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 |
|---|---|---|---|---|---|
Deltares__pyflwdir-18 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyflwdir/dem.py:fill_depressions"
],
"edited_modules": [
"pyflwdir/dem.py:fill_depressions"
]
},
"file": "pyflwdir/dem.py"
}
] | Deltares/pyflwdir | 90be06f24c7d7ce9bbeeccf19b1452d5be8859d2 | prioritize non-boundary cells with same elevation over boundary cells in dem.fill_depressions | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index c0327c7..f240f71 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,16 @@
Change Log
###########
+Unreleased
+********************
+
+Improved
+---------
+* prioritize non-boundary cells with same elevation over boundary cells in dem.fill_depressions, #17
+
+B... |
Deltares__pyflwdir-41 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyflwdir/dem.py:fill_depressions"
],
"edited_modules": [
"pyflwdir/dem.py:fill_depressions"
]
},
"file": "pyflwdir/dem.py"
}
] | Deltares/pyflwdir | 3dd0e04d6cd53aea1d692b0052a83df784a18f6b | No implementation of function Function(<built-in function heappush>) found for signature
I'm trying to get started with pyflwdir -- it looks very powerful. But the code in the quickstart at https://deltares.github.io/pyflwdir/latest/quickstart.html fails when executed in a newly created Python 3.11.6 virtualenv (on Lin... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 99d12cb..92533a9 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,11 @@
Change Log
###########
+in development
+**************
+
+* Fixed support for interger type DEMs in `from_dem` and `dem.fill_depressions` methods
+
0.5.8 (06-Oct-2023)
***************... |
Deric-W__ascii_progress-9 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "ascii_progress/__main__.py"
},
{
"changes": {
"added_entities": [
"ascii_progress/bar.py:BarContext.__init__",
"ascii_progress/b... | Deric-W/ascii_progress | a5f5f2815ba25cdfdcf57a0f02c025ef9dc2a3b0 | improved context managers
Problem:
The messages displayed when using `Spinner` or `Bar` as context managers are hard coded.
Solution:
Add a `.handle_exceptions(message, error)` method to both classes which returns a context manager. | diff --git a/ascii_progress/__main__.py b/ascii_progress/__main__.py
index f5d1e15..b550f91 100644
--- a/ascii_progress/__main__.py
+++ b/ascii_progress/__main__.py
@@ -16,7 +16,7 @@ for frames in (
(">))'>", " >))'>", " >))'>", " <'((<", " <'((<", "<'((<")
):
sys.stdout.write("Working ")... |
DevoInc__python-sdk-109 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"devo/sender/lookup.py:Lookup.send_headers",
"devo/sender/lookup.py:Lookup.list_to_headers",
"devo/sender/lookup.py:Lookup.process_fields"
],
"edited_modules": [
"devo... | DevoInc/python-sdk | 805bb8561837e83ced05d8326e5cd24658a870ba | Lookup.send_headers method not working as expected with key_index parameter
By checking the Lookup docs, I can see the following parameters recommendation for the `Lookup.send_headers` method:
https://github.com/DevoInc/python-sdk/blob/84a4e2c9da8d3013cd8f012e4399994d64817035/docs/sender/lookup.md#L107-L108
If we c... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index d82fb96..28e86d5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
## Unreleased - 2021-11-18
### Fixed
* Fix and skip some non-working tests
+* `Lookup.send_headers` method not ... |
DevoInc__python-sdk-113 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"devo/sender/lookup.py:Lookup.__init__",
"devo/sender/lookup.py:Lookup.send_data_line",
"devo/sender/lookup.py:Lookup.send_csv",
"devo/sender/lookup.py:Lookup.field_to_str",
... | DevoInc/python-sdk | 3fa89f73be41307044fec587eb13b563201cd8f9 | Lookup API is unable to send records with a double quote character in their content
Right now, the `Lookup.clean_field` method wraps the field's content in double quotes, unless it is a number:
https://github.com/DevoInc/python-sdk/blob/84a4e2c9da8d3013cd8f012e4399994d64817035/devo/sender/lookup.py#L400-L414
Howeve... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 28e86d5..6686fd3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,7 +10,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
* `Lookup.send_headers` method not working as expected with key_index parameter
* Add `type_of_key` parameter ... |
DiCarloLab-Delft__PycQED_py3-651 | [
{
"changes": {
"added_entities": [
"pycqed/instrument_drivers/physical_instruments/ZurichInstruments/UHFQuantumController.py:UHFQC._get_minimum_holdoff"
],
"added_modules": null,
"edited_entities": [
"pycqed/instrument_drivers/physical_instruments/ZurichInstruments/UHFQua... | DiCarloLab-Delft/PycQED_py3 | 2d0c14ecd6cf9ee902394d1146bec40eeb5dabce | Instruments contained in meta instrument as parameter
I've been experimenting with a better way to have instruments referenced in meta instruments (such as the qubit object. Currently the instruments need to be given upon initialization of the instrument and are an attribute of the instrument that is not logged and can... | diff --git a/pycqed/instrument_drivers/physical_instruments/ZurichInstruments/UHFQuantumController.py b/pycqed/instrument_drivers/physical_instruments/ZurichInstruments/UHFQuantumController.py
index c8a554e6..569d17e2 100644
--- a/pycqed/instrument_drivers/physical_instruments/ZurichInstruments/UHFQuantumController.py
... |
DiamondLightSource__python-workflows-107 | [
{
"changes": {
"added_entities": [
"src/workflows/logging/__init__.py:CallbackHandler.handleError"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/workflows/logging/__init__.py:CallbackHandler"
]
},
"file": "src/workflows/lo... | DiamondLightSource/python-workflows | 8549c1ee333c73635705def66cbea5a0929a0e31 | PikaTransport `ChannelClose` errors are not propagated | diff --git a/src/workflows/logging/__init__.py b/src/workflows/logging.py
similarity index 79%
rename from src/workflows/logging/__init__.py
rename to src/workflows/logging.py
index 2d50e99..5b03cf7 100644
--- a/src/workflows/logging/__init__.py
+++ b/src/workflows/logging.py
@@ -64,3 +64,18 @@ class CallbackHandler(lo... |
DiamondLightSource__python-zocalo-147 | [
{
"changes": {
"added_entities": [
"src/zocalo/util/rabbitmq.py:RabbitMQAPI.post",
"src/zocalo/util/rabbitmq.py:RabbitMQAPI.bindings",
"src/zocalo/util/rabbitmq.py:RabbitMQAPI.binding_declare",
"src/zocalo/util/rabbitmq.py:RabbitMQAPI.bindings_delete"
],
"added_... | DiamondLightSource/python-zocalo | fd345bdc6ce3d0a389219058ed2fdd2e42a512dc | Configuration script needs to add bindings to support delayed messages exchanges
`RabbitMQAPI` in `zocalo.util.rabbitmq` needs extending to support bindings to allow the configuration of queues bound to exchanges other than the default exchange | diff --git a/src/zocalo/util/rabbitmq.py b/src/zocalo/util/rabbitmq.py
index d132aac..7dbda08 100644
--- a/src/zocalo/util/rabbitmq.py
+++ b/src/zocalo/util/rabbitmq.py
@@ -12,7 +12,7 @@ from workflows.transport import pika_transport
import zocalo.configuration
-logger = logging.getLogger("workflows.transport.pika... |
Diaoul__babelfish-50 | [
{
"changes": {
"added_entities": [
"babelfish/country.py:Country.__post_init__",
"babelfish/country.py:Country.alpha2"
],
"added_modules": null,
"edited_entities": [
"babelfish/country.py:Country.__init__",
"babelfish/country.py:Country.__getstate__",
... | Diaoul/babelfish | 7584c2ae86d2171094287b035a0c78fad5db4b1c | Immutability issues
Currently babelfish implements the hash function to override default behavior and make it possible for objects to be keys in dictionaries and other useful features.
While this is a good thing, the way it is implemented makes it prone to some weird errors as explained in [this lyft blog post](https... | diff --git a/babelfish/country.py b/babelfish/country.py
index 4c3893d..0ffb33f 100644
--- a/babelfish/country.py
+++ b/babelfish/country.py
@@ -5,6 +5,7 @@
from __future__ import annotations
from collections import namedtuple
+from dataclasses import dataclass
from functools import partial
from typing import Any... |
Digital-Sapphire__PyUpdater-226 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyupdater/client/__init__.py:Client.__init__",
"pyupdater/client/__init__.py:Client._gen_file_downloader_options",
"pyupdater/client/__init__.py:Client._update_check",
"pyupdater... | Digital-Sapphire/PyUpdater | 1abe00d602327eb106a0a220b03366eca6ea6553 | Honor HTTP_TIMEOUT in FileDownloader
**Problem:** Developers can set the `HTTP_TIMEOUT` in their client configuration. This variable does not seem to be honored in the codebase. As a consequence, there are instances where this can cause an application to hang indefinitely waiting for a response, leaving the applicati... | diff --git a/docs/api.md b/docs/api.md
index 9c62f39..15a8466 100644
--- a/docs/api.md
+++ b/docs/api.md
@@ -95,7 +95,7 @@ progress_hooks (list): List of callbacks
data_dir (str): Path to custom update folder
-headers (dict): A urllib3.utils.make_headers compatible dictionary
+headers (dict): A dictionary of gener... |
DigitaleGesellschaft__Anonip-48 | [
{
"changes": {
"added_entities": [
"anonip.py:Anonip.process_line_regex",
"anonip.py:Anonip.process_line_column",
"anonip.py:regex_arg_type"
],
"added_modules": [
"anonip.py:regex_arg_type"
],
"edited_entities": [
"anonip.py:Anonip.__init__",... | DigitaleGesellschaft/Anonip | b516ea91a1fb74a37976a32055785d1241f7e067 | nginx error logs not masked
I have trouble getting anonip to mask IPs in my nginx error.log file.
When I execute anonip as root, I receive the following error message:
```
# anonip < /var/log/nginx/error.log
WARNING:anonip:'2020' does not appear to be an IPv4 or IPv6 network
2020/03/05 19:27:43 [error] 1253#12... | diff --git a/README.md b/README.md
index 9532467..0947cd0 100644
--- a/README.md
+++ b/README.md
@@ -34,6 +34,7 @@ Using shell redirects, it's also possible to rewrite existing log files.
- Masks IP addresses in log files
- Configurable amount of masked bits
- The column containing the IP address can freely be ch... |
DinoTools__python-overpy-18 | [
{
"changes": {
"added_entities": [
"overpy/__init__.py:OSMSAXHandler.__init__",
"overpy/__init__.py:OSMSAXHandler.startElement",
"overpy/__init__.py:OSMSAXHandler.endElement",
"overpy/__init__.py:OSMSAXHandler._handle_start_tag",
"overpy/__init__.py:OSMSAXHandler._h... | DinoTools/python-overpy | ac7df97ef4302d7eda46a6bb34a887e9b275748c | Less memory-consuming xml parsing
Currently the whole xml-result is first parsed into a xml.etree.ElementTree and than processed to create overpy structures. While this is perfectly fine for small amounts of data, larger files or requests consume a lot of memory that is not freed after the overpy result is constructed.... | diff --git a/overpy/__init__.py b/overpy/__init__.py
index 454e1f5..cf48898 100644
--- a/overpy/__init__.py
+++ b/overpy/__init__.py
@@ -1,5 +1,6 @@
from collections import OrderedDict
from decimal import Decimal
+from xml.sax import handler, make_parser
import json
import re
import sys
@@ -14,6 +15,9 @@ from over... |
DinoTools__python-overpy-64 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"overpy/__init__.py:Result.from_xml"
],
"edited_modules": [
"overpy/__init__.py:Result"
]
},
"file": "overpy/__init__.py"
}
] | DinoTools/python-overpy | d49ad8080ff9e9da3081a240380915b159172a87 | Result.from_xml data argument has a wrong type doc
Passing Element as a data argument to Result.from_xml() as docstring suggests raises Exception.
