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 |
|---|---|---|---|---|---|
faucetsdn__chewie-24 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"chewie/chewie.py:Chewie.__init__",
"chewie/chewie.py:Chewie.get_state_machine"
],
"edited_modules": [
"chewie/chewie.py:Chewie"
]
},
"file": "chewie/chewie.py"
... | faucetsdn/chewie | 1dfd612e1d03f11f7d3e5d091342bdc879eac4db | Statemachine logging isn't working with Faucet
Investigate. It is working when running standalone. | diff --git a/chewie/chewie.py b/chewie/chewie.py
index eff9b87..60c79f2 100644
--- a/chewie/chewie.py
+++ b/chewie/chewie.py
@@ -14,6 +14,7 @@ from chewie.radius_attributes import EAPMessage, State, CalledStationId, NASPort
from chewie.message_parser import MessageParser, MessagePacker
from chewie.mac_address import ... |
faucetsdn__chewie-39 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"chewie/chewie.py:Chewie.receive_eap_messages",
"chewie/chewie.py:Chewie.send_radius_messages",
"chewie/chewie.py:Chewie.get_state_machine_from_radius_packet_id",
"chewie/chewie.p... | faucetsdn/chewie | 79e0c35e0089af91349fcd233d6419a25b28c25a | Could verify that all EAP packets in a sequence come from the same port.
If we have 2 hosts with same MAC (e.g. 1 good, 1 Malicious) and they try to authenticate, it could be possible to authenticate on the malicious port when good is successful if malicious sends eap packet before the radius access-accept has been rec... | diff --git a/chewie/chewie.py b/chewie/chewie.py
index a046688..cfbb661 100644
--- a/chewie/chewie.py
+++ b/chewie/chewie.py
@@ -99,19 +99,19 @@ class Chewie:
def auth_failure(self, src_mac, port_id):
"""failure shim between faucet and chewie
- Args:
- src_mac (MacAddre... |
faucetsdn__chewie-50 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"chewie/chewie.py:Chewie.receive_radius_messages"
],
"edited_modules": [
"chewie/chewie.py:Chewie"
]
},
"file": "chewie/chewie.py"
},
{
"changes": {
"added... | faucetsdn/chewie | d965911e0b4670cca45bc1f7883f4c4daf4905fe | De-authenticate successful auths after period
period since last successful auth.
Renew/Expire authentications
After X time log supplicant off (notify logoff handler). | diff --git a/chewie/chewie.py b/chewie/chewie.py
index 8144daf..9fa2e46 100644
--- a/chewie/chewie.py
+++ b/chewie/chewie.py
@@ -239,7 +239,7 @@ class Chewie:
eap_msg = eap_msg.data_type.data()
state = radius.attributes.find(State.DESCRIPTION)
self.logger.info("radius ... |
faucetsdn__chewie-89 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"chewie/auth_8021x.py:Auth8021x.parse"
],
"edited_modules": [
"chewie/auth_8021x.py:Auth8021x"
]
},
"file": "chewie/auth_8021x.py"
},
{
"changes": {
"added... | faucetsdn/chewie | 05b8441802c2bba0a434826beafbcd51cf2c4f7a | Exception handling with MessageParser
There are times we raise exceptions during packet parsing which should result in the processed packet being dropped, and Chewie can safely continue processing other packets.
Exceptions (and example of when raised) include:
- KeyError: unknown EAP type.
- UnicodeDecodeError: Il... | diff --git a/chewie/auth_8021x.py b/chewie/auth_8021x.py
index 8ae4947..0de562f 100644
--- a/chewie/auth_8021x.py
+++ b/chewie/auth_8021x.py
@@ -1,5 +1,7 @@
import struct
+from chewie.utils import MessageParseError
+
def hwaddr_to_string(hwaddr):
return ":".join(["%02x" % x for x in hwaddr])
@@ -22,9 +24,15 ... |
faucetsdn__chewie-96 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"chewie/chewie.py:Chewie.get_state_machine"
],
"edited_modules": [
"chewie/chewie.py:Chewie"
]
},
"file": "chewie/chewie.py"
},
{
"changes": {
"added_entit... | faucetsdn/chewie | 9c1b6d96f27a585fc777a99ed8ca3cee6be39013 | Change the focus of EAP state machine
There are a couple of improvements we could make here:
- Build the test suite around outcomes (unit test should not care what internal states get transitioned, especially with UCTs)
- Move to a state machine framework (pytramsitions, pysm etc) so we don't need to think about te... | diff --git a/chewie/chewie.py b/chewie/chewie.py
index 918a9ae..8427c36 100644
--- a/chewie/chewie.py
+++ b/chewie/chewie.py
@@ -260,8 +260,8 @@ class Chewie:
state_machine = FullEAPStateMachine(self.eap_output_messages, self.radius_output_messages, src_mac,
... |
feast-dev__feast-5199 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"sdk/python/feast/infra/online_stores/milvus_online_store/milvus.py:MilvusOnlineStore.retrieve_online_documents_v2"
],
"edited_modules": [
"sdk/python/feast/infra/online_stores/milvus... | feast-dev/feast | 306acca510fb90f51ed3de431cfe20f76dc4c971 | Add Keyword Search Support to Milvus
**Is your feature request related to a problem? Please describe.**
Should follow the new V2 pattern here: https://github.com/feast-dev/feast/pull/5082
**Describe the solution you'd like**
Should work like:
```python
results = store.retrieve_online_documents_v2(
features=[
... | diff --git a/sdk/python/feast/infra/online_stores/milvus_online_store/milvus.py b/sdk/python/feast/infra/online_stores/milvus_online_store/milvus.py
index 99405dc2c..d39a2e3a1 100644
--- a/sdk/python/feast/infra/online_stores/milvus_online_store/milvus.py
+++ b/sdk/python/feast/infra/online_stores/milvus_online_store/m... |
feature-engine__feature_engine-339 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"feature_engine/selection/target_mean_selection.py:SelectByTargetMeanPerformance.fit"
],
"edited_modules": [
"feature_engine/selection/target_mean_selection.py:SelectByTargetMeanPerfo... | feature-engine/feature_engine | cceeed2515b9dd709779c91185eb7e3a0bcddcb7 | no numerical or categorical variable checks when user passes string instead of list
`_find_or_check_numerical_variable`s and `_find_or_check_categorical_variables` don't check variable type when user passes string instead of list
Copying @dodoarg code that spots this issue:
Please have a look at the demo below ... | diff --git a/feature_engine/selection/target_mean_selection.py b/feature_engine/selection/target_mean_selection.py
index c55717b..6eba350 100644
--- a/feature_engine/selection/target_mean_selection.py
+++ b/feature_engine/selection/target_mean_selection.py
@@ -201,7 +201,7 @@ class SelectByTargetMeanPerformance(BaseSel... |
feature-engine__feature_engine-340 | [
{
"changes": {
"added_entities": [
"feature_engine/outliers/base_outlier.py:WinsorizerBase.__init__",
"feature_engine/outliers/base_outlier.py:WinsorizerBase.fit"
],
"added_modules": [
"feature_engine/outliers/base_outlier.py:WinsorizerBase"
],
"edited_entit... | feature-engine/feature_engine | d26e5684091501d49ce40c1fc854d6f7510dc530 | Request: add indicator variables as output from `Winsorizer`
**Is your feature request related to a problem? Please describe.**
When clipping extreme values in data, oftentimes having an indicator of whether a feature ended up being clipped or not turns out to be a helpful feature. Currently, `Winsorizer` will clip th... | diff --git a/feature_engine/outliers/base_outlier.py b/feature_engine/outliers/base_outlier.py
index 881d201..a57caf2 100644
--- a/feature_engine/outliers/base_outlier.py
+++ b/feature_engine/outliers/base_outlier.py
@@ -2,6 +2,7 @@ import numpy as np
import pandas as pd
from sklearn.base import BaseEstimator, Transf... |
feature-engine__feature_engine-344 | [
{
"changes": {
"added_entities": [
"feature_engine/outliers/base_outlier.py:WinsorizerBase.__init__",
"feature_engine/outliers/base_outlier.py:WinsorizerBase.fit"
],
"added_modules": [
"feature_engine/outliers/base_outlier.py:WinsorizerBase"
],
"edited_entit... | feature-engine/feature_engine | d26e5684091501d49ce40c1fc854d6f7510dc530 | categorical encoders should not pick datetime variables automatically
If a datetime variable is encoded as object or categorical, and the parameter `variables` is set to None, the transformer will detect those datetime variables as categorical and then encode them.
It might be better practice to exclude datetime var... | diff --git a/feature_engine/outliers/base_outlier.py b/feature_engine/outliers/base_outlier.py
index 881d201..a57caf2 100644
--- a/feature_engine/outliers/base_outlier.py
+++ b/feature_engine/outliers/base_outlier.py
@@ -2,6 +2,7 @@ import numpy as np
import pandas as pd
from sklearn.base import BaseEstimator, Transf... |
feature-engine__feature_engine-477 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"feature_engine/_prediction/base_predictor.py:BaseTargetMeanEstimator._predict"
],
"edited_modules": [
"feature_engine/_prediction/base_predictor.py:BaseTargetMeanEstimator"
]
... | feature-engine/feature_engine | 84dd73b658272bf093785a7b7959733427979320 | functions in variable manipulation should check that user did not enter duplicated variable names
@FYI @Morgan-Sell
This one is important for your decision tree transformer | diff --git a/feature_engine/_prediction/base_predictor.py b/feature_engine/_prediction/base_predictor.py
index 3fab9a3..3ab45be 100644
--- a/feature_engine/_prediction/base_predictor.py
+++ b/feature_engine/_prediction/base_predictor.py
@@ -270,7 +270,7 @@ class BaseTargetMeanEstimator(BaseEstimator):
return... |
feature-engine__feature_engine-502 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"feature_engine/_prediction/base_predictor.py:BaseTargetMeanEstimator._make_numerical_pipeline",
"feature_engine/_prediction/base_predictor.py:BaseTargetMeanEstimator._make_categorical_pipeline",... | feature-engine/feature_engine | 8035f2d060493461fd9c6e363d5e8dc26db54ad0 | change name of parameter errors by unseen in categorical encoders
The change should be done with a deprecation cycle. | diff --git a/feature_engine/_prediction/base_predictor.py b/feature_engine/_prediction/base_predictor.py
index 3ab45be..2b0d143 100644
--- a/feature_engine/_prediction/base_predictor.py
+++ b/feature_engine/_prediction/base_predictor.py
@@ -177,7 +177,7 @@ class BaseTargetMeanEstimator(BaseEstimator):
Create p... |
feature-engine__feature_engine-827 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"feature_engine/selection/smart_correlation_selection.py:SmartCorrelatedSelection.__init__",
"feature_engine/selection/smart_correlation_selection.py:SmartCorrelatedSelection.fit"
],
... | feature-engine/feature_engine | fd62305cbcd4ac15ab6875c15d3bac8e752c0904 | Feature Request: Add Correlation with target as selection method for `SmartCorrelatedSelection`
**Is your feature request related to a problem? Please describe.**
No.
