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 |
|---|---|---|---|---|---|
NCAS-CMS__cfdm-243 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfdm/examplefield.py:example_field"
],
"edited_modules": [
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]
},
"file": "cfdm/examplefield.py"
},
{
"changes": {
"add... | NCAS-CMS/cfdm | 0cece5a8c04d4e1d26dd9ae50a825e4b8e1d335d | Incorrect `formula_terms` in output netCDF files in some cases
When a domain ancillary construct with bounds is the same netCDF variable as the parent dimension coordinate constructs, the domain ancillary construct is erroneously written to an output file in addition to the dimension coordinate construct.
```python
... | diff --git a/Changelog.rst b/Changelog.rst
index b18f7dd25..721dfade1 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -7,7 +7,9 @@ Version 1.10.0.2
(https://github.com/NCAS-CMS/cfdm/issues/228)
* Relocate the call to `NetCDFRead._customize_read_vars` to earlier in
`NetCDFRead.read` (https://github.com/NCAS-CMS... |
NCAS-CMS__cfdm-247 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfdm/cfdmimplementation.py:CFDMImplementation.initialise_NetCDFArray"
],
"edited_modules": [
"cfdm/cfdmimplementation.py:CFDMImplementation"
]
},
"file": "cfdm/cfdmimpl... | NCAS-CMS/cfdm | 1698508adff6148f782a1123be7f3cbd1ecd39f7 | Allow file missing data indicator values to be stored on `NetCDFArray` instances
It can be useful to applications to know the missing data indicator without opening the netCDF file. This is the case for active storage reductions currently being implemented in cf-python.
It is almost always the case that the netCDF f... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ae9504987..576c555fc 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -68,7 +68,7 @@ repos:
# compatible with 'black' with the lines set to ensure so in the repo's
# pyproject.toml. Other than that and the below, no extra co... |
NCAS-CMS__cfdm-250 | [
{
"changes": {
"added_entities": null,
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"edited_entities": [
"cfdm/data/data.py:Data.second_element"
],
"edited_modules": [
"cfdm/data/data.py:Data"
]
},
"file": "cfdm/data/data.py"
}
] | NCAS-CMS/cfdm | 55a5f5bc8ec0a231d403c2284634339342104f34 | Error from `Data.second_element` for some data shapes
For some `Data` shapes, the retrieval of the second element causes an error:
```python
>>> import cfdm
>>> import numpy as np
>>> d = cfdm.Data(np.arange(6).reshape(1, 3, 2)) # This shape is OK
>>> d.array
array([[[0],
[1],
[2],
[... | diff --git a/Changelog.rst b/Changelog.rst
index 05fef7152..0987737fc 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -1,3 +1,14 @@
+Version 1.10.?.?
+----------------
+
+**2023-??-??**
+
+* Fixed bug that caused `cf.Data.second_element` to fail for some data
+ shapes, namely for a final axis with size one.
+ (http... |
NCAS-CMS__cfdm-263 | [
{
"changes": {
"added_entities": [
"cfdm/read_write/netcdf/netcdfread.py:NetCDFRead.is_file",
"cfdm/read_write/netcdf/netcdfread.py:NetCDFRead.is_dir"
],
"added_modules": null,
"edited_entities": [
"cfdm/read_write/netcdf/netcdfread.py:NetCDFRead.read"
],
... | NCAS-CMS/cfdm | 55572dac1b57fd06e97300577c8c8b1e0b6bcab1 | Reading of `http://` remote files does not work
In cfdm `1.10.1.0` we get:
```python
>>> remote_file = 'http://psl.noaa.gov/thredds/dodsC/Datasets/cru/crutem5/Monthlies/air.mon.anom.nobs.nc'
>>> import netCDF4
>>> nc = netCDF4.Dataset(remote_file, 'r') # works
>>> import cfdm
>>> j = cfdm.read(remote_file) # do... | diff --git a/Changelog.rst b/Changelog.rst
index 73d3efdea..ff7f4a697 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -6,6 +6,8 @@ Version 1.10.1.1
* Fix bug that caused very slow reads of datasets with compession by
gathering or DSG ragged arrays
(https://github.com/NCAS-CMS/cfdm/issues/260)
+* Fix bug that p... |
NCAS-CMS__cfdm-269 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfdm/read_write/netcdf/netcdfread.py:NetCDFRead.is_netcdf_file"
],
"edited_modules": [
"cfdm/read_write/netcdf/netcdfread.py:NetCDFRead"
]
},
"file": "cfdm/read_write/n... | NCAS-CMS/cfdm | 142accf27fbbc052473b4eee47daf0e81c88df3a | Reading `https://` netCDF files does not work
At version 1.10.1.1, reading a `https://` files does not work, but reading an `http://` file does work:
```python
>>> import cfdm
>>> remote = "http://psl.noaa.gov/thredds/dodsC/Datasets/cru/crutem5/Monthlies/air.mon.anom.nobs.nc"
>>> cfdm.read(remote)
[<Field: air_t... | diff --git a/Changelog.rst b/Changelog.rst
index e4e178769..5cf7d255c 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -1,3 +1,13 @@
+Version 1.10.1.2
+----------------
+
+**2023-08-31**
+
+* Fix bug that prevented "https://" netCDF files from being read
+ (https://github.com/NCAS-CMS/cfdm/issues/268)
+
+----
+
Vers... |
NCAS-CMS__cfdm-288 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfdm/field.py:Field.__new__",
"cfdm/field.py:Field.compress",
"cfdm/field.py:Field.insert_dimension"
],
"edited_modules": [
"cfdm/field.py:Field"
]
},
"... | NCAS-CMS/cfdm | 92f8fdd4b9cdcea27479b3467988f1b453946427 | Allow discrete sampling geometries with 1-d data to be written as ragged arrays, and improve the compression process
Currently, a 1-d DSG can not be compressed so that it is written out to netCDF file as a ragged array. E.g.
```python
>>> print(dsg)
Field: mole_fraction_of_ozone_in_air (ncvar%O3_TECO)
-------------... | diff --git a/Changelog.rst b/Changelog.rst
index d5c425fe2..f028a514f 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -1,3 +1,13 @@
+Version 1.11.1.0
+----------------
+
+**2024-??-??**
+
+* New keyword parameter to `cfdm.Field.insert_dimension`:
+ ``constructs`` (https://github.com/NCAS-CMS/cfdm/issues/287)
+
+----... |
NCAS-CMS__cfdm-300 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfdm/field.py:Field.cell_methods"
],
"edited_modules": [
"cfdm/field.py:Field"
]
},
"file": "cfdm/field.py"
}
] | NCAS-CMS/cfdm | 8d3b7d26412dcdc9769a4e09e6b278be989ccd4e | `cf.Field.cell_methods` returns incorrect results when an invalid identifer is provided
At cfdm `v1.11.1.0`, when an invalid selection is passed to `cfdm.Field.cell_methods`, _all_ cell method constructs are returned, rather than none of them as expected:
```python
>>> import cfdm
>>> f = cfdm.example_field(1)
>>> ... | diff --git a/Changelog.rst b/Changelog.rst
index 522654d30..5b47696a5 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -3,6 +3,9 @@ Version NEXTVERSION
**2024-??-??**
+* Fix bug that returned incorrect results when an invalid identifer is
+ provided to `cf.Field.cell_methods`
+ (https://github.com/NCAS-CMS/cfdm... |
NCAS-CMS__cfdm-61 | [
{
"changes": {
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},
"file": "cfdm/__init__.py"
},
{
"changes": {
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"edited_modules": ... | NCAS-CMS/cfdm | cfec0493b584abe64fdb6e0027a91bdaa5be1e4c | Consolidate functions that get & set global settings
Equivalent to NCAS-CMS/cf-python#70. | diff --git a/Changelog.rst b/Changelog.rst
index 24dca59c7..61cb26149 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -8,6 +8,9 @@ version 1.8.6
(https://github.com/NCAS-CMS/cfdm/issues/55)
* Implemented the reading and writing of netCDF4 group hierarchies for
CF-1.8 (https://github.com/NCAS-CMS/cfdm/issues/13... |
NCAS-CMS__cfdm-86 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfdm/core/cellmethod.py:CellMethod.__init__"
],
"edited_modules": [
"cfdm/core/cellmethod.py:CellMethod"
]
},
"file": "cfdm/core/cellmethod.py"
},
{
"changes": ... | NCAS-CMS/cfdm | 57ca70e3a2ad24069207989fe4a6fce9b84a4424 | In cf.write, allow dimension coordinate constructs' netCDF names to be added to the "coordinates" attribute
In `cf.write`, allow dimension coordinate constructs' netCDF names to be added to the `coordinates` netCDF attribute, if the user desires. Currently they are always omitted. Either way is CF-compliant. | diff --git a/cfdm/core/cellmethod.py b/cfdm/core/cellmethod.py
index d2ce40fe4..3266d2d30 100644
--- a/cfdm/core/cellmethod.py
+++ b/cfdm/core/cellmethod.py
@@ -90,12 +90,12 @@ class CellMethod(abstract.Container):
if source:
try:
axes = source.get_axes(None)
- except A... |
NCAS-CMS__cfunits-46 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "cfunits/units.py"
}
] | NCAS-CMS/cfunits | 1f2d0868174c2d364d34e9fe5f8577baa3a786af | Change default calendar from "gregorian" to "standard"
The `gregorian` calendar was deprecated as of CF-1.9 | diff --git a/Changelog.rst b/Changelog.rst
index 7bb43a9..120d111 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -1,3 +1,12 @@
+version 3.3.5
+-------------
+----
+
+**2022-09-??**
+
+* Change default calendar from ``'gregorian'`` to ``'standard'``
+ (https://github.com/NCAS-CMS/cfunits/issues/45)
+
version 3.3.4
... |
NCSU-High-Powered-Rocketry-Club__AirbrakesV2-118 | [
{
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},
"file": "airbrakes/constants.py"
},
{
"changes": {
"added_entities": [
"airbrakes/data_handling/data_processor.py:IMUDataProcessor.average_vertic... | NCSU-High-Powered-Rocketry-Club/AirbrakesV2 | 54d7f9e2a4c45775cf8f89a1df4bd431d1af3f82 | `LandedState` should be detected based on acceleration spike
Genesis Flight 1 had trouble switching to `LandedState`, because the velocity calculated from the gyro was off by > 20m/s due to drift. Genesis Flight 2 lucked out and the velocity was mostly accurate and consistent with velocity from the altitude data.
A... | diff --git a/airbrakes/constants.py b/airbrakes/constants.py
index f76ab2f..8f6d457 100644
--- a/airbrakes/constants.py
+++ b/airbrakes/constants.py
@@ -158,9 +158,8 @@ deploying at apogee."""
GROUND_ALTITUDE_METERS = 10.0
"""The altitude in meters that the rocket must be under before we consider it to have landed.... |
NCSU-High-Powered-Rocketry-Club__AirbrakesV2-151 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"airbrakes/airbrakes.py:AirbrakesContext.__init__",
"airbrakes/airbrakes.py:AirbrakesContext.update"
],
"edited_modules": [
"airbrakes/airbrakes.py:AirbrakesContext"
]
... | NCSU-High-Powered-Rocketry-Club/AirbrakesV2 | 2d85a6c6bf946636c5e6b4aa74388b9d376289f3 | Refactor logging to be more clear and performant
After the changes in #146 in the logger to get #147 resolved, our logging process has slightly slowed down due to use of `msgpec.structs.asdict()` instead of `msgspec.to_builtins()`. We can still keep up with the IMU process, but the margin has reduced.