```
>>> overpy.Result.from_xml(xml.etree.ElementTree.fromstring("<osm />"))
Traceback (most recent call last):
File "<input>", line 1, in <module>
File "/home/w/osm... | diff --git a/overpy/__init__.py b/overpy/__init__.py
index 13de583..377c28d 100644
--- a/overpy/__init__.py
+++ b/overpy/__init__.py
@@ -349,23 +349,39 @@ class Result(object):
return result
@classmethod
- def from_xml(cls, data, api=None, parser=XML_PARSER_SAX):
+ def from_xml(cls, data, api=None... |
DinoTools__python-overpy-65 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"overpy/__init__.py:Element.__init__"
],
"edited_modules": [
"overpy/__init__.py:Element"
]
},
"file": "overpy/__init__.py"
}
] | DinoTools/python-overpy | daa6a72748c3e682f4ffe65fe4b9bfbc788d10b1 | Can't pickle overpy.Result
<!--- Verify first that your issue/request has not already been reported -->
##### Issue type
- Bug Report
##### OverPy version
<!--- Paste verbatim output from “python -c 'import overpy; print(overpy.__version__)'” or the hash of the git commit between quotes below. -->
```
0.4
`... | diff --git a/overpy/__init__.py b/overpy/__init__.py
index 377c28d..6aa887a 100644
--- a/overpy/__init__.py
+++ b/overpy/__init__.py
@@ -19,6 +19,16 @@ PY3 = sys.version_info[0] == 3
XML_PARSER_DOM = 1
XML_PARSER_SAX = 2
+# Try to convert some common attributes
+# http://wiki.openstreetmap.org/wiki/Elements#Common_... |
Domain-Connect__domainconnect_python-5 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"domainconnect/domainconnect.py:DomainConnect.identify_domain_root"
],
"edited_modules": [
"domainconnect/domainconnect.py:DomainConnect"
]
},
"file": "domainconnect/dom... | Domain-Connect/domainconnect_python | 23f91c72851c6303c876bd1d6957c2236ac0e1cc | Doesn't work for .app domains
Hi,
i was trying to use it with an .app domain but it did not work.
Looks like it is doing a DNS lookup for
_domainconnect.app
instead of
_domainconnect.domain.app
Full command line and error message below.
Can you check and fix it please?
regards
michael
\# domain-conne... | diff --git a/README.md b/README.md
index 4e0bd1c..c96f770 100644
--- a/README.md
+++ b/README.md
@@ -145,5 +145,6 @@ dc = DomainConnect(
## CHANGELOG
| version | date | changes |
| ------- | -----------| ------ |
+| 0.0.7 | 2019-10-29 | Bugfix: error when setting up .app domain |
| 0.0.6 | 2019-07-05 | UPDA... |
Dorthu__openapi3-30 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openapi3/schemas.py:Schema._parse_data"
],
"edited_modules": [
"openapi3/schemas.py:Schema"
]
},
"file": "openapi3/schemas.py"
}
] | Dorthu/openapi3 | 528da892d379f1b813055c781043139cb9dac41a | openapi3.errors.SpecError when minimum/maximum validation is float
The following file::
<details><summary><code>openapi.json</code></summary>
```json
{
"openapi": "3.0.3",
"info": {
"title": "Foo",
"version": "1.0.0"
},
"paths": {
"/foo": {
"post": {
... | diff --git a/openapi3/schemas.py b/openapi3/schemas.py
index 78ab0c3..081b28a 100644
--- a/openapi3/schemas.py
+++ b/openapi3/schemas.py
@@ -33,8 +33,8 @@ class Schema(ObjectBase):
Implementation of :any:`ObjectBase._parse_data`
"""
self.title = self._get('title', str)
- ... |
Dorthu__openapi3-57 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openapi3/object_base.py:ObjectBase._get"
],
"edited_modules": [
"openapi3/object_base.py:ObjectBase"
]
},
"file": "openapi3/object_base.py"
},
{
"changes": {
... | Dorthu/openapi3 | ab4065a8cefac09253b3709121ad5b8b9241fb5a | openapi3.errors.SpecError: Could not parse paths./api/v1/auth/login/.post.security.2, expected to be one of [['SecurityRequirement']]
Python test client:
```python
import yaml
import requests
from openapi3 import OpenAPI
url = 'http://localhost/schema_openapi/'
response = requests.get(url, allow_redirects=True)
... | diff --git a/openapi3/object_base.py b/openapi3/object_base.py
index b3e0a0d..9932822 100644
--- a/openapi3/object_base.py
+++ b/openapi3/object_base.py
@@ -217,75 +217,76 @@ class ObjectBase(object):
self._accessed_members.append(field)
ret = self.raw_element.get(field, None)
+ if ret is Non... |
Dorthu__openapi3-75 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openapi3/openapi.py:OpenAPI.resolve_path"
],
"edited_modules": [
"openapi3/openapi.py:OpenAPI"
]
},
"file": "openapi3/openapi.py"
}
] | Dorthu/openapi3 | 0e02198948258b69e666f53aa2b22fcf4da62f97 | Doesn't resolve JSON path escape codes
RFC 6901 says that `~1` must be de-escaped to `/` and `~0` is de-escaped to `~` (in this order). | diff --git a/openapi3/openapi.py b/openapi3/openapi.py
index 5b79b14..0b2c753 100644
--- a/openapi3/openapi.py
+++ b/openapi3/openapi.py
@@ -101,16 +101,27 @@ class OpenAPI(ObjectBase):
node = self
for part in path:
+ part = part.replace('~1','/').replace('~0','~')
if isinsta... |
Dorthu__openapi3-77 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openapi3/example.py:Example._parse_data"
],
"edited_modules": [
"openapi3/example.py:Example"
]
},
"file": "openapi3/example.py"
},
{
"changes": {
"added_... | Dorthu/openapi3 | 9b4dc86bc736eddb8b7f1e6c88392fc35dc65b1a | SpecError when the result is an array
```
openapi3.errors.SpecError: Expected paths./phone/batch_locations.post.responses.201.content.application/json.examples.response.value to be one of [Reference,<class 'dict'>,<class 'str'>], got <class 'list'>
```
The attached file is a reduced version of the spec that exhibi... | diff --git a/openapi3/example.py b/openapi3/example.py
index ea9a959..b2185d0 100644
--- a/openapi3/example.py
+++ b/openapi3/example.py
@@ -17,5 +17,5 @@ class Example(ObjectBase):
"""
self.summary = self._get("summary", str)
self.description = self._get("description", str)
- self.val... |
Dorthu__openapi3-83 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"openapi3/info.py:Contact"
]
},
"file": "openapi3/info.py"
}
] | Dorthu/openapi3 | dc791af2ff58e8170c21c2775df091c421829b48 | Contact fields that should be optional are considered required, resulting in raised SpecError.
When parsing a JSON spec, if the `contact` object is specified but missing _any_ of `name`, `url`, or `email`, a `SpecError` is raised:
```
openapi3.errors.SpecError: Expected info.contact to be of type Contact, with requir... | diff --git a/openapi3/info.py b/openapi3/info.py
index 4bc332f..66ea9f7 100644
--- a/openapi3/info.py
+++ b/openapi3/info.py
@@ -31,7 +31,7 @@ class Contact(ObjectBase):
"""
__slots__ = ["name", "url", "email"]
- required_fields = ["name", "url", "email"]
+ required_fields = []
def _parse_data(... |
Dorthu__openapi3-90 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"openapi3/general.py:ExternalDocumentation"
]
},
"file": "openapi3/general.py"
},
{
"changes": {
"added_entities": null,
"added_modules": n... | Dorthu/openapi3 | 7039a15e65477b505467b85bcd09215645f3ec9a | Bug causing "SpecError: Expected externalDocs to be of type ExternalDocumentation with required fields url"
Hello, after breaking my head for a couple of days trying to figure out why I was getting the aforementioned error saying that the `externalDocs` object could not be parsed.
Finally I found the problem and iso... | diff --git a/openapi3/general.py b/openapi3/general.py
index dd453a6..fbe2666 100644
--- a/openapi3/general.py
+++ b/openapi3/general.py
@@ -9,8 +9,8 @@ class ExternalDocumentation(ObjectBase):
.. _External Documentation Object: https://github.com/OAI/OpenAPI-Specification/blob/master/versions/3.0.1.md#externalDoc... |
Dorthu__openapi3-94 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "openapi3/schemas.py"
}
] | Dorthu/openapi3 | fba9f2785a822e951e9e13f44486840f4e03d80e | [Bug] - Expects incorrect type on parameter default
Trying to parse a spec containing a parameter component with a numeric default with incorrectly throw and states that a string default was expected.
Version: `1.7.0`
Minimal example spec:
```yaml
openapi: 3.0.0
info:
title: Test api
description: te... | diff --git a/openapi3/schemas.py b/openapi3/schemas.py
index 0796552..d454e47 100644
--- a/openapi3/schemas.py
+++ b/openapi3/schemas.py
@@ -8,6 +8,7 @@ TYPE_LOOKUP = {
"object": dict,
"string": str,
"boolean": bool,
+ "number": float,
}
|
DropD__reentry-50 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"reentry/config.py:get_config",
"reentry/config.py:make_data_file_name",
"reentry/config.py:get_datafile"
],
"edited_modules": [
"reentry/config.py:get_config",
... | DropD/reentry | 06cabf7841d1fdb78d68cbd8395598d16d8ab286 | What is the rational behind pkg_path_filename in get_datafile()?
Hi :)
First of all, thanks for a great package!
I would like to know if the name of the filename created in get_datafile function (config.py) has some important meaning and weather of not it can be changed.
This name can be a little problematic whe... | diff --git a/README.rst b/README.rst
index 79101b2..6b33db1 100644
--- a/README.rst
+++ b/README.rst
@@ -20,7 +20,7 @@ Features
Note that ``reentry_register`` creates a *build-time*
dependency on ``reentry``. The suggested way to resolve that is using the
method described in `PEP518 <https://www.python.org/dev/peps/... |
Duke-GCB__DukeDSClient-113 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/cmdparser.py:to_unicode"
],
"edited_modules": [
"ddsc/cmdparser.py:to_unicode"
]
},
"file": "ddsc/cmdparser.py"
},
{
"changes": {
"added_entities": n... | Duke-GCB/DukeDSClient | a1ffd407bc0dd886c892eb0667f79d08317f7b84 | Check for lowercase utf-8 in encoding
Testing Windows 7 with Anaconda(python 3.6) 4.3.0 ignores the PYTHONIOENCODING value and displays lowercase utf-8.
Change the code in ddsc/core/util.py verify_terminal_encoding to ignore case. | diff --git a/ddsc/cmdparser.py b/ddsc/cmdparser.py
index 91f6940..fdceb62 100644
--- a/ddsc/cmdparser.py
+++ b/ddsc/cmdparser.py
@@ -3,6 +3,7 @@ Command line parser for the application.
"""
import os
import argparse
+import six
from builtins import str
@@ -26,7 +27,7 @@ def to_unicode(s):
:param s: string ... |
Duke-GCB__DukeDSClient-116 | [
{
"changes": {
"added_entities": [
"ddsc/core/ddsapi.py:DataServiceApi.get_auth_providers",
"ddsc/core/ddsapi.py:DataServiceApi.auth_provider_add_user"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"ddsc/core/ddsapi.py:DataServiceApi... | Duke-GCB/DukeDSClient | 759ef9203db06b482365c4d04d669b24bdeedcca | For Share/Deliver, register users in DukeDS as needed
The API to create a DukeDS user is at https://apidev.dataservice.duke.edu/apidocs/users_software_agents.html#auth-provider-affiliates-not_impl_new-create-or-get-user-account-for-affiliate-post, and while we can register users through this API, DukeDS will not automa... | diff --git a/ddsc/core/ddsapi.py b/ddsc/core/ddsapi.py
index f79d7bf..2039628 100644
--- a/ddsc/core/ddsapi.py
+++ b/ddsc/core/ddsapi.py
@@ -747,6 +747,26 @@ class DataServiceApi(object):
}
return self._put("/activities/" + activity_id, put_data)
+ def get_auth_providers(self):
+ """
+ ... |
Duke-GCB__DukeDSClient-124 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/cmdparser.py:CommandParser.register_add_user_command",
"ddsc/cmdparser.py:CommandParser.register_remove_user_command"
],
"edited_modules": [
"ddsc/cmdparser.py:CommandPa... | Duke-GCB/DukeDSClient | fb617c41b09cfd859fc50b93308e3680e209069b | Remove duplicate commands in commandline.
