- # TODO USE context.invoked_function_arn.
+
aws_account = None
- aws_region = None
+ aws_region = os.getenv('AWS_REGION', None)
... |
biocore__deblur-156 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"deblur/workflow.py:trim_seqs",
"deblur/workflow.py:launch_workflow"
],
"edited_modules": [
"deblur/workflow.py:trim_seqs",
"deblur/workflow.py:launch_workflow"
... | biocore/deblur | fd259a74f516a22db8db790ab2cd3a1afab96b22 | Support "left trimming" on sequences
It would be useful if in addition to the normal trimming (at the end of the sequence), there was a parameter to trim initial bases of a sequence. | diff --git a/ChangeLog.md b/ChangeLog.md
index ea3e5aa..a8981f9 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -4,6 +4,8 @@
### Features
+* Added `--left-trim-length` to allow for trimming nucleotides on the 5' end of each sequence. Please see [issue #154](https://github.com/biocore/deblur/issues/154) for more in... |
biocore__microsetta-public-api-31 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"microsetta_public_api/api/metadata.py:filter_sample_ids"
],
"edited_modules": [
"microsetta_public_api/api/metadata.py:filter_sample_ids"
]
},
"file": "microsetta_publi... | biocore/microsetta-public-api | 0f7a462d4a610e5e799772253ad61e09d04411d6 | The Taxonomy model is initialized on each GET and it's very expensive
Each GET seems to initialize the `Taxonomy` model, and takes about 2 minutes on my laptop. The interaction with this object is read-only -- is there a reason it needs to be re-initialized on each call rather than being done once at server start up? | diff --git a/README.md b/README.md
index e690226..c3dc94f 100644
--- a/README.md
+++ b/README.md
@@ -50,6 +50,9 @@ feature data. Tables can either be QZA `FeatureTable`'s or biom tables. If a `bi
the `"table-format": "biom"` option must be specified. Taxonomy data is accepted with the
`"feature-data-taxonomy"` keywor... |
biolink__biolink-model-toolkit-172 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bmt/toolkit.py:Toolkit.get_associations"
],
"edited_modules": [
"bmt/toolkit.py:Toolkit"
]
},
"file": "bmt/toolkit.py"
}
] | biolink/biolink-model-toolkit | e421af4ebb7e33ce43a7d9de2e5a6ab4b9e94e5c | get_associations() returns an emtpy list
We are trying to use `get_associations()` and are getting some unexpected results.
A couple of examples I tried:
`tk.get_associations(
subject_categories = ["chemical entity"], predicates = ["affects"], object_categories= ["gene or gene product"]
)`, and was expecting a... | diff --git a/bmt/toolkit.py b/bmt/toolkit.py
index fed2f44..b61da7a 100644
--- a/bmt/toolkit.py
+++ b/bmt/toolkit.py
@@ -441,12 +441,26 @@ class Toolkit(object):
A list of elements
"""
- association_elements = self.get_descendants("association")
filtered_elements: List[str] = lis... |
biolink__biolink-model-toolkit-25 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bmt/toolkit.py:Toolkit.get_descendants"
],
"edited_modules": [
"bmt/toolkit.py:Toolkit"
]
},
"file": "bmt/toolkit.py"
}
] | biolink/biolink-model-toolkit | f22def149c6f48ff13e8d62c71e1151123a4650d | Inconsistent return values from `get_descendants` method
When asking for a descendant, if descendants exist the method will return a list with the original category in it:
```python
from bmt import Toolkit
t = Toolkit()
print( t.get_descendants("disease or phenotypic feature") )
```
prints out `['disease or pheno... | diff --git a/bmt/toolkit.py b/bmt/toolkit.py
index 514cde9..15baef7 100644
--- a/bmt/toolkit.py
+++ b/bmt/toolkit.py
@@ -304,7 +304,7 @@ class Toolkit(object):
element = self.get_element(name)
if element:
d = self.generator.descendants(element.name)
- if d and reflexive:
+ ... |
biolink__biolink-model-toolkit-28 | [
{
"changes": {
"added_entities": [
"bmt/toolkit.py:Toolkit.is_mixin",
"bmt/toolkit.py:Toolkit.has_inverse"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"bmt/toolkit.py:Toolkit"
]
},
"file": "bmt/toolkit.py"
}
] | biolink/biolink-model-toolkit | ea7bb3f936b19c1416794d9fa9a72a0897420894 | add "is_mixin" and "has_inverse"
These would be helpful functions to have while generating QC reports on the biolink-model. | diff --git a/bmt/toolkit.py b/bmt/toolkit.py
index 121054d..7b18352 100644
--- a/bmt/toolkit.py
+++ b/bmt/toolkit.py
@@ -9,7 +9,7 @@ from bmt.utils import format_element, parse_name
Url = str
Path = str
-REMOTE_PATH = 'https://raw.githubusercontent.com/biolink/biolink-model/1.5.0/biolink-model.yaml'
+REMOTE_PATH = ... |
biolink__biolink-model-toolkit-43 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bmt/toolkit.py:Toolkit.get_element",
"bmt/toolkit.py:Toolkit.is_translator_canonical_predicate"
],
"edited_modules": [
"bmt/toolkit.py:Toolkit"
]
},
"file": "bm... | biolink/biolink-model-toolkit | 6a6563c7423fcb0f1338e78fcfb6c8735fbd40e2 | fix get_element() method for use in KGX | diff --git a/bmt/toolkit.py b/bmt/toolkit.py
index 4c08077..c43fae1 100644
--- a/bmt/toolkit.py
+++ b/bmt/toolkit.py
@@ -398,10 +398,12 @@ class Toolkit(object):
"""
parsed_name = parse_name(name)
element = self.generator.obj_for(parsed_name)
- if element is None and name in self.gener... |
biolink__biolink-model-toolkit-51 | [
{
"changes": {
"added_entities": [
"bmt/utils.py:from_camel"
],
"added_modules": [
"bmt/utils.py:from_camel"
],
"edited_entities": [
"bmt/utils.py:camelcase_to_sentencecase"
],
"edited_modules": [
"bmt/utils.py:camelcase_to_sentencecase"
... | biolink/biolink-model-toolkit | d4495980870ca6805c40f434fc3325d73da3e9f4 | Camel-case names with acronyms are not parsed well
Classes like "RNA product", etc. behave in strange ways.
```python
>>> print(tk.get_element("RNA product").class_uri)
biolink:RNAProduct
>>> print(tk.get_element("biolink:RNAProduct"))
None
```
I suspect that we are failing to convert "RNAProduct" to the exp... | diff --git a/bmt/utils.py b/bmt/utils.py
index f2ac488..e9a1d7c 100644
--- a/bmt/utils.py
+++ b/bmt/utils.py
@@ -4,6 +4,18 @@ import stringcase
from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition, Element, ClassDefinitionName, \
SlotDefinitionName, ElementName, TypeDefinition
+lowercase... |
biolink__biolink-model-toolkit-52 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bmt/utils.py:sentencecase_to_camelcase"
],
"edited_modules": [
"bmt/utils.py:sentencecase_to_camelcase"
]
},
"file": "bmt/utils.py"
}
] | biolink/biolink-model-toolkit | d4495980870ca6805c40f434fc3325d73da3e9f4 | Camel-case class names are not converted to CURIEs well
```python
>>> tk.get_descendants("transcript", formatted=True)
['biolink:Transcript', 'biolink:RNAProduct', 'biolink:Noncoding_RNAProduct', 'biolink:SiRNA', 'biolink:MicroRNA', 'biolink:RNAProductIsoform']
```
`biolink:Noncoding_RNAProduct` should not have a... | diff --git a/bmt/utils.py b/bmt/utils.py
index f2ac488..a5ad4fa 100644
--- a/bmt/utils.py
+++ b/bmt/utils.py
@@ -65,7 +65,11 @@ def sentencecase_to_camelcase(s: str) -> str:
str
string in CamelCase form
"""
- return stringcase.pascalcase(stringcase.snakecase(s))
+ return re.sub(
+ r"(?:^... |
biolink__biolink-model-toolkit-64 | [
{
"changes": {
"added_entities": [
"bmt/toolkit.py:Toolkit.get_element_by_prefix"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"bmt/toolkit.py:Toolkit"
]
},
"file": "bmt/toolkit.py"
},
{
"changes": {
"added_entit... | biolink/biolink-model-toolkit | 9daec3ff3534c6c9d39efbec2f95bef7eed56bef | add functionality to return biolink class for any curie
slightly different than ```element_name = t.get_element_by_mapping('RO:0002410')```
instead of mapping via exact, narrow, close, etc. mappings, this feature would take a curie and return the most likely classes that would be instantiated for a curie of this kind... | diff --git a/bmt/toolkit.py b/bmt/toolkit.py
index 8d1e4c3..ce16174 100644
--- a/bmt/toolkit.py
+++ b/bmt/toolkit.py
@@ -12,6 +12,7 @@ from linkml_runtime.linkml_model.meta import (
from bmt.toolkit_generator import ToolkitGenerator
from bmt.utils import format_element, parse_name
+import logging
Url = str
Path... |
biolink__biolink-model-toolkit-68 | [
{
"changes": {
"added_entities": [
"bmt/toolkit.py:Toolkit.get_inverse"
],
"added_modules": null,
"edited_entities": [
"bmt/toolkit.py:Toolkit.__init__",
"bmt/toolkit.py:Toolkit.get_ancestors",
"bmt/toolkit.py:Toolkit.get_descendants"
],
"edite... | biolink/biolink-model-toolkit | bd7858ded0bd8d23908efdbad64b1d98c40f318e | bmt.readthedocs.io link in README leads to 404 | diff --git a/README.md b/README.md
index 3dfaa6d..97d6c8b 100644
--- a/README.md
+++ b/README.md
@@ -37,7 +37,7 @@ python setup.py install
## Documentation
-The technical documentation for BMT can be found at [bmt.readthedocs.io](bmt.readthedocs.io)
+The technical documentation for BMT can be found at [https://bio... |
biolink__biolinkml-130 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"biolinkml/generators/jsonschemagen.py:JsonSchemaGenerator.visit_class_slot",
"biolinkml/generators/jsonschemagen.py:JsonSchemaGenerator.xxxvisit_slot"
],
"edited_modules": [
... | biolink/biolinkml | 0039fa7f15b31f043fd11fe514597ed378804eaa | json-schema
```yaml
id: http://example.org/sample/types
prefixes:
biolinkml: https://w3id.org/biolink/biolinkml/
imports:
- biolinkml:types
types:
yearCount:
base: int
uri: xsd:int
classes:
c:
slots:
- id
- age in years
- scores
- has prop
- ha... | diff --git a/biolinkml/generators/jsonschemagen.py b/biolinkml/generators/jsonschemagen.py
index 6af50246..77d77de1 100644
--- a/biolinkml/generators/jsonschemagen.py
+++ b/biolinkml/generators/jsonschemagen.py
@@ -57,14 +57,25 @@ class JsonSchemaGenerator(Generator):
self.schemaobj.definitions[camelcase(cls.n... |
biolink__biolinkml-369 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"biolinkml/generators/pythongen.py:PythonGenerator.gen_import_list"
],
"edited_modules": [
"biolinkml/generators/pythongen.py:PythonGenerator"
]
},
"file": "biolinkml/ge... | biolink/biolinkml | 0b62bffabb4938208703acac990a6b2b6461fa7e | enums are not imported in generated python code
E.g
```yaml
id: https://microbiomedata/schema
prefixes:
biolinkml: https://w3id.org/biolink/biolinkml/
imports:
- biolinkml:types
- issues_368_imports
classes:
c:
is_a: parent_class
slots:
- s
slots:
s:
range: e
```
... | diff --git a/biolinkml/generators/pythongen.py b/biolinkml/generators/pythongen.py
index 63f4a7ca..48c9d2e1 100644
--- a/biolinkml/generators/pythongen.py
+++ b/biolinkml/generators/pythongen.py
@@ -197,12 +197,15 @@ dataclasses._init_fn = dataclasses_init_fn_with_kwargs
add_type_ref(self.schema.types[... |
biolink__ontobio-699 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ontobio/obograph_util.py:OboJsonMapper.add_obograph_digraph"
],
"edited_modules": [
"ontobio/obograph_util.py:OboJsonMapper"
]
},
"file": "ontobio/obograph_util.py"
}... | biolink/ontobio | 4d591cd3b31d6ac3771ea8d143318764f6fe460f | problems parsing output from latest obographs library
In GO, we are trying to update to the latest obographs in ROBOT. We have been using owltools, which uses an older obographs release. We noticed this change, which currently upsets the ontobio JSON reader:
owltools:
```json
{
"definedClassId" : "http://... | diff --git a/ontobio/obograph_util.py b/ontobio/obograph_util.py
index 307ae1e..da2ef4d 100644
--- a/ontobio/obograph_util.py
+++ b/ontobio/obograph_util.py
@@ -43,17 +43,17 @@ class OboJsonMapper(object):
Converts a single obograph to Digraph edges and adds to an existing networkx DiGraph
"""
... |
biomass-dev__biomass-232 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"biomass/construction/reaction_rules.py:ReactionRules.state_transition"
],
"edited_modules": [
"biomass/construction/reaction_rules.py:ReactionRules"
]
},
"file": "bioma... | biomass-dev/biomass | 9ac0db3e444f9eee6ed120ff223cb19fe7bb9772 | Raise `DetectionError` instead of creating wrong model
### Discussed in https://github.com/biomass-dev/biomass/discussions/223
Prepare `test_ubiquitination.txt` including:
