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 |
|---|---|---|---|---|---|
ESMValGroup__ESMValCore-2230 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/preprocessor/_area.py:extract_region"
],
"edited_modules": [
"esmvalcore/preprocessor/_area.py:extract_region"
]
},
"file": "esmvalcore/preprocessor/_area.py... | ESMValGroup/ESMValCore | 79455c1dfb4c29e801472cadccd723027997cc88 | extract_region forces the region to be represented from 0-360 longitude
`extract_region` uses an iris cube `intersection`, and then applies another so that the cube is represented from 0-360 longitude. If the extracted region crosses 360 degrees, this forces the bounds to be discontiguous, and prevents future regrid-in... | diff --git a/esmvalcore/preprocessor/_area.py b/esmvalcore/preprocessor/_area.py
index ae78526a2..145b87ec3 100644
--- a/esmvalcore/preprocessor/_area.py
+++ b/esmvalcore/preprocessor/_area.py
@@ -84,7 +84,6 @@ def extract_region(
latitude=(start_latitude, end_latitude),
ignore_bounds=True,
... |
ESMValGroup__ESMValCore-2236 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "doc/conf.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe/from_... | ESMValGroup/ESMValCore | 7a70d5b274869052e45d753ef3012a5f3b486696 | Improve the exception message when an option within the `rootpath` section is missing from the user configuration file
**Describe the bug**
I ran the `recipe_extreme_events.yml` at the MO for the first time this morning and I got the following error message:
```
KeyError: 'default rootpath must be specified in con... | diff --git a/CITATION.cff b/CITATION.cff
index 1f5a31582..70cf87276 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -201,11 +201,11 @@ authors:
given-names: Joerg
cff-version: 1.2.0
-date-released: 2023-07-04
+date-released: 2023-11-01
doi: "10.5281/zenodo.3387139"
license: "Apache-2.0"
message: "If you use ... |
ESMValGroup__ESMValCore-2238 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe/from_datasets.py:_SortableDict.__lt__",
"esmvalcore/_recipe/from_datasets.py:_change_dict_type",
"esmvalcore/_recipe/from_datasets.py:_group_ensemble_members"
],... | ESMValGroup/ESMValCore | 7a70d5b274869052e45d753ef3012a5f3b486696 | Sorting of ensemble members (#2095) breaks with mix of facet value types
**Describe the bug**
In #2095, we introduced sorting of datasets during the recipe filling process.
This breaks currently when the dataset specifiers in the input recipe contain lists, for example for experiments, which is relatively commonly us... | diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index e1b497c58..62887266d 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -50,8 +50,8 @@ https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda#
https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2... |
ESMValGroup__ESMValCore-2240 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe/from_datasets.py:_SortableDict.__lt__",
"esmvalcore/_recipe/from_datasets.py:_change_dict_type",
"esmvalcore/_recipe/from_datasets.py:_group_ensemble_members"
],... | ESMValGroup/ESMValCore | 7a70d5b274869052e45d753ef3012a5f3b486696 | Input data versions can confuse ESMValTool
Sometimes input data is available in more than one version. This is true both for (CMIP5/6) model data, where a newer version may supersede an older one without the older one being removed from storage, and observational data, where it is common to have several versions of dat... | diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index e1b497c58..62887266d 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -50,8 +50,8 @@ https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda#
https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2... |
ESMValGroup__ESMValCore-2258 | [
{
"changes": {
"added_entities": [
"esmvalcore/iris_helpers.py:_rechunk",
"esmvalcore/iris_helpers.py:_rechunk_dim_metadata",
"esmvalcore/iris_helpers.py:rechunk_cube"
],
"added_modules": [
"esmvalcore/iris_helpers.py:_rechunk",
"esmvalcore/iris_helpers.... | ESMValGroup/ESMValCore | 1f55ec9358df2c6cfcc5e341a1c08f6a3537d43b | ESMValCore: add preprocessor that converts time to local solar time
To correctly visualize diurnal cycles, it is necessary to convert the regular time coordinate to a solar time coordinate. This is non-trivial since we need to re-order the data along the time dimension depending on the longitude of the grid cell.
For ... | diff --git a/doc/recipe/preprocessor.rst b/doc/recipe/preprocessor.rst
index 5c4b14e35..7ad4bdbce 100644
--- a/doc/recipe/preprocessor.rst
+++ b/doc/recipe/preprocessor.rst
@@ -1219,6 +1219,7 @@ The ``_time.py`` module contains the following preprocessor functions:
* regrid_time_: Aligns the time axis of each dataset ... |
ESMValGroup__ESMValCore-2279 | [
{
"changes": {
"added_entities": [
"esmvalcore/_recipe/recipe.py:_log_input_files",
"esmvalcore/_recipe/recipe.py:_get_files_str"
],
"added_modules": [
"esmvalcore/_recipe/recipe.py:_log_input_files",
"esmvalcore/_recipe/recipe.py:_get_files_str"
],
... | ESMValGroup/ESMValCore | f51516962df2b5e7c8351a2d5281900498a199c0 | If custom location for custom CMOR tables is used, default location is ignored
**Describe the bug**
If a custom location for custom CMOR tables is used via `custom: cmor_path: ...` in `config-developer`, the default location `esmvalcore/cmor/tables/custom` is ignored. To avoid copying all existing tables to a custom l... | diff --git a/doc/quickstart/configure.rst b/doc/quickstart/configure.rst
index 4caf7e794..c14bcb6ea 100644
--- a/doc/quickstart/configure.rst
+++ b/doc/quickstart/configure.rst
@@ -683,7 +683,8 @@ related to CMOR table settings available:
extended with variables from the :ref:`custom_cmor_tables` (by default loaded
... |
ESMValGroup__ESMValCore-2303 | [
{
"changes": {
"added_entities": [
"esmvalcore/_recipe/recipe.py:_log_input_files",
"esmvalcore/_recipe/recipe.py:_get_files_str"
],
"added_modules": [
"esmvalcore/_recipe/recipe.py:_log_input_files",
"esmvalcore/_recipe/recipe.py:_get_files_str"
],
... | ESMValGroup/ESMValCore | 79455c1dfb4c29e801472cadccd723027997cc88 | No explicit logging of supplementary variable file paths
**Is your feature request related to a problem? Please describe.**
Currently, file paths of supplementary variables are logged together with their parent variable:
https://github.com/ESMValGroup/ESMValCore/blob/79455c1dfb4c29e801472cadccd723027997cc88/esmva... | diff --git a/esmvalcore/_recipe/recipe.py b/esmvalcore/_recipe/recipe.py
index 1613f6cf6..d245880fa 100644
--- a/esmvalcore/_recipe/recipe.py
+++ b/esmvalcore/_recipe/recipe.py
@@ -250,25 +250,42 @@ def _add_to_download_list(dataset):
def _schedule_for_download(datasets):
- """Schedule files for download and sh... |
ESMValGroup__ESMValCore-2309 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_main.py:ESMValTool.run"
],
"edited_modules": [
"esmvalcore/_main.py:ESMValTool"
]
},
"file": "esmvalcore/_main.py"
},
{
"changes": {
"added_en... | ESMValGroup/ESMValCore | 5171ee3d7fd1a02b0bbc35ec737d81f718f4d60a | ~/.esmvaltool/config-user.yml is always read even when --config-file is specified
**Describe the bug**
If a user specified a custom user configuration file via `--config-file`, the default user configuration file at `~/.esmvaltool/config-user.yml` is [still read](https://github.com/ESMValGroup/ESMValCore/blob/main/e... | diff --git a/esmvalcore/_main.py b/esmvalcore/_main.py
index afb0cc047..1fa4e80ce 100755
--- a/esmvalcore/_main.py
+++ b/esmvalcore/_main.py
@@ -353,8 +353,10 @@ class ESMValTool():
Recipe to run, as either the name of an installed recipe or the
path to a non-installed one.
config_fil... |
ESMValGroup__ESMValCore-2311 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe/recipe.py:_update_regrid_time"
],
"edited_modules": [
"esmvalcore/_recipe/recipe.py:_update_regrid_time"
]
},
"file": "esmvalcore/_recipe/recipe.py"
... | ESMValGroup/ESMValCore | afde69265f9fd948ff68f331b62584cd31f6725b | regrid_time does not have promised functionality
The stated goal of `regrid_time` is 'Align time axis for cubes so they can be subtracted', but it does not accomplish this goal. It takes two inputs: a `cube`, and a `frequency`. Since it does not accept two cubes, I imagine it's meant to simply remove evidence of time i... | diff --git a/doc/recipe/preprocessor.rst b/doc/recipe/preprocessor.rst
index 4d7ef23c5..972d49001 100644
--- a/doc/recipe/preprocessor.rst
+++ b/doc/recipe/preprocessor.rst
@@ -1248,8 +1248,7 @@ The ``_time.py`` module contains the following preprocessor functions:
* resample_time_: Resample data
* resample_hours_: C... |
ESMValGroup__ESMValCore-2313 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe/check.py:diagnostics",
"esmvalcore/_recipe/check.py:duplicate_datasets",
"esmvalcore/_recipe/check.py:variable"
],
"edited_modules": [
"esmvalcore/... | ESMValGroup/ESMValCore | 6f30fa6495fbe76d5694e7ba9260e09db70ea631 | var has not key 'diagnostic' error when checking var from the recipe
**Describe the bug**
When a necessary entry is missing in a variable, instead of raising the correct error defined in
https://github.com/ESMValGroup/ESMValCore/blob/989839f596a6b4433731c0efcb6b5cb4f3ca7045/esmvalcore/_recipe/check.py#L103-L112
an... | diff --git a/.zenodo.json b/.zenodo.json
index 31727467b..df7a49977 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -178,6 +178,11 @@
"name": "Kazeroni, Rémi",
"orcid": "0000-0001-7205-9528"
},
+ {
+ "affiliation": "GEOMAR, Germany",
+ "name": "Hohn, David... |
ESMValGroup__ESMValCore-2324 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe/check.py:regridding_schemes"
],
"edited_modules": [
"esmvalcore/_recipe/check.py:regridding_schemes"
]
},
"file": "esmvalcore/_recipe/check.py"
}
] | ESMValGroup/ESMValCore | 22e31c67b80c618ff27f2ab01066636da388d6c5 | Recipes fails with invalid regridding scheme `linear_extrapolate`
**Describe the bug**
See https://app.circleci.com/pipelines/github/ESMValGroup/ESMValTool/11191/workflows/e5b73b45-26f1-491b-99d6-b3bbcec2c442/jobs/71774.
I forgot to properly deprecate the regridding scheme `linear_extrapolate` in the recipe check... | diff --git a/esmvalcore/_recipe/check.py b/esmvalcore/_recipe/check.py
index f3de14e2a..9b4b2abb3 100644
--- a/esmvalcore/_recipe/check.py
+++ b/esmvalcore/_recipe/check.py
@@ -506,6 +506,13 @@ def regridding_schemes(settings: dict):
# Check built-in regridding schemes (given as str)
if isinstance(scheme, str... |
ESMValGroup__ESMValCore-2329 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_task.py:DiagnosticTask._initialize_cmd"
],
"edited_modules": [
"esmvalcore/_task.py:DiagnosticTask"
]
},
"file": "esmvalcore/_task.py"
},
{
"changes... | ESMValGroup/ESMValCore | 9b9a12526d9afdc87a5dd9e6904efe37acb629ac | Allow usage of relative paths for diagnostic scripts
Hi everyone,
Currently, in the diagnostic section of a recipe, the script must be either:
- A valid path to an existing diagnostic shipped with ESMValtool (diagnostic root)
- An absolute path to a diagnostic (not portable)
Looking at the code here, there is... | diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index 3a0d7b7b1..260725b5d 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -1,6 +1,6 @@
# Generated by conda-lock.
# platform: linux-64
-# input_hash: 090d7bbcb310d32c80fa50bdedeee5d4a266ff46613d62244bae0b69ede2d43d
+# input_hash: efb0d40da21331f380... |
ESMValGroup__ESMValCore-2343 | [
{
"changes": {
"added_entities": [
"esmvalcore/preprocessor/_io.py:_concatenate_cubes_by_experiment"
],
"added_modules": [
"esmvalcore/preprocessor/_io.py:_concatenate_cubes_by_experiment"
],
"edited_entities": [
"esmvalcore/preprocessor/_io.py:concatenate"
... | ESMValGroup/ESMValCore | 43f9e3b2af283eca3611bf66322620f2668db139 | concatenate experiments handles time ordering incorrectly
I am analysing the 1pctCO2 and esm-1pct-brch-1000PgC experiments, where the latter branches from the former after about 70 years. The simulation time for 1pctCO2 is longer than 70 years, so there will be several years that are present in both experiments. When c... | diff --git a/esmvalcore/preprocessor/_io.py b/esmvalcore/preprocessor/_io.py
index 900d02694..649bb577a 100644
--- a/esmvalcore/preprocessor/_io.py
+++ b/esmvalcore/preprocessor/_io.py
@@ -20,6 +20,7 @@ from iris.cube import CubeList
from esmvalcore.cmor.check import CheckLevels
from esmvalcore.iris_helpers import ... |
ESMValGroup__ESMValCore-2344 | [
{
"changes": {
"added_entities": [
"esmvalcore/preprocessor/_regrid.py:_get_regridder",
"esmvalcore/preprocessor/_regrid.py:_get_coord_key",
"esmvalcore/preprocessor/_regrid.py:_get_name_and_shape_key",
"esmvalcore/preprocessor/_regrid.py:_cache_clear"
],
"added... | ESMValGroup/ESMValCore | 6cf32c74551561e15276e4622047fd026ea54d3a | Use iris' regridder caching for faster regridding?
