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 |
|---|---|---|---|---|---|
NeurodataWithoutBorders__pynwb-2060 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/pynwb/image.py:ImageSeries.__init__",
"src/pynwb/image.py:ImageSeries._change_external_file_format"
],
"edited_modules": [
"src/pynwb/image.py:ImageSeries"
]
},... | NeurodataWithoutBorders/pynwb | c4007f030024580be7a8810342632c1ef260b081 | [Bug]: External file format error on ImageSeries
### What happened?
When creating a new `ImageSeries` with an external file, pynwb now throws an error if `format` is not specified as "external", even if no format value was provided.
Would it be better for this to remain a warning (or removed entirely), since it is ju... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 28f92b2e..52c00b21 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@
### Enhancements and minor changes
- Added option to disable typemap caching and updated type map cache location. @stephprince [#2057](https://github.com/NeurodataWithoutBorders/pynwb/pull/20... |
NeurodataWithoutBorders__pynwb-381 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/pynwb/ogen.py:OptogeneticStimulusSite"
]
},
"file": "src/pynwb/ogen.py"
}
] | NeurodataWithoutBorders/pynwb | a11f8e4edb84fa318b84035d0debe5c764bf7f31 | `nwbfile.create_ogen_site` device argument expects string
the `device` argument of `nwbfile.create_ogen_site` takes a string that is the name of the device. I think it should also take the device object. This will make usage more consistent with `nwbfile.create_electrode_group` and `nwbfile.add_electrode` (with `electr... | diff --git a/src/pynwb/ogen.py b/src/pynwb/ogen.py
index d05832fd..a4a21f9c 100644
--- a/src/pynwb/ogen.py
+++ b/src/pynwb/ogen.py
@@ -5,6 +5,7 @@ from .form.utils import docval, popargs, fmt_docval_args
from . import register_class, CORE_NAMESPACE
from .base import TimeSeries, _default_resolution, _default_conversio... |
NeurodataWithoutBorders__pynwb-439 | [
{
"changes": {
"added_entities": [
"src/pynwb/form/spec/namespace.py:NamespaceCatalog.__load_namespace"
],
"added_modules": null,
"edited_entities": [
"src/pynwb/form/spec/namespace.py:NamespaceCatalog.load_namespaces"
],
"edited_modules": [
"src/pynwb... | NeurodataWithoutBorders/pynwb | 0db2fc1528a7eb0204911fba88f54f07cd70bc94 | NWBNamespaceBuilder does not validate spec it is building/writing.
NWBNamespaceBuilder allows construction of specs that can't be loaded due to redefining types already defined in the spec. The problem isn't discovered until load time.
Example:
from pynwb.spec import NWBGroupSpec, NWBNamespaceBuilder
s... | diff --git a/src/pynwb/form/spec/namespace.py b/src/pynwb/form/spec/namespace.py
index b152adef..bf7388ad 100644
--- a/src/pynwb/form/spec/namespace.py
+++ b/src/pynwb/form/spec/namespace.py
@@ -337,6 +337,40 @@ class NamespaceCatalog(object):
for subspec_dict in it:
self.__resolve_includes(subspe... |
NeurodataWithoutBorders__pynwb-501 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/pynwb/behavior.py:BehavioralEvents",
"src/pynwb/behavior.py:BehavioralTimeSeries",
"src/pynwb/behavior.py:PupilTracking"
]
},
"file": "src... | NeurodataWithoutBorders/pynwb | 6f1c065fc321b8b9669935f0465b6a6ff24c087e | BehavioralEvents does not write to hdf5 file
Using minimal example below to create an nwb file and a BehavioralEvents time series, groups for the processing module and for the BehavioralEvents container are created. However, the data is missing from the hdf5 file after writing the data.
Can be fixed by changing 'ti... | diff --git a/src/pynwb/behavior.py b/src/pynwb/behavior.py
index e3cc84de..d73adcf1 100644
--- a/src/pynwb/behavior.py
+++ b/src/pynwb/behavior.py
@@ -102,7 +102,7 @@ class BehavioralEvents(MultiContainerInterface):
'get': 'get_timeseries',
'create': 'create_timeseries',
'type': TimeSeries,
-... |
NeurodataWithoutBorders__pynwb-57 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/form/data_utils.py:DataChunkIterator.__init__"
],
"edited_modules": [
"src/form/data_utils.py:DataChunkIterator"
]
},
"file": "src/form/data_utils.py"
}
] | NeurodataWithoutBorders/pynwb | 17699d46b6bc3902b8fa47fb24f4f376b1b7ddc0 | Bug: unittest test_standard_iterator_unbuffered seems buggy
Subtle bug, but here it goes:
On test_standard_iterator_unbuffered (tests/unit/form_tests/utils_test/test_core_DataChunkIterator), line 57 and 59, we have
dci = DataChunkIterator(data=range(10), buffer_size=1)
self.assertTupleEqual(dci.max_shape, (None,))... | diff --git a/src/form/data_utils.py b/src/form/data_utils.py
index 7e0f16f8..6b249dbc 100644
--- a/src/form/data_utils.py
+++ b/src/form/data_utils.py
@@ -98,7 +98,7 @@ class DataChunkIterator(AbstractDataChunkIterator):
# Try to get an accurate idea of max_shape for other Python datastructures if possible... |
NeurodataWithoutBorders__pynwb-575 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/pynwb/form/build/map.py:Proxy.candidates",
"src/pynwb/form/build/map.py:BuildManager.__get_proxy_container"
],
"edited_modules": [
"src/pynwb/form/build/map.py:Proxy",
... | NeurodataWithoutBorders/pynwb | 432699f83ecb4747943a6c3bfd052b9cd5d2d357 | FilteredEphys error on read
```python
from pynwb import NWBFile, NWBHDF5IO
from pynwb.ecephys import FilteredEphys, ElectricalSeries
import numpy as np
nwbfile = NWBFile("source", "a file with header data", "NB123A", '2018-06-01T00:00:00')
module_lfp = nwbfile.create_processing_module(
'lfp', source='sour... | diff --git a/src/pynwb/form/build/map.py b/src/pynwb/form/build/map.py
index 5efe6b8e..3de93323 100644
--- a/src/pynwb/form/build/map.py
+++ b/src/pynwb/form/build/map.py
@@ -15,6 +15,16 @@ from .warnings import OrphanContainerWarning, MissingRequiredWarning
class Proxy(object):
+ """
+ A temporary object to... |
NeurodataWithoutBorders__pynwb-596 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/pynwb/image.py:ImageSeries.__init__"
],
"edited_modules": [
"src/pynwb/image.py:ImageSeries"
]
},
"file": "src/pynwb/image.py"
}
] | NeurodataWithoutBorders/pynwb | c27448d25b080054028c330533f52ed14c4375b8 | TwoPhotonSeries data warning
TwoPhotonSeries should not throw warning`UserWarning: missing required attribute 'data' for 'object_name' warnings.warn("missing required attribute '%s' for '%s'" % (spec.name, builder.name))` when `format='external'` | diff --git a/src/pynwb/data/nwb.image.yaml b/src/pynwb/data/nwb.image.yaml
index ba78d096..964b12bf 100644
--- a/src/pynwb/data/nwb.image.yaml
+++ b/src/pynwb/data/nwb.image.yaml
@@ -19,6 +19,7 @@ groups:
- name: data
dtype: int8
doc: Either binary data containing image or empty.
+ quantity: '?'
di... |
Nicoretti__crc-153 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/crc/_crc.py:BasicRegister.digest"
],
"edited_modules": [
"src/crc/_crc.py:BasicRegister"
]
},
"file": "src/crc/_crc.py"
}
] | Nicoretti/crc | 8d928145df5caf588d9ff5af83bd72feb241fd1e | 🐞 Return of digest() is not stable
# Summary
Multiple calls to `digest()` don't return the same answers.
## Reproducing the Issue
```
>>> import crc
>>> r = crc.Register(crc.Crc8.BLUETOOTH)
>>> r.init()
>>> r.update(b"Hello World!")
138
>>> r.digest()
81
>>> r.digest()
138
>>> r.digest()
81
```
## ... | diff --git a/docs/docs/changelog/unreleased.md b/docs/docs/changelog/unreleased.md
index 30c1938..49f4d41 100644
--- a/docs/docs/changelog/unreleased.md
+++ b/docs/docs/changelog/unreleased.md
@@ -1,5 +1,12 @@
# Unreleased
+## 🐞 Bug Fixes
+* Fixed unstable return values of `digest` function. For more details, see i... |
Nicoretti__crc-157 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "docs/scripts/configurations.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edi... | Nicoretti/crc | 2368149d71ae9580bc9df1c69866c5267e299d0b | 🔧 Refactor CRC-16 Configuration Naming and Expand Variants
# Summary
The current `Crc16.CCITT` implementation in our library aligns with `CRC-16/XMODEM`. Considering that "CCITT" refers to a group of related configurations rather than a single, specific one, utilizing "CCITT" for a distinct configuration is misleadin... | diff --git a/README.md b/README.md
index 13b1cd3..860a3cb 100644
--- a/README.md
+++ b/README.md
@@ -34,13 +34,14 @@ Calculate CRC checksums, verify CRC checksum, predefined CRC configurations, cus
## Available CRC Configurations
For convenience various frequently used crc configurations ship with the library out of ... |
Nike-Inc__gimme-aws-creds-464 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"gimme_aws_creds/config.py:Config._handle_config"
],
"edited_modules": [
"gimme_aws_creds/config.py:Config"
]
},
"file": "gimme_aws_creds/config.py"
}
] | Nike-Inc/gimme-aws-creds | 763ae83ca4f5338ffdaeb788b4ac83542d72df6d | `force_classic` value is overridden by default when using profile inheritance
<!--- Provide a general summary of the issue in the Title above -->
## Expected Behavior
The following configuration should set `force_classic=False` in the `myprofile` profile
```
[mybase-level1]
client_id = bar
[mybase-level2]
inhe... | diff --git a/gimme_aws_creds/config.py b/gimme_aws_creds/config.py
index fe541d3..b5a881b 100644
--- a/gimme_aws_creds/config.py
+++ b/gimme_aws_creds/config.py
@@ -201,23 +201,22 @@ class Config(object):
profile_config[key] = True
elif profile_config[key] == 'False':
prof... |
Nike-Inc__koheesio-158 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/koheesio/spark/utils/common.py:check_if_pyspark_connect_is_supported"
],
"edited_modules": [
"src/koheesio/spark/utils/common.py:check_if_pyspark_connect_is_supported"
]
... | Nike-Inc/koheesio | ea5be3fe7758a0559a3fbda0d1cce7d43eab40f6 | [FEATURE] Add Support for Bearer Token in Http Module with Masking
## Is your feature request related to a problem? Please describe.
<!-- A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] -->
Currently, the `get_headers` method in the Http module does not support adding a bear... | diff --git a/src/koheesio/spark/utils/common.py b/src/koheesio/spark/utils/common.py
index 78bdf31..341ce47 100644
--- a/src/koheesio/spark/utils/common.py
+++ b/src/koheesio/spark/utils/common.py
@@ -89,7 +89,7 @@ def check_if_pyspark_connect_is_supported() -> bool:
Raises
------
ImportError
- If... |
Nike-Inc__koheesio-164 | [
{
"changes": {
"added_entities": [
"src/koheesio/models/__init__.py:_SecretMixin.__add__",
"src/koheesio/models/__init__.py:_SecretMixin.__radd__",
"src/koheesio/models/__init__.py:_SecretMixin.__mul__",
"src/koheesio/models/__init__.py:_SecretMixin.__rmul__",
"src/... | Nike-Inc/koheesio | 7fa963fabb41d0471ebbd2291741108e8a26b85d | [FEATURE] Bigger, better, SecretStr
We should create a custom SecretStr implementation that plays a bit nicer with str operations, but that's up for debate.