```
A ubiquitinates B --> uB
```
Since there is no rule like 'ubiquitinate', we expect
```
# This is what I expect.
DetectionError: Unre... | diff --git a/biomass/construction/reaction_rules.py b/biomass/construction/reaction_rules.py
index f780835..41921c8 100644
--- a/biomass/construction/reaction_rules.py
+++ b/biomass/construction/reaction_rules.py
@@ -1709,11 +1709,21 @@ class ReactionRules(ThermodynamicRestrictions):
if arrow in descriptio... |
biopragmatics__bioregistry-1035 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bioregistry/app/ui.py:resolve"
],
"edited_modules": [
"src/bioregistry/app/ui.py:resolve"
]
},
"file": "src/bioregistry/app/ui.py"
}
] | biopragmatics/bioregistry | cec184109840de15d1cc0c168845b61a3ae2bb3c | Add prefix [hgvs]
### Prefix
hgvs
### Name
Human Genome Variation Society Nomenclature
### Homepage
https://hgvs-nomenclature.org/stable/background/simple/
### Source Code Repository
https://github.com/HGVSnomenclature/hgvs-nomenclature
### Description
The HGVS Nomenclature is an internationa... | diff --git a/src/bioregistry/app/ui.py b/src/bioregistry/app/ui.py
index 023d64a02..5e19603f7 100644
--- a/src/bioregistry/app/ui.py
+++ b/src/bioregistry/app/ui.py
@@ -303,8 +303,15 @@ def reference(prefix: str, identifier: str):
)
+#: this is a hack to make it work when the luid starts with a slash for
+#: A... |
biopragmatics__bioregistry-1037 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bioregistry/app/ui.py:resolve"
],
"edited_modules": [
"src/bioregistry/app/ui.py:resolve"
]
},
"file": "src/bioregistry/app/ui.py"
}
] | biopragmatics/bioregistry | cec184109840de15d1cc0c168845b61a3ae2bb3c | Ark identifier example does not redirect via Bioregistry, but does via n2t and identifiers.org
The `ark` prefix (https://bioregistry.io/registry/ark) has an example for which the redirecting works for all but Bioregistry, which goes a 404: https://bioregistry.io/ark:/53355/cl010066723
Preliminary private discussion ... | diff --git a/src/bioregistry/app/ui.py b/src/bioregistry/app/ui.py
index 023d64a02..5e19603f7 100644
--- a/src/bioregistry/app/ui.py
+++ b/src/bioregistry/app/ui.py
@@ -303,8 +303,15 @@ def reference(prefix: str, identifier: str):
)
+#: this is a hack to make it work when the luid starts with a slash for
+#: A... |
biopragmatics__bioregistry-1076 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bioregistry/app/api.py:get_reference"
],
"edited_modules": [
"src/bioregistry/app/api.py:get_reference"
]
},
"file": "src/bioregistry/app/api.py"
},
{
"chan... | biopragmatics/bioregistry | c8fae322a64b493252c144582f9fa746991bf1bf | Can't construct reference page if slash in identifier
I believe this is still/again an issue: look at e.g. the registry page for [CTRI](https://bioregistry.io/registry/ctri) (India Clinical Trials Registry), and click on the example CURIE: https://bioregistry.io/reference/ctri:CTRI/2023/04/052053, at leas... | diff --git a/src/bioregistry/app/api.py b/src/bioregistry/app/api.py
index 9ee3b440c..1552d82b2 100644
--- a/src/bioregistry/app/api.py
+++ b/src/bioregistry/app/api.py
@@ -466,10 +466,12 @@ class IdentifierResponse(BaseModel):
@api_router.get(
- "/reference/{prefix}:{identifier}", response_model=IdentifierResp... |
biopragmatics__bioregistry-1208 | [
{
"changes": {
"added_entities": [
"src/bioregistry/schema/struct.py:Publication._matches_any_field"
],
"added_modules": null,
"edited_entities": [
"src/bioregistry/schema/struct.py:Resource.get_publications"
],
"edited_modules": [
"src/bioregistry/sch... | biopragmatics/bioregistry | 22f53b4105ab6b5eb0e41ea749582833c6cbcd0c | Extend provider data model
Include a list of publications in the `Provider` data model.
https://github.com/biopragmatics/bioregistry/blob/22f53b4105ab6b5eb0e41ea749582833c6cbcd0c/src/bioregistry/schema/struct.py#L232
This should be easy to incorporate since there's already a model for `Publication`
https://gi... | diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json
index a094c04d7..d71be1682 100644
--- a/src/bioregistry/data/bioregistry.json
+++ b/src/bioregistry/data/bioregistry.json
@@ -49460,6 +49460,22 @@
"description": "A large scale database of biomedical statements.",
... |
biopragmatics__bioregistry-1429 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bioregistry/app/ui.py:resource"
],
"edited_modules": [
"src/bioregistry/app/ui.py:resource"
]
},
"file": "src/bioregistry/app/ui.py"
},
{
"changes": {
... | biopragmatics/bioregistry | dc8399b2ac5b31b8d6bfe9bcdb6d93f2a181e60b | Allow provider-specific example ID
Should we extend the provider data model with an **optional provider-specific example ID** for the purpose of having working links in the provider table? There are other examples of this issue, for instance, for https://bioregistry.io/registry/uniprot, we have
![image](https://github... | diff --git a/src/bioregistry/app/templates/resource.html b/src/bioregistry/app/templates/resource.html
index d4b7b28d0..0091cf70e 100644
--- a/src/bioregistry/app/templates/resource.html
+++ b/src/bioregistry/app/templates/resource.html
@@ -613,7 +613,8 @@
{% if providers %}
<p>
... |
biopragmatics__bioregistry-955 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bioregistry/app/ui.py:metaresource"
],
"edited_modules": [
"src/bioregistry/app/ui.py:metaresource"
]
},
"file": "src/bioregistry/app/ui.py"
},
{
"changes":... | biopragmatics/bioregistry | fd3b4ee6b571f5d6ff2e10ccfff4b636194ad192 | obofoundry metaregistry pages shows incorrect example purl
Yes, I won't shut up about case sensitivity... it will be inscribed on my gravestone... all in lowercase
But this is different from #46 which is resolved
https://bioregistry.io/metaregistry/obofoundry
Example CURIE
chebi:24867
Example CURIE Link
h... | diff --git a/src/bioregistry/app/templates/metaresource.html b/src/bioregistry/app/templates/metaresource.html
index 30613a770..a405c10a9 100644
--- a/src/bioregistry/app/templates/metaresource.html
+++ b/src/bioregistry/app/templates/metaresource.html
@@ -144,7 +144,7 @@
</dd>
{% ... |
biopragmatics__bioregistry-977 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bioregistry/record_accumulator.py:get_converter"
],
"edited_modules": [
"src/bioregistry/record_accumulator.py:get_converter"
]
},
"file": "src/bioregistry/record_a... | biopragmatics/bioregistry | 0c4ff7203189c6470196c0d50200e1eaf85a866b | Rewiring from prescriptive context is ignored | diff --git a/exports/contexts/obo.context.jsonld b/exports/contexts/obo.context.jsonld
index 87f6613ff..1ec1187ef 100644
--- a/exports/contexts/obo.context.jsonld
+++ b/exports/contexts/obo.context.jsonld
@@ -254,7 +254,7 @@
"PLANA": "http://purl.obolibrary.org/obo/PLANA_",
"PLANP": "http://purl.oboli... |
biopragmatics__bioregistry-993 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bioregistry/external/ols.py:get_ols",
"src/bioregistry/external/ols.py:_process"
],
"edited_modules": [
"src/bioregistry/external/ols.py:get_ols",
"src/bioregistr... | biopragmatics/bioregistry | 848371021c929683fd62b4e2f4e6b1ccf646cc23 | The url that resolves the hpath ontology
### Prefix
MC
### Explanation
# Problem
The resource in question is the hpath ontology listed here: https://bioregistry.io/registry/hpath
The example case does not resolve to the correct resource, and that probably means none of the resource links do.
E.G. http://purl.... | diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json
index ad495fa18..244cedfdf 100644
--- a/src/bioregistry/data/bioregistry.json
+++ b/src/bioregistry/data/bioregistry.json
@@ -903,7 +903,7 @@
},
"ols": {
"description": "Alzheimer's Disease Ontology is a knowledg... |
biopragmatics__bioregistry-995 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bioregistry/external/ols.py:get_ols",
"src/bioregistry/external/ols.py:_process"
],
"edited_modules": [
"src/bioregistry/external/ols.py:get_ols",
"src/bioregistr... | biopragmatics/bioregistry | 896def9b2873386ebc88a7bc287d0a43f2379d85 | Add prefix devtox
### Prefix
devtox
### Name
DevTox
### Homepage
https://www.devtox.org/
### Repository
_No response_
### Description
The DevTox Project harmonizes the nomenclature used to describe developmental anomalies in laboratory animals, assists in the visual recognition of developmental anomalies with ... | diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json
index 2b93cab5f..972b53480 100644
--- a/src/bioregistry/data/bioregistry.json
+++ b/src/bioregistry/data/bioregistry.json
@@ -903,7 +903,7 @@
},
"ols": {
"description": "Alzheimer's Disease Ontology is a knowledg... |
bird-house__birdy-137 | [
{
"changes": {
"added_entities": [
"birdy/client/converters.py:BaseConverter.data",
"birdy/client/converters.py:GenericConverter.convert",
"birdy/client/converters.py:TextConverter.convert"
],
"added_modules": [
"birdy/client/converters.py:GenericConverter"
... | bird-house/birdy | 4454a969d01f066a92792e02ce8e1fdbc7d45cf8 | Retrieve the data if no converter is found
## Description
At the moment, if no converter is available, `get(asobj=True)` returns the link. I suggest that instead we return the output of `retrieveData()`.