**Describe the solution you'd like**
I would like to add as a selection method of `SmartCorrelatedSelection` a new selection method based on the cor... | diff --git a/docs/user_guide/outliers/Winsorizer.rst b/docs/user_guide/outliers/Winsorizer.rst
index 5fb07c9..7416902 100644
--- a/docs/user_guide/outliers/Winsorizer.rst
+++ b/docs/user_guide/outliers/Winsorizer.rst
@@ -127,7 +127,7 @@ The default values for fold are as follows:
- 'gaussian': `fold` is set to 3.0;
-... |
feder-observatory__stellarphot-141 | [
{
"changes": {
"added_entities": [
"stellarphot/core.py:Camera.__repr__",
"stellarphot/core.py:SourceListData.drop_ra_dec",
"stellarphot/core.py:SourceListData.drop_x_y"
],
"added_modules": null,
"edited_entities": [
"stellarphot/core.py:PhotometryData.__i... | feder-observatory/stellarphot | d73f2834195c1847980ec5ac8964b54d1c0bcec3 | Function `find_too_close()` never used
Function `find_too_close(star_locs, aperture_rad, pixel_scale=0.563)` in `photometry.py` doesn't appear to be called from anywhere in the stellarphot package. Purge or do we need to use it! | diff --git a/stellarphot/core.py b/stellarphot/core.py
index 525b0cb..4515fd7 100644
--- a/stellarphot/core.py
+++ b/stellarphot/core.py
@@ -1,11 +1,9 @@
+import numpy as np
from astropy import units as u
-from astropy.table import QTable, Table, Column
from astropy.coordinates import EarthLocation, SkyCoord
+from as... |
feder-observatory__stellarphot-233 | [
{
"changes": {
"added_entities": [
"stellarphot/core.py:camera_representer",
"stellarphot/core.py:camera_constructor"
],
"added_modules": [
"stellarphot/core.py:camera_representer",
"stellarphot/core.py:camera_constructor"
],
"edited_entities": [
... | feder-observatory/stellarphot | 78b4b7e9605d27f5d4891e6d7d214ec01291d2d3 | Maybe make `Camera` and `Observatory` table attributes
The `PhotometryTable` code has this comment:
```python
# Add the TableAttributes directly to meta (and adding attribute
# functions below) since using TableAttributes results in a
# inability to access the values to due a
# AttributeError: 'TableAttribute' o... | diff --git a/stellarphot/core.py b/stellarphot/core.py
index 569fb20..141bd12 100644
--- a/stellarphot/core.py
+++ b/stellarphot/core.py
@@ -2,7 +2,8 @@ import re
from astropy import units as u
from astropy.coordinates import EarthLocation, SkyCoord
-from astropy.table import Column, QTable, Table
+from astropy.io.... |
feder-observatory__stellarphot-242 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"stellarphot/core.py:CatalogData.from_vizier",
"stellarphot/core.py:apass_dr9",
"stellarphot/core.py:vsx_vizier"
],
"edited_modules": [
"stellarphot/core.py:CatalogDat... | feder-observatory/stellarphot | a35aa74c80bee74d40156197ef6311f95802c468 | CatalogData.from_vizier should accept a WCS as its first argument
Right now `CatalogData.from_vizier` accepts either a coordinate or a FITS header as its first argument. It needs to also accept a WCS. The reason is that when you read a FITS image with `CCDData.read` the WCS information is automatically stripped from th... | diff --git a/stellarphot/core.py b/stellarphot/core.py
index 569fb20..84f3006 100644
--- a/stellarphot/core.py
+++ b/stellarphot/core.py
@@ -1089,7 +1089,7 @@ class CatalogData(BaseEnhancedTable):
@classmethod
def from_vizier(
cls,
- header_or_center,
+ field_center,
desired_ca... |
feder-observatory__stellarphot-280 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"stellarphot/core.py:BaseEnhancedTable._update_passbands"
],
"edited_modules": [
"stellarphot/core.py:BaseEnhancedTable"
]
},
"file": "stellarphot/core.py"
}
] | feder-observatory/stellarphot | 0c3170ad98414c7b04aa42ed11a194fc592887d6 | Creating `PhotometryData` fails if the pasbband_map new passband names are longer than the longest of the original passband names
Consider this setup:
+ The input data to `PhotometryData` has a `passband` column whose contents are `['i']`.
+ The 1passband_map` is `{'i': 'SI'}`
This will issue a warning and fail ... | diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index e8b3e1d..f67b32a 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -14,7 +14,7 @@ build:
apt_packages:
- graphviz
tools:
- python: "mambaforge-22.9"
+ python: "mambaforge-latest"
python:
install:
diff --git a/.rtd-environment.yml b/... |
feder-observatory__stellarphot-297 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"stellarphot/settings/models.py:PassbandMapEntry"
]
},
"file": "stellarphot/settings/models.py"
}
] | feder-observatory/stellarphot | d37db07dacbcac51f3543b39cf7b35c213cf5c8f | The filter name in a PassbandMapEntry should be non-empty
Right now you can enter no name at all or an empty name in a PassbandMapEntry. That should be impossible. The fix is straightforward -- the type for that field should change from `str` to `NonEmptyStr`.
| diff --git a/stellarphot/settings/models.py b/stellarphot/settings/models.py
index 5a68464..fb38187 100644
--- a/stellarphot/settings/models.py
+++ b/stellarphot/settings/models.py
@@ -758,11 +758,9 @@ class PassbandMapEntry(BaseModel):
"""
your_filter_name: Annotated[
- str, Field(description="Instr... |
feder-observatory__stellarphot-298 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"stellarphot/settings/models.py:Camera",
"stellarphot/settings/models.py:Observatory",
"stellarphot/settings/models.py:PassbandMapEntry"
]
},
"... | feder-observatory/stellarphot | bd23f25fd68e88feac679c232514a8ecca43365a | data_unit example for Camera contains errors
In particular, it lists one of the options as "electrons" but that is not a valid unit -- "electron" is the correct name. Same error for "counts".
Found by @Tanner728 | diff --git a/stellarphot/settings/models.py b/stellarphot/settings/models.py
index db043c2..d64f9aa 100644
--- a/stellarphot/settings/models.py
+++ b/stellarphot/settings/models.py
@@ -252,23 +252,27 @@ class Camera(BaseModelWithTableRep):
NonEmptyStr,
Field(
description="Name of the came... |
feder-observatory__stellarphot-300 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"stellarphot/settings/models.py:Camera.validate_gain"
],
"edited_modules": [
"stellarphot/settings/models.py:Camera"
]
},
"file": "stellarphot/settings/models.py"
}
] | feder-observatory/stellarphot | bd23f25fd68e88feac679c232514a8ecca43365a | `Camera` model validation code contains an error
In writing #298 I stumbled on what is, I think, an error in the validation logic for the `Camera` model.
Consider this code, which *should* be a valid `Camera` but is not:
```python
from stellarphot.settings import Camera
c = Camera(
name="should_work",
... | diff --git a/stellarphot/settings/models.py b/stellarphot/settings/models.py
index db043c2..09c9e8a 100644
--- a/stellarphot/settings/models.py
+++ b/stellarphot/settings/models.py
@@ -7,7 +7,7 @@ from typing import Annotated, Any, Literal
from astropy.coordinates import EarthLocation, Latitude, Longitude, SkyCoord
f... |
feder-observatory__stellarphot-308 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"stellarphot/settings/custom_widgets.py:ChooseOrMakeNew._set_disable_state_nested_models"
],
"edited_modules": [
"stellarphot/settings/custom_widgets.py:ChooseOrMakeNew"
]
}... | feder-observatory/stellarphot | fb2d15f2ebec82428cd678fe4f428a31cc21494e | Fix some issues with the custom widget UI
A few things that @Tanner728 found:
- [x] You can type stuff in nullable fields (e.g. AAVSO code for observatory) even if the "switch" is off if you have hit the "Edit" button
- [x] The "Status" button in the ipyautoui save button bar (the leftmost button) is clickable when... | diff --git a/stellarphot/settings/custom_widgets.py b/stellarphot/settings/custom_widgets.py
index ef18099..888d121 100644
--- a/stellarphot/settings/custom_widgets.py
+++ b/stellarphot/settings/custom_widgets.py
@@ -4,6 +4,7 @@
import ipywidgets as ipw
import traitlets as tr
from ipyautoui.autoobject import AutoObj... |
feder-observatory__stellarphot-311 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"stellarphot/settings/custom_widgets.py:ChooseOrMakeNew.__init__"
],
"edited_modules": [
"stellarphot/settings/custom_widgets.py:ChooseOrMakeNew"
]
},
"file": "stellarph... | feder-observatory/stellarphot | d49279bb5e3080d6fc44330d31703ea0da134b1e | Save button is enabled after clicking edit even though no changes have been made
This sequence of events leads to an save button that is enabled even though no changes have been made:
1. Make a new camera or edit an existing one.
2. Click save (after making a change if necessary)
3. Click confirm if necessary
4. ... | diff --git a/stellarphot/settings/custom_widgets.py b/stellarphot/settings/custom_widgets.py
index f92c6c8..160192e 100644
--- a/stellarphot/settings/custom_widgets.py
+++ b/stellarphot/settings/custom_widgets.py
@@ -105,19 +105,11 @@ class ChooseOrMakeNew(ipw.VBox):
# but does no harm in the other cases (true... |
feder-observatory__stellarphot-315 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"stellarphot/settings/custom_widgets.py:ChooseOrMakeNew._edit_button_action",
"stellarphot/settings/custom_widgets.py:ChooseOrMakeNew._make_new_widget"
],
"edited_modules": [
... | feder-observatory/stellarphot | a7415f6222ef2c331ca5f228fbf245ed68d054d9 | Need way to cancel an edit of a camera, etc
Right now there is no easy way to stop editing something if you decide you don't want to make any changes. The obvious way to do that is with the "Revert" button (the yellow counter-clockwise arrow button).
Clicking on that button should set the UI to the same state it wou... | diff --git a/stellarphot/settings/custom_widgets.py b/stellarphot/settings/custom_widgets.py
index 1a26f59..e50a9c3 100644
--- a/stellarphot/settings/custom_widgets.py
+++ b/stellarphot/settings/custom_widgets.py
@@ -224,6 +224,9 @@ class ChooseOrMakeNew(ipw.VBox):
# Update the current state of the widget
... |
feder-observatory__stellarphot-318 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"stellarphot/settings/custom_widgets.py:ChooseOrMakeNew.__init__",
"stellarphot/settings/custom_widgets.py:ChooseOrMakeNew._handle_selection",
"stellarphot/settings/custom_widgets.py:Choo... | feder-observatory/stellarphot | 3c79d736978daaaa6873c26a9ee781f2da01e8c2 | Making a new item confuses the widget
If you have at least one item, e.g. camera, and you select the "Make new..." option and then select the original item again then the widget display is blank. The reason is that the private method `_init_ui` from ipyautoui resets the values of each individual text box (or whatever) ... | diff --git a/stellarphot/settings/custom_widgets.py b/stellarphot/settings/custom_widgets.py
index 160192e..1a26f59 100644
--- a/stellarphot/settings/custom_widgets.py
+++ b/stellarphot/settings/custom_widgets.py
@@ -72,7 +72,7 @@ class ChooseOrMakeNew(ipw.VBox):
message=f"Replace value of this {self._disp... |
feder-observatory__stellarphot-322 | [
{
"changes": {
"added_entities": [
"stellarphot/settings/custom_widgets.py:ChooseOrMakeNew._delete_button_action",
"stellarphot/settings/custom_widgets.py:ChooseOrMakeNew._set_confirm_message"
],
"added_modules": null,
"edited_entities": [
"stellarphot/settings/cu... | feder-observatory/stellarphot | 92f44fc5dc348f6f2e2c553e14c0152cfec390a7 | Add a delete button for the saveable settings
I suppose errors will happen and it would be nice to be able to delete them. | diff --git a/stellarphot/settings/custom_widgets.py b/stellarphot/settings/custom_widgets.py
index e50a9c3..46ff21a 100644
--- a/stellarphot/settings/custom_widgets.py
+++ b/stellarphot/settings/custom_widgets.py
@@ -14,6 +14,8 @@ from stellarphot.settings import (
ui_generator,
)
+DEFAULT_BUTTON_WIDTH = "300px... |
feder-observatory__stellarphot-364 | [
{
"changes": {
"added_entities": [
"stellarphot/gui_tools/comparison_functions.py:ComparisonViewer.photom_apertures_file",
"stellarphot/gui_tools/comparison_functions.py:ComparisonViewer.save",
"stellarphot/gui_tools/comparison_functions.py:ComparisonViewer._set_source_location_fil... | feder-observatory/stellarphot | 69db392c1011438fe4c355f73f4f501f8ccd716d | Notebook 02 problems
- [ ] Add visual indication that aperture and variable files need to be saved or autosave them
- [x] Add settings for file names
- [x] Bring back some way to save TIC information?
