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 |
|---|---|---|---|---|---|
Ouranosinc__xclim-297 | [
{
"changes": {
"added_entities": [
"xclim/subset.py:distance"
],
"added_modules": [
"xclim/subset.py:distance"
],
"edited_entities": [
"xclim/subset.py:subset_gridpoint"
],
"edited_modules": [
"xclim/subset.py:subset_gridpoint"
]
... | Ouranosinc/xclim | 608bac4c9976df778fb9fa442ef725c45dde9f36 | add optional threshold in utils.subset_gridpoint
* xclim version:
* Python version:
* Operating System:
### Description
Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.
### What I Did
```
Paste the command(s) you ran and the output.
If ... | diff --git a/HISTORY.rst b/HISTORY.rst
index ced91a46..0a2c589e 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -2,6 +2,11 @@
History
=======
+0.12.x-beta (2019-11-15)
+------------------------
+* Added a distance function computing the geodesic distance to a point.
+* Added a `tolerance` argument to `subset_gridpoin... |
Ouranosinc__xclim-312 | [
{
"changes": {
"added_entities": null,
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"edited_entities": null,
"edited_modules": null
},
"file": "xclim/atmos/_temperature.py"
},
{
"changes": {
"added_entities": [
"xclim/indices/_multivariate.py:tas"
],
"added_modules": ... | Ouranosinc/xclim | 5860a492a4b27bdc0b89ad912b955ac963b854cc | Indicator for average temperature based on tasmin and tasmax
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
Create a new indicator computing the daily average temperature from the daily min and max temperature.
| diff --git a/HISTORY.rst b/HISTORY.rst
index 4994460e..3ff1c54d 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -8,7 +8,7 @@ History
* Added a `tolerance` argument to `subset_gridpoint` raising an error if distance to closest point is larger than tolerance.
* Created land module for standardized access to streamflow in... |
Ouranosinc__xclim-336 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/ensembles.py:_ens_align_datasets"
],
"edited_modules": [
"xclim/ensembles.py:_ens_align_datasets"
]
},
"file": "xclim/ensembles.py"
}
] | Ouranosinc/xclim | 26d99831e33e989da59b0a7e2471e66231111784 | build failing against xarray master
ensembles creation tests seems to be failing with the travis build w/ xarray@master
We might want to take a minute to try to see why and try to get ahead of this... | diff --git a/HISTORY.rst b/HISTORY.rst
index 66f7cba4..556b131c 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -5,6 +5,7 @@ History
0.13.x (2020-01-10)
-------------------
* Reverted #311, removing the `_rolling` util function. Added optimal keywords to `rolling()` calls.
+* Fixed `ensembles.create_ensemble` errors f... |
Ouranosinc__xclim-339 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/ensembles.py:create_ensemble",
"xclim/ensembles.py:ensemble_percentiles",
"xclim/ensembles.py:_calc_percentiles_simple",
"xclim/ensembles.py:_calc_percentiles_blocks",
... | Ouranosinc/xclim | 0790e8c7cc4b5d933a034f1a6da1cdc1072c2e01 | Optimize/improve xclim ensemble stats utilities
There are currently functional versions of the following utilities but they could use improvement / polishing:
```python
xclim.utils.utils.create_ensemble()
xclim.utils.ensemble_percentiles()
xclim.utils.calc_percentiles_simple()
xclim.utils.calc_percentiles_blocks(... | diff --git a/HISTORY.rst b/HISTORY.rst
index 2da52984..50dd6f92 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -10,6 +10,7 @@ History
* Fixed `ensembles.create_ensemble` errors for builds against xarray master branch.
* Reformatted code to make better use of Python3.6 conventions (f-strings and object signatures).
* ... |
Ouranosinc__xclim-347 | [
{
"changes": {
"added_entities": null,
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"file": "setup.py"
},
{
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... | Ouranosinc/xclim | a4a8a7c4a7d2bb527ff11b77607189415c9def13 | Subset with individual features
* xclim version: 0.13.0
It would be great to have an option for us to explode the features of a shapefile and subset spatially according to their boundaries. This has been implemented in a few libraries but it wouldn't take much work to modify our current `subset_shape` and `create_ma... | diff --git a/HISTORY.rst b/HISTORY.rst
index 50dd6f92..ec7dbd31 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -2,6 +2,11 @@
History
=======
+0.14.x
+------
+* Fix in `subset.wrap_lons_and_split_at_greenwich` to preserve multi-region dataframes.
+
+
0.13.x (2020-01-10)
-------------------
* Documentation improvem... |
Ouranosinc__xclim-349 | [
{
"changes": {
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"file": "xclim/atmos/_temperature.py"
},
{
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"xclim/in... | Ouranosinc/xclim | 7d331b5a2753f334d6e066d14ed64f6b5718e051 | growing season length memory use
### Description
Calling growing season length calculation on large multiyear datasets (e.g. mf_datset of nrcan over canada) causes memory errors / accumulation.
Dask writing of chunks to netcdf (xr.to_netcdf) does not seem to work as expected and RAM use quickly accumulates and crashe... | diff --git a/HISTORY.rst b/HISTORY.rst
index ec7dbd31..4d84de91 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -5,6 +5,7 @@ History
0.14.x
------
* Fix in `subset.wrap_lons_and_split_at_greenwich` to preserve multi-region dataframes.
+* Improve the memory use of `indices.growing_season_length`.
0.13.x (2020-01-1... |
Ouranosinc__xclim-377 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/subset.py:subset_gridpoint"
],
"edited_modules": [
"xclim/subset.py:subset_gridpoint"
]
},
"file": "xclim/subset.py"
}
] | Ouranosinc/xclim | bbc8bc730d99f28dfc9d31f17fadfa188d92fcd5 | Add support in subset_gridpoint for 1D lat lon.
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
`subset_gridpoint` assumes that lats and lons are on a 2D grid. If used with 1D coordinates, it fails. This would be useful to ... | diff --git a/HISTORY.rst b/HISTORY.rst
index 026c37e2..ba05dad9 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -2,6 +2,10 @@
History
=======
+0.15.x
+------
+* Fix bug in subset_gridpoint to work on lat/lon coords of any dimension when they are not a dimension of the data.
+
0.14.x (2020-02-21)
-------------------... |
Ouranosinc__xclim-380 | [
{
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"added_modules": null,
"edited_entities": null,
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},
"file": "setup.py"
},
{
"changes": {
"added_entities": null,
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... | Ouranosinc/xclim | 314e4297f40d82a193f52a5cbb5cae4b9d3ac014 | Make run_length methods return the coordinate values
Right now, functions like `rl.first_run` return indexes (integers) along the given dimension. Retrieving the coordinate values (like the datetime objects) is not an easy task and usually gets done by unelegant hacky lines. There should be an option on the run_length ... | diff --git a/HISTORY.rst b/HISTORY.rst
index ba05dad9..9915f137 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -4,6 +4,7 @@ History
0.15.x
------
+* Add feature to retrieve coordinate values instead of index in `run_length.first_run`. Add `run_length.last_run`.
* Fix bug in subset_gridpoint to work on lat/lon coord... |
Ouranosinc__xclim-401 | [
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"file": "setup.py"
},
{
"changes": {
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... | Ouranosinc/xclim | 9b03ee6cb9929db1644d95238d49ba3310d597bf | crs coordinate added during the `subset_shape` call
* xclim version: 0.15.0
* Python version: 3.8
* Operating System: ubuntu
### Description
This happened in the finch test suite: https://github.com/bird-house/finch/pull/107/commits/7f5ffff1ed422df8ddd12286f5990cf3fbe389c2
When I call `xclim.subset.subset_sh... | diff --git a/HISTORY.rst b/HISTORY.rst
index c70e0593..d282d386 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -5,6 +5,7 @@ History
0.16.x
------
* Allow lazy units conversion
+* CRS definitions of projected DataSets are now written to file according to Climate and Forecast-convention standards
0.15.x (2020-03-12)... |
Ouranosinc__xclim-408 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/indices/_multivariate.py:cold_spell_duration_index",
"xclim/indices/_multivariate.py:heat_wave_frequency",
"xclim/indices/_multivariate.py:heat_wave_max_length",
"xclim/ind... | Ouranosinc/xclim | e940cdb3cfa9bf5b0284067673e99e9f9f02530d | `subset_shape` with large input data
* xclim version: 0.15.0
* Python version: 3.8
* Operating System: ubuntu
### Description
Calling the `subset_shape` function on a large input dataset crashes when the dataset doesn't fit in memory. Not with a large polygon subset, but a large source dataset. So I want to sub... | diff --git a/HISTORY.rst b/HISTORY.rst
index 1660b080..d6263236 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -8,6 +8,8 @@ History
* CRS definitions of projected DataSets are now written to file according to Climate and Forecast-convention standards
* Add utilities to merge attributes and update history in xclim.core... |
Ouranosinc__xclim-413 | [
{
"changes": {
"added_entities": [
"xclim/subset.py:convert_lat_lon_to_da"
],
"added_modules": [
"xclim/subset.py:convert_lat_lon_to_da"
],
"edited_entities": [
"xclim/subset.py:subset_gridpoint",
"xclim/subset.py:distance"
],
"edited_mod... | Ouranosinc/xclim | 7e7ff9762465e1621bf51cd4ca0cb490a4987811 | subset multipoint (scattered locations)
For a couple of recent projects I have had to extract multiple scattered site locations (weather stations, sample sites etc etc) from a netcdf and thought that the steps could form the basis of a `subset.subset_scattered()` or similar named function
For a large number of stat... | diff --git a/HISTORY.rst b/HISTORY.rst
index 178cf347..1aa592c2 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -4,6 +4,7 @@ History
0.16.x
------
+* Add multi gridpoints support in `subset.subset_gridpoint`.
* Better `wrapped_partial` for more meaningful inspection.
* Add indices for relative humidity, specific hu... |
Ouranosinc__xclim-416 | [
{
"changes": {
"added_entities": [
"xclim/core/checks.py:MissingBase.__init__",
"xclim/core/checks.py:MissingBase.split_freq",
"xclim/core/checks.py:MissingBase.is_null",
"xclim/core/checks.py:MissingBase.prepare",
"xclim/core/checks.py:MissingBase.is_missing",
... | Ouranosinc/xclim | 83aebec1966213b1be8131f998d6b69bf2406198 | Improve missing data check
### Description
Currently missing data checks in indicator classes are very strict (single missing day or single nan value) will result in nan for a given resample time step
Options include:
1. Percent missing : https://github.com/Ouranosinc/xclim/issues/364#issuecomment-585804628... | diff --git a/HISTORY.rst b/HISTORY.rst
index f0f5444e..6883462f 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -15,6 +15,8 @@ History
* Ensembles : Allow alignment of datasets with same frequency but different offsets.
* Bug fixes in run_length for run-with-dates methods when the date is not found in the run.
* Remov... |
Ouranosinc__xclim-428 | [
{
"changes": {
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"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "xclim/indicators/atmos/_conversion.py"
},
{
"changes": {
"added_entities": null,
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"edited_entities": [
... | Ouranosinc/xclim | 04dd41642ad2f5bd10c44c5501e1a6351f74ad57 | Error converting array to scalars in subset.subset_shape
* xclim version: 0.16.0
* Python version: PAVICS
* Operating System: PAVICS
### Description
I was subsetting a shapefile to be used to calculate ensemble percentiles. The shapefile has multiple watershed sub-boundaries.