| diff --git a/birdy/client/converters.py b/birdy/client/converters.py
index 8e6b3fc..f3e9471 100644
--- a/birdy/client/converters.py
+++ b/birdy/client/converters.py
@@ -17,7 +17,7 @@ else:
class BaseConverter(object):
mimetype = None
extensions = []
- priority = 1
+ priority = None
nested = False
... |
bird-house__birdy-172 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"birdy/client/base.py:WPSClient._build_inputs"
],
"edited_modules": [
"birdy/client/base.py:WPSClient"
]
},
"file": "birdy/client/base.py"
},
{
"changes": {
... | bird-house/birdy | d7d2a6f83d786ce3820eee5147d00c85302007a0 | Inputs are given default mimetype
## Description
If an input has multiple supported formats, birdy will always use the first one in the list when creating a request. If an input has to be embedded in the request, and its mimetype is a binary format while the default mimetype is not, it crashes the `embed` function. ... | diff --git a/CHANGES.rst b/CHANGES.rst
index bf4ed82..613a7d0 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -1,6 +1,14 @@
Change History
**************
+0.6.7 (2020-03-10)
+==================
+
+Changes:
+
+* Fixed passing Path objects (#169)
+* Trying to guess mime type of inputs rather than taking the first value... |
bird-house__birdy-173 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"birdy/client/base.py:WPSClient._build_inputs"
],
"edited_modules": [
"birdy/client/base.py:WPSClient"
]
},
"file": "birdy/client/base.py"
},
{
"changes": {
... | bird-house/birdy | 299acb5929877db576a645bc24d209d61b1f4a36 | Inputs are given default mimetype
## Description
If an input has multiple supported formats, birdy will always use the first one in the list when creating a request. If an input has to be embedded in the request, and its mimetype is a binary format while the default mimetype is not, it crashes the `embed` function. ... | diff --git a/CHANGES.rst b/CHANGES.rst
index 613a7d0..82eee94 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -1,7 +1,7 @@
Change History
**************
-0.6.7 (2020-03-10)
+0.6.8 (2020-03-10)
==================
Changes:
diff --git a/birdy/client/base.py b/birdy/client/base.py
index 9bbf39f..d4bdf2e 100644
--- a/... |
bird-house__birdy-202 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"birdy/utils.py:guess_type"
],
"edited_modules": [
"birdy/utils.py:guess_type"
]
},
"file": "birdy/utils.py"
}
] | bird-house/birdy | 1fa66cf314d5276c14b9008ac70408ec2278a489 | `guess_type` function does not support Path objects. | diff --git a/CHANGES.rst b/CHANGES.rst
index eee7b6e..74850b8 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -8,6 +8,7 @@ Changes:
* Added a converter for loading GeoTIFF using xarray/rioxarray (#193).
* Update notebook process forms. See `client.gui` function.
+* Add support for Path objects in `utils.guess_type`
... |
bird-house__birdy-209 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"birdy/client/converters.py:Netcdf4Converter.convert",
"birdy/client/converters.py:XarrayConverter.convert"
],
"edited_modules": [
"birdy/client/converters.py:Netcdf4Converter... | bird-house/birdy | 24dbbd1f1d431b22f918486ab2974019edea4888 | Cryptic error message when trying to open non-existent netCDF link
## Description
When opening a netCDF link that does not exist, netcdf-c raises this error on stdout, which ends up in the response from birdy.
## Environment
* Birdy version used, if any: 0.8.0
## Steps to Reproduce
If the site does not ... | diff --git a/CHANGES.rst b/CHANGES.rst
index 8f9368a..e5d68d4 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -1,6 +1,14 @@
Change History
**************
+0.8.1 (unreleased)
+==================
+
+Changes:
+
+* Before trying to open a netCDF dataset, determine whether link is a valid OPeNDAP endpoint to avoid unneces... |
bird-house__birdy-217 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"birdy/client/base.py:WPSClient.__init__"
],
"edited_modules": [
"birdy/client/base.py:WPSClient"
]
},
"file": "birdy/client/base.py"
},
{
"changes": {
"ad... | bird-house/birdy | 7398c8adc7264f31b9f7664998b3932cb6d89be8 | owslib removed verbose argument
## Description
The client has a `verbose` argument that it passes to `owslib.WebProcessingService`. In https://github.com/geopython/OWSLib/pull/864, it was removed without deprecation warning.
I think we'll need to update birdy and pin owslib.
## Additional Information
Link... | diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 0c235c8..2b48946 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -14,7 +14,7 @@ jobs:
- name: Install packages
run: |
sudo apt-get -y install pandoc
- if: matrix.python-version == 3.8
+ ... |
bird-house__birdy-75 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"birdy/client/base.py:WPSClient._execute",
"birdy/client/base.py:WPSClient._process_output"
],
"edited_modules": [
"birdy/client/base.py:WPSClient"
]
},
"file": ... | bird-house/birdy | a8b1f071bc316d9cc3453257b0430a644b3f9a7e | native client: how to return multiple values?
## Description
In the current *native* client implementation we either return a single value or a list of values. I would find it more descriptive to return a dictionary with:
```
key=parameter identifier
value=parameter value
```
@huard @davidcaron
What do you... | diff --git a/birdy/client/base.py b/birdy/client/base.py
index ba82dbb..20bbe60 100644
--- a/birdy/client/base.py
+++ b/birdy/client/base.py
@@ -1,5 +1,6 @@
import types
from collections import OrderedDict
+from collections import namedtuple
from copy import copy
from textwrap import dedent
import threading
@@ -12... |
bjlittle__geovista-1132 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/geovista/bridge.py:Transform.from_tiff"
],
"edited_modules": [
"src/geovista/bridge.py:Transform"
]
},
"file": "src/geovista/bridge.py"
},
{
"changes": {
... | bjlittle/geovista | 57fc7edd7c12d554f35e50afbce40967bc4df913 | rasterio 1.4.x regression
## 🐛 Bug Report
<!-- Provide a clear description of the bug/issue that you're experiencing -->
The recent release of [rasterio 1.4.0](https://github.com/rasterio/rasterio/releases/tag/1.4.0) has resulted in a behaviour regression, see https://github.com/rasterio/rasterio/issues/3191.
T... | diff --git a/src/geovista/bridge.py b/src/geovista/bridge.py
index eafc184..f95f56b 100644
--- a/src/geovista/bridge.py
+++ b/src/geovista/bridge.py
@@ -867,7 +867,19 @@ class Transform: # numpydoc ignore=PR01
cols, rows = np.meshgrid(
np.arange(src.width), np.arange(src.height), indexing... |
bjlittle__geovista-673 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/geovista/pantry/data.py:CloudPreference"
]
},
"file": "src/geovista/pantry/data.py"
},
{
"changes": {
"added_entities": null,
"added_m... | bjlittle/geovista | 884d6baed97aa96cddbdc5e0803658bbffc7c1d5 | geovista.pantry.meshes are broken
## 🐛 Bug Report
<!-- Provide a clear description of the bug/issue that you're experiencing -->
```
> python -c "from geovista.pantry.meshes import dynamico; print(dynamico())"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/net/home/h05/itwl/... | diff --git a/src/geovista/pantry/data.py b/src/geovista/pantry/data.py
index 0d9529f..5092d1d 100644
--- a/src/geovista/pantry/data.py
+++ b/src/geovista/pantry/data.py
@@ -73,11 +73,11 @@ class CloudPreference(_MixinStrEnum, Enum):
"""
- HIGH = "high"
LOW = "low"
MEDIUM = "medium"
- MESH = "me... |
bjmorgan__py-sc-fermi-25 | [
{
"changes": {
"added_entities": [
"py_sc_fermi/defect_system.py:DefectSystem.site_percentages"
],
"added_modules": null,
"edited_entities": [
"py_sc_fermi/defect_system.py:DefectSystem.get_sc_fermi",
"py_sc_fermi/defect_system.py:DefectSystem._get_report_string"
... | bjmorgan/py-sc-fermi | 9292dea25a4f93832179cea9ae4a4e46edc8f4ba | add a warning when defect concentrations are "beyond dilute limit"
It would be nice to warn the user if the code predicts defect concentrations beyond the dilute limit. This would be simple to implement, we would just need a definition of when the dilute limit approximation is becoming questionable. This could easily b... | diff --git a/README.md b/README.md
index 483d32c..db3d6cd 100644
--- a/README.md
+++ b/README.md
@@ -5,28 +5,12 @@
[](https://py-sc-fermi.readthedocs.io/en/latest/?badge=latest)
[![status](https://joss.theoj.org/papers/2fa8b3d8... |
bloomberg__attrs-strict-38 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"attrs_strict/_type_validation.py:_handle_tuple"
],
"edited_modules": [
"attrs_strict/_type_validation.py:_handle_tuple"
]
},
"file": "attrs_strict/_type_validation.py"
... | bloomberg/attrs-strict | 21abe902debcc2eb1a7f373dac37ea05edf21b86 | Support for Tuple is incorrect/incomplete
When declaring an attribute as a Tuple, there are 2 possible forms:
Simple form, like `Tuple[str]` or `Tuple[int, int]`, should be used for fixed size tuple declarations, which seems to be what attrs-strict currently supports. But there is also the form with an ellipsis to d... | diff --git a/attrs_strict/_type_validation.py b/attrs_strict/_type_validation.py
index fce8bc5..2dc75d2 100644
--- a/attrs_strict/_type_validation.py
+++ b/attrs_strict/_type_validation.py
@@ -105,6 +105,9 @@ def _handle_dict(attribute, container, expected_type):
def _handle_tuple(attribute, container, expected_type... |
blue-marble__gridpath-855 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"gridpath/project/availability/availability_types/binary.py:total_scheduled_availability_per_period_rule"
],
"edited_modules": [
"gridpath/project/availability/availability_types/bina... | blue-marble/gridpath | c0ec4d2d93592f9514169ab5cca5a655170e94d1 | Endogenous availability availability calculation should be weighted
In both the continuous and the binary availability types, the unavailability calculated in the availability constraints (respectively [AvlBin_Tot_Sched_Unavl_per_Prd_Constraint](https://github.com/blue-marble/gridpath/blob/c0ec4d2d93592f9514169ab5cca5a... | diff --git a/gridpath/project/availability/availability_types/binary.py b/gridpath/project/availability/availability_types/binary.py
index e53176a4..7ff8fb74 100644
--- a/gridpath/project/availability/availability_types/binary.py
+++ b/gridpath/project/availability/availability_types/binary.py
@@ -231,7 +231,7 @@ def t... |
blue-yonder__tsfresh-578 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tsfresh/feature_extraction/feature_calculators.py:longest_strike_below_mean",
"tsfresh/feature_extraction/feature_calculators.py:longest_strike_above_mean"
],
"edited_modules": [
... | blue-yonder/tsfresh | c3d35c42c799d1f36a1aca1d90ec0ab6450ce264 | Off-by-one error in longest strike features
The two features `longest_strike_below_mean` and `longest_strike_above_mean` are implemented in a "less-than" and "greater-than" fashion, which yields incorrect results.
Here is a MWE where µ = 3 and the longest strike below and above is 2 - `tsfresh` yields 3.
```
ass... | diff --git a/tsfresh/feature_extraction/feature_calculators.py b/tsfresh/feature_extraction/feature_calculators.py
index b5c8823..3df61b6 100644
--- a/tsfresh/feature_extraction/feature_calculators.py
+++ b/tsfresh/feature_extraction/feature_calculators.py
@@ -691,7 +691,7 @@ def longest_strike_below_mean(x):
"""
... |
blue-yonder__tsfresh-586 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "setup.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tsfresh/utilities/dataframe... | blue-yonder/tsfresh | 6309f82c104bf4e20648d8d2d2759b3f3162ae36 | underscore not allowed in time series kind names
there is a bug in tsfresh.feature_extraction.settings.from_columns which causes it to raise an error.
If the name of time series column ends with `_`, e.g. `temeprature_valve_`, you get such an error:
```
ValueError Traceback (most ... | diff --git a/setup.py b/setup.py
index be4e01e..9022dc0 100644
--- a/setup.py
+++ b/setup.py
@@ -25,6 +25,6 @@ setup(
long_description=long_description,
long_description_content_type="text/markdown",
setup_requires=["six", "setuptools_scm"] + sphinx,
- packages=find_packages(),
+ packages=find_pack... |
blue-yonder__tsfresh-599 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "setup.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tsfresh/utilities/dataframe... | blue-yonder/tsfresh | d81c57dc826c522484f0fd268144d189517df6cb | the install process is globally installing a "tests" module (using version 0.12)
Oh no, you encountered a problem while using *tsfesh*.