I propose the f... | diff --git a/airbrakes/airbrakes.py b/airbrakes/airbrakes.py
index a451905..f52d720 100644
--- a/airbrakes/airbrakes.py
+++ b/airbrakes/airbrakes.py
@@ -1,7 +1,6 @@
"""Module which provides a high level interface to the air brakes system on the rocket."""
import time
-from collections import deque
from typing impo... |
NCSU-High-Powered-Rocketry-Club__AirbrakesV2-98 | [
{
"changes": {
"added_entities": [
"airbrakes/hardware/servo.py:Servo._set_max_no_buzz",
"airbrakes/hardware/servo.py:Servo._set_min_no_buzz"
],
"added_modules": null,
"edited_entities": [
"airbrakes/hardware/servo.py:Servo.set_extended",
"airbrakes/hardwa... | NCSU-High-Powered-Rocketry-Club/AirbrakesV2 | f0891a6f1fa956c947bfacb671af18d96d3c2aea | Fix controls logic
If we are doing an actual control flight, and our target altitude is quite close to predicted apogee, then our controls logic would subtly fail because of race conditions. Consider this case, when our target altitude is 800m:
1. Predicted apogee is 801m:
- Airbrakes extend to `MAX`. Thread to ext... | diff --git a/airbrakes/hardware/servo.py b/airbrakes/hardware/servo.py
index cad697c..07bb2e1 100644
--- a/airbrakes/hardware/servo.py
+++ b/airbrakes/hardware/servo.py
@@ -2,7 +2,6 @@
the airbrakes."""
import threading
-import time
import warnings
import gpiozero
@@ -17,7 +16,7 @@ class Servo:
controlling... |
NERSC__pytokio-66 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tokio/cli/archive_collectdes.py:pages_to_hdf5"
],
"edited_modules": [
"tokio/cli/archive_collectdes.py:pages_to_hdf5"
]
},
"file": "tokio/cli/archive_collectdes.py"
}... | NERSC/pytokio | 2561457101cd85b82b841b67085d0bdfb6c69e83 | make tokio.timeseries independent of connectors
At present, `tokio.timeseries` imports `tokio.connectors.hdf5` to facilitate translating to/from HDF5 format. This causes a fragile circular dependency between the two which causes problems when importing other connectors that depend on `tokio.connectors.common`.
Ther... | diff --git a/tokio/cli/archive_collectdes.py b/tokio/cli/archive_collectdes.py
index 505932c..7bd3c77 100644
--- a/tokio/cli/archive_collectdes.py
+++ b/tokio/cli/archive_collectdes.py
@@ -382,19 +382,19 @@ def pages_to_hdf5(pages, output_file, init_start, init_end, query_start, query_e
... |
NLeSC-GO-common-infrastructure__stac2dcache-26 | [
{
"changes": {
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},
"file": "setup.py"
},
{
"changes": {
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"edited_entities": [
"stac2dcache/configure.py:co... | NLeSC-GO-common-infrastructure/stac2dcache | c4991520def371cbc06d774e538a03b9cca6e7d2 | fsspec config files seem to create conflicts when configuring
When a configuration file is present, calling the function `configure` seems not to correctly setup the filesystem/STAC_IO? | diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index d7bd3d8..82e0090 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -10,7 +10,7 @@ jobs:
strategy:
fail-fast: false
matrix:
- python-version: ['3.7', '3.8', '3.9']
+ python-version: [... |
NOhs__dkey-10 | [
{
"changes": {
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},
"file": "dkey/__init__.py"
},
{
"changes": {
"added_entities": [
"dkey/_dkey.py:deprecate_keys.__eq__",
"dkey/_dkey.py:deprecate_keys.__n... | NOhs/dkey | 167ebb26e04e1d268ce2456a36cdac8f7018756a | Set function should remove the deprecated key entry
Currently the setitem function only warns. However, once the key is overridden, the warning should be removed to not further propagate to code that is unrelated to the deprecation. | diff --git a/.travis.yml b/.travis.yml
index 1069918..50fc290 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -17,3 +17,4 @@ deploy:
secure: ZYN/wuXcpWOuWtuEJrrdd7uhdID5yOk6XN9zeGgFVQASnI5PvgqGe/DeflMkSAem5gaa/shGNVL0454tI2L047HxN11MiGyk6wlDUAHbx6iQm4REzgHufxfmoVtqUXHnJqxARboTWw3vosorAd+u6fyhdcqI66bs4OEH23op2uCPSz05... |
NOhs__dkey-18 | [
{
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"added_entities": null,
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"edited_modules": null
},
"file": "dkey/__init__.py"
}
] | NOhs/dkey | 098cecbe1c1ed8cca92029dbd90f77cc6c0d7673 | Dkey should provide version info
It is common practice to provide the version of an installed package via `__version__` etc. This should be added. | diff --git a/dkey/__init__.py b/dkey/__init__.py
index 266df21..f71a87d 100644
--- a/dkey/__init__.py
+++ b/dkey/__init__.py
@@ -10,6 +10,20 @@ dkey
====
Function to generate deprecated keys.
+__version__
+===========
+A string indicating which version of dkey is currently used.
+
+version_info
+============
+A tup... |
NREL__bifacial_radiance-527 | [
{
"changes": {
"added_entities": null,
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"edited_entities": [
"bifacial_radiance/main.py:SceneObj._makeSceneNxR",
"bifacial_radiance/main.py:MetObj.__init__"
],
"edited_modules": [
"bifacial_radiance/main.py:SceneObj",
"bifacial_... | NREL/bifacial_radiance | 2742b883b07c4a70e6bc737289734d7e624b1ec1 | Development tests are failing
First two are failing in all env's. Second two only fail in upgrade-strategy Eager.
FAILED tests/test_bifacial_radiance.py::test_SingleModule_HPC - AssertionError: assert 'groundplane' == 'a0.0.a0.test'
FAILED tests/test_performance.py::test_calculatePerformance - UnboundLocalError: c... | diff --git a/bifacial_radiance/main.py b/bifacial_radiance/main.py
index 574ca27..aa58a58 100644
--- a/bifacial_radiance/main.py
+++ b/bifacial_radiance/main.py
@@ -3002,11 +3002,11 @@ class SceneObj:
f'{nMods}modsx{nRows}rows_origin{originx},{originy}.rad' )
if self.hpc:
- ... |
NREL__floris-312 | [
{
"changes": {
"added_entities": null,
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"edited_entities": [
"src/floris/simulation/wake_velocity/jensen.py:JensenVelocityDeficit.function"
],
"edited_modules": [
"src/floris/simulation/wake_velocity/jensen.py:JensenVelocityDeficit"
]
... | NREL/floris | 563c10cfd43341d232ee80ace5c4dab0a62574ea | Jensen model has odd power value
**Bug description**
Working on an example script I noticed that some turbines in a farm returned oddly low power levels
**To Reproduce**
Here is an example script to reproduce the behavior, notice one of the turbines produces much less power than the rest. This is not consistent w... | diff --git a/src/floris/simulation/wake_velocity/jensen.py b/src/floris/simulation/wake_velocity/jensen.py
index 294c4ac7..c7cdb251 100644
--- a/src/floris/simulation/wake_velocity/jensen.py
+++ b/src/floris/simulation/wake_velocity/jensen.py
@@ -114,7 +114,7 @@ class JensenVelocityDeficit(BaseModel):
# np.nan... |
NREL__hescore-hpxml-100 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator._get_window_code"
],
"edited_modules": [
"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator"
]
},
"file": "hescorehpxm... | NREL/hescore-hpxml | b4c0dfd6a0e38b571a558b2127757c9c81a8640e | Window code mapping changes
- Aluminum, double pane, low-e is currently mapping to `dcaa`.
- Aluminum, thermal break is currently mapping to `dcab`
@lirainer What should these be mapping to? | diff --git a/hescorehpxml/__init__.py b/hescorehpxml/__init__.py
index 306fcba0..b178e9fc 100644
--- a/hescorehpxml/__init__.py
+++ b/hescorehpxml/__init__.py
@@ -236,7 +236,7 @@ class HPXMLtoHEScoreTranslator(object):
if glass_layers in ('double-pane', 'single-paned with storms', 'single-paned with lo... |
NREL__hescore-hpxml-103 | [
{
"changes": {
"added_entities": null,
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"edited_entities": [
"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator._get_cooling_system_type",
"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator._get_hvac"
],
"edited_modules": [
"hescorehpxm... | NREL/hescore-hpxml | 8b8d22ce729c851042f074b36709407fdda5be8f | Cooling only mini splits
We are mapping cooling only mini splits to `split_dx` as described [here](https://hescore-hpxml.readthedocs.io/en/latest/translation/cooling_system.html#id2). HEScore has been updated to handle a cooling only mini split and it should be translated as such now.
- [ ] Code changes
- [ ] Test... | diff --git a/docs/source/translation/cooling_system.rst b/docs/source/translation/cooling_system.rst
index 898bb821..33949281 100644
--- a/docs/source/translation/cooling_system.rst
+++ b/docs/source/translation/cooling_system.rst
@@ -59,7 +59,7 @@ is done according to the following mapping.
=======================... |
NREL__hescore-hpxml-113 | [
{
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"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator._get_building_zone_wall"
],
"edited_modules": [
"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator"
]
},
"file": "hesc... | NREL/hescore-hpxml | 0b79d17c5fff0876a18ccd2efca3d058323d7810 | Better handle windows attached to foundation walls
If a window is attached to a foundation wall it will try to determine the orientation from the wall but won't be able to find it (It's not looking for foundation walls and they don't have orientation anyway). We should fall back to using the orientation from the window... | diff --git a/docs/source/translation/zone_window.rst b/docs/source/translation/zone_window.rst
index 480fe5db..5062926c 100644
--- a/docs/source/translation/zone_window.rst
+++ b/docs/source/translation/zone_window.rst
@@ -13,17 +13,21 @@ assumed to mean the sum of the areas of the windows that the ``Window`` element
... |
NREL__hescore-hpxml-115 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator.hpxml_to_hescore_dict",
"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator._get_hvac"
],
"edited_modules": [
"hescorehpxml/_... | NREL/hescore-hpxml | 0b79d17c5fff0876a18ccd2efca3d058323d7810 | HVAC weighting priority
Right now the priority for weighting factor on HVAC systems is floor area served then fraction of load. If both have fraction and only cooling (for instance) has floor area, it will throw an error because it wants them to be the same instead of choosing fraction for all of them. This should be c... | diff --git a/docs/source/translation/hvac.rst b/docs/source/translation/hvac.rst
index ec1bc7e9..cdc7169f 100644
--- a/docs/source/translation/hvac.rst
+++ b/docs/source/translation/hvac.rst
@@ -1,26 +1,35 @@
HVAC Systems
############
-HEScore allows the definition of up to two HVAC systems which can each include a... |
NREL__hescore-hpxml-117 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator._get_building_zone_floor"
],
"edited_modules": [
"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator"
]
},
"file": "hes... | NREL/hescore-hpxml | 0b79d17c5fff0876a18ccd2efca3d058323d7810 | Throw descriptive error message on SlabOnGrade foundations when a Slab element is missing
Currently, when foundations are defined without attaching a slab element, translator will throw an error of "integer division or modulo by zero". A more descriptive error is expected to reflect the missing input.
Might be a sub-i... | diff --git a/hescorehpxml/__init__.py b/hescorehpxml/__init__.py
index 55a58b86..e7bfb5c8 100644
--- a/hescorehpxml/__init__.py
+++ b/hescorehpxml/__init__.py
@@ -1345,7 +1345,7 @@ class HPXMLtoHEScoreTranslator(object):
elif zone_floor['foundation_type'] == 'slab_on_grade':
del fw_eff_rva... |
NREL__hescore-hpxml-127 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/__init__.py:main"
],
"edited_modules": [
"hescorehpxml/__init__.py:main"
]
},
"file": "hescorehpxml/__init__.py"
},
{
"changes": {
"added_ent... | NREL/hescore-hpxml | d46f8002505438d16abbb397cd7bb23f3e279c6a | Export an HPXML file scrubbed of PII
It would be helpful to be able have the HPXML file a user submits for support and debugging. However, we want to remove any personally identifiable information, so let's add a flag that optionally writes the imported HPXML file with the following elements removed
- All data unde... | diff --git a/.circleci/config.yml b/.circleci/config.yml
index 80e9a7ba..191ddade 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -1,8 +1,8 @@
version: 2
jobs:
- build-py27:
+ build-py36:
docker:
- - image: circleci/python:2
+ - image: circleci/python:3.6
steps:
- checkout... |
NREL__hescore-hpxml-131 | [
{
"changes": {
"added_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_attic_knee_wall_rvalue_and_area"
],
"added_modules": null,
"edited_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_building_zone_roof"
],
"edited_modu... | NREL/hescore-hpxml | 584a2bdd34ae66c6b0ae9507f30976ec5a222cab | Area weighted R-value fix for knee walls
Proposed changes:
- Get rid of the center of cavity effective R-value lookups for walls and attics. Do area weighted R-values with nominal cavity R-values only.