There shouldn't be both add-user and add_user in the help. | diff --git a/ddsc/cmdparser.py b/ddsc/cmdparser.py
index 4f381b6..4d6e9c0 100644
--- a/ddsc/cmdparser.py
+++ b/ddsc/cmdparser.py
@@ -271,7 +271,6 @@ class CommandParser(object):
"""
description = "Gives user permission to access a remote project."
add_user_parser = self.subparsers.add_parser(... |
Duke-GCB__DukeDSClient-131 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/localstore.py:LocalFile.count_chunks"
],
"edited_modules": [
"ddsc/core/localstore.py:LocalFile"
]
},
"file": "ddsc/core/localstore.py"
}
] | Duke-GCB/DukeDSClient | e158990c3f68aef9ed4731aa446cea6d49be2950 | File Synchronization issue between portal and ddsclient
User feedback:
> As you may be aware, if a project has been modified via the web-portal, ddsclient seems to get confused. For example, If a file from a project has been removed via the web-portal, the ddsclient will ignore an upload request that would re-instan... | diff --git a/ddsc/core/localstore.py b/ddsc/core/localstore.py
index db0fa4b..9ced1a4 100644
--- a/ddsc/core/localstore.py
+++ b/ddsc/core/localstore.py
@@ -231,7 +231,14 @@ class LocalFile(object):
self.remote_id = remote_id
def count_chunks(self, bytes_per_chunk):
- return math.ceil(float(self.... |
Duke-GCB__DukeDSClient-144 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/ddsapi.py:DataServiceApi._get_single_page",
"ddsc/core/ddsapi.py:DataServiceApi._get_collection",
"ddsc/core/ddsapi.py:DataServiceApi._get_children",
"ddsc/core/ddsapi.... | Duke-GCB/DukeDSClient | c6a1ad6afa8af78f858a59f7f6c129501a537b83 | DDSClient is creating multiple projects with the same name
Email report from David Corcoran:
DDS client is currently creating multiple projects with the same name. Can you please make it so that there is an error when this is attempted?
I also got the occasional error (see attached). It happened for a handful... | diff --git a/ddsc/core/ddsapi.py b/ddsc/core/ddsapi.py
index b02dc6b..1633145 100644
--- a/ddsc/core/ddsapi.py
+++ b/ddsc/core/ddsapi.py
@@ -238,41 +238,40 @@ class DataServiceApi(object):
resp = self.http.get(url, headers=headers, params=data_str)
return self._check_err(resp, url_suffix, data, allow_... |
Duke-GCB__DukeDSClient-153 | [
{
"changes": {
"added_entities": [
"ddsc/cmdparser.py:_add_project_filter_auth_role_arg"
],
"added_modules": [
"ddsc/cmdparser.py:_add_project_filter_auth_role_arg"
],
"edited_entities": [
"ddsc/cmdparser.py:CommandParser.register_list_command"
],
... | Duke-GCB/DukeDSClient | 0293338fa21dd12611e2991d012a1c4e801a361f | Add option to filter projects by role
Me:
> ... Duke DS team has developed a UI change to include the project role in the project listing (screenshot attached). This is on their dev server (https://dev.dataservice.duke.edu), and they’ve asked for feedback.
>
> One suggestion I’d have would be a select box to let ... | diff --git a/ddsc/cmdparser.py b/ddsc/cmdparser.py
index b64cb30..9bf2a7b 100644
--- a/ddsc/cmdparser.py
+++ b/ddsc/cmdparser.py
@@ -160,6 +160,21 @@ def _add_auth_role_arg(arg_parser, default_permissions):
default=default_permissions)
+def _add_project_filter_auth_role_arg(arg_parser):... |
Duke-GCB__DukeDSClient-158 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/util.py:verify_terminal_encoding"
],
"edited_modules": [
"ddsc/core/util.py:verify_terminal_encoding"
]
},
"file": "ddsc/core/util.py"
}
] | Duke-GCB/DukeDSClient | 3137fc3d94da3754c85715f3912bbebbe22d19be | Checks for terminal encoding prevents piping/redirection
Noticed when I was reviewing #153 that I can't pipe the output of ddsclient anywhere because it fails the terminal encoding check:
```
$ ddsclient list > projects
ERROR: DukeDSClient requires UTF terminal encoding.
Follow this guide for adjusting your t... | diff --git a/ddsc/core/util.py b/ddsc/core/util.py
index 8307bb0..1af9afc 100644
--- a/ddsc/core/util.py
+++ b/ddsc/core/util.py
@@ -301,8 +301,7 @@ def verify_terminal_encoding(encoding):
Raises ValueError with error message when terminal encoding is not Unicode(contains UTF ignoring case).
:param encoding: ... |
Duke-GCB__DukeDSClient-160 | [
{
"changes": {
"added_entities": [
"ddsc/core/projectuploader.py:UploadContext.start_waiting"
],
"added_modules": null,
"edited_entities": [
"ddsc/core/projectuploader.py:UploadContext.started_waiting"
],
"edited_modules": [
"ddsc/core/projectuploader.... | Duke-GCB/DukeDSClient | 4125429b9a10ee60a92456a5bd2b4b207e625a45 | AttributeError: 'UploadContext' object has no attribute 'start_waiting'
In refactoring the name of the method I missed one case.
UploadContext method should be `start_waiting` (ddsc/core/projectuploader.py). | diff --git a/ddsc/core/projectuploader.py b/ddsc/core/projectuploader.py
index 926df55..7498835 100644
--- a/ddsc/core/projectuploader.py
+++ b/ddsc/core/projectuploader.py
@@ -78,7 +78,7 @@ class UploadContext(object):
"""
self.message_queue.put((self.task_id, data))
- def started_waiting(self):... |
Duke-GCB__DukeDSClient-179 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/cmdparser.py:CommandParser.__init__"
],
"edited_modules": [
"ddsc/cmdparser.py:CommandParser"
]
},
"file": "ddsc/cmdparser.py"
},
{
"changes": {
"add... | Duke-GCB/DukeDSClient | 72ec820e45dd44ba14ff86476c71f2dc40f2088e | Show the ddsclient version in help or with a --version argument
When running ddsclient, it will print a message about a newer version, but I can't find any command-line option to print the current version. Obviously I can `pip freeze` but the tool should be able to report its own version | diff --git a/ddsc/cmdparser.py b/ddsc/cmdparser.py
index dd3c1bf..8cc145e 100644
--- a/ddsc/cmdparser.py
+++ b/ddsc/cmdparser.py
@@ -6,7 +6,7 @@ import argparse
import six
from builtins import str
-
+DESCRIPTION_STR = "DukeDSClient ({}) Manage projects/folders/files in the duke-data-service"
INVALID_PATH_CHARS = (... |
Duke-GCB__DukeDSClient-204 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/cmdparser.py:_add_copy_project_arg",
"ddsc/cmdparser.py:CommandParser.register_deliver_command"
],
"edited_modules": [
"ddsc/cmdparser.py:_add_copy_project_arg",
... | Duke-GCB/DukeDSClient | b8274d3185ec78ca47a772c1fb644ba319dedd80 | Should --skip-copy be the default?
I want to revisit this choice. When delivering data, it's certainly unexpected that ddsclient will download the entire project and upload a copy. I'll reach out to the users but it may be a better default to skip the copy, and require a `--copy` argument to make a copy before deliveri... | diff --git a/ddsc/cmdparser.py b/ddsc/cmdparser.py
index f2f6ec5..456f8db 100644
--- a/ddsc/cmdparser.py
+++ b/ddsc/cmdparser.py
@@ -222,11 +222,11 @@ def _add_copy_project_arg(arg_parser):
Adds optional copy_project parameter to a parser.
:param arg_parser: ArgumentParser parser to add this argument to.
... |
Duke-GCB__DukeDSClient-207 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/upload.py:ProjectUpload.get_url_msg"
],
"edited_modules": [
"ddsc/core/upload.py:ProjectUpload"
]
},
"file": "ddsc/core/upload.py"
}
] | Duke-GCB/DukeDSClient | b8274d3185ec78ca47a772c1fb644ba319dedd80 | URL to view project returns 404
Issue due to changes in DukeDS portal url changes.
Similar to https://github.com/Duke-GCB/D4S2/issues/175 | diff --git a/ddsc/core/upload.py b/ddsc/core/upload.py
index d702e0d..cb46c47 100644
--- a/ddsc/core/upload.py
+++ b/ddsc/core/upload.py
@@ -103,7 +103,7 @@ class ProjectUpload(object):
"""
msg = 'URL to view project'
project_id = self.local_project.remote_id
- url = '{}: https://{}/po... |
Duke-GCB__DukeDSClient-210 | [
{
"changes": {
"added_entities": [
"ddsc/core/ddsapi.py:DataServiceApi.get_users",
"ddsc/core/ddsapi.py:DataServiceApi.get_auth_provider",
"ddsc/core/ddsapi.py:DataServiceApi.get_auth_provider_affiliates"
],
"added_modules": null,
"edited_entities": [
"dds... | Duke-GCB/DukeDSClient | 570bc4954d51f662e294b2f2352248623ea8bf8b | Make use of DukeDS user filtering improvements
DukeDS API has been updated to allow filtering users by email and/or username: https://github.com/Duke-Translational-Bioinformatics/duke-data-service/issues/1103
This will speed up how long it takes to list users.
NOTE: This is new feature currently deployed to DukeDS ... | diff --git a/ddsc/core/ddsapi.py b/ddsc/core/ddsapi.py
index c026b27..71710f4 100644
--- a/ddsc/core/ddsapi.py
+++ b/ddsc/core/ddsapi.py
@@ -609,12 +609,21 @@ class DataServiceApi(object):
}
return self._get_collection('/users', data)
- def get_all_users(self):
+ def get_users(self, full_name=... |
Duke-GCB__DukeDSClient-215 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/download.py:RetryChunkDownloader.download_chunk"
],
"edited_modules": [
"ddsc/core/download.py:RetryChunkDownloader"
]
},
"file": "ddsc/core/download.py"
}
... | Duke-GCB/DukeDSClient | e2cf592ba0d9b2ee1bfdf51a723677275fee3998 | User received TooLargeChunkDownloadError exception
User was downloading a project via `ddsclient download -p <projectname> --include <filepath>`.
Error:
```
File ".../conda/envs/bespin/lib/python3.7/site-packages/ddsc/core/download.py", line 455,
in _write_response_to_file
self._on_bytes_read(len(chunk))
... | diff --git a/ddsc/core/download.py b/ddsc/core/download.py
index f9bf81b..545d438 100644
--- a/ddsc/core/download.py
+++ b/ddsc/core/download.py
@@ -439,6 +439,7 @@ class RetryChunkDownloader(object):
if response.status_code == 401:
raise DownloadInconsistentError(response.text)
response.... |
Duke-GCB__DukeDSClient-230 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/download.py:RetryChunkDownloader.get_url_and_headers_for_range",
"ddsc/core/download.py:RetryChunkDownloader.download_chunk"
],
"edited_modules": [
"ddsc/core/downl... | Duke-GCB/DukeDSClient | 95e2d44613240a68d78da8c887acfbcab18f5136 | Error 403 downloading project from s3 backend
Error printed out by ddsclient:
```
requests.exceptions.HTTPError: 403 Client Error: Forbidden for
url: https://eso.duhs.duke.edu//ca....
```
Payload returned by S3:
```
<Error><Code>SignatureDoesNotMatch</Code><Message>The request signature we calculated
does not ... | diff --git a/ddsc/core/download.py b/ddsc/core/download.py
index 545d438..b8ec446 100644
--- a/ddsc/core/download.py
+++ b/ddsc/core/download.py
@@ -12,6 +12,8 @@ from ddsc.core.remotestore import RemoteStore, ProjectFile, RemoteFileUrl
FETCH_EXTERNAL_PUT_RETRY_TIMES = 5
FETCH_EXTERNAL_RETRY_SECONDS = 20
RESOURCE_NO... |
Duke-GCB__DukeDSClient-238 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/ddsapi.py:DataServiceApi.create_upload"
],
"edited_modules": [
"ddsc/core/ddsapi.py:DataServiceApi"
]
},
"file": "ddsc/core/ddsapi.py"
},
{
"changes":... | Duke-GCB/DukeDSClient | a14dc08e5c37446b489d9aed5def6bf5fd0fd445 | Empty files fail to upload to DukeDS S3 backend
This results in an error like `Failed to send file to external store. Error:400 https...`.
This error occurs when uploading the file to the S3 backend.
The text response from the exception:
```
<Error><Code>InvalidPartSizeZero</Code><Message>The upload part size canno... | diff --git a/ddsc/core/ddsapi.py b/ddsc/core/ddsapi.py
index 0ec7f94..d0dd066 100644
--- a/ddsc/core/ddsapi.py
+++ b/ddsc/core/ddsapi.py
@@ -470,7 +470,7 @@ class DataServiceApi(object):
return self._get_collection(url_prefix, data)
def create_upload(self, project_id, filename, content_type, size,
- ... |
Duke-GCB__DukeDSClient-259 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/sdk/client.py:Client.__init__"
],
"edited_modules": [
"ddsc/sdk/client.py:Client"
]
},
"file": "ddsc/sdk/client.py"
},
{
"changes": {
"added_entities... | Duke-GCB/DukeDSClient | 0c15a9a50957abe806c7b2b6cad6a58f9d3aa61b | Importing DukeDS module checks config file
When a user imports the DukeDS module it reads and verifies the associated config file.
https://github.com/Duke-GCB/DukeDSClient/blob/0c15a9a50957abe806c7b2b6cad6a58f9d3aa61b/ddsc/sdk/client.py#L19
Importing a module shouldn't perform an action. | diff --git a/ddsc/sdk/client.py b/ddsc/sdk/client.py
index e7b6e16..578c6d2 100644
--- a/ddsc/sdk/client.py
+++ b/ddsc/sdk/client.py
@@ -16,10 +16,12 @@ class Client(object):
Client that connects to the DDSConnection base on ~/.ddsclient configuration.