- [ ] Offer a choice of source selection (maybe) | diff --git a/.jp_app_launcher_stellarphot.yaml b/.jp_app_launcher_stellarphot.yaml
index 13797c8..8937515 100644
--- a/.jp_app_launcher_stellarphot.yaml
+++ b/.jp_app_launcher_stellarphot.yaml
@@ -13,3 +13,11 @@
cwd: not_used
type: notebook
catalog: Stellarphot photometry
+
+- title: Comparison stars
+ descri... |
feder-observatory__stellarphot-423 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"stellarphot/differential_photometry/aij_rel_fluxes.py:calc_aij_relative_flux"
],
"edited_modules": [
"stellarphot/differential_photometry/aij_rel_fluxes.py:calc_aij_relative_flux"
... | feder-observatory/stellarphot | 0a08565dc0929a181cf62ca80ef8b3157705985f | Calculation of AIJ relative fluxes fails
A consequence of #421 is the calculation of `aij_relative_flux` fails because it relies on aggregation to calculate the relative flux. | diff --git a/stellarphot/differential_photometry/aij_rel_fluxes.py b/stellarphot/differential_photometry/aij_rel_fluxes.py
index 730479d..cf6a37c 100644
--- a/stellarphot/differential_photometry/aij_rel_fluxes.py
+++ b/stellarphot/differential_photometry/aij_rel_fluxes.py
@@ -1,7 +1,7 @@
import astropy.units as u
imp... |
feder-observatory__stellarphot-440 | [
{
"changes": {
"added_entities": [
"stellarphot/core.py:CatalogData.passband_map"
],
"added_modules": null,
"edited_entities": [
"stellarphot/core.py:apass_dr9"
],
"edited_modules": [
"stellarphot/core.py:CatalogData",
"stellarphot/core.py:apas... | feder-observatory/stellarphot | 740b6deaa7877834eafeffb2f1270540d93d10ae | Current `apass_dr9` implementation does not change passbands to the AAVSO standard
The `apass_dr9` implementation does not change the passbands present in the Vizier catalog to the AAVSO standard names. It should. | diff --git a/stellarphot/core.py b/stellarphot/core.py
index 9675d99..4d69df5 100644
--- a/stellarphot/core.py
+++ b/stellarphot/core.py
@@ -9,7 +9,7 @@ from astropy.time import Time
from astropy.wcs import WCS
from astroquery.vizier import Vizier
-from .settings import Camera, Observatory
+from .settings import Ca... |
feder-observatory__stellarphot-459 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"stellarphot/core.py:CatalogData.__init__",
"stellarphot/core.py:CatalogData.from_vizier",
"stellarphot/core.py:vsx_vizier"
],
"edited_modules": [
"stellarphot/core.py... | feder-observatory/stellarphot | 7943077b29dedf1204b19774632f8de0a2bed0b0 | `CatalogData` should explicitly allow for an error column
I've been working a bit on magnitude transforms and realized that the current definition of CatalogData does not allo for a magnitude error column.
While an error column probably should not be required, it should exist where possible. | diff --git a/stellarphot/core.py b/stellarphot/core.py
index af29601..8ffd81f 100644
--- a/stellarphot/core.py
+++ b/stellarphot/core.py
@@ -613,6 +613,10 @@ class CatalogData(BaseEnhancedTable):
the documentation for `stellarphot.settings.PassbandMap` for more
information. The object behaves like a d... |
feder-observatory__stellarphot-461 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"stellarphot/core.py:PhotometryData.__init__",
"stellarphot/core.py:PhotometryData.add_bjd_col"
],
"edited_modules": [
"stellarphot/core.py:PhotometryData"
]
},
... | feder-observatory/stellarphot | 7943077b29dedf1204b19774632f8de0a2bed0b0 | BJD calculation is per star, not per frame
I noticed yesterday that the BJD calculation, which is done in [`PhotometryData`](https://github.com/feder-observatory/stellarphot/blob/main/stellarphot/core.py#L260), has an issue.
In the past, `BJD_TDB` was calculated using the center of the frame as the RA/Dec. Now it is... | diff --git a/stellarphot/core.py b/stellarphot/core.py
index af29601..e06ffdf 100644
--- a/stellarphot/core.py
+++ b/stellarphot/core.py
@@ -353,11 +353,10 @@ class PhotometryData(BaseEnhancedTable):
In addition to these required columns, the following columns are created based
on the input data during creati... |
feder-observatory__stellarphot-470 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"stellarphot/core.py:PhotometryData.__init__"
],
"edited_modules": [
"stellarphot/core.py:PhotometryData"
]
},
"file": "stellarphot/core.py"
}
] | feder-observatory/stellarphot | adc4858fef2a9b3f828903752b8f846da16e81b0 | `PhotometryData` does not use column name mapping
It turns out that `PhotometryData` does not used the remapped column names in its `__init__`. I'll open a PR with a test that reproduces the issue and fixes it in a moment. | diff --git a/stellarphot/core.py b/stellarphot/core.py
index c18e787..222b566 100644
--- a/stellarphot/core.py
+++ b/stellarphot/core.py
@@ -438,6 +438,9 @@ class PhotometryData(BaseEnhancedTable):
**kwargs,
)
+ # From this point forward we should be using self to get at any d... |
fedorpashin__linalg-15 | [
{
"changes": {
"added_entities": [
"linalg/solution.py:Solution.__repr__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"linalg/solution.py:Solution"
]
},
"file": "linalg/solution.py"
},
{
"changes": {
"added_enti... | fedorpashin/linalg | 195006339b7a61e485e0cf778c6aa27a45f7b5b6 | Add __repr__ for Solution | diff --git a/linalg/solution.py b/linalg/solution.py
index 314c165..6ea2dbe 100644
--- a/linalg/solution.py
+++ b/linalg/solution.py
@@ -3,6 +3,7 @@ from linalg.base.any_system import AnySystem
from linalg.base.any_algorithm import AnyAlgorithm
from linalg.factories.default_algorithm import DefaultAlgorithm
+from d... |
felipeangelimvieira__prophetverse-106 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/prophetverse/sktime/base.py:BaseBayesianForecaster._set_y_scales",
"src/prophetverse/sktime/base.py:BaseProphetForecaster._get_trend_model",
"src/prophetverse/sktime/base.py:BaseProp... | felipeangelimvieira/prophetverse | 3f6c300c40d08f8a842e32f54e21ee6bbd353c07 | [BUG] HierarchicalProphet parameter validation is not accepting custom trends
`HierarchicalProphet` is raising error when passing a custom trend. | diff --git a/src/prophetverse/sktime/base.py b/src/prophetverse/sktime/base.py
index e998aff..5dce588 100644
--- a/src/prophetverse/sktime/base.py
+++ b/src/prophetverse/sktime/base.py
@@ -474,6 +474,13 @@ class BaseBayesianForecaster(BaseForecaster):
lambda x: np.abs(x).max()
)
+ ... |
felipeangelimvieira__prophetverse-139 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/prophetverse/effects/base.py:BaseEffect.__init__",
"src/prophetverse/effects/base.py:BaseEffect.input_feature_column_names",
"src/prophetverse/effects/base.py:BaseEffect.should_skip_... | felipeangelimvieira/prophetverse | a1b381583e448a8ce2cf2d4f3ffb0f6b356f2886 | [ENH] Remove `_input_feature_column_names` and make optional to call `fit` before `transform`
The attribute `_input_feature_column_names` of BaseEffects is not needed anymore since the input columns are filtered before calling the effects. In addition, some effects do not have a fit method, that could be skipped.
| diff --git a/src/prophetverse/effects/base.py b/src/prophetverse/effects/base.py
index a592865..d2b1b2e 100644
--- a/src/prophetverse/effects/base.py
+++ b/src/prophetverse/effects/base.py
@@ -1,6 +1,6 @@
"""Module that stores abstract class of effects."""
-from typing import Any, Dict, List, Literal, Optional
+from... |
felipeangelimvieira__prophetverse-176 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "src/prophetverse/engine/map.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edi... | felipeangelimvieira/prophetverse | 8ad00d6f24887ec5c1d37938144112cd2ba37960 | [MNT] Deprecation of some trend and inference engine arguments
To reduce redundancy and provide a more concise interface, some arguments of Prophetverse's models are being deprecated.
## Trend arguments
Instead of
```python
model = Prophetverse(
trend="linear",
changepoint_interval=500,
changepoint_pri... | diff --git a/src/prophetverse/engine/map.py b/src/prophetverse/engine/map.py
index 8434222..293fb6b 100644
--- a/src/prophetverse/engine/map.py
+++ b/src/prophetverse/engine/map.py
@@ -17,7 +17,6 @@ from prophetverse.engine.optimizer.optimizer import (
AdamOptimizer,
BaseOptimizer,
LBFGSSolver,
- _Opt... |
felix-martel__pydanclick-12 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/complex.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"examples/simple.... | felix-martel/pydanclick | 53b9d7fcc8f9af98d8a0d0e2e68d8ddf9629411e | Provide default value for '__var' | diff --git a/README.md b/README.md
index ebf78ae..d69bae5 100644
--- a/README.md
+++ b/README.md
@@ -34,10 +34,10 @@ Add all its fields as options in your Click command:
from pydanclick import from_pydantic
@click.command()
-@from_pydantic("config", TrainingConfig)
-def cli(config: TrainingConfig):
+@from_pydantic(... |
felix-martel__pydanclick-33 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydanclick/main.py:from_pydantic"
],
"edited_modules": [
"pydanclick/main.py:from_pydantic"
]
},
"file": "pydanclick/main.py"
},
{
"changes": {
"added_ent... | felix-martel/pydanclick | e0d762f5983804d8716810304db57291a6e5982f | Support ignoring unsupported fields
It would be nice to have an option to ignore pydantic fields that are not supported e.g. `@pydanclick.from_pydantic(ChatOpenAI, ignore_unsupported=True)
`. I know I can `exclude` specific fieldnames, but I'm dynamically constructing click commands from pydantic models and so I don't... | diff --git a/pydanclick/main.py b/pydanclick/main.py
index bf7ae09..be83915 100644
--- a/pydanclick/main.py
+++ b/pydanclick/main.py
@@ -22,6 +22,7 @@ def from_pydantic(
parse_docstring: bool = True,
docstring_style: Literal["google", "numpy", "sphinx"] = "google",
extra_options: Optional[Dict[str, _Para... |
fema-ffrd__rashdf-24 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/rashdf/geom.py:RasGeomHdf.bc_lines",
"src/rashdf/geom.py:RasGeomHdf.breaklines",
"src/rashdf/geom.py:RasGeomHdf.refinement_regions"
],
"edited_modules": [
"src/ra... | fema-ffrd/rashdf | c63cd8455728d821bd23befd9e5269400fcf5174 | Implement `RasGeomHdf.bc_lines`
Return boundary condition lines from a HEC-RAS Geometry HDF file as a GeoDataFrame of polylines. | diff --git a/src/rashdf/geom.py b/src/rashdf/geom.py
index 5209655..725b6cd 100644
--- a/src/rashdf/geom.py
+++ b/src/rashdf/geom.py
@@ -5,7 +5,7 @@ import numpy as np
import pandas as pd
from geopandas import GeoDataFrame
from pyproj import CRS
-from shapely import Polygon, Point, LineString, polygonize
+from shape... |
femueller__python-n26-73 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"n26/api.py:Api.__init__"
],
"edited_modules": [
"n26/api.py:Api"
]
},
"file": "n26/api.py"
},
{
"changes": {
"added_entities": null,
"added_modules"... | femueller/python-n26 | e71df7ecb8b76ab821ea59ac3196a9478d8c0f65 | Unexpected Keyword
Hi,
I just try you script. And I have this error at first n26 call.
