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 |
|---|---|---|---|---|---|
CheetahTemplate3__cheetah3-2 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"Cheetah/Compiler.py:ModuleCompiler.setBaseClass"
],
"edited_modules": [
"Cheetah/Compiler.py:ModuleCompiler"
]
},
"file": "Cheetah/Compiler.py"
}
] | CheetahTemplate3/cheetah3 | 01eaf9e0d4e319d465443d50ad850b849d53b760 | Failing to catch an Exception
Hello,
The following `except` line is expected to be reached as the file `expect_exception_catch` doesn't exist. Instead, an `indentation error` is raised which was not happening at some point, but even then the ImportError was not catching either. I think this whole area has been bro... | diff --git a/Cheetah/Compiler.py b/Cheetah/Compiler.py
index f1b392d..5629272 100644
--- a/Cheetah/Compiler.py
+++ b/Cheetah/Compiler.py
@@ -1744,11 +1744,12 @@ class ModuleCompiler(SettingsManager, GenUtils):
# - We also assume that the final . separates the classname from the
# module na... |
Chilipp__autodocsumm-101 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"autodocsumm/__init__.py:AutoSummClassDocumenter.add_content"
],
"edited_modules": [
"autodocsumm/__init__.py:AutoSummClassDocumenter"
]
},
"file": "autodocsumm/__init__... | Chilipp/autodocsumm | 354e67b443fe212401b1fc0f9e2f0d669c5852c4 | Alias Expands Nested Class Documentation
Assigning a type to a class attribute is documented as an alias, but its nested class members are being expanded.
```py
class NestedClass:
"""Parent class"""
class Foo:
"""Nested class"""
def foo(self):
"""Nested method"""
... | diff --git a/autodocsumm/__init__.py b/autodocsumm/__init__.py
index 5808308..9727ec1 100755
--- a/autodocsumm/__init__.py
+++ b/autodocsumm/__init__.py
@@ -414,7 +414,11 @@ class AutoSummClassDocumenter(ClassDocumenter, AutosummaryDocumenter):
def add_content(self, *args, **kwargs):
super().add_content(*... |
Clarifai__clarifai-python-228 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"clarifai/utils/logging.py:_configure_logger",
"clarifai/utils/logging.py:get_logger"
],
"edited_modules": [
"clarifai/utils/logging.py:_configure_logger",
"clarifai/u... | Clarifai/clarifai-python | 445922866de2e88c75dbbae450568a311e7beaca | Handler added to root logger
This library adds a `RichHandler` to the root logger through `logging.basicConfig` every time `get_logger` is called (which seems to be every time any common class/object is initialized):
https://github.com/Clarifai/clarifai-python/blob/dbdcb493bdb9255244276086bd193a305e2cbcc0/clarifai/uti... | diff --git a/clarifai/utils/logging.py b/clarifai/utils/logging.py
index 9fbc6e9..44373af 100644
--- a/clarifai/utils/logging.py
+++ b/clarifai/utils/logging.py
@@ -1,6 +1,6 @@
import logging
from collections import defaultdict
-from typing import Dict, List, Optional
+from typing import Dict, List, Optional, Union
... |
CleanCut__green-254 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"green/result.py:ProtoTest.getDescription"
],
"edited_modules": [
"green/result.py:ProtoTest"
]
},
"file": "green/result.py"
}
] | CleanCut/green | 55625649869d44f8c9577f5f10626b1cbdcc48ad | Combine methode name and doc string in output
With `-vvv` the output gives the first line of the doc-string of each `test_*()` method like this
```
Green 3.3.0, Coverage 5.5, Python 3.9.2
buhtzology.tests.test_khq
TestKHK
. KHQ Question 1
```
When doing `-vv` the output is this.
```
buhtzology.test... | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f7b7ab0..78c6b30 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -2,9 +2,9 @@ name: CI
on:
push:
- branches: [master]
+ branches: [main]
pull_request:
- branches: [master]
+ branches: [main]
jobs:
t... |
CleanCut__green-40 | [
{
"changes": {
"added_entities": [
"green/loader.py:isNoseDisabledCase"
],
"added_modules": [
"green/loader.py:isNoseDisabledCase"
],
"edited_entities": [
"green/loader.py:loadFromTestCase"
],
"edited_modules": [
"green/loader.py:loadFrom... | CleanCut/green | 9450d48e8099b15e87ddbd12243fb61db29fe4ba | Make green work with nose_parameterized
Green doesn't work with `nose_parameterized` since it executes tests that `nose_parameterized` [marks](https://github.com/wolever/nose-parameterized/blob/master/nose_parameterized/parameterized.py#L232) as disabled using the nose-specific [`__test__`](https://github.com/nose-devs... | diff --git a/green/loader.py b/green/loader.py
index f93d26c..50e5e91 100644
--- a/green/loader.py
+++ b/green/loader.py
@@ -121,11 +121,21 @@ def findDottedModuleAndParentDir(file_path):
return (dotted_module, parent_dir)
+def isNoseDisabledCase(test_case_class, attrname):
+ test_func = getattr(test_case_c... |
ClimateImpactLab__impactlab-tools-450 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"impactlab_tools/utils/configdict.py:gather_configtree",
"impactlab_tools/utils/configdict.py:ConfigDict.accessed_all_keys"
],
"edited_modules": [
"impactlab_tools/utils/confi... | ClimateImpactLab/impactlab-tools | a56fa03cfe65515c324bfebda79e7906e20ac87d | `gather_configtree()` needs option to assign parents to nested lists of dicts
`gather_configtree()` will skip over any nested lists of dictionaries. @jrising suggested allowing `gather_configtree()` to convert these nested dicts to `ConfDicts` and assigning them parents, as we would do for any other nested dictionaries... | diff --git a/impactlab_tools/utils/configdict.py b/impactlab_tools/utils/configdict.py
index cb9e5ec..135dfde 100644
--- a/impactlab_tools/utils/configdict.py
+++ b/impactlab_tools/utils/configdict.py
@@ -10,15 +10,19 @@ except ImportError:
import collections as collections_abc
-def gather_configtree(d):
+def ... |
Clinical-Genomics__cgbeacon2-16 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cgbeacon2/cli/add.py:dataset"
],
"edited_modules": [
"cgbeacon2/cli/add.py:dataset"
]
},
"file": "cgbeacon2/cli/add.py"
},
{
"changes": {
"added_entities"... | Clinical-Genomics/cgbeacon2 | 4400432409161176c5da9ca974db1612ef916bcb | Code to create/edit a dataset | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 39f8afb..cdb3286 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,6 @@
## [x.x.x] -
### Added
-- Info endpoint (/) for API v1
+- Info endpoint (/) for API v1
- Add new datasets using the command line
+- Update existing datasets using the command line
diff --gi... |
Clinical-Genomics__patientMatcher-215 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"patientMatcher/utils/ensembl_rest_client.py:EnsemblRestApiClient.send_request"
],
"edited_modules": [
"patientMatcher/utils/ensembl_rest_client.py:EnsemblRestApiClient"
]
}... | Clinical-Genomics/patientMatcher | d4b57a0d4cd5ee8fece93db7345137d2d4eaed3c | HGNC symbol to Ensembl ID conversion might return more than 1 gene Ensembl ID
For instance SKI gene: https://grch37.rest.ensembl.org/xrefs/symbol/homo_sapiens/SKI?external_db=HGNC
At the moment only the second Ensembl ID is captured, but this might lead to less matching results
| diff --git a/CHANGELOG.md b/CHANGELOG.md
index d565b19..1def5e0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,8 +3,13 @@
### Changed
- Save Ensembl ids for demo patient data genes automatically
- Mock the Ensembl REST API converting gene symbols to Ensembl IDs in tests
+- Changed the tests for the gene conversi... |
Clinical-Genomics__patientMatcher-233 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"patientMatcher/utils/delete.py:drop_all_collections"
],
"edited_modules": [
"patientMatcher/utils/delete.py:drop_all_collections"
]
},
"file": "patientMatcher/utils/del... | Clinical-Genomics/patientMatcher | 46c5763abe349a0d919bae1b5a63754c15e31da8 | Deprecated functions
On a low prio but good to fix when I have time:
patientMatcher/utils/disease.py:12
/home/runner/work/patientMatcher/patientMatcher/patientMatcher/utils/disease.py:12: DeprecationWarning: invalid escape sequence \d
db_re = re.compile("([A-Z]+:\d+)")
tests/cli/test_commands.py::test_cli... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 39b84d9..87f5ada 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,6 @@
## [] -
+### Fixed
+- Fix some deprecated code causing warnings during automatic tests
### Changed
- Improve views code by reusing a controllers function when request auth fails
### Added
dif... |
Clinical-Genomics__patientMatcher-41 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "patientMatcher/cli/add.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"patientMat... | Clinical-Genomics/patientMatcher | 8b6d68621708af3dd6fc56ba83ddf5313a259714 | delete patient should delete its matches as well
Should work from the cli and from DELETE requests | diff --git a/README.md b/README.md
index de4b514..3529f9d 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
[](https://travis-ci.com/northwestwitch/patientMatcher) [![Coverage Status](https://coveralls.io/repos/github/Clinical-G... |
Clinical-Genomics__patientMatcher-50 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"patientMatcher/match/handler.py:external_matcher"
],
"edited_modules": [
"patientMatcher/match/handler.py:external_matcher"
]
},
"file": "patientMatcher/match/handler.p... | Clinical-Genomics/patientMatcher | 107cfd03fb26553b2a68505a930ebcfbbc2a524b | Introduce the possibility to choose the external node to send a request to
Maybe it's interesting for final users. I am aware of at least another MME service which allows users to do that (RD Connect) | diff --git a/README.md b/README.md
index 4fb74a3..bb2fa19 100644
--- a/README.md
+++ b/README.md
@@ -197,7 +197,7 @@ curl -X GET \
-H 'X-Auth-Token: custom_token' \
localhost:9020/nodes
```
-The response will return a list like this : [ { 'id' : node_1_id, 'description' : node1_description}, .. ] or an empty lis... |
Clinical-Genomics__patientMatcher-55 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"patientMatcher/match/handler.py:patient_matches",
"patientMatcher/match/handler.py:internal_matcher",
"patientMatcher/match/handler.py:external_matcher"
],
"edited_modules": ... | Clinical-Genomics/patientMatcher | 80d18b817ac611e2faf37e627fca5d39150a8ff6 | Group match results by searched node
Not really a bug here, but it would add more useful info to the match objects.
Match objects saved to database now look like this:
```bash
matches = [
{ # External match where test_patient is the query and with results
'_id' : 'match_1',
'h... | diff --git a/patientMatcher/match/handler.py b/patientMatcher/match/handler.py
index ca7f629..f87a12a 100644
--- a/patientMatcher/match/handler.py
+++ b/patientMatcher/match/handler.py
@@ -28,7 +28,7 @@ def patient_matches(database, patient_id, type=None, with_results=True):
query = {
'$or' : [
... |
Clinical-Genomics__patientMatcher-72 | [
{
"changes": {
"added_entities": [
"patientMatcher/server/controllers.py:heartbeat"
],
"added_modules": [
"patientMatcher/server/controllers.py:heartbeat"
],
"edited_entities": null,
"edited_modules": null
},
"file": "patientMatcher/server/controllers.... | Clinical-Genomics/patientMatcher | af9e9601516fb1f638ec6dc15a521a9bb5870e4e | patientMatcher MUST have a heartbeat
I completely missed this: https://github.com/ga4gh/mme-apis/blob/master/heartbeat-api.md
Good thing it's easy to implement! | diff --git a/patientMatcher/server/controllers.py b/patientMatcher/server/controllers.py
index ac9ff04..30bb61a 100644
--- a/patientMatcher/server/controllers.py
+++ b/patientMatcher/server/controllers.py
@@ -9,9 +9,24 @@ from patientMatcher.utils.patient import patients
from patientMatcher.parse.patient import json_p... |
Clinical-Genomics__patientMatcher-75 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"patientMatcher/server/views.py:add",
"patientMatcher/server/views.py:match_external",
"patientMatcher/server/views.py:match_internal"
],
"edited_modules": [
"patientM... | Clinical-Genomics/patientMatcher | ad0eaf3559992eb4d61289c06443ef787a53c617 | Add option to notify minimal or complete matching info by emails
For security reasons it's good to introduce an option to notify complete or partial info for MME matches by email.