This configuration can be customized by passing in a ddsc... |
Duke-GCB__DukeDSClient-270 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/d4s2.py:UploadedFileRelations._lookup_used_entity_id"
],
"edited_modules": [
"ddsc/core/d4s2.py:UploadedFileRelations"
]
},
"file": "ddsc/core/d4s2.py"
}
] | Duke-GCB/DukeDSClient | 16d75079cbc28b048fdc547e928e8778190d8e9c | Delivery with --copy flag fails with KeyError
This fails trying to create a relationship between the original file and the copy that will be delivered:
```
File ".../ddsc/core/d4s2.py", line 467, in run
used_entity_id = self._lookup_used_entity_id(file_details)
File ".../ddsc/core/d4s2.py", line 484, in _lo... | diff --git a/ddsc/core/d4s2.py b/ddsc/core/d4s2.py
index d913995..62642a0 100644
--- a/ddsc/core/d4s2.py
+++ b/ddsc/core/d4s2.py
@@ -12,7 +12,7 @@ from ddsc.core.download import ProjectDownload
from ddsc.core.ddsapi import DataServiceAuth
from ddsc.core.util import KindType
from ddsc.versioncheck import get_internal... |
Duke-GCB__DukeDSClient-271 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/d4s2.py:D4S2Project._upload_project"
],
"edited_modules": [
"ddsc/core/d4s2.py:D4S2Project"
]
},
"file": "ddsc/core/d4s2.py"
},
{
"changes": {
"... | Duke-GCB/DukeDSClient | 16d75079cbc28b048fdc547e928e8778190d8e9c | Improve upload performance for existing projects
Currently when uploading files to an existing project ddsclient runs a serial process that compares local file hashes against remote files hashes. It performs this comparison to skip files that have already been successfully uploaded. This process can take quite some tim... | diff --git a/ddsc/core/d4s2.py b/ddsc/core/d4s2.py
index d913995..edab984 100644
--- a/ddsc/core/d4s2.py
+++ b/ddsc/core/d4s2.py
@@ -372,10 +372,12 @@ class D4S2Project(object):
:param temp_directory: str path to directory who's files we will upload
"""
self.print_func("Uploading to '{}'.".fo... |
Duke-GCB__DukeDSClient-283 | [
{
"changes": {
"added_entities": [
"ddsc/core/download.py:ProjectDownload.get_included_project_files"
],
"added_modules": null,
"edited_entities": [
"ddsc/core/download.py:ProjectDownload.run",
"ddsc/core/download.py:ProjectDownload.get_files_to_download"
],... | Duke-GCB/DukeDSClient | 535994f973ae20d05ae4be968b2faa1192bb8a4d | improve communication when downloading a project
A user re-ran a failed `ddsclient download` command and was concerned about verifying the file hashes for the files downloaded in the first run. When ddsclient downloads a project the first thing it does is create file hashes for any local files and compares them to the... | diff --git a/ddsc/core/download.py b/ddsc/core/download.py
index dab4306..ca96cc6 100644
--- a/ddsc/core/download.py
+++ b/ddsc/core/download.py
@@ -4,7 +4,7 @@ import traceback
import math
import requests
from ddsc.core.localstore import HashUtil
-from ddsc.core.util import ProgressPrinter
+from ddsc.core.util impo... |
Duke-GCB__DukeDSClient-286 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/download.py:FileDownloader._create_task_runner"
],
"edited_modules": [
"ddsc/core/download.py:FileDownloader"
]
},
"file": "ddsc/core/download.py"
},
{
... | Duke-GCB/DukeDSClient | f93da42349cec1d9b86e9ccb789356592694c6de | download hangs after completing on windows
On windows after downloading larger files the terminal hangs after finishing downloading and verifying the data. This seems to be related to not closing the multiprocessing pool.
I found that closing the multiprocessing pool fixes this problem.
https://github.com/Duke-GCB/Du... | diff --git a/ddsc/core/download.py b/ddsc/core/download.py
index ca96cc6..c24935f 100644
--- a/ddsc/core/download.py
+++ b/ddsc/core/download.py
@@ -5,7 +5,7 @@ import math
import requests
from ddsc.core.localstore import HashUtil
from ddsc.core.util import ProgressPrinter, plural_fmt
-from ddsc.core.parallel import... |
Duke-GCB__DukeDSClient-289 | [
{
"changes": {
"added_entities": [
"ddsc/core/localstore.py:_on_non_regular_file"
],
"added_modules": [
"ddsc/core/localstore.py:_on_non_regular_file"
],
"edited_entities": [
"ddsc/core/localstore.py:LocalProject.add_path",
"ddsc/core/localstore.py:_... | Duke-GCB/DukeDSClient | bd6172fde42acdea23b89491579d127f5af6b281 | ddsclient upload stuck
A user reported an upload that appeared to be stuck.
I was able to look at the process in linux.
Using `lsof -u <user>` I saw that there were several TCP connections back to DukeDS API (heroku) that were stuck in CLOSE_WAIT.
| diff --git a/ddsc/core/localstore.py b/ddsc/core/localstore.py
index d8d38ec..27e0866 100644
--- a/ddsc/core/localstore.py
+++ b/ddsc/core/localstore.py
@@ -2,6 +2,7 @@ import hashlib
import math
import mimetypes
import os
+from os.path import isfile, isdir
from ddsc.core.ignorefile import FileFilter, IgnoreFilePat... |
Duke-GCB__DukeDSClient-303 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/download.py:ProjectFileDownloader.make_download_speed"
],
"edited_modules": [
"ddsc/core/download.py:ProjectFileDownloader"
]
},
"file": "ddsc/core/download.p... | Duke-GCB/DukeDSClient | 259f337f4d2782eb9249473046d8dd59daf01533 | Include speed for uploads in progress bar
The downloads progress bar has been updated to include speed (MB/s) - PR #295
This has been useful allowing users to easily provide meaningful performance metrics.
The uploads progress bar should also include this information. | diff --git a/ddsc/core/download.py b/ddsc/core/download.py
index f7d35b4..bd97279 100644
--- a/ddsc/core/download.py
+++ b/ddsc/core/download.py
@@ -7,7 +7,7 @@ import time
import queue
from ddsc.core.localstore import HashUtil
from ddsc.core.ddsapi import DDS_TOTAL_HEADER
-from ddsc.core.util import humanize_bytes
... |
Duke-GCB__DukeDSClient-306 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "DukeDS/__init__.py"
},
{
"changes": {
"added_entities": [
"ddsc/sdk/client.py:Folder.get_child_for_path",
"ddsc/sdk/client.py:Fo... | Duke-GCB/DukeDSClient | 397c28fd29ddfbb4c0e66d36ab34c7390ee9fb35 | Add create_folder developer API
Request from user to create a folder using the `DukeDS` developer API.
Example command to create a folder and subfolder for a project named 'mouse':
```
import DukeDS
DukeDS.create_folder('mouse', '/date/results')
```
Currently you can only create a folder indirectly by uploading a... | diff --git a/DukeDS/__init__.py b/DukeDS/__init__.py
index c0fc0f2..7ab856f 100644
--- a/DukeDS/__init__.py
+++ b/DukeDS/__init__.py
@@ -2,6 +2,7 @@ from ddsc.sdk.dukeds import DukeDS
list_projects = DukeDS.list_projects
create_project = DukeDS.create_project
delete_project = DukeDS.delete_project
+create_folder = D... |
Duke-GCB__DukeDSClient-309 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/core/download.py:ProjectFileDownloader._download_files",
"ddsc/core/download.py:ProjectFileDownloader._download_file",
"ddsc/core/download.py:ProjectFileDownloader.show_progress_bar... | Duke-GCB/DukeDSClient | c93e169ccacba2a9f3db2d4d9d5c8120a91d11c5 | python2 issues downloading
When downloading using python2 the following errors occur:
## multiprocessing.Pool doesn't work with `with`
```
File "ddsc/core/download.py", line 221, in _download_files
with multiprocessing.Pool(self.num_workers) as pool:
AttributeError: __exit__
```
Associated Code:
https:/... | diff --git a/ddsc/core/download.py b/ddsc/core/download.py
index bd97279..9bc1d31 100644
--- a/ddsc/core/download.py
+++ b/ddsc/core/download.py
@@ -218,13 +218,16 @@ class ProjectFileDownloader(object):
self._show_downloaded_files_status()
def _download_files(self):
- with multiprocessing.Pool(s... |
Duke-GCB__DukeDSClient-311 | [
{
"changes": {
"added_entities": [
"ddsc/core/ddsapi.py:DataServiceApi.close"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"ddsc/core/ddsapi.py:DataServiceApi"
]
},
"file": "ddsc/core/ddsapi.py"
},
{
"changes": {
... | Duke-GCB/DukeDSClient | f0be06dad96330c39bdbebe7928dd60954e6f3f0 | Check for Deprecations
Deprecated python 2 modules and features will eventually be removed from python 3. Once we drop python2 support we should check our code explained here: https://docs.python.org/3.9/whatsnew/3.9.html#you-should-check-for-deprecationwarning-in-your-code
Issue #304 removes python2 support. | diff --git a/ddsc/core/ddsapi.py b/ddsc/core/ddsapi.py
index 295b0c8..8db2fe7 100644
--- a/ddsc/core/ddsapi.py
+++ b/ddsc/core/ddsapi.py
@@ -278,6 +278,10 @@ class DataServiceApi(object):
"""
self.http = requests.Session()
+ def close(self):
+ self.http.close()
+ self.http = None
+
... |
Duke-GCB__DukeDSClient-317 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ddsc/config.py:Config.add_properties"
],
"edited_modules": [
"ddsc/config.py:Config"
]
},
"file": "ddsc/config.py"
}
] | Duke-GCB/DukeDSClient | 6df1eb9f210f98d4ff826f89f89309f48c4e8c5b | Fix error when the .ddsclient config file is empty
When a the .ddsclient config file is empty the following error is produced when running a command such as `ddsclient list`:
```
type object argument after ** must be a mapping, not NoneType
```
See #315 for more | diff --git a/ddsc/config.py b/ddsc/config.py
index f74ab5d..582c9aa 100644
--- a/ddsc/config.py
+++ b/ddsc/config.py
@@ -88,7 +88,11 @@ class Config(object):
filename = os.path.expanduser(filename)
if os.path.exists(filename):
with open(filename, 'r') as yaml_file:
- self.u... |
Duke-GCB__DukeDSClient-97 | [
{
"changes": {
"added_entities": [
"ddsc/config.py:default_num_workers"
],
"added_modules": [
"ddsc/config.py:default_num_workers"
],
"edited_entities": [
"ddsc/config.py:Config.upload_workers",
"ddsc/config.py:Config.download_workers"
],
... | Duke-GCB/DukeDSClient | 076b0db0c0ec9ef1807e2a557407394fab37eaeb | Limit default upload/download workers to 8.
Right now we use the number of CPUs as the default value.
For cluster environments this is overkill and can result in lesser performance.
Changing it to limit default to 8 for upload_workers and download_workers.
We will still ask the number of CPUS just limit it. | diff --git a/ddsc/config.py b/ddsc/config.py
index 22d09ec..7ccea6c 100644
--- a/ddsc/config.py
+++ b/ddsc/config.py
@@ -19,6 +19,7 @@ DDS_DEFAULT_UPLOAD_CHUNKS = 100 * MB_TO_BYTES
AUTH_ENV_KEY_NAME = 'DUKE_DATA_SERVICE_AUTH'
# when uploading skip .DS_Store, our key file, and ._ (resource fork metadata)
FILE_EXCLUDE... |
Duke-GCB__bespin-cli-15 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bespin/argparser.py:ArgParser._create_workflows_parser",
"bespin/argparser.py:ArgParser._run_list_workflows"
],
"edited_modules": [
"bespin/argparser.py:ArgParser"
]
... | Duke-GCB/bespin-cli | 70450d7b00c477580d6851b8aaa65433a54cf415 | Allow listing all workflow versions
Allow users to see all version of workflows so the can pick older tags.