Some regridding schemes of iris allow reusing the regridding weights (see [here ](https://scitools-iris.readthedocs.io/en/latest/further_topics/which_regridder_to_use.html)for an overview of them), which might significantly speed up our `regrid` preprocessor if multipl... | diff --git a/doc/recipe/preprocessor.rst b/doc/recipe/preprocessor.rst
index cd3566498..4d7ef23c5 100644
--- a/doc/recipe/preprocessor.rst
+++ b/doc/recipe/preprocessor.rst
@@ -780,10 +780,6 @@ regridding is based on the horizontal grid of another cube (the reference
grid). If the horizontal grids of a cube and its re... |
ESMValGroup__ESMValCore-2346 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/preprocessor/_time.py:get_time_weights"
],
"edited_modules": [
"esmvalcore/preprocessor/_time.py:get_time_weights"
]
},
"file": "esmvalcore/preprocessor/_tim... | ESMValGroup/ESMValCore | bb7866e6a136f6e011bc6419c4e3ed9eec25721e | Weights for `climate_statistics` and `axis_statistics` are not lazy
**Describe the bug**
`iris.coords.DimCoords` are [never lazy](https://scitools-iris.readthedocs.io/en/stable/userguide/real_and_lazy_data.html#coordinates). Thus, the results of `core_points()` and `core_bounds()` will always be numpy arrays. Since we... | diff --git a/esmvalcore/preprocessor/_time.py b/esmvalcore/preprocessor/_time.py
index ca4e95ce5..ee11e1146 100644
--- a/esmvalcore/preprocessor/_time.py
+++ b/esmvalcore/preprocessor/_time.py
@@ -392,8 +392,10 @@ def get_time_weights(cube: Cube) -> np.ndarray | da.core.Array:
Returns
-------
- np.ndarra... |
ESMValGroup__ESMValCore-2348 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/preprocessor/_area.py:_mask_cube"
],
"edited_modules": [
"esmvalcore/preprocessor/_area.py:_mask_cube"
]
},
"file": "esmvalcore/preprocessor/_area.py"
},
... | ESMValGroup/ESMValCore | 3a0b49f84b156c876e6785af0293feb5cb5e8445 | Preprocessor shape 'extract_shape' breaks if cell measure is time dependent
**Describe the bug**
Running extract_shape with `decompose: True` on data which has a time dependent cell measure (like `volcello`) attached to it fails with the following error:
```
iris.exceptions.CannotAddError: Unequal lengths. Cube dime... | diff --git a/esmvalcore/cmor/tables/custom/CMOR_clhmtisccp.dat b/esmvalcore/cmor/tables/custom/CMOR_clhmtisccp.dat
index 504b69164..3c8b049ec 100644
--- a/esmvalcore/cmor/tables/custom/CMOR_clhmtisccp.dat
+++ b/esmvalcore/cmor/tables/custom/CMOR_clhmtisccp.dat
@@ -17,6 +17,5 @@ comment: at the top of the atmo... |
ESMValGroup__ESMValCore-2356 | [
{
"changes": {
"added_entities": [
"esmvalcore/cmor/_fixes/icon/_base_fixes.py:IconFix._tmp_local_file",
"esmvalcore/cmor/_fixes/icon/_base_fixes.py:IconFix._get_grid_from_rootpath",
"esmvalcore/cmor/_fixes/icon/_base_fixes.py:IconFix._get_downloaded_grid",
"esmvalcore/cmor... | ESMValGroup/ESMValCore | 2be264db778c5be86600ff5134d28b3b1d8d1e0c | Potential memory leak in local solar time preprocessor
The iris team warned us that Dask appears to be keeping functions it uses in memory even after it is done with them, see https://github.com/SciTools/iris/pull/5767. Wrapping large arguments, such as numpy arrays in a `functools.partial` is an example of how functio... | diff --git a/.zenodo.json b/.zenodo.json
index df7a49977..bb00d5471 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -200,6 +200,10 @@
"affiliation": "BSC, Spain",
"name": "Martin-Martinez, Eneko",
"orcid": "0000-0002-9213-7818"
+ },
+ {
+ "affiliation": "D... |
ESMValGroup__ESMValCore-236 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/cmor/table.py:read_cmor_tables",
"esmvalcore/cmor/table.py:CMIP6Info.__init__",
"esmvalcore/cmor/table.py:CMIP6Info.get_table",
"esmvalcore/cmor/table.py:CMIP6Info.get... | ESMValGroup/ESMValCore | ecff56c773f606094f9bb1c5b9f40f407c0e112b | obs4mips CMOR table not used
At the moment, the obs4mips CMOR table is present but not used, the CMIP6 table is used instead to look up obs4mips variables. | diff --git a/esmvalcore/cmor/table.py b/esmvalcore/cmor/table.py
index 09e827016..f179f8193 100644
--- a/esmvalcore/cmor/table.py
+++ b/esmvalcore/cmor/table.py
@@ -34,9 +34,10 @@ def read_cmor_tables(cfg_developer):
project = cfg_developer[table]
cmor_type = project.get('cmor_type', 'CMIP5')
- ... |
ESMValGroup__ESMValCore-2440 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe/check.py:_check_literal"
],
"edited_modules": [
"esmvalcore/_recipe/check.py:_check_literal"
]
},
"file": "esmvalcore/_recipe/check.py"
},
{
... | ESMValGroup/ESMValCore | 405300886cfb2314eadc6ff2f9b137371ada0dfe | Interpolation in `resample_hours`
**Is your feature request related to a problem? Please describe.**
Our current [`resample_hours`](https://docs.esmvaltool.org/projects/ESMValCore/en/latest/recipe/preprocessor.html#resample-hours) is only able to subset existing data. For example, it is able to create 3-hr data from 1... | diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index 08917d47c..3888d61b9 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -1,6 +1,6 @@
# Generated by conda-lock.
# platform: linux-64
-# input_hash: fa2d3995f132377c678545539752f20f28ca6b8ae5fc481da604e892e2cade9f
+# input_hash: 69fbe724ec4bb47187... |
ESMValGroup__ESMValCore-2472 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe/from_datasets.py:_to_frozen"
],
"edited_modules": [
"esmvalcore/_recipe/from_datasets.py:_to_frozen"
]
},
"file": "esmvalcore/_recipe/from_datasets.p... | ESMValGroup/ESMValCore | 0dce90cb34b4c0db9e1c23ce37a0f5485629056a | Writing of filled recipe fails with `TypeError: '<' not supported between instances of 'str' and 'tuple'`
**Describe the bug**
The recipe
```yaml
documentation:
title: Test
description: Test
authors:
- schlund_manuel
preprocessors:
global_ocean:
mask_landsea:
mask_out: land
a... | diff --git a/esmvalcore/_recipe/from_datasets.py b/esmvalcore/_recipe/from_datasets.py
index f68bd9e09..76cf368a4 100644
--- a/esmvalcore/_recipe/from_datasets.py
+++ b/esmvalcore/_recipe/from_datasets.py
@@ -5,9 +5,10 @@ from __future__ import annotations
import itertools
import logging
import re
+from collections.... |
ESMValGroup__ESMValCore-2546 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe/check.py:_check_duration_periods",
"esmvalcore/_recipe/check.py:_check_timerange_values"
],
"edited_modules": [
"esmvalcore/_recipe/check.py:_check_duratio... | ESMValGroup/ESMValCore | da3440e4744726f3f645ba3a3f240e9d8ac17d16 | Tests involving `isodate` failed
```bash
=========================== short test summary info ============================
FAILED tests/integration/recipe/test_check.py::test_valid_time_selection[19900101T12H00M00S/19920101T12H00M00] - esmvalcore.exceptions.RecipeError: Invalid value encountered for `timerange`. Valid... | diff --git a/environment.yml b/environment.yml
index 636883f04..5cf256c22 100644
--- a/environment.yml
+++ b/environment.yml
@@ -21,7 +21,7 @@ dependencies:
- iris >=3.10.0
- iris-esmf-regrid >=0.11.0
- iris-grib >=0.20.0 # github.com/ESMValGroup/ESMValCore/issues/2535
- - isodate
+ - isodate >=0.7.0 # inc... |
ESMValGroup__ESMValCore-2626 | [
{
"changes": {
"added_entities": [
"esmvalcore/_task.py:TaskSet._get_dask_config"
],
"added_modules": null,
"edited_entities": [
"esmvalcore/_task.py:TaskSet._run_parallel"
],
"edited_modules": [
"esmvalcore/_task.py:TaskSet"
]
},
"file":... | ESMValGroup/ESMValCore | 04e0cbd85db9440c5911ffbf33e3222e0d8ad12b | `max_parallel_tasks` and Dask
Issue reported by @schlunma
> Since https://github.com/ESMValGroup/ESMValCore/pull/2522, `recipe_schlund20esd.yml` hangs indefinitely after a while when using the default threaded scheduler and `--max-parallel-tasks=16`. Another example is an ICON recipe that evaluates 3D data, which n... | diff --git a/doc/quickstart/configure.rst b/doc/quickstart/configure.rst
index 5fee34db5..a85e85e53 100644
--- a/doc/quickstart/configure.rst
+++ b/doc/quickstart/configure.rst
@@ -178,7 +178,7 @@ For example, Python's ``None`` is YAML's ``null``, Python's ``True`` is YAML's
| | :ref:`run... |
ESMValGroup__ESMValCore-2668 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/cmor/_fixes/fix.py:GenericFix._fix_time_units"
],
"edited_modules": [
"esmvalcore/cmor/_fixes/fix.py:GenericFix"
]
},
"file": "esmvalcore/cmor/_fixes/fix.py"... | ESMValGroup/ESMValCore | c6dd6f54ffb7f54af3e047edfe3d0fed849d1a56 | High value for 'branch_time_in_parent' attribute crashes CMOR check
The NESM3 model has a very high value for the `'branch_time_in_parent'` attribute (I'm not sure if this is correct):
```
$ ncdump /work/bd0854/DATA/ESMValTool2/CMIP6_DKRZ/ScenarioMIP/NUIST/NESM3/ssp126/r1i1p1f1/Omon/tos/gn/v20190731/tos_Omon_NESM3_ss... | diff --git a/esmvalcore/cmor/_fixes/fix.py b/esmvalcore/cmor/_fixes/fix.py
index 9a229b2dc..4453177f7 100644
--- a/esmvalcore/cmor/_fixes/fix.py
+++ b/esmvalcore/cmor/_fixes/fix.py
@@ -831,15 +831,23 @@ class GenericFix(Fix):
branch_parent = "branch_time_in_parent"
if branch_... |
ESMValGroup__ESMValCore-290 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/cmor/_fixes/cmip5/ec_earth.py:Tas.fix_metadata"
],
"edited_modules": [
"esmvalcore/cmor/_fixes/cmip5/ec_earth.py:Tas"
]
},
"file": "esmvalcore/cmor/_fixes/cm... | ESMValGroup/ESMValCore | 9f558b364ff221e88ee58487f953ba18baba94b8 | Add SUM operator for daily_statistics preprocessor function
This is useful to compute e.g. daily precipitation flux from hourly data. | diff --git a/README.md b/README.md
index 8dc3f49e5..0b81db984 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
# ESMValCore package
-[](https://esmvaltool.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](... |
ESMValGroup__ESMValCore-306 | [
{
"changes": {
"added_entities": null,
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"edited_entities": [
"esmvalcore/cmor/_fixes/cmip5/fgoals_g2.py:AllVars.fix_metadata"
],
"edited_modules": [
"esmvalcore/cmor/_fixes/cmip5/fgoals_g2.py:AllVars"
]
},
"file": "esmvalcore/cmor... | ESMValGroup/ESMValCore | 166d8938d133cf6eb595c9fb4ec9396653f62c66 | Bug in fix for FGOALS-g2
The fix for FGOALS-g2 (CMIP5) does not work on `fx` variable, since it attempts to fix the time coordinate, which is not defined in `fx` variables:
```
for cube in cubes:
time = cube.coord('time')
time.units = Unit(time.units.name, time.units.calendar)
``` | diff --git a/esmvalcore/cmor/_fixes/cmip5/fgoals_g2.py b/esmvalcore/cmor/_fixes/cmip5/fgoals_g2.py
index 8811d3953..23c032abb 100644
--- a/esmvalcore/cmor/_fixes/cmip5/fgoals_g2.py
+++ b/esmvalcore/cmor/_fixes/cmip5/fgoals_g2.py
@@ -1,6 +1,7 @@
"""Fix FGOALS-g2 model."""