```
root@weboob:~/.config$ /usr/local/bin/n26 -json balance
Traceback (most recent call last):
File "/usr/local/bin/n26", line 6, in <module>
from n26.cli import cli
File "/usr/local/lib/python3.7/dist-packages/n26/c... | diff --git a/Pipfile b/Pipfile
index e85533c..f3e36ec 100644
--- a/Pipfile
+++ b/Pipfile
@@ -4,14 +4,14 @@ verify_ssl = true
name = "pypi"
[packages]
-requests = ">=2.20.0"
+requests = "~=2.20"
click = "*"
tabulate = ">=0.8.3"
PyYAML = "*"
inflect = "*"
-urllib3 = ">=1.24.2"
-tenacity = ">=5.1.1"
-container-app... |
fepegar__torchio-1116 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/torchio/transforms/preprocessing/intensity/rescale.py:RescaleIntensity.__init__",
"src/torchio/transforms/preprocessing/intensity/rescale.py:RescaleIntensity.rescale"
],
"edited_... | fepegar/torchio | 80d71e0807571aca317e9ee7f7056711955a21b8 | RescaleIntensity - multiple calls
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Problem summary
If RescaleIntensity(out_min_max=(0, 1)) is called a second time, an error/unexpected behavior occurs in the normalization. This is because in line [115-116](https://github.com/fep... | diff --git a/src/torchio/transforms/preprocessing/intensity/rescale.py b/src/torchio/transforms/preprocessing/intensity/rescale.py
index 86e8d72..012cf22 100644
--- a/src/torchio/transforms/preprocessing/intensity/rescale.py
+++ b/src/torchio/transforms/preprocessing/intensity/rescale.py
@@ -5,7 +5,7 @@ import numpy as... |
fepegar__torchio-1170 | [
{
"changes": {
"added_entities": [
"src/torchio/data/image.py:Image._crop_from_slices"
],
"added_modules": null,
"edited_entities": [
"src/torchio/data/image.py:Image.__getitem__"
],
"edited_modules": [
"src/torchio/data/image.py:Image"
]
},
... | fepegar/torchio | f8638f33a60ef5e37b101a9deb5d74509b2b9970 | Add pythonic slicing support to torchio.Image
**🚀 Feature**
Allow torchio.Image to be sliced like numpy arrays
```python
image = torchio.Image(...)
print(image.spatial_shape) # -> (100, 100, 100)
crop = image[10:20, :, ::2] # returns a new ScalarImage where the affine matrix and data have been modified accord... | diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml
index 1396c21..eee95d1 100644
--- a/.github/workflows/code_quality.yml
+++ b/.github/workflows/code_quality.yml
@@ -18,7 +18,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v5
with:
- pytho... |
fepegar__torchio-1227 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/torchio/data/subject.py:Subject.__copy__",
"src/torchio/data/subject.py:_subject_copy_helper",
"src/torchio/data/subject.py:_RawSubjectCopySubject.__copy__"
],
"edited_mo... | fepegar/torchio | c7f3b821f96cd3bd7a71edc490c81c4aacc54f22 | Memory leak with TorchIO 0.20.1
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Bug summary
A memory leak issue is observed in TorchIO version 20.0.1 during prolonged training sessions. The memory usage gradually increases over time, leading to an eventual out-of-memory e... | diff --git a/src/torchio/data/subject.py b/src/torchio/data/subject.py
index 75ade08..25f871c 100644
--- a/src/torchio/data/subject.py
+++ b/src/torchio/data/subject.py
@@ -5,7 +5,6 @@ import pprint
from collections.abc import Sequence
from typing import TYPE_CHECKING
from typing import Any
-from typing import Calla... |
fepegar__torchio-163 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"torchio/data/dataset.py:ImagesDataset.save_sample"
],
"edited_modules": [
"torchio/data/dataset.py:ImagesDataset"
]
},
"file": "torchio/data/dataset.py"
},
{
"c... | fepegar/torchio | a1abc1604188397a7a58a72727cfa7977e19ecd7 | Add support for 2D images | diff --git a/torchio/data/dataset.py b/torchio/data/dataset.py
index 0bc00f0..6fdf1f2 100644
--- a/torchio/data/dataset.py
+++ b/torchio/data/dataset.py
@@ -207,7 +207,7 @@ class ImagesDataset(Dataset):
output_paths_dict: Dict[str, TypePath],
) -> None:
for key, output_path in output_... |
fepegar__torchio-385 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"torchio/data/image.py:Image._parse_path",
"torchio/data/image.py:Image.as_pil"
],
"edited_modules": [
"torchio/data/image.py:Image"
]
},
"file": "torchio/data/i... | fepegar/torchio | 48e8a7d27b4f45f90f961cce0faeac5156931c20 | AttributeError: 'NoneType' object has no attribute 'read' when converting to PIL
**🐛Bug**
<!-- A clear and concise description of what the bug is -->
**To reproduce**
<!-- Please provide a minimal working example: https://stackoverflow.com/help/minimal-reproducible-example -->
```python
In [1]: import tor... | diff --git a/torchio/data/image.py b/torchio/data/image.py
index 0f63adf..bb81619 100644
--- a/torchio/data/image.py
+++ b/torchio/data/image.py
@@ -335,7 +335,7 @@ class Image(dict):
def _parse_path(
self,
path: Union[TypePath, Sequence[TypePath]]
- ) -> Union[Path, List[Path]... |
fepegar__torchio-745 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"torchio/utils.py:get_subjects_from_batch"
],
"edited_modules": [
"torchio/utils.py:get_subjects_from_batch"
]
},
"file": "torchio/utils.py"
}
] | fepegar/torchio | 588227bbf66b6c3f15cb941ae152aede96f11057 | Transforms history is not retrieved from batch
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Bug summary
As reported by @Bigsealion in #743, the batch reconstructed from the `DataLoader` doesn't retrieve the transforms for inversion.
### Code for reproduction
```python
impo... | diff --git a/torchio/utils.py b/torchio/utils.py
index 7fc38f0..ce1da1c 100644
--- a/torchio/utils.py
+++ b/torchio/utils.py
@@ -256,6 +256,10 @@ def get_subjects_from_batch(batch: Dict) -> List:
image = klass(tensor=data, affine=affine, filename=path.name)
subject_dict[image_name] = image
... |
festinuz__gecaso-10 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "gecaso/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"gecaso/cache.py:_... | festinuz/gecaso | 36ddb83cbb99d7b82752948383410325408b6948 | Make BaseStorage Async
As suggested by [robin-gvx](https://www.reddit.com/r/Python/comments/6on8in/feedback_required_for_a_small_cache_library/dkirf2p/l) on reddit:
> library relies heavily on asyncio, but for some reason get and set aren't required to be coroutines, but are coerced to be coroutines by the library. ... | diff --git a/README.md b/README.md
index 9db7af6..b7d39df 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
# Gecaso
-
+[](https://badge.fury.io/py/gecaso)  that 'pack' and 'unpack' methods should not be part of BaseStorage. | diff --git a/README.md b/README.md
index 6b3b100..9db7af6 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
# Gecaso
-[](https://badge.fury.io/py/gecaso) 
+![master branch stat... |
fetchai__tools-pocketbook-28 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pocketbook/commands/list.py:run_list"
],
"edited_modules": [
"pocketbook/commands/list.py:run_list"
]
},
"file": "pocketbook/commands/list.py"
},
{
"changes": {... | fetchai/tools-pocketbook | 8dbcabfed3ace459251e0e91afaa9641a71087d4 | Pocketbook transfer to show transaction ID
It would be great if doing a transfer using pocketbook resulted in the transaction ID being posted so that it can be fed into the block-explorer, and also sent to people as "verification" of a transaction being sent.
| diff --git a/pocketbook/commands/list.py b/pocketbook/commands/list.py
index 8a8d8c1..7db9d6e 100644
--- a/pocketbook/commands/list.py
+++ b/pocketbook/commands/list.py
@@ -1,5 +1,5 @@
from fnmatch import fnmatch
-
+import warnings
def _should_display(item, patterns):
return any([fnmatch(item, p) for p in patt... |
fetzerch__kasserver-6 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"kasserver/__init__.py:KasServer._get_credentials",
"kasserver/__init__.py:KasServer._request"
],
"edited_modules": [
"kasserver/__init__.py:KasServer"
]
},
"fil... | fetzerch/kasserver | bcf115dac60e5da2d03c172e9ad2786e708f773e | Switch from 'sha1' to 'plain' authentication method
The following E-Mail from All-Inkl support reached me today:
> Our system has detected that you are using the KAS API, which means that your custom scripts gain access to several features of the technical administration panel (KAS). So please forward the following ... | diff --git a/kasserver/__init__.py b/kasserver/__init__.py
index 7f1364a..86d55c5 100644
--- a/kasserver/__init__.py
+++ b/kasserver/__init__.py
@@ -51,11 +51,8 @@ class KasServer:
self._get_credentials()
def _get_credentials(self):
- def _sha1(string):
- return None if not string else... |
fgmacedo__python-statemachine-353 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"statemachine/factory.py:StateMachineMetaclass._check"
],
"edited_modules": [
"statemachine/factory.py:StateMachineMetaclass"
]
},
"file": "statemachine/factory.py"
},... | fgmacedo/python-statemachine | 0a54b24fd195522c98db42d43ea6a75138750a2f | Supporting abstract classes
### Discussed in https://github.com/fgmacedo/python-statemachine/discussions/344
<div type='discussions-op-text'>
<sup>Originally posted by **galhyt** January 30, 2023</sup>
I have a class that inherites statemachine and has no states and no transitions, all are defined in the childre... | diff --git a/docs/releases/2.0.0.md b/docs/releases/2.0.0.md
index e5cd38b..7d3367e 100644
--- a/docs/releases/2.0.0.md
+++ b/docs/releases/2.0.0.md
@@ -47,6 +47,7 @@ See {ref}`internal transition` for more details.
- [#342](https://github.com/fgmacedo/python-statemachine/pull/342): Assignment of `Transition`
guard... |
fgmacedo__python-statemachine-387 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"statemachine/callbacks.py:CallbackWrapper.__init__",
"statemachine/callbacks.py:CallbackWrapper.__eq__",
"statemachine/callbacks.py:CallbackWrapper.setup",
"statemachine/callback... | fgmacedo/python-statemachine | c60f7febed5c176b5a45d5cf35d2f6474cc70370 | Multiple Observers not working on singular State machine
* Python State Machine version:
* Python version:
* Operating System:
### Description
I would like to have multiple observers responding to an event from a statemachine.
### What I Did
```
from statemachine import StateMachine, State
class MyO... | diff --git a/docs/releases/2.1.0.md b/docs/releases/2.1.0.md
index 5c3caf2..e182ca5 100644
--- a/docs/releases/2.1.0.md
+++ b/docs/releases/2.1.0.md
@@ -40,3 +40,4 @@ See {ref}`States from Enum types`.
- Fixes [#369](https://github.com/fgmacedo/python-statemachine/issues/369) adding support to wrap
methods used a... |
fgmacedo__python-statemachine-425 | [
{
"changes": {
"added_entities": [
"statemachine/callbacks.py:CallbacksRegistry.clear"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"statemachine/callbacks.py:CallbacksRegistry"
]
},
"file": "statemachine/callbacks.py"
},
... | fgmacedo/python-statemachine | f236cad26f5aea3e25824973b19fe5c3519e1e60 | Models instantiated in Djangos setUpTestData seem to skip conditions
* Python State Machine version: 2.1.2
* Python version: 3.12
* Operating System: OsX 12.7.2
* Django: 5.0.3
### Description
The MachineMixin for Django seems to behave differently when models are used within django tests.