Initially we thought users could just change the `v#` portion of the tags, but due to changes in the suffix portion of tags this is not possible. | diff --git a/bespin/argparser.py b/bespin/argparser.py
index 5fc8fa3..f97d735 100644
--- a/bespin/argparser.py
+++ b/bespin/argparser.py
@@ -40,6 +40,8 @@ class ArgParser(object):
jobs_subparser = jobs_parser.add_subparsers()
list_jobs_parser = jobs_subparser.add_parser('list', description='list wor... |
Duke-GCB__bespin-cli-16 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bespin/api.py:BespinApi.dds_job_input_files_post"
],
"edited_modules": [
"bespin/api.py:BespinApi"
]
},
"file": "bespin/api.py"
},
{
"changes": {
"added_e... | Duke-GCB/bespin-cli | 471cd4df56c852bee11fcb4725dc6b4e9053e08c | Jobs created appear to have 0-byte input files
I created job 46 in dev, with two files from data service. Viewing the job in the UI suggests the files are zero bytes (see screenshot).
:
return self._post_request('/job-file-stage-groups/', {})
def dds_job_input_files_post(self, project_id, file_id, destination_path, sequence_group,... |
Duke-GCB__bespin-cli-18 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bespin/commands.py:JobOrderWalker.format_file_path",
"bespin/commands.py:JobOrderPlaceholderCheck.on_class_value",
"bespin/commands.py:JobOrderFormatFiles.on_class_value",
"bespi... | Duke-GCB/bespin-cli | 3cb0cf75ca821e051ea48d4b1a990f34acedd98d | Allow using non-DukeDS File parameters
Currently all files are expected to begin with the `dds:` prefix. If a user attempts to use a ` class: File` input specifying either a url or a file path they will receive an error.
```
Invalid DukeDS file path (missing prefix): /data/exome-seq/b37/SUPERSNIPS.vcf
```
If a user... | diff --git a/bespin/commands.py b/bespin/commands.py
index e30d252..1766e96 100644
--- a/bespin/commands.py
+++ b/bespin/commands.py
@@ -3,6 +3,7 @@ from bespin.config import ConfigFile
from bespin.api import BespinApi
from bespin.exceptions import IncompleteJobFileException
from bespin.dukeds import DDSFileUtil
+fr... |
Duke-GCB__lando-155 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lando/k8s/jobmanager.py:JobManager._create_organize_output_config_map"
],
"edited_modules": [
"lando/k8s/jobmanager.py:JobManager"
]
},
"file": "lando/k8s/jobmanager.py... | Duke-GCB/lando | 9fd8cb5d0aa19bc83f1d8d1d6936fd60e0d2238a | k8s record job run time and file info
The organize project needs to save this info in the resulting project.
Functionality split off from #139
Currently the implementation just returns a placeholder value:
https://github.com/Duke-GCB/lando/blob/38747c5e75a93caf4a4228ce18bbae75442a507c/lando/k8s/jobmanager.py#L237
... | diff --git a/lando/k8s/jobmanager.py b/lando/k8s/jobmanager.py
index d9b893e..c73cbfb 100644
--- a/lando/k8s/jobmanager.py
+++ b/lando/k8s/jobmanager.py
@@ -233,10 +233,10 @@ class JobManager(object):
def _create_organize_output_config_map(self, name, filename, methods_document_content):
config_data = {... |
Duke-GCB__lando-159 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lando/k8s/jobmanager.py:JobManager.create_run_workflow_job"
],
"edited_modules": [
"lando/k8s/jobmanager.py:JobManager"
]
},
"file": "lando/k8s/jobmanager.py"
},
{
... | Duke-GCB/lando | 9294aabdb06947677d36dd738a3c927951bae7ec | k8s lando should pass cpu/memory from job_flavor to calrissian
Currently the flavor settings are not being used by the k8s run workflow job.
These values need to be passed via "--max-ram" and "--max-cores" flags for the `run_workflow` step.
https://github.com/Duke-GCB/lando/blob/9294aabdb06947677d36dd738a3c927951bae7... | diff --git a/lando/k8s/jobmanager.py b/lando/k8s/jobmanager.py
index b0c2095..456a8f2 100644
--- a/lando/k8s/jobmanager.py
+++ b/lando/k8s/jobmanager.py
@@ -169,7 +169,10 @@ class JobManager(object):
read_only=True))
command_parts = run_workflow_config.command
command_parts.extend(["-... |
Duke-GCB__lando-161 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lando/server/jobapi.py:CWLCommand.__init__"
],
"edited_modules": [
"lando/server/jobapi.py:CWLCommand"
]
},
"file": "lando/server/jobapi.py"
}
] | Duke-GCB/lando | ee4148bc7934c94be4e0bcbd129ce9ee1ba8afa5 | TypeError when parsing v2 CWLCommand
Error:
```
File "/usr/local/lib/python3.6/site-packages/lando-0.9.3-py3.6.egg/lando/server/jobapi.py", line 482, in __init__
self.base_command = json.loads(data.get('cwl_base_command'))
File "/usr/local/lib/python3.6/json/__init__.py", line 348, in loads
'not {!r}'.... | diff --git a/lando/server/jobapi.py b/lando/server/jobapi.py
index a049cd0..fe87b69 100644
--- a/lando/server/jobapi.py
+++ b/lando/server/jobapi.py
@@ -481,9 +481,9 @@ class CWLCommand(object):
Loads JSON-encoded CWL commands from dictionary
:param data:
"""
- self.base_command = json... |
Duke-GCB__lando-169 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lando/k8s/jobmanager.py:JobManager.create_run_workflow_job",
"lando/k8s/jobmanager.py:Names.__init__"
],
"edited_modules": [
"lando/k8s/jobmanager.py:JobManager",
"la... | Duke-GCB/lando | 76f981ebff4ae0abbabbc4461308e9e5ea0bc830 | k8s save calrissian record usage report
Calrissian has a usage report option that will record statistics about how memory/cpu usage when running a job. Add the `--usage-report <report.json>` flag to the calrissian command line.
Relevant code:
https://github.com/Duke-GCB/lando/blob/da2c40ef588578993a45c46f20676a691e... | diff --git a/lando/k8s/jobmanager.py b/lando/k8s/jobmanager.py
index 456a8f2..6774189 100644
--- a/lando/k8s/jobmanager.py
+++ b/lando/k8s/jobmanager.py
@@ -171,7 +171,8 @@ class JobManager(object):
command_parts.extend(["--tmp-outdir-prefix", Paths.TMPOUT_DATA + "/",
"--outdir",... |
Duke-GCB__lando-173 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lando/k8s/jobmanager.py:JobManager.create_run_workflow_job"
],
"edited_modules": [
"lando/k8s/jobmanager.py:JobManager"
]
},
"file": "lando/k8s/jobmanager.py"
}
] | Duke-GCB/lando | 10eb77896e2e4ff0810b6249fb92a303aa966d18 | k8s workflow runner logs are empty
We started redirecting stderr to a file so we can save this long term for successful jobs:
https://github.com/Duke-GCB/lando/blob/6f370eee825f78b694df3a640bc1cb75b4e61ec5/lando/k8s/jobmanager.py#L170-L175
This makes failed jobs have not logs to be saved. The error is recorded in a p... | diff --git a/lando/k8s/jobmanager.py b/lando/k8s/jobmanager.py
index 438eb1b..70c43e4 100644
--- a/lando/k8s/jobmanager.py
+++ b/lando/k8s/jobmanager.py
@@ -168,23 +168,21 @@ class JobManager(object):
mount_path=system_data_volume.mount_path,
volume_claim_name=system_data_volume.volume... |
Duke-GCB__lando-190 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lando/worker/cwlworkflow.py:CwlWorkflowDownloader.__init__",
"lando/worker/cwlworkflow.py:CwlWorkflowDownloader._handle_packed_download",
"lando/worker/cwlworkflow.py:CwlWorkflowDownload... | Duke-GCB/lando | ed29711ca564a5d18bf8752a3e0c09661c1d6fca | cwlreport uses badly formed path for packed workflows
Test job 70 with a packed workflow failed because `workflow_to_report` included `#main`
```
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist-packages/lando/worker/worker.py", line 186, in run
self.func(working_directory, self.payloa... | diff --git a/lando/worker/cwlworkflow.py b/lando/worker/cwlworkflow.py
index d54b2f5..a81f3f8 100644
--- a/lando/worker/cwlworkflow.py
+++ b/lando/worker/cwlworkflow.py
@@ -97,8 +97,10 @@ class CwlWorkflowDownloader(object):
self.workflow_url = workflow_url
self.workflow_path = workflow_path
... |
Duke-GCB__lando-194 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lando/worker/staging.py:DownloadDukeDSFile.run"
],
"edited_modules": [
"lando/worker/staging.py:DownloadDukeDSFile"
]
},
"file": "lando/worker/staging.py"
}
] | Duke-GCB/lando | 042ae53c0ad0ab0dc309100ecaa549bd0987cd4a | Error in new DukeDSClient download
```
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist-packages/lando/worker/worker.py", line 186, in run
self.func(working_directory, self.payload)
File "/usr/local/lib/python3.5/dist-packages/lando/worker/worker.py", line 82, in stage_files
downl... | diff --git a/lando/worker/staging.py b/lando/worker/staging.py
index 9d8680a..e54474f 100644
--- a/lando/worker/staging.py
+++ b/lando/worker/staging.py
@@ -146,7 +146,7 @@ class DownloadDukeDSFile(object):
dds_file = dds_client.get_file_by_id(self.file_id)
logging.info("Downloading file id:{} to {}".... |
Duke-GCB__lando-20 | [
{
"changes": {
"added_entities": [
"lando/server/cloudservice.py:NovaClient._delete_floating_ip"
],
"added_modules": null,
"edited_entities": [
"lando/server/cloudservice.py:NovaClient.terminate_instance",
"lando/server/cloudservice.py:CloudService.launch_instance... | Duke-GCB/lando | 5684145c4e27e6396a63b02ffc6d6e244ad69bc1 | Floating IP address exhaustion
The current implementation allocates a new floating IP address.
Once these are exhausted the VM will not launch.
Need to re-use existing floating IP addresses or delete them when we are done.
We don't technically need to have floating IPs for running jobs but it makes debugging easier. | diff --git a/README.md b/README.md
index 8130b3b..4adc5b5 100644
--- a/README.md
+++ b/README.md
@@ -87,6 +87,7 @@ vm_settings:
worker_image_name: lando_worker # Name of the image that has lando installed and lando_worker setup to run as a service
ssh_key_name: jpb67 # Name of the openstack SSH ... |
E3SM-Project__e3sm_to_cmip-203 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"e3sm_to_cmip/cmor_handlers/utils.py:load_all_handlers",
"e3sm_to_cmip/cmor_handlers/utils.py:_get_mpas_handlers",
"e3sm_to_cmip/cmor_handlers/utils.py:derive_handlers"
],
"ed... | E3SM-Project/e3sm_to_cmip | a151f8d1f74b78a172caec3a83b8b4110e3f34ce | KeyError raised when any of the variable handler fails
Initially reported by @forsyth2 in e3sm-unified rc testing, when any of the cmip variable handler fails, KeyError raised and the program exist. The expected behavior is to process every available target cmip variables, as previous versions.
My standalone e2c test... | diff --git a/e3sm_to_cmip/cmor_handlers/utils.py b/e3sm_to_cmip/cmor_handlers/utils.py
index dcbcb00..9f0240d 100644
--- a/e3sm_to_cmip/cmor_handlers/utils.py
+++ b/e3sm_to_cmip/cmor_handlers/utils.py
@@ -74,7 +74,7 @@ def load_all_handlers(
handlers = handlers + var_handler
if len(missing_handl... |
E3SM-Project__zstash-168 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"zstash/extract.py:extract",
"zstash/extract.py:multiprocess_extract"
],
"edited_modules": [
"zstash/extract.py:extract",
"zstash/extract.py:multiprocess_extract"
... | E3SM-Project/zstash | fb39bbc5272177e1de7f5f65e767b6013340d981 | zstash check reports success even if exceptions occur
`zstash check` reports success even if exceptions occur.