from cf_units import Unit
+from iris.excepti... |
ESMValGroup__ESMValCore-353 | [
{
"changes": {
"added_entities": null,
"added_modules": [
"esmvalcore/cmor/_fixes/cmip5/cesm1_bgc.py:Gpp"
],
"edited_entities": null,
"edited_modules": [
"esmvalcore/cmor/_fixes/cmip5/cesm1_bgc.py:Nbp"
]
},
"file": "esmvalcore/cmor/_fixes/cmip5/cesm1_b... | ESMValGroup/ESMValCore | 30de8d6a99c96e485781153b32ba7c389a6bfdea | Masking of CESM1-BGC's gpp wrong
The missing value for `gpp` of `CESM1-BGC` is not set correctly, just like `nbp`. | diff --git a/esmvalcore/cmor/_fixes/cmip5/cesm1_bgc.py b/esmvalcore/cmor/_fixes/cmip5/cesm1_bgc.py
index 3bc2d3474..d213ea04d 100644
--- a/esmvalcore/cmor/_fixes/cmip5/cesm1_bgc.py
+++ b/esmvalcore/cmor/_fixes/cmip5/cesm1_bgc.py
@@ -28,8 +28,8 @@ class Co2(Fix):
return cube
-class Nbp(Fix):
- """Fixes f... |
ESMValGroup__ESMValCore-4 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_recipe.py:Recipe.initialize_tasks"
],
"edited_modules": [
"esmvalcore/_recipe.py:Recipe"
]
},
"file": "esmvalcore/_recipe.py"
},
{
"changes": {
... | ESMValGroup/ESMValCore | d917aa9e14fdc6be3870949038bab78a16880522 | Prioritize task execution by recipe order
This will allow recipe authors to put long running tasks at the beginning of the recipe, so the total run time is minimized when executing recipes in which the duration of the various tasks greatly varies. | diff --git a/doc/esmvalcore/recipe.rst b/doc/esmvalcore/recipe.rst
index c1396a416..6ba46e184 100644
--- a/doc/esmvalcore/recipe.rst
+++ b/doc/esmvalcore/recipe.rst
@@ -147,7 +147,7 @@ arguments):
operator: mean
multi_model_statistics:
span: overlap
- statistics: [mean ]
+ ... |
ESMValGroup__ESMValCore-432 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_config.py:get_project_config"
],
"edited_modules": [
"esmvalcore/_config.py:get_project_config"
]
},
"file": "esmvalcore/_config.py"
},
{
"changes":... | ESMValGroup/ESMValCore | a0552bd1a33108156d9453ddf884e21087932150 | Use of areacella and areacello in area_statistics not supported for CMIP6
Using the following preprocessor
```yaml
spatial_mean_sea:
mask_landsea:
mask_out: land
area_statistics:
operator: mean
fx_files: ['areacello']
```
fails at the moment:
```
2020-01-15 13:48:55,511 UTC ... | diff --git a/esmvalcore/_config.py b/esmvalcore/_config.py
index 6f44f1673..c8e08381d 100644
--- a/esmvalcore/_config.py
+++ b/esmvalcore/_config.py
@@ -168,7 +168,10 @@ def configure_logging(cfg_file=None, output=None, console_log_level=None):
def get_project_config(project):
"""Get developer-configuration for p... |
ESMValGroup__ESMValCore-462 | [
{
"changes": {
"added_entities": [
"esmvalcore/cmor/_fixes/cmip5/gfdl_cm2p1.py:Sit.fix_metadata",
"esmvalcore/cmor/_fixes/cmip5/gfdl_cm2p1.py:Sit._fix_required"
],
"added_modules": [
"esmvalcore/cmor/_fixes/cmip5/gfdl_cm2p1.py:Sit"
],
"edited_entities": null... | ESMValGroup/ESMValCore | e2404b7924afd040b909e1eaf5d22db3110e86b7 | Dataset problem: GFDL-CM2p1 sit has invalid time bounds
I have found a sit file for CMIP5 GFDL-CM2p1 that has time bounds of about 1e9 with times of abot 40000. Iris breaks up at the checker, when changing the time units:
```yaml
- {dataset: GFDL-CM2p1, project: CMIP5, exp: historical, ensemble: r1i1p1, start_yea... | diff --git a/esmvalcore/cmor/_fixes/cmip5/gfdl_cm2p1.py b/esmvalcore/cmor/_fixes/cmip5/gfdl_cm2p1.py
index ad98dacae..e8c5008a5 100644
--- a/esmvalcore/cmor/_fixes/cmip5/gfdl_cm2p1.py
+++ b/esmvalcore/cmor/_fixes/cmip5/gfdl_cm2p1.py
@@ -1,5 +1,7 @@
"""Fixes for GFDL CM2p1 model."""
from copy import deepcopy
+import n... |
ESMValGroup__ESMValCore-656 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_task.py:DiagnosticTask._initialize_cmd"
],
"edited_modules": [
"esmvalcore/_task.py:DiagnosticTask"
]
},
"file": "esmvalcore/_task.py"
}
] | ESMValGroup/ESMValCore | 5016e8426d6369652afef9a7372d9856e79756ea | Use sys.executable to find python interpreter to run diagnostic
At the moment, we use the command `python` to run a diagnostic script. It would be more reliable to try to use the same interpreter (using ` sys.executable`) as the `esmvaltool` command. This would then also work even when the conda environment in which es... | diff --git a/esmvalcore/_task.py b/esmvalcore/_task.py
index de36e3d34..49682c0cc 100644
--- a/esmvalcore/_task.py
+++ b/esmvalcore/_task.py
@@ -8,6 +8,7 @@ import numbers
import os
import pprint
import subprocess
+import sys
import threading
import time
from copy import deepcopy
@@ -311,7 +312,10 @@ class Diagno... |
ESMValGroup__ESMValCore-745 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "setup.py"
}
] | ESMValGroup/ESMValCore | df32faa09e438d2fd15e7b54b4f10daefbdfceb4 | python setup.py test is deprecated
So our documentation on running tests as well as the test scripts that run on CircleCi need to be updated. | diff --git a/.circleci/config.yml b/.circleci/config.yml
index 09e597e53..f0ea8afc7 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -1,19 +1,22 @@
---
-version: 2
+version: 2.1
-aliases:
- check_changes: &check_changes
- name: Check changes
- command: |
- if (test "$CIRCLE_BRANCH" = maste... |
ESMValGroup__ESMValCore-771 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"esmvalcore/_data_finder.py:_replace_tags",
"esmvalcore/_data_finder.py:_replace_tag"
],
"edited_modules": [
"esmvalcore/_data_finder.py:_replace_tags",
"esmvalcore/_d... | ESMValGroup/ESMValCore | 5656fb8b546eeb4d750a424de7ed56a237edfabb | Dealing with startdates in filenames
**Is your feature request related to a problem? Please describe.**
Some experiments (DCPP, etc) contain startdates in the filenames and this is currently not supported.
**Would you be able to help out?**
Started working in branch dev_dccp_startdates, in which startdates are dea... | diff --git a/doc/recipe/overview.rst b/doc/recipe/overview.rst
index 779887862..e49abab13 100644
--- a/doc/recipe/overview.rst
+++ b/doc/recipe/overview.rst
@@ -82,6 +82,8 @@ data specifications:
``RCP8.5``)
- mip (for CMIP data, key ``mip``, value e.g. ``Amon``, ``Omon``, ``LImon``)
- ensemble member (key ``ensem... |
ESMValGroup__ESMValCore-880 | [
{
"changes": {
"added_entities": [
"esmvalcore/preprocessor/_derive/_shared.py:pressure_level_widths",
"esmvalcore/preprocessor/_derive/_shared.py:_create_pressure_array",
"esmvalcore/preprocessor/_derive/_shared.py:_get_pressure_level_widths"
],
"added_modules": [
... | ESMValGroup/ESMValCore | 86fe8558a82204169195b1a22ad92aa13d619dd7 | Numba causing installation issues with python=3.9
conda=4.9.2 env builds well but installing doesn't:
```
Running setup.py install for llvmlite ... error
ERROR: Command errored out with exit status 1:
command: /home/valeriu/miniconda3/envs/esmvalcore-492/bin/python3.9 -u -c 'import sys, setuptools, tok... | diff --git a/doc/requirements.txt b/doc/requirements.txt
index a055635a3..7d67ccad6 100644
--- a/doc/requirements.txt
+++ b/doc/requirements.txt
@@ -2,7 +2,6 @@ autodocsumm
dask[array]
fiona
netCDF4
-numba
numpy
pandas
pillow
diff --git a/esmvalcore/preprocessor/_derive/_shared.py b/esmvalcore/preprocessor/_deriv... |
ESSS__barril-30 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/barril/units/_quantity.py:ObtainQuantity",
"src/barril/units/_quantity.py:_Quantity.__init__"
],
"edited_modules": [
"src/barril/units/_quantity.py:ObtainQuantity",
... | ESSS/barril | fbcfac06110d4fa264d7b0b04fc3a9a3838ccee7 | Review units to use traditional Petroleum Engineering format
### Description
In the unit database, there are several units with the following format:
- `1000ft3/d`, `1000m3/d`, etc.
- `M(ft3)/d`, `M(m3)/d`, etc.
But the conventional format used in the petroleum industry is:
- `Mcf/d`, `Mm3/d`, etc.
- `MMc... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 309e284..875c151 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -4,6 +4,8 @@ UNRELEASED
* ``_foundation`` has been renamed to ``_util``, and a lot of functions which were not being
used anymore have been removed.
* Add new unit category mass temperature per mol (... |
ESSS__barril-46 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/barril/units/posc.py:FillUnitDatabaseWithPosc"
],
"edited_modules": [
"src/barril/units/posc.py:FillUnitDatabaseWithPosc"
]
},
"file": "src/barril/units/posc.py"
... | ESSS/barril | 87ebd247c3c3fa422f4ab3b5acdefbe9e85145c7 | Fix default category of `degF` and `degR` for `Scalar`
* Barril version: 1.9.0
* Python version: 3.6.7
* Operating System: Windows
### Description
When creating `Scalars` with only value and units `degF` or `degR` (omitting category) the generated `Scalar` has category `thermodynamic temperature` where it shoul... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 58b4af4..a0d3e56 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,15 +1,19 @@
+UNRELEASED
+------------------
+
+* Removing ``thermodynamic temperature`` as default category for ``degF`` and ``degR`` units.
+
1.9.0 (2020-02-20)
------------------
* New ``classme... |
ESSS__barril-49 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/barril/units/posc.py:FillUnitDatabaseWithPosc"
],
"edited_modules": [
"src/barril/units/posc.py:FillUnitDatabaseWithPosc"
]
},
"file": "src/barril/units/posc.py"
... | ESSS/barril | 94074b54b1037dab91c1354b78c6a865e025a7d0 | Unit 'St' is not valid for quantity type 'volume per time per length'.
