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 |
|---|---|---|---|---|---|
Sage-Bionetworks__Genie-464 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"genie_registry/clinical.py:_check_int_year_consistency"
],
"edited_modules": [
"genie_registry/clinical.py:_check_int_year_consistency"
]
},
"file": "genie_registry/cli... | Sage-Bionetworks/Genie | bdeacb848e48ddadc1652b6572d6a5deb5f37869 | Modify vital status inconsistency check
One site reports that they are able to supply the YEAR but not INT of the vital status values.
Therefore, should allow for a numeric year and `Unknown` INT pattern for both death and contact variable pairs. | diff --git a/genie_registry/clinical.py b/genie_registry/clinical.py
index cbf1a42..cac16e4 100644
--- a/genie_registry/clinical.py
+++ b/genie_registry/clinical.py
@@ -140,8 +140,14 @@ def _check_int_year_consistency(
for str_val in string_vals:
# n string values per row
n_str = (clinicaldf[cols... |
Sage-Bionetworks__challengeutils-143 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"challengeutils/__main__.py:command_mirrorwiki",
"challengeutils/__main__.py:build_parser"
],
"edited_modules": [
"challengeutils/__main__.py:command_mirrorwiki",
"cha... | Sage-Bionetworks/challengeutils | d6b6bcd33637859ca79a14fc56c1f57f1554655f | Refactor mirrorwiki
Add tests
implement a 'dry run' for mirroring the wiki
It would be nice to have a 'test' run of mirroring to indicate what would happen without actually making any changes. | diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 5db2751..6589b67 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -1,7 +1,7 @@
# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more infor... |
Sage-Bionetworks__challengeutils-165 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"challengeutils/challenge.py:ChallengeApi.create_challenge",
"challengeutils/challenge.py:ChallengeApi.update_challenge"
],
"edited_modules": [
"challengeutils/challenge.py:Ch... | Sage-Bionetworks/challengeutils | d6b6bcd33637859ca79a14fc56c1f57f1554655f | Add tests to cli
```
---------- coverage: platform darwin, python 3.7.6-final-0 -----------
Name Stmts Miss Cover
------------------------------------------------------------------------
challengeutils/__init__.py 3 0 100%
chal... | diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 5db2751..6589b67 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -1,7 +1,7 @@
# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more infor... |
Sage-Bionetworks__challengeutils-169 | [
{
"changes": {
"added_entities": [
"challengeutils/discussion.py:_copy_thread"
],
"added_modules": [
"challengeutils/discussion.py:_copy_thread"
],
"edited_entities": [
"challengeutils/discussion.py:copy_thread",
"challengeutils/discussion.py:copy_fo... | Sage-Bionetworks/challengeutils | d6b6bcd33637859ca79a14fc56c1f57f1554655f | copy_thread should also copy replies
Currently the logic in copying threads and replies are in copy_forum. Update copy threads to have copy replies:
```python
import synapseclient
syn = synapseclient.login
discussion_cls = challengeutils.discussion.DiscussionApi(syn)
thread_dict = discussion_cls.get_thread({threa... | diff --git a/challengeutils/discussion.py b/challengeutils/discussion.py
index 1a32828..46b507e 100644
--- a/challengeutils/discussion.py
+++ b/challengeutils/discussion.py
@@ -357,6 +357,23 @@ def create_thread_reply(syn, threadid, message):
def copy_thread(syn, thread, project):
+ """Copies a discussion threa... |
Sage-Bionetworks__challengeutils-171 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"challengeutils/challenge.py:ChallengeApi.create_challenge",
"challengeutils/challenge.py:ChallengeApi.update_challenge"
],
"edited_modules": [
"challengeutils/challenge.py:Ch... | Sage-Bionetworks/challengeutils | 0b2129349fef07c072f9dc0d42c7de8485e3cc57 | createchallenge does not work!
**Describe the bug**
creating a challenge object used to use the `Challenge` class, but restPOST does not like 'None' values.
**To Reproduce**
```
syn.restPOST('/challenge', str(new_challenge))
--------------------------------------------------------------... | diff --git a/LICENSE b/LICENSE
index 261eeb9..8b9a0c6 100644
--- a/LICENSE
+++ b/LICENSE
@@ -186,7 +186,7 @@
same "printed page" as the copyright notice for easier
identification within third-party archives.
- Copyright [yyyy] [name of copyright owner]
+ Copyright 2017 Sage Bionetworks
License... |
Sage-Bionetworks__challengeutils-197 | [
{
"changes": {
"added_entities": [
"challengeutils/utils.py:remove_team_member"
],
"added_modules": [
"challengeutils/utils.py:remove_team_member"
],
"edited_entities": null,
"edited_modules": null
},
"file": "challengeutils/utils.py"
}
] | Sage-Bionetworks/challengeutils | 81b0e0f78ffe9c96106dbcc6d3e49ae0c2dcc3f2 | removal of members from a Team | diff --git a/challengeutils/utils.py b/challengeutils/utils.py
index 984eae1..33e3d6c 100644
--- a/challengeutils/utils.py
+++ b/challengeutils/utils.py
@@ -11,6 +11,7 @@ import synapseclient
from synapseclient.annotations import (is_submission_status_annotations,
to_submission_... |
Sage-Bionetworks__challengeutils-247 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"challengeutils/submission.py:_validate_public_permissions",
"challengeutils/submission.py:_validate_admin_permissions"
],
"edited_modules": [
"challengeutils/submission.py:_v... | Sage-Bionetworks/challengeutils | 51915b06f431df229ad41ade949291f60950bf85 | `--admin` check for `validate-project` does not work as expected
**Describe the bug**
The project associated with submission ID 9731653 is a publicly accessible Synapse project, but comes back as INVALID when `--admin <some user/team>` is flagged. e.g.
```
$ challengeutils validate-project 9731653 syn28590455 --... | diff --git a/challengeutils/submission.py b/challengeutils/submission.py
index 6a625d0..3c3c74e 100644
--- a/challengeutils/submission.py
+++ b/challengeutils/submission.py
@@ -103,18 +103,14 @@ def validate_project(syn, submission, challenge, public=False, admin=None):
"""
writeup = syn.getSubmission(submiss... |
Sage-Bionetworks__synapsePythonClient-1139 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"synapseclient/core/download/download_functions.py:download_from_url"
],
"edited_modules": [
"synapseclient/core/download/download_functions.py:download_from_url"
]
},
"... | Sage-Bionetworks/synapsePythonClient | 1918ec2a667570637fa9c16a459bb55879c1e1d5 | KeyError: 'X-Amz-Date' when trying to download HTAN data
Hi team,
I've been trying to download some HTAN data, but have been unable to due to a dict KeyError.
Thank you in advance for your help,
Nikolas
# Operating system
RHEL 8.6
# Client version
4.5.1, Python 3.12 (replicated error in Python 3.9)
... | diff --git a/synapseclient/core/download/download_async.py b/synapseclient/core/download/download_async.py
index 3c8ca557..748c309d 100644
--- a/synapseclient/core/download/download_async.py
+++ b/synapseclient/core/download/download_async.py
@@ -214,6 +214,7 @@ def _generate_chunk_ranges(
def _pre_signed_url_expirati... |
Sage-Bionetworks__synapsePythonClient-950 | [
{
"changes": {
"added_entities": [
"synapseclient/client.py:Synapse.is_synapse_id"
],
"added_modules": null,
"edited_entities": [
"synapseclient/client.py:Synapse.get_download_list"
],
"edited_modules": [
"synapseclient/client.py:Synapse"
]
}... | Sage-Bionetworks/synapsePythonClient | 4362d1ec51639383383966a489160c8ff4d20b76 | [Feature request] Add `is_synapse_id` to the client
# Feature Request
Add a helper function to the client that will allow checking whether a given string is a valid Synapse ID. A "valid" synID must:
* have the expected format of `syn[0-9]+`
* be linked to an actual Synapse entity, that is, "syn123" is not a rea... | diff --git a/synapseclient/client.py b/synapseclient/client.py
index 1f7a4c0d..0034732a 100644
--- a/synapseclient/client.py
+++ b/synapseclient/client.py
@@ -626,6 +626,24 @@ class Synapse(object):
return False
raise
+ def is_synapse_id(self, syn_id: str) -> bool:
+ """Checks ... |
SathyaBhat__spotify-dl-311 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"spotify_dl/spotify_dl.py:spotify_dl"
],
"edited_modules": [
"spotify_dl/spotify_dl.py:spotify_dl"
]
},
"file": "spotify_dl/spotify_dl.py"
},
{
"changes": {
... | SathyaBhat/spotify-dl | 403547b8f73cfafba6f39d421aae419b29259d1d | Error SponsorBlock
The system downloads but does not convert to mp3 due to the error below, is there a way to skip this check?
Because it does not convert and is in webm format
[SponsorBlock] Fetching SponsorBlock segments
WARNING: Unable to communicate with SponsorBlock API: The read operation timed out. Retrying... | diff --git a/README.md b/README.md
index 1384fe5..b1752c0 100644
--- a/README.md
+++ b/README.md
@@ -30,6 +30,10 @@ If you want to make use of parallel download, pass `-mc <number>`, where `<numbe
spotify_dl -mc 4 -l spotify_playlist_link_1 spotify_playlist_link_2
+Spotify-dl can make use of SponsorBlock an... |
SathyaBhat__spotify-dl-368 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"spotify_dl/spotify.py:fetch_tracks"
],
"edited_modules": [
"spotify_dl/spotify.py:fetch_tracks"
]
},
"file": "spotify_dl/spotify.py"
},
{
"changes": {
"ad... | SathyaBhat/spotify-dl | b56afb2b459b93245dede75b7c27fd46753707ff | Add BPM to metadata of MP3 songs.
Since adding BPM to the metadata of the MP3 is an option provided with the Spotify API and mutagen supports it as well. This feature could help with many who are in the field of DJ Mixing.
| diff --git a/spotify_dl/spotify.py b/spotify_dl/spotify.py
index f777a59..448d5e4 100644
--- a/spotify_dl/spotify.py
+++ b/spotify_dl/spotify.py
@@ -42,8 +42,14 @@ def fetch_tracks(sp, item_type, item_id):
continue
track_album_info = track_info.get("album")
... |
Sceptre__sceptre-1219 | [
{
"changes": {
"added_entities": [
"sceptre/diffing/stack_differ.py:StackDiffer._extract_parameters_from_generated_stack",
"sceptre/diffing/stack_differ.py:StackDiffer._remove_terminating_linebreaks_from_deployed_parameters"
],
"added_modules": null,
"edited_entities": [
... | Sceptre/sceptre | 3ed957f22889a197f4b4ec585ef243a6cf34eb24 | `Sceptre diff` creates false-positives when Stack parameter ends with linebreak
### Subject of the issue
Right now, running `sceptre diff` will report that there _is_ a difference when there isn't when the parameter value ends with a line break, such as when you use the !file_contents resolver for a parameter value.
... | diff --git a/sceptre/diffing/stack_differ.py b/sceptre/diffing/stack_differ.py
index 69011c6..87931e1 100644
--- a/sceptre/diffing/stack_differ.py
+++ b/sceptre/diffing/stack_differ.py
@@ -1,7 +1,7 @@
import difflib
import logging
from abc import abstractmethod
-from typing import NamedTuple, Dict, List, Optional, C... |
Sceptre__sceptre-1246 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/cli/drift.py:drift_show"
],
"edited_modules": [
"sceptre/cli/drift.py:drift_show"
]
},
"file": "sceptre/cli/drift.py"
},
{
"changes": {
"added_ent... | Sceptre/sceptre | 45629a5530b16e7f439bd3ba2f6e68cddf551506 | It'd be great if `drift show` had an option to filter out IN_SYNC resources.