- If the continuous insulation is >= R-5, choose the appropriate construction type. Do not add additional continuo... | diff --git a/.gitignore b/.gitignore
index 3ce39c42..58094f71 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,4 +10,5 @@ docs/build
hescore_hpxml.egg-info
dist
build
-
+.env
+.devcontainer
diff --git a/examples/house8.json b/examples/house8.json
index b87518e7..7f070bf4 100644
--- a/examples/house8.json
+++ b/exampl... |
NREL__hescore-hpxml-137 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_building_about"
],
"edited_modules": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase"
]
},
"file": "hescorehp... | NREL/hescore-hpxml | 1bd1dd87237c00280c2150d96df6a33919659836 | NumberofBedrooms silently capped at 10
If `NumberofBedrooms` is greater than 10 then hpxml2hescore returns `number_bedrooms` set to 10 and no error.
Test file:
[bad_input_hpxml.txt](https://github.com/NREL/hescore-hpxml/files/6225296/bad_input_hpxml.txt)
* Currently: returns json with `number_bedrooms` set to 10
... | diff --git a/examples/house6.xml b/examples/house6.xml
index 0ab806c2..fdc7713d 100644
--- a/examples/house6.xml
+++ b/examples/house6.xml
@@ -32,7 +32,7 @@
<ResidentialFacilityType>single-family detached</ResidentialFacilityType>
<NumberofConditionedFloorsAboveGrade>2</Numbero... |
NREL__hescore-hpxml-139 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.hpxml_to_hescore",
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_building_zone_roof",
"hescorehpxml/base.py:HPXMLtoHEScoreTrans... | NREL/hescore-hpxml | 1bd1dd87237c00280c2150d96df6a33919659836 | Skylight is always assigned to first roof
Can/should the skylight be able to be assigned to the second roof? See original discussion [here](https://github.com/NREL/OpenStudio-HEScore/pull/237). | diff --git a/docs/source/translation/zone_window.rst b/docs/source/translation/zone_window.rst
index 2275a2c5..22a50602 100644
--- a/docs/source/translation/zone_window.rst
+++ b/docs/source/translation/zone_window.rst
@@ -36,7 +36,9 @@ window properties be assigned to each direction, the
windows will be specified sep... |
NREL__hescore-hpxml-149 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_building_address",
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_building_about"
],
"edited_modules": [
"hescor... | NREL/hescore-hpxml | e5af84582b4524ad92bac0a9f153051f2d39f5eb | Move external_building_id to building_address
[In this repo](https://github.com/NREL/hescore-hpxml/blob/e5af84582b4524ad92bac0a9f153051f2d39f5eb/hescorehpxml/base.py#L879) we're placing the `external_building_id` under `building.about`.
In the HEScore API documentation it says that it should be sent with `submit_ad... | diff --git a/docs/source/translation/about.rst b/docs/source/translation/about.rst
index c083c764..6eebb65c 100644
--- a/docs/source/translation/about.rst
+++ b/docs/source/translation/about.rst
@@ -10,15 +10,6 @@ HEScore requires an assessment date. If a date is stored in the element
``Building/ProjectStatus/Date``, ... |
NREL__hescore-hpxml-152 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/hpxml3.py:HPXML3toHEScoreTranslator.get_attic_knee_walls"
],
"edited_modules": [
"hescorehpxml/hpxml3.py:HPXML3toHEScoreTranslator"
]
},
"file": "hescorehp... | NREL/hescore-hpxml | 9a069f2b34e5de5352673c96461afbbbbe75c2ae | Update input validation
[new input validation rules](https://docs.google.com/spreadsheet/pub?key=0Aqq3Ugm1VCSwdE13bWsxNTRVaE54c2N2LWFBd3h6TXc&single=true&gid=1&output=html)
Check attic wall type when getting knee walls
When getting attic knee walls, this [method](https://github.com/NREL/hescore-hpxml/blob/master/hescor... | diff --git a/hescorehpxml/hpxml3.py b/hescorehpxml/hpxml3.py
index 9a227e76..2c84e53c 100644
--- a/hescorehpxml/hpxml3.py
+++ b/hescorehpxml/hpxml3.py
@@ -66,10 +66,11 @@ class HPXML3toHEScoreTranslator(HPXMLtoHEScoreTranslatorBase):
wall = self.xpath(
b,
'//h:Wall[h:Syste... |
NREL__hescore-hpxml-163 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_hvac_distribution"
],
"edited_modules": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase"
]
},
"file": "hescor... | NREL/hescore-hpxml | 37a5e1e821fd3c625e082336a1a7219697f0220e | Verify that hpxml2hescore works on workflow HPXML
The hpxml2hescore script should be able to process workflow HPXML without loosing any information. Run all the regression set HPXML files through scoring tool API submit_hpxml() method and compare the results to the regression set results and Identify any differences.
... | diff --git a/docs/source/translation/hvac_distribution.rst b/docs/source/translation/hvac_distribution.rst
index 12766e8e..3676c227 100644
--- a/docs/source/translation/hvac_distribution.rst
+++ b/docs/source/translation/hvac_distribution.rst
@@ -81,8 +81,8 @@ Duct Insulation
If the any of the ``Ducts`` elements in ... |
NREL__hescore-hpxml-169 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_building_address"
],
"edited_modules": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase"
]
},
"file": "hescore... | NREL/hescore-hpxml | 974933e77b66154cc2302c553374006d7151a15c | Handle ZIP+4 cleanly
HPXML allows for ZIP+4: https://hpxml.nrel.gov/datadictionary/3.0.0/Building/Site/Address/ZipCode
If an [HPXML file](https://github.com/NREL/hescore-hpxml/files/7171808/zip_plus_4.xml.txt) is submitted with a valid ZIP+4 entry then hpxml2hescore passes it with no changes to the JSON output:
```... | diff --git a/docs/source/translation/building_address.rst b/docs/source/translation/building_address.rst
index 33449491..8fdf52c7 100644
--- a/docs/source/translation/building_address.rst
+++ b/docs/source/translation/building_address.rst
@@ -33,8 +33,10 @@ format for HEScore.
HPXML allows for two lines of address e... |
NREL__hescore-hpxml-170 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_wall_assembly_code_and_rvalue"
],
"edited_modules": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase"
]
},
"fi... | NREL/hescore-hpxml | 7eb187cef9e8fcb145fcd333fc4477ac946b4bac | Incorrectly subtracting R-5 when using ExpandedPolystyreneSheathing element
If you have a wall like this
```xml
<Wall>
<SystemIdentifier id="wall_right"/>
<WallType>
<WoodStud>
<ExpandedPolystyreneSheathing>true</ExpandedPolystyreneSheathing>
</WoodStud>
</WallType>
<Orientation>east</O... | diff --git a/hescorehpxml/base.py b/hescorehpxml/base.py
index 6a885f3e..af079178 100644
--- a/hescorehpxml/base.py
+++ b/hescorehpxml/base.py
@@ -262,7 +262,7 @@ class HPXMLtoHEScoreTranslatorBase(object):
tobool(xpath(hpxmlwall, 'h:WallType/h:WoodStud/h:ExpandedPolystyreneSheathing/text()')):... |
NREL__hescore-hpxml-179 | [
{
"changes": {
"added_entities": [
"hescorehpxml/base.py:weighted_average"
],
"added_modules": [
"hescorehpxml/base.py:weighted_average"
],
"edited_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_generation"
],
"edited_modules... | NREL/hescore-hpxml | 72e5137bd0d00bd8c2640a7a18cfc9ab93c50906 | Read NumberOfPanels from PV in HPXML v3
**Is your feature request related to a problem? Please describe.**
The `NumberOfPanels` element was added in HPXML v3 (probably to support HEScore). Currently we're either reading from `MaxPowerOutput` or estimating the number of panels from `CollectorArea` because that input wa... | diff --git a/docs/source/translation/generation.rst b/docs/source/translation/generation.rst
index b4b2c751..039ac1a1 100644
--- a/docs/source/translation/generation.rst
+++ b/docs/source/translation/generation.rst
@@ -4,55 +4,75 @@ Generation
Solar Electric
**************
-HEScore allows for a single photovoltaic ... |
NREL__hescore-hpxml-190 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_building_about"
],
"edited_modules": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase"
]
},
"file": "hescorehp... | NREL/hescore-hpxml | b360ae3315b0b96ad90e9d53b210af9ffe73d57d | Translate AirInfiltrationMeasurement without TypeOfInfiltrationMeasurement
**Is your feature request related to a problem? Please describe.**
Currently, the translator requires `TypeOfInfiltrationMeasurement` to translate `AirInfiltrationMeasurement`. The translator does not correctly handle `AirInfiltrationMeasuremen... | diff --git a/docs/source/translation/about.rst b/docs/source/translation/about.rst
index 6eebb65c..637f8561 100644
--- a/docs/source/translation/about.rst
+++ b/docs/source/translation/about.rst
@@ -131,7 +131,7 @@ is available in HPXML.
Blower Door Test
================
-The translator first looks for a blower doo... |
NREL__hescore-hpxml-194 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_hvac_distribution"
],
"edited_modules": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase"
]
},
"file": "hescor... | NREL/hescore-hpxml | 90367bd091f74d9d82c0f1d64908f95ee4cabfb8 | Multiple ducts translation
**Describe the bug**
If there are two ducts located in the same space type, it seems that they get combined into one duct. When both ducts are either insulated or uninsulated, it's not a problem. But when one duct is insulated and the other duct is uninsulated, combining these ducts into one... | diff --git a/docs/source/translation/hvac_distribution.rst b/docs/source/translation/hvac_distribution.rst
index 22b0b4fa..7063d32b 100644
--- a/docs/source/translation/hvac_distribution.rst
+++ b/docs/source/translation/hvac_distribution.rst
@@ -73,8 +73,8 @@ following mapping.
Duct Fractions
**************
-For e... |
NREL__hescore-hpxml-197 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"hescorehpxml/hpxml2.py:HPXML2toHEScoreTranslator"
]
},
"file": "hescorehpxml/hpxml2.py"
}
] | NREL/hescore-hpxml | 644f8f8cffa6910006c0f8d69404de33127fb7a3 | Duct Location - Garage - HPXML Translator Mapping Adjustment
Requesting adjustment of Duct Location for HPXML to HES API translation (for "garage" and "garage - unconditioned") from "vented_crawl" to "unvented_crawl", as that will align us with Foundation translation (for "Garage" = "unvented_crawl") and existing Sim T... | diff --git a/docs/source/translation/hvac_distribution.rst b/docs/source/translation/hvac_distribution.rst
index 7063d32b..0b9388c7 100644
--- a/docs/source/translation/hvac_distribution.rst
+++ b/docs/source/translation/hvac_distribution.rst
@@ -31,7 +31,7 @@ following mapping.
crawlspace *not transla... |
NREL__hescore-hpxml-201 | [
{
"changes": {
"added_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.every_surface_layer_has_nominal_rvalue"
],
"added_modules": null,
"edited_entities": [
"hescorehpxml/base.py:HPXMLtoHEScoreTranslatorBase.get_building_zone_floor"
],
"edited_... | NREL/hescore-hpxml | f595831260d52a162d9f97efe2786d52383d04ca | Foundation wall insulation errors when AssemblyRValue is present
**Describe the bug**
If a foundation wall has _both_ `AssemblyRValue` and `Layer/NominalRValue` elements, it throws an error saying that a `NominalRValue` is required for all `Layer`s.
