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 |
|---|---|---|---|---|---|
mlrun__mlrun-149 | [
{
"changes": {
"added_entities": [
"mlrun/db/httpd.py:list_artifact_tags",
"mlrun/db/httpd.py:list_projects",
"mlrun/db/httpd.py:list_schedules"
],
"added_modules": [
"mlrun/db/httpd.py:list_artifact_tags",
"mlrun/db/httpd.py:list_projects",
"mlr... | mlrun/mlrun | e0b13616cc8c53ea69978d4ff8520ab6244aa6a0 | More HTTP API endpoints
@yaronha said:
> expose list_projects, list_artifact_tags, list_schedules in httpd/web-api (so the UI can access those)
| diff --git a/mlrun/db/httpd.py b/mlrun/db/httpd.py
index 2c89f1eeb..f447d4eb0 100644
--- a/mlrun/db/httpd.py
+++ b/mlrun/db/httpd.py
@@ -12,6 +12,7 @@
# See the License for the specific language governing permissions and
# limitations under the License.
"""mlrun database HTTP server"""
+from argparse import Argument... |
mlrun__mlrun-27 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mlrun/db/httpd.py:read_artifact"
],
"edited_modules": [
"mlrun/db/httpd.py:read_artifact"
]
},
"file": "mlrun/db/httpd.py"
},
{
"changes": {
"added_entiti... | mlrun/mlrun | bb4b1fd00e08134004e8723ec32af9f52c06eb63 | httpd/db artifacts broken
@tebeka the artifacts get/store etc is broken
a. you must use the `artifact.to_json()` vs dumps like in filedb, since `to_json()` accounts for model details, also `body` is not stored in the DB
b. artifacts object path should be `/artifact/<project>/<uid/tag>/<key>' (key not as arg)
,... | diff --git a/mlrun/db/httpd.py b/mlrun/db/httpd.py
index e9c533546..1ed01fcd5 100644
--- a/mlrun/db/httpd.py
+++ b/mlrun/db/httpd.py
@@ -20,7 +20,6 @@ from http import HTTPStatus
from flask import Flask, jsonify, request
-from mlrun.artifacts import Artifact
from mlrun.db import RunDBError
from mlrun.db.filedb i... |
mlrun__mlrun-52 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "mlrun/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mlrun/__main__.py:... | mlrun/mlrun | 74e3883ac65770707cefbb19e02608e891fe49e3 | Move HTTP routes under prefix
Move the HTTP DB routes under a prefix (such as `/api/v1`). We'd like to be able to add UI on top of it as well | diff --git a/mlrun/__init__.py b/mlrun/__init__.py
index 16c968e89..efde0b6fd 100644
--- a/mlrun/__init__.py
+++ b/mlrun/__init__.py
@@ -20,5 +20,5 @@ from .model import RunTemplate, NewRun, NewTask, RunObject
from .kfpops import mlrun_op
from .config import config as mlconf
from .runtimes import new_model_server
-f... |
mlrun__mlrun-82 | [
{
"changes": {
"added_entities": [
"mlrun/db/sqldb.py:SQLDB.list_projects",
"mlrun/db/sqldb.py:SQLDB.list_artifact_tags"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"mlrun/db/sqldb.py:SQLDB"
]
},
"file": "mlrun/db/sql... | mlrun/mlrun | 51a18e01ebe942e04301bf6c75adc5764a5936c6 | Add list_projects & list_artifact_tags(project)
The wevb API needs these | diff --git a/mlrun/db/sqldb.py b/mlrun/db/sqldb.py
index 712b970d3..b87f24cf5 100644
--- a/mlrun/db/sqldb.py
+++ b/mlrun/db/sqldb.py
@@ -320,6 +320,14 @@ class SQLDB(RunDBInterface):
)
return funcs
+ def list_projects(self):
+ return [row[0] for row in self.session.query(Run.project).disti... |
mmaelicke__scikit-gstat-114 | [
{
"changes": {
"added_entities": [
"skgstat/MetricSpace.py:_get_disk_sample",
"skgstat/MetricSpace.py:_get_successive_ring_samples",
"skgstat/MetricSpace.py:_get_idx_dists",
"skgstat/MetricSpace.py:_mp_wrapper_get_idx_dists",
"skgstat/MetricSpace.py:RasterEquidistan... | mmaelicke/scikit-gstat | 43cf393953e03c85ab8b72a73d1def30fb4edc3f | Easier support for raster data: custom bins, user-defined maxlag, return count, etc...
Hi there!
First, thanks for all the work on scikit-gstat :+1:.
It's great and I'm very happy to see geostatistics emerging in Python!
I used `skgstat` quite a bit recently (moving away from R), cited it in our last paper! :wink... | diff --git a/skgstat/MetricSpace.py b/skgstat/MetricSpace.py
index 2370a18..28d07c7 100644
--- a/skgstat/MetricSpace.py
+++ b/skgstat/MetricSpace.py
@@ -1,8 +1,10 @@
+from __future__ import annotations
+
from scipy.spatial.distance import pdist, cdist, squareform
from scipy.spatial import cKDTree
from scipy import s... |
mmaelicke__scikit-gstat-158 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skgstat/estimators.py:dowd"
],
"edited_modules": [
"skgstat/estimators.py:dowd"
]
},
"file": "skgstat/estimators.py"
}
] | mmaelicke/scikit-gstat | 81463bbadec56e892135122856613b57ed25bea7 | Scale of Dowd's estimator
Hey @mmaelicke,
Hope all is well, it's been a while!