Right now, when `drift show` is run, it shows the drift status of all the resources in all stacks. However, this is a bit overload if you're really just trying to find drifted resources. It would be a great addition if we added a `--filter` f... | diff --git a/sceptre/cli/drift.py b/sceptre/cli/drift.py
index 9aab47d..282d9b8 100644
--- a/sceptre/cli/drift.py
+++ b/sceptre/cli/drift.py
@@ -68,9 +68,12 @@ def drift_detect(ctx: Context, path: str):
@drift_group.command(name="show", short_help="Shows stack drift on running stacks.")
@click.argument("path")
+@cl... |
Sceptre__sceptre-1249 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/resolvers/__init__.py:ResolvableContainerProperty.get_resolved_value"
],
"edited_modules": [
"sceptre/resolvers/__init__.py:ResolvableContainerProperty"
]
},
"f... | Sceptre/sceptre | 880fba9bd11e5167adfee0167608aede2439228a | Sceptre fails when multiple resolvers return None
### Sceptre fails when multiple resolvers return None
When multiple resolvers in a stack config return None sceptre fails.
### Your environment
* version of sceptre (3.1.0)
* version of python (3.8.10)
* which OS/distro -- windows 10, linux
### Steps to reprod... | diff --git a/sceptre/resolvers/__init__.py b/sceptre/resolvers/__init__.py
index 5dde952..1515d61 100644
--- a/sceptre/resolvers/__init__.py
+++ b/sceptre/resolvers/__init__.py
@@ -238,8 +238,19 @@ class ResolvableContainerProperty(ResolvableProperty):
resolve, container, Resolver
)
# Rem... |
Sceptre__sceptre-1277 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/template_handlers/http.py:Http._get_template"
],
"edited_modules": [
"sceptre/template_handlers/http.py:Http"
]
},
"file": "sceptre/template_handlers/http.py"
... | Sceptre/sceptre | ebe7c25295b5dcf5da8aef3bcc050623f5641d7b | Better error handling with invalid templates
### Subject of the issue
The template handler does not provide a helpful message when sceptre cannot resolve a template from an http source. It would be nice to improve the error handling for that.
### Your environment
* version of sceptre: 3.1
* version of python: 3... | diff --git a/sceptre/template_handlers/http.py b/sceptre/template_handlers/http.py
index 31ac126..983e228 100644
--- a/sceptre/template_handlers/http.py
+++ b/sceptre/template_handlers/http.py
@@ -1,15 +1,15 @@
# -*- coding: utf-8 -*-
import pathlib
-import requests
import tempfile
-import sceptre.template_handlers.... |
Sceptre__sceptre-1296 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/context.py:SceptreContext.__init__"
],
"edited_modules": [
"sceptre/context.py:SceptreContext"
]
},
"file": "sceptre/context.py"
}
] | Sceptre/sceptre | 855a030c7cff5ffb7dc447c14ab0ae9d9befa267 | Intermittent AttributeError when resolving dependencies using the sceptre.plan.plan module.
### Subject of the issue
Hello,
I've got an intermittent AttributeError when resolving dependencies using the sceptre.plan.plan module. It only occurs when using a particular hierarchy of dependencies. The error does not o... | diff --git a/sceptre/context.py b/sceptre/context.py
index c958c97..73b86f9 100644
--- a/sceptre/context.py
+++ b/sceptre/context.py
@@ -60,7 +60,7 @@ class SceptreContext(object):
):
# project_path: absolute path to the base sceptre project folder
# e.g. absolute_path/to/sceptre_directory
- ... |
Sceptre__sceptre-1333 | [
{
"changes": {
"added_entities": [
"sceptre/config/reader.py:ConfigReader._read"
],
"added_modules": null,
"edited_entities": [
"sceptre/config/reader.py:ConfigReader.construct_stacks",
"sceptre/config/reader.py:ConfigReader.read",
"sceptre/config/reader.p... | Sceptre/sceptre | cb118579367adf28f887fa604c47f2d4be1abed0 | The dump config command is not loading the j2_environment
### Subject of the issue
Given a stack with custom `j2_environment`, this is not loaded or available during the `dump config` command.
### Your environment
* version of sceptre - latest
* version of python - 3.10
* which OS/distro - Debian
### Steps to... | diff --git a/sceptre/config/reader.py b/sceptre/config/reader.py
index f618d87..4b371a6 100644
--- a/sceptre/config/reader.py
+++ b/sceptre/config/reader.py
@@ -102,14 +102,6 @@ STACK_CONFIG_ATTRIBUTES = ConfigAttributes(
},
)
-INTERNAL_CONFIG_ATTRIBUTES = ConfigAttributes(
- {
- "project_path",
- ... |
Sceptre__sceptre-1337 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/diffing/stack_differ.py:StackDiffer._extract_parameters_from_generated_stack"
],
"edited_modules": [
"sceptre/diffing/stack_differ.py:StackDiffer"
]
},
"file": ... | Sceptre/sceptre | cb118579367adf28f887fa604c47f2d4be1abed0 | Stack differ raises if a value is None
### Subject of the issue
The Stack Differ raises an exception if a parameter value is None.
### Your environment
* version of sceptre - master branch
* version of python (python --version) - 3.10
* which OS/distro - Ubuntu
### Steps to reproduce
Create a config like thi... | diff --git a/sceptre/diffing/stack_differ.py b/sceptre/diffing/stack_differ.py
index eeb942e..6712aa6 100644
--- a/sceptre/diffing/stack_differ.py
+++ b/sceptre/diffing/stack_differ.py
@@ -167,6 +167,12 @@ class StackDiffer(Generic[DiffType]):
"""
formatted_parameters = {}
for key, value in s... |
Sceptre__sceptre-1357 | [
{
"changes": {
"added_entities": [
"sceptre/cli/list.py:write_outputs"
],
"added_modules": [
"sceptre/cli/list.py:write_outputs"
],
"edited_entities": [
"sceptre/cli/list.py:list_outputs"
],
"edited_modules": [
"sceptre/cli/list.py:list_o... | Sceptre/sceptre | 64ab818cb9be16276689932b7a15072c3fa6c86e | Stack outputs in stack groups hide the stack names
### An export format for stack outputs that shows stack name is needed
The main purpose of stack outputs is to consume them in other stacks. Example:
```yaml
VpcId: !stack_output network.yaml::VpcId
```
or in a var file:
```yaml
VpcId: '!stack_output_exter... | diff --git a/sceptre/cli/list.py b/sceptre/cli/list.py
index 6f11bd2..c9b7b0c 100644
--- a/sceptre/cli/list.py
+++ b/sceptre/cli/list.py
@@ -5,6 +5,8 @@ from sceptre.context import SceptreContext
from sceptre.cli.helpers import catch_exceptions, write
from sceptre.plan.plan import SceptrePlan
+from typing import Li... |
Sceptre__sceptre-1372 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/hooks/cmd.py:Cmd.run"
],
"edited_modules": [
"sceptre/hooks/cmd.py:Cmd"
]
},
"file": "sceptre/hooks/cmd.py"
}
] | Sceptre/sceptre | 64ab818cb9be16276689932b7a15072c3fa6c86e | !cmd hook runs in `sh`, which is not my default shell
### Subject of the issue
When I use a `!cmd` hook, it appears to be run by `sh` because I receive this error:
```shell
/bin/sh: 1: [[: not found
```
Is there a way to force the underlying `subprocess.run()` call to use Python? I know I can do this in Pytho... | diff --git a/docs/_source/docs/hooks.rst b/docs/_source/docs/hooks.rst
index a1eeef6..9a3bc82 100644
--- a/docs/_source/docs/hooks.rst
+++ b/docs/_source/docs/hooks.rst
@@ -44,23 +44,105 @@ Available Hooks
cmd
~~~
-Executes the argument string in the shell as a Python subprocess.
-
-For more information about how t... |
Sceptre__sceptre-1391 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/resolvers/stack_output.py:StackOutput.setup",
"sceptre/resolvers/stack_output.py:StackOutputExternal.resolve"
],
"edited_modules": [
"sceptre/resolvers/stack_output.p... | Sceptre/sceptre | 3f16beda2a51db8bf7b7de87fbaad2582387897f | Not enough values to unpack given a badly formatted stack ref
### Subject of the issue
If a stack output is incorrectly formatted, and missing `::`, a confusing and unhandled exception is seen:
```
[2023-11-24 01:53:39] - REDACTED - Successfully initiated creation of Change Set 'sceptre-foundations-3551-834819d897... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9c25517..da8c1e4 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -47,7 +47,7 @@ repos:
language_version: python3.10
args: ['--check']
- repo: https://github.com/sirosen/check-jsonschema
- rev: 0.27.3
+ ... |
Sceptre__sceptre-1437 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/diffing/stack_differ.py:StackDiffer._extract_parameters_from_generated_stack",
"sceptre/diffing/stack_differ.py:DeepDiffStackDiffer.__init__",
"sceptre/diffing/stack_differ.py:Di... | Sceptre/sceptre | b91915f6ee1126fcc2b264bde1af043f76c0ad6b | Stack differ raises AttributeError if a values is a bool
### Subject of the issue
This relates to an earlier issue
https://github.com/Sceptre/sceptre/issues/1336
The Stack Differ raises an exception if a parameter value is of type bool.
It apparently would also fail if a parameter value is of any type other str.... | diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index b3cd598..08fb35b 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -85,7 +85,7 @@ $ git clone git@github.org:<github_username>/sceptre.git
[virtual environment](http://docs.python-guide.org/en/latest/dev/virtualenvs/))
```bash
- $ poetry install --all-ex... |
Sceptre__sceptre-1442 | [
{
"changes": {
"added_entities": [
"sceptre/stack.py:Stack._ensure_parameters"
],
"added_modules": null,
"edited_entities": [
"sceptre/stack.py:Stack.__init__"
],
"edited_modules": [
"sceptre/stack.py:Stack"
]
},
"file": "sceptre/stack.py... | Sceptre/sceptre | 68db2e0bc0579e89ab64b408d328205eaa4dac1d | Input parameters should be validated
### Subject of the issue
For historical reasons, Sceptre has never validated input parameters that are passed in to CloudFormation stack parameters. Blocks that contain bools, ints etc give rise to confusing failures. For example:
```yaml
parameters:
someBool: true
```
W... | diff --git a/sceptre/stack.py b/sceptre/stack.py
index 8a63309..fa5639a 100644
--- a/sceptre/stack.py
+++ b/sceptre/stack.py
@@ -9,7 +9,7 @@ This module implements a Stack class, which stores a Stack's data.
import logging
-from typing import List, Any, Optional
+from typing import List, Dict, Union, Any, Optional... |
Sceptre__sceptre-1445 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/config/graph.py:StackGraph._generate_edges"
],
"edited_modules": [
"sceptre/config/graph.py:StackGraph"
]
},
"file": "sceptre/config/graph.py"
},
{
"cha... | Sceptre/sceptre | 08f64759c4fa1e100aed52e17d5f3f54ba0f4e9b | feature request: append stack_tag inheritance
Currently stack_tags inheritance strategy is override which means that stack tags can be defined in a Sceptre StackGroup and then overridden in the a child StackGroup or Stack config. I would like to make a feature request to append stack_tags on a dependencies.
Exa... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ace46ff..95677b3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
hooks:
- id: yamllint
- repo: https://github.com/awslabs/cfn-python-lint
- rev: v0.85.2
+ rev: v0.86.0
hooks:
... |
Sceptre__sceptre-1471 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/config/reader.py:ConfigReader._render"
],
"edited_modules": [
"sceptre/config/reader.py:ConfigReader"
]
},
"file": "sceptre/config/reader.py"
},
{
"chan... | Sceptre/sceptre | bac2c2b49df238df3c9ab8b9613b56cebc994f8b | Reimplement #1443 - parameter Schema Validation
### Subject of the issue
In already-resolved and merged issue #1443 we implemented parameter validation. In Slack, we then discussed a preferred implementation of using instead a parameter Schema Validator.