### What I Did
```python
impo... | diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb
index 344812d6..6bc3484a 100644
--- a/docs/notebooks/example.ipynb
+++ b/docs/notebooks/example.ipynb
@@ -51,40 +51,27 @@
"source": [
"## Setting up the Dask client: parallel processing\n",
"\n",
- "This step is not mandatory as d... |
Ouranosinc__xclim-433 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/core/checks.py:MissingBase.split_freq",
"xclim/core/checks.py:MissingBase.is_null",
"xclim/core/checks.py:MissingBase.prepare"
],
"edited_modules": [
"xclim/cor... | Ouranosinc/xclim | 3c2b233b45af8c1b6932d19ae43dc398bbcbed43 | Support `freq=None` in missing_* functions
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
This will simplify the Indicator class logic and facilitate switching the missing method.
| diff --git a/xclim/core/checks.py b/xclim/core/checks.py
index fb7eef91..d478910c 100644
--- a/xclim/core/checks.py
+++ b/xclim/core/checks.py
@@ -62,7 +62,7 @@ def assert_daily(var):
if np.timedelta64(dt.timedelta(days=1)) != (t1 - t0).data:
raise ValueError("time series is not daily.")
- # Check th... |
Ouranosinc__xclim-447 | [
{
"changes": {
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},
"file": "xclim/sdba/__init__.py"
},
{
"changes": {
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"edited_entities": [
"xclim/sdba/ad... | Ouranosinc/xclim | 761b2c1433223adad92124565572fc0aca519f61 | DetrendedQuantileMapping only applies the last correction factor
* xclim version: '0.16.1-beta' (master, as of 2020-05-08)
* Python version: 3.8.2
* Operating System: Linux
### Description
The figure below is the daily average : `plt.plot(data.groupby("time.dayofyear").mean("time").values)`. The black line is my ... | diff --git a/docs/sdba.rst b/docs/sdba.rst
index d25e699e..1ac5f555 100644
--- a/docs/sdba.rst
+++ b/docs/sdba.rst
@@ -2,18 +2,18 @@
Bias adjustment and downscaling algorithms
==========================================
-`xarray` data structures allow for relatively straightforward implementations of simple bias-adj... |
Ouranosinc__xclim-453 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/core/units.py:units2pint"
],
"edited_modules": [
"xclim/core/units.py:units2pint"
]
},
"file": "xclim/core/units.py"
}
] | Ouranosinc/xclim | 6393a9bbc9fe8fc344b64512f0277d55dd83e3e8 | Add support for unit = '1'
### Description
I'm trying to use xclim.indices.relative_humidity and I get the following error when `huss` is among the inputs :
```
Traceback (most recent call last):
File "/usr/local/pycharm-community-2017.3.4/helpers/pydev/pydevd.py", line 1668, in <module>
main()
File "/us... | diff --git a/xclim/core/units.py b/xclim/core/units.py
index be0d956f..d186db7e 100644
--- a/xclim/core/units.py
+++ b/xclim/core/units.py
@@ -143,6 +143,9 @@ def units2pint(value: Union[xr.DataArray, str]) -> pint.unit.UnitDefinition:
raise NotImplementedError(f"Value of type `{type(value)}` not supported.")
... |
Ouranosinc__xclim-463 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/ensembles.py:ensemble_percentiles",
"xclim/ensembles.py:_calc_perc"
],
"edited_modules": [
"xclim/ensembles.py:ensemble_percentiles",
"xclim/ensembles.py:_calc_... | Ouranosinc/xclim | 9a5a4140fa3fcef611de21495c077c22128de2c0 | Ensemble percentiles as dimension instead of variables
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
Currently, `xclim.ensembles.ensemble_percentiles` takes in a dataset and returns a new one with one variable per percentile and data varia... | diff --git a/HISTORY.rst b/HISTORY.rst
index 5c6413eb..47eda3f1 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -3,6 +3,7 @@ History
=======
0.18.x
------
+* `ensembles.ensemble_percentiles` modified to compute along a `percentiles` dimension by default, instead of creating different variables.
* Added indicator `fir... |
Ouranosinc__xclim-467 | [
{
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"file": "setup.py"
},
{
"changes": {
"added_entities": null,
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"edited_modules": null
... | Ouranosinc/xclim | 17bc5e9afdc76d7f802b5193ed4209b0e7d5a67c | sdba - Grouped Detrending
We need to implement grouped detrending into sdba. | diff --git a/HISTORY.rst b/HISTORY.rst
index 2e0e319a..1d6a6ebc 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -4,6 +4,7 @@ History
0.18.x
------
+* `xclim.sdba.detrending` objects can now act on groups.
* Replaced `dask[complete]` with `dask[array]` in basic installation and added `distributed` to `docs` build dep... |
Ouranosinc__xclim-488 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "xclim/indicators/seaIce/_seaice.py"
}
] | Ouranosinc/xclim | 0309ee4f6208ce1d468673aec9b2cb7353749616 | Sea ice extent and area should use CF units
* xclim version: master
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
Units are currently set as `m^2`. CF units should be written `m2`.
| diff --git a/HISTORY.rst b/HISTORY.rst
index 8d834796..0e27f351 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -12,8 +12,10 @@ History
* Added indicator `first_day_below` and run length helper `first_run_after_date`.
* Added ANUCLIM model climate indices mappings.
* Renamed `areacella` to `areacello` in sea ice tests... |
Ouranosinc__xclim-489 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/indices/_multivariate.py:daily_freezethaw_cycles",
"xclim/indices/_multivariate.py:daily_temperature_range",
"xclim/indices/_multivariate.py:daily_temperature_range_variability",
... | Ouranosinc/xclim | 6b5a5e952203d1be2c1bd9a4a03af6974cec6f5a | Some indices are defined with (tasmin, tasmax) while others use (tasmax, tasmin)
* xclim version: master
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
I think we should stick to one ordering. It creates problems when wr... | diff --git a/HISTORY.rst b/HISTORY.rst
index 85dd5f6d..1df4f827 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -14,9 +14,9 @@ History
* Renamed `areacella` to `areacello` in sea ice tests.
* Sea ice extent and area outputs now have units of m2 to comply with CF-Convention.
* Split `checks.py` into `cfchecks.py`, `dat... |
Ouranosinc__xclim-495 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/indices/run_length.py:rle"
],
"edited_modules": [
"xclim/indices/run_length.py:rle"
]
},
"file": "xclim/indices/run_length.py"
}
] | Ouranosinc/xclim | c8a0a5417baf28f8b10d8ca4f3e9dd2db8ff55dd | rle fails when first dimension is not 'time' on dask arrays
* xclim version: 0.17.0 & @master
* Python version: 3.6 & 3.8
* Operating System: boréas and Linux
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
When `xclim.in... | diff --git a/xclim/indices/run_length.py b/xclim/indices/run_length.py
index e1dc8f33..9b69522c 100644
--- a/xclim/indices/run_length.py
+++ b/xclim/indices/run_length.py
@@ -43,8 +43,11 @@ def get_npts(da: xr.DataArray) -> int:
def rle(da: xr.DataArray, dim: str = "time", max_chunk: int = 1_000_000):
n = len(d... |
Ouranosinc__xclim-513 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/indices/generic.py:fit"
],
"edited_modules": [
"xclim/indices/generic.py:fit"
]
},
"file": "xclim/indices/generic.py"
}
] | Ouranosinc/xclim | c3cce368e5ac64b27ecc93157095f55fefd07305 | generic.fit incorrectly orders dimensions
* xclim version: 0.18.1-beta
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
Works as long as time is the first dimension, breaks otherwise (I think).
For example,
`xclim.indice... | diff --git a/HISTORY.rst b/HISTORY.rst
index 8aa7b5b3..a53a3b5c 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -21,6 +21,8 @@ New features and enhancements
Bug fixes
~~~~~~~~~
+* Fix `generic.fit` dimension ordering. This caused errors when "time" was not the first dimension in a DataArray.
+
Internal changes
~~... |
Ouranosinc__xclim-531 | [
{
"changes": {
"added_entities": [
"xclim/core/datachecks.py:check_freq"
],
"added_modules": [
"xclim/core/datachecks.py:check_freq"
],
"edited_entities": [
"xclim/core/datachecks.py:check_daily"
],
"edited_modules": [
"xclim/core/datache... | Ouranosinc/xclim | 160cd4e5a271178bb9a0a61d9e34f0fa077bd62c | Extend support to hourly data
Raven will generate hourly streamflow time series, driven by hourly meteorological data. Ideally we would be able to define indicators operating on hourly data. | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3b23b630..2b76e53c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -42,7 +42,7 @@ repos:
# - id: autopep8
# args: ['--global-config=setup.cfg','--in-place']
- repo: https://github.com/timothycrosley/isort
- re... |
Ouranosinc__xclim-547 | [
{
"changes": {
"added_entities": [
"xclim/indices/generic.py:_fit_start"
],
"added_modules": [
"xclim/indices/generic.py:_fit_start"
],
"edited_entities": [
"xclim/indices/generic.py:fit"
],
"edited_modules": [
"xclim/indices/generic.py:f... | Ouranosinc/xclim | b5fa98ec7d0aa7a39e58fc9efbf7a36aa6aad6ec | Initial values for distribution fit
* xclim version: 0.19
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
The scipy.stats fit function using Maximum Likelihood (`generic.fit`) converges to poor values for some distributi... | diff --git a/HISTORY.rst b/HISTORY.rst
index 9b8bd3f8..5abe2ece 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -22,6 +22,7 @@ New features and enhancements
* New `generic.parametric_quantile` function taking parameters estimated by `generic.fit` as an input.
* Add support for using probability weighted moments method ... |
Ouranosinc__xclim-562 | [
{
"changes": {
"added_entities": [
"xclim/indices/run_length.py:index_of_date"
],
"added_modules": [
"xclim/indices/run_length.py:index_of_date"
],
"edited_entities": [
"xclim/indices/run_length.py:season_length",
"xclim/indices/run_length.py:run_end... | Ouranosinc/xclim | a7e126ceae6c743f7f7fd85b9bf45b52b39abb10 | Run calculations with dates are not calendar-aware
* xclim version: 0.20
* Python version: 3.8
* Operating System: Linux
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
Functions of `xclim.indices.run_length` that accept ... | diff --git a/HISTORY.rst b/HISTORY.rst
index 67715d9a..04b7dcd9 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -18,6 +18,7 @@ New features and enhancements
Bug fixes
~~~~~~~~~
* Fixed a bug in the attributes of `frost_season_length`.
+* `indices.run_length` methods using dates now respect the array's calendar.
Int... |
Ouranosinc__xclim-694 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/core/calendar.py:doy_to_days_since",
"xclim/core/calendar.py:days_since_to_doy"
],
"edited_modules": [
"xclim/core/calendar.py:doy_to_days_since",
"xclim/core/c... | Ouranosinc/xclim | 0a66c614f159f7243a09d837a7beb315f891ed45 | Implement a 'doy_to_days_after' and reverse functionality
### Description
Certain indices outputting 'day of year' or `doy` values are not directly usable for ensemble percentiles and statistics due to its circular nature.
Averaging `doy` results can potentially be handled by users via https://docs.scipy.org/d... | diff --git a/xclim/core/calendar.py b/xclim/core/calendar.py
index e2936660..86a3787f 100644
--- a/xclim/core/calendar.py
+++ b/xclim/core/calendar.py
@@ -872,7 +872,7 @@ def doy_to_days_since(
Passing `start` only makes sense if `da` has a yearly sampling frequency.
calendar: str, optional
The calen... |
Ouranosinc__xclim-720 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "xclim/core/options.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/sdba/_ad... | Ouranosinc/xclim | 2bd9efe0e241ce039f7e818df32d2b047729a6bf | sdba - "verbose" mode?