Oddly enough, any o... | diff --git a/statemachine/callbacks.py b/statemachine/callbacks.py
index 20d9126..3d8153d 100644
--- a/statemachine/callbacks.py
+++ b/statemachine/callbacks.py
@@ -240,6 +240,9 @@ class CallbacksRegistry:
executor_list.add(callbacks, resolver)
return executor_list
+ def clear(self):
+ sel... |
fgmacedo__python-statemachine-431 | [
{
"changes": {
"added_entities": [
"statemachine/dispatcher.py:_search_callable_attr_is_property",
"statemachine/dispatcher.py:_search_callable_attr_is_callable",
"statemachine/dispatcher.py:_search_callable_in_configs",
"statemachine/dispatcher.py:resolver_factory_from_obj... | fgmacedo/python-statemachine | d195b4a5ab9f068e617ae529aa30214e953a50e1 | Guards and conditions passed as strings really necessary?
* Python State Machine version: 2.1.2
* Python version: 3.11.4
* Operating System: Windows 10
### Description
I wonder why we have to give the "unless" parameter and similar as strings. It hinders me from using automatic renaming in my IDE which does not... | diff --git a/statemachine/dispatcher.py b/statemachine/dispatcher.py
index 4c3bc54..cc1cb29 100644
--- a/statemachine/dispatcher.py
+++ b/statemachine/dispatcher.py
@@ -19,12 +19,7 @@ class ObjectConfig(namedtuple("ObjectConfig", "obj skip_attrs resolver_id")):
if isinstance(obj, ObjectConfig):
re... |
fgnt__lazy_dataset-49 | [
{
"changes": {
"added_entities": [
"lazy_dataset/core.py:from_dataset"
],
"added_modules": [
"lazy_dataset/core.py:from_dataset"
],
"edited_entities": [
"lazy_dataset/core.py:new",
"lazy_dataset/core.py:from_list",
"lazy_dataset/core.py:Datas... | fgnt/lazy_dataset | ff1e16cc68fb98620ccd2e639112c1801d12c4a8 | Support lazy_dataset.new(other_dataset)
It would be logical if `lazy_dataset.new` would accept another dataset, like this:
```python
import lazy_dataset
lazy_dataset.new(lazy_dataset.new([1, 2, 3, 4]))
```
But it is unclear how `new` should handle datasets. It could
- return the input dataset
- make a copy of ... | diff --git a/lazy_dataset/core.py b/lazy_dataset/core.py
index 6a55273..56cb6c9 100644
--- a/lazy_dataset/core.py
+++ b/lazy_dataset/core.py
@@ -27,7 +27,7 @@ def _get_serialize_and_deserialize(immutable_warranty):
def new(
- examples: Union[list, dict],
+ examples: Union[list, dict, 'Dataset'],
... |
firebase__firebase-admin-python-122 | [
{
"changes": {
"added_entities": [
"firebase_admin/__init__.py:App._lookup_project_id"
],
"added_modules": null,
"edited_entities": [
"firebase_admin/__init__.py:App.__init__"
],
"edited_modules": [
"firebase_admin/__init__.py:App"
]
},
"... | firebase/firebase-admin-python | d2d0060ec805f85a73b6b203d6df1d3c9e74cb8b | Validate Project ID String Globally
We currently check if project_id is a string in each of the service modules. This can be done in one place -- namely when the project_id is first read in the `App.__init__()` method. | diff --git a/firebase_admin/__init__.py b/firebase_admin/__init__.py
index 0bf08cd..03471a6 100644
--- a/firebase_admin/__init__.py
+++ b/firebase_admin/__init__.py
@@ -218,15 +218,38 @@ class App(object):
self._options = _AppOptions(options)
self._lock = threading.RLock()
self._services = {}... |
firebase__firebase-admin-python-162 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"firebase_admin/db.py:Reference.update"
],
"edited_modules": [
"firebase_admin/db.py:Reference"
]
},
"file": "firebase_admin/db.py"
}
] | firebase/firebase-admin-python | 351d624a91acb0babfaee019998173555a967755 | Skip validation flag for None in db.update()
### [REQUIRED] Step 2: Describe your environment
* Operating System version: Ubuntu 16.04
* Firebase SDK version: 2.10.0
* Library version: _____
* Firebase Product: database
### [REQUIRED] Step 3: Describe the problem
Updating a key with the value null is... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index b886d51..26877b5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,7 @@
# Unreleased
--
+- [fixed] The `db.Reference.update()` function now accepts dictionaries with
+ `None` values. This can be used to delete child keys from a reference.
# v2.10.0
diff --gi... |
firebase__firebase-admin-python-247 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"firebase_admin/_http_client.py:HttpClient.__init__"
],
"edited_modules": [
"firebase_admin/_http_client.py:HttpClient"
]
},
"file": "firebase_admin/_http_client.py"
}... | firebase/firebase-admin-python | b199dfa6bf3399a05fdf8e631b4996a09e3684ff | Automatically retry 503 errors for RTDB
RTDB occasionally will service [503][1] status codes if the service is temporarily overloaded - currently the HTTPClient doesn't retry those operations, which are safe to be retried.
[1]: https://httpstatuses.com/503 | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 24190cf..b3bec93 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,8 @@
# Unreleased
--
+- [added] Implemented HTTP retries. The SDK now retries HTTP calls on
+ low-level connection and socket read errors, as well as HTTP 500 and
+ 503 errors.
# v2.15.0
dif... |
firebase__firebase-admin-python-249 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"firebase_admin/_token_gen.py:TokenGenerator.create_session_cookie"
],
"edited_modules": [
"firebase_admin/_token_gen.py:TokenGenerator"
]
},
"file": "firebase_admin/_to... | firebase/firebase-admin-python | c120cef6e240c334b7e902035137418d7c295f8f | auth module should use the _http_client.JsonHttpClient
Currently the `auth` module uses the `AuthorizedHttpSession` directly. Instead it should use the `JsonHttpClient` like the other modules. This gives us a single point to control the HTTP interactions of the entire SDK. | diff --git a/firebase_admin/_token_gen.py b/firebase_admin/_token_gen.py
index e979fb1..1ff9bc7 100644
--- a/firebase_admin/_token_gen.py
+++ b/firebase_admin/_token_gen.py
@@ -206,7 +206,7 @@ class TokenGenerator(object):
'validDuration': expires_in,
}
try:
- response = self.c... |
firebase__firebase-admin-python-510 | [
{
"changes": {
"added_entities": [
"firebase_admin/credentials.py:_is_file_path"
],
"added_modules": [
"firebase_admin/credentials.py:_is_file_path"
],
"edited_entities": [
"firebase_admin/credentials.py:Certificate.__init__",
"firebase_admin/credent... | firebase/firebase-admin-python | 939375c021f4c4425beb4bd77b76f0d1be9a7ddd | pathlib and Django v3.1 Compatibility
* Operating System version: Windows 10 home single language
* Firebase SDK version: _____
* Library version: 4.4.0
* Firebase Product: auth
Recently with Django 3.1 release, the previous os.path library was removed and pathlib is introduced for maintaining the file ... | diff --git a/firebase_admin/credentials.py b/firebase_admin/credentials.py
index 1f207e4..5477e1c 100644
--- a/firebase_admin/credentials.py
+++ b/firebase_admin/credentials.py
@@ -15,6 +15,7 @@
"""Firebase credentials module."""
import collections
import json
+import pathlib
import google.auth
from google.auth.... |
firebase__firebase-admin-python-531 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"firebase_admin/_auth_client.py:Client.__init__"
],
"edited_modules": [
"firebase_admin/_auth_client.py:Client"
]
},
"file": "firebase_admin/_auth_client.py"
},
{
... | firebase/firebase-admin-python | 3bdb182554ad188db9d7d66cfc136e999bf593b0 | FR: Support for authentication emulator
* Operating System version: Ubuntu 20.04
* Firebase SDK version: 8.1.1
* Library version: 4.4.0
* Firebase Product: auth
It would be excellent if the Firebase Admin Python SDK could connect to the local authentication emulator. Similar issues exists for [the Go vers... | diff --git a/firebase_admin/_auth_client.py b/firebase_admin/_auth_client.py
index 60be968..2f6713d 100644
--- a/firebase_admin/_auth_client.py
+++ b/firebase_admin/_auth_client.py
@@ -24,6 +24,7 @@ from firebase_admin import _token_gen
from firebase_admin import _user_identifier
from firebase_admin import _user_impo... |
firebase__firebase-admin-python-538 | [
{
"changes": {
"added_entities": [
"firebase_admin/_token_gen.py:CertificateFetchRequest.__init__",
"firebase_admin/_token_gen.py:CertificateFetchRequest.session",
"firebase_admin/_token_gen.py:CertificateFetchRequest.timeout_seconds",
"firebase_admin/_token_gen.py:Certific... | firebase/firebase-admin-python | 04c406978948a076db6198b5f9a1fa96a9addc2e | Auth call timeout option
Using firebase-admin sdk v4.0.0 for python3.8.
We have recently noticed that one of our time sensitive services is struggling due to long calls on `auth.verify_id_token` function. We'd like the option to have a timeout for the actual request call that happens here, since it does appear that ... | diff --git a/firebase_admin/_token_gen.py b/firebase_admin/_token_gen.py
index 562e77f..135573c 100644
--- a/firebase_admin/_token_gen.py
+++ b/firebase_admin/_token_gen.py
@@ -29,6 +29,7 @@ import google.oauth2.service_account
from firebase_admin import exceptions
from firebase_admin import _auth_utils
+from fireb... |
firebase__firebase-admin-python-96 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"firebase_admin/db.py:Query.start_at",
"firebase_admin/db.py:Query.end_at",
"firebase_admin/db.py:Query.equal_to"
],
"edited_modules": [
"firebase_admin/db.py:Query"
... | firebase/firebase-admin-python | d8a93457a5dfba8ddb12d229a6f717565f0975e2 | Unable to query by boolean False
* Operating System version: OSX 10.11.4
* Firebase SDK version: Firebase Admin Python SDK 2.4.0
* Firebase Product: database
In firebase-admin-python/firebase_admin/db.py , it's unable to use equal_to(), start_at(), and end_at() with a boolean False value. It throws `Valu... | diff --git a/firebase_admin/db.py b/firebase_admin/db.py
index d6f5f99..1efa31e 100644
--- a/firebase_admin/db.py
+++ b/firebase_admin/db.py
@@ -442,10 +442,10 @@ class Query(object):
Query: The updated Query instance.
Raises:
- ValueError: If the value is empty or None.
+ ValueE... |
firefly-cpp__NiaARM-105 | [
{
"changes": {
"added_entities": [
"niaarm/rule.py:Rule.zhang"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"niaarm/rule.py:Rule"
]
},
"file": "niaarm/rule.py"
},
{
"changes": {
"added_entities": null,
"add... | firefly-cpp/NiaARM | 2e7a503667b4831b0f11ceedac45885500447bdf | Zhang's metric
@zStupan, can Zhang's metric be added to the pool of implemented interestingness measures?