I've changed the email body to follow the MME directives, see #65. Still it's good to have the option of NOT showing variants and phenoty... | diff --git a/README.md b/README.md
index b2eed1c..bf20b6d 100644
--- a/README.md
+++ b/README.md
@@ -315,6 +315,8 @@ in the configuration file (config.py). If you want to test your email configurat
pmatcher test email -recipient your_email@email.com
```
+It is possible to choose to send complete or partial info for... |
Clinical-Genomics__scout-5254 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"scout/adapter/mongo/institute.py:InstituteHandler.update_institute"
],
"edited_modules": [
"scout/adapter/mongo/institute.py:InstituteHandler"
]
},
"file": "scout/adapt... | Clinical-Genomics/scout | 356fb0613b96e0897a70980b61d69634d001d8f7 | Enable filtering on matched normal
**⚠️ Important:** Please avoid sharing any sensitive or personal information, including text or images, in this issue.
**Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate.... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4247b63a6..174bfedb2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ About changelog [here](https://keepachangelog.com/en/1.0.0/)
- Enhanced SNV and SV filtering for cancer and rare disease cases, now supporting size thresholds (≥ or < a specified base pair... |
Clinical-Genomics__scout-593 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"scout/adapter/mongo/query.py:QueryHandler.build_query"
],
"edited_modules": [
"scout/adapter/mongo/query.py:QueryHandler"
]
},
"file": "scout/adapter/mongo/query.py"
... | Clinical-Genomics/scout | 7b2419a20dd5dbae88f21b9a2afe2c2d4ad5277f | CADD score filter monday-issue!
Thank you kindly for the quick inclusion of CADD score filtering! Will make a couple of our doctors very happy.
One major caveat though: the current version seems to filter out unknown CADD scores as well (similar to the unknown frequency bug)! Not intended usage..
| diff --git a/scout/adapter/mongo/query.py b/scout/adapter/mongo/query.py
index 3a07b82d8..055963b99 100644
--- a/scout/adapter/mongo/query.py
+++ b/scout/adapter/mongo/query.py
@@ -114,15 +114,16 @@ class QueryHandler(object):
cadd_query = {'cadd_score': {'$gt': float(cadd)}}
logger.debug("Add... |
Clinical-Genomics__scout-615 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"scout/adapter/mongo/query.py:QueryHandler.build_query"
],
"edited_modules": [
"scout/adapter/mongo/query.py:QueryHandler"
]
},
"file": "scout/adapter/mongo/query.py"
... | Clinical-Genomics/scout | 8e1c3acd430a1f57f712aac29847e71cac8308f3 | Always allow ClinVar Pathogenic, Likely Pathogenic through Clinical filter
It is counterintuitive to find known clinical pathogenic mutation filtered out as a result of a "clinical filter". Also apply to local "marked causatives" - but there we already have a sufficient mechanism? | diff --git a/scout/adapter/mongo/query.py b/scout/adapter/mongo/query.py
index 055963b99..267969642 100644
--- a/scout/adapter/mongo/query.py
+++ b/scout/adapter/mongo/query.py
@@ -13,11 +13,13 @@ class QueryHandler(object):
'thousand_genomes_frequency': float,
'exac_frequency': float,... |
Clinical-Genomics__scout-656 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"scout/build/variant.py:build_variant"
],
"edited_modules": [
"scout/build/variant.py:build_variant"
]
},
"file": "scout/build/variant.py"
},
{
"changes": {
... | Clinical-Genomics/scout | e41d7b94106581fa28da793e2ab19c466e2f2f5a | CSV - length -1 for a deletion of 80 genes
https://scout.scilifelab.se/cust003/17159/sv/variants?variant_type=clinical&gene_panels=EP&hgnc_symbols=&size=&chrom=&thousand_genomes_frequency=
please have a look. Something doesn't fit here.
A deletion of 1 bp can not contain 80 genes.
thanks,
Michela | diff --git a/scout/build/variant.py b/scout/build/variant.py
index 3cf04f188..391398ca7 100644
--- a/scout/build/variant.py
+++ b/scout/build/variant.py
@@ -258,10 +258,20 @@ def build_variant(variant, institute_id, gene_to_panels = None,
# Add the callers
call_info = variant.get('callers', {})
+ if call... |
Clinical-Genomics__scout-676 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"scout/adapter/mongo/query.py:QueryHandler.build_query"
],
"edited_modules": [
"scout/adapter/mongo/query.py:QueryHandler"
]
},
"file": "scout/adapter/mongo/query.py"
... | Clinical-Genomics/scout | 96e4730530858967fd3b1542c79cc5a7f77ece12 | SV frequency filter
- [x] add filter boxes for filter frequencies of interest (e.g. ClinGen NGI, array, SweGen)
- [x] clinical filter settings update for structural variants
- [x] clickable coordinates for start end of structural variant to enable view the edges of large variants
| diff --git a/scout/adapter/mongo/query.py b/scout/adapter/mongo/query.py
index 3ec4fe991..914733acc 100644
--- a/scout/adapter/mongo/query.py
+++ b/scout/adapter/mongo/query.py
@@ -12,6 +12,7 @@ class QueryHandler(object):
'genetic_models': list,
'thousand_genomes_frequency': float,
... |
Clinical-Genomics__trailblazer-449 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"trailblazer/server/api.py:add_comment"
],
"edited_modules": [
"trailblazer/server/api.py:add_comment"
]
},
"file": "trailblazer/server/api.py"
},
{
"changes": {... | Clinical-Genomics/trailblazer | b630d1caa89c218b6453538695fc9dc61485ce6d | Trailblazer cancel overwrites existing comments
When running `trailblazer cancel ANALYSIS_ID` - It overwrites any comment and writes `Analysis cancelled manually by user: USER!`
**Solution:**
- Instead of overwriting a comment, append to a comment to keep any previous comments added to that field. | diff --git a/trailblazer/server/api.py b/trailblazer/server/api.py
index bbfbcb4..636a3bb 100644
--- a/trailblazer/server/api.py
+++ b/trailblazer/server/api.py
@@ -255,7 +255,7 @@ def add_comment():
try:
case_id: str = put_request.get("case_id")
comment: str = put_request.get("comment")
- ... |
CodeForPhilly__chime-418 | [
{
"changes": {
"added_entities": [
"src/penn_chime/models.py:SimSirModel.gen_policy"
],
"added_modules": null,
"edited_entities": [
"src/penn_chime/models.py:SimSirModel.__init__",
"src/penn_chime/models.py:SimSirModel.run_projection",
"src/penn_chime/mode... | CodeForPhilly/chime | e6ff8aaa0be2be7c27ec9b98611147650d414270 | ["model"] social isolation started earlier than model assumes
<!--
Please note: Any changes to the model have a huge impact on rapidly evolving hospital system & public health decisions. The current model has been in use for a while now, and it has been validated against other similar models, so any changes to the mod... | diff --git a/src/penn_chime/models.py b/src/penn_chime/models.py
index da7311f..6582b1c 100644
--- a/src/penn_chime/models.py
+++ b/src/penn_chime/models.py
@@ -9,7 +9,7 @@ from __future__ import annotations
from datetime import date, datetime, timedelta
from logging import INFO, basicConfig, getLogger
from sys impo... |
CodeForPhilly__chime-559 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/penn_chime/model/parameters.py:Parameters.parser",
"src/penn_chime/model/parameters.py:Parameters.__init__"
],
"edited_modules": [
"src/penn_chime/model/parameters.py:Par... | CodeForPhilly/chime | 45aeb494a7bc3dd4dda6517a0cde75c2b6251ca8 | [dash] Add log scale checkbox in sidebar
Put it at the bottom of the sidebar. When checked switch the y-axis scale to log scale. Equivalent to [`altair.ScaleType`](https://altair-viz.github.io/user_guide/generated/core/altair.ScaleType.html#altair.ScaleType)`== 'log'` | diff --git a/src/penn_chime/model/parameters.py b/src/penn_chime/model/parameters.py
index 72f39e1..b15d559 100644
--- a/src/penn_chime/model/parameters.py
+++ b/src/penn_chime/model/parameters.py
@@ -137,6 +137,7 @@ VALIDATORS = {
"ventilated": ValDisposition,
"hospitalized": ValDisposition,
"icu": ValD... |
CodeWithEmad__apyrat-5 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"apyrat/cli.py:main",
"apyrat/cli.py:get_quality"
],
"edited_modules": [
"apyrat/cli.py:main",
"apyrat/cli.py:get_quality"
]
},
"file": "apyrat/cli.py"
... | CodeWithEmad/apyrat | 50409df64ee87706832adbe459f283a60d7b6638 | prompt when confirm flag is and quality is not provided
if quality is not provided prompt is always used, which is not desirable when batch downloading and only best quality is desired:
https://github.com/CodeWithEmad/apyrat/blob/50409df64ee87706832adbe459f283a60d7b6638/apyrat/cli.py#L82-L89
something like this wou... | diff --git a/apyrat/cli.py b/apyrat/cli.py
index 34bb93f..d891588 100644
--- a/apyrat/cli.py
+++ b/apyrat/cli.py
@@ -1,7 +1,8 @@
"""Console script for apyrat."""
+
import click
-from apyrat.apyrat import Downloader, URLType
+from apyrat.apyrat import Downloader, URLType, VideoQuality
from apyrat.utils import get_a... |
CoffeaTeam__coffea-1017 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/coffea/dataset_tools/manipulations.py:_default_filter"
],
"edited_modules": [
"src/coffea/dataset_tools/manipulations.py:_default_filter"
]
},
"file": "src/coffea/d... | CoffeaTeam/coffea | 49d71e0634f33dc4235382ef3e1224955f4556cf | Bug in NanoEventsFactory.from_root() when reading in multiple files with different trigger paths
**Describe the bug**
When including multiple files (from the NanoAODv9 dataset shown below) in the NanoEventsFactory.from_root() uproot file spec, the dask.compute() function results in a KeyInFileError which I believe res... | diff --git a/src/coffea/dataset_tools/manipulations.py b/src/coffea/dataset_tools/manipulations.py
index d71d06e3..e515ce2b 100644
--- a/src/coffea/dataset_tools/manipulations.py
+++ b/src/coffea/dataset_tools/manipulations.py
@@ -101,10 +101,8 @@ def slice_files(fileset: FilesetSpec, theslice: Any = slice(None)) -> Fi... |
CoffeaTeam__coffea-447 | [
{
"changes": {
"added_entities": [
"coffea/nanoevents/methods/vector.py:TwoVector.negative",
"coffea/nanoevents/methods/vector.py:TwoVector.subtract",
"coffea/nanoevents/methods/vector.py:TwoVector.divide",
"coffea/nanoevents/methods/vector.py:TwoVector.dot",
"coffe... | CoffeaTeam/coffea | 5465597e0e46799d4ac4a37d1c31182b2ec4cbb4 | Extending Nanoevents vector
(Continued from the mailing list)
The classes in `coffea.nanoevents.methods.vector` are still missing some common functions. What I have in mind here
- Subtractions, just like there is addition for two vector objects
- Division with numbers, just like there is multiplication
- Dot prod... | diff --git a/coffea/nanoevents/methods/vector.py b/coffea/nanoevents/methods/vector.py
index a34c527d..ee0c11ef 100644
--- a/coffea/nanoevents/methods/vector.py
+++ b/coffea/nanoevents/methods/vector.py
@@ -108,6 +108,14 @@ class TwoVector:
"""
return self.r
+ @awkward.mixin_class_method(numpy.ne... |
CoffeaTeam__coffea-572 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"coffea/lumi_tools/lumi_tools.py:LumiData.__init__",
"coffea/lumi_tools/lumi_tools.py:LumiData.build_lumi_table",
"coffea/lumi_tools/lumi_tools.py:LumiData._build_lumi_table_kernel",
... | CoffeaTeam/coffea | 2197e71dacf329910373369dfbbb4895ef0977e1 | not able to load LumiMask
**Describe the bug**
Cannot load LumiMask from a textfile.