We, the maintainers, are happy to help you. When opening an issue, please provide the following information to us:
1. Your operating system
Ubuntu 18
2. The version of *tsf... | diff --git a/setup.py b/setup.py
index be4e01e..9022dc0 100644
--- a/setup.py
+++ b/setup.py
@@ -25,6 +25,6 @@ setup(
long_description=long_description,
long_description_content_type="text/markdown",
setup_requires=["six", "setuptools_scm"] + sphinx,
- packages=find_packages(),
+ packages=find_pack... |
blue-yonder__tsfresh-610 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tsfresh/convenience/relevant_extraction.py:extract_relevant_features"
],
"edited_modules": [
"tsfresh/convenience/relevant_extraction.py:extract_relevant_features"
]
},
... | blue-yonder/tsfresh | b9f14775030d0d9798fb95d5cd6df2e84bb4fbc7 | Unable to disable warnings in extract_features
I am unable to disable the warning messages. I have tried all of the following:
```
import warnings
warnings.simplefilter("ignore")
warnings.filterwarnings("ignore")
warnings.filterwarnings("ignore", category=RuntimeWarning)
numpy.warnings.filterwarnings('ignore')... | diff --git a/tsfresh/convenience/relevant_extraction.py b/tsfresh/convenience/relevant_extraction.py
index 36ed1ca..82c83da 100644
--- a/tsfresh/convenience/relevant_extraction.py
+++ b/tsfresh/convenience/relevant_extraction.py
@@ -87,7 +87,7 @@ def extract_relevant_features(timeseries_container, y, X=None,
:para... |
blue-yonder__tsfresh-66 | [
{
"changes": {
"added_entities": [
"tsfresh/feature_extraction/feature_calculators.py:percentage_of_reoccurring_datapoints_to_all_datapoints",
"tsfresh/feature_extraction/feature_calculators.py:percentage_of_reoccurring_values_to_all_values",
"tsfresh/feature_extraction/feature_cal... | blue-yonder/tsfresh | 50b3ee7ee663aacf8d6ae28bcb2bfcc00bd3d9a1 | Add feature class: Count/Percentage same value
I had an idea for a class of features.
1. percentage of data points that occur at least second time
2. sum of data points that occur at least second time
3. percentage of observed values that occur at lest second time
... | diff --git a/tsfresh/feature_extraction/feature_calculators.py b/tsfresh/feature_extraction/feature_calculators.py
index 5882882..d216254 100644
--- a/tsfresh/feature_extraction/feature_calculators.py
+++ b/tsfresh/feature_extraction/feature_calculators.py
@@ -587,6 +587,92 @@ def first_location_of_minimum(x):
ret... |
blue-yonder__tsfresh-758 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tsfresh/utilities/dataframe_functions.py:make_forecasting_frame"
],
"edited_modules": [
"tsfresh/utilities/dataframe_functions.py:make_forecasting_frame"
]
},
"file": "... | blue-yonder/tsfresh | f82f9d4aa6cf656cfcea8a186038764eefdc4718 | ValueError: The following ids are in the time series container but are missing in y:
Hello, I'm using tsfresh to extract features from univariate energy time series. On the newer versions >0.15 the same code that was working fine some months ago outputs the error above and a huge list of ids (input data is a year of 15... | diff --git a/CHANGES.rst b/CHANGES.rst
index 974d248..15a7631 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -9,6 +9,7 @@ Unreleased
- Bugfixes:
- Fix typos in notebook (#757)
+ - Fix output format of `make_forecasting_frame` (#758)
Version 0.17.0
==============
diff --git a/tsfresh/utilities/dataframe_fu... |
bluesky__bluesky-darkframes-20 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bluesky_darkframes/__init__.py:DarkFramePreprocessor.__call__"
],
"edited_modules": [
"bluesky_darkframes/__init__.py:DarkFramePreprocessor"
]
},
"file": "bluesky_darkf... | bluesky/bluesky-darkframes | 881efbd47aedf9856f4f7f45d90318ea4dc5b209 | Add detector argument to dark_plan()
Pass the detector from DarkFramePreprocessor to dark_plan(). | diff --git a/.travis.yml b/.travis.yml
index f6314f9..acc748e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -13,6 +13,8 @@ env:
install:
+ # explicitly upgrade numpy to work around a problem with imagecodecs
+ - pip install --upgrade numpy
# Install this package and the packages listed in requirements.txt.
... |
bluesky__bluesky-darkframes-21 | [
{
"changes": {
"added_entities": [
"bluesky_darkframes/__init__.py:SnapshotDevice.unstage",
"bluesky_darkframes/__init__.py:SnapshotDevice._remake_docs"
],
"added_modules": null,
"edited_entities": [
"bluesky_darkframes/__init__.py:SnapshotDevice.__init__",
... | bluesky/bluesky-darkframes | 3cf9c7e8ab62474932b7541ef1c13fa66183c14b | Fix Resource document creation to make uid unique
Currently, we re-issue the same Resource document multiple times, resulting in Resource documents with colliding UIDs in the database. (Their `run_start` keys are different, though.) For awhile we entertained the idea of letting `uid` be nonunique so long as the pair `(... | diff --git a/.flake8 b/.flake8
index 5e2e49c..97bf913 100644
--- a/.flake8
+++ b/.flake8
@@ -1,2 +1,10 @@
[flake8]
-exclude = .git,__pycache__,build,dist,versioneer.py,bluesky_darkframes/_version.py,docs/source/conf.py
+exclude =
+ .git,
+ __pycache__,
+ build,
+ dist,
+ versioneer.py,
+ bluesky_dark... |
bluesky__bluesky-darkframes-24 | [
{
"changes": {
"added_entities": [
"bluesky_darkframes/__init__.py:trigger_and_read"
],
"added_modules": [
"bluesky_darkframes/__init__.py:trigger_and_read"
],
"edited_entities": [
"bluesky_darkframes/__init__.py:DarkFramePreprocessor.__call__"
],
... | bluesky/bluesky-darkframes | 53808f1f4450c3e1ec65aa4c6f8e9a91949d602a | Support multiple DarkFramePreprocessors
I believe (but have not rigorously verified) that if two `DarkFramePreprocessors` are applied, they will interfere. The outer one will see the `trigger` messages added by the inner one, and try to take a dark frame for a dark frame (if that makes sense...).
We briefly tried th... | diff --git a/bluesky_darkframes/__init__.py b/bluesky_darkframes/__init__.py
index ddb3fac..6603ab1 100644
--- a/bluesky_darkframes/__init__.py
+++ b/bluesky_darkframes/__init__.py
@@ -8,6 +8,7 @@ import event_model
from frozendict import frozendict
import bluesky.preprocessors
import bluesky.plan_stubs as bps
+from... |
blumx116__VotingIsAllYouNeed-55 | [
{
"changes": {
"added_entities": [
"VIAYN/project_types.py:ActionBet.__post_init__"
],
"added_modules": null,
"edited_entities": [
"VIAYN/project_types.py:WeightedBet.__post_init__",
"VIAYN/project_types.py:WeightedBet.to_action_bet"
],
"edited_modules... | blumx116/VotingIsAllYouNeed | aa85d8c09e3c5b161011ada76716027857e3ce29 | Agents use WeightedBet instead of ActionBet
`WeightedBet` is used everywhere except in `bet` of the agent. Also, `WeightedBet` has all the attributes that `ActionBet` has. I think having both might be redundant so if we make agents generate `WeightedBet` in `bet`, we could delete AgentBet. We also need to refactor the ... | diff --git a/VIAYN/project_types.py b/VIAYN/project_types.py
index 0a22df7..a5f77ad 100644
--- a/VIAYN/project_types.py
+++ b/VIAYN/project_types.py
@@ -88,12 +88,21 @@ class ActionBet:
Minimal version of a bet containing only the parts that are
directly under the control of the agent
"""
- bet: List[... |
blumx116__VotingIsAllYouNeed-62 | [
{
"changes": {
"added_entities": [
"VIAYN/samples/agents.py:LookupBasedVotingMechanism.__init__",
"VIAYN/samples/agents.py:LookupBasedVotingMechanism.vote",
"VIAYN/samples/agents.py:LookupBasedBetSelectionMech.__init__",
"VIAYN/samples/agents.py:LookupBasedBetSelectionMech.... | blumx116/VotingIsAllYouNeed | 4bf11f6d83d590c157665397f5e2f430ce16e247 | Make Simple Agents That Don't Ignore State
For each of vote, bet & prediction, add in the following configuration options:
- random range by state
- constant value by state
Currently supported state is IntAction | diff --git a/VIAYN/samples/agents.py b/VIAYN/samples/agents.py
index f4d13cf..072f146 100644
--- a/VIAYN/samples/agents.py
+++ b/VIAYN/samples/agents.py
@@ -5,12 +5,13 @@
# @Last Modified time: 2020-12-06 14:54:12
from abc import ABC, abstractmethod
from copy import copy
-from typing import List, Callable, Optional,... |
blumx116__VotingIsAllYouNeed-66 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"VIAYN/project_types.py:Agent.view"
],
"edited_modules": [
"VIAYN/project_types.py:Agent"
]
},
"file": "VIAYN/project_types.py"
},
{
"changes": {
"added_en... | blumx116/VotingIsAllYouNeed | e2f6aa773f87772f060b2c5bac0953aeccfdf754 | Tests: #39
#39 | diff --git a/VIAYN/project_types.py b/VIAYN/project_types.py
index a5f77ad..ef669f3 100644
--- a/VIAYN/project_types.py
+++ b/VIAYN/project_types.py
@@ -108,8 +108,6 @@ class Agent(Generic[A, S], ABC):
Minimal interface for an agent to be used with train.py
Agent's need to be able to do 2 things : predict & b... |
bluss__pyproject-local-kernel-19 | [
{
"changes": {
"added_entities": [
"src/pyproject_local_kernel/__init__.py:is_uv"
],
"added_modules": [
"src/pyproject_local_kernel/__init__.py:is_uv"
],
"edited_entities": [
"src/pyproject_local_kernel/__init__.py:ProjectKind.python_cmd",
"src/pypro... | bluss/pyproject-local-kernel | 6bdb9bcc105a68cf6a43191134c0037b1984cbae | Support uv run
The following configuration almost works right now:
```toml
[tool.pyproject-local-kernel]
python-cmd = ["uv", "run", "--with", "ipykernel", "python"]
```
(installing ipykernel if missing is a great feature.)