For example, this code would throw an error:
```python
from pydantic import SecretStr
body = SecretStr("foobarbazbladibla")
type = "bearer"
header = type + body
... | diff --git a/pyproject.toml b/pyproject.toml
index 89641a3..ea59dfd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -410,7 +410,7 @@ Available scripts:
- `coverage` or `cov` - run the test suite with coverage.
"""
path = ".venv"
-python = "3.11"
+python = "3.12"
template = "default"
features = [
"async",
di... |
Nikoleta-v3__blackbook-36 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/blackbook/__main__.py:main"
],
"edited_modules": [
"src/blackbook/__main__.py:main"
]
},
"file": "src/blackbook/__main__.py"
}
] | Nikoleta-v3/blackbook | 31468676b827657269a5730769111a759bb018c6 | Support ability to run blackbook over a single file
Currently it seems that there is no way to run `blackbook` over a specific file path. Attempting to format a single notebook at path `path/to/notebooks/Example-Notebook.ipynb` fails to do anything
```
$ pip freeze | grep blackbook
blackbook==0.0.5
$ blackbook pa... | diff --git a/README.md b/README.md
index 63d2f49..e0acc79 100644
--- a/README.md
+++ b/README.md
@@ -11,9 +11,16 @@
```bash
$ pip install blackbook
$ blackbook .
-2019-01-28 17:15:10.857 | INFO | blackbook.__main__:main:25 - All done! 📖
-2019-01-28 17:15:10.857 | INFO | blackbook.__main__:main:27 - 1 notebo... |
NoRedInk__make-lambda-package-4 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"make_lambda_package/cli.py:main"
],
"edited_modules": [
"make_lambda_package/cli.py:main"
]
},
"file": "make_lambda_package/cli.py"
}
] | NoRedInk/make-lambda-package | 058f04b29129c15cc3bcf3a4e21d36c553a60143 | Script breaks if --requirements-file is not given
- remove temporary `import click` statement from cli.py
| diff --git a/README.in b/README.in
index 2a4dc23..3a2a879 100644
--- a/README.in
+++ b/README.in
@@ -6,16 +6,20 @@ source code, configs, and dependencies with extension modules.
# Installation
-If you don't use `pipsi`, you're missing out.
-Here are [installation instructions](https://github.com/mitsuhiko/pipsi#re... |
OCA__oca-github-bot-215 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "setup.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/oca_github_bot/manifest... | OCA/oca-github-bot | 0d64b24e33fd339fcc5415c38421948ac511b6aa | ocabot migration duplicating lines in migration issue?
See for example https://github.com/OCA/server-env/issues/120 where the issue was created correctly but now lines with references to a PR are duplicated. | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7bc5bf2..4929ad8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ default_language_version:
python: python3
repos:
- repo: https://github.com/psf/black
- rev: 22.10.0
+ rev: 22.8.0
hooks:
- id: black
- r... |
OCA__oca-github-bot-59 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/oca_github_bot/commands.py:BotCommand.__init__",
"src/oca_github_bot/commands.py:BotCommandMerge.parse_options",
"src/oca_github_bot/commands.py:parse_commands"
],
"edite... | OCA/oca-github-bot | 0ab1c02e2ef25e2b3231a326e04c31b40710ce6f | merge bot: parse command inside a greater message
For now, the merge bot only reacts to the merge command putting that comment in an isolated message (example of greater message: https://github.com/OCA/account-invoicing/pull/552#issuecomment-507203903). | diff --git a/HISTORY.rst b/HISTORY.rst
index 0f9ae33..08d2ad2 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -1,6 +1,10 @@
next
~~~~
+**Features**
+
+- Improved command parser (#53)
+
**Bug fixes**
- Do not attempt to build wheels for uninstallable addons.
diff --git a/src/oca_github_bot/commands.py b/src/oca_gi... |
OCHA-DAP__hdx-python-country-61 | [
{
"changes": {
"added_entities": [
"src/hdx/location/country.py:Country.set_ocha_path"
],
"added_modules": null,
"edited_entities": [
"src/hdx/location/country.py:Country.countriesdata"
],
"edited_modules": [
"src/hdx/location/country.py:Country"
... | OCHA-DAP/hdx-python-country | 9c1759d23d952ff3e5755bc83ba052b1375ad809 | Uee local file for live data rather than url
As a follow on from https://github.com/OCHA-DAP/hdx-python-country/issues/57, we've been looking into implementing this but as it stands the live data feed can only use a url and not a local file. This works but is a bit awkward. Would you be open to extending this to be abl... | diff --git a/requirements.txt b/requirements.txt
index a5e5efb..a44eb5c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -18,7 +18,7 @@ charset-normalizer==3.4.0
# via requests
click==8.1.7
# via typer
-coverage==7.6.4
+coverage==7.6.5
# via pytest-cov
distlib==0.3.9
# via virtualenv
@@ -32... |
OCHA-DAP__hdx-python-country-63 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/hdx/location/country.py:Country.countriesdata",
"src/hdx/location/country.py:Country.get_country_info_from_iso3",
"src/hdx/location/country.py:Country.get_country_name_from_iso3",
... | OCHA-DAP/hdx-python-country | fa69943a6906c131d23bbb9926c8845e920b3106 | set_use_live_default not working as expected
I have called `Country.set_use_live_default(False)` but when calling any method to retrieve data, it's still using the live data. It seems to be setting `cls._use_live` correctly but the method param default is not picking this value up.
I will submit a PR for a fix. | diff --git a/src/hdx/location/country.py b/src/hdx/location/country.py
index dbdb239..b4e7500 100755
--- a/src/hdx/location/country.py
+++ b/src/hdx/location/country.py
@@ -212,7 +212,7 @@ class Country:
@classmethod
def countriesdata(
cls,
- use_live: bool = _use_live,
+ use_live: bool... |
OSOceanAcoustics__echopype-428 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"echopype/convert/api.py:_check_file"
],
"edited_modules": [
"echopype/convert/api.py:_check_file"
]
},
"file": "echopype/convert/api.py"
},
{
"changes": {
... | OSOceanAcoustics/echopype | dbf4eb1e7b1be92be979b0fbdf47d02831cfb2d8 | Using open_raw for AZFP data files with name other than .01A
We can convert AZFP data files using open_raw for the .01A file. However, not all AZFP data files are .01A files. There are 2 parts that the filename can change (the number and letter of the file)
1. The number:
When we collect data with multiple phases (... | diff --git a/echopype/convert/api.py b/echopype/convert/api.py
index 3799c938..1f96b3ad 100644
--- a/echopype/convert/api.py
+++ b/echopype/convert/api.py
@@ -308,12 +308,11 @@ def _check_file(
# TODO: https://github.com/OSOceanAcoustics/echopype/issues/229
# to add compatibility for pathlib.Path objects for... |
OSeMOSYS__otoole-110 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/otoole/cli.py:conversion_matrix",
"src/otoole/cli.py:get_parser",
"src/otoole/cli.py:main"
],
"edited_modules": [
"src/otoole/cli.py:conversion_matrix",
"... | OSeMOSYS/otoole | 266c1f3cf9db3f064547d5aa7013dde3f4792a07 | Converting OSeMBE datafile (.txt) to excel (.xlsx) using Otoole - Windows 10
Hi,
I am using the modified version of otoole adapted for OSeMBE. My otoole version is v0.10.1b3. When I try to convert the OSeMBE datafile (in .txt format) to excel (.xlsx), using the following input line, it gives an error.
```otoole c... | diff --git a/.gitignore b/.gitignore
index c42d6b2..5754bed 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,9 +13,22 @@ __pycache__/*
.*.swp
*/.ipynb_checkpoints/*
.DS_Store
-.vscode
+*.feather
+*.parquet
+*.kgrind
+*.sol
+*.lp
+*.txt
+*.csv
+datapackage.json
+*.ipynb
# Project files
+*.srctrlbm
+*.srctrldb
+*.sr... |
OSeMOSYS__otoole-120 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/otoole/cli.py:conversion_matrix",
"src/otoole/cli.py:get_parser"
],
"edited_modules": [
"src/otoole/cli.py:conversion_matrix",
"src/otoole/cli.py:get_parser"
... | OSeMOSYS/otoole | 77606e9966fc8bce0bd7471049d0051f3ca9aff3 | Use otoole with custom OSeMOSYS parameters
If you modify the name of a parameter or set, or add a new parameter or set in an OSeMOSYS model which you wish to use with otoole, there is currently no way for the user to edit the `config.yaml` file.
Suggest:
- [x] adding `--config` flag to the command line
- [x] `setup` ... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 007b09a..65bec4e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,12 +2,12 @@ exclude: '^docs/conf.py'
repos:
- repo: https://github.com/psf/black
- rev: 21.5b1
+ rev: 22.6.0
hooks:
- id: black
- language_ver... |
OSeMOSYS__otoole-172 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/otoole/write_strategies.py:WriteExcel._form_parameter"
],
"edited_modules": [
"src/otoole/write_strategies.py:WriteExcel"
]
},
"file": "src/otoole/write_strategies.... | OSeMOSYS/otoole | 99708f349fe4a9cb6cfe4804ba1c0ed62353762b | [Bug]: Data conversion to Excel
### The Issue
If I convert from CSV to excel, and a parameter is not indexed over years but the last column is MODE_OF_OPERATION, the mode gets pivoted on
For example, TechnologyToStorage is given as:
:
total_columns = len(names)
- if total_columns > 3:
+ if "YEAR... |
OSeMOSYS__otoole-213 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/otoole/results/result_package.py:ResultsPackage.capital_investment",
"src/otoole/results/result_package.py:capital_recovery_factor"
],
"edited_modules": [
"src/otoole/res... | OSeMOSYS/otoole | 48b05aa14e50d7443794fba77a31b6b1e924aabe | [Bug]: `CapitalInvestment` not being calculated
### The Issue
When converting a result solution file to a folder of CSVs, the variable `CapitalInvestment` is not written out
### Expected Behavior
I would expect the file `CapitalInvestment.csv` to be available in the folder of results
### Steps To Reproduce
1. c... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 4ebb5bb..bdc2c67 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -5,6 +5,7 @@ Changelog
(Development) Version 1.1.3
===========================
- Lock pandas to 2.1.4 or later
+- Capital Investment result calculation fixed
Version 1.1.2
=============
diff --git ... |
OSeMOSYS__otoole-234 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/otoole/results/result_package.py:capital_recovery_factor",
"src/otoole/results/result_package.py:pv_annuity",
"src/otoole/results/result_package.py:discount_factor",
"src/oto... | OSeMOSYS/otoole | 5fcd21e21907522e3097c479dec9ca307d368d6a | [Bug]: otoole.results calculation of CRF fails if no data in discount_rate parameter
### The Issue
Calculation of the capital recovery factor fails if no data is entered in the discount rate parameter file.