As suggested in slack by @dgergel and also discussed this morning with Patrick, it could be interesting to output more than just the training dataset / scenario timeseries. I am thinking of some kind of "verbose" or "debug" mode, where sdba trains and adjusts would provide ancillary "diagnostics"... | diff --git a/HISTORY.rst b/HISTORY.rst
index d6dafcde..073c2715 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -13,6 +13,7 @@ New features and enhancements
* Indicator modules built from YAML can now use custom indices. A mapping or module of them can be given to ``build_indicator_module_from_yaml`` with the ``indices`... |
Ouranosinc__xclim-723 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "xclim/indicators/atmos/_conversion.py"
},
{
"changes": {
"added_entities": [
"xclim/indices/_conversion.py:humidex"
],
"adde... | Ouranosinc/xclim | 8688e167d4210d43a5792416679ed483caac6f87 | Humidex indicator
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
Add humidex indicator.
https://www.canada.ca/en/environment-climate-change/services/seasonal-weather-hazards/warm-season-weather-hazards.html#toc7
http... | diff --git a/HISTORY.rst b/HISTORY.rst
index f812dc8a..bfb2f18d 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -34,6 +34,7 @@ New indicators
~~~~~~~~~~~~~~
* `atmos.corn_heat_units` computes the daily temperature-based index for corn growth.
* New indices and indicators for `tx_days_below`, `tg_days_above`, `tg_days_... |
Ouranosinc__xclim-757 | [
{
"changes": {
"added_entities": [
"xclim/sdba/_adjustment.py:npdf_transform"
],
"added_modules": [
"xclim/sdba/_adjustment.py:npdf_transform"
],
"edited_entities": null,
"edited_modules": null
},
"file": "xclim/sdba/_adjustment.py"
},
{
"chang... | Ouranosinc/xclim | 8504336b13c2a9e4b826024bbe5c84337a1b94f6 | Multivariate quantile mapping bias correction implementation
Implement https://link.springer.com/article/10.1007/s00382-017-3580-6
| diff --git a/HISTORY.rst b/HISTORY.rst
index af3ab196..842e6529 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -9,9 +9,12 @@ New features and enhancements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Automatic load of translations on import and possibility to pass translations for virtual modules.
* New ``xclim.testing.list_datas... |
Ouranosinc__xclim-766 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "xclim/indicators/land/_snow.py"
},
{
"changes": {
"added_entities": [
"xclim/indices/_simple.py:snow_depth"
],
"added_module... | Ouranosinc/xclim | 8acbae020e6472783fc11330a8f51f3a0aa14107 | Implement missing ICCLIM indices
A few icclim indices were never included in early xclim implementation @bzah indicates he can spend some time on this
List of indices:
- [x] SD : Snow depth
- [ ] CD : Cold and dry days
- [ ] CW: Cold and wet days
- [ ] WD: Warm and dry days
- [ ] WW: Warm and wet days
| diff --git a/.zenodo.json b/.zenodo.json
index 6f50705d..5b82038d 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -35,6 +35,11 @@
"name": "Rondeau-Genesse, Gabriel",
"orcid": "0000-0003-3389-9406"
},
+ {
+ "affiliation": "CERFACS",
+ "name": "Aoun, Abel",
+ "orcid": "0000-0003-2289-... |
Ouranosinc__xclim-836 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/core/missing.py:MissingBase.__init__",
"xclim/core/missing.py:MissingBase.prepare",
"xclim/core/missing.py:MissingWMO.execute",
"xclim/core/missing.py:missing_wmo"
],... | Ouranosinc/xclim | 45cc76286525c2b7cbc55eb34bfcbb7ed7712e0e | WMO check missing doesn't account for missing months
* xclim version: 0.29.0
* Python version: 3.9
* Operating System: BSD
### Description
The missing data checks using the `set_options(check_missing="wmo")` context are correctly dropping the months that don't have an adequate number of days or too many days mi... | diff --git a/HISTORY.rst b/HISTORY.rst
index 0c8f0a75..4d485e63 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -17,6 +17,7 @@ Bug fixes
* ``xc.core.units.rate2amount`` is now exact when the sampling frequency is monthly, seasonal or yearly. Earlier, monthly and yearly data were computed using constant month and year le... |
Ouranosinc__xclim-852 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xclim/core/indicator.py:build_indicator_module_from_yaml"
],
"edited_modules": [
"xclim/core/indicator.py:build_indicator_module_from_yaml"
]
},
"file": "xclim/core/ind... | Ouranosinc/xclim | 994c1d7681af0a0dd46d90725bf6a093719860f2 | Reading YAML file code seems need add encoding setting
* xclim version: 0.29.0
* Python version: 3.9.7
* Operating System: Windows 10(zh-cn)
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
Maybe Reading YAML file part nee... | diff --git a/HISTORY.rst b/HISTORY.rst
index 13b838e3..581e8cde 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -44,6 +44,7 @@ Bug fixes
* Fix bug in ``missing_wmo``, where a period would be considered valid if all months met WMO criteria, but complete months in a year were missing. Now if any month does not meet criter... |
Ouranosinc__xclim-969 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "setup.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
... | Ouranosinc/xclim | bd10c799d885531a0061a15f04a4b90bd9c32a48 | Circular imports
### Description
<!--Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.-->
`core.missing` imports `indices.generic`, while some indices import `core.missing`, which causes circular import problems.
The function required in `core.m... | diff --git a/HISTORY.rst b/HISTORY.rst
index 13d253ca..378d7eeb 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -6,6 +6,10 @@ History
-------------------
Contributors to this version: Trevor James Smith (:user:`Zeitsperre`).
+Breaking changes
+^^^^^^^^^^^^^^^^
+* To reduce import complexity, `select_time` has been re... |
OxfordIonTrapGroup__oitg-38 | [
{
"changes": {
"added_entities": [
"oitg/threshold.py:optimise_readout",
"oitg/threshold.py:optimise_treshold",
"oitg/threshold.py:optimise_t_bin",
"oitg/threshold.py:poisson_optimal_thresh_count"
],
"added_modules": [
"oitg/threshold.py:optimise_readout... | OxfordIonTrapGroup/oitg | 768b2d5be8cf189b192d025877518a227171177f | Account for spontaneous shelving and deshelving in threshold.py
As per title.
Currently [threshold.py](https://github.com/OxfordIonTrapGroup/oitg/blob/master/oitg/threshold.py) assumes poissonian statistics. This is innacurate for longer readout durations. | diff --git a/oitg/threshold.py b/oitg/threshold.py
index b74c080..7d4bf82 100644
--- a/oitg/threshold.py
+++ b/oitg/threshold.py
@@ -1,114 +1,156 @@
import numpy as np
-from scipy.optimize import least_squares
+from scipy.optimize import minimize
from scipy.stats import poisson
+from scipy.special import gammainc
... |
PEtab-dev__libpetab-python-136 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"petab/lint.py:check_observable_df"
],
"edited_modules": [
"petab/lint.py:check_observable_df"
]
},
"file": "petab/lint.py"
}
] | PEtab-dev/libpetab-python | 902f34967ecc60230339006dc21e233578075dc6 | Reduce tests to min+max python?
takes quite some time to start+run all ... | diff --git a/petab/lint.py b/petab/lint.py
index ba9ad8f..e13f540 100644
--- a/petab/lint.py
+++ b/petab/lint.py
@@ -292,7 +292,12 @@ def check_observable_df(observable_df: pd.DataFrame) -> None:
noise = getattr(row, NOISE_FORMULA)
try:
- sp.sympify(noise)
+ sympified_noise = s... |
PEtab-dev__libpetab-python-152 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"petab/problem.py:Problem.from_files",
"petab/problem.py:Problem.from_yaml"
],
"edited_modules": [
"petab/problem.py:Problem"
]
},
"file": "petab/problem.py"
}... | PEtab-dev/libpetab-python | 7a0b77ef6d968a4600497763df0ca791caa24768 | Add support for multiple condition files per petab.Problem
Allowed in YAML file, but not implemented in library. | diff --git a/petab/problem.py b/petab/problem.py
index 517b91c..f523803 100644
--- a/petab/problem.py
+++ b/petab/problem.py
@@ -87,8 +87,9 @@ class Problem:
@staticmethod
def from_files(
- sbml_file: Union[str, Path, None] = None,
- condition_file: Union[str, Path, None] = None,
+ ... |
PEtab-dev__libpetab-python-156 | [
{
"changes": {
"added_entities": [
"petab/parameters.py:_check_for_contradicting_parameter_definitions"
],
"added_modules": [
"petab/parameters.py:_check_for_contradicting_parameter_definitions"
],
"edited_entities": [
"petab/parameters.py:get_parameter_df"
... | PEtab-dev/libpetab-python | 5a87f8370aa5be56ed39b986801e7e36b18d94cb | Parameters dropped when using subset parameter files
On branch `develop`: When supplying multiple parameter files to `parameters.get_parameter_df`, parameters will be dropped if they only differ from other parameters by their `parameterId`.
___
Example using parameter files from [demo_parameters.zip](https://github.c... | diff --git a/petab/parameters.py b/petab/parameters.py
index f794530..8dbf441 100644
--- a/petab/parameters.py
+++ b/petab/parameters.py
@@ -55,18 +55,8 @@ def get_parameter_df(
return None
parameter_df = pd.concat(dfs)
- # Remove identical parameter definitions
- parameter_df.drop... |
PEtab-dev__libpetab-python-235 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"petab/core.py:get_visualization_df",
"petab/core.py:flatten_timepoint_specific_output_overrides",
"petab/core.py:unflatten_simulation_df"
],
"edited_modules": [
"peta... | PEtab-dev/libpetab-python | 4e6a0189eedf7078de8a674c200819cbdc26c83b | `flatten_timepoint_specific_output_overrides` does not support observableParameter overrides as placeholders in noise formulae
`flatten_timepoint_specific_output_overrides` does not support `observableParameter` placeholders in noise formulae.
Related to https://github.com/PEtab-dev/libpetab-python/pull/231 | diff --git a/petab/core.py b/petab/core.py
index 05deb16..0e7b7da 100644
--- a/petab/core.py
+++ b/petab/core.py
@@ -71,7 +71,7 @@ def write_simulation_df(df: pd.DataFrame, filename: Union[str, Path]) -> None:
def get_visualization_df(
- visualization_file: Union[str, Path, pd.DataFrame, None]
+ visualiz... |
PEtab-dev__libpetab-python-287 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"petab/v1/problem.py:Problem.to_files_generic"
],
"edited_modules": [
"petab/v1/problem.py:Problem"
]
},
"file": "petab/v1/problem.py"
},
{
"changes": {
"a... | PEtab-dev/libpetab-python | 62991395aeebb5b60a02ba39d6dc9a0347db4957 | Validation fails for remote files
`validate_yaml_semantics` uses `os.path.isfile` to check whether referenced files are available and fails for remote files. | diff --git a/petab/v1/problem.py b/petab/v1/problem.py
index 203e8d9..e49e4d7 100644
--- a/petab/v1/problem.py
+++ b/petab/v1/problem.py
@@ -5,7 +5,7 @@ import os
import tempfile
from collections.abc import Iterable
from math import nan
-from pathlib import Path
+from pathlib import Path, PurePosixPath
from typing ... |
PEtab-dev__libpetab-python-327 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"petab/v1/problem.py:Problem.from_yaml"
],
"edited_modules": [
"petab/v1/problem.py:Problem"
]
},
"file": "petab/v1/problem.py"
},
{
"changes": {
"added_en... | PEtab-dev/libpetab-python | 0b77d7fb48ef36c579f9748d7df12365c68a1e24 | Path management
When generating a `petab.Problem` from a yaml file, all files are automatically prefixed by the location of the yaml file. However when directly passing the corresponding `dict` (potentially after manipulation), it is no longer possible to specify a prefix and the only way for the import to work correct... | diff --git a/petab/v1/problem.py b/petab/v1/problem.py
index 4a5577e..6145656 100644
--- a/petab/v1/problem.py
+++ b/petab/v1/problem.py
@@ -251,21 +251,28 @@ class Problem:
)
@staticmethod
- def from_yaml(yaml_config: dict | Path | str) -> Problem:
+ def from_yaml(
+ yaml_config: dict | Pa... |
PEtab-dev__libpetab-python-350 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"petab/v1/problem.py:Problem.from_yaml"
],
"edited_modules": [
"petab/v1/problem.py:Problem"
]
},
"file": "petab/v1/problem.py"
},
{
"changes": {
"added_en... | PEtab-dev/libpetab-python | 9f11e7319b44b991fb0dc3315f1f3441ae9ac5fd | v2: version check
`pteab.v2.Problem.from_yaml` will only accept "2.0.0" as version string, even though it sounds like "2" would also be valid according to spec.