This issue tracks possible reimplementation of this feature.... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5daa10b..d6f8dbb 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ repos:
- id: mixed-line-ending
- id: trailing-whitespace
- repo: https://github.com/PyCQA/flake8
- rev: 7.0.0
+ rev: 7.1.0
... |
Sceptre__sceptre-1480 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/cli/update.py:update_command"
],
"edited_modules": [
"sceptre/cli/update.py:update_command"
]
},
"file": "sceptre/cli/update.py"
},
{
"changes": {
... | Sceptre/sceptre | deef08e31911493ac18220bf9ed46218210cb94d | Update with change sets for multiple stacks fails unless all cause updates
`update -c xxx` fails if there are multiple stacks resolved, and not all have updates (i.e. generates valid change sets). This is due to not all change sets statuses being READY, so it bails with `exit(1)`.
Party covered in #520, but this is ... | diff --git a/sceptre/cli/update.py b/sceptre/cli/update.py
index 35d4239..f685ecc 100644
--- a/sceptre/cli/update.py
+++ b/sceptre/cli/update.py
@@ -61,14 +61,33 @@ def update_command(
try:
# Wait for change set to be created
statuses = plan.wait_for_cs_completion(change_set_name)
- ... |
Sceptre__sceptre-1485 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/stack.py:Stack._cast_parameters"
],
"edited_modules": [
"sceptre/stack.py:Stack"
]
},
"file": "sceptre/stack.py"
}
] | Sceptre/sceptre | c06b3b5816a6ecb29cd9d1c4cd34eee19f8be642 | Sceptre should handle invalid types passed to the parameters dict gracefully
### Subject of the issue
All commands raise exceptions if `parameters` is a list instead of a dict. This did not occur in v4.4.2 and relates to the cast parameters feature.
### Your environment
* version of sceptre (sceptre --version) mas... | diff --git a/sceptre/stack.py b/sceptre/stack.py
index f085ced..7990e81 100644
--- a/sceptre/stack.py
+++ b/sceptre/stack.py
@@ -305,6 +305,11 @@ class Stack:
or isinstance(value, Resolver)
)
+ if not isinstance(parameters, dict):
+ raise InvalidConfigFileError(
+ ... |
Sceptre__sceptre-1494 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/plan/actions.py:StackActions.update"
],
"edited_modules": [
"sceptre/plan/actions.py:StackActions"
]
},
"file": "sceptre/plan/actions.py"
}
] | Sceptre/sceptre | deef08e31911493ac18220bf9ed46218210cb94d | DisableRollback not fully implemented in stack updates
### Subject of the issue
DisableRollback is handled only during the creation of a stack and not for stack updates. This appears to be an oversight. It is already half-implemented in the CLI.
### Your environment
* version of sceptre (sceptre --version)
* vers... | diff --git a/sceptre/cli/update.py b/sceptre/cli/update.py
index 35d4239..1502422 100644
--- a/sceptre/cli/update.py
+++ b/sceptre/cli/update.py
@@ -41,6 +41,7 @@ def update_command(
:type verbose: bool
:param yes: A flag to answer 'yes' to all CLI questions.
:type yes: bool
+ :param disable_rollback:... |
Sceptre__sceptre-1513 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sceptre/plan/actions.py:StackActions._log_new_events"
],
"edited_modules": [
"sceptre/plan/actions.py:StackActions"
]
},
"file": "sceptre/plan/actions.py"
}
] | Sceptre/sceptre | 417f599ec7371078d53701946f8a192fbc73e324 | Cloudformation Hook Status message in sceptre output is confusing
The cloudformation hook status reason and hook mode displayed as a part of sceptre cloudformation log is misleading.
As it appends the HookMode to the Hook Message, if the mode is FAIL and the hooks message is successful, it display as Hook Execution is... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7781568..87c1b23 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
hooks:
- id: yamllint
- repo: https://github.com/awslabs/cfn-python-lint
- rev: v1.12.4
+ rev: v1.15.0
hooks:
... |
SciCatProject__scitacean-148 | [
{
"changes": {
"added_entities": [
"src/scitacean/client.py:ScicatClient.validate_dataset_model"
],
"added_modules": null,
"edited_entities": [
"src/scitacean/client.py:Client.upload_new_dataset_now"
],
"edited_modules": [
"src/scitacean/client.py:Clie... | SciCatProject/scitacean | 8536a832fa36d4c9b4a16b91ee9fd74675c6d4b3 | Validate dataset with backend before upload
As discussed in #55, when the new backend is out, we should ask the backend if a dataset is valid before uploading any files. | diff --git a/src/scitacean/client.py b/src/scitacean/client.py
index 8c68c4b..9c461e1 100644
--- a/src/scitacean/client.py
+++ b/src/scitacean/client.py
@@ -249,7 +249,7 @@ class Client:
dataset = dataset.replace(
source_folder=self._expect_file_transfer().source_folder_for(dataset)
)
- ... |
SciCatProject__scitacean-150 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/scitacean/_dataset_fields.py:DatasetBase.type"
],
"edited_modules": [
"src/scitacean/_dataset_fields.py:DatasetBase"
]
},
"file": "src/scitacean/_dataset_fields.py"... | SciCatProject/scitacean | 88b3318cf1457dafc48adbffbad9a4c25767d952 | Make `dataset.type` read-only
It seems strange and error-prone that it is possible to change the `type` of a dataset. In particular because it can lead to datasets that have the wrong fields set. Is there a valid use case for it? | diff --git a/src/scitacean/_dataset_fields.py b/src/scitacean/_dataset_fields.py
index fa97195..a577e27 100644
--- a/src/scitacean/_dataset_fields.py
+++ b/src/scitacean/_dataset_fields.py
@@ -1054,11 +1054,6 @@ class DatasetBase:
"""Characterize type of dataset, either 'raw' or 'derived'. Autofilled when choo... |
SciCatProject__scitacean-153 | [
{
"changes": {
"added_entities": [
"src/scitacean/dataset.py:Dataset.keys",
"src/scitacean/dataset.py:Dataset.values",
"src/scitacean/dataset.py:Dataset.items",
"src/scitacean/dataset.py:Dataset._validate_field_name",
"src/scitacean/dataset.py:Dataset.__getitem__",
... | SciCatProject/scitacean | 62c757efa828a9de487b93f2acc77a921e5b58ac | dict-like API for Dataset
`Dataset.fields` is not very user friendly for iterating over values.
- Add methods like `keys`, `values`, etc.
- Should we also have __getitem__? | diff --git a/docs/release-notes.rst b/docs/release-notes.rst
index 96342da..23329aa 100644
--- a/docs/release-notes.rst
+++ b/docs/release-notes.rst
@@ -41,6 +41,9 @@ Security
Features
~~~~~~~~
+* Added dict-like methods, :meth:`Dataset.keys`, :meth:`Dataset.values` and :meth:`Dataset.items`.
+* Added dict-like ite... |
SciCatProject__scitacean-159 | [
{
"changes": {
"added_entities": [
"src/scitacean/client.py:Client._source_folder_for",
"src/scitacean/client.py:_files_to_upload",
"src/scitacean/client.py:_NullUploadConnection.upload_files",
"src/scitacean/client.py:_NullUploadConnection.revert_upload"
],
"ad... | SciCatProject/scitacean | effa5ca04e1eaa4908c9af1c01e945a92dd21ef1 | Allow uploading a dataset without uploading files
There are cases where it is not possible to upload files with Scitacean because of complicated permissions on the file server. In these cases, it would be useful to only upload the metadata with Scitacean.
This can be done by adding files with `Dataset.add_files` and... | diff --git a/docs/_templates/scitacean-class-template.rst b/docs/_templates/scitacean-class-template.rst
index c60a129..45f2086 100644
--- a/docs/_templates/scitacean-class-template.rst
+++ b/docs/_templates/scitacean-class-template.rst
@@ -2,7 +2,7 @@
{% set constructors = {"Client": ["from_credentials", "from_toke... |
SciCatProject__scitacean-184 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "src/scitacean/__init__.py"
},
{
"changes": {
"added_entities": [
"src/scitacean/client.py:Client.get_sample",
"src/scitacean/cli... | SciCatProject/scitacean | 2dbb7f7d0d07b705ab4c0fc0b7fb10f2c7f4a8f6 | Support Sample
We already have the models. All that's missing are functions in the clients. | diff --git a/docs/release-notes.rst b/docs/release-notes.rst
index 95f32bf..9685594 100644
--- a/docs/release-notes.rst
+++ b/docs/release-notes.rst
@@ -41,6 +41,8 @@ Security
Features
~~~~~~~~
+* Added functions for downloading and uploading samples: :meth:`Client.get_sample`, :meth:`Client.upload_new_sample_now`.... |
SciCatProject__scitacean-262 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/scitacean/client.py:Client.upload_new_dataset_now",
"src/scitacean/client.py:_files_to_upload"
],
"edited_modules": [
"src/scitacean/client.py:Client",
"src/scita... | SciCatProject/scitacean | ca36437f0fe762622881fdb2e464c6171620dfeb | Upload: Prevent files outside of source folder
When uploading, all files should go into a dataset's source folder. This needs to be guaranteed by disallowing any paths that would lead outside of the source folder, e.g., through going up a level: `remote_path=../not-in-source-folder/file'. | diff --git a/src/scitacean/client.py b/src/scitacean/client.py
index 898bd4d..0045b3b 100644
--- a/src/scitacean/client.py
+++ b/src/scitacean/client.py
@@ -277,7 +277,7 @@ class Client:
Note the error message if that happens.
"""
dataset = dataset.replace(source_folder=self._source_folde... |
SciCatProject__scitacean-43 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/scitacean/file.py:File.uploaded",
"src/scitacean/file.py:File.downloaded",
"src/scitacean/file.py:File._validate_after_download_file_size"
],
"edited_modules": [
... | SciCatProject/scitacean | 39fd91c79727d3536fcee00458e126c1f4ebf558 | Do not require matching files size in download / upload
File sizes can vary depending on the block size of the filesystem. With the current setup at ESS, the sizes in datasets are almost always different from the physical file sizes.
So we should not raise an exception if there is a mismatch but simply log a message. | diff --git a/src/scitacean/file.py b/src/scitacean/file.py
index 26e0cc1..8ce3dd0 100644
--- a/src/scitacean/file.py
+++ b/src/scitacean/file.py
@@ -255,6 +255,7 @@ class File:
remote_gid: Optional[str] = None,
remote_perm: Optional[str] = None,
remote_creation_time: Optional[datetime] = None... |
SciCatProject__scitacean-57 | [
{
"changes": {
"added_entities": [
"src/scitacean/client.py:_remove_up_to_date_local_files"
],
"added_modules": [
"src/scitacean/client.py:_remove_up_to_date_local_files"
],
"edited_entities": [
"src/scitacean/client.py:Client.download_files"
],
... | SciCatProject/scitacean | 660b6a58ded9d90c8f3389134c7a4920b4f8cf27 | File caching
I was think if we could implement a rudimentary file caching following this simple workflow:
- user indicate that a local copy of the file is needed by using the provide_locally function
```
dataset.files[x].provide_locally(
local_folder,
downloader=file_transfer_function,
checksum_algori... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4a3c6fd..4d67bf3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,12 +9,6 @@ repos:
- id: detect-private-key
- id: trailing-whitespace
args: [--markdown-linebreak-ext=md]
-- repo: https://github.com/charliermar... |
SciCatProject__scitacean-62 | [
{
"changes": {
"added_entities": [
"src/scitacean/dataset.py:Dataset.as_new",
"src/scitacean/dataset.py:Dataset.derive"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/scitacean/dataset.py:Dataset"
]
},
"file": "src/... | SciCatProject/scitacean | 5e867028a383677007627955c3e83e4cbe21cc98 | Clone dataset
As a user, it would be efficient to have a clone method on a dataset to create a new one which is the exact copy of the original one, but with the necessary lifecycle properties reset, including pid. | diff --git a/docs/release-notes.rst b/docs/release-notes.rst
index c1b4b4b..4cda0d2 100644
--- a/docs/release-notes.rst
+++ b/docs/release-notes.rst
@@ -29,6 +29,28 @@ Release notes
Stability, Maintainability, and Testing
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+vYY.0M.MICRO (Unreleased)
+--------------------... |
SciCatProject__scitacean-83 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/scitacean/_dataset_fields.py:DatasetFields.__init__"
],
"edited_modules": [
"src/scitacean/_dataset_fields.py:DatasetFields"
]
},
"file": "src/scitacean/_dataset_fi... | SciCatProject/scitacean | 9a3dec57db4b6807369f6b80015c40ce8df2f4a3 | Default checksum algorithm
It is annoying to re-download files just because the checksum algorithm has not been set. Instead, try a default algorithm if none is set. The chance of false-positives from using the wrong algorithm should be negligible. | diff --git a/docs/release-notes.rst b/docs/release-notes.rst
index 9f9139f..e70dd5e 100644
--- a/docs/release-notes.rst
+++ b/docs/release-notes.rst
@@ -43,10 +43,13 @@ Features
* Better HTML formatting of ESS-style scientific metadata.