### Expected Behavior
The capital recovery factor should be calculated using the default value for the discoun... | diff --git a/src/otoole/results/result_package.py b/src/otoole/results/result_package.py
index a63de92..c961d5e 100644
--- a/src/otoole/results/result_package.py
+++ b/src/otoole/results/result_package.py
@@ -775,6 +775,9 @@ def capital_recovery_factor(
return numerator / denominator
+ if discount_rate_... |
OSeMOSYS__otoole-236 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/otoole/results/result_package.py:ResultsPackage.capital_investment"
],
"edited_modules": [
"src/otoole/results/result_package.py:ResultsPackage"
]
},
"file": "src/o... | OSeMOSYS/otoole | 7dce87ec86a18c73af64230efdd6cd6de4cbd1b1 | [Bug]: Calculation of `CapitalInvestment` fails if `DiscountRateIdv` not defined in configuration file
### The Issue
When running otoole to convert UTOPIA results calculated by CBC I get an error. When putting a print statement in `result_package.py` in line 315 for the `DiscountRate` the df seems to be empty.
### ... | diff --git a/src/otoole/results/result_package.py b/src/otoole/results/result_package.py
index c961d5e..8a70bdd 100644
--- a/src/otoole/results/result_package.py
+++ b/src/otoole/results/result_package.py
@@ -307,11 +307,14 @@ class ResultsPackage(Mapping):
capital_cost = self["CapitalCost"]
n... |
OSeMOSYS__otoole-243 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/otoole/results/result_package.py:discount_factor"
],
"edited_modules": [
"src/otoole/results/result_package.py:discount_factor"
]
},
"file": "src/otoole/results/res... | OSeMOSYS/otoole | 3e1f05d51ba16d3e3fd80dc73af3d931f92e45b7 | [Bug]: Discount Factor calculation fails if multiple regions are defined
### The Issue
If you run a multiple region model, the discount factor calculation fails
### Expected Behavior
_No response_
### Steps To Reproduce
run this test
```
def test_df_two_regions(self, region_multiple, year, discount_rate... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 75233c7..d057917 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,10 @@
Changelog
=========
+Version 1.1.5
+=============
+- Correct discount factor calculation for multiple regions
+
Version 1.1.4
=============
- Add result calculations for ``DiscountedC... |
OSeMOSYS__otoole-71 | [
{
"changes": {
"added_entities": [
"src/otoole/read_strategies.py:ReadDatafile.extract_set",
"src/otoole/read_strategies.py:ReadDatafile.extract_param"
],
"added_modules": null,
"edited_entities": [
"src/otoole/read_strategies.py:ReadDatafile._convert_amply_to_dat... | OSeMOSYS/otoole | 71cd6a12a00f122d0a265fa929459a864073415a | `otoole results cbc csv {} {} --input_datafile` fails if datafile contains ResultsPath (or other parameter)
```python
DEBUG:otoole.read_strategies:Extracting data for ResultsPath
Traceback (most recent call last):
File "/Users/wusher/miniconda3/envs/snakemake/bin/otoole", line 8, in <module>
sys.exit(main())
... | diff --git a/src/otoole/read_strategies.py b/src/otoole/read_strategies.py
index 8e2900c..36143f3 100644
--- a/src/otoole/read_strategies.py
+++ b/src/otoole/read_strategies.py
@@ -258,39 +258,56 @@ class ReadDatafile(ReadStrategy):
dict of pandas.DataFrame
"""
- dict_of_dataframes = {}
+ ... |
OddBloke__ubuntu-standalone-builder-33 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "generate_build_config.py"
}
] | OddBloke/ubuntu-standalone-builder | 4930aaa0713dd1ea1a7bb598ffcb75de30b2d381 | Set a serial in /etc/cloud/build.info in built images
This should make it clear that they are custom-built images. | diff --git a/generate_build_config.py b/generate_build_config.py
index 3fcfe42..09a71fe 100755
--- a/generate_build_config.py
+++ b/generate_build_config.py
@@ -30,7 +30,7 @@ runcmd:
- {homedir}/launchpad-buildd/mount-chroot $BUILD_ID
- {homedir}/launchpad-buildd/update-debian-chroot $BUILD_ID
{ppa_conf}
-- {homedir... |
OnroerendErfgoed__pyramid_urireferencer-11 | [
{
"changes": {
"added_entities": [
"pyramid_urireferencer/models.py:RegistryResponse.to_json",
"pyramid_urireferencer/models.py:ApplicationResponse.to_json",
"pyramid_urireferencer/models.py:Item.to_json"
],
"added_modules": null,
"edited_entities": [
"pyr... | OnroerendErfgoed/pyramid_urireferencer | b9c5617a6f21cc081232826cee80fa7b2bf050e2 | Error message when a resource can't be deleted.
Currently, when the protected resources decorator finds that a resource is still in use, it raise a 409 Conflict with a text string as body.
The current error message looks like:
*Urireferencer: The uri https://id.erfgoed.net/actoren/1 is still in use by other applica... | diff --git a/pyramid_urireferencer/models.py b/pyramid_urireferencer/models.py
index 8ef53f0..9bbd245 100644
--- a/pyramid_urireferencer/models.py
+++ b/pyramid_urireferencer/models.py
@@ -14,12 +14,13 @@ class RegistryResponse:
:param int count: How many references were found?
:param list applications: A lis... |
OnroerendErfgoed__pyramid_urireferencer-12 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyramid_urireferencer/models.py:ApplicationResponse.to_json"
],
"edited_modules": [
"pyramid_urireferencer/models.py:ApplicationResponse"
]
},
"file": "pyramid_urirefer... | OnroerendErfgoed/pyramid_urireferencer | 067293d191dc9dd4f7c2554f71bf0c730786a872 | Error message when a backend application can't be reached
When a service is not reachable for the uriregistry.
AS IS:
HTTPInternalServerError: Urireferencer: Something went wrong while retrieving references of the uri https://id.erfgoed.net/besluiten/1
TO BE:
HTTP 503 Service Unavailable: Urireferencer: Somethi... | diff --git a/CHANGES.rst b/CHANGES.rst
index 72b550b..195a2b5 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -5,6 +5,7 @@
- Some minor doc fixes
- Changed an edge case where `items` or `applications` response attributes could
be `None` so that they are now always empty lists. (#6)
+- Updated error message and added... |
OnroerendErfgoed__skosprovider_rdf-119 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "setup.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skosprovider_rdf/utils.py:_... | OnroerendErfgoed/skosprovider_rdf | 9a68fb35e971caac8d7df45e6371f3132a85e9f2 | Don't export local id as dcterms.identifier when it's the URI
When reading a SKOS file, we assign the URI to the id attribute because our skosprovider expects an internal identifier. But, when exporting the provider to SKOS again, we export this id to dcterms:identifier. This creates extra information in the SKOS file ... | diff --git a/HISTORY.rst b/HISTORY.rst
index b0e2a7b..3c5a727 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -1,3 +1,9 @@
+1.3.0 (??-12-2022)
+------------------
+
+- Don't export local id as dcterms.identifier when it's equal to the URI (#117)
+- Add support for Python 3.10 and Python 3.11 (#120)
+
1.2.0 (11-10-2022)... |
Open-EO__openeo-pg-parser-python-7 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/openeo_pg_parser_python/translate_process_graph.py:translate_graph"
],
"edited_modules": [
"src/openeo_pg_parser_python/translate_process_graph.py:translate_graph"
]
},... | Open-EO/openeo-pg-parser-python | fbc4daccbc518e19099a72b9891530c57de9fc17 | Unclear error when JSON file not found
Currently, when the input JSON file (or related python dict) is not found, the following error is returned:
`UnboundLocalError: local variable 'pg_dict' referenced before assignment`
This is not clear and very unfriendly to debug, add check if input file exists or if input dic... | diff --git a/src/openeo_pg_parser_python/translate_process_graph.py b/src/openeo_pg_parser_python/translate_process_graph.py
index bbbffde..3982dcd 100644
--- a/src/openeo_pg_parser_python/translate_process_graph.py
+++ b/src/openeo_pg_parser_python/translate_process_graph.py
@@ -216,10 +216,12 @@ def link_nodes(graph)... |
Open-EO__openeo-python-client-131 | [
{
"changes": {
"added_entities": [
"openeo/rest/connection.py:Connection._build_request_with_process_graph"
],
"added_modules": null,
"edited_entities": [
"openeo/rest/connection.py:Connection.create_service",
"openeo/rest/connection.py:Connection.job_results",
... | Open-EO/openeo-python-client | 822cf42030274d12f461ac9ef0d28129d804823e | Update process graph (POST) requests to 1.0 API
> For batch jobs (/jobs), services (/services) and sync. processing (/result) the property process_graph got replaced by process. It contains a process graph and optionally all process metadata. #260
also see Open-EO/openeo-api#260
methods and paths that have to be ... | diff --git a/openeo/rest/connection.py b/openeo/rest/connection.py
index a12eb44d..5b80394f 100644
--- a/openeo/rest/connection.py
+++ b/openeo/rest/connection.py
@@ -242,6 +242,7 @@ class Connection(RestApiConnection):
:return: jobs: Dict All jobs of the user
"""
+ # TODO duplication with `l... |
Open-EO__openeo-python-client-183 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "openeo/_version.py"
},
{
"changes": {
"added_entities": [
"openeo/internal/graph_building.py:PGNode.namespace"
],
"added_mod... | Open-EO/openeo-python-client | 05ab328ebb3fb59257525a5da17ec09ccfad4cc0 | Add namespace support
add namespace support in `Datacube.process` (and related) so that process graphs can be built using process from other namespaces than the default ("backend") | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8da75d3b..0a4fa8c0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added
+- Add namespace support to `DataCube.process`, `PGNode`, `ProcessGraphVisitor` (minor API breaki... |
Open-EO__openeo-python-client-230 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openeo/rest/datacube.py:DataCube.fit_curve",
"openeo/rest/datacube.py:DataCube.predict_curve"
],
"edited_modules": [
"openeo/rest/datacube.py:DataCube"
]
},
"fi... | Open-EO/openeo-python-client | 7f15d6ecb839cd2916fa5bae59953cd647d49337 | Proper callable support in fit_curve and related
from https://github.com/openEOPlatform/documentation/issues/10
```python
curve_fitting = l2a_bands.fit_curve(
parameters=[1,1,1], # Initial guess of the parameters
dimension="t", # Fit the function along the temporal dimension
function=l2a_bands._... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 53f9ab94..831591f1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
([#225](https://github.com/Open-EO/openeo-python-client/issues/225), [openeo-api#410](https://github.com/Op... |
Open-EO__openeo-python-client-231 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openeo/internal/processes/generator.py:generate_process_py"
],
"edited_modules": [
"openeo/internal/processes/generator.py:generate_process_py"
]
},
"file": "openeo/int... | Open-EO/openeo-python-client | e0a58e85978ed06cdc0647f68a98c35bcc92fdc9 | ProcessBuilder __getitem__ support
from https://github.com/openEOPlatform/documentation/issues/10
```python
def fit_function(x:ProcessBuilder, parameters):
pi = math.pi
a0 = array_element(parameters, 0)
a1 = array_element(parameters, 1)
a2 = array_element(parameters, 2)
return a0 + a1*cos(2... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 831591f1..d475e078 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Add `DataCube.dimension_labels()` (EP-4008)
- Add `Connection.load_result()` (EP-4008)
- Add proper suppo... |
Open-EO__openeo-python-client-643 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openeo/internal/warnings.py:legacy_alias"
],
"edited_modules": [
"openeo/internal/warnings.py:legacy_alias"
]
},
"file": "openeo/internal/warnings.py"
},
{
"cha... | Open-EO/openeo-python-client | f7f035f67d5afc57a4943a1f2389249e8cb0c250 | wrong deprecation warning on send_job
reported by @Katrijne-at-Vito
https://github.com/Open-EO/openeo-python-client/blob/f7f035f67d5afc57a4943a1f2389249e8cb0c250/tests/rest/datacube/test_datacube100.py#L3396-L3403
should say "Call to deprecated method send_job" | diff --git a/openeo/internal/warnings.py b/openeo/internal/warnings.py
index 2c5335bc..fe9d5489 100644
--- a/openeo/internal/warnings.py
+++ b/openeo/internal/warnings.py
@@ -35,12 +35,12 @@ def test_warnings(stacklevel=1):
)
-def legacy_alias(orig: Callable, name: str = "n/a", *, since: str, mode: str = "... |
Open-EO__openeo-python-client-669 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openeo/metadata.py:_StacMetadataParser.get_temporal_dimension"
],
"edited_modules": [
"openeo/metadata.py:_StacMetadataParser"
]
},
"file": "openeo/metadata.py"
},
... | Open-EO/openeo-python-client | 37ba26039a93e0849727dae1ee4980642eb49392 | load_stac metadata detection
reported by @JorisCod:
```python
cube = connection.load_stac(
"https://stac.terrascope.be/collections/sentinel-2-l2a",
spatial_extent={"west": 3, "south": 50, "east": 3.01, "north": 50.01},
temporal_extent=["2020-06-01", "2020-06-30"],
bands=["B02", "B04", "B08"],
)... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index aa030952..7b83adab 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed
+- `load_stac`: use fallback temporal dimension when no "cube:dimensions" in STAC Collection ([... |
OpenFreeEnergy__cinnabar-112 | [
{
"changes": {
"added_entities": [
"cinnabar/femap.py:FEMap.__iter__",
"cinnabar/femap.py:FEMap.__eq__",
"cinnabar/femap.py:FEMap.to_networkx",
"cinnabar/femap.py:FEMap.from_networkx"
],
"added_modules": null,
"edited_entities": [
"cinnabar/femap.p... | OpenFreeEnergy/cinnabar | 95cca4e64bb64df5e9fc4b83bc3c34cfaaf0a4a6 | FEMap add to/from networkx method
hide the networkx Graph internally and offer to/from methods
this can eventually be extended to other backends | diff --git a/cinnabar/femap.py b/cinnabar/femap.py
index a403a6f..2600925 100644
--- a/cinnabar/femap.py
+++ b/cinnabar/femap.py
@@ -1,6 +1,6 @@
import pathlib
from typing import Union
-
+import copy
import openff.units
import pandas as pd
from openff.units import unit
@@ -95,13 +95,64 @@ class FEMap:
>>> fe.... |
OpenFreeEnergy__openfe-241 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openfe/utils/visualization.py:_get_unique_bonds_and_atoms",
"openfe/utils/visualization.py:_draw_molecules",
"openfe/utils/visualization.py:draw_mapping",
"openfe/utils/visualiza... | OpenFreeEnergy/openfe | 82a6a6db4c22cc5b30ddf26253db10130a24662f | atom mapping bonds seem red too often
In the mapping visualisation below, 19:14 is in the mapping, which is marked blue as a transmutation. The bond is coloured red as not mapped, but arguably should be blue as something which is changing?