**Error Message**
```
ERROR:TranslationError:Every foundati... | diff --git a/examples/house7.xml b/examples/house7.xml
index b3301351..4de32c3e 100644
--- a/examples/house7.xml
+++ b/examples/house7.xml
@@ -76,7 +76,12 @@
<Slab>
<SystemIdentifier id="slab1"/>
<Area>900</Area>
- ... |
NREL__hescore-hpxml-98 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator._get_building_zone_roof"
],
"edited_modules": [
"hescorehpxml/__init__.py:HPXMLtoHEScoreTranslator"
]
},
"file": "hesc... | NREL/hescore-hpxml | cb48cf3a4bdcdbc0951186dd59b0e5e64c2c3d67 | Workaround for conditioned attics in HPXML 2.3
There is [no way to translate a conditioned attic](https://hescore-hpxml.readthedocs.io/en/latest/translation/zone_roof.html#id1) from HPXML 2.3. It [will be possible](https://hpxml.nrel.gov/datadictionary/3/Building/BuildingDetails/Enclosure/Attics/Attic/AtticType/Attic/C... | diff --git a/docs/source/translation/zone_roof.rst b/docs/source/translation/zone_roof.rst
index b4f1e7df..4e1ed757 100644
--- a/docs/source/translation/zone_roof.rst
+++ b/docs/source/translation/zone_roof.rst
@@ -30,16 +30,19 @@ type according to the following mapping.
unvented attic vented_attic
vent... |
NREL__infrasys-25 | [
{
"changes": {
"added_entities": [
"src/infrasys/base_quantity.py:BaseQuantity.__init_subclass__",
"src/infrasys/base_quantity.py:BaseQuantity.__class_getitem__",
"src/infrasys/base_quantity.py:BaseQuantity.__get_pydantic_core_schema__",
"src/infrasys/base_quantity.py:BaseQ... | NREL/infrasys | fe2295d1a9b561dda82fe5ed8ea5a8eb26c27ac7 | bug: pint unit definitions are not capable of performing multiplications
It looks like the `__new__` method is preventing us to multiply `ActivePower` * `Time` to obtain energy. The reason is that the `__new__` method of `BaseQuantity` is checking unit consistency even on the result multiplication. | diff --git a/src/infrasys/base_quantity.py b/src/infrasys/base_quantity.py
index 22c4fac..5a3d9b4 100644
--- a/src/infrasys/base_quantity.py
+++ b/src/infrasys/base_quantity.py
@@ -1,25 +1,71 @@
-""" This module contains base class for handling pint quantity."""
+"""This module contains base class for handling pint qua... |
NREL__rdtools-152 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rdtools/normalization.py:irradiance_rescale"
],
"edited_modules": [
"rdtools/normalization.py:irradiance_rescale"
]
},
"file": "rdtools/normalization.py"
}
] | NREL/rdtools | 3c2f9ffca03714ae68023a94dba160d4f17062f3 | normalization.irradiance_rescale is not tested
About half of the untested lines of code in the dev branch are in `normalization.irradiance_rescale`. Covering those with a new test would get coverage to ~94% which would put us in pretty good shape.
```
$ coverage run -m pytest
...
$ coverage report -m
Name ... | diff --git a/docs/degradation_and_soiling_example.ipynb b/docs/degradation_and_soiling_example.ipynb
index afaffa3..c820271 100644
--- a/docs/degradation_and_soiling_example.ipynb
+++ b/docs/degradation_and_soiling_example.ipynb
@@ -7,7 +7,7 @@
"# Degradation and soiling example with clearsky workflow\n",
"\n... |
NREL__rex-68 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rex/multi_time_resource.py:MultiTimeH5.shape",
"rex/multi_time_resource.py:MultiTimeResource.__len__",
"rex/multi_time_resource.py:MultiTimeResource.h5",
"rex/multi_time_resource... | NREL/rex | 169ff3878112f0f3b0cb890423361c8d4355eca2 | download binary file
**Why this feature is necessary:**
Is it possible to download entire dataset (e.g., `/nrel/nsrdb/v3/nsrdb_2018.h5`) as some sort of binary file?
**I have considered the following alternatives:**
I tried using the CLI, but this appears to output `csv` files.
To give more insight, what I woul... | diff --git a/README.rst b/README.rst
index 5d62262..bf460b0 100644
--- a/README.rst
+++ b/README.rst
@@ -97,9 +97,9 @@ Option 2: Clone repo (recommended for developers)
1) Create a conda env: ``conda create -n rex``
2) Run the command: ``conda activate rex``
3) cd into the repo cloned in 1.
- 5) prior... |
NRWLDev__fastapi-problem-29 | [
{
"changes": {
"added_entities": [
"src/fastapi_problem/handler.py:customise_openapi"
],
"added_modules": [
"src/fastapi_problem/handler.py:customise_openapi"
],
"edited_entities": [
"src/fastapi_problem/handler.py:add_exception_handler"
],
"edit... | NRWLDev/fastapi-problem | e090904b1e62b5fe2434c6a21a0546ce05bdd065 | Swagger doc of fastapi is not updated regarding error examples
Hello,
thanks for the nice module, it seems to work well for me in the Fastapi Swagger, but the Validation Error example remains with the old format, not the RFC9457 one :
![Image](https://github.com/user-attachments/assets/c0fedaa3-d816-4b23-b8d5-622eca7... | diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 35f6386..aad3011 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -21,7 +21,7 @@ jobs:
- name: Publish
env:
- TWINE_USERNAME: EdgyEdgemond
+ TWINE_USERNAME: __token__
TW... |
NRWLDev__fastapi-problem-32 | [
{
"changes": {
"added_entities": [
"src/fastapi_problem/handler.py:_swagger_problem_response",
"src/fastapi_problem/handler.py:generate_swagger_response"
],
"added_modules": [
"src/fastapi_problem/handler.py:_swagger_problem_response",
"src/fastapi_problem/handl... | NRWLDev/fastapi-problem | fd0bda627bbbc7c229bda001205b874ade83e3ad | Pydantic friendly?
To integrate Fastapi with OpenAPI, you can use [Additional Response with model](https://fastapi.tiangolo.com/advanced/additional-responses/#additional-response-with-model), and example as following:
```
@router.post(
"/collection",
response_model=dict[str, Any],
responses={400: {"mode... | diff --git a/docs/error.md b/docs/error.md
index aaaead7..f69ee32 100644
--- a/docs/error.md
+++ b/docs/error.md
@@ -201,19 +201,3 @@ add_exception_handler(
...
}
```
-
-### Swagger defaults
-
-When the exception handlers are registered, the default `422` response type is
-updated to match the Problem format ins... |
NSLS-II__nslsii-89 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nslsii/__init__.py:configure_bluesky_logging",
"nslsii/__init__.py:configure_ipython_logging"
],
"edited_modules": [
"nslsii/__init__.py:configure_bluesky_logging",
"... | NSLS-II/nslsii | 8c5ccb2fc7416387b46f64d5f286de0a77162cda | provide a reasonable bluesky log file path for Windows
The bluesky log path is /var/log/bluesky/bluesky.log. This is not reasonable for Windows. | diff --git a/nslsii/__init__.py b/nslsii/__init__.py
index c3a3654..de86137 100644
--- a/nslsii/__init__.py
+++ b/nslsii/__init__.py
@@ -273,7 +273,8 @@ def configure_bluesky_logging(ipython, appdirs_appname="bluesky"):
The log file path is taken from environment variable BLUESKY_LOG_FILE, if
that variable ... |
NTNU-IHB__PythonFMU-103 | [
{
"changes": {
"added_entities": [
"pythonfmu/__main__.py:cli_main"
],
"added_modules": [
"pythonfmu/__main__.py:cli_main"
],
"edited_entities": null,
"edited_modules": null
},
"file": "pythonfmu/__main__.py"
},
{
"changes": {
"added_enti... | NTNU-IHB/PythonFMU | 14089e86c9df8a643f26f923e75aa7af24edcd6a | Change CLI API
> On a different note, I should probably refactor the csv stuff into a separate cli as you did with this one. `pythonfmu-csvbuilder`, which would allow for customization and separation of concern.
This is a great idea. One comment, should we move to a cli api like `pythonfmu _command_ options` rather ... | diff --git a/README.md b/README.md
index e03750d..72e3a6f 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
# PythonFMU
-> A lightweight framework that enables the packaging of Python3.x code as co-simulation FMUs.
+> A lightweight framework that enables the packaging of Python 3 code or CSV files as co-simulat... |
NTNU-IHB__PythonFMU-158 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pythonfmu/default_experiment.py:DefaultExperiment.__init__"
],
"edited_modules": [
"pythonfmu/default_experiment.py:DefaultExperiment"
]
},
"file": "pythonfmu/default_e... | NTNU-IHB/PythonFMU | ae50251eee8d9b6acbaf1ae174f84991db8c70ad | Trouble using the `default_experiment`
I have ran into two issues trying to set the `default_experiment` using the `DefaultExperiment` class.
First, the xml parser is throwing an error regarding serializing the floats specified in the start/stop time fields, as such:
```
Traceback (most recent call last):
File ... | diff --git a/pythonfmu/default_experiment.py b/pythonfmu/default_experiment.py
index 817cf08..c0aabb2 100644
--- a/pythonfmu/default_experiment.py
+++ b/pythonfmu/default_experiment.py
@@ -1,6 +1,7 @@
class DefaultExperiment:
- def __init__(self, start_time: float = None, stop_time: float = None, tolerance: float... |
NTNU-IHB__PythonFMU-24 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pythonfmu/builder.py:ModelDescriptionFetcher.get_model_description"
],
"edited_modules": [
"pythonfmu/builder.py:ModelDescriptionFetcher"
]
},
"file": "pythonfmu/builde... | NTNU-IHB/PythonFMU | 9a49e3aa0564a2730837a5232a82ab5791a1f71d | Pass instanceName to slave | diff --git a/README.md b/README.md
index a900c61..f9dfe19 100644
--- a/README.md
+++ b/README.md
@@ -53,8 +53,8 @@ class PythonSlave(Fmi2Slave):
author = "John Doe"
description = "A simple description"
- def __init__(self):
- super().__init__()
+ def __init__(self, instance_name):
+ supe... |
NTNU-IHB__PythonFMU-30 | [
{
"changes": {
"added_entities": [
"pythonfmu/fmi2slave.py:Fmi2Slave.get_value",
"pythonfmu/fmi2slave.py:Fmi2Slave.set_value",
"pythonfmu/fmi2slave.py:Fmi2Slave.get_integer",
"pythonfmu/fmi2slave.py:Fmi2Slave.get_real",
"pythonfmu/fmi2slave.py:Fmi2Slave.get_boolean"... | NTNU-IHB/PythonFMU | c4849cd58e67cc82e24d259594a558d6b534117a | Rename internal getters and setters
Rename internal getters and setter which uses \_\_XXX__ method names to __XXX | diff --git a/pythonfmu/fmi2slave.py b/pythonfmu/fmi2slave.py
index 756ddcb..bdb89ad 100644
--- a/pythonfmu/fmi2slave.py
+++ b/pythonfmu/fmi2slave.py
@@ -1,7 +1,7 @@
import datetime
from abc import ABC, abstractmethod
from collections import namedtuple, OrderedDict
-from typing import ClassVar, Dict, List, Optional
+... |
NTNU-IHB__PythonFMU-40 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pythonfmu/builder.py:FmuBuilder.build_FMU",
"pythonfmu/builder.py:main"
],
"edited_modules": [
"pythonfmu/builder.py:FmuBuilder",
"pythonfmu/builder.py:main"
]
... | NTNU-IHB/PythonFMU | 893ec30ca017a19382f332b36cf36f497032ba14 | Add PythonFMU version to modelDescription.xml
Version should be read from _version.py | diff --git a/pythonfmu/builder.py b/pythonfmu/builder.py
index 90a6b49..feb8fcf 100644
--- a/pythonfmu/builder.py
+++ b/pythonfmu/builder.py
@@ -53,7 +53,7 @@ class ModelDescriptionFetcher:
instance = getattr(fmu_interface, class_name)("dummyInstance")
finally:
sys.path.remove(str(fil... |
NTNU-IHB__PythonFMU-41 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pythonfmu/builder.py:ModelDescriptionFetcher.get_model_description",
"pythonfmu/builder.py:FmuBuilder.build_FMU",
"pythonfmu/builder.py:main"
],
"edited_modules": [
"... | NTNU-IHB/PythonFMU | ff236d21a298e1eed62800fa80d6012bf89fefc5 | Support rollback
Since we have full control over all variable reads and writes it is very much possible to support rollback without the user even knowing it. Although I'm not in a hurry implementing it. | diff --git a/README.md b/README.md
index a3e19be..76bc3f9 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,6 @@
[](https://opensource.org/licenses/MIT)
[![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?st... |
NVIDIA__NVFlare-288 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nvflare/app_common/aggregators/dxo_aggregator.py:DXOAggregator.__init__"
],
"edited_modules": [
"nvflare/app_common/aggregators/dxo_aggregator.py:DXOAggregator"
]
},
"f... | NVIDIA/NVFlare | 9eb93673fb366cd5b29e2911ea2c2e58e575b7b3 | Build tests for new aggregation classes
- The new `InTimeAccumulateWeightedAggregator` now uses `WeightedAggregationHelper` and `DXOAggregator` which need to be unit tested.