* Barril version: 1.10.0
* Python version: 3.6.7
* Operating System: Ubuntu 20.10
### Description
- `St` (Stokes) is one of the basic unit used by the kinematic viscosity magnitude.
- Barril supports `cSt` (a variant of Stoke), but doesn't... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 21465bd..3fb83c7 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,3 +1,8 @@
+UNRELEASED
+------------------
+
+* Add new unit: "Stokes" (``St``).
+
1.10.0 (2020-10-22)
-------------------
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index 23d7e2c..cb3085d 100... |
ESSS__conda-devenv-106 | [
{
"changes": {
"added_entities": [
"conda_devenv/devenv.py:_get_env",
"conda_devenv/devenv.py:parse_env_var_args"
],
"added_modules": [
"conda_devenv/devenv.py:_get_env",
"conda_devenv/devenv.py:parse_env_var_args"
],
"edited_entities": [
"co... | ESSS/conda-devenv | 163062c279ba3e0fd8959a17c2b1b6b0c7f72286 | Support additional command line arguments
I often find myself specifying flags in the devenv file via environment variables, e.g. I'd have a section like:
```
# development
{% if "PKG_DEV" in os.environ %}
- pytest
- bump2version
{% endif %}
```
for development dependencies that are separate from those whic... | diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index de61cbf..9a2969e 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -64,7 +64,7 @@ Ready to contribute? Here's how to set up ``conda-devenv`` for local development
3. Create a new conda environment for developing::
- $ conda create -n devenv --file req... |
ESSS__conda-devenv-114 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"conda_devenv/devenv.py:merge_dependencies_version_specifications"
],
"edited_modules": [
"conda_devenv/devenv.py:merge_dependencies_version_specifications"
]
},
"file":... | ESSS/conda-devenv | 1d57f4922384c7c3f3938ba140d9d2bd775e045f | Incorrect rendering of pip dependencies with flags
Defining multiple dependencies in the `pip` section with flags such as `--editable/-e`:
```
dependencies:
- pip:
- --editable path/to/first/package
- --editable path/to/second/package
name: pip_editable_test
```
generates this:
```
dependencies:
-... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index bc3e447..1cd5d4a 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,12 +2,20 @@
CHANGELOG
=========
+2.1.1 (2020-08-13)
+------------------
+
+* Correctly handle editable installs when using pip dependencies (`#113`_).
+
+.. _`#113`: https://github.com/ESSS/conda-d... |
ESSS__conda-devenv-46 | [
{
"changes": {
"added_entities": [
"conda_devenv/devenv.py:_call_conda"
],
"added_modules": [
"conda_devenv/devenv.py:_call_conda"
],
"edited_entities": [
"conda_devenv/devenv.py:__call_conda_env_update"
],
"edited_modules": [
"conda_deve... | ESSS/conda-devenv | f23bec79139cbb9e59e4e2bdafb27385afcee192 | devenv command fails if conda is not on path
I was just updating an env in a linux machine with `/full/path/to/conda devenv -f environment.devenv.yml` and got this traceback:
```
Traceback (most recent call last):
File "/home/company/Work/miniconda/bin/conda-devenv", line 11, in <module>
load_entry_point('con... | diff --git a/HISTORY.rst b/HISTORY.rst
index a808c8c..796bf32 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -2,6 +2,15 @@
History
=======
+
+0.9.3 (2017-04-10)
+------------------
+
+* ``conda-devenv`` no longer requires ``conda`` to be on ``PATH`` to work (`#45`_).
+
+.. _`#45`: https://github.com/ESSS/conda-deven... |
ESSS__conda-devenv-50 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"conda_devenv/devenv.py:__call_conda_env_update"
],
"edited_modules": [
"conda_devenv/devenv.py:__call_conda_env_update"
]
},
"file": "conda_devenv/devenv.py"
}
] | ESSS/conda-devenv | f58819151109dfc68edbbf4a58cd56853ff1c414 | 0.9.3 broken: no longer generates activate/deactivate scripts
#46 introduced a bug: `conda-devenv` now calls `conda_env.main` directly, which probably calls `sys.exit()`, which skips activate/deactivate scripts generation. | diff --git a/HISTORY.rst b/HISTORY.rst
index 796bf32..608aaa0 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -3,6 +3,14 @@ History
=======
+0.9.4 (2017-04-20)
+------------------
+
+* Fixed major bug where activate/deactivate scripts were not being generated (`#49`_).
+
+.. _`#49`: https://github.com/ESSS/conda-dev... |
ESSS__conda-devenv-51 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"conda_devenv/devenv.py:main"
],
"edited_modules": [
"conda_devenv/devenv.py:main"
]
},
"file": "conda_devenv/devenv.py"
}
] | ESSS/conda-devenv | 320f7fdd672abf4122506850982a6b4095614e55 | 0.9.3 broken: no longer generates activate/deactivate scripts
#46 introduced a bug: `conda-devenv` now calls `conda_env.main` directly, which probably calls `sys.exit()`, which skips activate/deactivate scripts generation. | diff --git a/HISTORY.rst b/HISTORY.rst
index 608aaa0..f9fafd4 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -3,6 +3,12 @@ History
=======
+0.9.5 (2017-04-24)
+------------------
+
+* Handle ``None`` correctly, which actually fixes (`#49`_).
+
+
0.9.4 (2017-04-20)
------------------
diff --git a/conda_devenv/de... |
ESSS__conda-devenv-57 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"conda_devenv/devenv.py:handle_includes",
"conda_devenv/devenv.py:write_activate_deactivate_scripts",
"conda_devenv/devenv.py:main"
],
"edited_modules": [
"conda_deven... | ESSS/conda-devenv | 7867067acadb89f7da61af330d85caa31b284dd8 | Add --version flag | diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index 2be5977..ddda924 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -55,9 +55,9 @@ If you are proposing a feature:
Get Started!
------------
-Ready to contribute? Here's how to set up `conda-devenv` for local development.
+Ready to contribute? Here's how t... |
ESSS__conda-devenv-68 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"conda_devenv/devenv.py:truncate_history_file"
],
"edited_modules": [
"conda_devenv/devenv.py:truncate_history_file"
]
},
"file": "conda_devenv/devenv.py"
}
] | ESSS/conda-devenv | 331b0d9904f2bc200801efb9580663b74f88d057 | conda devenv may fail if history file is not there.
Traceback:
```
09:23:35 -> call conda devenv --quiet -n _database10-win64-py36 -f "K:\etk\database10\\environment.devenv.yml"
09:23:36 Traceback (most recent call last):
09:23:36 File "W:\Miniconda\Scripts\conda-devenv-script.py", line 5, in <module>
09:23:3... | diff --git a/HISTORY.rst b/HISTORY.rst
index b94fed0..24d2588 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -5,11 +5,15 @@ History
Next
------------------
-* Obtain ``envs_dir`` without using a subprocess (`#67`_).
+* Do not fail if history file does not exists (`#66`_).
+
+* Obtain ``envs_dir`` without using a... |
ESSS__conda-devenv-69 | [
{
"changes": {
"added_entities": [
"conda_devenv/devenv.py:_get_envs_dirs_from_conda"
],
"added_modules": [
"conda_devenv/devenv.py:_get_envs_dirs_from_conda"
],
"edited_entities": [
"conda_devenv/devenv.py:get_env_directory"
],
"edited_modules":... | ESSS/conda-devenv | 22e0b1a2515f187a330acfcd99a920bcf2fd7795 | Call conda info directly istead of by subprocess
The method `get_env_directory` on line 457 should be calling the conda directly instead of by calling `subprocess`.
Maybe add a method `_call_conda_info` similar to the already created `_call_conda` | diff --git a/HISTORY.rst b/HISTORY.rst
index b74b545..b94fed0 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -2,6 +2,14 @@
History
=======
+Next
+------------------
+
+* Obtain ``envs_dir`` without using a subprocess (`#67`_).
+
+
+.. _`#67`: https://github.com/ESSS/conda-devenv/issues/67
+
1.0.3 (2018-06-20)
---... |
ESSS__conda-devenv-72 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"conda_devenv/devenv.py:render_jinja",
"conda_devenv/devenv.py:handle_includes",
"conda_devenv/devenv.py:load_yaml_dict"
],
"edited_modules": [
"conda_devenv/devenv.py... | ESSS/conda-devenv | f74b1ebc267d9c765e0f4851cf1154d3434a0e49 | Add a way to identify if the current file is the "main" devenv file | diff --git a/conda_devenv/devenv.py b/conda_devenv/devenv.py
index a89cf89..aad9646 100644
--- a/conda_devenv/devenv.py
+++ b/conda_devenv/devenv.py
@@ -7,16 +7,17 @@ import sys
import six
-def render_jinja(contents, filename):
+def render_jinja(contents, filename, is_included):
import jinja2
import sys
... |
ESSS__oop-ext-21 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/oop_ext/interface/_interface.py:_IsMethod"
],
"edited_modules": [
"src/oop_ext/interface/_interface.py:_IsMethod"
]
},
"file": "src/oop_ext/interface/_interface.py"... | ESSS/oop-ext | 00000f0c728003d078fa48a7a0b121725326d491 | Bug with mocked `classmethod`
If you mock a `classmethod`, `unittest.mock` creates a `MagickMock` object instead of a method, that makes the internal `_IsMethod` check fail.
The following test fails:
```python
def testRequiresDeclarationBug(mocker):
class IFoo(Interface):
@classmethod
def foo... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index f98b109..41e5a14 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,6 +1,11 @@
-0.5.0 (2019-12-12)
+0.5.1 (2019-12-20)
==================
+* Fixes an issue (#20) where mocked `classmethods` weren't considered a valid method during internal checks.
+
+0.5.0 (2019-12-... |
ESSS__oop-ext-23 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/oop_ext/interface/_interface.py:IsImplementation",
"src/oop_ext/interface/_interface.py:IsImplementationOfAny",
"src/oop_ext/interface/_interface.py:AssertImplements",
"src/o... | ESSS/oop-ext | a6b298e39a84fdc2344ca36857d3e31a0b741b29 | Use `requires_declaration=True` as default in `IsImplementation`
As discussed in our meeting today with @nicoddemus, @tigarmo and @igortg we need to change back the default for `requires_declaration=True` because in the current state (`False`) provides "duck typing" interfaces, that is, a given class is considered an i... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 41e5a14..0de729f 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,6 +1,11 @@
-0.5.1 (2019-12-20)
+0.6.0 (2020-01-31)
==================
+* Change back the default value of ``requires_declaration`` to ``True`` and fix an error (#22) where the cache wasn 't properly... |
ESSS__oop-ext-37 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/oop_ext/foundation/decorators.py:Abstract"
],
"edited_modules": [
"src/oop_ext/foundation/decorators.py:Abstract"
]
},
"file": "src/oop_ext/foundation/decorators.py... | ESSS/oop-ext | 279c80eae56783c02d99ba7b94a8d2df7eb1aec3 | Regression: Abstract/Override/Implement decorators in interface implementations
While updating to `1.1.0`, found a regression involving `Abstract`, `Override`, and `Implements` decorators being used in interface implementations.
In `1.1.0` the decorator implementations were type decorated, however this doesn't play ... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index f2ece4a..cd58cce 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,3 +1,9 @@
+1.1.1 (UNRELEASED)
+------------------
+
+* #36: Fix regression introduced in ``1.1.0`` where ``Abstract`` and ``Implements`` decorators
+ could no longer be used in interfaces implementati... |
ESSS__oop-ext-42 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/oop_ext/foundation/decorators.py:Abstract"
],
"edited_modules": [
"src/oop_ext/foundation/decorators.py:Abstract"
]
},
"file": "src/oop_ext/foundation/decorators.py... | ESSS/oop-ext | 4b34facdb24514cde532301ab0ee9a673aa1110f | Regression: callback.After changes signatures, breaking interface checks
Similar to #36, however it is more subtle because it requires someone to install a callback using `callback.After`
```python
class IFoo(Interface):
@classmethod
def GetCaption(cls) -> str:
...