![index](https://user-images.githubusercontent.com/9249543/212974973-d134391... | diff --git a/openfe/utils/visualization.py b/openfe/utils/visualization.py
index f5b85c9f..ad3e6d6a 100644
--- a/openfe/utils/visualization.py
+++ b/openfe/utils/visualization.py
@@ -9,6 +9,12 @@ from rdkit.Chem import AllChem
from openfe.utils.custom_typing import RDKitMol
+# highlight core element changes differ... |
OpenFreeEnergy__openfe-26 | [
{
"changes": {
"added_entities": [
"openfe/setup/scorer.py:Scorer.score",
"openfe/setup/scorer.py:Scorer.annotation"
],
"added_modules": [
"openfe/setup/scorer.py:ScoreAnnotation"
],
"edited_entities": [
"openfe/setup/scorer.py:Scorer.__call__"
... | OpenFreeEnergy/openfe | 3ab18e7b98d09980b4c8c19320762bee9abcb244 | Implement Scorer Base Implementation
```python
s = Scorer(stuff)
m = Mapper.suggest_mapping(m1, m2)
f : float = s.score(m)
``` | diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index da0a3741..7faa724d 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -48,10 +48,10 @@ jobs:
- name: "Test imports"
run: |
# if we add more to this, consider changing to for + env vars
- p... |
OpenFreeEnergy__openfe-28 | [
{
"changes": {
"added_entities": [
"openfe/setup/atommapping.py:AtomMapping.__hash__"
],
"added_modules": null,
"edited_entities": [
"openfe/setup/atommapping.py:AtomMapping.from_perses",
"openfe/setup/atommapping.py:AtomMapping.__getitem__"
],
"edited... | OpenFreeEnergy/openfe | a55a592571a660593b1b98138e9a2a91275e4581 | Implement AtomMapping container
Should be a read only simple data class holding enough information for mapping two sets of ints (atom indices) to each other...
```python
class AtomMapping:
AtoB : dict[int, int]
BtoA : dict[int, int]
``` | diff --git a/openfe/setup/atommapping.py b/openfe/setup/atommapping.py
index c398611d..8f7ac9fe 100644
--- a/openfe/setup/atommapping.py
+++ b/openfe/setup/atommapping.py
@@ -1,8 +1,34 @@
+# This code is part of OpenFE and is licensed under the MIT license.
+# For details, see https://github.com/OpenFreeEnergy/openfe
+... |
OpenKMIP__PyKMIP-194 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"kmip/services/server/engine.py:KmipEngine.process_request"
],
"edited_modules": [
"kmip/services/server/engine.py:KmipEngine"
]
},
"file": "kmip/services/server/engine.... | OpenKMIP/PyKMIP | 40919468a64046349191c946991e0415fe768a0b | Install/Run Instructions and SQLAlchemy Issue
I have installed the latest version of pykmip-server (0.5.0) but have some questions.
I noticed that the instructions on the Wiki mention to run the "run_server.py" script but it appears as though the newer versions of pykmip support installation of Pykmip-server using t... | diff --git a/kmip/services/server/engine.py b/kmip/services/server/engine.py
index c90d355..5787b30 100644
--- a/kmip/services/server/engine.py
+++ b/kmip/services/server/engine.py
@@ -249,7 +249,10 @@ class KmipEngine(object):
)
# Process the authentication credentials
- auth_credentials... |
OpenKMIP__PyKMIP-215 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"kmip/services/server/config.py:KmipServerConfig.__init__",
"kmip/services/server/config.py:KmipServerConfig.set_setting",
"kmip/services/server/config.py:KmipServerConfig._parse_settings... | OpenKMIP/PyKMIP | 023bb8fd04b1e61b127313f4a9a6313af07fb14a | policy_path error when running server
I'm receiving the following error when attempting to run the PyKMIP server 0.5.0:
"kmip.core.exceptions.ConfigurationError: Setting 'policy_path' is missing from the configuration file."
I cannot find policy_path documented anywhere and have not found any guidance online. I ha... | diff --git a/kmip/services/server/config.py b/kmip/services/server/config.py
index 4687999..25bab5e 100644
--- a/kmip/services/server/config.py
+++ b/kmip/services/server/config.py
@@ -41,7 +41,9 @@ class KmipServerConfig(object):
'certificate_path',
'key_path',
'ca_path',
- ... |
OpenMDAO__dymos-1018 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dymos/utils/introspection.py:_configure_constraint_introspection"
],
"edited_modules": [
"dymos/utils/introspection.py:_configure_constraint_introspection"
]
},
"file":... | OpenMDAO/dymos | 37bb5dd5e11467af36d0364d771ed7be4dbc18cc | Overlapping constraints in Birkhoff transcription
### Description
Adding a boundary constraint and a path constraint for variables of any type other than state causes the error.
The lines of code when added to the brachistochrone problem throw the error
`RuntimeError: <model> <class Group>: Indices for aliases [... | diff --git a/dymos/utils/introspection.py b/dymos/utils/introspection.py
index 73497d24..775fa29b 100644
--- a/dymos/utils/introspection.py
+++ b/dymos/utils/introspection.py
@@ -227,7 +227,10 @@ def _configure_constraint_introspection(phase):
con['shape'] = control_shape
con['units'... |
OpenMDAO__dymos-1020 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dymos/examples/finite_burn_orbit_raise/finite_burn_orbit_raise_problem.py:make_traj"
],
"edited_modules": [
"dymos/examples/finite_burn_orbit_raise/finite_burn_orbit_raise_problem.py... | OpenMDAO/dymos | 10c2df0ba7e498d155890814f82ddee70c7bec66 | Solver-based shooting with a Krylov solver fails due to the DirectSolver attached to `indep_states`
### Description
When using Newton solver-based shooting with a Krylov linear solver, the `LinearRunOnce` preconditioner fails with the following error.
It seems the error comes from the `DirectSolver` attached to `inde... | diff --git a/docs/dymos_book/examples/cannonball_implicit_duration/cannonball_implicit_duration.ipynb b/docs/dymos_book/examples/cannonball_implicit_duration/cannonball_implicit_duration.ipynb
index 98da7d17..22d3b3bd 100644
--- a/docs/dymos_book/examples/cannonball_implicit_duration/cannonball_implicit_duration.ipynb
... |
OpenMDAO__dymos-1021 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dymos/transcriptions/pseudospectral/birkhoff.py:Birkhoff.configure_polynomial_controls"
],
"edited_modules": [
"dymos/transcriptions/pseudospectral/birkhoff.py:Birkhoff"
]
... | OpenMDAO/dymos | bc67ea54d56a77a9ba0259ed85aa7f4c14d5c320 | Polynomial controls don't work with Birkhoff transcription
### Description
Attempting to use a polynomial control causes an error during configure. This occurs only in the Birkhoff transcription and only with polynomial controls
`AttributeError: 'Phase' object has no attribute 'ode_all'`
### Example
https://github.... | diff --git a/dymos/transcriptions/pseudospectral/birkhoff.py b/dymos/transcriptions/pseudospectral/birkhoff.py
index 08d3aabb..df914ead 100644
--- a/dymos/transcriptions/pseudospectral/birkhoff.py
+++ b/dymos/transcriptions/pseudospectral/birkhoff.py
@@ -211,34 +211,24 @@ class Birkhoff(TranscriptionBase):
"""... |
OpenMDAO__dymos-1087 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dymos/phase/phase.py:Phase.__init__",
"dymos/phase/phase.py:Phase.simulate",
"dymos/phase/phase.py:Phase.load_case"
],
"edited_modules": [
"dymos/phase/phase.py:Phase... | OpenMDAO/dymos | d61cd9792489e4cbd428d9f5b9fbe4799a75797f | `phase.load_case` should use the new `phase.set_xxx_vals` API
### Description
`phase.load_case` was not using the set_xxx_vals API.
As a result, under the Birkhoff transcription, the initial and final state values were not being properly set.