- `InTimeAccumulateWeightedAggregator` also introduced support for DXO DataKind "COLLECTION" which needs to be tested.
- Also add tests for `exc... | diff --git a/nvflare/app_common/aggregators/dxo_aggregator.py b/nvflare/app_common/aggregators/dxo_aggregator.py
index 44dc3ce7..786c5a70 100644
--- a/nvflare/app_common/aggregators/dxo_aggregator.py
+++ b/nvflare/app_common/aggregators/dxo_aggregator.py
@@ -13,6 +13,7 @@
# limitations under the License.
import log... |
NVIDIA__hpc-container-maker-221 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/netcdf.py:netcdf.__init__",
"hpccm/building_blocks/netcdf.py:netcdf.__setup",
"hpccm/building_blocks/netcdf.py:netcdf.__setup_optional"
],
"edited_modul... | NVIDIA/hpc-container-maker | 278af2acfae3296ebcdf6b6ab796d54a1ad2f343 | NetCDF issues
Hi guys, I'm having troubles installing NetCDF with HPCCM. The issue is that the default version of netcdf-c library is now 4.7.3, and the later releases are not available via ftp anymore, see ftp://ftp.unidata.ucar.edu/pub/netcdf/
Specifying explicit version='4.7.3' works fine.
A different solution w... | diff --git a/hpccm/building_blocks/netcdf.py b/hpccm/building_blocks/netcdf.py
index c18e907..3b074e9 100644
--- a/hpccm/building_blocks/netcdf.py
+++ b/hpccm/building_blocks/netcdf.py
@@ -122,7 +122,9 @@ class netcdf(bb_base, hpccm.templates.ConfigureMake, hpccm.templates.envvars,
self.configure_opts = kwar... |
NVIDIA__hpc-container-maker-244 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/llvm.py:llvm.__init__",
"hpccm/building_blocks/llvm.py:llvm.__setup"
],
"edited_modules": [
"hpccm/building_blocks/llvm.py:llvm"
]
},
"fil... | NVIDIA/hpc-container-maker | 5d48c54e7ae8412841be766f5434be5924cbc5d6 | Add ability to include llvm tools (clang-tidy/format)
Currently, adding the llvm building block only adds the base compiler to the image.
It would be great if it was also possible to add the corresponding tools as well, to allow the generated image to be used for source code linting. | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index 79a20c8..4d8b12d 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -2007,6 +2007,9 @@ packages. For Ubuntu, setting this flag to True enables the
distributions, setting this flag to True enables the Software
Collections (SCL) re... |
NVIDIA__hpc-container-maker-286 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/boost.py:boost.__init__",
"hpccm/building_blocks/boost.py:boost.__setup"
],
"edited_modules": [
"hpccm/building_blocks/boost.py:boost"
]
},
... | NVIDIA/hpc-container-maker | 5d7c29c4a16c59dbce7a21a51fed5d5e18e73763 | Building block Boost: add possibility to pass args to ./b2
I want to build my boost with C++ 14, so I need to pass the flag `cxxflags="-std=c++14"` to the `./b2` build process: `./b2 cxxflags="-std=c++14" -j$(nproc) -q install`. There is currently no way to pass arguments to `./b2`: https://github.com/NVIDIA/hpc-contai... | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index 8178a5a..c13ed81 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -209,6 +209,9 @@ The `boost` building block downloads and installs the
__Parameters__
+- __b2_opts__: List of options to pass to `b2`. The default is an empty... |
NVIDIA__hpc-container-maker-311 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/llvm.py:llvm.__init__",
"hpccm/building_blocks/llvm.py:llvm.__setup"
],
"edited_modules": [
"hpccm/building_blocks/llvm.py:llvm"
]
},
"fil... | NVIDIA/hpc-container-maker | f065b74de7fd09bebdde1be55b1e6c53dc629c68 | LLVM package: make OpenMP installation optinal
For our CI we install different versions of Clang/LLVM in parallel in a container. Unfortunately there is a dependency between `lipomp5-7` and `lipomp5-8`:
```bash
Step 20/28 : RUN apt-get update -y && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-... | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index e50a59c..8a15602 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -2163,6 +2163,9 @@ include the LLVM compilers when necessary. The default is True.
- __extra_tools__: Boolean flag to specify whether to also install
`clang-forma... |
NVIDIA__hpc-container-maker-312 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/conda.py:conda.__init__"
],
"edited_modules": [
"hpccm/building_blocks/conda.py:conda"
]
},
"file": "hpccm/building_blocks/conda.py"
},
{
... | NVIDIA/hpc-container-maker | f065b74de7fd09bebdde1be55b1e6c53dc629c68 | conda: allow changing python subversion
Hi,
our workflow needs for the moment a python 3.7 version of conda (nothing I can change on our side). Until last version, I was able to retrieve it by giving 'py37_4.8.3' as version argument, but since this version, the version argument is strictly checked in its format, and p... | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index e50a59c..00a7abf 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -595,6 +595,10 @@ empty list.
- __python2__: Boolean flag to specify that the Python 2 version of
Anaconda should be installed. The default is False.
+- __pyth... |
NVIDIA__hpc-container-maker-346 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/pnetcdf.py:pnetcdf.__init__"
],
"edited_modules": [
"hpccm/building_blocks/pnetcdf.py:pnetcdf"
]
},
"file": "hpccm/building_blocks/pnetcdf.py"
}... | NVIDIA/hpc-container-maker | dea6f6915b1f4131485885b40ca780d348900191 | Netcdf with pnetCDF support
What is the correct syntax to install netcdf with pnetcdf support using hpc-container-maker?
Assuming that pnetcdf is installed in /usr/local/pnetcdf, it does not seem sufficient to add
enable_pnetcdf='/usr/local/pnetcdf'
Whatever I tried nc-config --all always shows --has-pnetcdf ... | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index 3161373..0443ffa 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -3931,8 +3931,8 @@ configuring. For instance, `enable_foo=True` maps to
Underscores in the parameter name are converted to dashes.
- __environment__: Boolean f... |
NVIDIA__hpc-container-maker-368 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/nsight_compute.py:nsight_compute.__instructions_repository"
],
"edited_modules": [
"hpccm/building_blocks/nsight_compute.py:nsight_compute"
]
},
"... | NVIDIA/hpc-container-maker | 887196021837ddf8c6b88031d3134ede54bea876 | yum errors with same repo twice
When installing both nsys and nsight-compute in a centos container, it issues the following command:
```
RUN rpm --import https://developer.download.nvidia.com/devtools/repos/rhel7/x86_64/nvidia.pub && \
yum install -y yum-utils && \
yum-config-manager --add-repo https://d... | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index 8c492de..aac8f1c 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -3623,6 +3623,11 @@ packages are extracted they are deleted. This parameter is ignored
if `download` is False. If empty, then the downloaded packages are
not extr... |
NVIDIA__hpc-container-maker-378 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/boost.py:boost.__init__"
],
"edited_modules": [
"hpccm/building_blocks/boost.py:boost"
]
},
"file": "hpccm/building_blocks/boost.py"
}
] | NVIDIA/hpc-container-maker | db9fd15221e0b2c9794e0a04c4214ac40a39e4a7 | Boost URL outdated?
I try to build boost with the building block but I get an error code 8.
I found out, that wget fails:
```
wget -nc --no-check-certificate -P /tmp https://dl.bintray.com/boostorg/release/1.74.0/source/boost_1_74_0.tar.bz2
--2021-06-14 11:43:32-- https://dl.bintray.com/boostorg/release/1.74.0/sou... | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index 3a9d023..12e9734 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -245,7 +245,7 @@ repository. For versions of Boost older than 1.63.0, the
SourceForge repository should be used. The default is False.
- __version__: The vers... |
NVIDIA__hpc-container-maker-420 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/nccl.py:nccl.__init__",
"hpccm/building_blocks/nccl.py:nccl.runtime"
],
"edited_modules": [
"hpccm/building_blocks/nccl.py:nccl"
]
},
"fil... | NVIDIA/hpc-container-maker | 4f4bd953c2c90ba68b9fa6dc04cbb006c7911542 | nvhpc building block with C++20 library support
According to the [nvhpc docs](https://docs.nvidia.com/hpc-sdk/hpc-sdk-release-notes/index.html#platform-requirements), one needs gcc/glibc>=10.1 for C++20 library support in the new nvhpc 22.3.
Neither
```
Stage0 += baseimage(image='nvcr.io/nvidia/nvhpc:22.3-devel-c... | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index a12b606..891b241 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -2863,7 +2863,7 @@ source. The default value is False.
use the latest commit on the default branch for the repository.
- __cuda__: Flag to specify the CUDA ver... |
NVIDIA__hpc-container-maker-427 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/slurm_pmi2.py:slurm_pmi2.__init__"
],
"edited_modules": [
"hpccm/building_blocks/slurm_pmi2.py:slurm_pmi2"
]
},
"file": "hpccm/building_blocks/slu... | NVIDIA/hpc-container-maker | 8a2d433cfb5265fb10e85ef0925f74f82da0242b | Need to update default version of Slurm
The default Slurm v20.11.7 has been removed from their [website](https://download.schedmd.com/slurm/) in favor of v20.11.9 | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index 744d218..6abf3a7 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -4371,7 +4371,7 @@ non-default compilers or other toolchain options are needed. The
default value is empty.
- __version__: The version of SLURM source to downl... |
NVIDIA__hpc-container-maker-445 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/cmake.py:cmake.__init__",
"hpccm/building_blocks/cmake.py:cmake.__setup",
"hpccm/building_blocks/cmake.py:cmake.__binary"
],
"edited_modules": [
... | NVIDIA/hpc-container-maker | cfd2dd88147a83e9ce3216981438896bdaa34c13 | Allow use of CMake binary package for aarch64
Currently you are forced to compile CMake from source for any architecture other than x86_64. I'm having some issues getting cmake to compile for one of my recipes which I could avoid by using the pre-compiled binaries. aarch64 binaries have been available since 3.20.0 rele... | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index d89cd70..db58f55 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -545,12 +545,12 @@ The default values are `make` and `wget`.
- __source__: Boolean flag to specify whether to build CMake from
source. If True, includes the `lib... |
NVIDIA__hpc-container-maker-456 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/conda.py:conda.__init__",
"hpccm/building_blocks/conda.py:conda.__setup"
],
"edited_modules": [
"hpccm/building_blocks/conda.py:conda"
]
},
... | NVIDIA/hpc-container-maker | 44b84723f910c7a809d49992ae8222e6362466bc | Newer Miniconda versions aren't accessible via the conda module
After 4.12.0, there's an additional dashed version number, see [the repo page](https://repo.anaconda.com/miniconda/). Putting in
```python
stage += conda(..., version='22.11.1-1')
```
to try to target this directly leads to a hpccm error, since it... | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index 6c518a4..bb50646 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -598,10 +598,10 @@ Anaconda should be installed. The default is False.