@Imple... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 54b08e0..d6d4f7b 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,3 +1,10 @@
+1.1.2 (2021-02-23)
+------------------
+
+* #41: Fix regression introduced in ``1.1.0`` where installing a callback using
+ ``callback.After`` or ``callback.Before`` would make a method no... |
Edinburgh-Genome-Foundry__DnaChisel-61 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dnachisel/Location.py:Location.overlap_region",
"dnachisel/Location.py:Location.extended",
"dnachisel/Location.py:Location.to_biopython_feature"
],
"edited_modules": [
... | Edinburgh-Genome-Foundry/DnaChisel | 0678f74bc0b92e0e7daa975f1ea6c94992cb3792 | Issue with AvoidPattern (and potentially other builtin_specifications)
It looks as though AvoidPattern doesn't preserve its strand information when being localized if the original strand information is 'from_location'
https://github.com/Edinburgh-Genome-Foundry/DnaChisel/blob/db0b606ec993a509de9f3bb4d8acde9baadeef99... | diff --git a/dnachisel/Location.py b/dnachisel/Location.py
index 853064f..6a3fdca 100644
--- a/dnachisel/Location.py
+++ b/dnachisel/Location.py
@@ -40,20 +40,25 @@ class Location:
def overlap_region(self, other_location):
"""Return the overlap span between two locations (None if None)."""
- stra... |
EdinburghGenomics__EGCG-Core-11 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"egcg_core/ncbi.py:_fetch_from_eutils"
],
"edited_modules": [
"egcg_core/ncbi.py:_fetch_from_eutils"
]
},
"file": "egcg_core/ncbi.py"
}
] | EdinburghGenomics/EGCG-Core | a835cffab69da2193d4653f31230f0d487596b78 | Canis lupus familiaris NCBI query returns None
Because _C. l. familiaris_ has `subspecies` in its efetch, the regex system in `fetch_from_eutils` breaks down. We should query the XML more robustly. | diff --git a/egcg_core/ncbi.py b/egcg_core/ncbi.py
index 13f74d6..69cc44c 100644
--- a/egcg_core/ncbi.py
+++ b/egcg_core/ncbi.py
@@ -76,7 +76,7 @@ def _fetch_from_eutils(species):
rank = None
if match:
rank = match.group(1)
- if rank == 'species':
+ if rank in ['species', 's... |
EdinburghGenomics__EGCG-Core-12 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "egcg_core/__init__.py"
},
{
"changes": {
"added_entities": [
"egcg_core/clarity.py:get_species_name"
],
"added_modules": [
... | EdinburghGenomics/EGCG-Core | 43f124d6f77db73cff13117003295ad715d9aabc | clarity.get_list_of_samples crashes if a sample doesn't exist in the Lims
The error is because of the way we're processing sample names. The stacktrace is misleading:
```
File "clarity.py", line 98, in get_list_of_samples
results.extend(_get_list_of_samples(sample_names[start:start+max_query]))
File "clarity.... | diff --git a/egcg_core/__init__.py b/egcg_core/__init__.py
index e1424ed..58d168b 100644
--- a/egcg_core/__init__.py
+++ b/egcg_core/__init__.py
@@ -1,1 +1,1 @@
-__version__ = '0.3.1'
+__version__ = '0.4'
diff --git a/egcg_core/clarity.py b/egcg_core/clarity.py
index 4691f7c..e896d04 100644
--- a/egcg_core/clarity.py
+... |
EdinburghGenomics__EGCG-Core-52 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"egcg_core/archive_management.py:register_for_archiving"
],
"edited_modules": [
"egcg_core/archive_management.py:register_for_archiving"
]
},
"file": "egcg_core/archive_... | EdinburghGenomics/EGCG-Core | 5a073c8d79148ed29379e4818e4dcebd5180eb15 | Failure to register for archiving cause pipeline crash
We should make the registering for archiving more robust by sleeping trying again to register the file after 1 second.
https://github.com/EdinburghGenomics/EGCG-Core/blob/master/egcg_core/archive_management.py#L92
This raising can cause Analysis Driver to crash a... | diff --git a/egcg_core/archive_management.py b/egcg_core/archive_management.py
index 3437925..58c5eb9 100644
--- a/egcg_core/archive_management.py
+++ b/egcg_core/archive_management.py
@@ -1,6 +1,8 @@
import os
import re
import subprocess
+from time import sleep
+
from egcg_core.app_logging import logging_default a... |
EdinburghGenomics__EGCG-Core-6 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"egcg_core/rest_communication.py:api_url",
"egcg_core/rest_communication.py:_req",
"egcg_core/rest_communication.py:post_or_patch"
],
"edited_modules": [
"egcg_core/re... | EdinburghGenomics/EGCG-Core | 0309bf8fdd5d64705fc62184fe31e27c20172fbc | Authentication
Since EdinburghGenomics/Reporting-App will be adding authentication, we should add auth headers to `rest_communication`. | diff --git a/egcg_core/rest_communication.py b/egcg_core/rest_communication.py
index 942039b..39acd98 100644
--- a/egcg_core/rest_communication.py
+++ b/egcg_core/rest_communication.py
@@ -1,9 +1,10 @@
import requests
from urllib.parse import urljoin
-from egcg_core.config import default as cfg
+from egcg_core.config... |
EdinburghGenomics__EGCG-Core-60 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"egcg_core/rest_communication.py:Communicator.post_entry"
],
"edited_modules": [
"egcg_core/rest_communication.py:Communicator"
]
},
"file": "egcg_core/rest_communicatio... | EdinburghGenomics/EGCG-Core | dff158066e922124e05d2d93cca14b2ee4ad6bfc | rest_communication: post data as form instead of json
`post_entry` should have an option to specify a post where the data is stored in the form instead of the query string.
| diff --git a/CHANGELOG.md b/CHANGELOG.md
index 58a261b..6db3fe5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,10 +1,10 @@
Changelog for EGCG-Core
===========================
-0.8 (unreleased)
+0.7.3 (unreleased)
----------------
-- Nothing changed yet.
+- Add new option to rest_communication.post_entry to s... |
EdinburghGenomics__EGCG-Core-64 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"egcg_core/archive_management.py:register_for_archiving"
],
"edited_modules": [
"egcg_core/archive_management.py:register_for_archiving"
]
},
"file": "egcg_core/archive_... | EdinburghGenomics/EGCG-Core | 5be3adbce57f2efd3afc6d15f59bb288ce0c1b50 | Broken recursion in archive_management
In archive_management.register_for_archiving, the recursion is called with the built-in function `filter`, which can only be a typo. | diff --git a/CHANGELOG.md b/CHANGELOG.md
index f304aea..260484f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,10 +1,10 @@
Changelog for EGCG-Core
===========================
-0.8 (unreleased)
+0.7.4 (unreleased)
----------------
-- Nothing changed yet.
+- Bugfix in archive management.
0.7.3 (2017-09-01... |
EdinburghGenomics__EGCG-Core-73 | [
{
"changes": {
"added_entities": [
"egcg_core/util.py:query_dict"
],
"added_modules": [
"egcg_core/util.py:query_dict"
],
"edited_entities": null,
"edited_modules": null
},
"file": "egcg_core/util.py"
}
] | EdinburghGenomics/EGCG-Core | 56a36841e0fedb399d9e5aab2c80c0468e93f2ed | Dot-notated dict querying
We implement this quite a lot in multiple places, so can add this as a common function:
```python
>>> d = {'this': {'that': 'other'}}
>>> query_dict(d, 'this.that')
'other'
``` | diff --git a/egcg_core/util.py b/egcg_core/util.py
index d1719af..0bfb634 100644
--- a/egcg_core/util.py
+++ b/egcg_core/util.py
@@ -100,3 +100,22 @@ def move_dir(src_dir, dest_dir):
dest_file = os.path.join(dest_dir, os.path.basename(src_file))
shutil.move(fp, dest_file)
return 0
+
+
+de... |
EdinburghGenomics__EGCG-Core-82 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"egcg_core/clarity.py:get_expected_yield_for_sample"
],
"edited_modules": [
"egcg_core/clarity.py:get_expected_yield_for_sample"
]
},
"file": "egcg_core/clarity.py"
},... | EdinburghGenomics/EGCG-Core | 4b8ccd933f689a9d0c5a0c98e59ddbfa697124aa | Deprecate get_expected_yield_for_sample
function `get_expected_yield_for_sample` in `clarity` returns the Expected yield Q30.
This function should be deprecated and a more explicitly named one should be used.
It is mainly used in Analysis-Driver (https://github.com/EdinburghGenomics/Analysis-Driver)
| diff --git a/.travis.yml b/.travis.yml
index 68e56d7..0292bb1 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ install:
- "pip install -r requirements.txt"
- "pip install python-coveralls pytest-cov"
- "python setup.py install"
-script: py.test tests/ --doctest-modules -v --cov egcg_core --cov-repor... |
EdinburghGenomics__EGCG-Core-88 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"egcg_core/clarity.py:sanitize_user_id"
],
"edited_modules": [
"egcg_core/clarity.py:sanitize_user_id"
]
},
"file": "egcg_core/clarity.py"
}
] | EdinburghGenomics/EGCG-Core | f54591f5420dc4b4f8241e080e594a5fd6c5f87a | Replace (.) dots in user sample name with underscores
Change the sanitize_user_id function to remove dots
https://github.com/EdinburghGenomics/EGCG-Core/blob/f54591f5420dc4b4f8241e080e594a5fd6c5f87a/egcg_core/clarity.py#L114 | diff --git a/egcg_core/clarity.py b/egcg_core/clarity.py
index 0068e9d..39d03f8 100644
--- a/egcg_core/clarity.py
+++ b/egcg_core/clarity.py
@@ -113,7 +113,7 @@ def get_genome_version(sample_id, species=None):
def sanitize_user_id(user_id):
if isinstance(user_id, str):
- return re.sub("[^\w_\-.]", "_", u... |
EdinburghGenomics__EGCG-Core-90 | [
{
"changes": {
"added_entities": [
"egcg_core/rest_communication.py:Communicator.close",
"egcg_core/rest_communication.py:Communicator.__del__"
],
"added_modules": null,
"edited_entities": [
"egcg_core/rest_communication.py:Communicator.__init__",
"egcg_co... | EdinburghGenomics/EGCG-Core | 8f4fefbdc4383b345ed58c7352b8125fcbe95f44 | Rest_communication cause SSL error in multiprocessing
In some circumstances rest_communication will generate SSL error when communicating with the reporting app over https.
This occurs in the pipeline when it uses multiprocessing. | diff --git a/egcg_core/rest_communication.py b/egcg_core/rest_communication.py
index 0a9e0cc..096648e 100644
--- a/egcg_core/rest_communication.py
+++ b/egcg_core/rest_communication.py
@@ -1,5 +1,6 @@
import json
import mimetypes
+import os
from urllib.parse import urljoin
import requests
from multiprocessing impo... |
EdinburghGenomics__EGCG-Core-96 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"egcg_core/config.py:Configuration.load_config_file"
],
"edited_modules": [
"egcg_core/config.py:Configuration"
]
},
"file": "egcg_core/config.py"
},
{
"changes"... | EdinburghGenomics/EGCG-Core | 1c278a1f45f591d92e712391b1efc137d92aeb0d | Bash syntax in local_execute
At the moment, we can use Bash constructs like `>`, `|`, etc. in Slurm/PBS execution, but not local execution - we should make this consistent. | diff --git a/egcg_core/config.py b/egcg_core/config.py
index 059fe28..8376c98 100644
--- a/egcg_core/config.py
+++ b/egcg_core/config.py
@@ -27,7 +27,9 @@ class Configuration:
self.env_var = env_var
self.config_file = self._find_config_file(search_path)
if self.config_file:
- s... |
EdinburghGenomics__clarity_scripts-41 | [
{
"changes": {
"added_entities": [
"scripts/assign_container_name.py:AssignContainerName.find_available_container"
],
"added_modules": null,
"edited_entities": [
"scripts/assign_container_name.py:AssignContainerName._run",
"scripts/assign_container_name.py:AssignC... | EdinburghGenomics/clarity_scripts | 37d6a75d81d94652c5c29228f86954b0ea96f8bb | User prepared library UDF handling
In assign_workflow_receive_sample, the following logic is done:
```python
if sample.udf.get('User Prepared Library') == 'Yes':
artifacts_to_route_userprepared.add(art)
elif not sample.udf.get('User Prepared Library'):
artifacts_to_route_preseqlab.add(art)
```
This relie... | diff --git a/requirements.txt b/requirements.txt
index 0b298f8..f7c70e9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,1 +1,1 @@
-EGCG-Core==0.7.3
+EGCG-Core==0.8.1
diff --git a/scripts/assign_container_name.py b/scripts/assign_container_name.py
index 98d46c6..2952a84 100644
--- a/scripts/assign_container_n... |
EdinburghGenomics__clarity_scripts-44 | [
{
"changes": {
"added_entities": [
"scripts/populate_review_step.py:StepPopulator.delivered",
"scripts/populate_review_step.py:StepPopulator.processed"
],
"added_modules": null,
"edited_entities": [
"scripts/populate_review_step.py:StepPopulator.check_rest_data_an... | EdinburghGenomics/clarity_scripts | 57d8c8da1958bf1f5769d385c5d679ab4b012294 | Add new rules to sample assessment in Run review
The sample assessment is using the require yield Q30 instead of the yield and %Q30 which makes it inaccurate in some cases. Change to use Yield and %Q30
- [ ] Add strategy to deal with sample that have been delivered already
- [ ] Add strategy to protect previous cal... | diff --git a/scripts/populate_review_step.py b/scripts/populate_review_step.py
index 3ba1948..9cccfd0 100644
--- a/scripts/populate_review_step.py
+++ b/scripts/populate_review_step.py
@@ -1,5 +1,6 @@
#!/usr/bin/env python
import datetime
+from egcg_core import util
from cached_property import cached_property
from ... |
EdinburghGenomics__clarity_scripts-48 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"EPPs/common.py:StepEPP.open_or_download_file"
],
"edited_modules": [
"EPPs/common.py:StepEPP"
]
},
"file": "EPPs/common.py"
},
{
"changes": {
"added_entit... | EdinburghGenomics/clarity_scripts | 32c21fa719365176a9101a8a7ce72eb07f3ac85d | Add Check for poor quality genotype in convert_and_dispatch_genotypes.py
We need to check the quality of the genotype and make sure we have at least 20 good SNPs.