### Example
N/A
### Dymos Version
1.10.1-dev
### Relevant environment ... | diff --git a/dymos/phase/phase.py b/dymos/phase/phase.py
index 58047247..26088aaf 100644
--- a/dymos/phase/phase.py
+++ b/dymos/phase/phase.py
@@ -1,7 +1,6 @@
-from collections.abc import Iterable, Callable, Sequence
+from collections.abc import Iterable, Callable
from copy import deepcopy
import inspect
-from os imp... |
OpenMDAO__dymos-1121 | [
{
"changes": {
"added_entities": [
"dymos/examples/oscillator/oscillator_ode.py:OscillatorVectorODE.initialize",
"dymos/examples/oscillator/oscillator_ode.py:OscillatorVectorODE.setup",
"dymos/examples/oscillator/oscillator_ode.py:OscillatorVectorODE.compute"
],
"added_... | OpenMDAO/dymos | 8338af108c3876c9d7adaa10dc41798bf6676a0d | Two phases can only be linked to each other once
### Description
Hi everyone,
Lateley I have been experimenting with multi phase trajectories. I am modelling a racing car that drives a lap around a circuit, similar to the racing car example in the docs. I am splitting the lap up into two parts to be able to force ... | diff --git a/dymos/examples/oscillator/oscillator_ode.py b/dymos/examples/oscillator/oscillator_ode.py
index dac0fcd7..a46aac64 100644
--- a/dymos/examples/oscillator/oscillator_ode.py
+++ b/dymos/examples/oscillator/oscillator_ode.py
@@ -36,3 +36,37 @@ class OscillatorODE(om.ExplicitComponent):
f_damper = -c ... |
OpenMDAO__dymos-1127 | [
{
"changes": {
"added_entities": [
"dymos/examples/oscillator/oscillator_ode.py:OscillatorVectorODE.initialize",
"dymos/examples/oscillator/oscillator_ode.py:OscillatorVectorODE.setup",
"dymos/examples/oscillator/oscillator_ode.py:OscillatorVectorODE.compute"
],
"added_... | OpenMDAO/dymos | 8338af108c3876c9d7adaa10dc41798bf6676a0d | Simulation step fails with shape error when parameter is an N-dimensional array
### Description
Sometimes a parameter input to a Dymos ODE needs to be something other than a scalar or 1-D array. One such situation might be when the ODE describes 6 degree of freedom motion, where the Moment of Inertia matrix of the ... | diff --git a/dymos/examples/oscillator/oscillator_ode.py b/dymos/examples/oscillator/oscillator_ode.py
index dac0fcd7..a46aac64 100644
--- a/dymos/examples/oscillator/oscillator_ode.py
+++ b/dymos/examples/oscillator/oscillator_ode.py
@@ -36,3 +36,37 @@ class OscillatorODE(om.ExplicitComponent):
f_damper = -c ... |
OpenMDAO__dymos-1133 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dymos/transcriptions/explicit_shooting/explicit_shooting.py:ExplicitShooting.setup_controls"
],
"edited_modules": [
"dymos/transcriptions/explicit_shooting/explicit_shooting.py:Expli... | OpenMDAO/dymos | 42fea76c302d94fd31c58f67799a95b6a5debf35 | Polynomial control rates are not correctly evaluated in explicit shooting.
### Description
When a polynomial control has `rate_targets` in the ODE, the resulting simulation obtains an incorrect value for that rate because it relies on the ration of phase duration to phase "tau" space. (`0.5 * t_duration`).
`t_durat... | diff --git a/dymos/transcriptions/explicit_shooting/explicit_shooting.py b/dymos/transcriptions/explicit_shooting/explicit_shooting.py
index a194f9e5..d60f2912 100644
--- a/dymos/transcriptions/explicit_shooting/explicit_shooting.py
+++ b/dymos/transcriptions/explicit_shooting/explicit_shooting.py
@@ -355,7 +355,8 @@ c... |
OpenMDAO__dymos-1135 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dymos/run_problem.py:run_problem"
],
"edited_modules": [
"dymos/run_problem.py:run_problem"
]
},
"file": "dymos/run_problem.py"
},
{
"changes": {
"added_e... | OpenMDAO/dymos | d324563198e0c455ee2d38b69a282a16d3cacbe7 | Timeseries report should display each element of vectorized states/controls/parameters separately.
### Description
When a state is a vector/matrix/tensor quantity at each given point in time the resulting timeseries plot is nonsensical.
Dymos should extract each element from the state (or control/parameter/etc) in th... | diff --git a/dymos/run_problem.py b/dymos/run_problem.py
index 8a3fbfd2..63af00db 100755
--- a/dymos/run_problem.py
+++ b/dymos/run_problem.py
@@ -122,7 +122,6 @@ def run_problem(problem, refine_method='hp', refine_iteration_limit=0, run_drive
sims[subsys.pathname] = sim_prob
if make_plots:
-
... |
OpenMDAO__dymos-858 | [
{
"changes": {
"added_entities": [
"dymos/phase/phase.py:Phase.is_control_rate_fixed",
"dymos/phase/phase.py:Phase.is_polynomial_control_rate_fixed"
],
"added_modules": null,
"edited_entities": [
"dymos/phase/phase.py:Phase.is_control_fixed"
],
"edited... | OpenMDAO/dymos | 523217e13bb294694b4bd27a7960ad41cc70b1c4 | Trajectory `link_phases` method should support arguments of `add_linkage_constraint`.
### Proposed feature.
The `link_phases` method is a simpler wrapper for the more complex but more capable `add_linkage_constraint` method.
In order to allow the user to control things like the scaling factors for the imposed const... | diff --git a/dymos/phase/phase.py b/dymos/phase/phase.py
index 023549b3..69dac6ce 100644
--- a/dymos/phase/phase.py
+++ b/dymos/phase/phase.py
@@ -2316,15 +2316,39 @@ class Phase(om.Group):
bool
True if the state of the given name is guaranteed to be fixed at the given location.
"""
- ... |
OpenMDAO__dymos-964 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dymos/grid_refinement/grid_refinement_ode_system.py:GridRefinementODESystem.configure"
],
"edited_modules": [
"dymos/grid_refinement/grid_refinement_ode_system.py:GridRefinementODESy... | OpenMDAO/dymos | 1aca42a4fedcca6e493c5516fadc2d78e4709797 | Parameter issues.
### Description
1. Parameters should allow for a mixture of static and dynamic targets.
2. Trajectory parameters do not currently get sufficient introspected data from phases when under MPI.
### Example
```python
import unittest
import numpy as np
import openmdao.api as om
import dymos as dm
... | diff --git a/dymos/grid_refinement/grid_refinement_ode_system.py b/dymos/grid_refinement/grid_refinement_ode_system.py
index 3fb76b90..fd86ec72 100644
--- a/dymos/grid_refinement/grid_refinement_ode_system.py
+++ b/dymos/grid_refinement/grid_refinement_ode_system.py
@@ -3,7 +3,7 @@ import openmdao.api as om
from ..p... |
OpenMined__PySyft-122 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.shape",
"syft/tensor.py:TensorBase.sum"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"syft/tensor.py:TensorBase"
]
},
"file": "syft/tensor.py"
}
] | OpenMined/PySyft | 16dae46b154dd755c18e941409b4ec771f5e2ca5 | Implement Default sum Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, I want to leverage a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, sum() should return a new tensor. For a reference on the operation thi... | diff --git a/syft/tensor.py b/syft/tensor.py
index 6d1ce8dc30..7d549da9bb 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -8,7 +8,7 @@ def _ensure_ndarray(arr):
class TensorBase(object):
"""
- A base tensor class that perform basic element-wise operation such as
+ A base tensor class that perform bas... |
OpenMined__PySyft-188 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.log",
"syft/tensor.py:TensorBase.log_",
"syft/tensor.py:TensorBase.log1p",
"syft/tensor.py:TensorBase.log1p_",
"syft/tensor.py:TensorBase.log_normal_"
],
"added_modules": null,
"edited_e... | OpenMined/PySyft | a81fde47c4593a787f9bb61dd655af58497bef4a | Implement Default log Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, we want to implement a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, log(), log1p(), and log_normal() should return a new tensor and log_... | diff --git a/syft/tensor.py b/syft/tensor.py
index f9eff20a64..ee9cf8715d 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -518,3 +518,41 @@ class TensorBase(object):
if self.encrypted:
return NotImplemented
self.data = 1 / np.array(self.data)
+
+ def log(self):
+ """performs... |
OpenMined__PySyft-216 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.cumprod",
"syft/tensor.py:TensorBase.cumprod_"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"syft/tensor.py:TensorBase"
]
},
"file": "syft/tensor.py"
}
] | OpenMined/PySyft | 02ba82e94de28b2dca463f06c22c7f4df4f78dd3 | Implement Default cumprod Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, we want to implement a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, cumprod() should return a new tensor. For a reference on the ope... | diff --git a/syft/tensor.py b/syft/tensor.py
index c1aa0e310e..859dd0ff4f 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -858,6 +858,19 @@ class TensorBase(object):
else:
return self.data.size
+ def cumprod(self, dim=0):
+ """Returns the cumulative product of elements in the dimen... |
OpenMined__PySyft-232 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.scatter_"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"syft/tensor.py:TensorBase"
]
},
"file": "syft/tensor.py"
}
] | OpenMined/PySyft | 6c049ac8c4c2e9598bbd495d9a5fd716d3e46126 | Implement Default scatter Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, I want to leverage a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, scatter_() should operate inline. For a reference on the operation... | diff --git a/syft/tensor.py b/syft/tensor.py
index 0aed1c3ef8..7d31e2e430 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -1034,6 +1034,67 @@ class TensorBase(object):
hist, edges = np.histogram(np.array(self.data), bins=bins, range=(min, max))
return TensorBase(hist)
+ def scatter_(self, dim... |
OpenMined__PySyft-233 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.gather"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"syft/tensor.py:TensorBase"
]
},
"file": "syft/tensor.py"
}
] | OpenMined/PySyft | 57cb74b0ec8a69c285a002e0a190d4c6603a06bc | Implement Default gather Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, we want to implement a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, gather() should return a new tensor. For a reference on the opera... | diff --git a/syft/tensor.py b/syft/tensor.py
index 765d418508..a016eb8cfa 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -1051,9 +1051,8 @@ class TensorBase(object):
def scatter_(self, dim, index, src):
"""
- Writes all values from the Tensor src into self at the indices specified in the ind... |
OpenMined__PySyft-237 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.index_select"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"syft/tensor.py:TensorBase"
]
},
"file": "syft/tensor.py"
}
] | OpenMined/PySyft | 1df96853cc9f1e97f7b106eae3de5a6f62284809 | Implement Default select Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, I want to leverage a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, select() should return a new tensor. For a reference on the operati... | diff --git a/syft/tensor.py b/syft/tensor.py
index 8ed5efad8d..6cf00090e3 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -1160,6 +1160,22 @@ class TensorBase(object):
def deserialize(b):
return pickle.loads(b)
+ def index_select(self, dim, index):
+ """
+ Returns a new Tensor which... |
OpenMined__PySyft-240 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.remainder",
"syft/tensor.py:TensorBase.remainder_"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"syft/tensor.py:TensorBase"
]
},
"file": "syft/tensor.py"
... | OpenMined/PySyft | 50c50da091ae6734237302efa5324d7dbed59164 | Implement Default remainder Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, I want to leverage a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, remainder() should return a new tensor, but remainder_() should ... | diff --git a/syft/tensor.py b/syft/tensor.py
index 553420c417..8c97892ea3 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -1160,6 +1160,37 @@ class TensorBase(object):
def deserialize(b):
return pickle.loads(b)
+ def remainder(self, divisor):
+ """
+ Computes the element-wise remain... |
OpenMined__PySyft-250 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.eq",
"syft/tensor.py:TensorBase.eq_"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"syft/tensor.py:TensorBase"
]
},
"file": "syft/tensor.py"
}
] | OpenMined/PySyft | 6d94259b46fb6516ab20773cbbb9bb6ddac3d3cd | Implement Default eq Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, we want to implement a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, eq() should return a new tensor and eq_() should perform the operatio... | diff --git a/syft/tensor.py b/syft/tensor.py
index 02a63a36d7..553420c417 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -1200,6 +1200,21 @@ class TensorBase(object):
out_flat = [s if m == 0 else source_iter.__next__().item() for m, s in mask_self_iter]
self.data = np.reshape(out_flat, self.data.... |
OpenMined__PySyft-254 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.lt",
"syft/tensor.py:TensorBase.lt_",
"syft/tensor.py:TensorBase.ge",
"syft/tensor.py:TensorBase.ge_",
"syft/tensor.py:TensorBase.le",
"syft/tensor.py:TensorBase.le_"
],
"added_modules... | OpenMined/PySyft | 6c84afb0d4d541039bdcad4357cc7b62a3d24084 | Implement Default ge Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, we want to implement a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, ge() should return a new tensor and ge_() should perform the operatio... | diff --git a/syft/tensor.py b/syft/tensor.py
index 2bb335111e..a5f21740c9 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -725,19 +725,72 @@ class TensorBase(object):
else:
return [TensorBase(x) for x in np.array_split(self.data, n, dim)]
- def gt(self, t):
+ def gt(self, other):
... |
OpenMined__PySyft-2549 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "syft/frameworks/torch/hook/hook_args.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | OpenMined/PySyft | 7e14632b65f9bb95b73ef62b0678858704fc6b4c | URGENT: bug in encrypted autograd
**Describe the bug**
For some reason, calling loss.backward() on a pointer using normal autograd then breaks our ability to call loss.backward() on an encrypted loss variable even on two totally separate examples.