* Added the ``force`` argument to :func:`scitacean.Client.download_files`.
+* T... |
SciLifeLab__genologics-154 | [
{
"changes": {
"added_entities": [
"genologics/entities.py:Process.step",
"genologics/entities.py:StepActions.escalation",
"genologics/entities.py:StepActions.next_actions",
"genologics/entities.py:Step.reagent_lots"
],
"added_modules": [
"genologics/ent... | SciLifeLab/genologics | 33b08db9bc8d85427c79f5e10792b51f10b27a47 | Change to StepActions
Hi,
I need to rework the way Step stores actions and that might results in backward incompatible changes to the API.
I was wondering how much this would affect you and the potential users of the API as it seems to be still work in progress
Cheers
Tim | diff --git a/genologics/entities.py b/genologics/entities.py
index 22e0625..4b7bcf7 100644
--- a/genologics/entities.py
+++ b/genologics/entities.py
@@ -271,7 +271,6 @@ class BaseDescriptor(object):
def __get__(self, instance, cls):
raise NotImplementedError
-
class TagDescriptor(BaseDescriptor):
... |
SciLifeLab__genologics-190 | [
{
"changes": {
"added_entities": [
"genologics/entities.py:Entity._create",
"genologics/entities.py:Sample.create"
],
"added_modules": null,
"edited_entities": [
"genologics/entities.py:Entity.create"
],
"edited_modules": [
"genologics/entities... | SciLifeLab/genologics | dc79dc55dc1218582f30a5e76e9a0fff428cbf30 | Create new samples
Hi guys!
I was wondering how it would be possible to create new samples using the REST API. I got it working using this package but it required some hacking. Perhaps I'm missing something.. Are you using the API to do something like that?
This is briefly my approach:
1. The API needs a "loca... | diff --git a/genologics/entities.py b/genologics/entities.py
index 3cdef28..89c4fd9 100644
--- a/genologics/entities.py
+++ b/genologics/entities.py
@@ -297,10 +297,12 @@ class Entity(object):
self.lims.post(self.uri, data)
@classmethod
- def create(cls, lims, **kwargs):
- """Create an instanc... |
SciTools__cf-units-164 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cf_units/__init__.py:Unit.convert"
],
"edited_modules": [
"cf_units/__init__.py:Unit"
]
},
"file": "cf_units/__init__.py"
}
] | SciTools/cf-units | 02ae952af96766bfe998da0c6856373b62373bee | Casting to integer on conversion
Hi there,
I have a question about behaviour which I was hoping you could help with. It focuses on this comment:
https://github.com/SciTools/cf-units/blob/a3eeaf15622bd3ec6f23c18cbd3b3658086aa7cf/cf_units/__init__.py#L1845
My question is: why isn't this also applied to `np.float... | diff --git a/cf_units/__init__.py b/cf_units/__init__.py
index f43b2e9..5395353 100644
--- a/cf_units/__init__.py
+++ b/cf_units/__init__.py
@@ -1738,10 +1738,12 @@ class Unit(_OrderedHashable):
result, self.cftime_unit, self.calendar)
result = cftime.date2num(
... |
SciTools__nc-time-axis-80 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nc_time_axis/__init__.py:NetCDFTimeConverter.default_units"
],
"edited_modules": [
"nc_time_axis/__init__.py:NetCDFTimeConverter"
]
},
"file": "nc_time_axis/__init__.py... | SciTools/nc-time-axis | 59c567d307eb8ced44f2c95b393c93ba571e486c | Why can't we just visualise a vanilla netcdftime.datetime
I think it is worth putting the rationale here for why we can't handle a calendar-less netcdftime datetime as I'm certain this will come up regularly.
| diff --git a/README.md b/README.md
index d1fc951..132b072 100644
--- a/README.md
+++ b/README.md
@@ -58,18 +58,16 @@ Or `pip`:
import cftime
import matplotlib.pyplot as plt
-
- from nc_time_axis import CalendarDateTime
+ import nc_time_axis
calendar = "360_day"
dt = [
cftime.datet... |
Scille__umongo-170 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"umongo/abstract.py:BaseField.__init__",
"umongo/abstract.py:BaseField._extract_marshmallow_field_params"
],
"edited_modules": [
"umongo/abstract.py:BaseField"
]
},
... | Scille/umongo | 3e765b3aa7250564c2eabddd1e776e6c806fa7fa | Rework _extract_marshmallow_field_params
I think we should rework `_extract_marshmallow_field_params` to avoid copying `default`, `missing`, `load_from`, `dump_to` and perhaps other attributes.
Current version:
```py
def _extract_marshmallow_field_params(self, mongo_world):
params = {field: getattr... | diff --git a/HISTORY.rst b/HISTORY.rst
index 1b69669..d10faee 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -7,7 +7,14 @@ dev
* ``missing`` attribute is no longer used in umongo fields, only ``default`` is
used. ``marshmallow_missing`` and ``marshmallow_default`` attribute can be
used to overwrite the value to u... |
Scille__umongo-190 | [
{
"changes": {
"added_entities": [
"umongo/fields.py:_round_to_millisecond"
],
"added_modules": [
"umongo/fields.py:_round_to_millisecond"
],
"edited_entities": [
"umongo/fields.py:DateTimeField._deserialize",
"umongo/fields.py:LocalDateTimeField._de... | Scille/umongo | 3f5339442d1ec3ce66d4e41dabcdb8242bf2e684 | ValueError: microsecond must be in 0..999999
Hello, all
I've got a new error after the v2.0.0 milestone, likely relating to #172. Here's the error text:
```python
File "/Users/space/Documents/Programming/dt-blog-platform/api-server/db/objs.py", line 268, in commit
self.updatedon = datetime.datetime.utcnow... | diff --git a/umongo/fields.py b/umongo/fields.py
index 4a57703..2cb87e3 100644
--- a/umongo/fields.py
+++ b/umongo/fields.py
@@ -165,6 +165,18 @@ class FloatField(BaseField, ma_fields.Float):
pass
+def _round_to_millisecond(datetime):
+ """Round a datetime to millisecond precision
+
+ MongoDB stores date... |
Scille__umongo-191 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"umongo/fields.py:StrictDateTimeField._deserialize"
],
"edited_modules": [
"umongo/fields.py:StrictDateTimeField"
]
},
"file": "umongo/fields.py"
}
] | Scille/umongo | 7f8c4cd62e61d1a62a70706f1780248bb3c3ad2a | ValueError: microsecond must be in 0..999999
Hello, all
I've got a new error after the v2.0.0 milestone, likely relating to #172. Here's the error text:
```python
File "/Users/space/Documents/Programming/dt-blog-platform/api-server/db/objs.py", line 268, in commit
self.updatedon = datetime.datetime.utcnow... | diff --git a/umongo/fields.py b/umongo/fields.py
index 2cb87e3..c2ba09a 100644
--- a/umongo/fields.py
+++ b/umongo/fields.py
@@ -248,9 +248,7 @@ class StrictDateTimeField(BaseField, ma_bonus_fields.StrictDateTime):
ret = self._set_tz_awareness(value)
else:
ret = super()._deserialize(v... |
Scille__umongo-231 | [
{
"changes": {
"added_entities": [
"umongo/fields.py:DictField.__init__",
"umongo/fields.py:ListField.__init__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"umongo/fields.py:DictField",
"umongo/fields.py:ListField"
]
... | Scille/umongo | 3c546921f4c9fb8bc686329beac903bf86597c5d | DictField / ListField: how to pass dict / list as default?
Since #154, default values must be passed in deserialized form for consistency with marshmallow 3.
One can't write this anymore:
```py
list_field = ListField(IntField, default=list)
```
One must now write
```py
from umongo.data_objects import Lis... | diff --git a/HISTORY.rst b/HISTORY.rst
index 4100c7e..62ac03e 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -2,25 +2,6 @@
History
=======
-3.0.0b1 (unreleased)
---------------------
-
-Features:
-
-* Support marshmallow 3 (see #154).
-* All field parameters beginning with ``"marshmallow_"`` are passed to the
- mar... |
Scille__umongo-245 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"umongo/builder.py:BaseBuilder._patch_field"
],
"edited_modules": [
"umongo/builder.py:BaseBuilder"
]
},
"file": "umongo/builder.py"
},
{
"changes": {
"add... | Scille/umongo | 9485f028b253fdf82f01bcdeae81e2fec6c4f39d | DictField limitations
`DictField` suffers from a few limitations.
- Must be marked as modified manually
- Does not deserialize values into objects (no Schema)
- Can't use non-string keys
It might be useful to have a schema-less structure, but sometimes, I'd like to have `DictField` enforce a schema. Maybe we co... | diff --git a/umongo/builder.py b/umongo/builder.py
index cbe8003..954258f 100644
--- a/umongo/builder.py
+++ b/umongo/builder.py
@@ -12,7 +12,7 @@ from .embedded_document import (
from .exceptions import DocumentDefinitionError, NotRegisteredDocumentError
from .schema import Schema, on_need_add_id_field, add_child_fi... |
Scille__umongo-330 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"umongo/frameworks/motor_asyncio.py:_list_io_validate",
"umongo/frameworks/motor_asyncio.py:_reference_io_validate",
"umongo/frameworks/motor_asyncio.py:_embedded_document_io_validate"
... | Scille/umongo | 38099cd9cd484e83c88df20ed6bd6ff1e6316877 | Trying to set a ReferenceField to None fails in _reference_io_validate
Using Python 3.8.6 and `motor_asyncio`, when trying to set a `ReferenceField` in a document to None, I get an `AttributeError` while committing.