- __python_subversion__: The Python version to install. This value is
ignored if the Co... |
NVIDIA__hpc-container-maker-472 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/llvm.py:llvm.__init__"
],
"edited_modules": [
"hpccm/building_blocks/llvm.py:llvm"
]
},
"file": "hpccm/building_blocks/llvm.py"
}
] | NVIDIA/hpc-container-maker | 4f5ef11bab5c4803e170ba8ab6c6a93855e5a9f4 | LLVM trunk version out-of-date
Since Jul 26th 2023, LLVM trunk is version 18.
`self.__trunk_version` in `hpccm/building_blocks/llvm.py` should be bumped to allow installing Clang 17 or 18. | diff --git a/hpccm/building_blocks/llvm.py b/hpccm/building_blocks/llvm.py
index f0d68fc..5897a99 100644
--- a/hpccm/building_blocks/llvm.py
+++ b/hpccm/building_blocks/llvm.py
@@ -104,7 +104,7 @@ class llvm(bb_base, hpccm.templates.envvars):
self.__runtime_rpms = [] # Filled in below
self.__toolset... |
NVIDIA__hpc-container-maker-486 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/config.py:set_linux_distro"
],
"edited_modules": [
"hpccm/config.py:set_linux_distro"
]
},
"file": "hpccm/config.py"
},
{
"changes": {
"added_entiti... | NVIDIA/hpc-container-maker | ce582fa83c9dc96c74e0343fdc25c69c9ea277e8 | Add support for Ubuntu 24.04
Please add support for the recently released new LTS flavor of Ubuntu, ie. 24.04. hpccm is used by the GROMACS development team to build their CI images and we're keen to start testing on that version soon because it will become our minimum supported version. If there's things we can do to ... | diff --git a/.github/workflows/python3.yml b/.github/workflows/python3.yml
index 6e756ef..bfc0559 100644
--- a/.github/workflows/python3.yml
+++ b/.github/workflows/python3.yml
@@ -8,16 +8,7 @@ jobs:
strategy:
matrix:
os: [ubuntu-latest, macos-latest, windows-latest]
- python-version: ['3.7'... |
NVIDIA__hpc-container-maker-498 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/apt_get.py:apt_get.__init__"
],
"edited_modules": [
"hpccm/building_blocks/apt_get.py:apt_get"
]
},
"file": "hpccm/building_blocks/apt_get.py"
}... | NVIDIA/hpc-container-maker | e7129547a7c708ecfafcdeceed662b40cf42975b | Replace use of deprecated apt-key
The use of apt-key has been deprecated for two years, so it would be good to update. Debian's official advice is [here](https://wiki.debian.org/DebianRepository/UseThirdParty).
See for example https://askubuntu.com/questions/1328806/how-to-solve-apt-key-deprecated for an approach that... | diff --git a/docs/building_blocks.md b/docs/building_blocks.md
index d60819e..e2d4a37 100644
--- a/docs/building_blocks.md
+++ b/docs/building_blocks.md
@@ -3335,7 +3335,7 @@ they are not available. For Ubuntu 16.04 and ppc64le processors,
the `libibcm1` and `libibcm-dev` packages are not installed
because they are ... |
NVIDIA__hpc-container-maker-511 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpccm/building_blocks/gdrcopy.py:gdrcopy.__init__"
],
"edited_modules": [
"hpccm/building_blocks/gdrcopy.py:gdrcopy"
]
},
"file": "hpccm/building_blocks/gdrcopy.py"
}... | NVIDIA/hpc-container-maker | 65e02c49d8912c77fbd638dfeae77d1af5f50d2a | Update default hpcx to v2.22.1
A few things have changed since in the URL format:
```
hpcx(version='2.22.1', oslabel='ubuntu24.04', ofedlabel='gcc-doca_ofed')
``` | diff --git a/.github/workflows/docker_build.yml b/.github/workflows/docker_build.yml
index b5fab08..bf34a84 100644
--- a/.github/workflows/docker_build.yml
+++ b/.github/workflows/docker_build.yml
@@ -79,12 +79,12 @@ jobs:
- uses: actions/checkout@v2
- name: Set up Python
- uses: actions/setup-python@v... |
NVIDIA__nv-ingest-400 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/nv_ingest/stages/multiprocessing_stage.py:MultiProcessingBaseStage._build_single"
],
"edited_modules": [
"src/nv_ingest/stages/multiprocessing_stage.py:MultiProcessingBaseStage"
... | NVIDIA/nv-ingest | 9ac378de300dc39f5365bb72d5560e809ad7de2d | [DOC]: Skaffold doc page non existent
### How would you describe the priority of this documentation request
None
### Please provide a link or source to the relevant docs
https://github.com/NVIDIA/nv-ingest/tree/main/skaffold
### Describe the problems in the documentation
I got this 404 error:
The main branch of... | diff --git a/client/client_examples/examples/python_client_usage.ipynb b/client/client_examples/examples/python_client_usage.ipynb
index 867c5e2..0675089 100644
--- a/client/client_examples/examples/python_client_usage.ipynb
+++ b/client/client_examples/examples/python_client_usage.ipynb
@@ -9,11 +9,9 @@
"\n",
... |
NVIDIA__nv-ingest-71 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/nv_ingest/extraction_workflows/pdf/doughnut_utils.py:crop_image"
],
"edited_modules": [
"src/nv_ingest/extraction_workflows/pdf/doughnut_utils.py:crop_image"
]
},
"... | NVIDIA/nv-ingest | 064add5cd5b00d5dcb4f52698ee32e064b2b5fa7 | [BUG]: Error extracting image: Failed to convert NumPy array to image: Cannot handle this data type: (1, 1, 1), |u1
### Version
24.08
### Which installation method(s) does this occur on?
_No response_
### Describe the bug.
The log shows error:
```
ERROR - Error extracting image: Failed to convert NumPy array to im... | diff --git a/src/nv_ingest/extraction_workflows/pdf/doughnut_utils.py b/src/nv_ingest/extraction_workflows/pdf/doughnut_utils.py
index 8ba3d2c..d1f7ac2 100644
--- a/src/nv_ingest/extraction_workflows/pdf/doughnut_utils.py
+++ b/src/nv_ingest/extraction_workflows/pdf/doughnut_utils.py
@@ -3,7 +3,6 @@
# SPDX-License-Ide... |
Netflix-Skunkworks__policyuniverse-147 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "policyuniverse/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"policyuni... | Netflix-Skunkworks/policyuniverse | 96336a5c51f0daa5cc832050b5668cd9a326e6cc | Unhandled exception ValueError when Token not found in statement._userid_internet_accessible()
https://github.com/Netflix-Skunkworks/policyuniverse/blob/96336a5c51f0daa5cc832050b5668cd9a326e6cc/policyuniverse/statement.py#L325
_userid_internet_accessible uses string.index() which throws an ValueError if the token is... | diff --git a/policyuniverse/__init__.py b/policyuniverse/__init__.py
index f442d13..e63a96b 100644
--- a/policyuniverse/__init__.py
+++ b/policyuniverse/__init__.py
@@ -13,7 +13,6 @@ from policyuniverse.action import build_service_actions_from_service_data
# Logging
-logging.basicConfig(level=logging.INFO)
logger... |
Netflix-Skunkworks__policyuniverse-99 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"policyuniverse/statement.py:Statement._principals"
],
"edited_modules": [
"policyuniverse/statement.py:Statement"
]
},
"file": "policyuniverse/statement.py"
}
] | Netflix-Skunkworks/policyuniverse | 37eccbc5be0552c85d58fcf2b6c5425ff7fe0984 | Perform Principal extraction with any Mapping type
Previous work in #94 did not include a expansion to all `Mapping` types for `Principal` extraction in `Statement`:
https://github.com/Netflix-Skunkworks/policyuniverse/blob/37eccbc5be0552c85d58fcf2b6c5425ff7fe0984/policyuniverse/statement.py#L118
The following ... | diff --git a/policyuniverse/statement.py b/policyuniverse/statement.py
index a571b1d..4ad4d4d 100644
--- a/policyuniverse/statement.py
+++ b/policyuniverse/statement.py
@@ -28,6 +28,11 @@ from policyuniverse.common import ensure_array, is_array
import re
from collections import namedtuple
+try:
+ from collection... |
Netuitive__netuitive-client-python-18 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"netuitive/check.py:Check.__init__"
],
"edited_modules": [
"netuitive/check.py:Check"
]
},
"file": "netuitive/check.py"
},
{
"changes": {
"added_entities":... | Netuitive/netuitive-client-python | 53087a9f6e6bc2e805ae3793f5c4417927f6f3f7 | Define the check ttl as ttl
This client should use the agreed upon "ttl" for the check ttl, instead of "duration". | diff --git a/netuitive/check.py b/netuitive/check.py
index b851282..2dd7858 100644
--- a/netuitive/check.py
+++ b/netuitive/check.py
@@ -7,15 +7,15 @@ class Check(object):
:type name: string
:param elementId: Associated Element ID
:type elementId: string
- :param interval: Check interv... |
Netuitive__netuitive-statsd-14 | [
{
"changes": {
"added_entities": [
"libs/config.py:get_hostname"
],
"added_modules": [
"libs/config.py:get_hostname"
],
"edited_entities": [
"libs/config.py:config"
],
"edited_modules": [
"libs/config.py:config"
]
},
"file":... | Netuitive/netuitive-statsd | 0b8c90d3a351de7f0b6d6ec5915af31263702590 | Support More Flexible Hostname Methods
Ideally this will match the Metricly Diamond project:
https://github.com/Netuitive/netuitive-diamond/blob/f48a0bc7de6038164e0919e2d3d0fd524c83e1d9/conf/diamond.conf.example#L146-L169 | diff --git a/libs/config.py b/libs/config.py
index c43a9a0..5d68cb9 100644
--- a/libs/config.py
+++ b/libs/config.py
@@ -6,30 +6,18 @@ import socket
import os
import configobj
import sys
+import subprocess
logger = logging.getLogger(__name__)
def config(args=None):
- # try to find the hostname
- host... |
NeuralEnsemble__elephant-282 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"elephant/spade.py:spade",
"elephant/spade.py:_build_context",
"elephant/spade.py:_fpgrowth",
"elephant/spade.py:_fpgrowth_filter",
"elephant/spade.py:_fast_fca",
... | NeuralEnsemble/elephant | 8200eefd7200d2c32b5f23aeb5409af5ea0c9758 | [Feautre] build with py 3.8
Hi team ---
Does not work with py 3.8
Cheers, | diff --git a/.gitignore b/.gitignore
index acceba1..987bbec 100644
--- a/.gitignore
+++ b/.gitignore
@@ -66,7 +66,7 @@ cover
######################
.directory
.gdb_history
-.DS_Store?
+.DS_Store
ehthumbs.db
Icon?
Thumbs.db
@@ -75,3 +75,5 @@ Thumbs.db
###################################
# ignored folder for fast... |
NeuralEnsemble__elephant-333 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "elephant/__init__.py"
},
{
"changes": {
"added_entities": [
"elephant/asset.py:_num_iterations",
"elephant/asset.py:_combination... | NeuralEnsemble/elephant | dea2ec4de6dffd2f6a19b7bb61e0c5ae1f4d5b20 | [Bug] cannot run ASSET on binder
In https://github.com/NeuralEnsemble/elephant/pull/327 Alex found that binder `postBuild` should be updated in order to run asset tutorial.