Exceptions like the following may occur, but `zstash check` still ends with `INFO: No failures detected when checking the files.`:
```
Process Process-3:
Traceback (most recent call last):
File "/glob... | diff --git a/zstash/extract.py b/zstash/extract.py
index 5382609..9918bf4 100644
--- a/zstash/extract.py
+++ b/zstash/extract.py
@@ -57,7 +57,11 @@ def extract(keep_files: bool = True):
logger.error(tar)
else:
verb: str = "extracting" if keep_files else "checking"
- logger.info("No fai... |
E3SM-Project__zstash-197 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"zstash/extract.py:extract_database"
],
"edited_modules": [
"zstash/extract.py:extract_database"
]
},
"file": "zstash/extract.py"
}
] | E3SM-Project/zstash | 0b18fd20031b48b91f604b886fb66b666284de43 | Improve Zstash extract warnings
Print a short explanation on the screen if the match doesn't return any files. | diff --git a/zstash/extract.py b/zstash/extract.py
index 56704d7..bc44ac7 100644
--- a/zstash/extract.py
+++ b/zstash/extract.py
@@ -232,7 +232,11 @@ def extract_database(
u"select * from files where name GLOB ? or tar GLOB ?",
(args_file, args_file),
)
- matche... |
E3SM-Project__zstash-275 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "setup.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
... | E3SM-Project/zstash | dfca67dae0d5fa57c7f8f55e372e67f66078b581 | Add Compy endpoint to Globus file
Add Compy endpoint to Globus file.
In https://github.com/E3SM-Project/zstash/blob/main/zstash/globus.py, add Compy's Globus endpoint. | diff --git a/conda/dev.yml b/conda/dev.yml
index 52453d7..e4b5995 100644
--- a/conda/dev.yml
+++ b/conda/dev.yml
@@ -9,7 +9,7 @@ dependencies:
- python=3.9.13
- six=1.16.0
- globus-sdk=3.2.1
- - fair-research-login=0.2.0
+ - fair-research-login=0.2.6
# Developer Tools
# =================
# If versio... |
ECCO-GROUP__ECCOv4-py-63 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ecco_v4_py/get_section_masks.py:get_section_endpoints"
],
"edited_modules": [
"ecco_v4_py/get_section_masks.py:get_section_endpoints"
]
},
"file": "ecco_v4_py/get_secti... | ECCO-GROUP/ECCOv4-py | 82c2327427fba0d90acdf7b87ffab607387fa331 | 'Faroe Scotland' is included in the get_available_sections() but not included in get_section_endpoints()
get_section_endpoints() returns and error for 'Faroe Scotland'. I think this is because the coordinates for this section is actually not included in the function. I assume that the info exists but was accidentally r... | diff --git a/ecco_v4_py/get_section_masks.py b/ecco_v4_py/get_section_masks.py
index a03db6f..6ffa665 100644
--- a/ecco_v4_py/get_section_masks.py
+++ b/ecco_v4_py/get_section_masks.py
@@ -90,6 +90,9 @@ def get_section_endpoints(section_name):
elif section_name == 'icelandfaroe':
pt1 = [-16, 65]
... |
EFForg__starttls-policy-cli-24 | [
{
"changes": {
"added_entities": [
"starttls_policy_cli/configure.py:PostfixGenerator._policy_for_domain"
],
"added_modules": null,
"edited_entities": [
"starttls_policy_cli/configure.py:ConfigGenerator.__init__",
"starttls_policy_cli/configure.py:_policy_for_doma... | EFForg/starttls-policy-cli | be1143dcfb2d54fe638a850f63f603aedb068e0c | Implement Early Adopter mode
Actual issue is created for tracking implementation progress of feature described [here](https://github.com/EFForg/starttls-everywhere/issues/124). | diff --git a/starttls_policy_cli/configure.py b/starttls_policy_cli/configure.py
index 8ec010d..bb13dec 100644
--- a/starttls_policy_cli/configure.py
+++ b/starttls_policy_cli/configure.py
@@ -20,8 +20,9 @@ class ConfigGenerator(object):
"""
__metaclass__ = abc.ABCMeta
- def __init__(self, policy_dir):
+... |
EFForg__starttls-policy-cli-27 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"starttls_policy_cli/policy.py:PolicyNoAlias.policy_alias"
],
"edited_modules": [
"starttls_policy_cli/policy.py:PolicyNoAlias"
]
},
"file": "starttls_policy_cli/policy.... | EFForg/starttls-policy-cli | be1143dcfb2d54fe638a850f63f603aedb068e0c | Config parser schema contains field not present in format spec
[Field Enforcer](https://github.com/EFForg/starttls-policy-cli/blob/687dbbf99b683eebceb524fb93286d5ebfe57204/starttls_policy_cli/util.py#L102-L105) ∉ [Format Spec](https://github.com/EFForg/starttls-everywhere/blob/master/RULES.md) | diff --git a/starttls_policy_cli/policy.py b/starttls_policy_cli/policy.py
index b4ab17a..8b5aedb 100644
--- a/starttls_policy_cli/policy.py
+++ b/starttls_policy_cli/policy.py
@@ -210,7 +210,6 @@ class PolicyNoAlias(Policy):
@property
def policy_alias(self):
""" This type of policy can't be aliased.... |
ELIFE-ASU__Neet-105 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neet/boolean/logicnetwork.py:LogicNetwork._encode_table"
],
"edited_modules": [
"neet/boolean/logicnetwork.py:LogicNetwork"
]
},
"file": "neet/boolean/logicnetwork.py"
... | ELIFE-ASU/Neet | 041332432596020896894dbaa66282010db9e065 | LogicNetwork table encoding issue
See comments on the team_grn slack channel. I'll add more here later. | diff --git a/neet/boolean/logicnetwork.py b/neet/boolean/logicnetwork.py
index b9342f1..b173fdf 100644
--- a/neet/boolean/logicnetwork.py
+++ b/neet/boolean/logicnetwork.py
@@ -109,13 +109,13 @@ class LogicNetwork(object):
# Encode the mask.
mask_code = long(0)
for idx in indices:... |
ELIFE-ASU__Neet-114 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neet/synchronous.py:trajectory",
"neet/synchronous.py:transitions",
"neet/synchronous.py:attractors"
],
"edited_modules": [
"neet/synchronous.py:trajectory",
... | ELIFE-ASU/Neet | 5a45a92c1b3a564290487ecc1483b4866e26eaf5 | Death to Generators
Generators are great when you may have to iterate over computations that are too large to store in memory. This is certainly a possibility for much of Neet's algorithms. It was for this reason that @dglmoore over-engineered Neet's functions to `yield` instead of `return` where possible.
While it ... | diff --git a/neet/synchronous.py b/neet/synchronous.py
index 1c6ed88..8f59454 100644
--- a/neet/synchronous.py
+++ b/neet/synchronous.py
@@ -35,7 +35,7 @@ def trajectory(net, state, timesteps=1, encode=False):
:param state: the network state
:param timesteps: the number of steps in the trajectory
:param ... |
ELIFE-ASU__Neet-30 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neet/automata.py:ECA._unsafe_update",
"neet/automata.py:ECA.update"
],
"edited_modules": [
"neet/automata.py:ECA"
]
},
"file": "neet/automata.py"
}
] | ELIFE-ASU/Neet | 27902597953c9188545e4f0543f14dd6d180952f | Add an optional index argument to network update methods
This adds ability for asynchronous updating | diff --git a/neet/automata.py b/neet/automata.py
index aaa9971..e94dfd7 100644
--- a/neet/automata.py
+++ b/neet/automata.py
@@ -182,7 +182,7 @@ class ECA(object):
return True
- def _unsafe_update(self, lattice):
+ def _unsafe_update(self, lattice, index=None):
"""
Update the state ... |
EMCECS__python-ecsclient-30 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ecsclient/authentication.py:Authentication.logout"
],
"edited_modules": [
"ecsclient/authentication.py:Authentication"
]
},
"file": "ecsclient/authentication.py"
},
... | EMCECS/python-ecsclient | 546e342440f7ca0274d222179c6eca790d1d6573 | Two logouts issued when only one logout() executed.
I am using a single logout() command, but the requests sent by the code I see two been issued. The problem is the first one succeed (200) and the second call fails (probably because the first 200). | diff --git a/ecsclient/authentication.py b/ecsclient/authentication.py
index 0e8ae84..31fb0c4 100644
--- a/ecsclient/authentication.py
+++ b/ecsclient/authentication.py
@@ -23,6 +23,11 @@ class Authentication(object):
:param force: If you have multiple sessions running simultaneously this
forces the t... |
EMCECS__python-ecsclient-48 | [
{
"changes": {
"added_entities": [
"ecsclient/common/provisioning/node.py:Node.list"
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"edited_entities": [
"ecsclient/common/provisioning/node.py:Node.get_nodes"
],
"edited_modules": [
"ecsclient/common/provisioning/node.py:Nod... | EMCECS/python-ecsclient | 671ad67baabb986cc33409ea5b41411b87013fcf | Add support for the Nodes endpoint
Implement the Node endpoint for versions 2.x, 3.0, and 3.1. | diff --git a/VERSION b/VERSION
index e25d8d9..0664a8f 100644
--- a/VERSION
+++ b/VERSION
@@ -1,1 +1,1 @@
-1.1.5
+1.1.6
diff --git a/ecsclient/common/provisioning/data_store.py b/ecsclient/common/provisioning/data_store.py
index 69f0402..6968d2b 100644
--- a/ecsclient/common/provisioning/data_store.py
+++ b/ecsclient/co... |
ESMValGroup__ESMValCore-1092 | [
{
"changes": {
"added_entities": null,
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"edited_entities": [
"esmvalcore/cmor/_fixes/cmip5/bcc_csm1_1.py:Tos.fix_data"
],
"edited_modules": [
"esmvalcore/cmor/_fixes/cmip5/bcc_csm1_1.py:Tos"
]
},
"file": "esmvalcore/cmor/_fixes/cm... | ESMValGroup/ESMValCore | fee5d541dc871efe72ab972a6a52195c452d16eb | Erroneous use of `grid_latitude` and `grid_longitude`
In `esmvalcore.cmor._fixes.common.OceanFixGrid.fix_metadata` we introduce `grid_latitude` and `grid_longitude` as names for index coordinates. This is confusing because those names are used to identified rotated pole grids (see [CF-1.7](http://cfconventions.org/Data... | diff --git a/esmvalcore/cmor/_fixes/cmip5/bcc_csm1_1.py b/esmvalcore/cmor/_fixes/cmip5/bcc_csm1_1.py
index c61eeaa19..28593a9d2 100644
--- a/esmvalcore/cmor/_fixes/cmip5/bcc_csm1_1.py
+++ b/esmvalcore/cmor/_fixes/cmip5/bcc_csm1_1.py
@@ -1,68 +1,7 @@
"""Fixes for bcc-csm1-1."""
-import numpy as np
-from scipy.interpola... |
ESMValGroup__ESMValCore-1095 | [
{
"changes": {
"added_entities": [
"esmvalcore/cmor/_fixes/cmip6/cesm2.py:Omon.fix_metadata"
],
"added_modules": [
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],
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},
"file": "esmvalcore/cmor/_fixes/cmip6/... | ESMValGroup/ESMValCore | fee5d541dc871efe72ab972a6a52195c452d16eb | Introduce `mip` level fixes
As proposed by @tomaslovato in #1069, it would be nice to have fixes at `mip` level for each dataset. For example, this fix
```py
class Amon(Fix):
"""Fixes for all `Amon` variables."""