see https://github.com/PEtab-dev/libpetab-python/blob/99373c4340512def5a23bf2a75805c3f88251251/petab/v2/problem.py#L139 | diff --git a/petab/v1/problem.py b/petab/v1/problem.py
index 5c0dcf6..373b6b4 100644
--- a/petab/v1/problem.py
+++ b/petab/v1/problem.py
@@ -13,10 +13,10 @@ from warnings import warn
import pandas as pd
from pydantic import AnyUrl, BaseModel, Field, RootModel
+from ..versions import get_major_version
from . import... |
PEtab-dev__libpetab-python-92 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"petab/lint.py:check_condition_df"
],
"edited_modules": [
"petab/lint.py:check_condition_df"
]
},
"file": "petab/lint.py"
}
] | PEtab-dev/libpetab-python | f6fd4896f557497a16afe3773467eb06a2614a79 | no lint error for non-unique condition ids
`petab.lint.check_condition_df` does not check whether index entries are unique, but this is required according to documentation. | diff --git a/petab/lint.py b/petab/lint.py
index fe353ac..ba9ad8f 100644
--- a/petab/lint.py
+++ b/petab/lint.py
@@ -108,6 +108,10 @@ def check_condition_df(
check_ids(df.index.values, kind='condition')
+ if not df.index.is_unique:
+ raise AssertionError("Non-unique condition IDs: "
+ ... |
PEtab-dev__libpetab-python-93 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"petab/conditions.py:get_condition_df",
"petab/conditions.py:write_condition_df"
],
"edited_modules": [
"petab/conditions.py:get_condition_df",
"petab/conditions.py:wr... | PEtab-dev/libpetab-python | 4f6b841495647a163d29c11c847dc4f45fda4286 | Add consistent support for pathlib.Path
Would be quite convenient if `Path`s could be used in addition path strings. | diff --git a/petab/conditions.py b/petab/conditions.py
index 4cb7853..c9ed93c 100644
--- a/petab/conditions.py
+++ b/petab/conditions.py
@@ -1,11 +1,12 @@
"""Functions operating on the PEtab condition table"""
-from typing import Iterable, Optional, List, Union
+from pathlib import Path
+from typing import Iterable,... |
PMEAL__OpenPNM-1665 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/algorithms/GenericTransport.py:GenericTransport.run",
"openpnm/algorithms/GenericTransport.py:GenericTransport._run_generic"
],
"edited_modules": [
"openpnm/algorithm... | PMEAL/OpenPNM | 707321ce9beb29a4b36730c5ea87b48f04953187 | Solvers don't check for convergence when maximum iterations is reached
This is a corner-case that @mkaguer has recently found. Basically, when `max_iter` is reached, the solver gets tricked that the solution has converged. This is because unless `update_iterative_props` is called, the solution `x`, not surprisingly, sa... | diff --git a/examples/tutorials/Working with Mixtures.ipynb b/examples/tutorials/Working with Mixtures.ipynb
index b3298216d..5b1ad732f 100644
--- a/examples/tutorials/Working with Mixtures.ipynb
+++ b/examples/tutorials/Working with Mixtures.ipynb
@@ -589,7 +589,6 @@
"1 pore.bc_rate ... |
PMEAL__OpenPNM-1689 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/core/Base.py:Base.__init__",
"openpnm/core/Base.py:Base._set_name"
],
"edited_modules": [
"openpnm/core/Base.py:Base"
]
},
"file": "openpnm/core/Base.py... | PMEAL/OpenPNM | 9393cc8308a61651681b2595b0f7cfa3eaa4a55f | Object names must be unique within a project
Currently, this is not enforced. | diff --git a/openpnm/core/Base.py b/openpnm/core/Base.py
index f99efe03c..7a19fa281 100644
--- a/openpnm/core/Base.py
+++ b/openpnm/core/Base.py
@@ -1,7 +1,6 @@
import warnings
import uuid
import numpy as np
-import scipy as sp
from collections import namedtuple
from openpnm.models.misc import from_neighbor_throat... |
PMEAL__OpenPNM-1702 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/topotools/topotools.py:dimensionality"
],
"edited_modules": [
"openpnm/topotools/topotools.py:dimensionality"
]
},
"file": "openpnm/topotools/topotools.py"
}
... | PMEAL/OpenPNM | 2b26808ccdf541e955bf8c897d1dca1b1cac2f3c | topotools.dimensionality sometimes treats 1D networks as 2D
Although extremely rare, it's still a bug. It's even hard to reproduce, but I had this problem when I was doing manual coordinate manipulations for the CL project.
```python
import openpnm as op
net = op.network.Cubic([1, 1, 5], spacing=1.2345678e-20)
... | diff --git a/openpnm/topotools/topotools.py b/openpnm/topotools/topotools.py
index 54d885cd6..05e8744fc 100644
--- a/openpnm/topotools/topotools.py
+++ b/openpnm/topotools/topotools.py
@@ -551,10 +551,12 @@ def dimensionality(network):
Returns an 3-by-1 array containing ``True`` for each axis that contains
mu... |
PMEAL__OpenPNM-1789 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/core/ModelsMixin.py:ModelsMixin._regen"
],
"edited_modules": [
"openpnm/core/ModelsMixin.py:ModelsMixin"
]
},
"file": "openpnm/core/ModelsMixin.py"
},
{
... | PMEAL/OpenPNM | 0cdb50bea1b1ec2aa8fca57358faa0fc757dc7e1 | Problem with 'throat.partition_coef.all' not being set as iterative_prop nor updating when regenerate_models is called manually
I am writing a model where the partition coefficient changes with concentration. So it's important that 'throat.partition_coef.all' updates as 'throat.diffusive_conductance' (based on multipha... | diff --git a/openpnm/algorithms/ReactiveTransport.py b/openpnm/algorithms/ReactiveTransport.py
index 4f50c065f..5b495bc99 100644
--- a/openpnm/algorithms/ReactiveTransport.py
+++ b/openpnm/algorithms/ReactiveTransport.py
@@ -368,14 +368,16 @@ class ReactiveTransport(GenericTransport):
def _get_iterative_props(se... |
PMEAL__OpenPNM-1794 | [
{
"changes": {
"added_entities": [
"openpnm/algorithms/AdvectionDiffusion.py:AdvectionDiffusion.remove_BC",
"openpnm/algorithms/AdvectionDiffusion.py:AdvectionDiffusion._set_BC"
],
"added_modules": null,
"edited_entities": [
"openpnm/algorithms/AdvectionDiffusion.... | PMEAL/OpenPNM | 86411dbd0af894ac569ab2cb09d2d33441cd8716 | Outflow BC and other BC types must be prevented to coexist in a given set of pores | diff --git a/openpnm/algorithms/AdvectionDiffusion.py b/openpnm/algorithms/AdvectionDiffusion.py
index 7554b0429..5373467f1 100644
--- a/openpnm/algorithms/AdvectionDiffusion.py
+++ b/openpnm/algorithms/AdvectionDiffusion.py
@@ -74,7 +74,7 @@ class AdvectionDiffusion(ReactiveTransport):
**kwargs
):
... |
PMEAL__OpenPNM-1831 | [
{
"changes": {
"added_entities": [
"openpnm/algorithms/ReactiveTransport.py:ReactiveTransport.remove_source"
],
"added_modules": null,
"edited_entities": [
"openpnm/algorithms/ReactiveTransport.py:ReactiveTransport.set_source"
],
"edited_modules": [
"o... | PMEAL/OpenPNM | 5ecee86e7b99c122804ce39971e351faff09da7d | Add remove_source to Algorithm objects? | diff --git a/openpnm/algorithms/ReactiveTransport.py b/openpnm/algorithms/ReactiveTransport.py
index a5f422105..15ea1402a 100644
--- a/openpnm/algorithms/ReactiveTransport.py
+++ b/openpnm/algorithms/ReactiveTransport.py
@@ -185,7 +185,7 @@ class ReactiveTransport(GenericTransport):
if variable_props:
... |
PMEAL__OpenPNM-1844 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/network/Cubic.py:Cubic.__init__",
"openpnm/network/Cubic.py:Cubic._get_spacing"
],
"edited_modules": [
"openpnm/network/Cubic.py:Cubic"
]
},
"file": "op... | PMEAL/OpenPNM | 11530fa4ce00a80700429710bad3b26bc540d600 | network.spacing breaks for 1D networks with only two pores
```python
import openpnm as op
net = op.network.Cubic([2, 1, 1], spacing=1)
print(net.spacing)
``` | diff --git a/openpnm/network/Cubic.py b/openpnm/network/Cubic.py
index 389562f19..41278b9c0 100644
--- a/openpnm/network/Cubic.py
+++ b/openpnm/network/Cubic.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
"""
===============================================================================
Cubic: Generate lattice-like ne... |
PMEAL__OpenPNM-1850 | [
{
"changes": {
"added_entities": [
"openpnm/algorithms/ReactiveTransport.py:ReactiveTransport._set_variable_props"
],
"added_modules": null,
"edited_entities": [
"openpnm/algorithms/ReactiveTransport.py:ReactiveTransport.reset",
"openpnm/algorithms/ReactiveTranspo... | PMEAL/OpenPNM | 52eb1bca667fd098d027b83f9f344e0d54d42ca3 | The default markersize in plot_coordinates is way too small
Maybe change it to 10. | diff --git a/examples/notebooks/algorithms/multiphysics/advection_diffusion.ipynb b/examples/notebooks/algorithms/multiphysics/advection_diffusion.ipynb
index e38cc56a4..5f7e54b4d 100644
--- a/examples/notebooks/algorithms/multiphysics/advection_diffusion.ipynb
+++ b/examples/notebooks/algorithms/multiphysics/advection... |
PMEAL__OpenPNM-1902 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/models/physics/ad_dif_conductance.py:ad_dif"
],
"edited_modules": [
"openpnm/models/physics/ad_dif_conductance.py:ad_dif"
]
},
"file": "openpnm/models/physics/a... | PMEAL/OpenPNM | 9392f1cf79eb2a0f39ba9f6d6211c6ead596c147 | Remove lines that store peclet numbers
https://github.com/PMEAL/OpenPNM/blob/c01c5d3433c411bc69968feb7847cd2e3ba2eaa3/openpnm/models/physics/ad_dif_mig_conductance.py#L175
https://github.com/PMEAL/OpenPNM/blob/c01c5d3433c411bc69968feb7847cd2e3ba2eaa3/openpnm/models/physics/ad_dif_conductance.py#L97
These lines of... | diff --git a/openpnm/models/physics/ad_dif_conductance.py b/openpnm/models/physics/ad_dif_conductance.py
index 315ecde99..7dbe99fd3 100644
--- a/openpnm/models/physics/ad_dif_conductance.py
+++ b/openpnm/models/physics/ad_dif_conductance.py
@@ -94,10 +94,6 @@ def ad_dif(target,
Peij[(Peij < 1e-10) & (Peij >= 0)] =... |
PMEAL__OpenPNM-2157 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/core/Base.py:Base._get_name",
"openpnm/core/Base.py:Base.to_global",
"openpnm/core/Base.py:Base.to_local",
"openpnm/core/Base.py:LegacyMixin.tomask",
"openpnm/cor... | PMEAL/OpenPNM | 371c97fc696d027fb37d46d9b352b3c56f853de6 | Remove target argument from pores/throats
This should be replaced with the ``global=True/False`` keyword | diff --git a/openpnm/core/Base.py b/openpnm/core/Base.py
index a486260b7..d1e2840ad 100644
--- a/openpnm/core/Base.py
+++ b/openpnm/core/Base.py
@@ -268,7 +268,10 @@ class Base(dict):
item['throat.' + name] = item.pop('throat.' + old_name)
def _get_name(self):
- return self.settings['name... |
PMEAL__OpenPNM-2160 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "openpnm/models/geometry/misc.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"ed... | PMEAL/OpenPNM | ddefbc73da05c936dcea0373cb89cb92121a35b0 | Add a function for fitting PSD to experimental histograms
Following the discussion had in #2112, it might be a good idea to offer a function like the one I proposed.