If not we need to set a UDF (to be named) so that the next step script can check if its value. | diff --git a/EPPs/common.py b/EPPs/common.py
index ead0ee4..b734a33 100644
--- a/EPPs/common.py
+++ b/EPPs/common.py
@@ -71,9 +71,12 @@ class StepEPP(AppLogger):
f = open(file_or_uid)
else:
a = Artifact(self.lims, id=file_or_uid)
- f = StringIO(self.get_file_contents(uri=a.... |
EdinburghGenomics__clarity_scripts-52 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"scripts/populate_review_step.py:PullSampleInfo.field_from_entity"
],
"edited_modules": [
"scripts/populate_review_step.py:PullSampleInfo"
]
},
"file": "scripts/populate... | EdinburghGenomics/clarity_scripts | 5b85e1e462c701d9e01f9a786d82688cfab4d391 | Matching species field is missing aggregated
https://github.com/EdinburghGenomics/clarity_scripts/blob/5b85e1e462c701d9e01f9a786d82688cfab4d391/scripts/populate_review_step.py#L209
Need to add the `aggregated` in the field name | diff --git a/scripts/populate_review_step.py b/scripts/populate_review_step.py
index 9cccfd0..3c0e723 100644
--- a/scripts/populate_review_step.py
+++ b/scripts/populate_review_step.py
@@ -206,7 +206,7 @@ class PullSampleInfo(PullInfo):
('SR % Mapped', 'aggregated.pc_mapped_reads'),
('SR % Duplicates'... |
EdinburghGenomics__clarity_scripts-62 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"scripts/convert_and_dispatch_genotypes.py:UploadVcfToSamples._upload_genotyping_for_one_sample"
],
"edited_modules": [
"scripts/convert_and_dispatch_genotypes.py:UploadVcfToSamples"
... | EdinburghGenomics/clarity_scripts | 6fd2d0a0f7fc2f12213daa9f265b8c5a35e3e7ef | ConvertGenotype does not overwrite best run = 0
In `convert_and_dispatch_genotypes.py` the overwriting of the best run UDF does not work when the best run is `0`
| diff --git a/scripts/convert_and_dispatch_genotypes.py b/scripts/convert_and_dispatch_genotypes.py
index 18720e0..aa7959e 100644
--- a/scripts/convert_and_dispatch_genotypes.py
+++ b/scripts/convert_and_dispatch_genotypes.py
@@ -241,8 +241,8 @@ class UploadVcfToSamples(StepEPP):
# This is the first genotyp... |
EdinburghGenomics__clarity_scripts-71 | [
{
"changes": {
"added_entities": [
"scripts/assign_workflow_preseqlab.py:AssignWorkflowPreSeqLab._finish_step"
],
"added_modules": null,
"edited_entities": [
"scripts/assign_workflow_preseqlab.py:AssignWorkflowPreSeqLab._run"
],
"edited_modules": [
"sc... | EdinburghGenomics/clarity_scripts | 1e4cc541ba056e8d89301fb41fc2b8a560c81857 | Route samples after "Awaiting User Response" to Remove Step
At the end of "Awaiting User Response" artifacts that do not have UDF "Proceed To SeqLab" == true
Should be routed and run through the Remove from workflow step.
this can be done in `assign_workflow_preseqlab.py` or another independent script | diff --git a/scripts/assign_workflow_preseqlab.py b/scripts/assign_workflow_preseqlab.py
index e539d68..5652fbb 100644
--- a/scripts/assign_workflow_preseqlab.py
+++ b/scripts/assign_workflow_preseqlab.py
@@ -1,15 +1,41 @@
#!/usr/bin/env python
+import platform
+
+import time
+from pyclarity_lims.entities import Step
... |
EdinburghGenomics__clarity_scripts-85 | [
{
"changes": {
"added_entities": [
"scripts/spectramax.py:SpectramaxOutput._add_plates_to_step"
],
"added_modules": null,
"edited_entities": [
"scripts/spectramax.py:SpectramaxOutput.add_plates_to_step"
],
"edited_modules": [
"scripts/spectramax.py:Spe... | EdinburghGenomics/clarity_scripts | 61e954cb2e2f649c91abcee531e46dc54e9f3650 | spectramax.py missing underscore
Add underscore to def add_plates_to_step(self): | diff --git a/scripts/spectramax.py b/scripts/spectramax.py
index 0267479..534dc0b 100644
--- a/scripts/spectramax.py
+++ b/scripts/spectramax.py
@@ -8,7 +8,7 @@ class SpectramaxOutput(ParseSpectramaxEPP):
# Standards will not be present in the results table to be parsed
starting_well = 'A1'
- def add_pla... |
EdinburghGenomics__pyclarity-lims-11 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyclarity_lims/lims.py:Lims.get_file_contents"
],
"edited_modules": [
"pyclarity_lims/lims.py:Lims"
]
},
"file": "pyclarity_lims/lims.py"
}
] | EdinburghGenomics/pyclarity-lims | 14dae08ac127b86df96b326ce466d4c4854dff2c | Support for different file encodings
We should be able to read `utf-16`-encoded files, e.g. from the Spectramax. `requests` can return text with any encoding:
```python
>>> request.encoding
'utf-8'
>>> request.text
'some_glitchy_looking_binary_data'
>>> request.encoding = 'utf-16'
>>> request.text
'some_well_... | diff --git a/pyclarity_lims/lims.py b/pyclarity_lims/lims.py
index 4f64117..67f26ad 100644
--- a/pyclarity_lims/lims.py
+++ b/pyclarity_lims/lims.py
@@ -89,18 +89,21 @@ class Lims(object):
else:
return self.parse_response(r)
- def get_file_contents(self, id=None, uri=None):
+ def get_file_... |
EdinburghGenomics__pyclarity-lims-24 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyclarity_lims/descriptors.py:XmlDictionary.clear",
"pyclarity_lims/descriptors.py:SubTagDictionary.__init__",
"pyclarity_lims/descriptors.py:SubTagDictionary._update_elems",
"py... | EdinburghGenomics/pyclarity-lims | 66586f02da5660a87a4347e246dd76eac0bb29c4 | UdfConfig presets clear method clears the entire UdfConfig object
Calling the UdfConfig.preset.clear() method seems to clear values from the entire UdfConfig object. Even if I set the preset list manually to a new empty list the object is also cleared...Is this expected? | diff --git a/pyclarity_lims/descriptors.py b/pyclarity_lims/descriptors.py
index c2ce1ad..1c4eea6 100644
--- a/pyclarity_lims/descriptors.py
+++ b/pyclarity_lims/descriptors.py
@@ -78,7 +78,8 @@ class XmlDictionary(XmlMutable, dict):
def clear(self):
dict.clear(self)
- self.rootnode(self.instance... |
EdinburghGenomics__pyclarity-lims-33 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyclarity_lims/lims.py:Lims.get_udfs",
"pyclarity_lims/lims.py:Lims.get_reagent_types",
"pyclarity_lims/lims.py:Lims.get_labs",
"pyclarity_lims/lims.py:Lims.get_researchers",
... | EdinburghGenomics/pyclarity-lims | d73f5b7d76f0d65b4fe51fbc80e4bf9f49903a6c | Lims _get_instances() returns empty array when start_index is set.
An empty array is always returned when retrieving a list of entities using the `get_*` methods of the`Lims` class. For example:
```
samples = l.get_samples(start_index=500)
# samples == []
```
The problem is in the [_get_instances()](https://gi... | diff --git a/pyclarity_lims/lims.py b/pyclarity_lims/lims.py
index c00b1a1..532b315 100644
--- a/pyclarity_lims/lims.py
+++ b/pyclarity_lims/lims.py
@@ -210,7 +210,8 @@ class Lims(object):
root = ElementTree.fromstring(response.content)
return root
- def get_udfs(self, name=None, attach_to_name=N... |
EdinburghGenomics__pyclarity-lims-41 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyclarity_lims/descriptors.py:XmlPooledInputDict._setitem",
"pyclarity_lims/descriptors.py:XmlPooledInputDict._parse_element"
],
"edited_modules": [
"pyclarity_lims/descripto... | EdinburghGenomics/pyclarity-lims | 1a9f7d14e5597f7607ab85171432c7791d523d08 | Pooling samples
Hi all, (Edited from my original post, earlier today, because I was using the wrong data structure for StepPools.pooled_inputs)
Not an issue for you, rather for me! I'm trying to pool 2 plates into 2 tubes. First I create the two pools, set up the step and add the Illumina indexes to the tubes, I think... | diff --git a/.travis.yml b/.travis.yml
index 429bf09..3fc825d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,6 +6,7 @@ python:
install:
- "pip install -r requirements.txt"
- "pip install python-coveralls pytest-cov"
+ - "pip install coverage --upgrade"
- "python setup.py install"
script: PYTHONPATH=. py.t... |
EdinburghGenomics__pyclarity-lims-43 | [
{
"changes": {
"added_entities": [
"pyclarity_lims/entities.py:Process._output_files"
],
"added_modules": null,
"edited_entities": [
"pyclarity_lims/entities.py:Process.outputs_per_input",
"pyclarity_lims/entities.py:Process.shared_result_files",
"pyclarit... | EdinburghGenomics/pyclarity-lims | 1a9f7d14e5597f7607ab85171432c7791d523d08 | Lims.get_reagent_types is defined twice
Which one do we want? | diff --git a/pyclarity_lims/entities.py b/pyclarity_lims/entities.py
index 9d22d8d..80bfaa1 100644
--- a/pyclarity_lims/entities.py
+++ b/pyclarity_lims/entities.py
@@ -200,6 +200,9 @@ class Note(Entity):
class File(Entity):
"""File attached to a project or a sample."""
+ _URI = 'files'
+ _PREFIX = 'file'... |
EdinburghGenomics__pyclarity-lims-51 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyclarity_lims/lims.py:Lims.get_file_contents",
"pyclarity_lims/lims.py:Lims.get_batch"
],
"edited_modules": [
"pyclarity_lims/lims.py:Lims"
]
},
"file": "pycla... | EdinburghGenomics/pyclarity-lims | c408de1880701d5702479a3ad7f03c931aee9e4e | all_inputs documentat - list vs dict_values
The documentation for "Process.all_inputs" infers that the output is always a list type variable but the output variable type can be list or dict_values
Process.all_inputs(self, unique=True, resolve=False) produces a list type variable
Process.all_inputs(self, uniqued=Tru... | diff --git a/docs/PracticalExamples.rst b/docs/PracticalExamples.rst
index 7c9a7e7..ee759a2 100644
--- a/docs/PracticalExamples.rst
+++ b/docs/PracticalExamples.rst
@@ -172,7 +172,7 @@ as the list of dictionary provided.