**To Reproduce**
```
import torch
import torch as th
import torc... | diff --git a/syft/frameworks/torch/hook/hook_args.py b/syft/frameworks/torch/hook/hook_args.py
index e078984ea8..49a4627dcd 100644
--- a/syft/frameworks/torch/hook/hook_args.py
+++ b/syft/frameworks/torch/hook/hook_args.py
@@ -55,6 +55,7 @@ ambiguous_functions = {
"chunk",
"torch.functional.split",
"spli... |
OpenMined__PySyft-2560 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "syft/messaging/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"syft/serd... | OpenMined/PySyft | e6a107c14eec6dde40bc3c73c4e2b54dae3996df | relu and relu_deriv require serializable workers
**This is a blocker for having [EMLaaS implemented](https://github.com/OpenMined/Grid/issues/203)**.
Relu and relu_derive require serializable workers. Apparently these operations require serializable workers in order to execute `.share` with pointer tensors. GridWork... | diff --git a/syft/frameworks/torch/crypto/securenn.py b/syft/frameworks/torch/crypto/securenn.py
index 5c0ba54ae5..8487f6c7bd 100644
--- a/syft/frameworks/torch/crypto/securenn.py
+++ b/syft/frameworks/torch/crypto/securenn.py
@@ -438,7 +438,7 @@ def relu(a_sh):
# 2**62 would almost always lead to overflow).
def divi... |
OpenMined__PySyft-257 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "syft/__init__.py"
},
{
"changes": {
"added_entities": [
"syft/math.py:mm"
],
"added_modules": [
"syft/math.py:mm"
... | OpenMined/PySyft | b0d646922b7529f5198dcc21fc856c7e9e598976 | Implement Default mm Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, we want to implement a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, mm() should return a new tensor. For a reference on the operation thi... | diff --git a/syft/__init__.py b/syft/__init__.py
index a172d04425..39d8074ab4 100644
--- a/syft/__init__.py
+++ b/syft/__init__.py
@@ -6,7 +6,7 @@ from syft import test
from syft.tensor import equal, TensorBase
from syft.math import cumprod, cumsum, ceil, dot, matmul, addmm, addcmul
from syft.math import addcdiv, ad... |
OpenMined__PySyft-2612 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"syft/frameworks/torch/tensors/interpreters/large_precision.py:LargePrecisionTensor._create_internal_representation"
],
"edited_modules": [
"syft/frameworks/torch/tensors/interpreters... | OpenMined/PySyft | 6feeb9357b83615f5acc9cde6d05ff4a61263eaa | Fix precision with large storage fails
**Describe the bug**
The following operation fails
`lpt = torch.Tensor([-2., 4]).fix_prec(storage="large")`
**To Reproduce**
Steps to reproduce the behavior:
Use the above expression in a test and see the result:
`TypeError`
**Expected behavior**
The expression should ... | diff --git a/syft/frameworks/torch/tensors/interpreters/large_precision.py b/syft/frameworks/torch/tensors/interpreters/large_precision.py
index f836022c4e..bbc46e6b7f 100644
--- a/syft/frameworks/torch/tensors/interpreters/large_precision.py
+++ b/syft/frameworks/torch/tensors/interpreters/large_precision.py
@@ -74,7 ... |
OpenMined__PySyft-285 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.geometric_"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"syft/tensor.py:TensorBase"
]
},
"file": "syft/tensor.py"
}
] | OpenMined/PySyft | 28ee3b4ade61bbbf0cce1c745a0b9fac310841e9 | Implement Default geometric Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, we want to implement a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, geometric_() should perform the operation inline. For a refere... | diff --git a/syft/tensor.py b/syft/tensor.py
index b2142167d4..6d040cf1ed 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -862,6 +862,25 @@ class TensorBase(object):
out = np.random.uniform(low=low, high=high, size=self.shape())
return TensorBase(out)
+ def geometric_(self, p):
+ """Fi... |
OpenMined__PySyft-286 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.new"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"syft/tensor.py:TensorBase"
]
},
"file": "syft/tensor.py"
}
] | OpenMined/PySyft | 40261aab99e6857e0ed2e34c26a315f16d9500f7 | Implement Default new Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, I want to leverage a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, new() should return a new tensor. For a reference on the operation thi... | diff --git a/syft/tensor.py b/syft/tensor.py
index 9dc2bab3ba..c01a50dd83 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -109,6 +109,30 @@ class TensorBase(object):
self.data = _ensure_ndarray(arr_like)
self.encrypted = encrypted
+ def new(self, *args, **kwargs):
+ """Constructs a new... |
OpenMined__PySyft-296 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.index",
"syft/tensor.py:TensorBase.index_add_",
"syft/tensor.py:TensorBase.index_copy_",
"syft/tensor.py:TensorBase.index_fill_"
],
"added_modules": null,
"edited_entities": null,
"edited_... | OpenMined/PySyft | 65b9352e9e349c7f932f52904d6f913a09f9a025 | Implement Default index Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, we want to implement a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, index() and index_select() should return a new tensor and index_ad... | diff --git a/syft/tensor.py b/syft/tensor.py
index f5313aa491..719ae2d409 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -2848,6 +2848,97 @@ class TensorBase(object):
self.data = np.remainder(self.data, divisor)
return self
+ def index(self, m):
+ """
+ Returns a new Tensor wit... |
OpenMined__PySyft-314 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"syft/tensor.py:TensorBase.__getitem__"
],
"edited_modules": [
"syft/tensor.py:TensorBase"
]
},
"file": "syft/tensor.py"
}
] | OpenMined/PySyft | 543a66153c17d6e2885d6b7d571749fe02629ba5 | 1dim TensorBase slice returns ndarray instead of TensorBase
Currently a slice of TensorBase returns an ndarray if `dim() == 1`. This is not the behavior expected in PyTorch
Example pytorch session:
```python
t1 = Tensor([1,2,3,4])
t1[1:]
2
3
4
[torch.FloatTensor of size 3]
```
Same with TensorBase
```... | diff --git a/syft/tensor.py b/syft/tensor.py
index 081679d946..d374bb5ae0 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -449,7 +449,7 @@ class TensorBase(object):
return NotImplemented
else:
out = self.data[position]
- if (len(self.shape()) == 1):
+ if (len... |
OpenMined__PySyft-391 | [
{
"changes": {
"added_entities": [
"syft/math.py:split"
],
"added_modules": [
"syft/math.py:split"
],
"edited_entities": null,
"edited_modules": null
},
"file": "syft/math.py"
},
{
"changes": {
"added_entities": null,
"added_modules... | OpenMined/PySyft | f1f230c45e29abce37f83a2ed4606c8a6512d3fa | Implement Default split Functionality for Base Tensor Type.
<!-- Please make sure that you review this: https://github.com/OpenMined/Docs/blob/master/contributing/guidelines.md -->
<!-- If you are looking to file a bug make sure to look at the .github/BUG_ISSUE_TEMPLATE.md -->
#### User story:
As a Data Scient... | diff --git a/syft/math.py b/syft/math.py
index e880c85ed9..4d395a6a0d 100644
--- a/syft/math.py
+++ b/syft/math.py
@@ -968,3 +968,43 @@ def zeros(dim):
Output Tensor
"""
return TensorBase(np.zeros(dim))
+
+
+def split(tensor, split_size, axis=0):
+ """
+ Splits the tensor into multiple equally ... |
OpenMined__PySyft-392 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "syft/__init__.py"
},
{
"changes": {
"added_entities": [
"syft/math.py:cross"
],
"added_modules": [
"syft/math.py:cro... | OpenMined/PySyft | 34af4f778c2b2f1a16a5a8aa505c37b7d9b18009 | Implement Default cross Functionality for Base Tensor Type.
<!-- Please make sure that you review this: https://github.com/OpenMined/Docs/blob/master/contributing/guidelines.md -->
<!-- If you are looking to file a bug make sure to look at the .github/BUG_ISSUE_TEMPLATE.md -->
#### User story:
As a Data Scient... | diff --git a/syft/__init__.py b/syft/__init__.py
index 43b3fa7b10..cada8b5181 100644
--- a/syft/__init__.py
+++ b/syft/__init__.py
@@ -7,7 +7,8 @@ from syft import nonlin
from syft.tensor import equal, TensorBase
from syft.math import cumprod, cumsum, ceil, dot, matmul, addmm, addcmul
from syft.math import addcdiv, ... |
OpenMined__PySyft-396 | [
{
"changes": {
"added_entities": [
"syft/tensor.py:TensorBase.storage_offset",
"syft/tensor.py:TensorBase.set_"
],
"added_modules": null,
"edited_entities": [
"syft/tensor.py:TensorBase.stride"
],
"edited_modules": [
"syft/tensor.py:TensorBase"... | OpenMined/PySyft | 7222ce4e3f5ce54ab79f3039be6723a312600a32 | Implement Default set Functionality for Base Tensor Type
**User Story A:** As a Data Scientist using Syft's Base Tensor type, I want to leverage a default method for computing operations on a Tensor of arbitrary type. For this ticket to be complete, set_() should operate inline. For a reference on the operation this pe... | diff --git a/syft/tensor.py b/syft/tensor.py
index 3bbdaffd6f..e54015a827 100644
--- a/syft/tensor.py
+++ b/syft/tensor.py
@@ -3095,7 +3095,7 @@ class TensorBase(object):
return NotImplemented
out = self.data.strides
- output = tuple(map(lambda x: x / 8, out))
+ output = tuple(map(... |
OpenNMT__OpenNMT-py-1841 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"onmt/inputters/image_dataset.py:ImageDataReader.read"
],
"edited_modules": [
"onmt/inputters/image_dataset.py:ImageDataReader"
]
},
"file": "onmt/inputters/image_datase... | OpenNMT/OpenNMT-py | 60125c807d1cb18099a69dbfba699bcdf30560b1 | Alpha channel and grayscale in image-to-text with -image_channel_size=3
For training image to text, the argument `-image_channel_size=3` imply that the images already have the good number of channel. However, some of my images are black and white and saved with only one channel or saved in RGB but with the alpha channe... | diff --git a/onmt/inputters/image_dataset.py b/onmt/inputters/image_dataset.py
index 13fc806a..1a21ae64 100644
--- a/onmt/inputters/image_dataset.py
+++ b/onmt/inputters/image_dataset.py
@@ -75,7 +75,8 @@ class ImageDataReader(DataReaderBase):
img = transforms.ToTensor()(
Image.fro... |
OpenNMT__OpenNMT-tf-563 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"opennmt/decoders/self_attention_decoder.py:SelfAttentionDecoder.__init__"
],
"edited_modules": [
"opennmt/decoders/self_attention_decoder.py:SelfAttentionDecoder"
]
},
... | OpenNMT/OpenNMT-tf | cb7519335266139feaf6f189c0f5c12cb0337f2d | Relative Positional Encoding
Hi,
Instead of Sinusoidal Positional Encoding, Relative Positional Encoding is becoming dominant in Transformer models. I would like to ask for adding this feature to the project.