See example: https://medium.com/@iuyasik/market-basket-analysis-apriori-algorithm-using-zhangs-metric-708406fc5dfc | diff --git a/docs/getting_started.rst b/docs/getting_started.rst
index d75a887..c48d740 100644
--- a/docs/getting_started.rst
+++ b/docs/getting_started.rst
@@ -334,6 +334,7 @@ The framework currently implements the following interest measures (metrics):
- Comprehensibility
- Netconf [#fn]_
- Yule's Q [#fn]_
+- Zhan... |
firefly-cpp__NiaARM-78 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/text_mining.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"niaarm/mine.... | firefly-cpp/NiaARM | 5ee5abb2c76cbc7da850498f6603206bb7f3f940 | Test for text mining is missing | diff --git a/examples/text_mining.py b/examples/text_mining.py
index 07b1f39..17af7ea 100644
--- a/examples/text_mining.py
+++ b/examples/text_mining.py
@@ -5,7 +5,14 @@ from niapy.algorithms.basic import ParticleSwarmOptimization
df = pd.read_json('datasets/text/artm_test_dataset.json', orient='records')
documents... |
fitbenchmarking__fitbenchmarking-1013 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/core/fitting_benchmarking.py:benchmark",
"fitbenchmarking/core/fitting_benchmarking.py:loop_over_benchmark_problems",
"fitbenchmarking/core/fitting_benchmarking.py:loop_o... | fitbenchmarking/fitbenchmarking | 7c0ac4983cb9a835ec105db6238d85d4804ebeb2 | Performance profiler fails if 2 minimizers share a name
**Description of the error**
When running scipy and mantid, the performance profiler fails due to both having a minimizer called BFGS.
| diff --git a/fitbenchmarking/core/fitting_benchmarking.py b/fitbenchmarking/core/fitting_benchmarking.py
index 89ff84ab..428f18fd 100644
--- a/fitbenchmarking/core/fitting_benchmarking.py
+++ b/fitbenchmarking/core/fitting_benchmarking.py
@@ -66,12 +66,9 @@ def benchmark(options, data_dir):
#######################... |
fitbenchmarking__fitbenchmarking-1041 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/controllers/bumps_controller.py:BumpsController.setup"
],
"edited_modules": [
"fitbenchmarking/controllers/bumps_controller.py:BumpsController"
]
},
"fi... | fitbenchmarking/fitbenchmarking | d4e104323741131792a1b92e596bc5760afab9a2 | Support for latest bumps
Bumps 0.9.0 now has different options:
- Rename mp option to lm
- Rename lm to scipy.leastsq
We should update our docs to point this out.
We should update our options. | diff --git a/docs/source/users/options/minimizer_option.rst b/docs/source/users/options/minimizer_option.rst
index 6be2cd39..7ac082b8 100644
--- a/docs/source/users/options/minimizer_option.rst
+++ b/docs/source/users/options/minimizer_option.rst
@@ -29,13 +29,13 @@ FitBenchmarking currently supports the Bumps minimize... |
fitbenchmarking__fitbenchmarking-1085 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/controllers/ralfit_controller.py:RALFitController.setup"
],
"edited_modules": [
"fitbenchmarking/controllers/ralfit_controller.py:RALFitController"
]
},
... | fitbenchmarking/fitbenchmarking | b6009bff0dab092f772f5bb46bb21312acb0e607 | Expose more features in RALFit controller
RALFit can exploit higher order derivatives, and we don't take advantage of that in FitBenchmarking. We should add extra options to the RALFit controller. | diff --git a/docs/source/users/options/minimizer_option.rst b/docs/source/users/options/minimizer_option.rst
index eeda979c..a3a1df10 100644
--- a/docs/source/users/options/minimizer_option.rst
+++ b/docs/source/users/options/minimizer_option.rst
@@ -609,8 +609,17 @@ order derivatives are currently utilized in FitBench... |
fitbenchmarking__fitbenchmarking-1094 | [
{
"changes": {
"added_entities": [
"fitbenchmarking/results_processing/base_table.py:Table.to_csv_file"
],
"added_modules": null,
"edited_entities": [
"fitbenchmarking/results_processing/base_table.py:Table.to_txt"
],
"edited_modules": [
"fitbenchmarki... | fitbenchmarking/fitbenchmarking | 6911a5099e8d9f0430f94dff41d207d38448701c | CSV output
**Is your feature request related to a problem? Please describe.**
The current text format is human readable, but for further processing, it would make more sense as a csv.
**Describe the solution you'd like**
The text file should have the same structure but with a comma somewhere in each column (prefe... | diff --git a/fitbenchmarking/results_processing/base_table.py b/fitbenchmarking/results_processing/base_table.py
index 35c4a6e3..b2f49742 100644
--- a/fitbenchmarking/results_processing/base_table.py
+++ b/fitbenchmarking/results_processing/base_table.py
@@ -160,7 +160,7 @@ class Table:
"""
Generate a... |
fitbenchmarking__fitbenchmarking-1110 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"fitbenchmarking/controllers/scipy_controller.py:ScipyController"
]
},
"file": "fitbenchmarking/controllers/scipy_controller.py"
},
{
"changes": {
... | fitbenchmarking/fitbenchmarking | df465dc1b60d580dfb885ee9d03866c25988566f | scipy Hessian solvers
The minimizer docs for scipy (https://fitbenchmarking.readthedocs.io/en/latest/users/options/minimizer_option.html) currently say:
We now have support for Hessians, so should add s... | diff --git a/docs/source/users/options/minimizer_option.rst b/docs/source/users/options/minimizer_option.rst
index 2a48debb..12f52da4 100644
--- a/docs/source/users/options/minimizer_option.rst
+++ b/docs/source/users/options/minimizer_option.rst
@@ -569,6 +569,12 @@ Hessian information as inputs.
* `L-BFGS-B algorith... |
fitbenchmarking__fitbenchmarking-1119 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"fitbenchmarking/utils/options.py:Options"
]
},
"file": "fitbenchmarking/utils/options.py"
}
] | fitbenchmarking/fitbenchmarking | e52a2f24eb5b727d719faacf66c49b878e332056 | Remove hessian required minimizers from the default scipy minimizers
Currently when running scipy software it runs with the hessian required minimzers. A default scip run doesn't have the hessian enabled.
![image](https://user-images.githubusercontent.com/83226114/212135247-9a6d0683-2f3b-484c-8fef-b3cf187528ac.png... | diff --git a/docs/source/users/options/minimizer_option.rst b/docs/source/users/options/minimizer_option.rst
index 5f62380c..7059eb57 100644
--- a/docs/source/users/options/minimizer_option.rst
+++ b/docs/source/users/options/minimizer_option.rst
@@ -65,7 +65,7 @@ The Bumps minimizers are set as follows:
`de` is no... |
fitbenchmarking__fitbenchmarking-1150 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/core/results_output.py:open_browser"
],
"edited_modules": [
"fitbenchmarking/core/results_output.py:open_browser"
]
},
"file": "fitbenchmarking/core/res... | fitbenchmarking/fitbenchmarking | 1ebe9d7a7263650029516ac293e4d0d41c8ff8c7 | Windows tests fail due to requesting a relative path between drives
**Description of the error**
The windows tests fail during generating results when a relative path is requested between 2 locations on different drives.
**Describe the expected result**
Paths should be explicit in where they are relative too so th... | diff --git a/fitbenchmarking/core/results_output.py b/fitbenchmarking/core/results_output.py
index b67d7931..0d729612 100644
--- a/fitbenchmarking/core/results_output.py
+++ b/fitbenchmarking/core/results_output.py
@@ -456,13 +456,21 @@ def open_browser(output_file: str, options) -> None:
:param output_file: The a... |
fitbenchmarking__fitbenchmarking-1172 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/core/fitting_benchmarking.py:loop_over_hessians",
"fitbenchmarking/core/fitting_benchmarking.py:perform_fit"
],
"edited_modules": [
"fitbenchmarking/core/fitt... | fitbenchmarking/fitbenchmarking | ed89ecec64c91e6806925954709920827806e193 | Store all runtimes and select average in results processing
Currently we take the mean of the runtimes after each fit.
We should store all runtimes at this point and pass it through to the results processing.
Results processing can then take the mean for now with the idea of having a user facing option to select th... | diff --git a/fitbenchmarking/core/fitting_benchmarking.py b/fitbenchmarking/core/fitting_benchmarking.py
index e79062db..6c600ee9 100644
--- a/fitbenchmarking/core/fitting_benchmarking.py
+++ b/fitbenchmarking/core/fitting_benchmarking.py
@@ -517,11 +517,11 @@ def loop_over_hessians(controller, options, grabbed_output,... |
fitbenchmarking__fitbenchmarking-1192 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/core/results_output.py:save_results"
],
"edited_modules": [
"fitbenchmarking/core/results_output.py:save_results"
]
},
"file": "fitbenchmarking/core/res... | fitbenchmarking/fitbenchmarking | 95ba0156cff281707d7bd64f20a9c12a2d71a008 | Use plotly for performance profiles | diff --git a/fitbenchmarking/core/results_output.py b/fitbenchmarking/core/results_output.py
index 16e65980..b9a328b7 100644
--- a/fitbenchmarking/core/results_output.py
+++ b/fitbenchmarking/core/results_output.py
@@ -61,7 +61,8 @@ def save_results(options, results, group_name, failed_problems,
best_results, re... |
fitbenchmarking__fitbenchmarking-1203 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/core/results_output.py:save_results",
"fitbenchmarking/core/results_output.py:create_plots"
],
"edited_modules": [
"fitbenchmarking/core/results_output.py:sav... | fitbenchmarking/fitbenchmarking | e349416a48d3bcb826ed088c7822876123473443 | Fix function that writes plots to html and introduce test for it
The function for writing plotly plots to html files ("write_html_with_link_plotlyjs") is not working. It needs to be fix so that the internal function 'write_html' receives the correct plotly.js path.