.. code::
# Assuming the Container c and the Project p exists.
- l.create_batch(... |
EdinburghGenomics__pyclarity-lims-54 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyclarity_lims/descriptors.py:XmlAction._parse_element",
"pyclarity_lims/descriptors.py:XmlAction._setitem"
],
"edited_modules": [
"pyclarity_lims/descriptors.py:XmlAction"
... | EdinburghGenomics/pyclarity-lims | a03be6eda34f0d8adaf776d2286198a34e40ecf5 | StepAction rework-step take a Step
It currently accept a protocolStep which is incorrect | diff --git a/pyclarity_lims/descriptors.py b/pyclarity_lims/descriptors.py
index 91e2a4d..6ac8565 100644
--- a/pyclarity_lims/descriptors.py
+++ b/pyclarity_lims/descriptors.py
@@ -278,21 +278,25 @@ class XmlAction(XmlElementAttributeDict):
action: The type of action to perform. (leave, repeat, remove, review, com... |
EducationalTestingService__rsmtool-425 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "rsmtool/configuration_parser.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rsmt... | EducationalTestingService/rsmtool | 18f05517dbdb65444d549871bd8c612d7043b879 | Wishlist for interactive generation
Few things to add to interactive generation:
- Add `-i` flag (in addition to ``--interactive``)
- Make subgroups an option rather than flag: "Do you have subgroups?" I always forget to set the flag.
- Add a question at the end: "Save output to a file?" | diff --git a/doc/automated_configuration.rst b/doc/automated_configuration.rst
index 50c673d6..4f714ac0 100644
--- a/doc/automated_configuration.rst
+++ b/doc/automated_configuration.rst
@@ -60,6 +60,8 @@ We end with a list of important things to note about interactive generation:
- Optional fields will accept blank... |
EducationalTestingService__rsmtool-429 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rsmtool/configuration_parser.py:ConfigurationParser.__init__"
],
"edited_modules": [
"rsmtool/configuration_parser.py:ConfigurationParser"
]
},
"file": "rsmtool/configu... | EducationalTestingService/rsmtool | 44e60059d10d919a8de24996e153f4fadcdbbcac | More meaningful error message for non-numeric features
It would be helpful to print a more explicit message, if one of the features only contains non-numeric values specifying the name of the feature.
This should be done here:
https://github.com/EducationalTestingService/rsmtool/blob/0eb9a96e236828483123e46a4b1... | diff --git a/rsmtool/configuration_parser.py b/rsmtool/configuration_parser.py
index 633c309a..11783b07 100644
--- a/rsmtool/configuration_parser.py
+++ b/rsmtool/configuration_parser.py
@@ -694,10 +694,12 @@ class ConfigurationParser:
Raises
------
FileNotFoundError
- If the given... |
EducationalTestingService__rsmtool-454 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rsmtool/utils/prmse.py:variance_of_errors",
"rsmtool/utils/prmse.py:true_score_variance",
"rsmtool/utils/prmse.py:mse_true",
"rsmtool/utils/prmse.py:prmse_true",
"rsmtool... | EducationalTestingService/rsmtool | e1ee0b754cf9a86bfe3b81e43782ce7a89c1c5df | Skip PRMSE if there are no double-scored responses
We need to change PRMSE code to deal with an edge case where the second_human_score column is present and populated, but no valid second human scores are left after filtering out non-numeric features (rsmtool) or non-numeric system scores (rsmeval). A particular use ca... | diff --git a/rsmtool/utils/prmse.py b/rsmtool/utils/prmse.py
index c95e969c..5c69d415 100644
--- a/rsmtool/utils/prmse.py
+++ b/rsmtool/utils/prmse.py
@@ -1,4 +1,6 @@
"""
+PRMSE utilities.
+
Utility classes and functions related to computing test
theory based evaluations.
@@ -13,6 +15,8 @@ The derivations and form... |
EducationalTestingService__rsmtool-669 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rsmtool/rsmcompare.py:main"
],
"edited_modules": [
"rsmtool/rsmcompare.py:main"
]
},
"file": "rsmtool/rsmcompare.py"
},
{
"changes": {
"added_entities": n... | EducationalTestingService/rsmtool | d7e776b24b64cdb97cd7659d04d3e8f9bf80f327 | Refactor CLI tests to call `main()` functions instead of calling the entry points
CodeCov wants people to switch to their [binary uploader](https://docs.codecov.com/docs/codecov-uploader) instead of using the `codecov` package. However, in my tests (as part of #636), I found that when I switch to the new uploader, we ... | diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0e642c7e..a01ddc97 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,13 +6,16 @@ stages:
variables:
PYVERSION: "3.8"
BINPATH: "/root/rsmenv/bin"
+ LOGCAPTURE_LEVEL: "WARNING"
CODECOV_TOKEN: "488304b7-b1c5-4fc7-bfb6-9e7cbcb36a08"
# set up basic job
.... |
EducationalTestingService__skll-557 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "skll/data/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skll/data/read... | EducationalTestingService/skll | ee5b4a1300f3ab69e2ea14b4b6315fe9e25740c0 | Remove MegaM Reader and Writer classes?
Is anyone using the `MegaMReader` or `MegaMWriter` classes in `skll`? If not, is there any reason to maintain these? Is there any code that still uses the megam classifier?
@aoifecahill @desilinguist @mulhod @bndgyawali? | diff --git a/README.rst b/README.rst
index 356b3277..d19e7c77 100644
--- a/README.rst
+++ b/README.rst
@@ -109,7 +109,7 @@ You can also follow this `interactive Jupyter tutorial <https://mybinder.org/v2/
We also provide utilities for:
- `converting between machine learning toolkit formats <https://skll.readthedocs... |
EducationalTestingService__skll-604 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skll/learner/__init__.py:Learner.save"
],
"edited_modules": [
"skll/learner/__init__.py:Learner"
]
},
"file": "skll/learner/__init__.py"
}
] | EducationalTestingService/skll | bb0353711680746d30d7ef932ad7ea38049c2915 | Saving models in current directory requires `./`
Specifying just a model file name, e.g., `Learner.save(foo.model)` should just assume that we want to save `foo.model` in the current directory. However, it's expecting an explicit directory so we instead need to do `Learner.save('./foo.model')` which is silly. | diff --git a/skll/learner/__init__.py b/skll/learner/__init__.py
index a5202dfe..b265372c 100644
--- a/skll/learner/__init__.py
+++ b/skll/learner/__init__.py
@@ -598,6 +598,8 @@ class Learner(object):
"""
# create the directory if it doesn't exist
learner_dir = os.path.dirname(learner_path)
... |
EducationalTestingService__skll-619 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skll/learner/__init__.py:Learner.__init__",
"skll/learner/__init__.py:Learner.train"
],
"edited_modules": [
"skll/learner/__init__.py:Learner"
]
},
"file": "skl... | EducationalTestingService/skll | 6bf31ab3cdaf42d56c739b7ff2a621704bfe86c0 | Simplify parameter grids to be dictionaries instead of lists of dictionaries
Right now, we always use a list with a single dictionary to represent the default parameter grid for a learner. However, [`GridSearchCV`](https://scikit-learn.org/stable/modules/generated/sklearn.model_selection.GridSearchCV.html) can take a p... | diff --git a/doc/run_experiment.rst b/doc/run_experiment.rst
index 652966ed..a3cb82d6 100644
--- a/doc/run_experiment.rst
+++ b/doc/run_experiment.rst
@@ -1015,106 +1015,106 @@ to be included in the model. Defaults to 1.
param_grids *(Optional)*
""""""""""""""""""""""""
-List of parameter grids to search for each l... |
EducationalTestingService__skll-658 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skll/learner/__init__.py:Learner._check_input_formatting"
],
"edited_modules": [
"skll/learner/__init__.py:Learner"
]
},
"file": "skll/learner/__init__.py"
}
] | EducationalTestingService/skll | 32823c0baa7e668357fcae3dcd28efa8916e15ee | `Learner._check_input_formatting()` does not work for dense featuresets
This method is called by `Learner._train_setup()` and it checks that regression labels are not strings and that feature values (for both classification and regression) are not strings. However, this method does not work as expected if the featurese... | diff --git a/skll/learner/__init__.py b/skll/learner/__init__.py
index 6345629e..982c5a96 100644
--- a/skll/learner/__init__.py
+++ b/skll/learner/__init__.py
@@ -661,8 +661,14 @@ class Learner(object):
"labels. Convert them to integers or "
"fl... |
EducationalTestingService__skll-662 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "skll/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": ... | EducationalTestingService/skll | 3e26acd663007bee5dd70dae3dc958edbb7f442b | Remove top-level imports
As I work on #488, I find that one unfortunate by-product of adding a new `VotingLearner` object that depends on the `Learner` object is that the following no longer works: `from skll import Learner` due to a circular import issue. From v2.5, we will need to do `from skll.learner import Lear... | diff --git a/skll/__init__.py b/skll/__init__.py
index fca5e543..e486415e 100644
--- a/skll/__init__.py
+++ b/skll/__init__.py
@@ -11,13 +11,8 @@ common scikit-learn experiments with pre-generated features.
from sklearn.metrics import SCORERS, f1_score, fbeta_score, make_scorer
-from .data import FeatureSet
-from ... |
EducationalTestingService__skll-705 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skll/config/__init__.py:SKLLConfigParser.__init__",
"skll/config/__init__.py:parse_config_file"
],
"edited_modules": [
"skll/config/__init__.py:SKLLConfigParser",
"sk... | EducationalTestingService/skll | f116e573bb82ca3f60c59f486b9e597a66e0e310 | Deprecate and remove 'log' field from configuration files
In #520, we added support for the 'logs' field as a replacement for 'log` and showed a warning if the user specified the latter. In the next version after v2.5, we should remove the 'log' field altogether and raise an error instead. | diff --git a/skll/config/__init__.py b/skll/config/__init__.py
index e30a0a11..31319fb3 100644
--- a/skll/config/__init__.py
+++ b/skll/config/__init__.py
@@ -68,7 +68,6 @@ class SKLLConfigParser(configparser.ConfigParser):
'id_col': 'id',
'ids_to_floats': 'False',
... |
EducationalTestingService__skll-706 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skll/config/__init__.py:SKLLConfigParser.__init__",
"skll/config/__init__.py:parse_config_file"
],
"edited_modules": [
"skll/config/__init__.py:SKLLConfigParser",
"sk... | EducationalTestingService/skll | 47175c8ad499c1134956e433cd8e2681fb767206 | Rename `pos_label_str` to `pos_label` and move to Input section
We should implement this in a backwards compatible way along with deprecation warnings in the next release and then fully deprecate the old behavior in the release after that. | diff --git a/doc/run_experiment.rst b/doc/run_experiment.rst
index 99841d89..b4e76783 100644
--- a/doc/run_experiment.rst
+++ b/doc/run_experiment.rst
@@ -1146,17 +1146,17 @@ SVR
experiment and are best left up to the user.
-.. _pos_label_str:
+.. _pos_label:
-pos_label_str *(Optional)*
-""""""""""""""""""""... |
Electrostatics__mmcif_pdbx-23 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pdbx/reader.py:PdbxReader.read",
"pdbx/reader.py:PdbxReader.__parser",
"pdbx/reader.py:PdbxReader.__tokenizer"
],
"edited_modules": [
"pdbx/reader.py:PdbxReader"
... | Electrostatics/mmcif_pdbx | 2d5204cb5fb9ec85ae219bcc51a3733a40645687 | Refactor usage of StopIteration in pdbx.reader
`pdbx.reader` follows a pre-[PEP 479](https://www.python.org/dev/peps/pep-0479/) pattern of `StopIteration` usage with a `RuntimeError` band-aid. This should be refactored.