**To Reproduce**
Steps to reproduce the behavior:
```
from coffea.lumi_tools import LumiMask
# load lumimask from e.g. this file https://github.com/cmantill/boostedhiggs/blob/main/boostedhiggs/data/Cert_294927-306462_13TeV_UL20... | diff --git a/coffea/lumi_tools/lumi_tools.py b/coffea/lumi_tools/lumi_tools.py
index 932eab9f..e4d92fe2 100644
--- a/coffea/lumi_tools/lumi_tools.py
+++ b/coffea/lumi_tools/lumi_tools.py
@@ -34,28 +34,6 @@ class LumiData(object):
], # not sure what lumi:0 means, appears to be always zero (DAQ off befo... |
Colin-b__httpx_auth-105 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"httpx_auth/_oauth2/client_credentials.py:OAuth2ClientCredentials.__init__"
],
"edited_modules": [
"httpx_auth/_oauth2/client_credentials.py:OAuth2ClientCredentials"
]
},
... | Colin-b/httpx_auth | 01f3646e8313dcf7ed29cb25dd6b6bf88e9976e1 | OAuth2ClientCredentials client id and secret are not taken into account to distinguish tokens
Hi @Colin-b thanks for this library - it helps people implementing OAuth flows which is great!
I think we might have discovered an issue that causes unintended or unexpected token reuse across requests/auth objects.
The g... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index ae6150e..b308ae1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased]
### Fixed
- Bearer tokens with nested JSON string are now properly handled. Thanks to [`Patrick... |
Colin-b__httpx_auth-16 | [
{
"changes": {
"added_entities": [
"httpx_auth/aws.py:AWS4Auth._get_canonical_request",
"httpx_auth/aws.py:AWS4Auth._get_canonical_headers",
"httpx_auth/aws.py:AWS4Auth._get_sig_string",
"httpx_auth/aws.py:AWS4Auth._amz_cano_path",
"httpx_auth/aws.py:AWS4Auth._amz_c... | Colin-b/httpx_auth | 4774b1d23946c7355fc488142cbae3bf3f9d6d34 | AWS auth fails for temporary cedentials
I tested with the latest versions and the aws auth is failing for temporary credentials ( those that require a session token). The version from the original PR I pushed still works so its not a change in AWS. I will take a look soon ( next couple of days) to see if I can figure... | diff --git a/.travis.yml b/.travis.yml
index 46dceed..6f9a825 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,10 +6,10 @@ python:
install:
- pip install .[testing]
script:
- - pytest --cov=httpx_auth --cov-fail-under=100
+ - pytest --cov=httpx_auth --cov-fail-under=100 --cov-report=term-missing
deploy:
prov... |
Colin-b__httpx_auth-93 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"httpx_auth/_oauth2/tokens.py:decode_base64"
],
"edited_modules": [
"httpx_auth/_oauth2/tokens.py:decode_base64"
]
},
"file": "httpx_auth/_oauth2/tokens.py"
}
] | Colin-b/httpx_auth | 9a5bf50e4d6f3094dfff56e9ca339b89ea9ee69a | JSONDecodeError due to Improper Handling of Nested JSON Strings in JWT Payloads
## Description
There is an issue in the `httpx-auth` library where the decoding of base64-encoded JSON within JWT tokens corrupts JSON strings that contain nested JSON. This happens because the double quotes inside the nested JSON string... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3541ca5..9c64ded 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased]
+### F... |
Colin-b__keepachangelog-4 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"keepachangelog/_changelog.py:is_release",
"keepachangelog/_changelog.py:to_dict"
],
"edited_modules": [
"keepachangelog/_changelog.py:is_release",
"keepachangelog/_ch... | Colin-b/keepachangelog | f8083cb3eb643aecec9ae6d9e0e53437baad56cf | Allow to retrieve unreleased information
As an option deactivated by default | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 205430e..2249674 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased]
+### Added
+- It is now possible to retrieve "Unreleased" information thanks to the `show_unr... |
Colin-b__keepachangelog-8 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"keepachangelog/_changelog.py:add_information"
],
"edited_modules": [
"keepachangelog/_changelog.py:add_information"
]
},
"file": "keepachangelog/_changelog.py"
},
{... | Colin-b/keepachangelog | 998fd84a568be62fb333422dbe8202200cf17bba | parse category entries
Ciao, I'd like to share a thought w/ you. Given the problem domain I think stripping the leading `- ` in category entries could be the right thing to do, you already assert an entry is an entry by placing it in relevant section after all.
That could be a future-proof evolution of the lib (eg. ... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index d694d84..6f721e2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased]
+## [0.3.0] - 2020-03-01
+### Changed
+- Information is now stored without star, space or ca... |
Colin-b__requests_auth-44 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"requests_auth/authentication.py:_pop_parameter",
"requests_auth/authentication.py:_get_query_parameter",
"requests_auth/authentication.py:request_new_grant_with_post"
],
"edi... | Colin-b/requests_auth | b0d96481708ace9912d4a69979a0305d58b4442b | Handle OAuth2 Browser query rejection properly
Same as #15 but for the browser queries | diff --git a/CHANGELOG.md b/CHANGELOG.md
index fe23f32..25a73e5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,7 +10,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed
- OAuth2ClientCredentials username parameter is now client_id
- OAuth2ClientCredentials password ... |
Collen-Roller__flydenity-3 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"flydenity/parser.py:ARParser.__init__",
"flydenity/parser.py:ARParser.load_datasets",
"flydenity/parser.py:ARParser.parse",
"flydenity/parser.py:ARParser.print_dataset_error"
... | Collen-Roller/flydenity | f19d02fea91e9988f97c8ef90ae9dbf01973a5ba | Split 'iso codes'
Current state:
{'iso codes': "['US', 'USA']"}
The string "['US', 'USA']" need further steps until we get the iso2 or iso3
Better (in my opinion):
{'iso codes': ['US', 'USA']}
or
{'iso2': 'US', 'iso3': 'USA'} | diff --git a/flydenity/parser.py b/flydenity/parser.py
index 1afc87a..5fe97b9 100644
--- a/flydenity/parser.py
+++ b/flydenity/parser.py
@@ -7,56 +7,93 @@ collen.roller@gmail.com
Main parser for Regexs that exist within the dataset
"""
-import pandas as pd
-import ast
import os
import re
-import sys
+import csv
... |
Cornices__cornice.ext.swagger-12 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cornice_swagger/converters/schema.py:convert_regex_validator",
"cornice_swagger/converters/schema.py:ValidatorConversionDispatcher.convert_all_validator"
],
"edited_modules": [
... | Cornices/cornice.ext.swagger | 1ee8267504d47acc13ba364f89f189b31c87b7ea | Reach and ensure 100% coverage | diff --git a/cornice_swagger/converters/schema.py b/cornice_swagger/converters/schema.py
index 343b357..45686cb 100644
--- a/cornice_swagger/converters/schema.py
+++ b/cornice_swagger/converters/schema.py
@@ -62,7 +62,7 @@ def convert_regex_validator(validator):
converted = {}
if hasattr(colander, '... |
CrepeGoat__FEHnt-10 | [
{
"changes": {
"added_entities": [
"fehnt/core.py:OutcomeCalculator.push_state",
"fehnt/core.py:OutcomeCalculator.pull_outcome",
"fehnt/core.py:OutcomeCalculator.__iter__"
],
"added_modules": null,
"edited_entities": [
"fehnt/core.py:OutcomeCalculator.proc... | CrepeGoat/FEHnt | 8b5692806a6ef0af0a4c90856ca42324f52d3f06 | reverse orb iteration
Currently the program starts with a known orb count and iterates through states of *remaining orbs* down to zero.
The code can be rewritten to:
- iterate over orbs *spent*; start from 0 and iterate *upwards*
- aggregate results (%-chance of x targets pulled, (for finite targets) avg. orbs spe... | diff --git a/fehnt/core.py b/fehnt/core.py
index 157f216..be7324e 100644
--- a/fehnt/core.py
+++ b/fehnt/core.py
@@ -64,7 +64,7 @@ class OutcomeCalculator:
alt_session.prob(self.event_details)
/ session.prob(self.event_details)
)
- self.states[StateStruct(event,... |
CrossGL__crosstl-104 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"crosstl/src/translator/ast.py:IfNode.__init__",
"crosstl/src/translator/ast.py:IfNode.__repr__"
],
"edited_modules": [
"crosstl/src/translator/ast.py:IfNode"
]
},
... | CrossGL/crosstl | c5bc4c57eba6f052907f2545d32c5b1af2c8bf22 | Add `Assignment AND` Token at translator frontend
Implement the ASSIGN_AND token to recognize the &= operator for performing bitwise AND assignments. | diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 32aefc7..5cfc4fd 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -1,5 +1,5 @@
* @NripeshN
-crosstl/* @samthakur587 @vaatsalya123
+crosstl/**/* @samthakur587 @vaatsalya123
-tests/* @samthakur587
+tests/**/* @samthakur587
diff --git a/crosstl/src... |
CrossGL__crosstl-166 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"crosstl/src/backend/DirectX/DirectxAst.py:shaderTypeNode.__init__",
"crosstl/src/backend/DirectX/DirectxAst.py:shaderTypeNode.__repr__",
"crosstl/src/backend/DirectX/DirectxAst.py:Functi... | CrossGL/crosstl | 86bb54fe27461b31e48427e84e31a2203c8f8926 | Add translator support for `Bitwise Shift Left` token | diff --git a/crosstl/src/backend/DirectX/DirectxAst.py b/crosstl/src/backend/DirectX/DirectxAst.py
index b5d3ac2..b314f05 100644
--- a/crosstl/src/backend/DirectX/DirectxAst.py
+++ b/crosstl/src/backend/DirectX/DirectxAst.py
@@ -23,27 +23,6 @@ class ShaderNode:
return f"ShaderNode(structs={self.structs}, funct... |