Not quite sure how to implement this though...it doesn't quite fit with the pore-scale modeling framework. | diff --git a/openpnm/models/geometry/misc.py b/openpnm/models/geometry/misc.py
index fa4df4578..f300a85bb 100644
--- a/openpnm/models/geometry/misc.py
+++ b/openpnm/models/geometry/misc.py
@@ -1,6 +1,5 @@
r"""
-Helper methods for openpnm.geometry module.
-
+Helper methods for openpnm.models.geometry module
"""
di... |
PMEAL__OpenPNM-2162 | [
{
"changes": {
"added_entities": [
"openpnm/core/Base.py:Base.__delitem__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"openpnm/core/Base.py:Base"
]
},
"file": "openpnm/core/Base.py"
}
] | PMEAL/OpenPNM | aa445a2acec85ebf1e8f358e641fa5e2c4e141b7 | Add the ability to delete hirarchical dictionary keys in one go
# Intended
```python
del geo['throat.conduit_lengths'] # this currently doesn't work
```
# Current
```python
del geo['throat.conduit_lengths.pore1']
del geo['throat.conduit_lengths.pore2']
del geo['throat.conduit_lengths.throat']
``` | diff --git a/openpnm/core/Base.py b/openpnm/core/Base.py
index d1e2840ad..7b66f3993 100644
--- a/openpnm/core/Base.py
+++ b/openpnm/core/Base.py
@@ -251,6 +251,14 @@ class Base(dict):
raise KeyError(key)
return vals
+ def __delitem__(self, key):
+ try:
+ super().__delitem__(... |
PMEAL__OpenPNM-2173 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"openpnm/algorithms/GenericAlgorithm.py:GenericAlgorithm"
]
},
"file": "openpnm/algorithms/GenericAlgorithm.py"
},
{
"changes": {
"added_entities... | PMEAL/OpenPNM | 486ed107160e587096d85cf308af7eadb5bef390 | Algorithms probably don't need to inherit from the Base class
We did some digging and the algorithms rarely call any of the ``Base`` methods like ``num_pores`` etc. I think we might be able to just define ``GenericAlgorithm`` as a direct subclass of ``dict`` and that would free up the algorithms quite a bit. For inst... | diff --git a/openpnm/algorithms/GenericAlgorithm.py b/openpnm/algorithms/GenericAlgorithm.py
index c2551b1ab..70bc915b5 100644
--- a/openpnm/algorithms/GenericAlgorithm.py
+++ b/openpnm/algorithms/GenericAlgorithm.py
@@ -21,7 +21,7 @@ class GenericAlgorithmSettings:
@docstr.get_sections(base='GenericAlgorithm', sect... |
PMEAL__OpenPNM-2186 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/models/geometry/throat_volume.py:lens",
"openpnm/models/geometry/throat_volume.py:pendular_ring"
],
"edited_modules": [
"openpnm/models/geometry/throat_volume.py:lens... | PMEAL/OpenPNM | 4588835e40c14421dcc6c34b555595147006c417 | Throat lens volume is higher that throat volume when pore sizes are >=0.8*max_pore_size.
**Describe the bug**
Throat lens volume is higher that throat volume when pore sizes are >=0.8*max_pore_size. Throat lens_volume should always be less than throat volume (as they are corrections on volume calculations). Lens va... | diff --git a/openpnm/models/geometry/throat_volume.py b/openpnm/models/geometry/throat_volume.py
index 3cdfff587..13d4322f4 100644
--- a/openpnm/models/geometry/throat_volume.py
+++ b/openpnm/models/geometry/throat_volume.py
@@ -163,8 +163,8 @@ def lens(target, throat_diameter='throat.diameter',
"""
network =... |
PMEAL__OpenPNM-2216 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/core/_base.py:Base.interleave_data"
],
"edited_modules": [
"openpnm/core/_base.py:Base"
]
},
"file": "openpnm/core/_base.py"
}
] | PMEAL/OpenPNM | af5c148155e16793697f0e754846a0ca83eb50e1 | Interleave data could infer the wrong shape
In line 803, depending on which object comes first, the inferred shape could be wrong. For instance, if we have `(Nt,1)` and `(Nt,2)` conductances, it'll break (the opposite accidentally works fine, since it'll broadcast the values). See #1676.
https://github.com/PMEAL/Ope... | diff --git a/openpnm/core/_base.py b/openpnm/core/_base.py
index 3b64fb4a5..1a4a429b3 100644
--- a/openpnm/core/_base.py
+++ b/openpnm/core/_base.py
@@ -682,14 +682,14 @@ class Base(dict):
[False False False False]
"""
- # Fetch sources list depending on type of self
+ # Fetch subdomai... |
PMEAL__OpenPNM-2230 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/core/_base.py:Base.interleave_data"
],
"edited_modules": [
"openpnm/core/_base.py:Base"
]
},
"file": "openpnm/core/_base.py"
}
] | PMEAL/OpenPNM | 703437e816546e12ec2ff71350961d666edbda9d | Interleave data breaks when dealing with a combination of (Nt,1) and (Nt,2) conductance models
**Describe the bug**
Suppose you have two geometries, one involves a conductance model that returns (Nt,1), and the other (Nt,2). Calling `throat.conductance` on the phase object fails.
**To Reproduce**
Steps to reproduc... | diff --git a/openpnm/core/_base.py b/openpnm/core/_base.py
index a10d5a9d8..8e72baeb7 100644
--- a/openpnm/core/_base.py
+++ b/openpnm/core/_base.py
@@ -715,11 +715,14 @@ class Base(dict):
# Let's start by handling the easy cases first
if not any([a is None for a in arrs]):
+ # If any arr... |
PMEAL__OpenPNM-2240 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "example.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/algorithms/_gener... | PMEAL/OpenPNM | 7a5aacb5a02bb4e242de949dcc1b48af13d43a7d | Make main arguments mandatory for main objects
I think we should make main arguments, namely `network`, `geometry`, `phase`, `physics` (where applicable), mandatory for main objects. Here's what I propose:
- `network`: looks good as is
- `geometry`: `network`
- `phase`: `network`
- `physics`: `network`, `geometry... | diff --git a/example.py b/example.py
index c781347fe..d3e8746af 100644
--- a/example.py
+++ b/example.py
@@ -5,11 +5,10 @@ from openpnm.models.physics import source_terms
# %% Initialization: create Workspace and project objects.
ws = op.Workspace()
ws.settings.loglevel = 50
-proj = ws.new_project()
np.random.seed(... |
PMEAL__OpenPNM-2243 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/core/_base.py:Base.__getitem__"
],
"edited_modules": [
"openpnm/core/_base.py:Base"
]
},
"file": "openpnm/core/_base.py"
},
{
"changes": {
"added_... | PMEAL/OpenPNM | 846dc907049f1a411907be762e7cc013b72429e1 | Allow passing scalar values as argument to built-in source term models
Something like:
```python
mod = op.models.physics.generic_source_term.standard_kinetics
k, n = 1e-4, 2
phys.add_model(
X="pore.concentration",
propname="pore.rxn",
model=mod, prefactor=k, exponent=n,
regen_mode="deferred"
)
... | diff --git a/openpnm/core/_base.py b/openpnm/core/_base.py
index 3fac92c54..3152d64ab 100644
--- a/openpnm/core/_base.py
+++ b/openpnm/core/_base.py
@@ -182,6 +182,11 @@ class Base(dict):
raise Exception('Provided array is wrong length for ' + key)
def __getitem__(self, key):
+ # If the k... |
PMEAL__OpenPNM-2265 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "openpnm/__version__.py"
},
{
"changes": {
"added_entities": [
"openpnm/algorithms/_generic_transport.py:GenericTransport._validate_x0",
... | PMEAL/OpenPNM | a592f5d7b7d57b9ef2a7101eaad4950d4acb27c5 | Check that x0 contains valid numbers in transport algs
the ``_validate_data_health`` check should also check if x0 doesn't contain nan/infs.
This is the main point we settled on in #2126 | diff --git a/openpnm/__version__.py b/openpnm/__version__.py
index 5f18c6783..ee33cb361 100644
--- a/openpnm/__version__.py
+++ b/openpnm/__version__.py
@@ -1,1 +1,1 @@
-__version__ = '2.8.2.dev6'
+__version__ = '2.8.2.dev5'
diff --git a/openpnm/algorithms/_generic_transport.py b/openpnm/algorithms/_generic_transport.p... |
PMEAL__OpenPNM-2266 | [
{
"changes": {
"added_entities": [
"openpnm/topotools/_topotools.py:find_interface_throats"
],
"added_modules": [
"openpnm/topotools/_topotools.py:find_interface_throats"
],
"edited_entities": null,
"edited_modules": null
},
"file": "openpnm/topotools/... | PMEAL/OpenPNM | bc4a7da27aa23ff0fc74b1ae0bc18a4451db3223 | Find rate between two sets of pores
Here's a handy function that calculates the rate between two sets of pores `P1` and `P2`. I'm not sure if it's worth adding it to `openpnm`.
```python
def rate_interface(alg, P1, P2):
if np.intersect1d(P1, P2).size != 0:
raise Exception("P1 and P2 must not share any... | diff --git a/openpnm/topotools/_topotools.py b/openpnm/topotools/_topotools.py
index ce44e9c9a..2cbf51a9b 100644
--- a/openpnm/topotools/_topotools.py
+++ b/openpnm/topotools/_topotools.py
@@ -1890,6 +1890,39 @@ def filter_pores_by_z(network, pores, z=1):
hits = pores[orphans]
return hits
+
+def find_interf... |
PMEAL__OpenPNM-2306 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/algorithms/_generic_transport.py:GenericTransport.run",
"openpnm/algorithms/_generic_transport.py:GenericTransport._run_special"
],
"edited_modules": [
"openpnm/algor... | PMEAL/OpenPNM | b60786a2194e9812ef3728b76f75d483aebd6b38 | Change solution objects to be nested inside a dict
All solutions should be returned inside a dict, so that ``sol = alg.run()`` and ``sol['pore.concentration']`` points to the actual Solution object. This way (a) the solution knows the quantity it contains (pore.concentration) and (b) multiphysics can be combined into o... | diff --git a/openpnm/algorithms/_generic_transport.py b/openpnm/algorithms/_generic_transport.py
index 7dcf7a3d1..272d8ea2d 100644
--- a/openpnm/algorithms/_generic_transport.py
+++ b/openpnm/algorithms/_generic_transport.py
@@ -7,7 +7,7 @@ from openpnm.algorithms import BCsMixin
from openpnm.utils import logging, pre... |
PMEAL__OpenPNM-2319 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "openpnm/contrib/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited... | PMEAL/OpenPNM | eefbd1ed219cd40ad514b8bd5f80008d5e24dcd5 | Move Multiphase into the contrib folder
We are still trying to figure out how Multiphase should work, and how it should interact with Mixtures, etc. In the spirit of actually getting 3.0 released, I think we should move it to contrib to allow us to break compatibility later. | diff --git a/openpnm/contrib/__init__.py b/openpnm/contrib/__init__.py
index f1d1793be..994381c77 100644
--- a/openpnm/contrib/__init__.py
+++ b/openpnm/contrib/__init__.py
@@ -10,3 +10,4 @@ removed.