The following problems remain
- With no configuration change, interrupting computa... | diff --git a/README.md b/README.md
index 596469f..b7d5f1e 100644
--- a/README.md
+++ b/README.md
@@ -27,7 +27,7 @@ figure out which kind of project it is:
- Use venv at path (for other setups)
Designed to be used with JupyterLab. Can also work with Jupyter Notebook and
-papermill. Doesn't seem to be compatible with... |
bluss__pyproject-local-kernel-48 | [
{
"changes": {
"added_entities": [
"src/pyproject_local_kernel/__init__.py:ProjectDetection.resolve",
"src/pyproject_local_kernel/__init__.py:PythonEnvironment.update_environment"
],
"added_modules": [
"src/pyproject_local_kernel/__init__.py:PythonEnvironment"
],
... | bluss/pyproject-local-kernel | 107bce6a8dbd69b15a6b8d9bb160a31bda484794 | Enable $PATH from .venv for use-venv configurations | diff --git a/src/pyproject_local_kernel/__init__.py b/src/pyproject_local_kernel/__init__.py
index b14a67a..d6d4c23 100644
--- a/src/pyproject_local_kernel/__init__.py
+++ b/src/pyproject_local_kernel/__init__.py
@@ -81,7 +81,11 @@ class ProjectDetection:
config: Config = dataclasses.field(default_factory=Config)
... |
bmcfee__pumpp-41 | [
{
"changes": {
"added_entities": [
"pumpp/core.py:Pump.sampler"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"pumpp/core.py:Pump"
]
},
"file": "pumpp/core.py"
}
] | bmcfee/pumpp | 18d19fb188342683d19af1388c8c085092b3b0be | connect Pump to Sampler
instead of having to say `Sampler(..., *P.ops)`, we should be able to just pull in a Pump object. | diff --git a/pumpp/core.py b/pumpp/core.py
index 445af3c..410b612 100644
--- a/pumpp/core.py
+++ b/pumpp/core.py
@@ -16,6 +16,7 @@ import jams
from .exceptions import ParameterError
from .task import BaseTaskTransformer
from .feature import FeatureExtractor
+from .sampler import Sampler
def transform(audio_f, j... |
bmcfee__pumpp-57 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pumpp/core.py:Pump.sampler"
],
"edited_modules": [
"pumpp/core.py:Pump"
]
},
"file": "pumpp/core.py"
},
{
"changes": {
"added_entities": null,
"adde... | bmcfee/pumpp | 7486f998acdd0f82241aeb0efdd6912da758c961 | extend pump.sampler interface
Or at least expose all the args and kwargs | diff --git a/pumpp/core.py b/pumpp/core.py
index cf39549..ab389c4 100644
--- a/pumpp/core.py
+++ b/pumpp/core.py
@@ -150,7 +150,7 @@ class Pump(object):
return transform(audio_f, jam, *self.ops)
- def sampler(self, n_samples, duration):
+ def sampler(self, n_samples, duration, random_state=None):
... |
bmcfee__pumpp-59 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "pumpp/feature/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pumpp/feat... | bmcfee/pumpp | 6be75b4724c19cec1f5edb3c2c438433ca4604ac | harmonic cqt | diff --git a/pumpp/feature/__init__.py b/pumpp/feature/__init__.py
index b3a9b34..197a14a 100644
--- a/pumpp/feature/__init__.py
+++ b/pumpp/feature/__init__.py
@@ -11,6 +11,9 @@ Feature extractors
CQT
CQTMag
CQTPhaseDiff
+ HCQT
+ HCQTMag
+ HCQTPhaseDiff
STFT
STFTMag
STFTPhaseDiff... |
bmcfee__pumpp-65 | [
{
"changes": {
"added_entities": [
"pumpp/core.py:Pump.__call__"
],
"added_modules": null,
"edited_entities": [
"pumpp/core.py:transform",
"pumpp/core.py:Pump.add",
"pumpp/core.py:Pump.transform"
],
"edited_modules": [
"pumpp/core.py:tr... | bmcfee/pumpp | 797a732eb907bd816b75b10da4707517789e871d | Deprecate transform function
We may as well move entirely to the object API. | diff --git a/pumpp/core.py b/pumpp/core.py
index ab389c4..014dbe8 100644
--- a/pumpp/core.py
+++ b/pumpp/core.py
@@ -19,49 +19,6 @@ from .feature import FeatureExtractor
from .sampler import Sampler
-def transform(audio_f, jam, *ops):
- '''Apply a set of operations to a track
-
- Parameters
- ----------
-... |
bmcfee__pumpp-91 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pumpp/task/beat.py:BeatTransformer.inverse"
],
"edited_modules": [
"pumpp/task/beat.py:BeatTransformer"
]
},
"file": "pumpp/task/beat.py"
},
{
"changes": {
... | bmcfee/pumpp | 460d07619ca6d1916150f56b45f333ba500d94a3 | Automatic confidence in task inversion
#### Description
The prediction inverters / jams converters could populate the `confidence` field of the jams annotations.
They don't currently, but it would be easy to do so. | diff --git a/pumpp/task/beat.py b/pumpp/task/beat.py
index 2d4b56b..cd5a0f3 100644
--- a/pumpp/task/beat.py
+++ b/pumpp/task/beat.py
@@ -4,6 +4,7 @@
import numpy as np
+from librosa import time_to_frames
import jams
from mir_eval.util import boundaries_to_intervals, adjust_intervals
from sklearn.preprocessing i... |
bmcfee__pumpp-92 | [
{
"changes": {
"added_entities": [
"pumpp/core.py:Pump.__str__",
"pumpp/core.py:Pump._repr_html_"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"pumpp/core.py:Pump"
]
},
"file": "pumpp/core.py"
}
] | bmcfee/pumpp | 0d6ef78f21fb7bf4736b2ca383c3377f7e0f8f9d | Meaningful repr for pump objects
#### Description
It would be useful if `repr(Pump)` showed the operator map directly. | diff --git a/pumpp/core.py b/pumpp/core.py
index 0db13b0..227cb81 100644
--- a/pumpp/core.py
+++ b/pumpp/core.py
@@ -11,6 +11,7 @@ Core functionality
import librosa
import jams
+import six
from .base import Slicer
from .exceptions import ParameterError
@@ -225,3 +226,28 @@ class Pump(Slicer):
def __call_... |
bmcfee__resampy-109 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"resampy/core.py:resample",
"resampy/core.py:resample_nu"
],
"edited_modules": [
"resampy/core.py:resample",
"resampy/core.py:resample_nu"
]
},
"file": "... | bmcfee/resampy | 29d34876a61fcd74e72003ceb0775abaf6fdb961 | Bringing import time back down
The guvectorize implementation in 0.3.1 uses a full set of build targets for all supported dtypes:
https://github.com/bmcfee/resampy/blob/29d34876a61fcd74e72003ceb0775abaf6fdb961/resampy/interpn.py#L117-L142
This works to preserve dtypes of inputs, but it causes a huge compilation o... | diff --git a/.github/workflows/ci-minimal.yml b/.github/workflows/ci-minimal.yml
index 6f64ce9..7bd8b1d 100644
--- a/.github/workflows/ci-minimal.yml
+++ b/.github/workflows/ci-minimal.yml
@@ -34,7 +34,7 @@ jobs:
shell: bash -l {0}
run: |
mamba install typing_extensions!=4.2 pytest
- mamba... |
bmcfee__resampy-113 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"resampy/core.py:resample"
],
"edited_modules": [
"resampy/core.py:resample"
]
},
"file": "resampy/core.py"
}
] | bmcfee/resampy | 2ca177f53f60ce39317cb35a548c8c69c011b63c | Edge Case, rounding error in length calculation
When apply resampy.resample( data, original_sr, target_sr) if original_sr = 12499, target_sr = 15001, the returned output is of sampling rate 15000.
- What cause the failure at this edge case?
- Is there any recommended fix or by-pass solution?
To reproduce this... | diff --git a/resampy/core.py b/resampy/core.py
index ce113e5..af65de5 100644
--- a/resampy/core.py
+++ b/resampy/core.py
@@ -107,7 +107,9 @@ def resample(
# Set up the output shape
shape = list(x.shape)
- shape[axis] = int(shape[axis] * sample_ratio)
+ # Explicitly recalculate length here instead of u... |
bmcfee__resampy-69 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"resampy/core.py:resample"
],
"edited_modules": [
"resampy/core.py:resample"
]
},
"file": "resampy/core.py"
},
{
"changes": {
"added_entities": null,
... | bmcfee/resampy | e5238a7120dcf0d76813bcd3e277998ead8fc308 | Resampling does not preserve array byte ordering
The title says it all: if you give a multidimensional array `x` as input, the output may have a different (ie c-contiguous) ordering.
The culprit is this line: https://github.com/bmcfee/resampy/blob/e5238a7120dcf0d76813bcd3e277998ead8fc308/resampy/core.py#L100 which d... | diff --git a/.travis.yml b/.travis.yml
index 9e1e4d3..f486f6d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,9 +9,9 @@ notifications:
python:
- 2.7
- - 3.4
- 3.5
- 3.6
+ - 3.7
cache:
directories:
@@ -20,7 +20,7 @@ cache:
env:
global:
# Directory where tests are run from
- - CONDA_DEP... |
bmcfee__resampy-88 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"resampy/core.py:resample"
],
"edited_modules": [
"resampy/core.py:resample"
]
},
"file": "resampy/core.py"
}
] | bmcfee/resampy | 6d20c2c4d28203dadd4208c91906445bf0fba846 | resampling to the same hz
Resampling with the same `hz` should likely give the exact result back. It doesn't (likely up to some floating point value).
```python
import librosa
import resampy
x, sr_orig = librosa.load(librosa.util.example_audio_file(), sr=None, mono=False)
y_same = resampy.resample(x, sr_... | diff --git a/resampy/core.py b/resampy/core.py
index e45d08e..82e3385 100644
--- a/resampy/core.py
+++ b/resampy/core.py
@@ -27,6 +27,9 @@ def resample(x, sr_orig, sr_new, axis=-1, filter='kaiser_best', **kwargs):
sr_new : int > 0
The target sampling rate of the output signal(s)
+ If `sr_new == s... |
bobthemighty__punq-191 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"punq/__init__.py:_match_defaults",
"punq/__init__.py:_Registry.register_concrete_service",
"punq/__init__.py:_Registry.register",
"punq/__init__.py:Container._build_impl"
]... | bobthemighty/punq | f5920143c85015ac21fc776ca1dc39a3234105da | support kwonlyargs
When building the implementation, you are getting `args` but if someone has used `*,` to make the args keyword only args, then you need to get them from `kwonlyargs`.
https://github.com/bobthemighty/punq/blob/c26cf2d0ad2f8a615751a8403e966f82216e55c4/punq/__init__.py#L420 | diff --git a/punq/__init__.py b/punq/__init__.py
index debbacf..5ccaae5 100644
--- a/punq/__init__.py
+++ b/punq/__init__.py
@@ -156,20 +156,24 @@ class _Empty:
empty = _Empty()
-def _match_defaults(args, defaults):
+def _match_defaults(spec):
"""Matches args with their defaults in the result of getfullargspe... |
bodo-ai__PyDough-238 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "pydough/pydough_operators/__init__.py"
},
{
"changes": {
"added_entities": null,
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... | bodo-ai/PyDough | 72ef839c4c6f819c5fae71dff5ad90de45615206 | Add support for HOUR, MINUTE and SECOND functions in PyDough
Goal: add the following functionalities to PyDough, which should be tested e2e (see `test_pipeline.py` for examples):
- `HOUR(x)` extracts the hour component of a timestamp (like `EXTRACT(HOUR FROM x)` in SQL)
- `MINUTE(x)` extracts the hour component of a t... | diff --git a/demos/notebooks/2_pydough_operations.ipynb b/demos/notebooks/2_pydough_operations.ipynb
index 457533e..84c21eb 100644
--- a/demos/notebooks/2_pydough_operations.ipynb
+++ b/demos/notebooks/2_pydough_operations.ipynb
@@ -232,7 +232,7 @@
"\n",
"# Datetime Operations\n",
"# Note: Since this is ... |
bodo-ai__PyDough-249 | [
{
"changes": {
"added_entities": [
"pydough/unqualified/unqualified_transform.py:AddRootVisitor.current_scope",
"pydough/unqualified/unqualified_transform.py:AddRootVisitor.enter_scope",
"pydough/unqualified/unqualified_transform.py:AddRootVisitor.exit_scope",
"pydough/unqu... | bodo-ai/PyDough | 048214839b7ca1b0d22ad7e7ceffa6fbb0aae920 | Ensure PyDough code is compatible with full Python syntax including function definitions/lambdas
Goal: ensure that PyDough code can be fully interleaved with all regular Python code, such as the following, and work as expected.