CrossGL__crosstl-201 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "crosstl/src/backend/DirectX/DirectxLexer.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | CrossGL/crosstl | 2e6ede3fc697cf110938bfd6df6074504906e2a2 | ASSIGN_XOR : ^= | diff --git a/crosstl/src/backend/DirectX/DirectxLexer.py b/crosstl/src/backend/DirectX/DirectxLexer.py
index 07dbd6d..eeb43b9 100644
--- a/crosstl/src/backend/DirectX/DirectxLexer.py
+++ b/crosstl/src/backend/DirectX/DirectxLexer.py
@@ -42,6 +42,7 @@ TOKENS = [
("MINUS_EQUALS", r"-="),
("MULTIPLY_EQUALS", r"\... |
CrossGL__crosstl-202 | [
{
"changes": {
"added_entities": [
"crosstl/src/backend/DirectX/DirectxAst.py:WhileNode.__init__",
"crosstl/src/backend/DirectX/DirectxAst.py:WhileNode.__repr__"
],
"added_modules": [
"crosstl/src/backend/DirectX/DirectxAst.py:WhileNode"
],
"edited_entities"... | CrossGL/crosstl | a4da57d8408a35c00f0146a2e1ef08989301fb56 | Add translator support for `Bitwise AND` token | diff --git a/crosstl/src/backend/DirectX/DirectxAst.py b/crosstl/src/backend/DirectX/DirectxAst.py
index b314f05..2484e0a 100644
--- a/crosstl/src/backend/DirectX/DirectxAst.py
+++ b/crosstl/src/backend/DirectX/DirectxAst.py
@@ -86,6 +86,15 @@ class ForNode(ASTNode):
return f"ForNode(init={self.init}, conditio... |
CrossGL__crosstl-205 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "crosstl/src/backend/DirectX/DirectxLexer.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | CrossGL/crosstl | 676f90134e4cdcce53bcd972199dae69093d9bd5 | SHIFT_LEFT : << | diff --git a/crosstl/src/backend/DirectX/DirectxLexer.py b/crosstl/src/backend/DirectX/DirectxLexer.py
index 41c8a78..c9756df 100644
--- a/crosstl/src/backend/DirectX/DirectxLexer.py
+++ b/crosstl/src/backend/DirectX/DirectxLexer.py
@@ -34,6 +34,7 @@ TOKENS = [
("COMMA", r","),
("COLON", r":"),
("QUESTIO... |
CrossGL__crosstl-206 | [
{
"changes": {
"added_entities": [
"crosstl/src/backend/DirectX/DirectxAst.py:DoWhileNode.__init__",
"crosstl/src/backend/DirectX/DirectxAst.py:DoWhileNode.__repr__"
],
"added_modules": [
"crosstl/src/backend/DirectX/DirectxAst.py:DoWhileNode"
],
"edited_ent... | CrossGL/crosstl | 48ff92c4f95d6d216c5ee17a3951b10bdb239ab3 | do-while loop | diff --git a/crosstl/src/backend/DirectX/DirectxAst.py b/crosstl/src/backend/DirectX/DirectxAst.py
index 2484e0a..ac88d52 100644
--- a/crosstl/src/backend/DirectX/DirectxAst.py
+++ b/crosstl/src/backend/DirectX/DirectxAst.py
@@ -95,6 +95,15 @@ class WhileNode(ASTNode):
return f"WhileNode(condition={self.condit... |
CrossGL__crosstl-207 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "crosstl/src/backend/DirectX/DirectxLexer.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | CrossGL/crosstl | e2f2c2452273935cbb394848c9bb79903ee0a545 | ASSIGN_AND : &= | diff --git a/crosstl/src/backend/DirectX/DirectxLexer.py b/crosstl/src/backend/DirectX/DirectxLexer.py
index c5a1574..d6632a3 100644
--- a/crosstl/src/backend/DirectX/DirectxLexer.py
+++ b/crosstl/src/backend/DirectX/DirectxLexer.py
@@ -45,6 +45,7 @@ TOKENS = [
("DIVIDE_EQUALS", r"/="),
("ASSIGN_XOR", r"\^=")... |
CrossGL__crosstl-208 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "crosstl/src/backend/DirectX/DirectxLexer.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | CrossGL/crosstl | cf3f439f9fc4289df5445fcde1ebfdd9acf72fca | BITWISE_XOR : ^ | diff --git a/crosstl/src/backend/DirectX/DirectxLexer.py b/crosstl/src/backend/DirectX/DirectxLexer.py
index c9756df..be17881 100644
--- a/crosstl/src/backend/DirectX/DirectxLexer.py
+++ b/crosstl/src/backend/DirectX/DirectxLexer.py
@@ -48,6 +48,7 @@ TOKENS = [
("ASSIGN_XOR", r"\^="),
("ASSIGN_OR", r"\|="),
... |
CrossGL__crosstl-213 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "crosstl/src/backend/DirectX/DirectxLexer.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | CrossGL/crosstl | c4325a413d735e2bd8a5e46ccff907c0fec13260 | SHIFT_RIGHT : >> | diff --git a/crosstl/src/backend/DirectX/DirectxLexer.py b/crosstl/src/backend/DirectX/DirectxLexer.py
index b8a23b2..a2c6084 100644
--- a/crosstl/src/backend/DirectX/DirectxLexer.py
+++ b/crosstl/src/backend/DirectX/DirectxLexer.py
@@ -35,6 +35,7 @@ TOKENS = [
("COLON", r":"),
("QUESTION", r"\?"),
("SHI... |
CrossGL__crosstl-219 | [
{
"changes": {
"added_entities": [
"crosstl/backend/DirectX/DirectxAst.py:PragmaNode.__init__",
"crosstl/backend/DirectX/DirectxAst.py:PragmaNode.__repr__",
"crosstl/backend/DirectX/DirectxAst.py:PragmaNode.__str__"
],
"added_modules": [
"crosstl/backend/DirectX... | CrossGL/crosstl | 6f0d2a68198ea398d1ac0f54b4d0d360c121d1c1 | #pragma
<!-- BOT_STATE: {"assignee": "plon-Susk7", "assigned_at": "2024-12-26T13:56:47.762956+00:00", "reminder_sent": false, "unassigned": false} --> | diff --git a/crosstl/backend/DirectX/DirectxAst.py b/crosstl/backend/DirectX/DirectxAst.py
index 829894f..30f69aa 100644
--- a/crosstl/backend/DirectX/DirectxAst.py
+++ b/crosstl/backend/DirectX/DirectxAst.py
@@ -161,6 +161,18 @@ class UnaryOpNode(ASTNode):
return f"({self.op}{self.operand})"
+class Pragma... |
CrossGL__crosstl-220 | [
{
"changes": {
"added_entities": [
"crosstl/backend/DirectX/DirectxAst.py:IncludeNode.__init__",
"crosstl/backend/DirectX/DirectxAst.py:IncludeNode.__repr__",
"crosstl/backend/DirectX/DirectxAst.py:IncludeNode.__str__"
],
"added_modules": [
"crosstl/backend/Dire... | CrossGL/crosstl | 0ddc76be73115c830de6f7e64c975b78443251db | #include
<!-- BOT_STATE: {"assignee": "SumitBahl02", "assigned_at": "2024-12-26T13:56:49.951114+00:00", "reminder_sent": false, "unassigned": false} --> | diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index c75ed28..a934205 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,48 +1,73 @@
-### PR Description
-<!-- Provide a brief summary of the changes you have made. Explain the purpose and motivatio... |
CrossGL__crosstl-226 | [
{
"changes": {
"added_entities": [
"crosstl/backend/DirectX/DirectxAst.py:SwitchNode.__init__",
"crosstl/backend/DirectX/DirectxAst.py:SwitchNode.__repr__",
"crosstl/backend/DirectX/DirectxAst.py:CaseNode.__init__",
"crosstl/backend/DirectX/DirectxAst.py:CaseNode.__repr__"
... | CrossGL/crosstl | 6fce0a1f21d429e7db6842f557969302e3065732 | switch statement
<!-- BOT_STATE: {"assignee": "RatneshKJaiswal", "assigned_at": "2024-12-26T13:56:57.047108+00:00", "reminder_sent": false, "unassigned": false} --> | diff --git a/crosstl/backend/DirectX/DirectxAst.py b/crosstl/backend/DirectX/DirectxAst.py
index 3269663..829894f 100644
--- a/crosstl/backend/DirectX/DirectxAst.py
+++ b/crosstl/backend/DirectX/DirectxAst.py
@@ -170,3 +170,22 @@ class IncludeNode(ASTNode):
def __str__(self):
return f"#include {self.pat... |
CrossGL__crosstl-236 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "crosstl/backend/DirectX/DirectxLexer.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | CrossGL/crosstl | 5db64c9ecb2e16096884d7532dfb39a579aa5da7 | BITWISE_AND : &
<!-- BOT_STATE: {} --> | diff --git a/crosstl/backend/DirectX/DirectxLexer.py b/crosstl/backend/DirectX/DirectxLexer.py
index a85cc9d..e6c4c28 100644
--- a/crosstl/backend/DirectX/DirectxLexer.py
+++ b/crosstl/backend/DirectX/DirectxLexer.py
@@ -103,6 +103,7 @@ TOKENS = tuple(
("DEFAULT", r"\bdefault\b"),
("BREAK", r"\bbreak\... |
CrossGL__crosstl-249 | [
{
"changes": {
"added_entities": [
"crosstl/backend/DirectX/DirectxLexer.py:HLSLLexer.token_generator",
"crosstl/backend/DirectX/DirectxLexer.py:HLSLLexer._next_token",
"crosstl/backend/DirectX/DirectxLexer.py:HLSLLexer.from_file"
],
"added_modules": null,
"edited... | CrossGL/crosstl | cfd399eb752ab2fb60a58dd6cc5317e2fe8ffd64 | Add translator support for `Const` type qualifier token
<!-- BOT_STATE: {"assignee": "ArchitGupta07", "assigned_at": "2024-12-26T13:57:50.024117+00:00", "reminder_sent": false, "unassigned": false} --> | diff --git a/crosstl/backend/DirectX/DirectxLexer.py b/crosstl/backend/DirectX/DirectxLexer.py
index 88eadcc..a85cc9d 100644
--- a/crosstl/backend/DirectX/DirectxLexer.py
+++ b/crosstl/backend/DirectX/DirectxLexer.py
@@ -1,75 +1,11 @@
import re
+from typing import Iterator, Tuple, List
-TOKENS = [
- ("COMMENT_SIN... |
CrossGL__crosstl-257 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "crosstl/translator/lexer.py"
}
] | CrossGL/crosstl | bf894dbc90466d1ed9ae942f44396fbd04f18298 | ToDO for translator frontend
- this task is to add support for `translator` frontend add token in `lexer` so it can also identify these tokens. for this task the one file `crosstl/src/translator/lexer.py`
List of task
- [x] #42
- [x] #43
- [x] #44
- [x] #45
- [x] #46
- [x] #47
- [x] #48
- [x] #4... | diff --git a/crosstl/translator/lexer.py b/crosstl/translator/lexer.py
index 84cad4f..c260361 100644
--- a/crosstl/translator/lexer.py
+++ b/crosstl/translator/lexer.py
@@ -21,6 +21,7 @@ TOKENS = OrderedDict(
("FRAGMENT", r"\bfragment\b"),
("FLOAT_NUMBER", r"\d*\.\d+|\d+\.\d*"),
("FLOAT", r"\... |
CrossGL__crosstl-41 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py:HLSLToCrossGLConverter.generate_if_statement"
],
"edited_modules": [
"crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py:HLSLTo... | CrossGL/crosstl | d456c2b5f509104dd97b74ce40c597531784e2ca | Add `else if` Conditional Statements to the DirectX backend
To add `else if` support to CrossGL, modify the following files in the `crosstl/src/backend/DirectX` directory:
- [ ] **DirectxLexer.py** : Add token recognition for `else if`.
- [ ] **DirectxParser.py** : Update grammar and AST to handle `else if`.