"""
from ._transient_multiphysics import *
+from ._multiphase import MultiPhase
diff --git a/openpnm/phase/_multipha... |
PMEAL__OpenPNM-2333 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/models/geometry/pore_surface_area/_funcs.py:sphere",
"openpnm/models/geometry/pore_surface_area/_funcs.py:circle",
"openpnm/models/geometry/pore_surface_area/_funcs.py:cube",
... | PMEAL/OpenPNM | 007c521a4cb93d45beb26cb878b9b1ee1762a4f8 | pore_area models are needlessly slow
We're using list comprehensions in these models, but could use unbuffered vector operations:
``` python
import numpy as np
import openpnm as op
net = op.network.Cubic(shape=[3, 3])
net['pore.diameter'] = 1
net['throat.diameter'] = np.random.rand(net.Nt)*0.5
net['throa... | diff --git a/openpnm/models/geometry/pore_surface_area/_funcs.py b/openpnm/models/geometry/pore_surface_area/_funcs.py
index 877347415..b5cc123a2 100644
--- a/openpnm/models/geometry/pore_surface_area/_funcs.py
+++ b/openpnm/models/geometry/pore_surface_area/_funcs.py
@@ -42,11 +42,11 @@ def sphere(
"""
net... |
PMEAL__OpenPNM-2445 | [
{
"changes": {
"added_entities": [
"openpnm/contrib/_multiphase.py:MultiPhase.phases",
"openpnm/contrib/_multiphase.py:MultiPhase.K",
"openpnm/contrib/_multiphase.py:MultiPhase._get_phase_labels",
"openpnm/contrib/_multiphase.py:MultiPhase._get_interface_throats",
"... | PMEAL/OpenPNM | 9b209ae9a469018f6e49a3dd05124d7787a42e60 | Fix MultiPhase to work with v3 changes | diff --git a/openpnm/contrib/_multiphase.py b/openpnm/contrib/_multiphase.py
index f07acc2ac..1b0d6c203 100644
--- a/openpnm/contrib/_multiphase.py
+++ b/openpnm/contrib/_multiphase.py
@@ -2,7 +2,7 @@ import logging
import numpy as np
import openpnm.models.misc as misc
from openpnm.phase import GenericPhase as Gener... |
PMEAL__OpenPNM-2467 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/algorithms/_advection_diffusion.py:AdvectionDiffusion._get_settings"
],
"edited_modules": [
"openpnm/algorithms/_advection_diffusion.py:AdvectionDiffusion"
]
},
... | PMEAL/OpenPNM | bdd1eb8b7652198846e19bbf6f7552347b643e0e | Fine-tune iterative props machinery
- [x] Move ``update_iterative_props`` to a higher level, like GenericAlgorithm, or perhaps as a Mixin
- [x] Add functools.cached_property to ``get_iterative_props``
- [ ] Decide if/how to update models on algorithm. Ex. Drainage could use 'update_iterative_props' method, or could ... | diff --git a/openpnm/algorithms/_advection_diffusion.py b/openpnm/algorithms/_advection_diffusion.py
index 2cd6c415b..efdf9cd0d 100644
--- a/openpnm/algorithms/_advection_diffusion.py
+++ b/openpnm/algorithms/_advection_diffusion.py
@@ -47,15 +47,6 @@ class AdvectionDiffusion(ReactiveTransport):
kwargs['na... |
PMEAL__OpenPNM-2532 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openpnm/core/_base2.py:Base2.get_conduit_data"
],
"edited_modules": [
"openpnm/core/_base2.py:Base2"
]
},
"file": "openpnm/core/_base2.py"
},
{
"changes": {
... | PMEAL/OpenPNM | 0d09f937f96b36cfb33ce49dfa9ebf334fee3c20 | Models that return conduit data should return Nt by 3 instead of a dict
Because it's more concise... | diff --git a/openpnm/core/_base2.py b/openpnm/core/_base2.py
index 94c40516d..f2f2e9a13 100644
--- a/openpnm/core/_base2.py
+++ b/openpnm/core/_base2.py
@@ -402,12 +402,35 @@ class Base2(dict):
values = from_neighbor_throats(target=self, prop='throat.'+prop, mode=mode)
return values
- def get... |
PMEAL__porespy-368 | [
{
"changes": {
"added_entities": [
"porespy/metrics/__funcs__.py:radial_density_distribution",
"porespy/metrics/__funcs__.py:lineal_path_distribution"
],
"added_modules": [
"porespy/metrics/__funcs__.py:radial_density_distribution",
"porespy/metrics/__funcs__.py... | PMEAL/porespy | f0089c7ceb9b9e186e6302b98cfe6cf2d89bd130 | Rename radial_density to radial_distribution
The term density comes from the statistical "probability density". This functions takes a distance transform, which is really a distribution of radii, and computes the pdf and cdf of those values. I propose to rename this to ``radial_distribution`` to indicate what it's an... | diff --git a/porespy/metrics/__funcs__.py b/porespy/metrics/__funcs__.py
index d0dc0e87e..8964ebc09 100644
--- a/porespy/metrics/__funcs__.py
+++ b/porespy/metrics/__funcs__.py
@@ -103,7 +103,7 @@ def porosity_profile(im, axis=0):
return prof
-def radial_density(im, bins=10, voxel_size=1):
+def radial_density_... |
PMEAL__porespy-369 | [
{
"changes": {
"added_entities": [
"porespy/tools/__funcs__.py:ps_rect"
],
"added_modules": [
"porespy/tools/__funcs__.py:ps_rect"
],
"edited_entities": null,
"edited_modules": null
},
"file": "porespy/tools/__funcs__.py"
},
{
"changes": {
... | PMEAL/porespy | f0089c7ceb9b9e186e6302b98cfe6cf2d89bd130 | Add new strel generators, that accepts ndims?
we have ps_sphere and ps_disk, so I propose ps_round, which accepts r and dims. If dims=2, it returns a disk, if dims=3 it returns a ball. This would save about 5 lines of code in dozens of functions. Could also do ps_rect for squares and cubes. | diff --git a/porespy/tools/__funcs__.py b/porespy/tools/__funcs__.py
index 1de41cb0c..0aa421013 100644
--- a/porespy/tools/__funcs__.py
+++ b/porespy/tools/__funcs__.py
@@ -911,6 +911,32 @@ def ps_round(r, ndim, smooth=True):
return ball
+def ps_rect(w, ndim):
+ r"""
+ Creates rectilinear structuring ele... |
PMEAL__porespy-371 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"porespy/generators/__imgen__.py:RSA"
],
"edited_modules": [
"porespy/generators/__imgen__.py:RSA"
]
},
"file": "porespy/generators/__imgen__.py"
}
] | PMEAL/porespy | f0089c7ceb9b9e186e6302b98cfe6cf2d89bd130 | Add a clearance argument to RSA | diff --git a/examples/generators/RSA.ipynb b/examples/generators/RSA.ipynb
index 6dfc999f7..50b8c8c12 100644
--- a/examples/generators/RSA.ipynb
+++ b/examples/generators/RSA.ipynb
@@ -29,7 +29,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": 2,
"metadata": {},
"outputs"... |
PMEAL__porespy-465 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"porespy/filters/_snows.py:trim_nearby_peaks"
],
"edited_modules": [
"porespy/filters/_snows.py:trim_nearby_peaks"
]
},
"file": "porespy/filters/_snows.py"
}
] | PMEAL/porespy | 51276c464ccaf8feea1cb246c6178a81af3b51dc | enhance trim_nearby_peaks to accept a tolerance or threshold
At the moment it trims peaks that are closer to another peak than to solid, but it'd be nice if we could put some sort of absolute AND relative tolerance, so it only trims peaks if they are too close to a nearby peak within some acceptable amount. | diff --git a/porespy/filters/_snows.py b/porespy/filters/_snows.py
index 346716570..aa17cb1a8 100644
--- a/porespy/filters/_snows.py
+++ b/porespy/filters/_snows.py
@@ -350,7 +350,7 @@ def trim_saddle_points(peaks, dt, max_iters=10):
return peaks
-def trim_nearby_peaks(peaks, dt):
+def trim_nearby_peaks(peaks,... |
PMEAL__porespy-802 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "porespy/__version__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modu... | PMEAL/porespy | aad78183ae47b4cf8c28558a25d5ee7287ff06b5 | add seed argument to all generators
This would be handy for several reason:
- so that we don't have to import numpy just to initialize the rng
- numba doesn't respect the numpy rng so needs special treatment
- the docs could explain how to get a repeatable image | diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml
index c5a81e49c..14230c7ac 100644
--- a/.github/workflows/gh-pages.yml
+++ b/.github/workflows/gh-pages.yml
@@ -22,30 +22,21 @@ jobs:
with:
python-version: 3.8
- - name: Cache conda
+ - name: Cache pip
... |
PMEAL__porespy-809 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"porespy/networks/_snow2.py:_parse_pad_width"
],
"edited_modules": [
"porespy/networks/_snow2.py:_parse_pad_width"
]
},
"file": "porespy/networks/_snow2.py"
}
] | PMEAL/porespy | 63ce07d4a1c0337bc5942a33777fae81adc6aba9 | boundary_width in snow2 breaks when trying to specify padding on both ends of all axes
This works:
`b = ps.networks.snow2(im, boundary_width=[[5, 15], 10])`
This breaks:
`b = ps.networks.snow2(im, boundary_width=[[5, 15], [10, 10]])`
The complaint is coming from `np.pad`: `TypeError: `pad_width` must be of inte... | diff --git a/porespy/networks/_snow2.py b/porespy/networks/_snow2.py
index 5aa197559..404ef5d99 100644
--- a/porespy/networks/_snow2.py
+++ b/porespy/networks/_snow2.py
@@ -244,4 +244,4 @@ def _parse_pad_width(pad_width, shape):
else:
raise Exception("pad_width components can't have 2+ elements")
... |
PMEAL__porespy-863 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"porespy/metrics/_funcs.py:satn_profile"
],
"edited_modules": [
"porespy/metrics/_funcs.py:satn_profile",
"porespy/metrics/_funcs.py:results"
]
},
"file": "pores... | PMEAL/porespy | 2b340e9cd1c6923f375496b0c040ea614d75e4d5 | Update `satn_profile` to accept an already thresholded image | diff --git a/porespy/metrics/_funcs.py b/porespy/metrics/_funcs.py
index d1001a351..e44651570 100644
--- a/porespy/metrics/_funcs.py
+++ b/porespy/metrics/_funcs.py
@@ -1104,7 +1104,7 @@ def pc_curve(im, sizes=None, pc=None, seq=None,
return pc_curve
-def satn_profile(satn, s, axis=0, span=10, mode='tile'):
+d... |
PMEAL__porespy-864 | [
{
"changes": {
"added_entities": [
"porespy/tools/_utils.py:_format_time",
"porespy/tools/_utils.py:tic",
"porespy/tools/_utils.py:toc"
],
"added_modules": [
"porespy/tools/_utils.py:_format_time",
"porespy/tools/_utils.py:tic",
"porespy/tools/_u... | PMEAL/porespy | 2b340e9cd1c6923f375496b0c040ea614d75e4d5 | Readd tic and toc to tools
I've been interested in timings a lot lately and it would be helpful if `tic` and `toc` were readded back to the tools module. | diff --git a/porespy/tools/_utils.py b/porespy/tools/_utils.py
index 630ac30af..9055157ef 100644
--- a/porespy/tools/_utils.py
+++ b/porespy/tools/_utils.py
@@ -16,9 +16,88 @@ __all__ = [
'get_tqdm',
'show_docstring',
'Results',
+ 'tic',
+ 'toc',
]
+def _format_time(timespan, precision=3):
+ ... |
PMEAL__porespy-865 | [
{
"changes": {