```
would be applied to all `Amon` variables of the given dataset. This would probably avoid l... | diff --git a/esmvalcore/cmor/_fixes/cmip6/cesm2.py b/esmvalcore/cmor/_fixes/cmip6/cesm2.py
index 9b4bc499f..4ab1f0a4b 100644
--- a/esmvalcore/cmor/_fixes/cmip6/cesm2.py
+++ b/esmvalcore/cmor/_fixes/cmip6/cesm2.py
@@ -10,6 +10,7 @@ from ..shared import (
add_scalar_height_coord,
add_scalar_typeland_coord,
... |
ESMValGroup__ESMValCore-1105 | [
{
"changes": {
"added_entities": null,
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"edited_entities": null,
"edited_modules": null
},
"file": "esmvalcore/cmor/_fixes/cmip6/cesm2.py"
},
{
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... | ESMValGroup/ESMValCore | b2d3642460c6cfa4aa97f1e58e6d1eda2f6c3ab6 | Dataset problem: `typesi` missing for the `siconc` variable of some CMIP6 models
**Describe the dataset issue**
A clear and concise description of what the problem with the data is is. Here are some guidelines that you can use
right out the box by filling in the blanks (note that, if needed we will assist you with w... | diff --git a/doc/recipe/preprocessor.rst b/doc/recipe/preprocessor.rst
index 8664530ba..997149225 100644
--- a/doc/recipe/preprocessor.rst
+++ b/doc/recipe/preprocessor.rst
@@ -1258,9 +1258,9 @@ The area manipulation module contains the following preprocessor functions:
``extract_region``
------------------
-This f... |
ESMValGroup__ESMValCore-1113 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "esmvalcore/cmor/_fixes/cmip6/cesm2.py"
},
{
"changes": {
"added_entities": null,
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"edited_entities": null,
... | ESMValGroup/ESMValCore | 933b37b225a89aeed84029d8c83105407ed7ae5f | Dataset problem: Fixe wrong sign for nbp
**Describe the dataset issue**
- Project: CMIP6
- Full dataset description (fill out as many as you know, please):
- dataset: SAM0-UNICON, GISS-E2-1-G
- experiment: historical
- mip: Lmon
- grid: gn
- variable used: nbp
- data version:
- Problems encounter... | diff --git a/doc/quickstart/install.rst b/doc/quickstart/install.rst
index 3069b2aba..1c78cd38b 100644
--- a/doc/quickstart/install.rst
+++ b/doc/quickstart/install.rst
@@ -203,5 +203,8 @@ You will find the tool available on HPC clusters and there will be no need to in
yourself if you are just running diagnostics:
... |
ESMValGroup__ESMValCore-156 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe.py:_add_cmor_info"
],
"edited_modules": [
"esmvalcore/_recipe.py:_add_cmor_info"
]
},
"file": "esmvalcore/_recipe.py"
},
{
"changes": {
... | ESMValGroup/ESMValCore | 0808e2d5f93c22ad6cddf71c628730c4467bf40b | Running with CMIP6 data and OBS data fails if using mip: AERmonZ
...since OBS data is using `cmor.table.CMIP5Info` that doesn't know of `AERmonZ` since that is not a CMIP5 mip | diff --git a/esmvalcore/_recipe.py b/esmvalcore/_recipe.py
index 4b240e91b..36aba2043 100644
--- a/esmvalcore/_recipe.py
+++ b/esmvalcore/_recipe.py
@@ -118,16 +118,15 @@ def _add_cmor_info(variable, override=False):
if derive and table_entry is None:
custom_table = CMOR_TABLES['custom']
table_en... |
ESMValGroup__ESMValCore-1894 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/cmor/_fixes/icon/_base_fixes.py:IconFix._get_grid_from_rootpath"
],
"edited_modules": [
"esmvalcore/cmor/_fixes/icon/_base_fixes.py:IconFix"
]
},
"file": "es... | ESMValGroup/ESMValCore | 405300886cfb2314eadc6ff2f9b137371ada0dfe | Specify directory stucture per path instead of per project in config-user.yml
At the moment all drs need to be the same per project, while it would make much more sense to be able to specify the drs per rootpath.
To make this more clear, now we have this:
```yaml
rootpath:
# Rootpath to CMIP5 data
CMIP5:
... | diff --git a/doc/quickstart/configure.rst b/doc/quickstart/configure.rst
index 834109e2d..cb5c73340 100644
--- a/doc/quickstart/configure.rst
+++ b/doc/quickstart/configure.rst
@@ -26,7 +26,7 @@ User configuration file
The ``config-user.yml`` configuration file contains all the global level
-information needed by ... |
ESMValGroup__ESMValCore-1988 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/cmor/_fixes/fix.py:Fix.__init__",
"esmvalcore/cmor/_fixes/fix.py:Fix.get_fixes"
],
"edited_modules": [
"esmvalcore/cmor/_fixes/fix.py:Fix"
]
},
"file... | ESMValGroup/ESMValCore | 88827d64d794da435e44dbf938cb02581f8eaabd | Use `auxiliary_data_dir` in fixes
It would be very helpful if the [`Fix`](https://github.com/ESMValGroup/ESMValCore/blob/d36db3b0a6aed86706800386074ff32b9aac5ad7/esmvalcore/cmor/_fixes/fix.py#L12) base class had access to the `auxiliary_data_dir` specified in the user-config file. An example use case would be the ICON ... | diff --git a/README.md b/README.md
index 22552e5dd..3c438fe6f 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@
[](https://github.com/ESMValGroup/ESMValCore/actions/workflows/run-tests.yml)
[![Github Acti... |
ESMValGroup__ESMValCore-1999 | [
{
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],
"edited_modules": [
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]
},
"file": "esmval... | ESMValGroup/ESMValCore | f192e400f114b482152f83941332bdd4743b020b | Altitude <--> pressure conversion in `extract_levels` fails for masked arrays
**Describe the bug**
The [conversion between altitudes and pressure levels](https://github.com/ESMValGroup/ESMValCore/blob/af5d6ccdc6643c0e416918ff472a087b8c75e9f1/esmvalcore/preprocessor/_regrid.py#L930-L938) in the `extract_levels` preproc... | diff --git a/esmvalcore/cmor/_fixes/icon/_base_fixes.py b/esmvalcore/cmor/_fixes/icon/_base_fixes.py
index d7b3a496a..f2502ac0a 100644
--- a/esmvalcore/cmor/_fixes/icon/_base_fixes.py
+++ b/esmvalcore/cmor/_fixes/icon/_base_fixes.py
@@ -219,6 +219,7 @@ class IconFix(NativeDatasetFix):
# Note: we use a lock her... |
ESMValGroup__ESMValCore-2023 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/preprocessor/_regrid.py:extract_location",
"esmvalcore/preprocessor/_regrid.py:get_cmor_levels"
],
"edited_modules": [
"esmvalcore/preprocessor/_regrid.py:extract_... | ESMValGroup/ESMValCore | 664f7c909f4ab6ce4d03c6c4e6d431d6ba70b154 | The `extract_location` preprocessor doesn't work at the Met Office :(
**Describe the bug**
A new ESMValTool user at the Met Office was following the [quick start guide](https://esmvalgroup.github.io/ESMValTool_Tutorial/01-quickstart/index.html) and using our new ESMValTool v2.8.0 environment, but the recipe raised t... | diff --git a/esmvalcore/preprocessor/_regrid.py b/esmvalcore/preprocessor/_regrid.py
index 302e0c86b..a14abfbe6 100644
--- a/esmvalcore/preprocessor/_regrid.py
+++ b/esmvalcore/preprocessor/_regrid.py
@@ -5,6 +5,7 @@ import inspect
import logging
import os
import re
+import ssl
from copy import deepcopy
from decim... |
ESMValGroup__ESMValCore-2038 | [
{
"changes": {
"added_entities": [
"esmvalcore/cmor/_fixes/icon/icon.py:AllVars._shift_time_coord",
"esmvalcore/cmor/_fixes/icon/icon.py:AllVars._get_previous_timestep",
"esmvalcore/cmor/_fixes/icon/icon.py:AllVars._fix_invalid_time_units"
],
"added_modules": null,
... | ESMValGroup/ESMValCore | 70861d4dfd45d080ee352bbb67c17dca3a3247cc | ICON output is shifted in time
After doing some evaluation of monthly ICON data I noticed that the ICON data is shifted by half a month. This becomes very obvious for the top-of-the-atmosphere incoming solar radiation, e.g.:
![grafik](https://github.com/ESMValGroup/ESMValCore/assets/32543114/8576a7a6-f6bb-495f-aed1-... | diff --git a/doc/quickstart/find_data.rst b/doc/quickstart/find_data.rst
index 948cb7f62..5a810081b 100644
--- a/doc/quickstart/find_data.rst
+++ b/doc/quickstart/find_data.rst
@@ -342,8 +342,33 @@ Please note the duplication of the name ``ICON`` in ``project`` and
``dataset``, which is necessary to comply with ESMVal... |
ESMValGroup__ESMValCore-2046 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe/recipe.py:_update_warning_settings",
"esmvalcore/_recipe/recipe.py:_get_preprocessor_products"
],
"edited_modules": [
"esmvalcore/_recipe/recipe.py:_update... | ESMValGroup/ESMValCore | 153c3a89a34747b1f5f862e091d47a1c90d85917 | `ignore_warnings` in cfg-developer.yml is not considered anymore
The `ignore_warnings` key ([example](https://github.com/ESMValGroup/ESMValCore/blob/8b6be3c3e994cae1609d8acc1cc0a7007a4d697d/esmvalcore/config-developer.yml#L138-L143)) in the `config-developer.yml` file is not considered anymore, which leads to a clutter... | diff --git a/doc/quickstart/configure.rst b/doc/quickstart/configure.rst
index 3ca78b9f2..eb1f618df 100644
--- a/doc/quickstart/configure.rst
+++ b/doc/quickstart/configure.rst
@@ -613,7 +613,7 @@ Currently supported preprocessor steps:
* :func:`~esmvalcore.preprocessor.load`
Here is an example on how to ignore spe... |
ESMValGroup__ESMValCore-2067 | [
{
"changes": {
"added_entities": [
"esmvalcore/cmor/_fixes/icon/_base_fixes.py:IconFix._get_path_from_facet",
"esmvalcore/cmor/_fixes/icon/_base_fixes.py:IconFix.add_additional_cubes"
],
"added_modules": null,
"edited_entities": [
"esmvalcore/cmor/_fixes/icon/_bas... | ESMValGroup/ESMValCore | 2e7e3848b0a7ab1bd5485605eb0d151d3dbb8bab | ICON: specifiy vertical grid file in recipe
ICON 3D output does not always have the vertical grid information (i.e., the altitude) available. In this case, this information is stored in a separate file. It would be helpful to specify this file (absolute or relative to `auxiliary_data_dir` in the recipe). | diff --git a/doc/quickstart/find_data.rst b/doc/quickstart/find_data.rst
index fcd27a66a..9f9963928 100644
--- a/doc/quickstart/find_data.rst
+++ b/doc/quickstart/find_data.rst
@@ -370,33 +370,15 @@ This is useful for diagnostics that do not support input data in UGRID format
if you want to use the built-in :ref:`unst... |
ESMValGroup__ESMValCore-2068 | [
{
"changes": {
"added_entities": [
"esmvalcore/cmor/_fixes/icon/_base_fixes.py:IconFix._get_path_from_facet",
"esmvalcore/cmor/_fixes/icon/_base_fixes.py:IconFix.add_additional_cubes"
],
"added_modules": null,
"edited_entities": [
"esmvalcore/cmor/_fixes/icon/_bas... | ESMValGroup/ESMValCore | 2e7e3848b0a7ab1bd5485605eb0d151d3dbb8bab | `climate_statistics` with period `hourly`
It would be great if `climate_statistics` supported the period `hourly`. This would be very useful to create diurnal cycle plots. | diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index f5d65d84a..b14aa7cfe 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -1,6 +1,6 @@
# Generated by conda-lock.
# platform: linux-64
-# input_hash: a129f6503ab0709f6a6d72bb9ec4a539c6fbb437842ba32fbed8b7f43f1ebc61
+# input_hash: 90193d2d9bc96fcccd... |
ESMValGroup__ESMValCore-2070 | [
{
"changes": {
"added_entities": [
"esmvalcore/preprocessor/_regrid.py:_check_grid_discontiguities"
],
"added_modules": [
"esmvalcore/preprocessor/_regrid.py:_check_grid_discontiguities"
],
"edited_entities": [
"esmvalcore/preprocessor/_regrid.py:regrid"
... | ESMValGroup/ESMValCore | 83650df4186b21e0098115b6c3fdddcd39f771c7 | Dataset problem: Nemo grid datasets cannot be regridded using iris-esmf
**Describe the dataset issue**
When trying to regrid ocean variables that are in a dataset that use the Nemo grid (CNRM, CMCC, EC-Earth, IPSL), the regridder in iris-esmf fails due to the coordinates not being contiguous. In those particular data... | diff --git a/doc/recipe/preprocessor.rst b/doc/recipe/preprocessor.rst
index 44eb9d0dd..1c9140868 100644
--- a/doc/recipe/preprocessor.rst
+++ b/doc/recipe/preprocessor.rst
@@ -1015,6 +1015,13 @@ scheme available in :doc:`iris-esmf-regrid:index`:
reference: esmf_regrid.schemes:regrid_rectilinear_to_rectiline... |
ESMValGroup__ESMValCore-2078 | [
{
"changes": {
"added_entities": [
"esmvalcore/cmor/_fixes/icon/_base_fixes.py:IconFix._get_grid_from_facet",
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],
"added_modules": null,
"edited_entities": [
"esmvalcore/cmor/_fixes/icon/... | ESMValGroup/ESMValCore | 76f32ac2a235199ae454e1a04d883cdf406319d4 | ICON: specify horizontal grid file in recipe
Currently, the ICON grid file is read from the file attribute `grid_file_uri`. However, some ICON files do not have this attribute. Thus, it would be good to be able to specify the location of this grid file (absolute or relative to `auxiliary_data_dir`) in the recipe. | diff --git a/doc/quickstart/find_data.rst b/doc/quickstart/find_data.rst
index 5a810081b..20da29ac0 100644
--- a/doc/quickstart/find_data.rst
+++ b/doc/quickstart/find_data.rst
@@ -370,6 +370,17 @@ is always disabled.