The traceback looks something like this:
```
Traceback (most recent call last):
... various pr... | diff --git a/umongo/frameworks/motor_asyncio.py b/umongo/frameworks/motor_asyncio.py
index 976ee5d..ccb61a5 100644
--- a/umongo/frameworks/motor_asyncio.py
+++ b/umongo/frameworks/motor_asyncio.py
@@ -338,12 +338,16 @@ async def _io_validate_data_proxy(schema, data_proxy, partial=None):
async def _reference_io_val... |
SebastianCzoch__influx-line-protocol-11 | [
{
"changes": {
"added_entities": [
"influx_line_protocol/metric.py:Metric.__escape"
],
"added_modules": null,
"edited_entities": [
"influx_line_protocol/metric.py:Metric.add_tag",
"influx_line_protocol/metric.py:Metric.add_value",
"influx_line_protocol/met... | SebastianCzoch/influx-line-protocol | cfb52c5e223de5f4dd6a73ddee0b458ce773b61b | needs to properly escape all characters
it only escapes spaces in tag keys. It also needs to escape = and ,
https://docs.influxdata.com/influxdb/v1.7/write_protocols/line_protocol_tutorial/#special-characters | diff --git a/influx_line_protocol/metric.py b/influx_line_protocol/metric.py
index dd96e5f..e8b06eb 100644
--- a/influx_line_protocol/metric.py
+++ b/influx_line_protocol/metric.py
@@ -10,20 +10,37 @@ class Metric(object):
self.timestamp = timestamp
def add_tag(self, name, value):
- if ' ' in str... |
Seluj78__shellhub-python-10 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "shellhub/__init__.py"
},
{
"changes": {
"added_entities": [
"shellhub/models/device.py:ShellHubDevice._safe_isoformat_to_datetime"
... | Seluj78/shellhub-python | 41e0ef66b9ba4fe9617456113ef85e2b3613fe0e | Convert datetime strings to datetime objects
Strings returned by the ShellHub API need to be converted to datetime objects | diff --git a/shellhub/__init__.py b/shellhub/__init__.py
index e7ca9b2..bfe43a1 100644
--- a/shellhub/__init__.py
+++ b/shellhub/__init__.py
@@ -1,5 +1,5 @@
# Increment versions here according to SemVer
-__version__ = "0.2.4"
+__version__ = "0.3.0"
from .models.device import ShellHubDevice, ShellHubDeviceInfo
from... |
Seluj78__shellhub-python-7 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "shellhub/__init__.py"
},
{
"changes": {
"added_entities": [
"shellhub/models/base.py:ShellHub._format_and_validate_url",
"shellh... | Seluj78/shellhub-python | 521a6f204523f22f633b48785f75570292957037 | Add checks for the endpoint
Right now, an endpoint can only be `https://XXX` but we would like it to also accept `XXX` as well and append the `https://` where needed. | diff --git a/shellhub/__init__.py b/shellhub/__init__.py
index 237565d..0d63d72 100644
--- a/shellhub/__init__.py
+++ b/shellhub/__init__.py
@@ -1,5 +1,5 @@
# Increment versions here according to SemVer
-__version__ = "0.0.1"
+__version__ = "0.1.0"
from .models.device import ShellHubDevice, ShellHubDeviceInfo
from... |
Seluj78__shellhub-python-9 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "shellhub/__init__.py"
},
{
"changes": {
"added_entities": [
"shellhub/models/device.py:ShellHubDevice.sshid"
],
"added_modul... | Seluj78/shellhub-python | e5af59cb92cf4954bf732613af2e28714d1dfea1 | Add a .sshid method
Add a method to get a device's sshid like so:
`shellhub_device.sshid` -> `NAMESPACE.NAME@ENDPOINT` | diff --git a/shellhub/__init__.py b/shellhub/__init__.py
index 0d63d72..0222d04 100644
--- a/shellhub/__init__.py
+++ b/shellhub/__init__.py
@@ -1,5 +1,5 @@
# Increment versions here according to SemVer
-__version__ = "0.1.0"
+__version__ = "0.2.0"
from .models.device import ShellHubDevice, ShellHubDeviceInfo
from... |
SethMMorton__natsort-146 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"natsort/utils.py:path_splitter"
],
"edited_modules": [
"natsort/utils.py:path_splitter"
]
},
"file": "natsort/utils.py"
}
] | SethMMorton/natsort | 4f0b3a8b005a0a43d2c21cf0b1e11c89186603b3 | Wrong os_sorted sorting with special character in filename
**Describe the bug**
It can happen that the `os_sorted` functionality does not sort correctly files with special character inside
**Expected behavior**
File sorting equal to Windows Explorer
**Environment (please complete the following information):**
... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2f81376..b1475fc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,18 +1,22 @@
Unreleased
---
+### Changed
+- When using `ns.PATH`, only split off a maximum of two suffixes from
+ a file name (issues #145, #146).
+
[8.0.2] - 2021-12-14
---
### Fixed
-- Bug where... |
SethMMorton__natsort-49 | [
{
"changes": {
"added_entities": [
"natsort/compat/locale.py:custom_strcoll"
],
"added_modules": [
"natsort/compat/locale.py:custom_strcoll"
],
"edited_entities": null,
"edited_modules": null
},
"file": "natsort/compat/locale.py"
},
{
"changes"... | SethMMorton/natsort | 2e474460d65998dd72f1db56556b03cb3f69f806 | Feature request natsorted(): Sort by letters, then numbers
I'd like to submit a feature request to add an option that would allow natsorted() to sort by letters first, then numbers instead of numbers first, then letters. Here is an example of the list that I am looking to sort - I am sorting by index 2 ('ABCDE', 'BCD... | diff --git a/natsort/compat/locale.py b/natsort/compat/locale.py
index 4cbe5f5..ab392ee 100644
--- a/natsort/compat/locale.py
+++ b/natsort/compat/locale.py
@@ -6,8 +6,21 @@ from __future__ import (
absolute_import
)
+# Std. lib imports.
+import sys
+
# Local imports.
-from natsort.compat.py23 import PY_VERSIO... |
ShailChoksi__text2digits-32 | [
{
"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": [
"text2digits/tokens_basic.py... | ShailChoksi/text2digits | d96df03444b621b23e3ad444f39da73ca15c8011 | Problems to convert date in format like "January sixth twenty twenty"
from text2digits import text2digits
t2d = text2digits.Text2Digits()
print(t2d.convert("january six twenty nineteen"))
print(t2d.convert("january 6 2019"))
print(t2d.convert("january six twenty twenty"))
print(t2d.convert("january 6 2020"))
prin... | diff --git a/setup.py b/setup.py
index 7c315ef..f61f06c 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
setuptools.setup(
name="text2digits",
- version="0.0.9",
+ version="0.1.0",
author="Shail Choksi",
author_email="choksishail@gmail.com",
descriptio... |
ShawHahnLab__igseq-12 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"igseq/igblast.py:igblast"
],
"edited_modules": [
"igseq/igblast.py:igblast"
]
},
"file": "igseq/igblast.py"
}
] | ShawHahnLab/igseq | 1280f70936a87dc47a557ea0603dff0e5c367a2c | Stderr/stdout should be shown if igblast crashes
Right now if a `subprocess.CalledProcessError` is raised because of a nonzero exit code from igblastn, the error message is inside the stderr attribute of the exception, but it's never actually shown so the cause of the problem isn't clear. The stdout/stderr attributes ... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index cd2aeb6..7aebd00 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
# Changelog
-## 0.1.1 - 2021-12-06
+## 0.1.1 - 2021-12-07
### Changed
@@ -8,6 +8,7 @@
### Fixed
+ * IgBLAST output is now shown even if it crashes ([#12])
* Header-only CSV/TSV fil... |
ShawHahnLab__igseq-2 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"igseq/vdj.py:parse_vdj_paths"
],
"edited_modules": [
"igseq/vdj.py:parse_vdj_paths"
]
},
"file": "igseq/vdj.py"
},
{
"changes": {
"added_entities": null,
... | ShawHahnLab/igseq | 3f0407f10e41f98acad8283d4f66e4adf1a4e3fc | Duplicate inferred FASTA paths should only be handled once
`vdj-gather` can take fragments of builtin file paths as input, so you could do, for example:
igseq vdj-gather sonarramesh/IGK sonarramesh/IGH/IGHD -o igdiscover-db-start
...and get IGK genes plus a placeholder D file. But something like this results... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 65385be..ac25fbe 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,14 @@
## Changelog
+# dev
+
+Fixed:
+
+ * Duplicate FASTA paths found in vdj-gather will no longer result in
+ duplicated output sequences ([#2])
+
+[#2]: https://github.com/ShawHahnLab/igseq/pul... |
ShawHahnLab__igseq-26 | [
{
"changes": {
"added_entities": [
"igseq/record.py:RecordHandler._infer_fmt"
],
"added_modules": null,
"edited_entities": [
"igseq/record.py:RecordHandler.infer_fmt",
"igseq/record.py:RecordReader.open"
],
"edited_modules": [
"igseq/record.py:... | ShawHahnLab/igseq | 2e620fb40ae79cebd5d9478a238c50e45882e914 | .afa should be recognized as a FASTA format
.afa (used in some SONAR filenames for example) should be recognized by default as a filename extension for FASTA. | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7824f3c..890f5fb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,11 +2,17 @@
## dev
+### Added
+
+ * Support for .afa (as FASTA) and .fq (as FASTQ) in input/output handling
+ ([#26])
+
### Fixed
* vdj-match now skips references that are missing gene segments... |
ShawHahnLab__igseq-37 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"igseq/identity.py:score_identity"
],
"edited_modules": [
"igseq/identity.py:score_identity"
]
},
"file": "igseq/identity.py"
}
] | ShawHahnLab/igseq | 2e36b272d6170625d96b3df3fb6a513ff37b7a27 | Identity calculation should disregard gaps and uppercase/lowercase
In using the new `identity` command I realized it should ignore gaps and uppercase/lowercase differences when comparing sequences. | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 51fd6d2..675a8c1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,7 @@
### Added
* `identity` command for calculating pairwise identity between arbitrary
- queries and references ([#31])
+ queries and references ([#31], [#37])
* Support for showing basic ... |
ShawHahnLab__igseq-43 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"igseq/__main__.py:main",
"igseq/__main__.py:_main_getreads"
],
"edited_modules": [
"igseq/__main__.py:main",
"igseq/__main__.py:_main_getreads"
]
},
"fi... | ShawHahnLab/igseq | b7fba32e2a004bb4197c7c7dd51b4b6aeb0e523b | Support extra command-line arguments for bcl2fastq in getreads command
It should be possible to specify custom bcl2fastq arguments (.e.g. `--with-failed-reads`) to be added to the command. Should be easy enough by following the pattern already used for the igblast command. | diff --git a/CHANGELOG.md b/CHANGELOG.md
index c1b315d..908cee6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,9 +4,12 @@
### Added
+ * support for additional arguments for `getreads` command passed through to
+ bcl2fastq ([#43])
* `msa` command for building multiple sequence alignments with
[MUSCLE](h... |
ShawHahnLab__igseq-49 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"igseq/identity.py:identity"
],
"edited_modules": [
"igseq/identity.py:identity"
]
},
"file": "igseq/identity.py"
},
{
"changes": {
"added_entities": null,... | ShawHahnLab/igseq | a97327884fb97b137613389607800e4215425ccf | identity command ignores sequence ID column name for tabular input
The identity command uses a hardcoded reference to the `sequence_id` column and ignores any custom column like from `--col-seq-id`. (The existing tests check a custom sequence column, which works, but not a custom sequence ID column, which evidently do... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4ba83d8..c57d74b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,12 @@
* `msa` command for building multiple sequence alignments with
[MUSCLE](https://drive5.com/muscle5/) ([#41])
+### Fixed
+
+ * `identity` command now uses a custom sequence ID column if... |
ShawHahnLab__igseq-50 | [
{
"changes": {
"added_entities": [
"igseq/igblast.py:fuzzy_species_match"
],
"added_modules": [
"igseq/igblast.py:fuzzy_species_match"
],
"edited_entities": [
"igseq/igblast.py:igblast",
"igseq/igblast.py:detect_organism",
"igseq/igblast.py:_... | ShawHahnLab/igseq | 6c4826c9118bc5c94943fd8e3f4948cefab8a844 | summarize command should follow same species-based default as igblast command
Same as #38, but for `summarize` as well as `igblast`. | diff --git a/CHANGELOG.md b/CHANGELOG.md
index c57d74b..fa1abf1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,8 @@
### Added
+ * `summarize` command will automatically use all available references for a
+ given species if a species is given but no references ([#50])