"added_entities": [
"porespy/filters/_size_seq_satn.py:pc_to_seq"
],
"added_modules": [
"porespy/filters/_size_seq_satn.py:pc_to_seq"
],
"edited_entities": null,
"edited_modules": null
},
"file": "porespy/filters/_size_seq_satn.py"
},
... | PMEAL/porespy | ff3029fad904dab8ac6f5acf02e3270a704cb07f | Add a `pc_to_seq` function
Not sure why we don't have this already. The only complication is that it does not work with ibip results since the Pcs are not filled sequentially. Not sure how to inidcate this. | diff --git a/porespy/filters/_size_seq_satn.py b/porespy/filters/_size_seq_satn.py
index 6b83bc26d..ace920e73 100644
--- a/porespy/filters/_size_seq_satn.py
+++ b/porespy/filters/_size_seq_satn.py
@@ -8,6 +8,7 @@ __all__ = [
'size_to_satn',
'seq_to_satn',
'pc_to_satn',
+ 'pc_to_seq',
'satn_to_seq... |
PSLmodels__ParamTools-80 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"paramtools/parameters.py:Parameters.to_array"
],
"edited_modules": [
"paramtools/parameters.py:Parameters"
]
},
"file": "paramtools/parameters.py"
}
] | PSLmodels/ParamTools | 06d113a25a3a6e3193fc3704c40a92cbcfdbe80b | Scalar values are set as zero dimension arrays
When `array_first` is `True`, scalar values are set to zero dimension NumPy arrays. For the most part, these values act like normal Python `int`s or `float`s, but they cause problems in edge cases. Further, this behavior may confusing for new users. I'll open a PR this wee... | diff --git a/paramtools/parameters.py b/paramtools/parameters.py
index a44fc7c..1d91538 100644
--- a/paramtools/parameters.py
+++ b/paramtools/parameters.py
@@ -369,10 +369,14 @@ class Parameters:
f"\nYou may be able to describe this parameter's values with additional "
f"labels\nand t... |
PSLmodels__microdf-158 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"microdf/inequality.py:gini",
"microdf/inequality.py:top_x_pct_share",
"microdf/inequality.py:bottom_x_pct_share",
"microdf/inequality.py:bottom_50_pct_share",
"microdf/in... | PSLmodels/microdf | a2422e8b0bf20eca60a9bf39e8a3ad14d98a62e9 | Add groupby to gini | diff --git a/.github/workflows/check_jupyterbook.yml b/.github/workflows/check_jupyterbook.yml
index d2174d5..49f4e0d 100644
--- a/.github/workflows/check_jupyterbook.yml
+++ b/.github/workflows/check_jupyterbook.yml
@@ -15,7 +15,7 @@ jobs:
with:
activate-environment: microdf
environment-... |
PSLmodels__microdf-166 | [
{
"changes": {
"added_entities": [
"microdf/generic.py:MicroSeries.handles_zero_weights",
"microdf/generic.py:MicroSeries.groupby",
"microdf/generic.py:MicroSeries.__getitem__",
"microdf/generic.py:MicroSeriesGroupBy.__init__",
"microdf/generic.py:MicroSeriesGroupBy... | PSLmodels/microdf | db688dbab9b0fc84bbd7d5d096084ff8d6a9ff13 | MicroSeries(list) causes TypeError: __init__() got an unexpected keyword argument 'column'
This crashes my ipython session:
```
import microdf as mdf
mdf.Series([1, 2, 3])
```
Error is long, includes `TypeError: __init__() got an unexpected keyword argument 'column'` | diff --git a/microdf/generic.py b/microdf/generic.py
index 2b72bbd..654cba5 100644
--- a/microdf/generic.py
+++ b/microdf/generic.py
@@ -12,21 +12,29 @@ class MicroSeries(pd.Series):
:type weights: np.array
"""
super().__init__(*args, **kwargs)
- self.weights = weights
+ self.se... |
PSLmodels__microdf-188 | [
{
"changes": {
"added_entities": [
"microdf/generic.py:MicroSeries.cumsum",
"microdf/generic.py:MicroSeries.rank",
"microdf/generic.py:MicroDataFrame.catch_series_relapse",
"microdf/generic.py:MicroDataFrame.__setattr__",
"microdf/generic.py:MicroDataFrame.reset_ind... | PSLmodels/microdf | 995a0c703af8bcc84809915df155336d9473d043 | Changing a MicroDataFrame's index makes its columns Series instead of MicroSeries
```
d = mdf.MicroDataFrame(dict(x=[1, 2, 3]), weights=[4, 5, 6])
d.x.__class__
```
>microdf.generic.MicroSeries
```
d = mdf.MicroDataFrame(dict(x=[1, 2, 3]), weights=[4, 5, 6])
d.index = [1, 2, 3]
d.x.__class__
```
>pandas.core.... | diff --git a/microdf/generic.py b/microdf/generic.py
index 9c19d0d..f6a91ad 100644
--- a/microdf/generic.py
+++ b/microdf/generic.py
@@ -239,6 +239,19 @@ class MicroSeries(pd.Series):
b50 = self.bottom_50_pct_share()
return t10 / b50
+ @vector_function
+ def cumsum(self) -> pd.Series:
+ ... |
PSLmodels__microdf-191 | [
{
"changes": {
"added_entities": [
"microdf/generic.py:MicroSeries.decile_rank",
"microdf/generic.py:MicroSeries.quintile_rank",
"microdf/generic.py:MicroSeries.quartile_rank",
"microdf/generic.py:MicroSeries.percentile_rank"
],
"added_modules": null,
"edi... | PSLmodels/microdf | 2c66482b72f12355ad0035bf281390197908788c | Add MicroSeries.{percentile, decile, quintile, quartile}_rank
Based off of recently-added `MicroSeries.rank(pct=True)` | diff --git a/microdf/generic.py b/microdf/generic.py
index 32d688c..4b31aba 100644
--- a/microdf/generic.py
+++ b/microdf/generic.py
@@ -1,6 +1,7 @@
from typing import Callable, Union
from functools import wraps
import warnings
+import copy
import numpy as np
import pandas as pd
@@ -247,10 +248,26 @@ class Micro... |
PSLmodels__microdf-205 | [
{
"changes": {
"added_entities": [
"microdf/generic.py:MicroSeries.copy",
"microdf/generic.py:MicroSeries.equals",
"microdf/generic.py:MicroDataFrame.copy",
"microdf/generic.py:MicroDataFrame.equals"
],
"added_modules": null,
"edited_entities": [
"... | PSLmodels/microdf | 02280c5d13dbc715258cd47b57a8ddd9291ecce2 | MicroDataFrame[[cols]] produces KeyError
This works in `pandas` and should produce a `MicroDataFrame` with only the column `x`:
```
d = mdf.MicroDataFrame(dict(x=[1, 2], y=[3, 4]), weights=[5, 6])
d[["x"]]
```
But it errors out instead:
```
KeyError: "None of [Index(['x'], dtype='object')] are in the [index]"
`... | diff --git a/microdf/generic.py b/microdf/generic.py
index f6a91ad..32d688c 100644
--- a/microdf/generic.py
+++ b/microdf/generic.py
@@ -1,8 +1,8 @@
-import numpy as np
-import pandas as pd
from typing import Callable, Union
from functools import wraps
import warnings
+import numpy as np
+import pandas as pd
cl... |
PSLmodels__microdf-219 | [
{
"changes": {
"added_entities": [
"microdf/generic.py:MicroSeries.__repr__",
"microdf/generic.py:MicroDataFrame.__repr__"
],
"added_modules": null,
"edited_entities": [
"microdf/generic.py:MicroDataFrame.__getitem__"
],
"edited_modules": [
"mi... | PSLmodels/microdf | 8802af33cdae9b37733a33aa307ee991246b0716 | Subsetting a MicroDataFrame doesn't subset weights
Example:
```
d = mdf.MicroDataFrame({"x": [1, 2, 3], "y": [1, 2, 2]}, weights=[4, 5, 6])
d2 = d[d.y > 1]
d2.shape # (2, 2)
d2.weights.shape # (3,)
```
Among other things, this breaks commands like `d[d.y > 1].mean()` with:
>TypeError: Axis must be specified w... | diff --git a/microdf/generic.py b/microdf/generic.py
index 4b31aba..b0906cf 100644
--- a/microdf/generic.py
+++ b/microdf/generic.py
@@ -373,6 +373,11 @@ class MicroSeries(pd.Series):
def __pos__(self, other):
return MicroSeries(super().__pos__(other), weights=self.weights)
+ def __repr__(self):
+ ... |
PaccMann__paccmann_datasets-13 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pytoda/smiles/transforms.py:ToTensor.__call__"
],
"edited_modules": [
"pytoda/smiles/transforms.py:ToTensor"
]
},
"file": "pytoda/smiles/transforms.py"
}
] | PaccMann/paccmann_datasets | def0673e39f2e6a6e86f6d2456eab4e7b770980f | Shape of tensors returned by SMILES_dataset
The `SMILESDataset` class currently returns per default tensors of shape `sequence_length x 1`. This is not ideal since the additional dimension is not understood by most models per default.
As a workaround, we use `torch.squeeze()` in the code that currently uses `SMILESDat... | diff --git a/pytoda/smiles/transforms.py b/pytoda/smiles/transforms.py
index 6a9288f..a40439f 100644
--- a/pytoda/smiles/transforms.py
+++ b/pytoda/smiles/transforms.py
@@ -95,7 +95,7 @@ class ToTensor(Transform):
"""
return torch.tensor(
token_indexes, dtype=self.dtype, device=self.devic... |
PagerDuty__pdpyras-54 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pdpyras.py:PDSession.stagger_cooldown",
"pdpyras.py:EventsAPISession.auth_header",
"pdpyras.py:EventsAPISession.send_event",
"pdpyras.py:APISession.find",
"pdpyras.py:API... | PagerDuty/pdpyras | 4fb715ab215a500262cb61005b1a9c70ba190179 | EventsAPISession uses `X-Routing-Key` instead of setting `routing_key` in payload
EventsAPISession uses the `X-Routing-Key` header to specify the routing key and does not set the `routing_key` parameter in the REST Payload.
API specification requires that the `routing_key` parameter is a required parameter.
https... | diff --git a/pdpyras.py b/pdpyras.py
index 506440d..2143baf 100644
--- a/pdpyras.py
+++ b/pdpyras.py
@@ -211,7 +211,7 @@ def tokenize_url_path(url, baseurl='https://api.pagerduty.com'):
:type method: str
:type url: str
:type baseurl: str
- :rtype: tuple
+ :rtype: tuple
"""
urlnparams = u... |
PandABlocks__PandABlocks-client-20 | [
{
"changes": {
"added_entities": [
"pandablocks/commands.py:RawResponse.line",
"pandablocks/commands.py:RawResponse.multiline",
"pandablocks/commands.py:Disarm.lines",
"pandablocks/commands.py:Disarm.response"
],
"added_modules": [
"pandablocks/commands.... | PandABlocks/PandABlocks-client | 89bb7d6cbe69199959d62859fabfd2a59526ae52 | look at changing return value of send
to always be a list.
this may reduce the amount of code checking the type of the return. | diff --git a/.github/workflows/code.yml b/.github/workflows/code.yml
index 0768ee0..4cfab26 100644
--- a/.github/workflows/code.yml
+++ b/.github/workflows/code.yml
@@ -25,7 +25,7 @@ jobs:
run: |
env
pip install pipenv
- pipenv install --dev --deploy && pipenv graph
+ pi... |
PandABlocks__PandABlocks-client-55 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pandablocks/connections.py:DataConnection.__init__",
"pandablocks/connections.py:DataConnection._handle_data_frame",
"pandablocks/connections.py:DataConnection._handle_data_end"
],... | PandABlocks/PandABlocks-client | 158122304c0c730e6adaddea30eae3d27db9d3da | How to get data frames immediately, instead of one frame late?