```py
%%pydough
def n_customers_with_inc(low, high):
return COUNT(customers.WHERE(MONOTON... | diff --git a/pydough/unqualified/unqualified_transform.py b/pydough/unqualified/unqualified_transform.py
index 7be19de..5d21af4 100644
--- a/pydough/unqualified/unqualified_transform.py
+++ b/pydough/unqualified/unqualified_transform.py
@@ -16,7 +16,9 @@ class AddRootVisitor(ast.NodeTransformer):
"""
QDAG vis... |
bodo-ai__PyDough-275 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "pydough/pydough_operators/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
... | bodo-ai/PyDough | e2102e138286f82487899f05562912308cb42e76 | Implement LPAD/RPAD functions in PyDough
Goal: add functions that do left/right string padding. The behavior of these functions is as follows:
- `LPAD(s, c, n)` pads string `s` with the padding character `c` on its left until its length is `n`. If the length of `s` is greater than `n` already, truncates to only include... | diff --git a/documentation/functions.md b/documentation/functions.md
index 49c1af1..8f954ea 100644
--- a/documentation/functions.md
+++ b/documentation/functions.md
@@ -21,6 +21,8 @@ Below is the list of every function/operator currently supported in PyDough as a
* [CONTAINS](#contains)
* [LIKE](#like)
* [J... |
bodo-ai__PyDough-277 | [
{
"changes": {
"added_entities": [
"pydough/sqlglot/transform_bindings.py:positive_index"
],
"added_modules": [
"pydough/sqlglot/transform_bindings.py:positive_index"
],
"edited_entities": [
"pydough/sqlglot/transform_bindings.py:convert_slice"
],
... | bodo-ai/PyDough | 1636bfa0f7f361a28956cb62415cf647333ed4b6 | Add support for more slicing cases with SUBSTR
Currently, PyDough only allows string slicing in cases where the step is absent (or 1), and the start/stop are both non-negative (or absent), by translating to `SUBSTR`. However, `SUBSTR` has support for negatives, which we should also support. This means we can expand the... | diff --git a/documentation/functions.md b/documentation/functions.md
index 8f4afc7..49c1af1 100644
--- a/documentation/functions.md
+++ b/documentation/functions.md
@@ -157,12 +157,17 @@ Below are all other operators currently supported in PyDough that use other synt
### Slicing
-A string expression can have a sub... |
bodo-ai__PyDough-288 | [
{
"changes": {
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"added_modules": null,
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"edited_modules": null
},
"file": "pydough/pydough_operators/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
... | bodo-ai/PyDough | dab212df86abcf7d36a395dbe9d36c1a729cdc0c | Add SIGN function in PyDough
Goal: add a `SIGN` function to PyDough with the following functionality, which should be tested e2e (see `test_pipeline.py` for examples):
- `SIGN(X)` is equivalent to the python string expression `0 if X == 0 else (1 if X > 0 else -1)`, or the SQL expression `CASE WHEN X == 0 THEN 0 WHEN ... | diff --git a/demos/notebooks/5_what_if.ipynb b/demos/notebooks/5_what_if.ipynb
index 1581178..fd9305b 100644
--- a/demos/notebooks/5_what_if.ipynb
+++ b/demos/notebooks/5_what_if.ipynb
@@ -113,7 +113,7 @@
"\n",
"```python\n",
"revenue_def = extended_price*(1-discount)\n",
- "orders(total_line_price=SU... |
bokeh__bokeh-12843 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/bokeh/core/serialization.py:Serializer._encode_other"
],
"edited_modules": [
"src/bokeh/core/serialization.py:Serializer"
]
},
"file": "src/bokeh/core/serialization... | bokeh/bokeh | ea707dffc5dc4b09d8fd4ee917e853f3ce53e142 | [BUG] Cannot serialize pd.NA
### Software versions
Python version : 3.10.9 | packaged by conda-forge | (main, Feb 2 2023, 20:20:04) [GCC 11.3.0]
IPython version : 8.10.0
Tornado version : 6.2
Bokeh version : 3.1.0.dev3+1.g0539444b.dirty
BokehJS static path : /home/ben/Projects/bokeh/src/bo... | diff --git a/src/bokeh/core/serialization.py b/src/bokeh/core/serialization.py
index 670047097..269ff0123 100644
--- a/src/bokeh/core/serialization.py
+++ b/src/bokeh/core/serialization.py
@@ -448,13 +448,14 @@ class Serializer:
if np.issubdtype(type(obj), np.bool_):
return self._encode_bool(bool(... |
bokeh__bokeh-1641 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bokeh/resources.py:Resources.js_wrapper"
],
"edited_modules": [
"bokeh/resources.py:Resources"
]
},
"file": "bokeh/resources.py"
}
] | bokeh/bokeh | f531eea62a0c5713575a72fc0e309b8fd9d3aaa9 | $ can get overridden in the Notebook
It is (evidently) possible for other libraries to override `$`, and then our use of `$(function() ...)` as `js_wrapper` here:
https://github.com/bokeh/bokeh/blob/master/bokeh/resources.py#L248
is fragile, and can cause problems, specifically plots not reloading. This was repo... | diff --git a/bokeh/resources.py b/bokeh/resources.py
index b78021b7a..3fdf39ebf 100644
--- a/bokeh/resources.py
+++ b/bokeh/resources.py
@@ -245,7 +245,7 @@ class Resources(object):
def pad(text, n=4):
return "\n".join([ " "*n + line for line in text.split("\n") ])
- wrapper = lambda code... |
bokeh__bokeh-1760 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bokeh/properties.py:DashPattern.__init__"
],
"edited_modules": [
"bokeh/properties.py:DashPattern"
]
},
"file": "bokeh/properties.py"
}
] | bokeh/bokeh | f161e86976a3ebcc15844339c757ff2e7fb0d9b7 | bokeh.plotting.patches line_dash argument only takes a list
The `bokeh.plotting.patches` renderer requires the argument to `line_dash` to be a list, it should probably take list and tuple | diff --git a/bokeh/properties.py b/bokeh/properties.py
index a7304e85d..d234beeb3 100644
--- a/bokeh/properties.py
+++ b/bokeh/properties.py
@@ -1091,7 +1091,7 @@ class DashPattern(Either):
}
def __init__(self, default=[], help=None):
- types = Enum(enums.DashPattern), Regex(r"^(\d+(\s+\d+)*)?$"), Li... |
bokeh__bokeh-6229 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "bokeh/core/enums.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules... | bokeh/bokeh | ca485c9a048fb353d7b1662f8a844f9ad266ee15 | Headless static (svg, png) image generation
Enable generation of PNG images directly on the server, similar to the Vega.js headless mode (https://github.com/trifacta/vega/wiki/Headless-Mode).
| diff --git a/bokeh/core/enums.py b/bokeh/core/enums.py
index 107cf475c..2087556b1 100644
--- a/bokeh/core/enums.py
+++ b/bokeh/core/enums.py
@@ -229,6 +229,9 @@ NumeralLanguage = enumeration("be-nl", "chs", "cs", "da-dk", "de-ch", "de", "en"
"fr", "hu", "it", "ja", "nl-nl", "pl", "pt-br",... |
bokeh__bokeh-6394 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bokeh/core/property/bases.py:Property.matches"
],
"edited_modules": [
"bokeh/core/property/bases.py:Property"
]
},
"file": "bokeh/core/property/bases.py"
}
] | bokeh/bokeh | be0d7255b917dd915a6b6cee5e40073e5a31eba6 | Modifying datasources broken
In bokeh master and presumably any rc/dev releases cut in the last few days, modifying a CDS is broken completely. This is because https://github.com/bokeh/bokeh/pull/6374 introduced a change in the way bokeh properties check whether an old and new value has changed. The approach there guar... | diff --git a/bokeh/core/property/bases.py b/bokeh/core/property/bases.py
index c5d7c92c9..4aace587a 100644
--- a/bokeh/core/property/bases.py
+++ b/bokeh/core/property/bases.py
@@ -178,7 +178,19 @@ class Property(PropertyDescriptorFactory):
if isinstance(new, np.ndarray) or isinstance(old, np.ndarray):
... |
bokeh__bokeh-6488 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bokeh/util/serialization.py:convert_datetime_type"
],
"edited_modules": [
"bokeh/util/serialization.py:convert_datetime_type"
]
},
"file": "bokeh/util/serialization.py"... | bokeh/bokeh | 74cf9e9e173fe3dbff132bf94257310869f9614f | bokeh.util.serialization.py convert_datetime_type breaks when passed timezone aware datetime
After updating to bokeh 0.12.6 the convert_datetime_type became unable to handle datetime objecs that are timezone aware. The subtraction of DT_EPOCH which is a naive datetime from a obj which might be aware or naive fails wh... | diff --git a/bokeh/util/serialization.py b/bokeh/util/serialization.py
index 96c406a88..dd6d27e78 100644
--- a/bokeh/util/serialization.py
+++ b/bokeh/util/serialization.py
@@ -101,7 +101,8 @@ def convert_datetime_type(obj):
# Datetime (datetime is a subclass of date)
elif isinstance(obj, dt.datetime):
- ... |
boolangery__py-lua-parser-32 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"luaparser/builder.py:Builder.parse_table_constructor"
],
"edited_modules": [
"luaparser/builder.py:Builder"
]
},
"file": "luaparser/builder.py"
}
] | boolangery/py-lua-parser | 5f6747fdff1e464cacdc785e0a24e029247d2172 | Rendering Some Lua Tables False
**Example code:**
```lua
local Table = {"a", "b", "c"};
```
**I have used ast.to_lua_source for turning the ast into a lua code**
**The output i got:**
```lua
local Table = {
1 = "a",
2 = "b",
3 = "c",
}
;
```
**What it should be:**
```lua
local Table = {... | diff --git a/luaparser/builder.py b/luaparser/builder.py
index 490b369..f6e8289 100644
--- a/luaparser/builder.py
+++ b/luaparser/builder.py
@@ -1472,6 +1472,7 @@ class Builder:
for field in fields:
if field.key is None:
field.key = Number(array... |
borgbackup__borg-2166 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:Archiver.build_parser"
],
"edited_modules": [
"src/borg/archiver.py:Archiver"
]
},
"file": "src/borg/archiver.py"
},
{
"changes": {
"... | borgbackup/borg | 833d0ab76cbf5af2a253d2c245722e16bdcf9887 | borg init repo -> unencrypted repo
Only applies to master branch (borg 1.1beta).
When blake2b was introduced, we removed the default of aes256-hmac-sha256.
Then intention was that the user does an informed decision between hmac-sha256 and blake2b MACs.
But: if a user does not specify --encryption, we now fall ... | diff --git a/src/borg/archiver.py b/src/borg/archiver.py
index 5de24d26..9dbbd202 100644
--- a/src/borg/archiver.py
+++ b/src/borg/archiver.py
@@ -1850,9 +1850,8 @@ def process_epilog(epilog):
subparser.add_argument('location', metavar='REPOSITORY', nargs='?', default='',
type=l... |
borgbackup__borg-2184 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archive.py:Archive.delete"
],
"edited_modules": [
"src/borg/archive.py:Archive"
]
},
"file": "src/borg/archive.py"
},
{
"changes": {
"added_entit... | borgbackup/borg | 4862efe718797e9fff6ca0dbfa24e8af8491be09 | Traceback when attempting to delete a corrupted .checkpoint archive
After upgrading to 1.0.9, I noticed the daily backup on one of the machines failed. I'm not sure 1.0.9 is the culprit here however, it may have just let me know about the corrupted archive since it looks like it rebuilt the indexes.
When attempting ... | diff --git a/src/borg/archive.py b/src/borg/archive.py
index 07d62e16..4bebecd7 100644
--- a/src/borg/archive.py
+++ b/src/borg/archive.py
@@ -662,7 +662,7 @@ def chunk_decref(id, stats):
raise ChunksIndexError(cid)
except Repository.ObjectNotFound as e:
# object not in re... |
borgbackup__borg-2206 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/borg/helpers.py:Location"
]
},
"file": "src/borg/helpers.py"
}
] | borgbackup/borg | 4862efe718797e9fff6ca0dbfa24e8af8491be09 | Borg (cygwin) 1.0.10 don't like smb paths
I know that cygwin is not really supported, but it worked with smb paths with no problems until version 1.0.10.