| diff --git a/opennmt/decoders/self_attention_decoder.py b/opennmt/decoders/self_attention_decoder.py
index 1fa052ee..897ca2ff 100644
--- a/opennmt/decoders/self_attention_decoder.py
+++ b/opennmt/decoders/self_attention_decoder.py
@@ -23,6 +23,7 @@ class SelfAttentionDecoder(decoder.Decoder):
ffn_activa... |
OpenNMT__OpenNMT-tf-62 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"opennmt/decoders/self_attention_decoder.py:SelfAttentionDecoder.__init__"
],
"edited_modules": [
"opennmt/decoders/self_attention_decoder.py:SelfAttentionDecoder"
]
},
... | OpenNMT/OpenNMT-tf | c46f9b0ce71e23faa0202832ac0cad179bb3bb42 | Positional encoding with sinusoids
Implement a new `opennmt.layers.PositionEncoder` with sinusoids as described in "Attention Is All You Need" (https://arxiv.org/abs/1706.03762). | diff --git a/opennmt/decoders/self_attention_decoder.py b/opennmt/decoders/self_attention_decoder.py
index fe1b3a6e..1e40d5d6 100644
--- a/opennmt/decoders/self_attention_decoder.py
+++ b/opennmt/decoders/self_attention_decoder.py
@@ -4,7 +4,7 @@ import tensorflow as tf
import opennmt.layers.transformer as transformer... |
OpenSourceEconomics__estimagic-212 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "estimagic/optimization/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
... | OpenSourceEconomics/estimagic | e512c444bb5498a356cadbbcf7ff64c5efee2856 | Add selected nlopt optimizers
### Current situation
Nlopt is not supported
### Desired Situation
Add local derivative free and derivative based optimizers from nlopt.
| diff --git a/estimagic/optimization/__init__.py b/estimagic/optimization/__init__.py
index 543eb5a..71541b2 100644
--- a/estimagic/optimization/__init__.py
+++ b/estimagic/optimization/__init__.py
@@ -44,3 +44,5 @@ if IS_DFOLS_INSTALLED:
if IS_CYIPOPT_INSTALLED:
AVAILABLE_ALGORITHMS["ipopt"] = cyipopt_optimizer... |
OpenSourceEconomics__estimagic-222 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"estimagic/visualization/estimation_table.py:_process_model",
"estimagic/visualization/estimation_table.py:_convert_model_to_series",
"estimagic/visualization/estimation_table.py:_extract... | OpenSourceEconomics/estimagic | a281eda1feb12be23e0a4ab7e985a67591c67a4e | Unify usage of `p_value` / `pvalue`
### Bug description
`p_value` and `pvalue` are used as column names in different places; may lead to errors.
### To Reproduce
`estimagic.inference.likelihood_inference.do_likelihood_inference` returns table with column `p_value`
`estimagic.visualization.estimation_table` ex... | diff --git a/estimagic/visualization/estimation_table.py b/estimagic/visualization/estimation_table.py
index b74ffd2..530cd5e 100644
--- a/estimagic/visualization/estimation_table.py
+++ b/estimagic/visualization/estimation_table.py
@@ -331,28 +331,30 @@ def tabular_html(
def _process_model(model):
"""Check mod... |
OpenSourceEconomics__estimagic-333 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/estimagic/benchmarking/get_benchmark_problems.py:_create_problem_inputs",
"src/estimagic/benchmarking/get_benchmark_problems.py:_create_problem_solution",
"src/estimagic/benchmarking... | OpenSourceEconomics/estimagic | b97c488b1444c8784a4c65cced3dd45778866f34 | Improve Benchmarking
### Problems:
1. The optimization histories for benchmarks are from a log database. The intention behind this was to get thread safety for optimizers that parallelize. However, when running benchmarks it is almost always a good idea not to parallelize on the level of function evaluations but on... | diff --git a/src/estimagic/benchmarking/get_benchmark_problems.py b/src/estimagic/benchmarking/get_benchmark_problems.py
index c10c0e6..bdb5f3e 100644
--- a/src/estimagic/benchmarking/get_benchmark_problems.py
+++ b/src/estimagic/benchmarking/get_benchmark_problems.py
@@ -2,7 +2,6 @@ import warnings
from functools imp... |
OpenSourceEconomics__estimagic-343 | [
{
"changes": {
"added_entities": [
"src/estimagic/estimation/estimate_ml.py:LikelihoodResult.__post_init__",
"src/estimagic/estimation/estimate_ml.py:LikelihoodResult._get_free_cov",
"src/estimagic/estimation/estimate_ml.py:LikelihoodResult.jacobian",
"src/estimagic/estimat... | OpenSourceEconomics/estimagic | b69b16e571bf5c88235715dac9ff20c44ae80672 | Return better results object for `estimate_ml` and `estimate_msm`
### Current situation
- `estimate_ml` and `estimate_msm` return a dictionary with information
- The keys are either confusing or not
### Describe the solution you'd like
- `estimate_ml` and `estimate_msm` should return a custom object (`Estima... | diff --git a/CHANGES.rst b/CHANGES.rst
index 60e4efe..dfa2193 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -10,7 +10,8 @@ releases are available on `Anaconda.org
0.3.0
-----
-Fist release with pytree support in optimization, estimation and differentiation.
+Fist release with pytree support in optimization, estimat... |
OpenSourceEconomics__estimagic-344 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/estimagic/visualization/plotting_utilities.py:combine_plots"
],
"edited_modules": [
"src/estimagic/visualization/plotting_utilities.py:combine_plots"
]
},
"file": "... | OpenSourceEconomics/estimagic | 76e65f3038cea98d17311757860767d5b569b847 | Generalize plotting code
### Problem
`slice_plot` and its 3d version (see #274) still assume that params are a DataFrame.
### Solution
Use `get_tree_converter` to make these plots more flexible. The rough idea is:
- get the tree_converter (with `primary_key="value"`) and `flat_params`
- calculate the evalu... | diff --git a/docs/source/how_to_guides/optimization/how_to_visualize_an_optimization_problem.ipynb b/docs/source/how_to_guides/optimization/how_to_visualize_an_optimization_problem.ipynb
index 15452cc..15446cd 100644
--- a/docs/source/how_to_guides/optimization/how_to_visualize_an_optimization_problem.ipynb
+++ b/docs/... |
OpenSourceEconomics__estimagic-347 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/estimagic/estimation/estimate_ml.py:LikelihoodResult.se",
"src/estimagic/estimation/estimate_ml.py:LikelihoodResult.ci",
"src/estimagic/estimation/estimate_ml.py:LikelihoodResult.p_v... | OpenSourceEconomics/estimagic | 3cfc1c8475159db508bdd39aef99c41368bf2674 | Allow pytrees in bootstrap
## Problem
- Parameters are assumed to be DataFrames
- Statistics are assumed to be Series
## Solution
- Allow both to be general pytrees | diff --git a/src/estimagic/estimation/estimate_ml.py b/src/estimagic/estimation/estimate_ml.py
index a45fa08..7a8ab7f 100644
--- a/src/estimagic/estimation/estimate_ml.py
+++ b/src/estimagic/estimation/estimate_ml.py
@@ -17,6 +17,7 @@ from estimagic.inference.shared import calculate_ci
from estimagic.inference.shared ... |
OpenSourceEconomics__estimagic-411 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/estimagic/optimization/tiktak.py:run_multistart_optimization",
"src/estimagic/optimization/tiktak.py:update_convergence_state"
],
"edited_modules": [
"src/estimagic/optim... | OpenSourceEconomics/estimagic | 737f4d73386d8782f7f2436ea515096177d67a9b | Error in multistart with `ls` optimizers
Hi! this is Mateo from last year's DSE Summer School. I'm starting to use estimagic and it is just, well, magical! Thank you!
I've run into this small bug.
### Bug description
Least squares algorithms appear not to work with multistarts. I think the issue is that some u... | diff --git a/src/estimagic/optimization/tiktak.py b/src/estimagic/optimization/tiktak.py
index ea21eb5..31f511f 100644
--- a/src/estimagic/optimization/tiktak.py
+++ b/src/estimagic/optimization/tiktak.py
@@ -170,6 +170,7 @@ def run_multistart_optimization(
starts=starts,
results=batch_results... |
OpenSourceEconomics__estimagic-69 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"estimagic/optimization/reparametrize.py:_covariance_to_internal"
],
"edited_modules": [
"estimagic/optimization/reparametrize.py:_covariance_to_internal"
]
},
"file": "... | OpenSourceEconomics/estimagic | db33ebce433eb3eac776b3de030c2a84937894cf | Add a robust cholesky decomposition to the utilities
## Background
The standard cholesky decompositions in `numpy.linalg` and `scipy.linalg` only work for positive-definite covariance matrices. However, there are two places where we might want to take a cholesky factor of a covariance matrix that is only positive se... | diff --git a/estimagic/optimization/reparametrize.py b/estimagic/optimization/reparametrize.py
index db6eded..49b3360 100644
--- a/estimagic/optimization/reparametrize.py
+++ b/estimagic/optimization/reparametrize.py
@@ -8,6 +8,7 @@ from estimagic.optimization.utilities import cov_matrix_to_params
from estimagic.optim... |
OpenSourceEconomics__estimagic-74 | [
{
"changes": {
"added_entities": [
"estimagic/optimization/optimize.py:create_internal_criterion",
"estimagic/optimization/optimize.py:calculate_scaling_factor"
],
"added_modules": [
"estimagic/optimization/optimize.py:create_internal_criterion",
"estimagic/opti... | OpenSourceEconomics/estimagic | d4ff6a9704122b34cf5dc2b8faead97e0333dc11 | Add scaling of the parameter vector
Scale the parameter vector by the inverse of the start parameters in reparametrize_to_internal and undo the scaling in reparametrize_from_internal. | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 39686e2..28af28e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -34,13 +34,12 @@ repos:
hooks:
- id: black
types: [python]
+- repo: https://github.com/PyCQA/doc8
+ rev: 0.8.1rc2
+ hooks:
+ - ... |
OpenSourceEconomics__estimagic-76 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"estimagic/differentiation/differentiation.py:gradient",
"estimagic/differentiation/differentiation.py:jacobian",
"estimagic/differentiation/differentiation.py:hessian"
],
"ed... | OpenSourceEconomics/estimagic | 5b602797666a7573ae34b05655885ff83659f8d6 | Allow user to specify steps for numdifftools, scaling
I set the Richardson extrapolation version running yesterday. Still running.