Hi Team PandABlocks
At MAX IV, we are trying to implement a near "real-time" indicator of the number of samples received from the PandABox via the data capture port. We are currently underestimating the expected value while capturing.
### Symptoms
... | diff --git a/docs/explanations/performance.rst b/docs/explanations/performance.rst
index 18f384c..f2952d9 100644
--- a/docs/explanations/performance.rst
+++ b/docs/explanations/performance.rst
@@ -51,7 +51,7 @@ Scale the data on the client
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
`AsyncioClient.data` and `BlockingClient.data` ... |
PandABlocks__PandABlocks-client-96 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/pandablocks/commands.py:GetFieldInfo._time"
],
"edited_modules": [
"src/pandablocks/commands.py:GetFieldInfo"
]
},
"file": "src/pandablocks/commands.py"
},
{
... | PandABlocks/PandABlocks-client | aa2eb1a823c08751b0deba072f39d1b4285d52f6 | PandABlocks-client raises error when using PandA3.1 (b1) firmware
I have recently updated the Firmware on BL20J-TS-PANDA-01 (172.23.90.24) to 3.1b1 and it produces the following error:
```
pandablocks-ioc softioc BL20J-TS-PANDA-01 BL20J-EA-PANDA-01
INFO: PVXS QSRV2 is loaded, permitted, and ENABLED.
Traceback (most... | diff --git a/src/pandablocks/commands.py b/src/pandablocks/commands.py
index b94a0f6..7a5d32e 100644
--- a/src/pandablocks/commands.py
+++ b/src/pandablocks/commands.py
@@ -510,13 +510,12 @@ class GetFieldInfo(Command[dict[str, FieldInfo]]):
def _time(
self, field_name: str, field_type: str, field_subtype... |
Parallel-in-Time__pySDC-235 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pySDC/implementations/convergence_controller_classes/adaptivity.py:AdaptivityResidual.setup"
],
"edited_modules": [
"pySDC/implementations/convergence_controller_classes/adaptivity.p... | Parallel-in-Time/pySDC | 994530de81e58b85952343cd34e3ba7890cc1975 | Default methods in convergence controller
It looks like the default methods of the `AdaptivityResidual` class are [never called](https://parallel-in-time.org/pySDC/coverage/d_c28af68f8f845bbd_adaptivity_py.html#t290). The same for the [`BasicRestartingMPI`](https://parallel-in-time.org/pySDC/coverage/d_c28af68f8f845bbd... | diff --git a/pySDC/implementations/convergence_controller_classes/adaptivity.py b/pySDC/implementations/convergence_controller_classes/adaptivity.py
index b26fec527..06fc27f07 100644
--- a/pySDC/implementations/convergence_controller_classes/adaptivity.py
+++ b/pySDC/implementations/convergence_controller_classes/adapt... |
Parietal-INRIA__fmralign-106 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fmralign/_utils.py:_make_parcellation"
],
"edited_modules": [
"fmralign/_utils.py:_make_parcellation"
]
},
"file": "fmralign/_utils.py"
},
{
"changes": {
... | Parietal-INRIA/fmralign | 51b01ffc4ae74e00f6c2dc2f25dcba2a76af79f6 | Using surface data
Currently, the code takes Niimg-like objects. PairwiseAlignment also takes as input a mask (also Niimg-like object). How can we straightforwardly use surface space data with fmralign?
One idea: Make the input images numpy arrays (ntimepoints/ncontrasts x nvertices). 'clustering' could also become ... | diff --git a/fmralign/_utils.py b/fmralign/_utils.py
index 7f8e4ac..6fc8111 100644
--- a/fmralign/_utils.py
+++ b/fmralign/_utils.py
@@ -1,5 +1,4 @@
# -*- coding: utf-8 -*-
-import os
import warnings
import nibabel as nib
@@ -8,6 +7,7 @@ from nilearn._utils.niimg_conversions import check_same_fov
from nilearn.ima... |
Parietal-INRIA__fmralign-115 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fmralign/preprocessing.py:ParcellationMasker._fit_masker"
],
"edited_modules": [
"fmralign/preprocessing.py:ParcellationMasker"
]
},
"file": "fmralign/preprocessing.py"... | Parietal-INRIA/fmralign | 077501ef5c14d00a2f34bb1e13f221a86ffe43f5 | [BUG] Inconsistence between 3D inputs and 4D templates
When dealing with one contrast, input images are usually 3D however the template is initialized as a 1 sample 4D image which raises an error when comparing the shapes during preprocessing. | diff --git a/fmralign/preprocessing.py b/fmralign/preprocessing.py
index 63521e8..0cc4a0a 100644
--- a/fmralign/preprocessing.py
+++ b/fmralign/preprocessing.py
@@ -123,6 +123,14 @@ class ParcellationMasker(BaseEstimator, TransformerMixin):
if isinstance(imgs, Nifti1Image):
imgs = [imgs]
+ ... |
Parquery__icontract-109 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"icontract/_decorators.py:require.__init__",
"icontract/_decorators.py:snapshot.__init__",
"icontract/_decorators.py:ensure.__init__"
],
"edited_modules": [
"icontract... | Parquery/icontract | 846e3187869a9ba790e9b893c98e5055e1cce274 | include decorator definition in ViolationError description
Consider this module (defined in ictb.py):
```
from icontract import require, ensure
@require(lambda x: x > 0)
def frobulate(x: int) -> int:
return x
```
Which I use
```
$ python -c "import ictb; ictb.frobulate(-1)" ... | diff --git a/README.rst b/README.rst
index 4cee487..17e1bbe 100644
--- a/README.rst
+++ b/README.rst
@@ -84,7 +84,8 @@ If you want to customize the error, see Section "Custom Errors".
>>> some_func(x=1)
Traceback (most recent call last):
...
- icontract.errors.ViolationError: x > 3: x was 1
+ ico... |
Parquery__icontract-112 | [
{
"changes": {
"added_entities": [
"icontract/_checkers.py:_not_check"
],
"added_modules": [
"icontract/_checkers.py:_not_check"
],
"edited_entities": [
"icontract/_checkers.py:_assert_precondition",
"icontract/_checkers.py:_assert_invariant",
... | Parquery/icontract | 013cb1bb0294097eaa8c43776bfd4d73342a1655 | catch exceptions in boolyness of check
This is very much related to #97
Consider this:
```
$ cat i.py
from icontract import require, ensure
import numpy as np
@require(lambda x: np.array([True, False]))
def frobulate(x: int) -> int:
return x
$ python -c "import i; i.frobulate(1)" ... | diff --git a/icontract/_checkers.py b/icontract/_checkers.py
index 1b27f5a..1dc79d3 100644
--- a/icontract/_checkers.py
+++ b/icontract/_checkers.py
@@ -66,6 +66,27 @@ def _kwargs_from_call(param_names: List[str], kwdefaults: Dict[str, Any], args:
return mapping
+def _not_check(check: Any, contract: Contract) ... |
Parquery__icontract-114 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"icontract/_checkers.py:_assert_precondition",
"icontract/_checkers.py:_assert_postcondition"
],
"edited_modules": [
"icontract/_checkers.py:_assert_precondition",
"ic... | Parquery/icontract | 5eecd149ac76db451a978ba208b95768fa1685af | checking of contract arguments is too strict
consider:
```
$ cat i.py (time_gym)
from icontract import require, e... | diff --git a/icontract/_checkers.py b/icontract/_checkers.py
index 1dc79d3..e5909e2 100644
--- a/icontract/_checkers.py
+++ b/icontract/_checkers.py
@@ -92,11 +92,12 @@ def _assert_precondition(contract: Contract, resolved_kwargs: Mapping[str, Any])
Assert that the contract holds as a precondition.
:param c... |
Parquery__icontract-115 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"icontract/_checkers.py:_kwargs_from_call"
],
"edited_modules": [
"icontract/_checkers.py:_kwargs_from_call"
]
},
"file": "icontract/_checkers.py"
}
] | Parquery/icontract | 21f6b8f51d4d458ee36b8a31cc091a5679a01000 | Crashes when functions are given wrong number of (positional) arguments
The following case, where `f` is given one too many arguments, should give the _original error message_ `TypeError: f() takes 0 positional arguments but 1 was given`:
```python
import icontract
@icontract.require(lambda: True)
def f():
... | diff --git a/icontract/_checkers.py b/icontract/_checkers.py
index e5909e2..19b1dcf 100644
--- a/icontract/_checkers.py
+++ b/icontract/_checkers.py
@@ -58,7 +58,13 @@ def _kwargs_from_call(param_names: List[str], kwdefaults: Dict[str, Any], args:
# Override the defaults with the values actually suplied to the f... |
Parquery__icontract-137 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"icontract/_checkers.py:decorate_with_checker",
"icontract/_checkers.py:_decorate_with_invariants"
],
"edited_modules": [
"icontract/_checkers.py:decorate_with_checker",
... | Parquery/icontract | 0bf4b66fd1590fc18a73208b69a0a17b228dd79b | Class invariant changes __dict__ unexpectedly
Usually `__dict__` can be used to compare if two instances have equal attributes. Adding an class invariant falsifies a `__eq__` method which is based on this assumption:
```Python
from icontract import invariant
@invariant(lambda self: all(" " not in n for n... | diff --git a/icontract/_checkers.py b/icontract/_checkers.py
index de92e3e..af1bceb 100644
--- a/icontract/_checkers.py
+++ b/icontract/_checkers.py
@@ -2,7 +2,8 @@
import contextlib
import functools
import inspect
-from typing import Callable, Any, Iterable, Optional, Tuple, List, Mapping, MutableMapping, Dict
+imp... |
Parquery__icontract-151 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"icontract/_checkers.py:_decorate_with_invariants"
],
"edited_modules": [
"icontract/_checkers.py:_decorate_with_invariants"
]
},
"file": "icontract/_checkers.py"
}
] | Parquery/icontract | f99d7436e3ef1fee8b83f7dc6b2ea8500ebdfa68 | AttributeError in contract caused by method call in constructor
When a method is called in the constructor, an `AttributeError` is raised in the contract. Here is a reproducer:
```Python
from icontract import invariant
@invariant(lambda self: all(" " not in part for part in self.parts))
class ID:
def __i... | diff --git a/README.rst b/README.rst
index 12c3b36..62fdfc3 100644
--- a/README.rst
+++ b/README.rst
@@ -711,6 +711,19 @@ in progress and removed once the invariants checking finished. As long as the du
``__dbc_invariant_check_is_in_progress__`` is present, the wrappers that check invariants simply return the result o... |
Parquery__icontract-166 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"icontract/_recompute.py:Visitor"
]
},
"file": "icontract/_recompute.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
... | Parquery/icontract | 9e8451b28b9cb5bdd02c1ae0b194af58ea80854d | Violating contract with assignment expression produces NotImplementedError
An assignment expression in a lambda expression in a contract produces a `NotImplementedError` from `incontract._recompute` when a call violates the contract. A call that conforms to the contract does not produce the error. Using Python 3.8.5... | diff --git a/.travis.yml b/.travis.yml
index 32624d8..7155fe1 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,7 +3,7 @@ python:
- "3.5"
- "3.6"
- "3.7"
- - "3.8"
+ - "3.8.5"
install:
- pip3 install -e .[dev]
- pip3 install coveralls
diff --git a/icontract/_recompute.py b/icontract/_recompute.py
index... |
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