See :ref:`timerange_examples` for more information on the ``timerange``
option.
+Usually, ES... |
ESMValGroup__ESMValCore-2087 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/preprocessor/_regrid.py:_rechunk"
],
"edited_modules": [
"esmvalcore/preprocessor/_regrid.py:_rechunk"
]
},
"file": "esmvalcore/preprocessor/_regrid.py"
}
... | ESMValGroup/ESMValCore | 92e20fd3511190bde4fdc073b59a97609a27f557 | Rechunking to keep chunk size normal may fail
For example, when running recipe_autoassess_stratosphere.yml from ESMValTool with the current `main` branch, the run fails to regrid dataset MPI-ESM-LR with:
```
ValueError: Chunks do not add up to shape. Got chunks=((1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, ... | diff --git a/esmvalcore/preprocessor/_regrid.py b/esmvalcore/preprocessor/_regrid.py
index cb5205559..daa6b6acf 100644
--- a/esmvalcore/preprocessor/_regrid.py
+++ b/esmvalcore/preprocessor/_regrid.py
@@ -681,13 +681,27 @@ def regrid(cube, target_grid, scheme, lat_offset=True, lon_offset=True):
return cube
-de... |
ESMValGroup__ESMValCore-2096 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_main.py:ESMValTool.__init__"
],
"edited_modules": [
"esmvalcore/_main.py:ESMValTool"
]
},
"file": "esmvalcore/_main.py"
},
{
"changes": {
"add... | ESMValGroup/ESMValCore | 9d6b9630bbeb84d69f3a1a4591dbf9506f0d8b29 | `pkg_resources` is deprecated
The `pkg_resources` package used in `esmvalcore/_main.py` is [deprecated](https://setuptools.pypa.io/en/latest/pkg_resources.html). Therefore the function `pkg_resources.iter_entry_points` needs to be replaced with [`importlib.metadata.entry_points`](https://docs.python.org/3/library/impor... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 31f3d57a8..2b01ae61c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -50,5 +50,4 @@ repos:
- id: mypy
additional_dependencies:
- 'types-PyYAML'
- - 'types-pkg_resources'
- 'types-req... |
ESMValGroup__ESMValCore-2097 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_citation.py:_extract_tags"
],
"edited_modules": [
"esmvalcore/_citation.py:_extract_tags"
]
},
"file": "esmvalcore/_citation.py"
}
] | ESMValGroup/ESMValCore | 179312e41f964bcb9cbd44f0ee234d62127d20ab | Reference bibtex filenames can only contain the characters that match `\w` regex
Issue reported by @alistairsellar
> Could you have a look at the following warnings from [`main_log.txt`](https://esmvaltool.dkrz.de/shared/esmvaltool/esmvalbot-output/autoassess_soilmoisture_obs_fly-litxq94v/recipe_autoassess_landsurfa... | diff --git a/esmvalcore/_citation.py b/esmvalcore/_citation.py
index 96e9286f4..5637f115b 100644
--- a/esmvalcore/_citation.py
+++ b/esmvalcore/_citation.py
@@ -137,7 +137,7 @@ def _extract_tags(tags):
For example, a single entry in the list `tags` could be the string
"['acknow_project', 'acknow_author']".
... |
ESMValGroup__ESMValCore-2099 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_citation.py:_extract_tags"
],
"edited_modules": [
"esmvalcore/_citation.py:_extract_tags"
]
},
"file": "esmvalcore/_citation.py"
},
{
"changes": {
... | ESMValGroup/ESMValCore | 179312e41f964bcb9cbd44f0ee234d62127d20ab | Dataset problem:
**Describe the dataset issue**
A clear and concise description of what the problem with the data is is. Here are some guidelines that you can use
right out the box by filling in the blanks (note that, if needed we will assist you with writing a fix; also note that
if the problem is with a CMIP6 dat... | diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index 028f61f0f..35c233a4b 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -1,6 +1,6 @@
# Generated by conda-lock.
# platform: linux-64
-# input_hash: 8e2958f9fa6064ce6efdec1ac7b93eb378b7281acae05ab7f6ae326ce198e536
+# input_hash: f879739c343850b4d3... |
ESMValGroup__ESMValCore-2105 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/esgf/_search.py:select_latest_versions"
],
"edited_modules": [
"esmvalcore/esgf/_search.py:select_latest_versions"
]
},
"file": "esmvalcore/esgf/_search.py"
... | ESMValGroup/ESMValCore | 41f46ab0e2e1a1cfca279394e2bc92c4d792a306 | Version selection does not work if some files are not available for a particular version
Run this script
```python
import logging
from esmvalcore.esgf import find_files
logging.getLogger().setLevel(logging.DEBUG)
if __name__ == '__main__':
files = find_files(
dataset='EC-Earth3-Veg',
p... | diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index 028f61f0f..35c233a4b 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -1,6 +1,6 @@
# Generated by conda-lock.
# platform: linux-64
-# input_hash: 8e2958f9fa6064ce6efdec1ac7b93eb378b7281acae05ab7f6ae326ce198e536
+# input_hash: f879739c343850b4d3... |
ESMValGroup__ESMValCore-2126 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_main.py:ESMValTool.__init__"
],
"edited_modules": [
"esmvalcore/_main.py:ESMValTool"
]
},
"file": "esmvalcore/_main.py"
},
{
"changes": {
"add... | ESMValGroup/ESMValCore | 9d6b9630bbeb84d69f3a1a4591dbf9506f0d8b29 | [Github Actions] Compress all bash shell setters into one default option per workflow
@bouweandela rightly suggested doing that so the workflow files are a bit more readable, and supplied and [example](https://github.com/dask/dask/blob/11f2b83ee034aea7837691f9a0d4ede6309d6194/.github/workflows/conda.yml#L18-L21) how th... | diff --git a/.github/workflows/create-condalock-file.yml b/.github/workflows/create-condalock-file.yml
index 5d71fb9d2..ccdffd617 100644
--- a/.github/workflows/create-condalock-file.yml
+++ b/.github/workflows/create-condalock-file.yml
@@ -10,6 +10,11 @@ on:
schedule:
- cron: '0 4 */10 * *'
+# Required shell... |
ESMValGroup__ESMValCore-2139 | [
{
"changes": {
"added_entities": [
"esmvalcore/preprocessor/_area.py:_try_adding_calculated_cell_area"
],
"added_modules": [
"esmvalcore/preprocessor/_area.py:_try_adding_calculated_cell_area"
],
"edited_entities": [
"esmvalcore/preprocessor/_area.py:extract... | ESMValGroup/ESMValCore | 579bb61f8455e82d28e3b9a1dbf06df4e441b67e | Smarter area weighted sum
Follows comment made [here](https://github.com/ESMValGroup/ESMValCore/pull/1574#issuecomment-1123428679) (other issues could also be spun out of that comment).
**Is your feature request related to a problem? Please describe.**
Currently, when doing an area-weighted sum, the units are no... | diff --git a/doc/recipe/preprocessor.rst b/doc/recipe/preprocessor.rst
index 8a0c1a54b..19020ba8f 100644
--- a/doc/recipe/preprocessor.rst
+++ b/doc/recipe/preprocessor.rst
@@ -1388,7 +1388,7 @@ statistics.
Parameters:
* operator: operation to apply. Accepted values are 'mean', 'median',
- 'std_dev', 'min'... |
ESMValGroup__ESMValCore-2166 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/preprocessor/_area.py:extract_region"
],
"edited_modules": [
"esmvalcore/preprocessor/_area.py:extract_region"
]
},
"file": "esmvalcore/preprocessor/_area.py... | ESMValGroup/ESMValCore | ea29584ea616122aad319558477aed7b937bc52b | supplementary variables disappear from cubes after extract_region
After poking around a bit more, I believe that the `cell_measures` and all other supplementary variables actually are disappearing from the cubes upon applying `extract_region`, whereas I would have expected information from spatially-anchored supplement... | diff --git a/esmvalcore/preprocessor/_area.py b/esmvalcore/preprocessor/_area.py
index 621a5e47e..947781141 100644
--- a/esmvalcore/preprocessor/_area.py
+++ b/esmvalcore/preprocessor/_area.py
@@ -65,6 +65,10 @@ def extract_region(cube, start_longitude, end_longitude, start_latitude,
iris.cube.Cube
smalle... |
ESMValGroup__ESMValCore-2181 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/dataset.py:Dataset._update_timerange"
],
"edited_modules": [
"esmvalcore/dataset.py:Dataset"
]
},
"file": "esmvalcore/dataset.py"
},
{
"changes": {
... | ESMValGroup/ESMValCore | 13a444eebd0806e5b7633ca12b3ca1dab7bf5668 | Unify `_get_start_end_date` and `_get_start_end_year` in `local.py`
While working on the ERA5 GRIB CMORizer, I found that we have the two functions [`_get_start_end_date`](https://github.com/ESMValGroup/ESMValCore/blob/4fd8701efd9e618ade0b3ec83a3733274d4f6b25/esmvalcore/local.py#L62C5-L62C24) and [`_get_start_end_year`... | diff --git a/esmvalcore/dataset.py b/esmvalcore/dataset.py
index 849a9a579..2b2230a59 100644
--- a/esmvalcore/dataset.py
+++ b/esmvalcore/dataset.py
@@ -857,7 +857,7 @@ class Dataset:
dataset.facets.pop('timerange')
dataset.supplementaries = []
check.data_availability(dataset)
- ... |
ESMValGroup__ESMValCore-2183 | [
{
"changes": {
"added_entities": [
"esmvalcore/_recipe/check.py:bias_type"
],
"added_modules": [
"esmvalcore/_recipe/check.py:bias_type"
],
"edited_entities": null,
"edited_modules": null
},
"file": "esmvalcore/_recipe/check.py"
},
{
"changes":... | ESMValGroup/ESMValCore | 0668223d83b27446218a0629086deb148651033d | Make `bias` preprocessor work with cubes
In it's current form, the [`bias`](https://github.com/ESMValGroup/ESMValCore/blob/291ce38cd6e77176b232de2a443044cb37f3e3fd/esmvalcore/preprocessor/_bias.py#L12) preprocessor can only be used on `PreprocessorFile` instances, which makes it hard to use outside of a recipe. It woul... | diff --git a/doc/recipe/preprocessor.rst b/doc/recipe/preprocessor.rst
index 8412ceba3..271641c85 100644
--- a/doc/recipe/preprocessor.rst
+++ b/doc/recipe/preprocessor.rst
@@ -2386,9 +2386,9 @@ The bias module contains the following preprocessor functions:
``bias``
--------
-This function calculates biases with re... |
ESMValGroup__ESMValCore-2189 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/preprocessor/_area.py:zonal_statistics",
"esmvalcore/preprocessor/_area.py:meridional_statistics",
"esmvalcore/preprocessor/_area.py:area_statistics"
],
"edited_mo... | ESMValGroup/ESMValCore | 3700cc9800b0d6e8af6020e68e7e7348e9118adb | New preprocessor: subtract global mean from field
A common operation in climate science is to subtract global means from a field. I will implement that. | diff --git a/doc/recipe/preprocessor.rst b/doc/recipe/preprocessor.rst
index 5c994ff00..638a9c6c1 100644
--- a/doc/recipe/preprocessor.rst
+++ b/doc/recipe/preprocessor.rst
@@ -1962,11 +1962,15 @@ along the longitude coordinate.
Parameters:
* `operator`: Operation to apply.
See :ref:`stat_preprocs` for mor... |
ESMValGroup__ESMValCore-2200 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe/recipe.py:_get_default_settings"
],
"edited_modules": [
"esmvalcore/_recipe/recipe.py:_get_default_settings"
]
},
"file": "esmvalcore/_recipe/recipe.... | ESMValGroup/ESMValCore | ac31d5352e5dc79a3f75eba809069a8731c432ea | Preprocessor function `anomalies` does not work well with Dask Distributed
When I run this recipe
```
preprocessors:
test:
anomalies:
period: month
reference:
start_year: 1950
start_month: 1
start_day: 1
end_year: 1979
end_month: 12
end_day: ... | diff --git a/esmvalcore/_recipe/recipe.py b/esmvalcore/_recipe/recipe.py
index ed858e0c3..6f003e17e 100644
--- a/esmvalcore/_recipe/recipe.py
+++ b/esmvalcore/_recipe/recipe.py
@@ -213,9 +213,6 @@ def _get_default_settings(dataset):
settings = {}
- # Configure (deprecated, remove for v2.10.0) load callback
... |
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