* `tree` command for creating and ... |
ShawHahnLab__igseq-57 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"igseq/tree.py:make_seq_set_colors"
],
"edited_modules": [
"igseq/tree.py:make_seq_set_colors"
]
},
"file": "igseq/tree.py"
}
] | ShawHahnLab/igseq | 01c186acaf91ed5813d00eb86c12bae060dacfde | tree color-coding crashes when exactly one set is defined
When there's exactly one set of sequences defined, `make_seq_set_colors` crashes:
```
$ igseq tree -P '.*' --input-format newick <(echo '((A:1,B:1):1)') out.nex
$ igseq tree -P A --input-format newick <(echo '((A:1,B:1):1)') out.nex
Traceback (most recent ... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 18d86e2..543636d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,14 @@
# Changelog
+## dev
+
+### Fixed
+
+ * `tree` command can now handle assigning a color code when exactly one
+ sequence set is defined ([#57])
+
+[#57]: https://github.com/ShawHahnLab/igseq... |
ShawHahnLab__igseq-7 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"igseq/igblast.py:igblast",
"igseq/igblast.py:setup_db_dir_and_igblast"
],
"edited_modules": [
"igseq/igblast.py:igblast",
"igseq/igblast.py:setup_db_dir_and_igblast"
... | ShawHahnLab/igseq | 4a85f3472dc04d1b7da8a3370bc9c0b430620e31 | summarize crashes with multiple references
It doesn't take into account the modified sequence IDs from the IgBLAST database. | diff --git a/CHANGELOG.md b/CHANGELOG.md
index ec3749f..014d7c6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,7 @@
Fixed:
+ * summarize command now works with multiple references ([#7])
* vdj-match and summarize commands now work as intended via igblast, and all
have basic automated tests ([#5])
... |
ShawHahnLab__igseq-74 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"igseq/phix.py:phix"
],
"edited_modules": [
"igseq/phix.py:phix"
]
},
"file": "igseq/phix.py"
}
] | ShawHahnLab/igseq | 7be0a05bb0a3f678aeee737f51a0c7677fef726b | PhiX mapping counts path should be cast to Path object
The command `igseq phix ... -c something.counts.csv` doesn't actually work because `counts_out` is treated as a Path object in the code but left as a string as passed from the command line. It should probably be cast as a Path immediately in the phix function. | diff --git a/.circleci/config.yml b/.circleci/config.yml
index 5ecf490..50154d5 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -2,7 +2,7 @@ version: 2.1
jobs:
build:
machine:
- image: ubuntu-2004:202201-02
+ image: default
steps:
- checkout:
path: igseq
diff --... |
ShawHahnLab__igseq-87 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"igseq/__main__.py:main",
"igseq/__main__.py:_main_trim"
],
"edited_modules": [
"igseq/__main__.py:main",
"igseq/__main__.py:_main_trim"
]
},
"file": "ig... | ShawHahnLab/igseq | 101b8b18390472dc8c9e69ac471f22d093930b6a | Trim should support custom command-line cutadapt arguments
Like I already have for the igblast and getreads commands, passing extra arguments through to igblastn and bcl2fastq, the trim command should allow custom arguments for cutadapt. | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 26ca696..b81ef6b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,12 +2,20 @@
## dev
+### Added
+
+ * `trim` now supports passing additional command-line arguments through to
+ cutadapt ([#87])
+
### Changed
* `trim` now allows the species to be left unspecif... |
Shoobx__mypy-zope-80 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/mypy_zope/plugin.py:ZopeInterfacePlugin._apply_interface"
],
"edited_modules": [
"src/mypy_zope/plugin.py:ZopeInterfacePlugin"
]
},
"file": "src/mypy_zope/plugin.py... | Shoobx/mypy-zope | 5139181a07febfde688af3035d00319942df4dcf | Caching errors with latest version of mypy
Hi. With the latest version of mypy and mypy-zope we're getting mypy errors that I think are cache related. The error goes away after `rm -rf .mypy_cache`
Here's the smallest repro I could make:
src/zg/foo.py:
```
from zg.bar import ZGScriptProtocol
print(ZGScriptP... | diff --git a/src/mypy_zope/plugin.py b/src/mypy_zope/plugin.py
index 312c0b5..46bdc1b 100644
--- a/src/mypy_zope/plugin.py
+++ b/src/mypy_zope/plugin.py
@@ -695,7 +695,7 @@ class ZopeInterfacePlugin(Plugin):
# there is a decorator for the class that will create a "type promotion",
# but ensure this on... |
Shoobx__mypy-zope-88 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/mypy_zope/plugin.py:ZopeInterfacePlugin._apply_interface"
],
"edited_modules": [
"src/mypy_zope/plugin.py:ZopeInterfacePlugin"
]
},
"file": "src/mypy_zope/plugin.py... | Shoobx/mypy-zope | 3c767525b740a35e7039bf792ccfbce8590044d7 | Caching error (Metaclass conflict) with mypy 0.991
Hi. With the latest version of mypy (0.991) and mypy-zope (0.3.11) we're getting mypy errors that I think are cache related. The error goes away after `rm -rf .mypy_cache`
Here's the easiest repro I could make:
iface.py
```
from zope.interface import Interface
... | diff --git a/src/mypy_zope/plugin.py b/src/mypy_zope/plugin.py
index 46bdc1b..0c7971e 100644
--- a/src/mypy_zope/plugin.py
+++ b/src/mypy_zope/plugin.py
@@ -698,7 +698,10 @@ class ZopeInterfacePlugin(Plugin):
if not any(promote in ti._promote for ti in impl.mro):
faketi = TypeInfo(SymbolTable(), i... |
Shoobx__xmldiff-103 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xmldiff/patch.py:Patcher.patch",
"xmldiff/patch.py:Patcher._handle_DeleteNode",
"xmldiff/patch.py:Patcher._handle_InsertNode",
"xmldiff/patch.py:Patcher._handle_RenameNode",
... | Shoobx/xmldiff | c66ba6b9d686e4fb612779272866093f9ee8a064 | Patching doesn't account for namespaces in xpaths and breaks
Xmldiff patching breaks when there are namespace prefixes in xpaths within xmldiff actions. e.g.: `ns:` in`MoveNode(node='/ns:a/ns:b/ns:x', target='/ns:a/ns:c', position=0)`.
When I attempt to apply the patch. I get the following:
```
Traceback (most rec... | diff --git a/CHANGES.rst b/CHANGES.rst
index c780fb0..9d65f6a 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -15,6 +15,8 @@ Changes
- Added a parameter for ignoring attributes in comparison.
+- Solved a bug in xmlpatch in certain namespace situations.
+
- Added a --diff-encoding parameter to xmlpatch, to support d... |
Shoobx__xmldiff-117 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xmldiff/patch.py:Patcher.patch"
],
"edited_modules": [
"xmldiff/patch.py:Patcher"
]
},
"file": "xmldiff/patch.py"
}
] | Shoobx/xmldiff | 8cb3fe009a1b2349499f2dcebd4752fcaed31ffc | -f xml fails with: "TypeError: empty namespace prefix is not supported in XPath"
I wanted to try adding the argon2 S2K allocation to https://www.iana.org/assignments/pgp-parameters/pgp-parameters.xml, which means adding a row for codepoint 4 in the S2K parameters section, so i fetched it, modified it by hand, and trie... | diff --git a/CHANGES.rst b/CHANGES.rst
index c35c7e7..88b864e 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -4,13 +4,13 @@ Changes
2.6.3 (unreleased)
------------------
-- Nothing changed yet.
+- And there was a namespace bug in the patch as well. #118
2.6.2 (2023-05-21)
------------------
-- Solved an erro... |
Shopify__shopify_python_api-110 | [
{
"changes": {
"added_entities": [
"shopify/resources/image.py:Image._prefix",
"shopify/resources/image.py:Image.save"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"shopify/resources/image.py:Image"
]
},
"file": "shopi... | Shopify/shopify_python_api | 657517e9b83e0e99404d994047b3bfea3b73d310 | Support for independently creating/modifying product images.
Please correct me if I'm wrong, but at the moment the only way to create/update product images through the Python API is directly through a POST/PUT call to the product endpoint.
As per the [Shopify API documentation on product images](http://docs.shopify.... | diff --git a/shopify/resources/image.py b/shopify/resources/image.py
index c5f9fd2..a0e82ef 100644
--- a/shopify/resources/image.py
+++ b/shopify/resources/image.py
@@ -8,6 +8,14 @@ import re
class Image(ShopifyResource):
_prefix_source = "/admin/products/$product_id/"
+ @classmethod
+ def _prefix(cls, op... |
Shopify__shopify_python_api-136 | [
{
"changes": {
"added_entities": [
"shopify/mixins.py:Metafields.metafields_count"
],
"added_modules": null,
"edited_entities": [
"shopify/mixins.py:Metafields.metafields"
],
"edited_modules": [
"shopify/mixins.py:Metafields"
]
},
"file":... | Shopify/shopify_python_api | a78109e725cf9e400f955062399767f36f3a1f44 | metafields() method should be able to take options parameters for limit and page
```
import shopify
product = shopify.Product.find(5972485446)
metafields = product.metafields()
print(len(metafields))
> 50
metafields = product.metafields(limit=250)
> TypeError: metafields() got an unexpected keyword argument 'lim... | diff --git a/shopify/mixins.py b/shopify/mixins.py
index 9d3c179..c7806a0 100644
--- a/shopify/mixins.py
+++ b/shopify/mixins.py
@@ -11,8 +11,15 @@ class Countable(object):
class Metafields(object):
- def metafields(self):
- return shopify.resources.Metafield.find(resource=self.__class__.plural, resource... |
Shopify__shopify_python_api-177 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"shopify/resources/image.py:Image.attach_image"
],
"edited_modules": [
"shopify/resources/image.py:Image"
]
},
"file": "shopify/resources/image.py"
}
] | Shopify/shopify_python_api | c29e0ecbed9de67dd923f980a3ac053922dab75e | Attaching Images - Decode required for Python 3 compatibility
When attaching an image from a local file:
```
with open("some_image.jpg","rb") as f:
img = f.read()
image1.attach_image(data=img)
```
img will be bytes while the attachment needs to be a string to the JSONified. So in image.py:
```
def attach_ima... | diff --git a/shopify/resources/image.py b/shopify/resources/image.py
index a0e82ef..b408261 100644
--- a/shopify/resources/image.py
+++ b/shopify/resources/image.py
@@ -23,7 +23,7 @@ class Image(ShopifyResource):
return super(Image, self).__getattr__(name)
def attach_image(self, data, filename=None)... |
Shopify__shopify_python_api-330 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"shopify/base.py:ShopifyResourceMeta.set_site"
],
"edited_modules": [
"shopify/base.py:ShopifyResourceMeta"
]
},
"file": "shopify/base.py"
}
] | Shopify/shopify_python_api | 748fc93d09a3e4467cd0e605a855b84cf029f415 | Shopify API url not working
Hi,
Currently, I'm just playing around, with this library. I created a development store and a private app.
When I'm trying to create a product I got the following error:
Python 3.7.2
ShopifyAPI==5.0.1
Traceback (most recent call last):
File "C:\Users\danish\AppData\Local\Progr... | diff --git a/README.md b/README.md
index 4959665..45111bc 100644
--- a/README.md
+++ b/README.md
@@ -85,15 +85,17 @@ service. pyactiveresource has to be configured with a fully authorized
URL of a particular store first. To obtain that URL you can follow
these steps:
-1. First create a new application in either th... |
Shopify__shopify_python_api-354 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"shopify/base.py:ShopifyResource.find",
"shopify/base.py:ShopifyResource._parse_pagination"
],
"edited_modules": [
"shopify/base.py:ShopifyResource"
]
},
"file":... | Shopify/shopify_python_api | 3cec005f5af28622fba023c67f739784a23f98a4 | Cursor pagination issue with single page results
I was trying out the new cursor pagination 6.0.0 release and came across an issue.
page1 = shopify.Product.find(limit=100)
while page1.has_next_page():
// do stuff
I can an error
AttributeError: 'Collection' object has no attribute 'has_next_page'
This ha... | diff --git a/shopify/base.py b/shopify/base.py
index bcab899..65349e6 100644
--- a/shopify/base.py
+++ b/shopify/base.py
@@ -208,43 +208,7 @@ class ShopifyResource(ActiveResource, mixins.Countable):
@classmethod
def find(cls, id_=None, from_=None, **kwargs):
"""Checks the resulting collection for pag... |
Shopify__shopify_python_api-358 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"shopify/base.py:ShopifyResource.find"
],
"edited_modules": [
"shopify/base.py:ShopifyResource"
]
},
"file": "shopify/base.py"
},
{
"changes": {
"added_ent... | Shopify/shopify_python_api | cd049439a62b84475b3693f82d455fb342f4abc7 | cursor-based pagination not working (header name case-sensitivity?)