Also a test should be introduced, that checks the s... | diff --git a/fitbenchmarking/core/results_output.py b/fitbenchmarking/core/results_output.py
index cae709b4..ece8d42c 100644
--- a/fitbenchmarking/core/results_output.py
+++ b/fitbenchmarking/core/results_output.py
@@ -62,10 +62,10 @@ def save_results(options, results, group_name, failed_problems,
best_results, re... |
fitbenchmarking__fitbenchmarking-1216 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/results_processing/acc_table.py:AccTable.__init__"
],
"edited_modules": [
"fitbenchmarking/results_processing/acc_table.py:AccTable"
]
},
"file": "fitbe... | fitbenchmarking/fitbenchmarking | 8065db0f8b56fc0b158b1201abee2facad425a68 | Performance profiles for emissions
**Description of the error**
When looking at the emissions table I see a runtime pp
**Describe the expected result**
We should have a separate emissions pp
**Suggested fix**
Copy code for runtime and accuracy to make emissions a first class citizen
| diff --git a/fitbenchmarking/results_processing/acc_table.py b/fitbenchmarking/results_processing/acc_table.py
index 2e5f350c..98fafe61 100644
--- a/fitbenchmarking/results_processing/acc_table.py
+++ b/fitbenchmarking/results_processing/acc_table.py
@@ -34,9 +34,8 @@ class AccTable(Table):
:param group_dir: p... |
fitbenchmarking__fitbenchmarking-1244 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/core/fitting_benchmarking.py:loop_over_benchmark_problems",
"fitbenchmarking/core/fitting_benchmarking.py:loop_over_starting_values",
"fitbenchmarking/core/fitting_benchm... | fitbenchmarking/fitbenchmarking | bf51c519b48a817bcceaf59332081343a358c608 | Update emissions tracking to use new codecarbon features
The emissions tracking in FitBenchmarking is currently verrrry slow due to the fact that a new `EmissionsTracker` object is created for each minimizer. A new version of codecarbon now includes a task manager to track emissions of small pieces of code [outlined he... | diff --git a/fitbenchmarking/core/fitting_benchmarking.py b/fitbenchmarking/core/fitting_benchmarking.py
index d064c0d0..a31f1f55 100644
--- a/fitbenchmarking/core/fitting_benchmarking.py
+++ b/fitbenchmarking/core/fitting_benchmarking.py
@@ -8,7 +8,6 @@ import os
import timeit
import warnings
-from contextlib impo... |
fitbenchmarking__fitbenchmarking-1271 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/cli/main.py:run"
],
"edited_modules": [
"fitbenchmarking/cli/main.py:run"
]
},
"file": "fitbenchmarking/cli/main.py"
}
] | fitbenchmarking/fitbenchmarking | 98e3393ac3df0c3ad6be298ceb208742873c35e5 | Corrupt checkpoint files after crash
If FitBenchmarking crashes during results processing, the checkpoint file is missing a final `}` we should add a try catch to finalise the file before reraising the exception. | diff --git a/fitbenchmarking/cli/main.py b/fitbenchmarking/cli/main.py
index 1ae7d531..04aabe33 100755
--- a/fitbenchmarking/cli/main.py
+++ b/fitbenchmarking/cli/main.py
@@ -383,76 +383,85 @@ def run(problem_sets, additional_options=None, options_file="", debug=False):
pp_dfs_all_prob_sets = {}
cp = Checkpoi... |
fitbenchmarking__fitbenchmarking-1279 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/results_processing/plots.py:Plot.__init__",
"fitbenchmarking/results_processing/plots.py:Plot.plot_initial_guess",
"fitbenchmarking/results_processing/plots.py:Plot.plotl... | fitbenchmarking/fitbenchmarking | 0b3ea8a82a1d74db4f5859927347a8b15628a063 | Add error bars
We need to add error bars to the fitting report. | diff --git a/fitbenchmarking/results_processing/plots.py b/fitbenchmarking/results_processing/plots.py
index a2350fa8..da108f4a 100644
--- a/fitbenchmarking/results_processing/plots.py
+++ b/fitbenchmarking/results_processing/plots.py
@@ -18,32 +18,36 @@ class Plot:
"""
Class providing plotting functionality.... |
fitbenchmarking__fitbenchmarking-1336 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/results_processing/performance_profiler.py:adjust_values_to_plot",
"fitbenchmarking/results_processing/performance_profiler.py:create_plot"
],
"edited_modules": [
... | fitbenchmarking/fitbenchmarking | f3f92bfbb2a4b0573142330fe4e824904a92fb59 | Acc and runtime performance profiles show different n failures for same solver
When running the NIST/average_difficulty problems, one can see that in the performance profile plots, certain solvers are marked as having a certain number of failures based on the accuracy plot, but no failure based on the runtime plot. See... | diff --git a/fitbenchmarking/results_processing/performance_profiler.py b/fitbenchmarking/results_processing/performance_profiler.py
index ffa60eb0..f50ee511 100644
--- a/fitbenchmarking/results_processing/performance_profiler.py
+++ b/fitbenchmarking/results_processing/performance_profiler.py
@@ -277,13 +277,11 @@ def... |
fitbenchmarking__fitbenchmarking-1337 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/core/results_output.py:display_page"
],
"edited_modules": [
"fitbenchmarking/core/results_output.py:display_page"
]
},
"file": "fitbenchmarking/core/res... | fitbenchmarking/fitbenchmarking | 546e9783dafe0ab502cceff43e4464c6ef5de843 | Colours in Dash plots in compare table disagree if either plot has already been modified
Once the Dash app is running, if one plays with the Dash plot in either accuracy or runtime table (i.e., removing and adding minimizers), and then switches to the compare table, the colors in two plots (accuracy and runtime) will n... | diff --git a/fitbenchmarking/core/results_output.py b/fitbenchmarking/core/results_output.py
index 73d4b72c..b9d0cd73 100644
--- a/fitbenchmarking/core/results_output.py
+++ b/fitbenchmarking/core/results_output.py
@@ -588,8 +588,12 @@ def check_max_solvers(opts, solvers, max_solvers):
return opts
-def display... |
fitbenchmarking__fitbenchmarking-1338 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/core/results_output.py:display_page",
"fitbenchmarking/core/results_output.py:run_dash_app"
],
"edited_modules": [
"fitbenchmarking/core/results_output.py:dis... | fitbenchmarking/fitbenchmarking | 798f3bc6058a5a3b2207e5fc19d059bdfc18d4b0 | When using load_checkpoint on old results (previous to last run), Dash pp plots are not shown
When one uses load_checkpoint to visualise results that are older than the one from the last run, the Dash app fails to display the performance profiles. When one clicks the online button, a blank space is shown in place of th... | diff --git a/fitbenchmarking/core/results_output.py b/fitbenchmarking/core/results_output.py
index b9d0cd73..6d660eb8 100644
--- a/fitbenchmarking/core/results_output.py
+++ b/fitbenchmarking/core/results_output.py
@@ -592,7 +592,8 @@ def display_page(
pathname: str,
profile_instances_all_groups: "dict[str, d... |
fitbenchmarking__fitbenchmarking-1353 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/parsing/fitting_problem.py:FittingProblem.ini_y"
],
"edited_modules": [
"fitbenchmarking/parsing/fitting_problem.py:FittingProblem"
]
},
"file": "fitben... | fitbenchmarking/fitbenchmarking | c451994dba5cf826520ab10f894f3b1260b29215 | Multifit and make plots produces a bug
**Description of the error**
When doing multifit problems with make plots set to true I get the error message
```
No registered converter was able to produce a C++ rvalue of type double from this Python object of type numpy.ndarray
Benchmark problems: 100%|██████████████████... | diff --git a/fitbenchmarking/parsing/fitting_problem.py b/fitbenchmarking/parsing/fitting_problem.py
index 788a01a8..c962eb64 100644
--- a/fitbenchmarking/parsing/fitting_problem.py
+++ b/fitbenchmarking/parsing/fitting_problem.py
@@ -296,12 +296,11 @@ class FittingProblem:
"""
if parameter_set not in... |
fitbenchmarking__fitbenchmarking-1355 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/parsing/fitbenchmark_parser.py:FitbenchmarkParser._get_data_problem_entries"
],
"edited_modules": [
"fitbenchmarking/parsing/fitbenchmark_parser.py:FitbenchmarkParser... | fitbenchmarking/fitbenchmarking | cbbfa71754bb236973ac80ffdf357cf1229ca98c | Wrong error when the problem name contains special characters
When testing another bug fix, I found a new bug.
If I put the following in a problem definition file
```
name = '$Q = 0.4628 \\AA$'
```
I will always get the error
```
The filepath for saving a file is too long.
Details:
Please change th... | diff --git a/fitbenchmarking/parsing/fitbenchmark_parser.py b/fitbenchmarking/parsing/fitbenchmark_parser.py
index 78961a35..4f9c03cc 100644
--- a/fitbenchmarking/parsing/fitbenchmark_parser.py
+++ b/fitbenchmarking/parsing/fitbenchmark_parser.py
@@ -236,7 +236,11 @@ class FitbenchmarkParser(Parser):
c... |
fitbenchmarking__fitbenchmarking-1356 | [
{
"changes": {
"added_entities": null,
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"edited_entities": null,
"edited_modules": null
},
"file": "fitbenchmarking/results_processing/base_table.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities"... | fitbenchmarking/fitbenchmarking | e1d18fc15c08e399c146b47d661e1893ca8e407c | Divide by zero error when data is fit perfectly
When fitting a problem exactly, the normalised accuracy gives a div by zero exception. | diff --git a/fitbenchmarking/results_processing/base_table.py b/fitbenchmarking/results_processing/base_table.py
index 00a07564..1b5ef053 100644
--- a/fitbenchmarking/results_processing/base_table.py
+++ b/fitbenchmarking/results_processing/base_table.py
@@ -15,9 +15,11 @@ from fitbenchmarking.utils.misc import get_js
... |
fitbenchmarking__fitbenchmarking-1358 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/utils/options.py:Options.read_value"
],
"edited_modules": [
"fitbenchmarking/utils/options.py:Options"
]
},
"file": "fitbenchmarking/utils/options.py"
... | fitbenchmarking/fitbenchmarking | f88b68edb089a0fa66f94df45fb504490d495839 | Bad options error message
When running a fit with a typo in my options file, I got this:
```
Error while running FitBenchmarking. Exiting. See below for more information.
Failed to process options.
Details: The option 'bumps: ['amoeba', 'de', 'dream', 'lm-bumps', 'newton', 'scipy-leastsp']' in the ini file is inval... | diff --git a/fitbenchmarking/utils/options.py b/fitbenchmarking/utils/options.py
index 059a23dc..021fe716 100644
--- a/fitbenchmarking/utils/options.py
+++ b/fitbenchmarking/utils/options.py
@@ -709,17 +709,16 @@ class Options:
value = None
if option in self.VALID[section]:
- if isins... |
fitbenchmarking__fitbenchmarking-1411 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/cli/main.py:get_parser",
"fitbenchmarking/cli/main.py:main"
],
"edited_modules": [
"fitbenchmarking/cli/main.py:get_parser",
"fitbenchmarking/cli/main... | fitbenchmarking/fitbenchmarking | aede3efa3ae005b7fa3f0d6da315d538b917e112 | Add Jacobian check
We should check Jacobians before fitting (outside of timed loop) and use scipy if not any good
| diff --git a/docs/source/users/running.rst b/docs/source/users/running.rst
index bdb319d9..ed6f6530 100644
--- a/docs/source/users/running.rst
+++ b/docs/source/users/running.rst
@@ -192,6 +192,16 @@ They can be changed using the arguments in the table below.
- ``--dont_run_dash``
- | Use this option if you... |
fitbenchmarking__fitbenchmarking-1419 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"examples/benchmark_problems/Data_Assimilation/functions/lorentz.py:lorentz3d"
],
"edited_modules": [
"examples/benchmark_problems/Data_Assimilation/functions/lorentz.py:lorentz3d"
... | fitbenchmarking/fitbenchmarking | ba49952c595970919779006370b39fb687150cc3 | Refactor and add more tests for the FitbenchmarkParser class
There is a need to refactor the class and simplify/clean up the logic.
The test coverage needs to be increased to around 95%(preferably to 100%) for the `FitbenchmarkParser`. It is currently 76%.
This will avoid regression when adding the new feature to all... | diff --git a/examples/benchmark_problems/Data_Assimilation/functions/lorentz.py b/examples/benchmark_problems/Data_Assimilation/functions/lorentz.py
index 62e4df07..0569875c 100644
--- a/examples/benchmark_problems/Data_Assimilation/functions/lorentz.py
+++ b/examples/benchmark_problems/Data_Assimilation/functions/lore... |
fitbenchmarking__fitbenchmarking-1456 | [
{
"changes": {
"added_entities": [
"fitbenchmarking/parsing/horace_parser.py:HoraceParser._get_subplot_titles_SpinW",
"fitbenchmarking/parsing/horace_parser.py:HoraceParser._add_plot_info_as_additional_info"
],
"added_modules": null,
"edited_entities": [
"fitbench... | fitbenchmarking/fitbenchmarking | ccf0faf3fcc8b230a285c707d7f0082a256069b5 | Refactor plots.py | diff --git a/fitbenchmarking/parsing/horace_parser.py b/fitbenchmarking/parsing/horace_parser.py
index ae46b459..0d81da04 100644
--- a/fitbenchmarking/parsing/horace_parser.py
+++ b/fitbenchmarking/parsing/horace_parser.py
@@ -31,7 +31,7 @@ def horace_on():
):
raise ParsingError(
"Could not p... |
fitbenchmarking__fitbenchmarking-1462 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/results_processing/fitting_report.py:create_prob_group",
"fitbenchmarking/results_processing/fitting_report.py:get_figure_paths"
],
"edited_modules": [
"fitbe... | fitbenchmarking/fitbenchmarking | 82716374bf37f0fe0e6f6a5fc5cc14fa7d036976 | Update the fitting report template
1. The `Graph 1` and `Graph 2` can be consolidated into one interactive graph or can be two sub plots stacked horizontally or vertically (if the axis ranges of them are expected to be different).