I would be willing to sacrifice some precision for speed here; surely for testing. So it would be great if it was possible to pass the options `step_ratio=2.0, step=1, order=1, num_terms... | diff --git a/docs/source/differentiation.rst b/docs/source/differentiation.rst
index fb7a17d..74d0fa0 100644
--- a/docs/source/differentiation.rst
+++ b/docs/source/differentiation.rst
@@ -15,8 +15,6 @@ backward or central differences for the following problems:
- Jacobian matrix of real vector-valued multivariate fun... |
OpenSourceEconomics__respy-182 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"respy/pre_processing/model_processing.py:process_model_spec",
"respy/pre_processing/model_processing.py:write_out_model_spec",
"respy/pre_processing/model_processing.py:_read_params_spec... | OpenSourceEconomics/respy | c3a6f820ffa6e6085cc2e400a68a53450daade3b | Make model_processing compatible with pathlib
Currently respy objects can be generated with a standard file path but not with a pathlib object. Changing this requires several adjustments:
- don't check for file types using endswith
- adjust type checking
- don't modify paths using string operations | diff --git a/respy/pre_processing/model_processing.py b/respy/pre_processing/model_processing.py
index 1d630123..b62c3003 100644
--- a/respy/pre_processing/model_processing.py
+++ b/respy/pre_processing/model_processing.py
@@ -1,5 +1,6 @@
"""Process model specification files or objects."""
import json
+from pathlib i... |
OpenSourceEconomics__respy-186 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "development/modules/auxiliary_reliability.py"
},
{
"changes": {
"added_entities": [
"respy/python/shared/shared_auxiliary.py:ols",
... | OpenSourceEconomics/respy | 712ac1aa368ba2d4b3aa4928024f6fb40a564212 | Drop statsmodels dependency
Currently we use statsmodels to calculate the OLS regressions in the value function interpolation and to calculate an rmse in several places. I propose we drop statsmodels for the following reasons:
- Statsmodels causes many deprecation warnings, all of them related to stuff we don't even... | diff --git a/development/modules/auxiliary_reliability.py b/development/modules/auxiliary_reliability.py
index 1db71d38..19d21543 100644
--- a/development/modules/auxiliary_reliability.py
+++ b/development/modules/auxiliary_reliability.py
@@ -3,7 +3,6 @@ import shlex
from copy import deepcopy
import numpy as np
-fr... |
OpenSourceEconomics__respy-363 | [
{
"changes": {
"added_entities": [
"respy/method_of_simulated_moments.py:_create_comparison_plot_data_msm",
"respy/method_of_simulated_moments.py:_create_tidy_data",
"respy/method_of_simulated_moments.py:_reconstruct_inputs"
],
"added_modules": [
"respy/method_o... | OpenSourceEconomics/respy | 81f12633ee43ce93801fa62c0038493aeff22aea | Add comparison_plot_data to msm().
* respy version used, if any: any
* Python version, if any: any
* Operating System: any
### Is your feature request related to a problem? Please describe.
estimagic allows the criterion function to have two returns.
1. A criterion value or array which is passed to the optim... | diff --git a/docs/how_to_guides/msm.ipynb b/docs/how_to_guides/msm.ipynb
index f448ac74..a95e86fb 100644
--- a/docs/how_to_guides/msm.ipynb
+++ b/docs/how_to_guides/msm.ipynb
@@ -46,6 +46,8 @@
"* weighting_matrix (numpy.ndarray)\n",
"* n_simulation_periods (int, default None)\n",
"* return_scalar (bool, ... |
OskarLiew__PyGenOpt-3 | [
{
"changes": {
"added_entities": [
"examples/linear_regression_variable_selection.py:get_x_subset",
"examples/linear_regression_variable_selection.py:main"
],
"added_modules": [
"examples/linear_regression_variable_selection.py:get_x_subset",
"examples/linear_re... | OskarLiew/PyGenOpt | 6edd9a82bf4b593209353fca4c0af97c4522d4cb | Add unit tests for functions
Needs tests for:
* crossover
* evaluation
* mutation
* population (not prio)
* selection | diff --git a/.gitignore b/.gitignore
index b6e4761..e02647d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -127,3 +127,6 @@ dmypy.json
# Pyre type checker
.pyre/
+
+# vscode settings
+.vscode/
\ No newline at end of file
diff --git a/README.md b/README.md
index 32889f6..7af9e51 100644
--- a/README.md
+++ b/README.md
@... |
Ouranosinc__Magpie-493 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"magpie/api/exception.py:verify_param"
],
"edited_modules": [
"magpie/api/exception.py:verify_param"
]
},
"file": "magpie/api/exception.py"
},
{
"changes": {
... | Ouranosinc/Magpie | 24c4ec2d3f98eb71fba7b199281882dbc62b6693 | [BUG] Rendering UI improvements
## Describe the bug
Some places where rendering of UI views can be improved.
## Screenshots
Unnecessary line (both group and user views)
Unnecessary "Apply Permis... | diff --git a/.readthedocs.yml b/.readthedocs.yml
index 4fa193fd..4f2190ef 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -11,8 +11,9 @@ formats:
#- pdf
#- epub
python:
- version: 3.7
+ version: "3.7"
install:
+ - requirements: requirements-sys.txt
- requirements: requirements-doc.txt
#... |
Ouranosinc__xclim-2117 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "src/xclim/indicators/atmos/_conversion.py"
},
{
"changes": {
"added_entities": [
"src/xclim/indices/_conversion.py:uas_vas_to_sfcwind",
... | Ouranosinc/xclim | 81d801f6c64ab6337293e21fc17f21c9938fb725 | Consistent namings for conversion functions
### Addressing a Problem?
This is a pet peeve of mine, with a very simple (albeit API-breaking) fix.
We currently offer several conversion tools that use the following naming conventions:
- `x2x`:
- `amount2rate`
- `flux2rate`
- `lwethickness2amount`
- `... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 354ebb0a..0aebcd90 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -20,6 +20,9 @@ Breaking changes
* `xclim` no longer supports Python 3.10. The minimum required version is now Python 3.11. (:pull:`2082`).
* Reverted: Extended support for Python3.10 will continue... |
Ouranosinc__xclim-214 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/checks.py:missing_any"
],
"edited_modules": [
"xclim/checks.py:missing_any"
]
},
"file": "xclim/checks.py"
},
{
"changes": {
"added_entities": null,... | Ouranosinc/xclim | fdb5bdcbdffb011aa394de794fec987e9422855a | Implement missing check for specific periods (e.g. season=djf)
At the moment the missing function checks for all dates in the `freq`, even though we might only be interested in a given month. | diff --git a/setup.cfg b/setup.cfg
index 78d6b84c..c8c7e55b 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -3,13 +3,13 @@ current_version = 0.9-beta
commit = True
tag = True
parse = (?P<major>\d+)\.(?P<minor>\d+)(\-(?P<release>[a-z]+))?
-serialize =
+serialize =
{major}.{minor}-{release}
{major}.{minor}
[bumpvers... |
Ouranosinc__xclim-216 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "xclim/atmos/_precip.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modu... | Ouranosinc/xclim | 66c6288eff15344d3830572ee5d54a3c606c0c7d | Solve problem with {} tags in identifier
### Description
In the indicator class, we use the identifier attribute as the unique identifier of a given class. Since this was also used as the output variable name for the created netCDF, we introduced formatting tags in the identifier attribute. The problem is that the sam... | diff --git a/xclim/atmos/_precip.py b/xclim/atmos/_precip.py
index 8397c951..8fb6396d 100644
--- a/xclim/atmos/_precip.py
+++ b/xclim/atmos/_precip.py
@@ -39,20 +39,21 @@ max_1day_precipitation_amount = Pr(identifier='rx1day',
compute=indices.max_1day_precipitation_amount,
... |
Ouranosinc__xclim-232 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "setup.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
... | Ouranosinc/xclim | a7946086aa64b40f50f90530f38f77358d929d92 | Add fit indicator
### Description
The `fit` function has no related indicator instance.
| diff --git a/HISTORY.rst b/HISTORY.rst
index 13f89f90..710cdc1a 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -6,6 +6,7 @@ History
--------------
* Migrated to a `major.minor.patch-release` semantic versioning system.
* Removed attributes in netCDF output from Indicators that are not in the CF-convention.
+* Added `... |
Ouranosinc__xclim-235 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/utils.py:Indicator.__call__"
],
"edited_modules": [
"xclim/utils.py:Indicator"
]
},
"file": "xclim/utils.py"
}
] | Ouranosinc/xclim | 0609a154b7be8c2be2e3db0f7786bb3bfcae123a | Add xclim version to history metadata attribute
### Description
In order to potentially backtrack slight differences in calculations between versions - add xclim version info the inicator attributes. I suggest in the ```history``` attr
| diff --git a/HISTORY.rst b/HISTORY.rst
index 3d38f84c..7231208e 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -2,15 +2,12 @@
History
=======
-0.10.2-beta (2019-06-18)
+0.10.x-beta (2019-06-18)
------------------------
-* Added utilities with ensemble, run length, and subset algorithms to the documentation.
-
-0.10... |
Ouranosinc__xclim-258 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/indices/_multivariate.py:cold_spell_duration_index",
"xclim/indices/_multivariate.py:days_over_precip_thresh",
"xclim/indices/_multivariate.py:fraction_over_precip_thresh",
... | Ouranosinc/xclim | b8f26a623fcb1329a94c17f4e6a7c5e2ac61dbd2 | Percentile threshold indices : Frequencies?
For indices such as 'R95p' (with the following definition taken from icclim)
- Days with RR > 95th percentile of daily amounts (very wet days)
(days)
- Let RRwj be the daily precipitation amount at wet day w (RR ≥ 1.0 mm)
of period j and let RRwn95 be the 95th percenti... | diff --git a/xclim/indices/_multivariate.py b/xclim/indices/_multivariate.py
index ef34fe6c..04473704 100644
--- a/xclim/indices/_multivariate.py
+++ b/xclim/indices/_multivariate.py
@@ -91,19 +91,10 @@ def cold_spell_duration_index(tasmin, tn10, window=6, freq="YS"):
>>> tn10 = percentile_doy(historical_tasmin, p... |
Ouranosinc__xclim-266 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"docs/itable.py:_indicator_table"
],
"edited_modules": [
"docs/itable.py:_indicator_table"
]
},
"file": "docs/itable.py"
},
{
"changes": {
"added_entities"... | Ouranosinc/xclim | 1fd3ef228ee48f547167bc43afa89615bdafb30b | Harmonize freeze-thaw cycle computation with PCC
PCC is using thresholds different than 0. | diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
index ac3a75cd..4be835ef 100644
--- a/.github/ISSUE_TEMPLATE.md
+++ b/.github/ISSUE_TEMPLATE.md
@@ -2,7 +2,7 @@
* Python version:
* Operating System:
-### Description
+### Description
<!--Describe what you were trying to get done.
Tell us what ha... |
Ouranosinc__xclim-294 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/generic.py:fit",
"xclim/generic.py:frequency_analysis"
],
"edited_modules": [
"xclim/generic.py:fit",
"xclim/generic.py:frequency_analysis"
]
},
"... | Ouranosinc/xclim | 608bac4c9976df778fb9fa442ef725c45dde9f36 | frequency_analysis crashes if there are empty grid cells
* xclim version: 0.11.2
* Python version: 3.6
* Operating System:
### Description
I have a Dataset on a rotated grid (EC-EARTH_HIRHAM5, from CORDEX-NA). I've made a subset for my region, and on the borders of that subset, some grid cells are empty (meaning ... | diff --git a/HISTORY.rst b/HISTORY.rst
index ced91a46..a42ac318 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -15,6 +15,7 @@ History
* Reformatted packaging configuration to pure Py3 wheel that ignore tests and test data
* Now officially supporting Python3.8
* Enhancement to precip_accumulation() to allow estimated ... |
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