I am trying to implement the new cursor-based pagination, with ShopifyPythonAPI/6.0.1 on Python/2.7.16 and pyactiveresource 2.2.0. I am testing with the API version 2020-10.
`has_next_page()` always returns false for me even when there are more item... | diff --git a/shopify/base.py b/shopify/base.py
index 65349e6..d14401e 100644
--- a/shopify/base.py
+++ b/shopify/base.py
@@ -210,5 +210,5 @@ class ShopifyResource(ActiveResource, mixins.Countable):
"""Checks the resulting collection for pagination metadata."""
collection = super(ShopifyResource, cls).... |
Shopify__shopify_python_api-363 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"shopify/resources/event.py:Event._prefix"
],
"edited_modules": [
"shopify/resources/event.py:Event"
]
},
"file": "shopify/resources/event.py"
}
] | Shopify/shopify_python_api | 16053bb8c6a27a0af992e4d6efc5bfdbb7931136 | TypeError: not all arguments converted during string formatting in /resources/events.py
Getting the following error trying query order events
```
>>> import shopify
>>> shopify.Order.find(2098647662664).events()
Traceback (most recent call last):
File "<console>", line 1, in <module>
File "/usr/local/lib/pyth... | diff --git a/shopify/resources/event.py b/shopify/resources/event.py
index 5d266d0..0fc1e6f 100644
--- a/shopify/resources/event.py
+++ b/shopify/resources/event.py
@@ -7,6 +7,6 @@ class Event(ShopifyResource):
def _prefix(cls, options={}):
resource = options.get("resource")
if resource:
- ... |
Shopify__shopify_python_api-89 | [
{
"changes": {
"added_entities": [
"shopify/session.py:Session.validate_hmac",
"shopify/session.py:Session.calculate_hmac"
],
"added_modules": null,
"edited_entities": [
"shopify/session.py:Session.request_token",
"shopify/session.py:Session.validate_param... | Shopify/shopify_python_api | 63c4a8dd026a60bce7880eeba792e1aeeaccc471 | Update MD5 Signature validation to HMAC
Docs say that MD5 signature validation 'To be removed after June 1st, 2015'
It appears ```Session``` is still doing it this way vs HMAC
| diff --git a/CHANGELOG b/CHANGELOG
index 4301098..00fe323 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -2,6 +2,7 @@
* Added Checkout resource
* Updated to pyactiveresource v2.1.1 which includes a test-related bugfix
+* Changed OAuth validation from MD5 to HMAC-SHA256
== Version 2.1.0
diff --git a/shopify/session.... |
Shopify__shopify_python_api-94 | [
{
"changes": {
"added_entities": [
"shopify/resources/recurring_application_charge.py:_get_first_by_status"
],
"added_modules": [
"shopify/resources/recurring_application_charge.py:_get_first_by_status"
],
"edited_entities": [
"shopify/resources/recurring_ap... | Shopify/shopify_python_api | 77dfd01e6e2bda80767663bd8214234f11b9ebdc | RecurringApplicationCharge.current() does not work as expected
In RecurringApplicationCharge class there is class method "current" that doesn't work as expexted.
## Problem
I have few RecurringApplicationCharge instances for my test shop but none of them has status=active. I was expecting to get None as a result w... | diff --git a/.gitignore b/.gitignore
index f62c50b..ba6c0eb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@ tags
/ShopifyAPI.egg-info
*.egg
/.idea
+.DS_Store
diff --git a/CHANGELOG b/CHANGELOG
index 00fe323..4301098 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -2,7 +2,6 @@
* Added Checkout resource
* Updat... |
SiftScience__sift-python-34 | [
{
"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": [
"sift/client.py:Client.track... | SiftScience/sift-python | a9993ecae67cc4804fd572cd3ef95ec9535758a2 | Warnings cause TypeError
I'm seeing some TypeError exceptions, it seems that the new warnings / exception handling code has some issues?
```
...
File "tasks.py", line 296, in track_sift_event
response = sift_client.track(event_type, attrs)
File "/home/ubuntu/closeio/venv/local/lib/python2.7/site-packag... | diff --git a/README.rst b/README.rst
index 30404c0..4d3f726 100644
--- a/README.rst
+++ b/README.rst
@@ -68,9 +68,9 @@ Here's an example:
"$payment_gateway" : "$braintree",
"$card_bin" : "542486",
"$card_last4" : "4444"
- },
- "$currency_code" : "USD",
- "$a... |
SiftScience__sift-python-68 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sift/client.py:Client.__init__",
"sift/client.py:Client.track",
"sift/client.py:Client.score",
"sift/client.py:Client.get_user_score",
"sift/client.py:Client.rescore_user... | SiftScience/sift-python | 09b6a55cbadebcb5289c548a346f0ade3fd22685 | Provide a way for users to use requests.Session
We're trying to use [connection pooling](http://docs.python-requests.org/en/master/user/advanced/#session-objects) which reduces our latency from 800ms to 200ms but we're finding it very difficult to "swap out" the `requests.get` for a `session.get` due to the design of t... | diff --git a/sift/client.py b/sift/client.py
index e2bfe50..2337e53 100644
--- a/sift/client.py
+++ b/sift/client.py
@@ -27,7 +27,8 @@ class Client(object):
api_url=API_URL,
timeout=2.0,
account_id=None,
- version=sift.version.API_VERSION):
+ version=sift.ver... |
SirAnthony__slpp-32 | [
{
"changes": {
"added_entities": [
"slpp.py:SLPP.skip_comments"
],
"added_modules": null,
"edited_entities": [
"slpp.py:SLPP.decode",
"slpp.py:SLPP.white"
],
"edited_modules": [
"slpp.py:SLPP"
]
},
"file": "slpp.py"
}
] | SirAnthony/slpp | b9474965a8fd5759847c8cbdfa873069a43a0bb8 | lua.decode('"--3"') fails
This looks like a bug in the string parsing to me - as if the parser tries to detect comments inside literal strings.
`'--3'` is a perfectly valid lua string, of course. | diff --git a/slpp.py b/slpp.py
index 19a6405..9f35cc0 100644
--- a/slpp.py
+++ b/slpp.py
@@ -43,9 +43,6 @@ class SLPP(object):
def decode(self, text):
if not text or not isinstance(text, six.string_types):
return
- # FIXME: only short comments removed
- reg = re.compile('--.*$',... |
SixTrack__pysixtrack-60 | [
{
"changes": {
"added_entities": [
"pysixtrack/line.py:Line._add_offset_error_to",
"pysixtrack/line.py:Line._add_aperture_offset_error_to",
"pysixtrack/line.py:Line._add_tilt_error_to",
"pysixtrack/line.py:Line._add_multipole_error_to",
"pysixtrack/line.py:Line._app... | SixTrack/pysixtrack | 4ab545da7489efeceb3f36580ba59f4fc046a12e | merge_consecutive_drifts() can prevent aperture misalignment
Example assumes #38 to be fixed
```
import cpymad.madx
import pysixtrack
# code from help(pysixtrack.Line.apply_madx_errors) with minimal madx sequence
madx = cpymad.madx.Madx()
madx.input('''
!----EXAMPLE----------------------------------------... | diff --git a/pysixtrack/line.py b/pysixtrack/line.py
index 7301b16..bd37201 100644
--- a/pysixtrack/line.py
+++ b/pysixtrack/line.py
@@ -328,6 +328,7 @@ class Line(Element):
exact_drift=False,
drift_threshold=1e-6,
install_apertures=False,
+ apply_madx_errors=False,
):
... |
Skyscanner__cfripper-80 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfripper/boto3_client.py:Boto3Client.get_template"
],
"edited_modules": [
"cfripper/boto3_client.py:Boto3Client"
]
},
"file": "cfripper/boto3_client.py"
},
{
"c... | Skyscanner/cfripper | db0bcdecf65ab6ba808c268476ccc28b3ad78460 | Error while parsing template with pycfmodel
Hi guys. I get the following error when I ran the lambda
```
[ERROR] TypeError: ModelMetaclass object argument after ** must be a mapping, not str
Traceback (most recent call last):
File "/var/task/cfripper/main.py", line 119, in handler
cfmodel = pycfmodel.parse... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7877480..8b362c3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,10 @@
# Changelog
All notable changes to this project will be documented in this file.
+## [0.11.2] - 2019-11-26
+### Fixes
+- Fix `get_template` when AWS doesn't return a dict.
+
## [0.11.1] - 2... |
SmileyChris__django-countries-339 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"django_countries/fields.py:CountryField.__init__"
],
"edited_modules": [
"django_countries/fields.py:CountryField"
]
},
"file": "django_countries/fields.py"
}
] | SmileyChris/django-countries | 72040a01239681bf0a8b1da93e46154fbaac6a48 | Applying migrations with CountryField fails with Django 3.2
I've created a simple model with a `CountryField`. Creating a migration for this model works fine (at least when using the latest version from Git). However, applying the migration fails (traceback included below).
**Environment:**
- Django 3.2b1 (from P... | diff --git a/django_countries/fields.py b/django_countries/fields.py
index 3b3db00..ee211f1 100644
--- a/django_countries/fields.py
+++ b/django_countries/fields.py
@@ -279,7 +279,7 @@ class CountryField(CharField):
kwargs["max_length"] = len(self.countries) * 3 - 1
else:
... |
SmileyChris__django-countries-394 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"django_countries/fields.py:CountryField.get_clean_value"
],
"edited_modules": [
"django_countries/fields.py:CountryField"
]
},
"file": "django_countries/fields.py"
}
... | SmileyChris/django-countries | 1c9255af3be37f7158296e660f3bbe76812c37ff | Duplicates should be stripped before saving a from a CountryField which has multiple=True
I'm using `CountrySelectWidget` in the admin interface, along with the following settings:
```python
COUNTRIES_FIRST = ['IE']
COUNTRIES_FIRST_REPEAT = True
```
This particular scenario leads to some unexpected behavior: When ... | diff --git a/django_countries/fields.py b/django_countries/fields.py
index aabd8d1..36a8c4a 100644
--- a/django_countries/fields.py
+++ b/django_countries/fields.py
@@ -1,4 +1,5 @@
import re
+from collections import OrderedDict
from typing import Any, Iterable, Optional, Tuple, Type, Union, cast
from urllib import p... |
SmileyChris__easy-thumbnails-562 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"easy_thumbnails/files.py:Thumbnailer.get_thumbnail_name"
],
"edited_modules": [
"easy_thumbnails/files.py:Thumbnailer"
]
},
"file": "easy_thumbnails/files.py"
},
{
... | SmileyChris/easy-thumbnails | ffd70cb7e7473e5e066e0b2087955a434b1b1917 | thumbnail_cleanup on aws s3
Hello
Is it possible to use thumbnail_cleanup commant if i store by thimbnails on AWS s3 and if so then how?