I also tested the cygwin version from billyc [https://github.com/borgbackup/borg/issues/440](https://github.com/borgbackup/borg/issues/440)
Same result.
/cygdri... | diff --git a/src/borg/helpers.py b/src/borg/helpers.py
index 89b557e5..5d05b3ce 100644
--- a/src/borg/helpers.py
+++ b/src/borg/helpers.py
@@ -1004,10 +1004,17 @@ class Location:
# path must not contain :: (it ends at :: or string end), but may contain single colons.
# to avoid ambiguities with other regexe... |
borgbackup__borg-2374 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:Archiver.get_args"
],
"edited_modules": [
"src/borg/archiver.py:Archiver"
]
},
"file": "src/borg/archiver.py"
}
] | borgbackup/borg | f878678b0c1df0e4c4971e7ef668e49a889e0545 | giving env var doesn't work for forced cmd
From IRC / bket:
```
macbook:~/bin$ borg-wrapper list --debug
using builtin fallback logging configuration
35 self tests completed in 0.23 seconds
SSH command line: ['ssh', '-i', '/Users/bket/.snapshot/keys/snapshot_ssh', '-o', 'IdentitiesOnly=yes', 'snapshot@aurora.lan',... | diff --git a/src/borg/archiver.py b/src/borg/archiver.py
index 7dccd55a..e73aaf2d 100644
--- a/src/borg/archiver.py
+++ b/src/borg/archiver.py
@@ -4,6 +4,7 @@
import functools
import hashlib
import inspect
+import itertools
import json
import logging
import os
@@ -3306,6 +3307,9 @@ def get_args(self, argv, cmd):
... |
borgbackup__borg-2500 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:with_repository",
"src/borg/archiver.py:Archiver._setup_implied_logging",
"src/borg/archiver.py:Archiver.run"
],
"edited_modules": [
"src/borg/ar... | borgbackup/borg | 781a41de50849b5c96c83a0f8fff91306ee52eb7 | Decouple SecurityManager and Cache and always check with SecurityManager
Currently SecurityManager is only queried if the Cache is used, which elides checks for various commands, e.g. list, key management, extract, mount, ...
The debug commands may be excluded. | diff --git a/src/borg/archiver.py b/src/borg/archiver.py
index 9946dd47..601c9848 100644
--- a/src/borg/archiver.py
+++ b/src/borg/archiver.py
@@ -36,7 +36,7 @@
from .algorithms.crc32 import crc32
from .archive import Archive, ArchiveChecker, ArchiveRecreater, Statistics, is_special
from .archive import BackupOSErro... |
borgbackup__borg-2508 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"setup.py:build_usage.generate_level",
"setup.py:build_man.generate_level"
],
"edited_modules": [
"setup.py:build_usage",
"setup.py:build_man"
]
},
"file... | borgbackup/borg | 00e76f77fc742b3297a407f2924b24ba497693c7 | main command options?
stuff like --remote-path should be an option of main command, not subcommand, so it can be used like:
```
borg --remote-path=... create
```
Currently, it only works like this:
```
borg create --remote-path=...
```
Thus, it is a bit impractical if one wants to define a abbreviation like:
`... | diff --git a/docs/man_intro.rst b/docs/man_intro.rst
index b726e331..85ba9bd3 100644
--- a/docs/man_intro.rst
+++ b/docs/man_intro.rst
@@ -14,7 +14,7 @@ deduplicating and encrypting backup tool
SYNOPSIS
--------
-borg <command> [options] [arguments]
+borg [common options] <command> [options] [arguments]
DESCRIPT... |
borgbackup__borg-2527 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:Archiver._setup_implied_logging",
"src/borg/archiver.py:Archiver.run"
],
"edited_modules": [
"src/borg/archiver.py:Archiver"
]
},
"file": "... | borgbackup/borg | eaf90cb73dfbe2e7996ae444d5c6bffd0ea89f7a | --progress for serve/RPC doesn't work
I think this was broken with the implied logging stuff?
---
:moneybag: [there is a bounty for this](https://www.bountysource.com/issues/42549881-progress-for-serve-rpc-doesn-t-work)
| diff --git a/src/borg/archiver.py b/src/borg/archiver.py
index 0ddfe1fe..9946dd47 100644
--- a/src/borg/archiver.py
+++ b/src/borg/archiver.py
@@ -3815,15 +3815,15 @@ def _setup_implied_logging(self, args):
""" turn on INFO level logging for args that imply that they will produce output """
# map of o... |
borgbackup__borg-2555 | [
{
"changes": {
"added_entities": [
"src/borg/helpers.py:Location.host"
],
"added_modules": null,
"edited_entities": [
"src/borg/helpers.py:Location.__init__",
"src/borg/helpers.py:Location._parse",
"src/borg/helpers.py:Location.canonical_path"
],
... | borgbackup/borg | 5a667d6f6aad54ba1246fee4dbf54a67f75b80f4 | Please enable IPv6 addresses for remote repositories
Hello,
I was trying to specify a remote borg repo as something like that
ssh://user@[ipv6_address_string]:/path/to/repo
(and tried with leaving out the ssh:// in front, as well)
borg then somehow tried to read the ipv6 address as a hostname, and the hostname ... | diff --git a/src/borg/helpers.py b/src/borg/helpers.py
index a93ba710..3fc22e7c 100644
--- a/src/borg/helpers.py
+++ b/src/borg/helpers.py
@@ -769,7 +769,7 @@ def bin_to_hex(binary):
class Location:
"""Object representing a repository / archive location
"""
- proto = user = host = port = path = archive = ... |
borgbackup__borg-2566 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/helpers.py:Location.to_key_filename"
],
"edited_modules": [
"src/borg/helpers.py:Location"
]
},
"file": "src/borg/helpers.py"
}
] | borgbackup/borg | 2dcbe02e5ae2c5674b350866b145c028966e1664 | Restrict file names generated by Location.to_keyfile_name
The generated file can currently include special characters like those mentioned in #2290, which should be stripped for compatibility reasons.
From #2555 | diff --git a/src/borg/helpers.py b/src/borg/helpers.py
index 15f56437..db66b822 100644
--- a/src/borg/helpers.py
+++ b/src/borg/helpers.py
@@ -916,7 +916,12 @@ def __str__(self):
def to_key_filename(self):
name = re.sub('[^\w]', '_', self.path).strip('_')
if self.proto != 'file':
- nam... |
borgbackup__borg-2617 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/helpers.py:truncate_and_unlink"
],
"edited_modules": [
"src/borg/helpers.py:truncate_and_unlink"
]
},
"file": "src/borg/helpers.py"
},
{
"changes": {
... | borgbackup/borg | fb26b3c7286cbeb9687e3a062b868a4a413edf39 | version parsing code blows up with a dirty workdir | diff --git a/docs/changes.rst b/docs/changes.rst
index 51170348..6e3394cd 100644
--- a/docs/changes.rst
+++ b/docs/changes.rst
@@ -172,7 +172,6 @@ New features:
- add --debug-profile option (and also "borg debug convert-profile"), #2473
Fixes:
-
- hashindex: read/write indices >2 GiB on 32bit systems, better error... |
borgbackup__borg-2654 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:Archiver.do_create",
"src/borg/archiver.py:Archiver.build_parser"
],
"edited_modules": [
"src/borg/archiver.py:Archiver"
]
},
"file": "src/... | borgbackup/borg | 4b38a17ab515d57cb1d6dbf1aac0d3129fca6a13 | borg create without syncing cache
code exists, needs testing, integration, but not a priority now | diff --git a/docs/internals/frontends.rst b/docs/internals/frontends.rst
index 4000bede..c41d427e 100644
--- a/docs/internals/frontends.rst
+++ b/docs/internals/frontends.rst
@@ -504,6 +504,7 @@ Errors
Operations
- cache.begin_transaction
+ - cache.download_chunks, appears with ``borg create --no-cache-sync`... |
borgbackup__borg-2900 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:Archiver.do_diff"
],
"edited_modules": [
"src/borg/archiver.py:Archiver"
]
},
"file": "src/borg/archiver.py"
}
] | borgbackup/borg | 4f57e3a7c4ff9ae2384b6c9b913780136e7e2d75 | Comparing modified items incorrectly assumes comparable chunk ids
This came up in #2842 (see during https://github.com/borgbackup/borg/pull/2842/files#diff-0c1790c20ac3974e84f97b2ded80507bR449) but the problem was there before https://github.com/borgbackup/borg/blob/master/src/borg/archiver.py#L1028.
The current solut... | diff --git a/src/borg/archiver.py b/src/borg/archiver.py
index 0f2ebd9a..ebb4b5e1 100644
--- a/src/borg/archiver.py
+++ b/src/borg/archiver.py
@@ -1021,18 +1021,19 @@ def contents_changed(item1, item2):
def compare_content(path, item1, item2):
if contents_changed(item1, item2):
if... |
borgbackup__borg-2918 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:Archiver.do_serve",
"src/borg/archiver.py:Archiver.do_diff"
],
"edited_modules": [
"src/borg/archiver.py:Archiver"
]
},
"file": "src/borg/a... | borgbackup/borg | eee4542f3b89908aa278c55cda5a6e16968072bd | Invoking "borg serve" compares None with int in version 1.0.11
```
$LOG ERROR Remote: Local Exception.
Traceback (most recent call last):
File "/usr/lib64/python3.4/site-packages/borg/archiver.py", line 2168, in main
exit_code = archiver.run(args)
File "/usr/lib64/python3.4/site-packages/borg/archiver.py",... | diff --git a/src/borg/archiver.py b/src/borg/archiver.py
index ebb4b5e1..96a8eb25 100644
--- a/src/borg/archiver.py
+++ b/src/borg/archiver.py
@@ -231,12 +231,13 @@ def build_matcher(inclexcl_patterns, include_paths):
def do_serve(self, args):
"""Start in server mode. This command is usually not used ma... |
borgbackup__borg-2924 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/fuse.py:FuseOperations.mount"
],
"edited_modules": [
"src/borg/fuse.py:FuseOperations"
]
},
"file": "src/borg/fuse.py"
},
{
"changes": {
"added_e... | borgbackup/borg | 72c8ec258355802beccdca6f1805731349783eeb | lock.roster left behind after umount in 1.1.0 rc1
I have been testing v1.1.0 rc1 and found the following issue:
Before doing a backup I check if a backup is neccessary by mounting the repo and comparing the latest archive with the source.
Then the repo is unmounted.
At the beginning of the next backup I get a messag... | diff --git a/src/borg/fuse.py b/src/borg/fuse.py
index 7868eb37..129e3b20 100644
--- a/src/borg/fuse.py
+++ b/src/borg/fuse.py
@@ -22,6 +22,7 @@
from .helpers import daemonize, hardlinkable, signal_handler, format_file_size
from .item import Item
from .lrucache import LRUCache
+from .remote import RemoteRepository
... |
borgbackup__borg-2959 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archive.py:Archive.info",
"src/borg/archive.py:Archive.__str__",
"src/borg/archive.py:Archive.save",
"src/borg/archive.py:Archive.compare_archives_iter"
],
"... | borgbackup/borg | e9b892feb5107fc407e2913a8d1b6fa16165efd7 | --timestamp time (vs list time)
The time set with `--timestamp` is the end time, whereas `list` shows the start time, e.g.:
```
$ borg create --timestamp 2017-01-01T00:00:00 ::foo bar
$ borg list
foo Sat, 2016-12-31 23:59:59
$ borg info ::foo
[...]