Also, scikit-learn should be added in the requirements-tutorials.txt | diff --git a/elephant/__init__.py b/elephant/__init__.py
index f1d8758..e500976 100644
--- a/elephant/__init__.py
+++ b/elephant/__init__.py
@@ -31,7 +31,6 @@ from . import (statistics,
# parallel: avoid warns when elephant is imported
try:
- from . import pandas_bridge
from . import asset
from . imp... |
NeuralEnsemble__elephant-390 | [
{
"changes": {
"added_entities": [
"elephant/conversion.py:BinnedSpikeTrain.__eq__",
"elephant/conversion.py:BinnedSpikeTrain.copy",
"elephant/conversion.py:BinnedSpikeTrain.__iter_sparse_matrix",
"elephant/conversion.py:BinnedSpikeTrain.__getitem__",
"elephant/conv... | NeuralEnsemble/elephant | 1ef33db135674ffcb69982993a13b8506efd9575 | [Feature] Add `to_spiketrain_list()` to `BinnedSpiketrain` object
**Feature**
Currently, the conversion module can convert `Spiketrain` to a matrix, but the reverse conversion is not possible. Needed would be a member function `to_spiketrain_list()`.
**Motivation**
See #309 | diff --git a/doc/_templates/autosummary/class.rst b/doc/_templates/autosummary/class.rst
index 1d66b14..06dd133 100644
--- a/doc/_templates/autosummary/class.rst
+++ b/doc/_templates/autosummary/class.rst
@@ -5,7 +5,7 @@
.. autoclass:: {{ objname }}
:members:
:inherited-members:
- :special-members: __call__
... |
NeuralEnsemble__elephant-614 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "doc/conf.py"
},
{
"changes": {
"added_entities": [
"elephant/spike_train_generation.py:_spike_extraction_from_single_channel",
"... | NeuralEnsemble/elephant | bdd98eefe99706621f5c840ce28134dac0e794af | [Bug] peak_detection without analogsignals.times
**Describe the bug**
Hello. After acquired data with an Intan, I would like to use Elephant for the first treatment of these.
In this way, I would like to fill the spiketrain object of neo using the spike_extraction method of elephant, which is empty after the acqui... | diff --git a/doc/conf.py b/doc/conf.py
index 67b766a..907952f 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -351,7 +351,7 @@ epub_copyright = copyright
intersphinx_mapping = {
'viziphant': ('https://viziphant.readthedocs.io/en/stable/', None),
'numpy': ('https://numpy.org/doc/stable', None),
- 'neo': ('ht... |
NeuralEnsemble__libNeuroML-154 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "neuroml/__version__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modu... | NeuralEnsemble/libNeuroML | 2a13bcd034b893a7b5e8609ae05c2bbfc7952d20 | cell util improvements
- call `setup_nml_cell` for all related helper functions: when we're adding a conductance density, for example, if morphology does not exist, create it
- add option to segment etc. addition functions to check membership
- add option to `setup_nml_cell` to disable setting up of individual defaul... | diff --git a/neuroml/__version__.py b/neuroml/__version__.py
index ad8e55e..79ab902 100644
--- a/neuroml/__version__.py
+++ b/neuroml/__version__.py
@@ -7,7 +7,7 @@ Copyright 2022 NeuroML contributors
"""
-__version__: str = "0.4.1"
+__version__: str = "0.4.2"
__version_info__: tuple = tuple(int(i) for i in __ver... |
NeuralEnsemble__python-neo-1297 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neo/io/__init__.py:list_candidate_ios"
],
"edited_modules": [
"neo/io/__init__.py:list_candidate_ios"
]
},
"file": "neo/io/__init__.py"
}
] | NeuralEnsemble/python-neo | f608309c5ce031ecd905349c140b07a3dafb057d | neo.get_io fails on file yet to be written
**Describe the bug**
Calling neo.get_io no longer works with the name of a file yet to be written
which means it can no longer be uses before a
io.write(... call
**To Reproduce**
import neo
neo.get_io("tobewritten.pkl")
**Expected behaviour**
return an io
**E... | diff --git a/neo/io/__init__.py b/neo/io/__init__.py
index 22b6df66..4aa31692 100644
--- a/neo/io/__init__.py
+++ b/neo/io/__init__.py
@@ -451,8 +451,23 @@ def list_candidate_ios(file_or_folder, ignore_patterns=['*.ini', 'README.txt', '
# if only file prefix was provided, e.g /mydatafolder/session1-
# to sele... |
NeuralEnsemble__python-neo-1554 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neo/core/analogsignal.py:_new_AnalogSignalArray",
"neo/core/analogsignal.py:AnalogSignal.__new__",
"neo/core/analogsignal.py:AnalogSignal.__init__",
"neo/core/analogsignal.py:Ana... | NeuralEnsemble/python-neo | de6b3b5be4e565ba8884aebd4be17a02f03c2079 | Fix tests for quantities 0.16.0
core-tests failing with new version of quantities. We will need to fix.
| diff --git a/neo/core/analogsignal.py b/neo/core/analogsignal.py
index 79f53440..12edb552 100644
--- a/neo/core/analogsignal.py
+++ b/neo/core/analogsignal.py
@@ -52,7 +52,7 @@ def _new_AnalogSignalArray(
signal,
units=None,
dtype=None,
- copy=True,
+ copy=None,
t_start=0 * pq.s,
sampling... |
NeuralEnsemble__python-neo-341 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neo/core/analogsignal.py:AnalogSignal.__getitem__"
],
"edited_modules": [
"neo/core/analogsignal.py:AnalogSignal"
]
},
"file": "neo/core/analogsignal.py"
},
{
"... | NeuralEnsemble/python-neo | 9bd5f01a3b3dc311a89c0be3b0008e516fd3a098 | Slicing `AnalogSignal` with numpy.int64 gives an incorrect result
Example:
```python
>>> signal[:, 0].shape
(1000, 1)
>>> signal[:, np.int64(0)].shape
(1000,)
```
| diff --git a/neo/core/analogsignal.py b/neo/core/analogsignal.py
index 8e129a52..aa971c80 100644
--- a/neo/core/analogsignal.py
+++ b/neo/core/analogsignal.py
@@ -285,11 +285,11 @@ class AnalogSignal(BaseNeo, pq.Quantity):
Get the item or slice :attr:`i`.
'''
obj = super(AnalogSignal, self)._... |
NeuralEnsemble__python-neo-382 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neo/core/analogsignal.py:AnalogSignal.rescale"
],
"edited_modules": [
"neo/core/analogsignal.py:AnalogSignal"
]
},
"file": "neo/core/analogsignal.py"
},
{
"chan... | NeuralEnsemble/python-neo | fec5dfca4edd6a2a04cc0b8e274d01009a1c0362 | AnalogSignal.rescale() does not preserve parent objects
The same is true for IrregularlySampledSignal and SpikeTrain. | diff --git a/neo/core/analogsignal.py b/neo/core/analogsignal.py
index aa971c80..fec332ea 100644
--- a/neo/core/analogsignal.py
+++ b/neo/core/analogsignal.py
@@ -251,7 +251,7 @@ class AnalogSignal(BaseNeo, pq.Quantity):
self.file_origin = getattr(obj, 'file_origin', None)
self.description = getattr(o... |
NeuralEnsemble__python-neo-446 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neo/core/analogsignal.py:AnalogSignal.__deepcopy__"
],
"edited_modules": [
"neo/core/analogsignal.py:AnalogSignal"
]
},
"file": "neo/core/analogsignal.py"
},
{
... | NeuralEnsemble/python-neo | ab720e75e2c947385a2eb977ee2002770d16dde2 | Implement deepcopy for all classes
#399 implements `__deepcopy__` for `AnalogSignal` and so fixes #220.
This should also be done for the other Neo classes. | diff --git a/neo/core/analogsignal.py b/neo/core/analogsignal.py
index a202fffe..86dcfcae 100644
--- a/neo/core/analogsignal.py
+++ b/neo/core/analogsignal.py
@@ -250,7 +250,7 @@ class AnalogSignal(BaseSignal):
for k, v in self.__dict__.items():
try:
setattr(new_signal, k, deepcop... |
NeuralEnsemble__python-neo-454 | [
{
"changes": {
"added_entities": [
"neo/core/epoch.py:Epoch.__getitem__"
],
"added_modules": null,
"edited_entities": [
"neo/core/epoch.py:_new_epoch",
"neo/core/epoch.py:Epoch.time_slice"
],
"edited_modules": [
"neo/core/epoch.py:_new_epoch",
... | NeuralEnsemble/python-neo | 6b6c7ef2d148de5431cbd8f254430251c3d34dde | Slicing epochs does only slice times not durations
When slicing an epoch only the times array is sliced and the durations array is not modified. This results in incompatible number of time stamps and durations. | diff --git a/neo/core/epoch.py b/neo/core/epoch.py
index a5cd367c..359947f9 100644
--- a/neo/core/epoch.py
+++ b/neo/core/epoch.py
@@ -24,10 +24,10 @@ def _new_epoch(cls, times=None, durations=None, labels=None, units=None,
name=None, description=None, file_origin=None, annotations=None, segment=None):
... |
NeuralEnsemble__python-neo-475 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"neo/io/spike2io.py:Spike2IO"
]
},
"file": "neo/io/spike2io.py"
},
{
"changes": {
"added_entities": [
"neo/rawio/spike2rawio.py:Spike2Raw... | NeuralEnsemble/python-neo | c66dbfe3e625607e13a74dcdc409c255d89dc608 | Hitting Spike2IO asserion on sampling_rate
I'm trying to import a spike2 smr file using `Spike2IO(filename=filename)` but am hitting an assertion:
```
Traceback (most recent call last):
File "G:/Python/libs/Playground/src/playground2.py", line 3, in <module>
reader = Spike2IO(filename=r'G:\Python\1-9-2018-m... | diff --git a/neo/io/spike2io.py b/neo/io/spike2io.py
index 405f98f0..d21f3fc4 100644
--- a/neo/io/spike2io.py
+++ b/neo/io/spike2io.py
@@ -5,7 +5,7 @@ from neo.rawio.spike2rawio import Spike2RawIO
class Spike2IO(Spike2RawIO, BaseFromRaw):
- _prefered_signal_group_mode = 'split-all'
+ _prefered_signal_group_m... |
NeuralEnsemble__python-neo-488 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neo/core/spiketrain.py:_check_time_in_range",
"neo/core/spiketrain.py:SpikeTrain.__new__"
],
"edited_modules": [
"neo/core/spiketrain.py:_check_time_in_range",
"neo/c... | NeuralEnsemble/python-neo | 643f889779ded1333bd433e004fe1f05b5c33026 | t_start > t_stop issue in SpikeTrain
I am transferring the issue from https://github.com/NeuralEnsemble/elephant/issues/81 here. Is following intended?
```python
import neo
import quantities as pq
print(neo.SpikeTrain([]*pq.s, t_start=5*pq.s, t_stop=4*pq.s))
>>> [] s
```
I am on version `0.5.2`.
Shouldn'... | diff --git a/neo/core/spiketrain.py b/neo/core/spiketrain.py
index 5d285ae0..7256511b 100644
--- a/neo/core/spiketrain.py
+++ b/neo/core/spiketrain.py
@@ -54,6 +54,9 @@ def _check_time_in_range(value, t_start, t_stop, view=False):
certain that the dtype and units are the same
'''
+ if t_start > t_stop:
+... |
NeuralEnsemble__python-neo-664 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neo/core/container.py:Container.filter"
],
"edited_modules": [
"neo/core/container.py:Container"
]
},
"file": "neo/core/container.py"
}
] | NeuralEnsemble/python-neo | 26a747c67597355b55204ea76ddf739f9c0cf141 | segments[0].filter recursion if String key not found.
example:script (taken from doc except for last line)
```python
from neo.core import (Block, Segment, ChannelIndex, AnalogSignal)
from quantities import nA, kHz
import numpy as np
blk = Block()
for ind in range(3):
seg = Segment(name='segment %d' % ind... | diff --git a/neo/core/container.py b/neo/core/container.py
index 5e7084cf..f990f0b4 100644
--- a/neo/core/container.py
+++ b/neo/core/container.py
@@ -8,6 +8,10 @@ object inherit from. It provides shared methods for all container types.