@sobolevnrm I'd be happy to send a pull request, unless this code is already being worked on. | diff --git a/pdbx/reader.py b/pdbx/reader.py
index 2a91215..c5bd339 100644
--- a/pdbx/reader.py
+++ b/pdbx/reader.py
@@ -46,9 +46,7 @@ class PdbxReader:
try:
self.__parser(self.__tokenizer(self.__input_file), container_list)
except StopIteration:
- pass
- else:
- ... |
Electrostatics__old_pdb-6 | [
{
"changes": {
"added_entities": [
"old_pdb/annotation.py:RevisionData.revisions"
],
"added_modules": null,
"edited_entities": [
"old_pdb/annotation.py:RevisionData.__init__",
"old_pdb/annotation.py:RevisionData.parse_line",
"old_pdb/annotation.py:Revision... | Electrostatics/old_pdb | b1876b2718e2de2eb91b63b769d59fafa97ce540 | Provide default attributes for pdb_entry.Entry
Implement as property. | diff --git a/docs/changelog.rst b/docs/changelog.rst
index 67ecbf5..365ab60 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -4,10 +4,12 @@
Change log
==========
-Current version
-===============
+1.0.0
+=====
* Fixed readthedocs.io rendering of documentation (`#3 <https://github.com/Electrostatics/ol... |
EliCDavis__AssociationEngine-30 | [
{
"changes": {
"added_entities": [
"Snapper/Snapper.py:Snapper.add_sensor"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"Snapper/Snapper.py:Snapper"
]
},
"file": "Snapper/Snapper.py"
}
] | EliCDavis/AssociationEngine | 941e395d804635ead728ce0c69156974b9c1d59c | Implement Generation of Variables from Sensors in Snapper
The snapper module must generate variable objects as needed from sensor objects supplied, rather than expect to be provided with the variables from outside the module. | diff --git a/Snapper/Snapper.py b/Snapper/Snapper.py
index 7306c09..56feaa3 100644
--- a/Snapper/Snapper.py
+++ b/Snapper/Snapper.py
@@ -1,3 +1,6 @@
+from ..Relationship.Variable import Variable
+
+
class Snapper:
def __init__(self):
self.sensors = []
@@ -23,6 +26,16 @@ class Snapper:
"""
... |
EliCDavis__AssociationEngine-52 | [
{
"changes": {
"added_entities": [
"Snapper/Manager.py:Manager.get_value_matrix",
"Snapper/Manager.py:Manager.get_relationships_by_value_range"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"Snapper/Manager.py:Manager"
]
},... | EliCDavis/AssociationEngine | f0df6c26fad05a818edfebaafb81b9342919cf9e | Create Wrapper Methods for Matrix in Manager
Need to implement wrappers for Matrix methods:
- [x] get_value_matrix
- [x] get_relationships_by_value_range
This needs to be done to avoid the end user needing to acquire an instance of AssociationMatrix and operate on it directly. Instead, the end user should only e... | diff --git a/Snapper/Manager.py b/Snapper/Manager.py
index cc9b635..e503ecf 100644
--- a/Snapper/Manager.py
+++ b/Snapper/Manager.py
@@ -61,6 +61,22 @@ class Manager:
"""
return self.matrix
+ def get_value_matrix(self):
+ """
+ Returns the underlying matrix on demand.
+
+ :re... |
EltonChou__EorzeaEnv-15 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"EorzeaEnv/eorzea_time.py:EorzeaTime.bell",
"EorzeaEnv/eorzea_time.py:EorzeaTime.minute"
],
"edited_modules": [
"EorzeaEnv/eorzea_time.py:EorzeaTime"
]
},
"file"... | EltonChou/EorzeaEnv | 34e623e8a5d4bc188381db6a12f59608a0517ac9 | Time rollover is handled incorrectly
While trying to calculate some windows where the time, moon phase and weather all matched (for an S rank) I discovered that the windows returned were incomplete (when compared to other tools).
After further testing I found that the provided `weather_period` generator was returni... | diff --git a/EorzeaEnv/eorzea_time.py b/EorzeaEnv/eorzea_time.py
index 8b805e1..eed9608 100644
--- a/EorzeaEnv/eorzea_time.py
+++ b/EorzeaEnv/eorzea_time.py
@@ -106,7 +106,7 @@ class EorzeaTime:
self._bell += 24
self.sun = self.sun - 1
- while self._bell > 24:
+ while self._bel... |
EmilStenstrom__conllu-19 | [
{
"changes": {
"added_entities": [
"conllu/models.py:TokenList.__ne__",
"conllu/models.py:TokenList.clear",
"conllu/models.py:TokenList.copy",
"conllu/models.py:TokenList.extend",
"conllu/models.py:TokenList.tokens"
],
"added_modules": null,
"edite... | EmilStenstrom/conllu | 1604bada91968725102b626da9537f361fc3178d | TokenList could inherit "list"
Hey. I have found this library quite useful. There is a suggestion that I ran into: `TokenList` could maybe inherit `list`, and so be treated like that.
I tried manipulating the sentences (TokenLists) as if they were lists, such as using `len` but then I saw they weren't. I thought abo... | diff --git a/conllu/models.py b/conllu/models.py
index d57a49a..cd98ae4 100644
--- a/conllu/models.py
+++ b/conllu/models.py
@@ -5,25 +5,53 @@ from conllu.parser import ParseException, head_to_token, serialize
DEFAULT_EXCLUDE_FIELDS = ('id', 'deprel', 'xpostag', 'feats', 'head', 'deps', 'misc')
-class TokenList(ob... |
EmilStenstrom__conllu-35 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "conllu/parser.py"
}
] | EmilStenstrom/conllu | 6da39c07ccafc4c280f10eb51b12165472a609a9 | Column 'deps' is not being parsed most of the time
Given the following sentence:
```
Removed.
```
The code at `parser.py:152` looks like this:
```python
def parse_paired_list_value(value):
if fullmatch(MULTI_DEPS_PATTERN, value):
return [
(part.split(":", 1)[1], parse_id_value(par... | diff --git a/conllu/parser.py b/conllu/parser.py
index 16ec94b..7456879 100644
--- a/conllu/parser.py
+++ b/conllu/parser.py
@@ -141,7 +141,7 @@ def parse_id_value(value):
ANY_ID = re.compile(ID_SINGLE.pattern + "|" + ID_RANGE.pattern + "|" + ID_DOT_ID.pattern)
-DEPS_RE = re.compile("(" + ANY_ID.pattern + r"):[a-z... |
EmilStenstrom__conllu-64 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"conllu/serializer.py:serialize"
],
"edited_modules": [
"conllu/serializer.py:serialize"
]
},
"file": "conllu/serializer.py"
}
] | EmilStenstrom/conllu | e9c8f2c6ab390c706680c6077d344cecffb71397 | BUG: Error when serializing metadata that is not a string
```
37 for key, value in tokenlist.metadata.items():
38 if value:
---> 39 line = "# " + key + " = " + value
40 else:
41 line = "# " + key
TypeError: can only concatenate ... | diff --git a/conllu/serializer.py b/conllu/serializer.py
index 39e9854..aa8fd4c 100644
--- a/conllu/serializer.py
+++ b/conllu/serializer.py
@@ -36,9 +36,9 @@ def serialize(tokenlist: 'TokenList') -> str:
if tokenlist.metadata:
for key, value in tokenlist.metadata.items():
if value:
- ... |
EmilStenstrom__conllu-99 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"conllu/models.py:TokenList.extend",
"conllu/models.py:TokenList.filter",
"conllu/models.py:SentenceList.extend"
],
"edited_modules": [
"conllu/models.py:TokenList",
... | EmilStenstrom/conllu | 2fcbda620fd687f132477bdcd75dd0c5695c1f10 | Failure with serializing/deserializing using Python `pickle`
I think something may be broken when serializing (pickle-dumping) and loading back conllu-parsed sentences.
```python
File "python3.9/site-packages/conllu/models.py", line 103, in extend
self.metadata.update(iterable.metadata)
AttributeError: 'TokenLi... | diff --git a/conllu/models.py b/conllu/models.py
index 25e5b3b..1b73591 100644
--- a/conllu/models.py
+++ b/conllu/models.py
@@ -95,11 +95,11 @@ class TokenList(T.List[Token]):
return TokenList(tokens_copy, self.metadata, self.default_fields)
def extend(self, iterable: T.Union['TokenList', T.Iterable[To... |
EmilStenstrom__django-components-489 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/django_components/template_loader.py:Loader.get_dirs"
],
"edited_modules": [
"src/django_components/template_loader.py:Loader"
]
},
"file": "src/django_components/t... | EmilStenstrom/django-components | 085c60a8c96442d9fd4f72d66a7eb295e7cfb2d9 | template_loader blocks on STATICFILES_DIRS if there are tuples
## How to reproduce
Simply run django with, in your _settings.py_, something like :
```
STATICFILES_DIRS = [
# ...
("downloads", "/opt/webfiles/stats"),
]
```
(as made possible [natively in Django](https://docs.djangoproject.com/en/3.2/r... | diff --git a/src/django_components/template_loader.py b/src/django_components/template_loader.py
index ea897b8..ae8ab3f 100644
--- a/src/django_components/template_loader.py
+++ b/src/django_components/template_loader.py
@@ -37,6 +37,16 @@ class Loader(FilesystemLoader):
directories: Set[Path] = set()
... |
EmilStenstrom__django-components-504 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/django_components/component.py:Component._fills_from_slots_data",
"src/django_components/component.py:ComponentNode.render"
],
"edited_modules": [
"src/django_components/... | EmilStenstrom/django-components | c07f0e634121ced0119bb665ed544ca4447c416b | Refactor accessing of default slot from `as var` to kwarg
See https://github.com/EmilStenstrom/django-components/pull/495#discussion_r1607117487 | diff --git a/README.md b/README.md
index ca94ae6..b65cbdb 100644
--- a/README.md
+++ b/README.md
@@ -44,6 +44,12 @@ Read on to learn about the details!
## Release notes
+🚨📢 **Version 0.77** CHANGED the syntax for accessing default slot content.
+- Previously, the syntax was
+`{% fill "my_slot" as "alias" %}` and... |
Epistimio__orion-564 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/orion/plotting/backend_plotly.py:lpi",
"src/orion/plotting/backend_plotly.py:parallel_coordinates",
"src/orion/plotting/backend_plotly.py:rankings",
"src/orion/plotting/backe... | Epistimio/orion | 91618980116b8d852cc67fe8c4e65180ba5bc53e | Add option to support plotting with all evc tree trials
Currently all plots are done using `with_evc_tree=False`. This should be configurable. | diff --git a/src/orion/plotting/backend_plotly.py b/src/orion/plotting/backend_plotly.py
index 25922067..20777883 100644
--- a/src/orion/plotting/backend_plotly.py
+++ b/src/orion/plotting/backend_plotly.py
@@ -20,6 +20,7 @@ from orion.core.worker.transformer import build_required_space
def lpi(
experiment,
+ ... |
Epistimio__orion-586 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/orion/core/cli/db/setup.py:main"
],
"edited_modules": [
"src/orion/core/cli/db/setup.py:main"
]
},
"file": "src/orion/core/cli/db/setup.py"
},
{
"changes": ... | Epistimio/orion | bc886daf791d66490b59e43657f6f6db45d34ea8 | Adjust `orion db setup` prompts based on the storage backend used.
The prompts are tailored for MongoDB specifically and misleading for pickleddb. The series of prompts should be adjusted based on which storage backend is specified at the first prompt. | diff --git a/src/orion/core/cli/db/setup.py b/src/orion/core/cli/db/setup.py
index b129a814..7e98ab4d 100644
--- a/src/orion/core/cli/db/setup.py
+++ b/src/orion/core/cli/db/setup.py
@@ -14,6 +14,7 @@ import os
import yaml
import orion.core
+from orion.core.io.database import Database
from orion.core.utils.termina... |
Epistimio__orion-625 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/orion/core/evc/conflicts.py:CommandLineConflict.get_nameless_args",
"src/orion/core/evc/conflicts.py:ScriptConfigConflict.get_nameless_config"
],
"edited_modules": [
"src... | Epistimio/orion | 20e28d4e406e186276e09e94abdefea2d2a89ae6 | EVC crashes when main script is not found on file system
If the path to main script in a previous experiment cannot be found, attempting to branch from it will make the EVC crash. The parent experiment should be loaded with a parser using option `allow_non_existing_files=True`
```
Traceback (most recent call last):
... | diff --git a/src/orion/core/evc/conflicts.py b/src/orion/core/evc/conflicts.py
index 93772d98..90aa4361 100644
--- a/src/orion/core/evc/conflicts.py
+++ b/src/orion/core/evc/conflicts.py
@@ -1318,7 +1318,7 @@ class CommandLineConflict(Conflict):
log.debug("User script config: %s", user_script_config)
... |
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