- [ ]... | diff --git a/crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py b/crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py
index 910eec2..e936097 100644
--- a/crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py
+++ b/crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py
@@ -157,9 +157,13 @@ class HLSLToCrossGLConverter:
... |
CrossGL__crosstl-63 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "crosstl/src/translator/lexer.py"
}
] | CrossGL/crosstl | 49a1c56a2b186090a472094a5156129495e11e27 | add `BITWISE_AND` Operators support at `translator ` frontend
Implement the BITWISE_AND token to recognize the & operator for performing bitwise AND operations.
| diff --git a/crosstl/src/translator/lexer.py b/crosstl/src/translator/lexer.py
index f613e17..f8e77d5 100644
--- a/crosstl/src/translator/lexer.py
+++ b/crosstl/src/translator/lexer.py
@@ -37,6 +37,8 @@ TOKENS = [
("ELSE", r"\belse\b"),
("FOR", r"\bfor\b"),
("RETURN", r"\breturn\b"),
+ ("BITWISE_SHIFT... |
CrossGL__crosstl-68 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py:HLSLToCrossGLConverter.generate_if_statement"
],
"edited_modules": [
"crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py:HLSLTo... | CrossGL/crosstl | d456c2b5f509104dd97b74ce40c597531784e2ca | Add `Double` Data Type Token at translator frontend
Implement the DOUBLE token to recognize the double data type for representing double-precision floating-point numbers. | diff --git a/crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py b/crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py
index 910eec2..e936097 100644
--- a/crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py
+++ b/crosstl/src/backend/DirectX/DirectxCrossGLCodeGen.py
@@ -157,9 +157,13 @@ class HLSLToCrossGLConverter:
... |
CrossGL__crosstl-95 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"crosstl/src/translator/parser.py:Parser.parse_assignment_or_function_call",
"crosstl/src/translator/parser.py:Parser.parse_variable_declaration",
"crosstl/src/translator/parser.py:Parser... | CrossGL/crosstl | 7f75249ddd6e3f1ea080495f6b320273b266468e | Add Parsing for `Assignment Shift Right` Token
Update the parser to handle the ASSIGN_SHIFT_RIGHT token, allowing it to correctly parse expressions involving the >>= operator. | diff --git a/crosstl/src/translator/parser.py b/crosstl/src/translator/parser.py
index a46a9d2..d07c84e 100644
--- a/crosstl/src/translator/parser.py
+++ b/crosstl/src/translator/parser.py
@@ -644,6 +644,7 @@ class Parser:
"ASSIGN_MOD",
"BITWISE_SHIFT_RIGHT",
"BITWISE_SHIFT_LEFT",... |
CrossGL__crosstl-98 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"crosstl/src/translator/parser.py:Parser.parse_assignment_or_function_call",
"crosstl/src/translator/parser.py:Parser.parse_variable_declaration",
"crosstl/src/translator/parser.py:Parser... | CrossGL/crosstl | d4a35e6554bc249fff7764276173ba42c6b5d422 | Add Parsing for `Assignment AND` Token
Update the parser to handle the ASSIGN_AND token, allowing it to correctly parse expressions involving the &= operator. | diff --git a/crosstl/src/translator/parser.py b/crosstl/src/translator/parser.py
index 82899e6..a46a9d2 100644
--- a/crosstl/src/translator/parser.py
+++ b/crosstl/src/translator/parser.py
@@ -638,6 +638,10 @@ class Parser:
"GREATER_THAN",
"LESS_EQUAL",
"GREATER_EQUAL",
+ ... |
CybOXProject__mixbox-35 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mixbox/dates.py:serialize_date"
],
"edited_modules": [
"mixbox/dates.py:serialize_date"
]
},
"file": "mixbox/dates.py"
},
{
"changes": {
"added_entities":... | CybOXProject/mixbox | bab51cfd20757f9a64a61571631203dbbc3644f8 | DateField does not properly serialize datetime objects
When storing a Python `datetime` object in a property specified by a `DateField`, the value incorrectly serializes to an ISO timestamp (`YYYY-MM-DDThh:mm:ss`) instead of to a `xs:date` format (`YYYY-MM-DD`).
class Foo(Entity):
my_date = DateField("m... | diff --git a/mixbox/dates.py b/mixbox/dates.py
index be279e1..794e0b0 100644
--- a/mixbox/dates.py
+++ b/mixbox/dates.py
@@ -73,10 +73,10 @@ def serialize_date(value):
"""
if not value:
return None
- elif isinstance(value, datetime.date):
- return value.isoformat()
elif isinstance(valu... |
CybOXProject__python-cybox-265 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "cybox/bindings/extensions/location/ciq_address_3_0.py"
}
] | CybOXProject/python-cybox | c889ade168e7e0a411af9c836c95d61d7b5c4583 | CIQ Address extension non mixboxified
I think the `cybox.extensions.location.ciq_address_3_0` module was left out of the mixboxification effort. | diff --git a/cybox/bindings/extensions/location/ciq_address_3_0.py b/cybox/bindings/extensions/location/ciq_address_3_0.py
index ae0ad70..a148347 100644
--- a/cybox/bindings/extensions/location/ciq_address_3_0.py
+++ b/cybox/bindings/extensions/location/ciq_address_3_0.py
@@ -2,7 +2,9 @@
# See LICENSE.txt for complete... |
CybOXProject__python-cybox-325 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cybox/helper.py:create_ipv4_list_observables"
],
"edited_modules": [
"cybox/helper.py:create_ipv4_list_observables"
]
},
"file": "cybox/helper.py"
},
{
"changes... | CybOXProject/python-cybox | eeffc25459a3ac3867b0548b62b8fd8e9a113af6 | Implement Artifact.Packaging as TypedField
Currently this is handled as a simple list... | diff --git a/cybox/helper.py b/cybox/helper.py
index 2ed7c5d..9e06a05 100644
--- a/cybox/helper.py
+++ b/cybox/helper.py
@@ -29,7 +29,8 @@ def create_ipv4_list_observables(list_ipv4_addresses):
list_observables = []
for ipv4_address in list_ipv4_addresses:
ipv4_observable = create_ipv4_observable(ipv... |
CybOXProject__python-cybox-327 | [
{
"changes": {
"added_entities": [
"cybox/objects/artifact_object.py:EncryptionFactory.register_extension",
"cybox/objects/artifact_object.py:CompressionFactory.register_extension",
"cybox/objects/artifact_object.py:EncodingFactory.register_extension"
],
"added_modules"... | CybOXProject/python-cybox | ee82c7da40ca4638e3ca8d70766150c0dace1b55 | Parsing fails if algorithm, compression_mechanism, or encryption_mechanism are not present
For Encoding, Encryption and Compression API classes we have a Factory that currently is limited in its extensibility. If the class is not found in the if/else clause it will fail hard. Propose a way to register new API classes, ... | diff --git a/cybox/objects/artifact_object.py b/cybox/objects/artifact_object.py
index 1c65723..92561b6 100644
--- a/cybox/objects/artifact_object.py
+++ b/cybox/objects/artifact_object.py
@@ -12,6 +12,10 @@ from mixbox.compat import xor
import cybox.bindings.artifact_object as artifact_binding
from cybox.common impo... |
CycloneDX__cyclonedx-python-332 | [
{
"changes": {
"added_entities": [
"cyclonedx_py/utils/conda.py:split_package_string",
"cyclonedx_py/utils/conda.py:split_package_build_string"
],
"added_modules": [
"cyclonedx_py/utils/conda.py:split_package_string",
"cyclonedx_py/utils/conda.py:split_package_b... | CycloneDX/cyclonedx-python | c02d770cf18a57e118347a0a57db29ae65919c35 | bug: conda-parser raises error when unexpected build-number is detected
## Environment
XUbuntu 20.04
Python 3.8.10
conda 4.12.0 #miniconda
Name: cyclonedx-bom
Version: 3.1.0
## What I did
* update conda base
```
->$ conda update -n base -c defaults conda -y
Collecting package metadata (current_repodata.json... | diff --git a/cyclonedx_py/utils/conda.py b/cyclonedx_py/utils/conda.py
index 3cf2fc5..b5c26a0 100644
--- a/cyclonedx_py/utils/conda.py
+++ b/cyclonedx_py/utils/conda.py
@@ -20,15 +20,14 @@
import json
import sys
from json import JSONDecodeError
-from typing import Optional
+from typing import Optional, Tuple
+from u... |
CycloneDX__cyclonedx-python-348 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cyclonedx_py/parser/pipenv.py:PipEnvParser.__init__"
],
"edited_modules": [
"cyclonedx_py/parser/pipenv.py:PipEnvParser"
]
},
"file": "cyclonedx_py/parser/pipenv.py"
... | CycloneDX/cyclonedx-python | 194d2878fe088f8f1a680cc4eb95504c046d34a2 | bug: hashes not always included in BOM when present in Pipfile.lock
Hashes appear to only be included in BOM output if they were originally called in the Pipfile as direct dependencies. According to the usage document (docs/usage.rst) hashes should be included if they are present.
Given the following Pipfile, only b... | diff --git a/cyclonedx_py/parser/pipenv.py b/cyclonedx_py/parser/pipenv.py
index 8e1676f..9339201 100644
--- a/cyclonedx_py/parser/pipenv.py
+++ b/cyclonedx_py/parser/pipenv.py
@@ -44,7 +44,7 @@ class PipEnvParser(BaseParser):
type='pypi', name=package_name, version=str(package_data.get('version') ... |
CycloneDX__cyclonedx-python-366 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cyclonedx_py/parser/conda.py:_BaseCondaParser._conda_packages_to_components"
],
"edited_modules": [
"cyclonedx_py/parser/conda.py:_BaseCondaParser"
]
},
"file": "cyclon... | CycloneDX/cyclonedx-python | b028c2b96fb2caea2d7f084b6ef88cba1bcade2b | [CONDA] Incorrect purl type in SBoM from Conda Explicit MD5 list
* What I did
```
# Create Conda environment with openssl included
$ conda create -y --name openssl openssl=1.1.1o
# Create an explicit MD5 list
$ conda list -n openssl --explicit --md5 > openssl-1.1.1_explict_md5_spec.txt
# Create a SBoM from ... | diff --git a/cyclonedx_py/parser/conda.py b/cyclonedx_py/parser/conda.py
index 1c9197b..487ad08 100644
--- a/cyclonedx_py/parser/conda.py
+++ b/cyclonedx_py/parser/conda.py
@@ -25,10 +25,12 @@ from cyclonedx.model import ExternalReference, ExternalReferenceType, HashAlgori
from cyclonedx.model.component import Compone... |
CycloneDX__cyclonedx-python-367 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cyclonedx_py/parser/conda.py:_BaseCondaParser._conda_packages_to_components"
],
"edited_modules": [
"cyclonedx_py/parser/conda.py:_BaseCondaParser"
]
},
"file": "cyclon... | CycloneDX/cyclonedx-python | e2be444b8db7dd12031f3e9b481dfdae23f3e59e | [CONDA] Include component hashes when generating SBoM from Conda Explicit MD5 List
* What I did
```
# Create Conda environment with openssl included
conda create -y --name openssl openssl=1.1.1o
# Create an explicit MD5 list
conda list -n openssl --explicit --md5 > openssl-1.1.1_explict_md5_spec.txt
# Create ... | diff --git a/cyclonedx_py/parser/conda.py b/cyclonedx_py/parser/conda.py
index 59fc527..1c9197b 100644
--- a/cyclonedx_py/parser/conda.py
+++ b/cyclonedx_py/parser/conda.py
@@ -21,7 +21,7 @@ import json
from abc import ABCMeta, abstractmethod
from typing import List
-from cyclonedx.model import ExternalReference, E... |
DAI-Lab__SteganoGAN-27 | [
{
"changes": {
"added_entities": [
"steganogan/critics.py:BasicCritic._conv2d",
"steganogan/critics.py:BasicCritic._build_models",
"steganogan/critics.py:BasicCritic.upgrade_legacy"
],
"added_modules": null,
"edited_entities": [
"steganogan/critics.py:Basi... | DAI-Lab/SteganoGAN | 7b5457edc88715a3e8885dcbc20468c739155024 | Refactorize critics and decoders
As we added a new Decoder, we can see that the code it's quiet similar and it should be refactorized in order to follow the same structure as `encoders.py`.
Same it's happening for `critics.py`. Refactorizing this now, will save us time in unit tests and if we want to add more architec... | diff --git a/steganogan/critics.py b/steganogan/critics.py
index 0963fd7..301cb61 100644
--- a/steganogan/critics.py
+++ b/steganogan/critics.py
@@ -1,7 +1,7 @@
# -*- coding: utf-8 -*-
import torch
-import torch.nn as nn
+from torch import nn
class BasicCritic(nn.Module):
@@ -13,29 +13,45 @@ class BasicCritic(... |
DAI-Lab__SteganoGAN-37 | [
{
"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": null,
"edited_modules": null
... | DAI-Lab/SteganoGAN | 4b0e6019078e99e36a8b095636620b107f3fa3d1 | Move `_get_steganogan` logic to `SteganoGAN.load`
The code that loads the pretrained models is currently inside a "private" function in the `cli.py` module.
This should be moved inside the `SteganoGAN.load` method to allow loading pretrained models directly from the class.