# needed for python 3 compatibility
from __future__ import absolute_import, di... |
NeuralEnsemble__python-neo-764 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neo/core/spiketrain.py:check_has_dimensions_time"
],
"edited_modules": [
"neo/core/spiketrain.py:check_has_dimensions_time"
]
},
"file": "neo/core/spiketrain.py"
}
] | NeuralEnsemble/python-neo | 03bef5fe3f654df24e8f66ee3d07fc6aabef6479 | Regression in the `check_has_dimensions_time` method of the SpikeTrain class for Compound Units
Regression in the `check_has_dimensions_time` method of the SpikeTrain class.
Calling
`neo.SpikeTrain([1,2,3]*pq.CompoundUnit("1/10*s"), t_start=0*pq.ms, t_stop=10000*pq.s)-5*pq.CompoundUnit("1/100*s")`
used to issue
`... | diff --git a/neo/core/spiketrain.py b/neo/core/spiketrain.py
index d863abb9..20a87594 100644
--- a/neo/core/spiketrain.py
+++ b/neo/core/spiketrain.py
@@ -38,10 +38,13 @@ def check_has_dimensions_time(*values):
'''
errmsgs = []
for value in values:
- dim = value.dimensionality
- if (len(dim... |
NeuralEnsemble__python-neo-815 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neo/io/neuralynxio.py:NeuralynxIO.__init__"
],
"edited_modules": [
"neo/io/neuralynxio.py:NeuralynxIO"
]
},
"file": "neo/io/neuralynxio.py"
},
{
"changes": {
... | NeuralEnsemble/python-neo | ebc3c51e73310b8f7921a4c4ac4f992e202f3a4e | Neuralynx loader output for a given file differs depending on what other files are present in folder
When loading a Neuralynx data file, the timestamps assigned by neo depend on what other files are present in the same folder.
For instance, loading a .ntt file with no other files present gives a first timestamp of ... | diff --git a/neo/io/neuralynxio.py b/neo/io/neuralynxio.py
index 463ede1e..8469c6a4 100644
--- a/neo/io/neuralynxio.py
+++ b/neo/io/neuralynxio.py
@@ -26,7 +26,26 @@ class NeuralynxIO(NeuralynxRawIO, BaseFromRaw):
_prefered_signal_group_mode = 'group-by-same-units'
mode = 'dir'
- def __init__(self, dirna... |
NeuralEnsemble__python-neo-824 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"neo/rawio/spike2rawio.py:Spike2RawIO._parse_header"
],
"edited_modules": [
"neo/rawio/spike2rawio.py:Spike2RawIO"
]
},
"file": "neo/rawio/spike2rawio.py"
}
] | NeuralEnsemble/python-neo | 3196aa84d0f4a092575fcf8ac0d519bd34404fc5 | SpikeIO does not load .smr
Dear Neo developers,
I can not load some of my .smr files with Spike2IO. I work with **python 3.5.2** and tried Neo versions **0.8.0** and **0.9.0.dev**. The error message is: “_IndexError: index 0 is out of bounds for axis 0 with size 0_”.
Note that I got the same error for some other .sm... | diff --git a/neo/rawio/spike2rawio.py b/neo/rawio/spike2rawio.py
index 2e315a49..6ff64939 100644
--- a/neo/rawio/spike2rawio.py
+++ b/neo/rawio/spike2rawio.py
@@ -52,6 +52,10 @@ class Spike2RawIO(BaseRawIO):
info['dtime_base'] = 1e-6
info['datetime_detail'] = 0
info['d... |
NeuroTechX__moabb-278 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"moabb/analysis/results.py:get_string_rep"
],
"edited_modules": [
"moabb/analysis/results.py:get_string_rep"
]
},
"file": "moabb/analysis/results.py"
}
] | NeuroTechX/moabb | 5b384b2428ebeab2521977cbc8fde384558aa848 | Results not saved due to issues with get_digest
The `get_digest` function yields duplicate hash values even if two classifier objects have different internal state via different lambda functions. https://github.com/NeuroTechX/moabb/blob/fd0ffe66572a273a6a2d19174a21cd9c4e4e94c9/moabb/analysis/results.py#L111
Short exam... | diff --git a/moabb/analysis/results.py b/moabb/analysis/results.py
index 03f378dc..eb117865 100644
--- a/moabb/analysis/results.py
+++ b/moabb/analysis/results.py
@@ -2,6 +2,7 @@ import hashlib
import os
import os.path as osp
import re
+import warnings
from datetime import datetime
import h5py
@@ -17,6 +18,15 @@... |
NeuroTechX__moabb-447 | [
{
"changes": {
"added_entities": [
"moabb/analysis/results.py:get_pipeline_digest"
],
"added_modules": [
"moabb/analysis/results.py:get_pipeline_digest"
],
"edited_entities": [
"moabb/analysis/results.py:Results.add",
"moabb/analysis/results.py:Resul... | NeuroTechX/moabb | 221cfc06f8465c7f3c467d7f3c7704d9675428c7 | Compute digest from the full processing+classification pipeline
With PR #408 and commit 8c88349426c0202aa8f1a54d90ef43f3159c53b2, the data processing steps (filtering, resampling, epoching...) are done by a sklearn pipeline.
So we could use the full pipeline (procesing+classification) to create the code that identi... | diff --git a/docs/source/utils.rst b/docs/source/utils.rst
index 0a115350..cd80e0fa 100644
--- a/docs/source/utils.rst
+++ b/docs/source/utils.rst
@@ -27,3 +27,4 @@ Utils
set_log_level
setup_seed
set_download_dir
+ make_process_pipelines
diff --git a/docs/source/whats_new.rst b/docs/source/whats_new.r... |
NeurodataWithoutBorders__pynwb-1538 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/pynwb/base.py:TimeSeries.__init__",
"src/pynwb/base.py:TimeSeries._check_time_series_dimension"
],
"edited_modules": [
"src/pynwb/base.py:TimeSeries"
]
},
"... | NeurodataWithoutBorders/pynwb | e43a602f459d05d9f3ff6fad83d2b52d0bc351b5 | [Bug]: Timeseries can have timestamps + data that don't match in length
### What happened?
I use the convenient timeseries pointer feature, where you can just store timestamps in one timeseries and have many others point to them. This saves a lot of memory! However, I just fixed a bug that arose because some data I st... | diff --git a/src/pynwb/base.py b/src/pynwb/base.py
index 8b4daf48..6b64b3ee 100644
--- a/src/pynwb/base.py
+++ b/src/pynwb/base.py
@@ -199,28 +199,34 @@ class TimeSeries(NWBDataInterface):
else:
raise TypeError("either 'timestamps' or 'rate' must be specified")
- if not self._check_time_s... |
NeurodataWithoutBorders__pynwb-1770 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "docs/source/conf.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/pynwb/ecephy... | NeurodataWithoutBorders/pynwb | dc98e84e73154cd13d532eed09a86878dcfbf738 | [Bug]: Writing ElectrodeGroup position saves incorrectly modified data to file
### What happened?
There seem to be some inconsistencies in writing ElectrodeGroup position to a file depending on the input type:
* For `np.ndarray` inputs, the `__init__` function checks whether position was provided using `if position` ... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index e5909f57..16e50465 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,9 @@
### Performance
- Cache global type map to speed import 3X. @sneakers-the-rat [#1931](https://github.com/NeurodataWithoutBorders/pynwb/pull/1931)
+### Bug fixes
+- Fixed bug in how `Electro... |
NeurodataWithoutBorders__pynwb-1975 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/pynwb/icephys.py:CurrentClampStimulusSeries.__init__",
"src/pynwb/icephys.py:VoltageClampStimulusSeries.__init__"
],
"edited_modules": [
"src/pynwb/icephys.py:PatchClampS... | NeurodataWithoutBorders/pynwb | 3c0dbfaff23d7bdf4b0972c92cc51a85820ff5ec | [Bug]: PatchClampSeries gain is optional in the schema but required in pynwb
### What happened?
I believe the schema indicates that `PatchClampSeries.gain` is an optional dataset with a quantity of 0 or 1:
https://github.com/NeurodataWithoutBorders/nwb-schema/blob/35889d36dfa088ec4a3614fa0350c02ced4a068c/core/nwb.i... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 971c9d79..d0989e10 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,8 @@
- Fixed bug in how `ElectrodeGroup.__init__` validates its `position` argument. @oruebel [#1770](https://github.com/NeurodataWithoutBorders/pynwb/pull/1770)
- Changed `SpatialSeries.referen... |
NeurodataWithoutBorders__pynwb-1986 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/pynwb/behavior.py:SpatialSeries"
]
},
"file": "src/pynwb/behavior.py"
}
] | NeurodataWithoutBorders/pynwb | e938202b257e44c5536dc35476d55aa98e57d18d | [Bug]: SpatialSeries.reference_frame should be optional
### What happened?
The [spec for `SpatialSeries`](https://github.com/NeurodataWithoutBorders/nwb-schema/blob/dev/core/nwb.behavior.yaml#L59-L62) says that the "reference_frame" dataset is optional. However, it is a required argument in pynwb to the `SpatialSeries... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 16e50465..9f627141 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@
### Bug fixes
- Fixed bug in how `ElectrodeGroup.__init__` validates its `position` argument. @oruebel [#1770](https://github.com/NeurodataWithoutBorders/pynwb/pull/1770)
+- Changed `Spatia... |
NeurodataWithoutBorders__pynwb-2052 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/pynwb/base.py:ProcessingModule.add_data_interface"
],
"edited_modules": [
"src/pynwb/base.py:ProcessingModule"
]
},
"file": "src/pynwb/base.py"
}
] | NeurodataWithoutBorders/pynwb | 01d9ab92de25dcd465cfad6d68d9df54679ea54f | [Bug]: `add_data_interface` fails silently on pynwb 3.0
### What happened?
It seems that now in pynwb 3.0 the method `add_data_interface` was replaced by `add`.
But the method `add_data_interface` does not add the structure or throws an error.
### Steps to Reproduce
```python
from pynwb.testing.mock.file import moc... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3de5f592..c1430ea4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,10 @@
# PyNWB Changelog
+## Upcoming
+
+### Bug fixes
+- Fix `add_data_interface` functionality that was mistakenly removed in PyNWB 3.0. @stephprince [#2052](https://github.com/NeurodataWithoutB... |
NeurodataWithoutBorders__pynwb-2056 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/pynwb/file.py:NWBFile.__init__"
],
"edited_modules": [
"src/pynwb/file.py:NWBFile"
]
},
"file": "src/pynwb/file.py"
}
] | NeurodataWithoutBorders/pynwb | a86b54034e654f888bdbff2c04d6e1d35921ed0b | [Bug]: Fail to read NWB file where TimeZone is missing from session_start_time
### What happened?
Not sure if this is a bug, but it seems strict to enforce TimeZone on read.
### Steps to Reproduce
In MATLAB:
```matlab
nwb = NwbFile( ...
'session_description', 'Simple demo file', ...
'identifier', 'test_file'... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 52c00b21..d4f6ad56 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
## Upcoming
### Enhancements and minor changes
+- Automatically add timezone information to timestamps reference time if no timezone information is specified. @stephprince [#2056](https://g... |
NeurodataWithoutBorders__pynwb-2057 | [
{
"changes": {
"added_entities": [
"src/pynwb/__init__.py:clear_cache_dir"
],
"added_modules": [
"src/pynwb/__init__.py:clear_cache_dir"
],
"edited_entities": [
"src/pynwb/__init__.py:__get_resources",
"src/pynwb/__init__.py:__load_core_namespace"
... | NeurodataWithoutBorders/pynwb | 2888ad0b5bb094af52839fb942c9ca3a4607195a | [Bug]: Fail to import in read-only file system
### What happened?
I'm trying to import `pynwb` within an Apptainer container and I'm getting a Read-only filesystem error:
```
apptainer shell /allen/aind/scratch/alessio.buccino/singularity_cache_dir/ghcr.io-allenneuraldynamics-aind-ephys-pipeline-nwb-si-0.102.1.img
```... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index c1430ea4..d884c0d5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,9 @@
## Upcoming
+### Enhancements and minor changes
+- Added option to disable typemap caching and updated type map cache location. @stephprince [#2057](https://github.com/NeurodataWithoutBord... |
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