Thx | diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index dd702c8..54cad96 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -13,7 +13,7 @@ jobs:
strategy:
max-parallel: 4
matrix:
- python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']... |
SnarkAttack__pybgg-json-25 | [
{
"changes": {
"added_entities": [
"pybgg_json/pybgg_json.py:PyBggInterface.guild_request"
],
"added_modules": null,
"edited_entities": [
"pybgg_json/pybgg_json.py:PyBggInterface.user_request"
],
"edited_modules": [
"pybgg_json/pybgg_json.py:PyBggInter... | SnarkAttack/pybgg-json | 589b104e62dbfe6a9d96cedfcf2eaba3572442bf | Guilds Requests | diff --git a/pybgg_json/pybgg_json.py b/pybgg_json/pybgg_json.py
index c54103a..ebd9649 100755
--- a/pybgg_json/pybgg_json.py
+++ b/pybgg_json/pybgg_json.py
@@ -74,10 +74,21 @@ class PyBggInterface(object):
def user_request(self, name, buddies=0, guilds=0, hot=0, top=0, domain='boardgame', page=1):
user... |
SnarkAttack__pybgg-json-27 | [
{
"changes": {
"added_entities": [
"pybgg_json/pybgg_json.py:PyBggInterface.collection_request"
],
"added_modules": null,
"edited_entities": [
"pybgg_json/pybgg_json.py:PyBggInterface.plays_request"
],
"edited_modules": [
"pybgg_json/pybgg_json.py:PyBg... | SnarkAttack/pybgg-json | 7896b4e1fde6c0bf79a9d47af375599ee47d9d12 | Collections Requests | diff --git a/pybgg_json/pybgg_json.py b/pybgg_json/pybgg_json.py
index 3f23f4b..bd105bc 100755
--- a/pybgg_json/pybgg_json.py
+++ b/pybgg_json/pybgg_json.py
@@ -111,4 +111,25 @@ class PyBggInterface(object):
root = pybgg_utils._make_request(plays_url)
+ return json.dumps(pybgg_utils._generat... |
SophT-Team__SophT-105 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"examples/2d_examples/FlowPastRodCase/flow_past_rod.py:flow_past_rod_case"
],
"edited_modules": [
"examples/2d_examples/FlowPastRodCase/flow_past_rod.py:flow_past_rod_case"
]
... | SophT-Team/SophT | a42e862d9a37484830e99dc009245c9f77d44823 | h5 field dumping functionality for eulerian grid fields
For more info:
<img width="726" alt="Screen Shot 2022-11-04 at 12 11 41 AM" src="https://user-images.githubusercontent.com/33580851/199894267-dc64d41f-ca6d-479f-862b-ac2f2bbc7319.png">
@armantekinalp do you want to have a shot at this? | diff --git a/examples/2d_examples/FlowPastRodCase/flow_past_rod.py b/examples/2d_examples/FlowPastRodCase/flow_past_rod.py
index c97b976..12b5085 100644
--- a/examples/2d_examples/FlowPastRodCase/flow_past_rod.py
+++ b/examples/2d_examples/FlowPastRodCase/flow_past_rod.py
@@ -131,20 +131,13 @@ def flow_past_rod_case(
... |
SpiNNakerManchester__SpiNNUtils-93 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"spinn_utilities/citation/citation_aggregator.py:CitationAggregator.create_aggregated_citation_file",
"spinn_utilities/citation/citation_aggregator.py:CitationAggregator._handle_dependency",
... | SpiNNakerManchester/SpiNNUtils | f6e4e8e0f67b4f84466f831d80e38ebe490faa86 | Broken citation code
The citation code does not handle comments in `requirements.txt`. The format supports comments (with `#`), therefore not handling it is ***wrong!*** | diff --git a/spinn_utilities/citation/citation_aggregator.py b/spinn_utilities/citation/citation_aggregator.py
index 295dffa..0c37124 100644
--- a/spinn_utilities/citation/citation_aggregator.py
+++ b/spinn_utilities/citation/citation_aggregator.py
@@ -7,9 +7,9 @@ import argparse
import sys
from spinn_utilities.cit... |
SpikeInterface__spikeextractors-649 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"spikeextractors/extractors/cedextractors/cedrecordingextractor.py:CEDRecordingExtractor.get_num_frames"
],
"edited_modules": [
"spikeextractors/extractors/cedextractors/cedrecordinge... | SpikeInterface/spikeextractors | e6f9255b0ff1a0140b313ae33b62b4676eeabfcd | CEDExtractor traces are missing the last element
The trace array imported from an smrx file using CEDExtractor has one element less than when the same file is imported directly with sonpy | diff --git a/spikeextractors/extractors/cedextractors/cedrecordingextractor.py b/spikeextractors/extractors/cedextractors/cedrecordingextractor.py
index 7cb2444..b563707 100644
--- a/spikeextractors/extractors/cedextractors/cedrecordingextractor.py
+++ b/spikeextractors/extractors/cedextractors/cedrecordingextractor.py... |
SpikeInterface__spikeinterface-1049 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"spikeinterface/core/base.py:BaseExtractor.save_to_zarr"
],
"edited_modules": [
"spikeinterface/core/base.py:BaseExtractor"
]
},
"file": "spikeinterface/core/base.py"
... | SpikeInterface/spikeinterface | b4b1d3aa29db8021aa32c791d7f4e9e9989212a8 | [feat-core]: refactor API for saving to zarr
Instead of `zarr_path`, use `folder` + `format="zarr"` | diff --git a/spikeinterface/core/base.py b/spikeinterface/core/base.py
index 53d0b926a..82081e240 100644
--- a/spikeinterface/core/base.py
+++ b/spikeinterface/core/base.py
@@ -1,6 +1,6 @@
from pathlib import Path
import importlib
-from copy import deepcopy
+import warnings
import weakref
import json
import pickle... |
SpikeInterface__spikeinterface-1057 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"spikeinterface/extractors/nwbextractors.py:NwbRecordingExtractor.__init__"
],
"edited_modules": [
"spikeinterface/extractors/nwbextractors.py:NwbRecordingExtractor"
]
},
... | SpikeInterface/spikeinterface | 7268ab900443ca3f0239de3007352d05f2d7d875 | nwbextractors: handling offsets in the electrode table
Hi, these lines are leading to a TypeError for me when multiplying the offsets by a scalar (`1e6`). I think when grabbing `offset = self._nwbfile.electrodes["offset"]` you actually need to do a slice syntax `[:]` to get a regular ndarray. I.e. the fix would be
`... | diff --git a/spikeinterface/extractors/nwbextractors.py b/spikeinterface/extractors/nwbextractors.py
index b40ffa74a..cb32aab79 100644
--- a/spikeinterface/extractors/nwbextractors.py
+++ b/spikeinterface/extractors/nwbextractors.py
@@ -168,7 +168,8 @@ class NwbRecordingExtractor(BaseRecording):
# Set offsets
... |
SpikeInterface__spikeinterface-1762 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/modules_gallery/core/plot_1_recording_extractor.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edite... | SpikeInterface/spikeinterface | dc498f292b4968d2222497cbf4b7d9a26ae8821c | PCA computation : pickle run out of inputs
Hello,
I used to get some 'shared memory issues" (#1704 ) to extract my waveforms. Since the PR #1704 has been merged, I updated my Spikeinterface. Now the waveform extraction goes well, but I have big issue with the PCAs computation. I compute the PCA with default parameter... | diff --git a/examples/modules_gallery/core/plot_1_recording_extractor.py b/examples/modules_gallery/core/plot_1_recording_extractor.py
index f20bf6497..a7c2403c4 100644
--- a/examples/modules_gallery/core/plot_1_recording_extractor.py
+++ b/examples/modules_gallery/core/plot_1_recording_extractor.py
@@ -79,7 +79,7 @@ s... |
SpikeInterface__spikeinterface-2610 | [
{
"changes": {
"added_entities": [
"src/spikeinterface/core/base.py:BaseExtractor.get_parent"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/spikeinterface/core/base.py:BaseExtractor"
]
},
"file": "src/spikeinterface/core/b... | SpikeInterface/spikeinterface | 93f9cc51a7a5c98518eab72a674891dd914059ab | Is it possible to access original data through preprocesed `BaseRecording` instance
The pipeline
```
Binary File -> Preprocessing -(1)-> Sorting -(2)-> Wave Extractor -(3)-> Neuron feature assessment.
```
The last class gets `BaseRecording` after (1) and uses `get_traces` to compute a spike "fingerprint". Unfortun... | diff --git a/src/spikeinterface/core/base.py b/src/spikeinterface/core/base.py
index 80341811b..f234d77da 100644
--- a/src/spikeinterface/core/base.py
+++ b/src/spikeinterface/core/base.py
@@ -82,6 +82,10 @@ class BaseExtractor:
# This is implemented in BaseRecording or BaseSorting
raise NotImplemente... |
SpikeInterface__spikeinterface-2716 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/spikeinterface/curation/remove_excess_spikes.py:RemoveExcessSpikesSortingSegment.get_unit_spike_train"
],
"edited_modules": [
"src/spikeinterface/curation/remove_excess_spikes.py... | SpikeInterface/spikeinterface | 482bd7406b790528800d0c6eed99617ee6efff9d | Unable to open kilosort4 results with phy
Dear,
I'm using `spikeinterface==0.100.5` and `kilosort4== .4.0.3`, on 64 channel 6 shanks probe. The phy output is works perfectly with the `ironclust ` generated results.
However, I have encountered some issues when open the kilosort4 phy output folder. And I saw there... | diff --git a/src/spikeinterface/curation/remove_excess_spikes.py b/src/spikeinterface/curation/remove_excess_spikes.py
index b9f00212e..52653d684 100644
--- a/src/spikeinterface/curation/remove_excess_spikes.py
+++ b/src/spikeinterface/curation/remove_excess_spikes.py
@@ -79,8 +79,9 @@ class RemoveExcessSpikesSortingSe... |
SpikeInterface__spikeinterface-2775 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/spikeinterface/core/sortinganalyzer.py:_get_children_dependencies"
],
"edited_modules": [
"src/spikeinterface/core/sortinganalyzer.py:_get_children_dependencies"
]
},
... | SpikeInterface/spikeinterface | c6f8f1fae2ed8fa80b59c42cf8d1cff523b3c754 | Split function and `new_unit_ids` definition
Hi !
I was looking into the curation module and didn't quite get how to use the split function. Let's say I want to split my unit into 3. To do so I just have to properly define my `indices_list` and then I could just do as so:
`cs.split(unit_id, indices_list)`
The cl... | diff --git a/src/spikeinterface/core/sortinganalyzer.py b/src/spikeinterface/core/sortinganalyzer.py
index 9edb52787..85ea9b843 100644
--- a/src/spikeinterface/core/sortinganalyzer.py
+++ b/src/spikeinterface/core/sortinganalyzer.py
@@ -1187,7 +1187,7 @@ def _get_children_dependencies(extension_name):
name... |
SpikeInterface__spikeinterface-3047 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/spikeinterface/core/sortinganalyzer.py:AnalyzerExtension.load_data"
],
"edited_modules": [
"src/spikeinterface/core/sortinganalyzer.py:AnalyzerExtension"
]
},
"file... | SpikeInterface/spikeinterface | e139e75d6d9a5bcbde9ce133db84a83ab7724a9e | `select_units` fails in `SortingAnalyzer` after using `load_sorting_analyzer`
## Problem
After saving a sorter (to binary_folder) and then reloading, you can no longer use the `select_units` function.
## MRE
```python
rec, sorting = si.generate_ground_truth_recording()
analyzer = si.create_sorting_analyzer(s... | diff --git a/src/spikeinterface/core/sortinganalyzer.py b/src/spikeinterface/core/sortinganalyzer.py
index 46d02099d..009401201 100644
--- a/src/spikeinterface/core/sortinganalyzer.py
+++ b/src/spikeinterface/core/sortinganalyzer.py
@@ -1608,7 +1608,9 @@ class AnalyzerExtension:
if self.format == "binary_folde... |
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