For this, the following changes are need... | diff --git a/setup.py b/setup.py
index dbe8ad7..9b57672 100644
--- a/setup.py
+++ b/setup.py
@@ -74,7 +74,7 @@ setup(
description="Steganography tool based on DeepLearning GANs",
entry_points={
'console_scripts': [
- 'steganogan=steganogan:cli.main'
+ 'steganogan=steganogan.cli:... |
DARMA-tasking__LB-analysis-framework-232 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/lbaf/IO/lbsVTDataReader.py:LoadReader.json_reader"
],
"edited_modules": [
"src/lbaf/IO/lbsVTDataReader.py:LoadReader"
]
},
"file": "src/lbaf/IO/lbsVTDataReader.py"
... | DARMA-tasking/LB-analysis-framework | 92b83de227bc8af517bb7ac5d8f444c1d1f9b2f8 | Add user-defined fields to JSON parser, create Python data structures of objects that hold this info
We have added a new region, `user_defined`, to the JSON files. Please make the parser read this data into Python data structures. Here is an example set of json files with this data: [fake-4x-block-overdecomp-3-uncompre... | diff --git a/src/lbaf/IO/lbsVTDataReader.py b/src/lbaf/IO/lbsVTDataReader.py
index 215e62e..a1f5770 100644
--- a/src/lbaf/IO/lbsVTDataReader.py
+++ b/src/lbaf/IO/lbsVTDataReader.py
@@ -189,11 +189,12 @@ class LoadReader:
for task in phase["tasks"]:
task_time = task.get("time")
... |
DARMA-tasking__LB-analysis-framework-235 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/lbaf/IO/lbsVTDataReader.py:LoadReader.read_iteration",
"src/lbaf/IO/lbsVTDataReader.py:LoadReader.json_reader"
],
"edited_modules": [
"src/lbaf/IO/lbsVTDataReader.py:Load... | DARMA-tasking/LB-analysis-framework | cea7f8155876a58c7d8df2f31d53ebc2bcb11f56 | is reading data from json file working correctly?
Random question after analysing the code in `lbsVTDataReader.py`:
- `comm_dict` is first created at top level
https://github.com/DARMA-tasking/LB-analysis-framework/blob/f93c5aad550a283dabb8d27d55167b47ebc8b422/src/lbaf/IO/lbsVTDataReader.py#L142-L144
- then for ev... | diff --git a/src/lbaf/IO/lbsVTDataReader.py b/src/lbaf/IO/lbsVTDataReader.py
index 9fd56b1..a977197 100644
--- a/src/lbaf/IO/lbsVTDataReader.py
+++ b/src/lbaf/IO/lbsVTDataReader.py
@@ -90,15 +90,16 @@ class LoadReader:
sys.exit(1)
# Merge rank communication with existing ones
- ... |
DARMA-tasking__LB-analysis-framework-274 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/lbaf/IO/lbsVTDataReader.py:LoadReader.json_reader"
],
"edited_modules": [
"src/lbaf/IO/lbsVTDataReader.py:LoadReader"
]
},
"file": "src/lbaf/IO/lbsVTDataReader.py"
... | DARMA-tasking/LB-analysis-framework | fee97e6634592292b47ab33ab3240519c7d18f41 | Load subphase data from input files | diff --git a/src/lbaf/IO/lbsVTDataReader.py b/src/lbaf/IO/lbsVTDataReader.py
index bd1c7cf..7d3f443 100644
--- a/src/lbaf/IO/lbsVTDataReader.py
+++ b/src/lbaf/IO/lbsVTDataReader.py
@@ -201,11 +201,13 @@ class LoadReader:
entity = task.get("entity")
task_object_id = entity.get("id")
... |
DARMA-tasking__LB-analysis-framework-278 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/lbaf/Applications/LBAF_app.py:internalParameters.parse_conf_file"
],
"edited_modules": [
"src/lbaf/Applications/LBAF_app.py:internalParameters"
]
},
"file": "src/lb... | DARMA-tasking/LB-analysis-framework | 14d165420e32962d8058c928a9ad73b387c833b4 | Accept range in phase indices in lbaf config
e.g. if we want to simulate 100 phases we would want to be able to have something like:
```yml
from_data:
phase_ids:
- [0,100]
```
@ppebay mentioned I should file an issue for this
| diff --git a/src/lbaf/Applications/LBAF_app.py b/src/lbaf/Applications/LBAF_app.py
index e971488..78fcca2 100644
--- a/src/lbaf/Applications/LBAF_app.py
+++ b/src/lbaf/Applications/LBAF_app.py
@@ -112,7 +112,11 @@ class internalParameters:
# Parse data parameters if present
if self.configuration.get("... |
DARMA-tasking__LB-analysis-framework-436 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/lbaf/Execution/lbsClusteringTransferStrategy.py:ClusteringTransferStrategy.__init__",
"src/lbaf/Execution/lbsClusteringTransferStrategy.py:ClusteringTransferStrategy.__find_suitable_subclust... | DARMA-tasking/LB-analysis-framework | 0cd1502c45e683eda9963896251c7d9c87d330ac | Make cluster swap relative threshold a configurable parameter
As suggested by @lifflander in PR #433 , the 5% value in line 117 0f [Execution/lbsClusteringTransferStrategy.py](https://github.com/DARMA-tasking/LB-analysis-framework/pull/433/files/41e8215c721da7c1c729dca393b8affe55f75675#diff-52bdf682017c84ecfdd2f4caa52b... | diff --git a/src/lbaf/Execution/lbsClusteringTransferStrategy.py b/src/lbaf/Execution/lbsClusteringTransferStrategy.py
index fb2f41c..7397eec 100644
--- a/src/lbaf/Execution/lbsClusteringTransferStrategy.py
+++ b/src/lbaf/Execution/lbsClusteringTransferStrategy.py
@@ -22,6 +22,9 @@ class ClusteringTransferStrategy(Tran... |
DARMA-tasking__LB-analysis-framework-455 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/lbaf/Execution/lbsInformAndTransferAlgorithm.py:InformAndTransferAlgorithm.__init__",
"src/lbaf/Execution/lbsInformAndTransferAlgorithm.py:InformAndTransferAlgorithm.execute"
],
... | DARMA-tasking/LB-analysis-framework | 22967e7811ecbb3822cd89a883ef3a54263788b3 | Add a target imbalance threshold to yaml
Add an optional target imbalance threshold to the yaml file that can be used to conclude the iteration process in fewer iterations than requested iff the imbalance has been brought down below the threshold already. | diff --git a/src/lbaf/Execution/lbsInformAndTransferAlgorithm.py b/src/lbaf/Execution/lbsInformAndTransferAlgorithm.py
index c854aca..4b21239 100644
--- a/src/lbaf/Execution/lbsInformAndTransferAlgorithm.py
+++ b/src/lbaf/Execution/lbsInformAndTransferAlgorithm.py
@@ -7,7 +7,6 @@ from .lbsCriterionBase import Criterion... |
DARMA-tasking__LB-analysis-framework-485 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/lbaf/Execution/lbsAlgorithmBase.py:AlgorithmBase.factory"
],
"edited_modules": [
"src/lbaf/Execution/lbsAlgorithmBase.py:AlgorithmBase"
]
},
"file": "src/lbaf/Execu... | DARMA-tasking/LB-analysis-framework | eb706ffa576f52e1a616546700d75c4be67edec8 | Keep tempered algorithm in sync with implementation in vt
This is because [vt#2201](https://github.com/DARMA-tasking/vt/issues/2201) will result in a version of the tempered algorithm (and transfer strategies) not necessarily synchronized -- or with some improvements. | diff --git a/config/challenging-toy-hundreds-tasks.yaml b/config/challenging-toy-hundreds-tasks.yaml
index 15d2cbe..2c65c9e 100644
--- a/config/challenging-toy-hundreds-tasks.yaml
+++ b/config/challenging-toy-hundreds-tasks.yaml
@@ -26,6 +26,8 @@ algorithm:
fanout: 4
order_strategy: arbitrary
transfer_st... |
DARMA-tasking__LB-analysis-framework-514 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/lbaf/Applications/LBAF_app.py:InternalParameters.init_parameters"
],
"edited_modules": [
"src/lbaf/Applications/LBAF_app.py:InternalParameters"
]
},
"file": "src/lb... | DARMA-tasking/LB-analysis-framework | 4467b0bef8e783468960f96ad820339f402b9707 | LBAF should report an error or a warning when vt-tv is not found but is requested (instead of a mere warning)
## Steps to reproduce:
* Identical to those of #509
* Except vt-tv should not be installed
## Error:
Output does not report that `vt-tv` is not found but it should, instead of a mere warming. If a visual... | diff --git a/src/lbaf/Applications/LBAF_app.py b/src/lbaf/Applications/LBAF_app.py
index 9c00900..167b2ad 100644
--- a/src/lbaf/Applications/LBAF_app.py
+++ b/src/lbaf/Applications/LBAF_app.py
@@ -121,7 +121,7 @@ class InternalParameters:
# Ensure that vttv module was found
if not using_vttv... |
DARMA-tasking__LB-analysis-framework-515 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/lbaf/Applications/LBAF_app.py:InternalParameters.init_parameters"
],
"edited_modules": [
"src/lbaf/Applications/LBAF_app.py:InternalParameters"
]
},
"file": "src/lb... | DARMA-tasking/LB-analysis-framework | 4467b0bef8e783468960f96ad820339f402b9707 | Different runtime errors occurring depending on whether vtk package is installed or not
## Steps to repeat
Identical as those of #509
## Observed errors
### If `vtk` package is **not** installed via `pip`
```
(lbaf39) [pppebay@aneto]~/Documents/Git/LB-analysis-framework/src/lbaf/Applications$ pip uninstall vtk
... | diff --git a/src/lbaf/Applications/LBAF_app.py b/src/lbaf/Applications/LBAF_app.py
index 9c00900..167b2ad 100644
--- a/src/lbaf/Applications/LBAF_app.py
+++ b/src/lbaf/Applications/LBAF_app.py
@@ -121,7 +121,7 @@ class InternalParameters:
# Ensure that vttv module was found
if not using_vttv... |
DARMA-tasking__LB-analysis-framework-568 | [
{
"changes": {
"added_entities": [
"src/lbaf/Applications/LBAF_app.py:LBAFApplication.__print_qoi"
],
"added_modules": null,
"edited_entities": [
"src/lbaf/Applications/LBAF_app.py:InternalParameters.init_parameters",
"src/lbaf/Applications/LBAF_app.py:LBAFApplica... | DARMA-tasking/LB-analysis-framework | f9d76b3aaf560f8ee764a49979699db450b2d603 | Support LB iterations
This is related to [vt#2375](https://github.com/DARMA-tasking/vt/issues/2375)
@lifflander if you want to add something
In the JSON for a phase:
```json
"phases":
[
{
"id": ...,
"tasks": ...,
"communications": ...,
"lb_iterations": [
{
... | diff --git a/config/conf.yaml b/config/conf.yaml
index 95824c4..1abb23b 100644
--- a/config/conf.yaml
+++ b/config/conf.yaml
@@ -9,11 +9,12 @@ check_schema: false
work_model:
name: AffineCombination
parameters:
- alpha: 0.0
- beta: 1.0
+ alpha: 1.0
+ beta: 0.0
gamma: 0.0
# Specify algorithm
+... |
DARMA-tasking__LB-analysis-framework-585 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/lbaf/Execution/lbsClusteringTransferStrategy.py:ClusteringTransferStrategy.execute"
],
"edited_modules": [
"src/lbaf/Execution/lbsClusteringTransferStrategy.py:ClusteringTransfer... | DARMA-tasking/LB-analysis-framework | 7c811843c9b6cd8ad7732b4a351eb74fc8c6f614 | Add option to run cluster transfer based algorithms without subclustering
@lifflander do you agree that this should be OFF by default (i.e. by default subclustering should be allowed)? | diff --git a/config/synthetic-blocks.yaml b/config/synthetic-blocks.yaml
index 20e1963..85ab304 100644
--- a/config/synthetic-blocks.yaml
+++ b/config/synthetic-blocks.yaml
@@ -23,7 +23,8 @@ algorithm:
n_rounds: 2
fanout: 2
order_strategy: arbitrary
- transfer_strategy: Recursive
+ transfer_strateg... |
DARMA-tasking__LB-analysis-framework-597 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/lbaf/Applications/LBAF_app.py:LBAFApplication.run"
],
"edited_modules": [
"src/lbaf/Applications/LBAF_app.py:LBAFApplication"
]
},
"file": "src/lbaf/Applications/LB... | DARMA-tasking/LB-analysis-framework | 7f2ce23cc1e44d4ca97113a6cc17604c2e996bbc | Replace hard-coded 1.0 with actual local alpha values for the computation of max arrangement work statistics
## Description of the issue:
As reported by @cwschilly, currently in `LBAF_app`, the `compute_min_max_arrangements_work()` is called with all `alpha` values set to 1.