2. `Table 1` can be removed.
3. The **Number of Parameters** and **Number of Data Points... | diff --git a/docs/source/users/running.rst b/docs/source/users/running.rst
index ed6f6530..ac9f7096 100644
--- a/docs/source/users/running.rst
+++ b/docs/source/users/running.rst
@@ -111,7 +111,7 @@ They can be changed using the arguments in the table below.
| to create plots during runtime.
* - *Don't make... |
fitbenchmarking__fitbenchmarking-165 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "example_scripts/example_runScripts.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
... | fitbenchmarking/fitbenchmarking | 51100cd9cee8722f5dce1272a7c6f84cf2b8f138 | Allow users to comparing minimizers from scipy, mantid, other in one table
Allow user to run a fit benchmarking with a mixture of different sources of minimizers (e.g. mantid and scipy) and where the relative scores of these against selected benchmarking problems is shown in a table.
At present FitBenchmarking only... | diff --git a/example_scripts/example_runScripts.py b/example_scripts/example_runScripts.py
index 3e178346..5d74ae5c 100644
--- a/example_scripts/example_runScripts.py
+++ b/example_scripts/example_runScripts.py
@@ -44,34 +44,26 @@ from fitting_benchmarking import do_fitting_benchmark as fitBenchmarking
from results_ou... |
fitbenchmarking__fitbenchmarking-225 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"example_scripts/example_runScripts.py:main"
],
"edited_modules": [
"example_scripts/example_runScripts.py:main"
]
},
"file": "example_scripts/example_runScripts.py"
}... | fitbenchmarking/fitbenchmarking | 5b418a978197bd00dff9603ebe3ba2ab8b7cc56e | Documentation of code out of sync in top level files
Code documentation of functions, function parameters and code comment has gone out of sync for fitting_benchmarking.py and fitbenchmark_one_problem.py and some of the functions it calls.
Fix:
* documentation for all function parameters
* check these are not out... | diff --git a/example_scripts/example_runScripts.py b/example_scripts/example_runScripts.py
index 0da68d4b..3aea5da5 100644
--- a/example_scripts/example_runScripts.py
+++ b/example_scripts/example_runScripts.py
@@ -9,8 +9,8 @@ import os
import sys
import glob
-from fitbenchmarking.fitting_benchmarking import do_fit... |
fitbenchmarking__fitbenchmarking-320 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/fitting/misc.py:compute_chisq",
"fitbenchmarking/fitting/misc.py:create_result_entry"
],
"edited_modules": [
"fitbenchmarking/fitting/misc.py:compute_chisq",
... | fitbenchmarking/fitbenchmarking | be3361d4fd7a34a8a2fcfa7a8510908accf9222a | Wrong `chi_sq` value produced
**Description of the error**
Noticed by @AndrewLister-STFC in the review of #316 that the `chi_sq` computed in `utils/fitting/misc.py` is incorrect.
**Describe the expected result**
Fixed reported `chi_sq` value
| diff --git a/fitbenchmarking/fitting/misc.py b/fitbenchmarking/fitting/misc.py
index 73ccd9e5..3120ebfc 100644
--- a/fitbenchmarking/fitting/misc.py
+++ b/fitbenchmarking/fitting/misc.py
@@ -20,10 +20,8 @@ def compute_chisq(actual, fitted, errors=None):
"""
r = fitted - actual
if errors is not None:
- ... |
fitbenchmarking__fitbenchmarking-329 | [
{
"changes": {
"added_entities": null,
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"edited_entities": [
"fitbenchmarking/fitting/controllers/dfogn_controller.py:DFOGNController._prediction_error",
"fitbenchmarking/fitting/controllers/dfogn_controller.py:DFOGNController.cleanup"
],
"edit... | fitbenchmarking/fitbenchmarking | 6a41e646051513f80570287b96796f879534b072 | Add a default value for x in FittingProblem.eval_f
Every evaluation of this is going to occur at self.data_x.
This already wrapped by some controllers to give a function which only takes parameters as an argument.
We should make self.data_x a default, which will accommodate all of the controllers | diff --git a/fitbenchmarking/fitting/controllers/dfogn_controller.py b/fitbenchmarking/fitting/controllers/dfogn_controller.py
index 328f62ae..ae6fc1cc 100644
--- a/fitbenchmarking/fitting/controllers/dfogn_controller.py
+++ b/fitbenchmarking/fitting/controllers/dfogn_controller.py
@@ -31,8 +31,7 @@ class DFOGNControll... |
fitbenchmarking__fitbenchmarking-338 | [
{
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"edited_modules": null
},
"file": "docs/source/conf.py"
},
{
"changes": {
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"edited_entities": [
"fitbenchmarking/... | fitbenchmarking/fitbenchmarking | 5e7ca3b5a5a9be23d6a06891367824e4ea0d169a | Create a Jacobian and residual evaluation function in the fitting problem
When adding RALFit (#215) you have to supply Jacobians and residuals to the software. Currently the Jacobians is done by using `SciPy` in the RALFit controller. We should create two new functions `eval_j` and `eval_r` which evaluate the Jacobian ... | diff --git a/docs/source/conf.py b/docs/source/conf.py
index 96dba92b..c39956f4 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -16,10 +16,9 @@
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#... |
fitbenchmarking__fitbenchmarking-339 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/fitbenchmark_one_problem.py:fitbm_one_prob",
"fitbenchmarking/fitbenchmark_one_problem.py:benchmark"
],
"edited_modules": [
"fitbenchmarking/fitbenchmark_one_... | fitbenchmarking/fitbenchmarking | 1be08f4a354735e73696c041285c72c1374a8ad5 | Revisit the way result objects are used for table generation
Add attributes within results object (normalised values, html colours, etc) to create pandas tables of the result object instead of chi_sq and runtime values. | diff --git a/.travis.yml b/.travis.yml
index 61aa7643..c6289a1e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -25,15 +25,16 @@ before_install:
- sudo apt-get install lcov
- sudo apt-get install libblas-dev
- sudo apt-get install liblapack-dev
+ - sudo apt-get install pandoc
install:
# Builds RALfit
-... |
fitbenchmarking__fitbenchmarking-514 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/core/fitbenchmark_one_problem.py:fitbm_one_prob",
"fitbenchmarking/core/fitbenchmark_one_problem.py:benchmark"
],
"edited_modules": [
"fitbenchmarking/core/fi... | fitbenchmarking/fitbenchmarking | 944b1cf42fd1429b84e0dad092a5cd789f4ad6a7 | Create an option to toggle the 3rd party output grabber
As observed in #500 the output grabber is not working on windows and as part of #511 to enable windows test a solution was to have the output grabber to pass through. It would also be useful to have this as a option within FitBenchmarking.
| diff --git a/examples/all_softwares.ini b/examples/all_softwares.ini
index b054ae82..dc589f6d 100644
--- a/examples/all_softwares.ini
+++ b/examples/all_softwares.ini
@@ -196,7 +196,7 @@ software: dfo
# file_name specifies the file path to write the logs to
# default is fitbenchmarking.log
-#file_name: fitbenchmark... |
fitbenchmarking__fitbenchmarking-603 | [
{
"changes": {
"added_entities": [
"fitbenchmarking/utils/options.py:Options._create_config",
"fitbenchmarking/utils/options.py:Options.write_to_stream"
],
"added_modules": null,
"edited_entities": [
"fitbenchmarking/utils/options.py:Options.write"
],
... | fitbenchmarking/fitbenchmarking | 9f8f5254e2512fd761be211c8274573eabff62b8 | Azure test incorrect report
**Description of the error**
The Windows tests in Azure say they pass when they actually fail.
**Describe the expected result**
Azure correctly reports passes and fails... | diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 229fd6e2..32d6dd95 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -11,8 +11,6 @@ strategy:
matrix:
Python36:
python.version: '3.6'
- Python37:
- python.version: '3.7'
steps:
- task: UsePythonVersion@0
@@ -21,15 +19,20... |
fitbenchmarking__fitbenchmarking-604 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/core/fitting_benchmarking.py:benchmark",
"fitbenchmarking/core/fitting_benchmarking.py:loop_over_benchmark_problems"
],
"edited_modules": [
"fitbenchmarking/c... | fitbenchmarking/fitbenchmarking | eddaae19cee2e5dc1c8d15519a2ad07bb5c58ed0 | Use a better first example
**Description of the documentation**
The suggested example is to use the `simple_tests` problem set.
This includes Mantid data, and so will fail if Mantid isn't installed. Change the default to be, e.g., a set of NIST problems, so that it can be run independently of third party software... | diff --git a/docs/source/users/running.rst b/docs/source/users/running.rst
index 20b9cb21..387cef6f 100644
--- a/docs/source/users/running.rst
+++ b/docs/source/users/running.rst
@@ -10,7 +10,7 @@ directory along with a template for passing in options.
To run with any of these problem sets, you should pass the path to... |
fitbenchmarking__fitbenchmarking-619 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/cli/main.py:run"
],
"edited_modules": [
"fitbenchmarking/cli/main.py:run"
]
},
"file": "fitbenchmarking/cli/main.py"
},
{
"changes": {
"ad... | fitbenchmarking/fitbenchmarking | a15f012656a7363ed694a90306a73907282c8c54 | Multiple problem groups error
**Description of the error**
When you run multiple problem groups, for example `fitbenchmark examples/benchmark_problems/NIST/*` the minimizers in the options are written over and produces the following errors
```
Minimizer: Newton-CG: scipy 2-point
Minimizer cannot be run ... | diff --git a/fitbenchmarking/cli/main.py b/fitbenchmarking/cli/main.py
index 1626ea33..818d199f 100755
--- a/fitbenchmarking/cli/main.py
+++ b/fitbenchmarking/cli/main.py
@@ -132,6 +132,9 @@ def run(problem_sets, options_file='', debug=False):
result_dir.append(group_results_dir)
groups.append(label)
... |
fitbenchmarking__fitbenchmarking-638 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fitbenchmarking/cli/main.py:run"
],
"edited_modules": [
"fitbenchmarking/cli/main.py:run"
]
},
"file": "fitbenchmarking/cli/main.py"
},
{
"changes": {
"ad... | fitbenchmarking/fitbenchmarking | 57b6a420919b94bde62dccd6bd610f78605fec8c | Make the css links relative
At the moment the css files are linked to using an absolute file path. We should change this to a relative path, which will allow easy deployment of the result on the web, as well as viewing the results generated in a Docker container on a native filesystem.
Probably the cleanest way to ... | diff --git a/fitbenchmarking/cli/main.py b/fitbenchmarking/cli/main.py
index b8fece31..603f7912 100755
--- a/fitbenchmarking/cli/main.py
+++ b/fitbenchmarking/cli/main.py
@@ -22,6 +22,7 @@ from fitbenchmarking.core.fitting_benchmarking import benchmark
from fitbenchmarking.core.results_output import save_results
from... |
fitbenchmarking__fitbenchmarking-661 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"fitbenchmarking/utils/options.py:Options"
]
},
"file": "fitbenchmarking/utils/options.py"
}
] | fitbenchmarking/fitbenchmarking | 6641c44ab97f156badf34a1075791a21304df4a3 | Tests run by default
If you install via
`pip install fitbenchmarking`
then only scipy minimizers are available. The default options should reflect this. | diff --git a/fitbenchmarking/utils/options.py b/fitbenchmarking/utils/options.py
index d650efa9..22ce6467 100644
--- a/fitbenchmarking/utils/options.py
+++ b/fitbenchmarking/utils/options.py
@@ -84,7 +84,7 @@ class Options(object):
DEFAULT_FITTING = \
{'num_runs': 5,
'algorithm_type': 'all',
- ... |
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