Time (start): Sat, 2016-12-31... | diff --git a/docs/changes.rst b/docs/changes.rst
index 9d32ccfd..ec436b7e 100644
--- a/docs/changes.rst
+++ b/docs/changes.rst
@@ -139,12 +139,7 @@ Compatibility notes:
- dropped support and testing for Python 3.4, minimum requirement is 3.5.0.
In case your OS does not provide Python >= 3.5, consider using our bina... |
borgbackup__borg-2964 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/remote.py:RemoteRepository.call_many"
],
"edited_modules": [
"src/borg/remote.py:RemoteRepository"
]
},
"file": "src/borg/remote.py"
},
{
"changes": {
... | borgbackup/borg | 818e5c8e0199fff8dc15d07fd1d8c65242405f25 | Generic error message when trying to use non-upgraded attic repository
Hi,
while playing with borg (as attic user) i accidentally run borg commands on attic*s repository and i get ugly trackback:
```
Traceback (most recent call last):
File "/usr/lib64/python3.4/site-packages/borg/archiver.py", line 1928, in mai... | diff --git a/docs/internals/frontends.rst b/docs/internals/frontends.rst
index c41d427e..677db738 100644
--- a/docs/internals/frontends.rst
+++ b/docs/internals/frontends.rst
@@ -499,6 +499,8 @@ Errors
Insufficient free space to complete transaction (required: {}, available: {}).
Repository.InvalidReposit... |
borgbackup__borg-2998 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archive.py:Archive.save"
],
"edited_modules": [
"src/borg/archive.py:Archive"
]
},
"file": "src/borg/archive.py"
},
{
"changes": {
"added_entitie... | borgbackup/borg | 2eab60ff49a4ad8f86c7dd562d8dd38eae66d70b | timestamp microseconds parsing issue
Spurious failure seen in a unrelated 1.1-maint PR on py 3.4:
```
.tox/py34/lib/python3.4/site-packages/borg/archiver.py:1232: in _delete_archives
manifest.write()
.tox/py34/lib/python3.4/site-packages/borg/helpers.py:393: in write
prev_ts = self.last_timestamp
.tox/py3... | diff --git a/src/borg/archive.py b/src/borg/archive.py
index 0f4c2d0f..3cb0b7cf 100644
--- a/src/borg/archive.py
+++ b/src/borg/archive.py
@@ -461,8 +461,8 @@ def save(self, name=None, comment=None, timestamp=None, additional_metadata=None
'cmdline': sys.argv,
'hostname': socket.gethostname(),... |
borgbackup__borg-3002 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/repository.py:LoggedIO.cleanup",
"src/borg/repository.py:LoggedIO.get_write_fd"
],
"edited_modules": [
"src/borg/repository.py:LoggedIO"
]
},
"file": "... | borgbackup/borg | 9afec263c98c0cb6c733c5c451d26f1cb0a251fd | with-lock crashes with 1.1.0-rc2
I just upgraded from borgbackup-1.1.0-b3 to rc2, found an issue within minutes.
A simple example, borgbackup is version 1.1.0-rc2
> $ borgbackup --version
borgbackup 1.1.0rc2
> $ borgbackup with-lock mail-01.borg ls
[Files are listed here]
> Data integrity error: Segment entry d... | diff --git a/src/borg/repository.py b/src/borg/repository.py
index ca55c698..dada3c14 100644
--- a/src/borg/repository.py
+++ b/src/borg/repository.py
@@ -1176,6 +1176,8 @@ def cleanup(self, transaction_id):
count = 0
for segment, filename in self.segment_iterator(reverse=True):
if segmen... |
borgbackup__borg-3024 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archive.py:FilesystemObjectProcessors.process_file"
],
"edited_modules": [
"src/borg/archive.py:FilesystemObjectProcessors"
]
},
"file": "src/borg/archive.py"
... | borgbackup/borg | dcf5e77253d35ca625d53f356cd2b969f4f4c6fd | Files cache: use ctime instead of mtime
ctime can't be set via userspace, while mtime is easily manipulated.
For most files (e.g. not extracted from tarballs, or installed by a package manager) these two are the same, which limits the impact of the change on existing file caches.
- Works with sshfs? -> (YES) (see b... | diff --git a/docs/internals/data-structures.rst b/docs/internals/data-structures.rst
index 045b476b..7c6d46b6 100644
--- a/docs/internals/data-structures.rst
+++ b/docs/internals/data-structures.rst
@@ -738,7 +738,7 @@ b) with ``create --chunker-params 19,23,21,4095`` (default):
mem_usage = 0.31GiB
-.. note:: ... |
borgbackup__borg-3234 | [
{
"changes": {
"added_entities": [
"src/borg/archive.py:Statistics.__add__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/borg/archive.py:Statistics"
]
},
"file": "src/borg/archive.py"
},
{
"changes": {
"adde... | borgbackup/borg | 4a58310433f21857fc124eed4bafde2956bac46a | wrong original size in borg create
Hello,
[borg 1.1.1 python 3.4.5 CentOs 6]
I tried 2 times with same command but different files ( oracle dump ) and both times I had
an original size reported twice bigger than the real one.
The file is 109 GB.
I tried even with smaller files but the problem did not appear.
`... | diff --git a/src/borg/archive.py b/src/borg/archive.py
index e04731e8..a8fbba91 100644
--- a/src/borg/archive.py
+++ b/src/borg/archive.py
@@ -65,6 +65,16 @@ def update(self, size, csize, unique):
if unique:
self.usize += csize
+ def __add__(self, other):
+ if not isinstance(other, Sta... |
borgbackup__borg-3246 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:Archiver.do_prune"
],
"edited_modules": [
"src/borg/archiver.py:Archiver"
]
},
"file": "src/borg/archiver.py"
},
{
"changes": {
"adde... | borgbackup/borg | 4a58310433f21857fc124eed4bafde2956bac46a | Borg 1.1.x failing to handle exceptions for servers < 1.0.7
When `borg list server:repo` is run on version 1.0.11:
```
Remote: Borg 0.29.0: exception in RPC call:
Remote: Traceback (most recent call last):
Remote: File "/usr/home/username/borgbackup-0.29.0/borg/remote.py", line 96, in serve
Remote: TypeError: ... | diff --git a/src/borg/archiver.py b/src/borg/archiver.py
index d678bb28..b09490bf 100644
--- a/src/borg/archiver.py
+++ b/src/borg/archiver.py
@@ -49,7 +49,7 @@
from .helpers import BaseFormatter, ItemFormatter, ArchiveFormatter
from .helpers import format_timedelta, format_file_size, parse_file_size, format_archive
... |
borgbackup__borg-4299 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:Archiver.build_parser"
],
"edited_modules": [
"src/borg/archiver.py:Archiver"
]
},
"file": "src/borg/archiver.py"
},
{
"changes": {
"... | borgbackup/borg | 1471fc0b0368a7ea3a973b0480f0ffb7451ab107 | Add --rsh option for setting BORG_RSH from the command line | diff --git a/docs/man/borg.1 b/docs/man/borg.1
index 5e89a2eb..24dae7d1 100644
--- a/docs/man/borg.1
+++ b/docs/man/borg.1
@@ -434,6 +434,7 @@ When set, use the given filename as \fI\%INI\fP\-style logging configuration.
.B BORG_RSH
When set, use this command instead of \fBssh\fP\&. This can be used to specify ssh op... |
borgbackup__borg-4324 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archive.py:ArchiveChecker.rebuild_refcounts"
],
"edited_modules": [
"src/borg/archive.py:ArchiveChecker"
]
},
"file": "src/borg/archive.py"
},
{
"chang... | borgbackup/borg | 585dd6b59b88fbf5d11fe91a8b1fa81975e5bf17 | do back/forward ports (15)
https://github.com/borgbackup/borg/issues?utf8=%E2%9C%93&q=label%3Abackport%2F1.0-maint
https://github.com/borgbackup/borg/issues?utf8=%E2%9C%93&q=label%3Abackport%2F1.1-maint
https://github.com/borgbackup/borg/issues?utf8=%E2%9C%93&q=label%3Aforwardport%2Fmaster
do 3 simple/small or 1 b... | diff --git a/docs/faq.rst b/docs/faq.rst
index 55b6fd40..9638dc3f 100644
--- a/docs/faq.rst
+++ b/docs/faq.rst
@@ -289,6 +289,15 @@ the :ref:`borg_recreate` command to rewrite all archives with a
different ``--exclude`` pattern. See the examples in the
:ref:`borg_recreate` manpage for more information.
+Can I safel... |
borgbackup__borg-4378 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "docs/conf.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:Ar... | borgbackup/borg | 091bd2bd79d6f3ac66ac6f3ed48ed96b2976570a | borg key export confusing error msg
from IRC:
```
borg key export REPO PATH
```
if the second argument is a directory it will throw an error.
I understand it needs a file, but the error it throws may be confusing to other users. :)
| diff --git a/LICENSE b/LICENSE
index 698326d4..051e44c6 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,4 +1,4 @@
-Copyright (C) 2015-2019 The Borg Collective (see AUTHORS file)
+Copyright (C) 2015-2018 The Borg Collective (see AUTHORS file)
Copyright (C) 2010-2014 Jonas Borgström <jonas@borgstrom.se>
All rights reserved.
... |
borgbackup__borg-4416 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:Archiver._process"
],
"edited_modules": [
"src/borg/archiver.py:Archiver"
]
},
"file": "src/borg/archiver.py"
},
{
"changes": {
"adde... | borgbackup/borg | a2c84215afdd8e79c1dbd7657b6b8f3ba627af01 | freebsd --read-special test failure
the read-special test fails when reading the fifo on freebsd (master branch):
```
freebsd64: __________________ ArchiverTestCase.test_create_read_special ___________________
freebsd64: [gw0] freebsd10 -- Python 3.6.6 /vagrant/borg/borg/.tox/py36/bin/python
freebsd64... | diff --git a/docs/installation.rst b/docs/installation.rst
index 857e7d08..dbab127b 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -41,7 +41,6 @@ package which can be installed with the package manager.
============ ============================================= =======
Distribution Source ... |
borgbackup__borg-4751 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archive.py:ChunksProcessor.maybe_checkpoint",
"src/borg/archive.py:ChunksProcessor.process_file_chunks"
],
"edited_modules": [
"src/borg/archive.py:ChunksProcessor"
... | borgbackup/borg | aa7df50a2d4c453523dc0d5fdf4f2e664f1f9059 | Consider making `--no-atime` the default
The [docs already mention](https://borgbackup.readthedocs.io/en/stable/usage/notes.html#noatime-noctime) the problem that storing `atime` can create:
> it might also affect metadata stream deduplication: if only this timestamp changes between backups and is stored into the me... | diff --git a/docs/changes.rst b/docs/changes.rst
index dc18f892..f84a2c70 100644
--- a/docs/changes.rst
+++ b/docs/changes.rst
@@ -192,6 +192,8 @@ Compatibility notes:
which does not need an external Python interpreter.
Maybe this requirement will be raised to Python 3.6 later.
- freeing repository space only ha... |
borgbackup__borg-5160 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/borg/archiver.py:Archiver.do_config",
"src/borg/archiver.py:Archiver.build_parser"
],
"edited_modules": [
"src/borg/archiver.py:Archiver"
]
},
"file": "src/... | borgbackup/borg | 0e76dff33ef6ddde409215cdaa83f7b2f6d04556 | Borg config --list does not show last_segment_checked
## Have you checked borgbackup docs, FAQ, and open Github issues?
Yes
## Is this a BUG / ISSUE report or a QUESTION?
BUG
## System information. For client/server mode post info for both machines.
1.2.0a8 / also master
#### Full borg commandline tha... | diff --git a/src/borg/archiver.py b/src/borg/archiver.py
index 0c3e2639..0d80a960 100644
--- a/src/borg/archiver.py
+++ b/src/borg/archiver.py
@@ -1659,7 +1659,7 @@ def do_config(self, args, repository):
def repo_validate(section, name, value=None, check_value=True):
if section not in ['repository... |
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