## How to fix the issue:
This must be repla... | diff --git a/config/conf.yaml b/config/conf.yaml
index b0e9cc9..8b823ac 100644
--- a/config/conf.yaml
+++ b/config/conf.yaml
@@ -13,7 +13,6 @@ work_model:
gamma: 0.0
# Specify algorithm
-brute_force_optimization: true
algorithm:
name: InformAndTransfer
phase_id: 0
diff --git a/config/synthetic-blocks.yam... |
DCC-Lab__RayTracing-133 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/rays.py:Rays.__init__",
"raytracing/rays.py:Rays.rayCountHistogram",
"raytracing/rays.py:Rays.rayAnglesHistogram",
"raytracing/rays.py:Rays.append"
],
"edi... | DCC-Lab/RayTracing | 25d5ffdd500afc561b8ce7d25dded3b532fd44a1 | rayCountHistogram() and rayAnglesHistogram() of Rays raise exception when already computed
When we compute `rayCountHistogram()` for a first time, it works perfectly. But when we run it a second time, it throws an exception because a variable is referenced before asignment. | diff --git a/raytracing/rays.py b/raytracing/rays.py
index 7787434..11de6ad 100644
--- a/raytracing/rays.py
+++ b/raytracing/rays.py
@@ -29,6 +29,12 @@ class Rays:
self._thetaHistogram = None
self._directionBinEdges = None
+ self._countHistogramParameters = None
+ self._xValuesCountHis... |
DCC-Lab__RayTracing-135 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/rays.py:Rays.__init__",
"raytracing/rays.py:Rays.append"
],
"edited_modules": [
"raytracing/rays.py:Rays"
]
},
"file": "raytracing/rays.py"
}
] | DCC-Lab/RayTracing | 203b3739d0804718664037706e2d43068fcd6ac5 | Rays() accepts objects from every type
This can cause further problems. In `__init__` itself it is not a big deal (except for coherence and logic) if `Rays` receive a string of nonsense or a list of numbers, but other methods will inevitably fail with exceptions of different types. | diff --git a/raytracing/rays.py b/raytracing/rays.py
index 11de6ad..1963e25 100644
--- a/raytracing/rays.py
+++ b/raytracing/rays.py
@@ -4,20 +4,36 @@ import matplotlib.pyplot as plt
import pickle
import time
import os
-
-""" A group of rays kept as a list, to be used as a starting
-point (i.e. an object) or as a cu... |
DCC-Lab__RayTracing-141 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/rays.py:RandomRays.__getitem__",
"raytracing/rays.py:RandomRays.randomRay"
],
"edited_modules": [
"raytracing/rays.py:RandomRays"
]
},
"file": "raytr... | DCC-Lab/RayTracing | 3a1d740763e8a3138f7c2c025f0dce707249acd9 | RandomRays raises a constant, not an exception
In `RandomRays`, some methods have `raise NotImplemented("...")`, but `NotImplemented` is a constant used in some binary methods (see https://docs.python.org/3/library/constants.html). I suspect what we want is `raise NotImplementedError("...")`. | diff --git a/raytracing/rays.py b/raytracing/rays.py
index aaf1971..83ffaf1 100644
--- a/raytracing/rays.py
+++ b/raytracing/rays.py
@@ -288,9 +288,9 @@ class RandomRays(Rays):
def __getitem__(self, item):
if self.rays is None:
- raise NotImplemented("You cannot access RandomRays")
+ ... |
DCC-Lab__RayTracing-174 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/rays.py:Rays.rayCountHistogram",
"raytracing/rays.py:Rays.rayAnglesHistogram",
"raytracing/rays.py:Rays.display",
"raytracing/rays.py:LambertianRays.__init__"
],... | DCC-Lab/RayTracing | a37805c13a908d1b8beb23c50bfb8079fbb455a1 | Unit tests needed for Rays.py
We want to reach 90% coverage for this file.
Check coverage with `coverage run -m unittest` then `coverage html` and `coverage_report_html/index.html` | diff --git a/raytracing/rays.py b/raytracing/rays.py
index 8cb6a51..9129491 100644
--- a/raytracing/rays.py
+++ b/raytracing/rays.py
@@ -94,6 +94,7 @@ class Rays:
maxValue = max(self.yValues)
if self._countHistogramParameters != (binCount, minValue, maxValue):
+ self._countHistogramPa... |
DCC-Lab__RayTracing-176 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/rays.py:Rays.load"
],
"edited_modules": [
"raytracing/rays.py:Rays"
]
},
"file": "raytracing/rays.py"
}
] | DCC-Lab/RayTracing | ce69bb2fc28ba9864f2631abd5e87819aad1de74 | Rays can load any "pickled" file
This can lead to unwanted behaviors. We should check if the content of the file is an iterable of `Ray` objects.
`load` directly extends (or override) the inner list or rays in `Rays`. This can cause unexpected problems without proper guidance to what caused the issue. | diff --git a/raytracing/rays.py b/raytracing/rays.py
index 9129491..a424fad 100644
--- a/raytracing/rays.py
+++ b/raytracing/rays.py
@@ -207,6 +207,10 @@ class Rays:
def load(self, filePath, append=False):
with open(filePath, 'rb') as infile:
loadedRays = pickle.Unpickler(infile).load()
+ ... |
DCC-Lab__RayTracing-180 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/laserpath.py:LaserPath.eigenModes",
"raytracing/laserpath.py:LaserPath.laserModes",
"raytracing/laserpath.py:LaserPath.drawBeamTrace",
"raytracing/laserpath.py:LaserPa... | DCC-Lab/RayTracing | 03535abea0f84ad4eeb61c8da671579d95d6217e | EigenModes of LaserPath fails with exception when C = 0
When we create a `LaserPath` and its C component is 0, we have a division by 0, which raises an exception. We should check if the laser path has power (`self.hasPower`) before and return `(None, None)` (maybe?) if not. We then need to change other methods, like `... | diff --git a/raytracing/laserpath.py b/raytracing/laserpath.py
index 4f74727..edcf1b2 100644
--- a/raytracing/laserpath.py
+++ b/raytracing/laserpath.py
@@ -1,6 +1,7 @@
from .matrixgroup import *
from .imagingpath import *
+
class LaserPath(MatrixGroup):
"""LaserPath: the main class of the module for coherent... |
DCC-Lab__RayTracing-187 | [
{
"changes": {
"added_entities": [
"raytracing/matrixgroup.py:MatrixGroup.__iter__",
"raytracing/matrixgroup.py:MatrixGroup.__next__"
],
"added_modules": null,
"edited_entities": [
"raytracing/matrixgroup.py:MatrixGroup.__init__",
"raytracing/matrixgroup.p... | DCC-Lab/RayTracing | fe768d07b48df2be9428da6dc3d7f738c652915e | ImagingPath and LaserPath methods in MatrixGroup raise exception.
They respectively return a ImagingPath instance and a LaserPath instance, but those classes are in other files not imported. It is also worth mentioning that they both inherit from MatrixGroup, so it is kind of incoherent to use them in MatrixGroup.
Q... | diff --git a/raytracing/matrixgroup.py b/raytracing/matrixgroup.py
index fe54cb8..b34038c 100644
--- a/raytracing/matrixgroup.py
+++ b/raytracing/matrixgroup.py
@@ -10,6 +10,7 @@ class MatrixGroup(Matrix):
"""
def __init__(self, elements=None, label=""):
+ self.iteration = 0
super(MatrixGrou... |
DCC-Lab__RayTracing-192 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/imagingpath.py:ImagingPath.chiefRay"
],
"edited_modules": [
"raytracing/imagingpath.py:ImagingPath"
]
},
"file": "raytracing/imagingpath.py"
}
] | DCC-Lab/RayTracing | 8b8d8f660c634a5cee6b0e3f926e298824ffa4d7 | ImagingPath: chiefRay not working with no aperture stop
When we create an `ImagingPath` without any aperture stop, `chiefRay` raises a `TypeError`, because there is no aperture stop. For example:
```python
path = ImagingPath(System2f(10)) # A 2f system with f = 10 and infinite diameter
path.chiefRay() # Fails with... | diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py
index 82765ea..6a7e46b 100644
--- a/raytracing/imagingpath.py
+++ b/raytracing/imagingpath.py
@@ -151,8 +151,12 @@ class ImagingPath(MatrixGroup):
If the element B in the transfer matrix for the imaging path
is zero, there is no value ... |
DCC-Lab__RayTracing-196 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/imagingpath.py:ImagingPath.imageSize"
],
"edited_modules": [
"raytracing/imagingpath.py:ImagingPath"
]
},
"file": "raytracing/imagingpath.py"
}
] | DCC-Lab/RayTracing | adc82c7e2d87b0d90f2a9790fe6f36c67a7d94d2 | ImagingPath: imageSize fails when D is 0
When `D == 0`, there is no forward conjugate (nor backward), so we return `conjugateMatrix` as `None`. Because of that, `imageSize` raises an `AttributeError`. We should check if `conjugateMatrix` is `None`, but what should we return? Since there is no image, return `None`? | diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py
index 9960d83..6c89bff 100644
--- a/raytracing/imagingpath.py
+++ b/raytracing/imagingpath.py
@@ -585,6 +585,9 @@ class ImagingPath(MatrixGroup):
"""
fieldOfView = self.fieldOfView()
(distance, conjugateMatrix) = self.forwardC... |
DCC-Lab__RayTracing-199 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/imagingpath.py:ImagingPath.chiefRay"
],
"edited_modules": [
"raytracing/imagingpath.py:ImagingPath"
]
},
"file": "raytracing/imagingpath.py"
}
] | DCC-Lab/RayTracing | 84522313da81dcea8cf30d398e63b5223c102976 | ImagingPath: chiefRay doesn't return None when B is very close but not 0
When `B == 0` in an `ImagingPath` instance, there is no chief ray. But because we use a computer, some calculations can lead to something close to 0 but not quite 0. For example:
```python
path = ImagingPath(System4f(pi * 2, pi * 1.25)) # This i... | diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py
index aa348eb..5c3b21d 100644
--- a/raytracing/imagingpath.py
+++ b/raytracing/imagingpath.py
@@ -161,7 +161,7 @@ class ImagingPath(MatrixGroup):
A = transferMatrixToApertureStop.A
B = transferMatrixToApertureStop.B
- if B == ... |
DCC-Lab__RayTracing-200 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/imagingpath.py:ImagingPath.chiefRay"
],
"edited_modules": [
"raytracing/imagingpath.py:ImagingPath"
]
},
"file": "raytracing/imagingpath.py"
}
] | DCC-Lab/RayTracing | 427fbe9fdcb21c452788b180ba683dff6a0c7321 | ImagingPath: chiefRay returns y=inf and theta=-inf with really big (but not infinite) aperture and no specific y given
When we create an `ImagingPath` with a really big aperture stop (but not infinite), the chief ray obtained has y = -theta = inf. This doesn't really make sense.
This happens because the aperture is ... | diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py
index eaea927..aa348eb 100644
--- a/raytracing/imagingpath.py
+++ b/raytracing/imagingpath.py
@@ -166,6 +166,8 @@ class ImagingPath(MatrixGroup):
if y is None:
y = self.fieldOfView()
+ if abs(y) == float("+inf"):
+ ... |
DCC-Lab__RayTracing-202 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/imagingpath.py:ImagingPath.marginalRays",
"raytracing/imagingpath.py:ImagingPath.displayRange",
"raytracing/imagingpath.py:ImagingPath.drawObject",
"raytracing/imaging... | DCC-Lab/RayTracing | 2c3d3f64b5aa09fc0a45a2422fe8bef834972b0b | ImagingPath: marginalRays raises exception when no apertureStop
When we want the marginal rays of an `ImagingPath` that has no aperture stop, a `TypeError` is raised. Example:
```python
path = ImagingPath(System4f(10, 10))
path.marginalRays() # Raises TypeError, no field stop
``` | diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py
index b9ee7de..eaea927 100644
--- a/raytracing/imagingpath.py
+++ b/raytracing/imagingpath.py
@@ -188,7 +188,6 @@ class ImagingPath(MatrixGroup):
"""
return self.chiefRay(y=None)
-
def marginalRays(self, y=0):
"""This f... |
DCC-Lab__RayTracing-204 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/imagingpath.py:ImagingPath.marginalRays"
],
"edited_modules": [
"raytracing/imagingpath.py:ImagingPath"
]
},
"file": "raytracing/imagingpath.py"
}
] | DCC-Lab/RayTracing | 4e999c92bde9e68c018859054193bf4a00d560a3 | ImagingPath: division by 0 in marginalRays
When we have an `ImagingPath` that has a transfer matrix to the aperture stop with `B == 0`, there is a division by 0 in the calculations of theta + and -. We should check when it's the case and return `None`. | diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py
index 6c89bff..b9ee7de 100644
--- a/raytracing/imagingpath.py
+++ b/raytracing/imagingpath.py
@@ -260,6 +260,9 @@ class ImagingPath(MatrixGroup):
A = transferMatrixToApertureStop.A
B = transferMatrixToApertureStop.B
+ if trans... |
DCC-Lab__RayTracing-220 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/gaussianbeam.py:GaussianBeam.__init__"
],
"edited_modules": [
"raytracing/gaussianbeam.py:GaussianBeam"
]
},
"file": "raytracing/gaussianbeam.py"
}
] | DCC-Lab/RayTracing | 52e850c6260b476c4925eb543702195f73cc779b | GaussianBeam: q or w should be specified (not both None)
This can lead to some incoherence: we should check (if q and w are given) that q computed with w is relatively close to q given.
Also, we should not be able to set both as `None`. Having w and q has `None` does nothing good, only lead to issues with methods, b... | diff --git a/raytracing/gaussianbeam.py b/raytracing/gaussianbeam.py
index 77dbfab..3cfc6b9 100644
--- a/raytracing/gaussianbeam.py
+++ b/raytracing/gaussianbeam.py
@@ -12,12 +12,17 @@ class GaussianBeam(object):
def __init__(self, q:complex=None, w:float=None, R:float=float("+Inf"), n:float=1.0, wavelength=632.... |
DCC-Lab__RayTracing-223 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/matrix.py:Matrix.hasPower"
],
"edited_modules": [
"raytracing/matrix.py:Matrix"
]
},
"file": "raytracing/matrix.py"
}
] | DCC-Lab/RayTracing | ba11e628ea9be0cf8f45efc2013c49529bd2d801 | Matrix: hasPower returns True when it should be False
When we want to know if a `Matrix` has power, we check if `self.C != 0`. In some cases, computational errors occurs due to the fact that we are handling floats and `self.C` is really close to 0. Example:
```python
d1 = 1.0000000000000017 # Some computation errors ... | diff --git a/raytracing/matrix.py b/raytracing/matrix.py
index 43f9790..c84cede 100644
--- a/raytracing/matrix.py
+++ b/raytracing/matrix.py
@@ -846,7 +846,8 @@ class Matrix(object):
@property
def hasPower(self):
- """ If True, then there is a non-null focal length because C!=0
+ """ If True, ... |
DCC-Lab__RayTracing-258 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/matrixgroup.py:MatrixGroup.intermediateConjugates"
],
"edited_modules": [
"raytracing/matrixgroup.py:MatrixGroup"
]
},
"file": "raytracing/matrixgroup.py"
... | DCC-Lab/RayTracing | 12e2e1fe89e74637d25304b4e101c71103de480c | MatrixGroup: intermediateConjugates gives duplicates
When we want the intermediate conjugates of some matrix groups, we have a list with duplicates. Is it normal?
Example:
```python
path = ImagingPath(System4f(10, 5))
print(path.intermediateConjugates())
```
the output is:
```python
[[30.0, -0.5], [30.0, -0.5... | diff --git a/raytracing/matrixgroup.py b/raytracing/matrixgroup.py
index e6d9e57..0270ed3 100644
--- a/raytracing/matrixgroup.py
+++ b/raytracing/matrixgroup.py
@@ -262,7 +262,10 @@ class MatrixGroup(Matrix):
planePosition = transferMatrix.L + distance
if planePosition != 0 and conjuga... |
DCC-Lab__RayTracing-259 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/figure.py:Figure.displayRange"
],
"edited_modules": [
"raytracing/figure.py:Figure"
]
},
"file": "raytracing/figure.py"
}
] | DCC-Lab/RayTracing | 12e2e1fe89e74637d25304b4e101c71103de480c | Generating unnecessary images
illumination = ImagingPath()
illumination.append(Space(d=10))
illumination.append(Lens(f=10, diameter=100, label="Collector"))
illumination.append(Space(d=10+30))
illumination.append(Lens(f=30, diameter=100, label="Condenser"))
illumination.append(Space(d=30+7))
illumination.appen... | diff --git a/raytracing/figure.py b/raytracing/figure.py
index a0b9014..dee5eb4 100644
--- a/raytracing/figure.py
+++ b/raytracing/figure.py
@@ -180,6 +180,8 @@ class Figure:
conjugates = self.path.intermediateConjugates()
if len(conjugates) != 0:
for (planePosition, magnification) in con... |
DCC-Lab__RayTracing-273 | [
{
"changes": {
"added_entities": [
"raytracing/matrix.py:Matrix.isIdentity"
],
"added_modules": null,
"edited_entities": [
"raytracing/matrix.py:Matrix.mul_matrix",
"raytracing/matrix.py:Matrix.mul_ray",
"raytracing/matrix.py:Space.transferMatrix"
],... | DCC-Lab/RayTracing | 92c62c400ca31119d4896422f4fba2bd030d3739 | Matrix multiplication returns a matrix with n1 = n2 = 1
I don't really know what we should do: in some cases, both matrices have the same n1 and n2, then the result should have n1 and n2. But sometimes they differ. I saw it happen in `MatrixGroup` when we append and build a transfer matrix: we create an identity matrix... | diff --git a/raytracing/matrix.py b/raytracing/matrix.py
index ff6293f..5878f23 100644
--- a/raytracing/matrix.py
+++ b/raytracing/matrix.py
@@ -136,6 +136,10 @@ class Matrix(object):
self.isFlipped = False
super(Matrix, self).__init__()
+ @property
+ def isIdentity(self):
+ return self... |
DCC-Lab__RayTracing-280 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "raytracing/__main__.py"
},
{
"changes": {
"added_entities": [
"raytracing/figure.py:MatrixGraphic.halfHeight",
"raytracing/figur... | DCC-Lab/RayTracing | 0da4c11f47ae13a1db8272b8edc52387ad1863dd | demo #3-13-16-18-19 not working with 1.2.10
I installed raytracing with pip.
i called "python -m raytracing"
demo 1 and 2 worked, but not 3, so others didnt display.
i called every demo 1 by 1 to see which one is working.
It looks like some demos are not displaying correclty (i think).
| diff --git a/raytracing/__main__.py b/raytracing/__main__.py
index 1db0a3d..dd34f4f 100644
--- a/raytracing/__main__.py
+++ b/raytracing/__main__.py
@@ -1,5 +1,6 @@
from .imagingpath import *
from .laserpath import *
+from .lasercavity import *
from .specialtylenses import *
from .axicon import *
@@ -392,7 +393,7... |
DCC-Lab__RayTracing-282 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"raytracing/matrix.py:Matrix.__init__"
],
"edited_modules": [
"raytracing/matrix.py:Matrix"
]
},
"file": "raytracing/matrix.py"
}
] | DCC-Lab/RayTracing | 0da4c11f47ae13a1db8272b8edc52387ad1863dd | Matrix accepts a negative aperture diameter
This doesn't make any sense. Even the doc specifies that it must be positive. | diff --git a/raytracing/matrix.py b/raytracing/matrix.py
index 2f8ff11..7f32c1b 100644
--- a/raytracing/matrix.py
+++ b/raytracing/matrix.py
@@ -122,6 +122,8 @@ class Matrix(object):
# Length of this element
self.L = float(physicalLength)
# Aperture
+ if apertureDiameter <= 0:
+ ... |
DCC-Lab__RayTracing-293 | [
{
"changes": {
"added_entities": [
"raytracing/axicon.py:Axicon.mul_matrix",
"raytracing/axicon.py:Axicon.mul_beam"
],
"added_modules": null,
"edited_entities": [
"raytracing/axicon.py:Axicon.__init__",
"raytracing/axicon.py:Axicon.deviationAngle",
... | DCC-Lab/RayTracing | 0574559c65ccce3efb17d36176d0985c9c20a781 | Axicon does not change the values of backIndex and frontIndex
The `Axicon` class does not change the default values of `backIndex` and `frontIndex` with the input value `n`. | diff --git a/raytracing/axicon.py b/raytracing/axicon.py
index 4bf6013..680a686 100644
--- a/raytracing/axicon.py
+++ b/raytracing/axicon.py
@@ -2,130 +2,170 @@ from .matrix import *
import matplotlib.pyplot as plt
-
class Axicon(Matrix):
- """
- This class is an advanced module that describes an axicon lens, not... |
DHI__mikeio-227 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mikeio/dfs.py:_Dfs123._read_header"
],
"edited_modules": [
"mikeio/dfs.py:_Dfs123"
]
},
"file": "mikeio/dfs.py"
},
{
"changes": {
"added_entities": null,
... | DHI/mikeio | 50037f2b193fe644aeebe4c5fee3e1d02821c488 | end_time property does not work in dfs0
https://github.com/DHI/mikeio/blob/ed60b7caeb1e2a2003266a69607157f2f3302c20/mikeio/dfs0.py#L424
Will throw an error since _end_time is not defined. Its implementation should be similar to that in dfs.py as it depends on the type of TimeAxis. | diff --git a/mikeio/dfs.py b/mikeio/dfs.py
index cd60dacc..36b7e482 100644
--- a/mikeio/dfs.py
+++ b/mikeio/dfs.py
@@ -1,4 +1,4 @@
-from datetime import datetime, timedelta
+from datetime import datetime
from abc import abstractmethod
import warnings
@@ -12,7 +12,7 @@ from .dfsutil import _valid_item_numbers, _vali... |
DHI__mikeio-238 | [
{
"changes": {
"added_entities": [
"mikeio/dataset.py:Dataset.__setitem__"
],
"added_modules": null,
"edited_entities": [
"mikeio/dataset.py:Dataset.__getitem__",
"mikeio/dataset.py:Dataset._add_dataset",
"mikeio/dataset.py:Dataset._check_datasets_match",
... | DHI/mikeio | 1805f86b1e3e2f6c9946759f99e9bdf957be9347 | Dataset item assignment
| diff --git a/mikeio/dataset.py b/mikeio/dataset.py
index b447f1c7..39255424 100644
--- a/mikeio/dataset.py
+++ b/mikeio/dataset.py
@@ -162,31 +162,44 @@ class Dataset(TimeSeries):
def __len__(self):
return len(self.items)
- def __getitem__(self, x):
+ def __setitem__(self, key, value):
- ... |
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