I use a lot robust estimators through my work, and noticed that Dowd's is not scaled the same as others: it returns 2gamma instead of gamma, and so will have twice the values of e.g. Matheron's for the same data. We can see it in the doc... | diff --git a/skgstat/estimators.py b/skgstat/estimators.py
index 74cf62c..adb4dd1 100644
--- a/skgstat/estimators.py
+++ b/skgstat/estimators.py
@@ -175,7 +175,7 @@ def dowd(x):
"""
# convert
- return 2.198 * np.nanmedian(x)**2
+ return 2.198 * np.nanmedian(x)**2 / 2
@jit(forceobj=True)
|
mmaelicke__scikit-gstat-160 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skgstat/DirectionalVariogram.py:DirectionalVariogram.__init__"
],
"edited_modules": [
"skgstat/DirectionalVariogram.py:DirectionalVariogram"
]
},
"file": "skgstat/Direc... | mmaelicke/scikit-gstat | c2d63d1307206621befed4d2fdba022f3bf0ae97 | Fit of a sum of variogram models
Hi again @mmaelicke,
Do you think allowing the fit of a combinaison (sum, product) of variogram models could be a functionality that has its place in `scikit-gstat`?
We use that a lot for analyzing multiple correlation ranges in satellite data (for example, https://github.com/Glac... | diff --git a/docs/userguide/variogram.rst b/docs/userguide/variogram.rst
index bb1d5d8..b195c48 100644
--- a/docs/userguide/variogram.rst
+++ b/docs/userguide/variogram.rst
@@ -766,6 +766,53 @@ variogram is rather showing a Gaussian or exponential behavior.
If you would like to export a Variogram instance to gstoo... |
mmaelicke__scikit-gstat-71 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skgstat/Variogram.py:Variogram.n_lags",
"skgstat/Variogram.py:Variogram.lag_classes",
"skgstat/Variogram.py:Variogram._experimental"
],
"edited_modules": [
"skgstat/V... | mmaelicke/scikit-gstat | 590510f09227a0448f6eeeaa6ead0ea5a30f6021 | Yet another Python loop
There is yet another Python loop in the code:
https://github.com/mmaelicke/scikit-gstat/blob/a43a7f30013061d28531504bfe97b6c10e3c28a5/skgstat/Variogram.py#L1127
and within the same function:
https://github.com/mmaelicke/scikit-gstat/blob/a43a7f30013061d28531504bfe97b6c10e3c28a5/skgstat/... | diff --git a/docs/changelog.rst b/docs/changelog.rst
index 09c6dbf..fad69bf 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -2,6 +2,21 @@
Changelog
=========
+Version 0.3.6
+=============
+.. warning::
+ There is some potential breaking behaviour
+
+- [Variogram] some internal code cleanup. Removed so... |
mmaelicke__scikit-gstat-73 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skgstat/Variogram.py:Variogram.__init__",
"skgstat/Variogram.py:Variogram.set_bin_func",
"skgstat/Variogram.py:Variogram.n_lags",
"skgstat/Variogram.py:Variogram.describe"
... | mmaelicke/scikit-gstat | 2ca3efb04192e2870656c8e9901526b5ad07e5ca | Better interaction between Variogram() and Kriging()
* Make Variogram().describe() output all relevant parameters needed to
* Recreate the Variogram given coordinates and values
* Perform kriging
* Make Kriging() not take a Variogram() instance as parameter, but the dictionary returned by describe(), plus coordi... | diff --git a/docs/changelog.rst b/docs/changelog.rst
index e9856b7..8dcc68d 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -8,6 +8,9 @@ Version 0.3.7
of the class. As of Version `0.3.7` this is used to pass arguments down to the
:func:`entropy <skgstat.estimators.entropy>` and :func:`percentile <skg... |
mmaelicke__scikit-gstat-82 | [
{
"changes": {
"added_entities": [
"skgstat/Variogram.py:Variogram.get_empirical"
],
"added_modules": null,
"edited_entities": [
"skgstat/Variogram.py:Variogram.bins"
],
"edited_modules": [
"skgstat/Variogram.py:Variogram"
]
},
"file": "s... | mmaelicke/scikit-gstat | 18d237b32bb9b891a465a22fef71d0dce2d65131 | Output function for experimental Variogram
Implement a new return function for `Variogram`, that returns the bin edges (or centers) along with the current experimental data. This is helpful to align skgstat with the `gstools.vario_etimate` function.
Could look like:
```Python
Variogram:
def get_empirical(se... | diff --git a/docs/changelog.rst b/docs/changelog.rst
index 30b4c8e..faa7ce6 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -2,9 +2,23 @@
Changelog
=========
-Version 0.4.0
+Version 0.4.2 [WIP]
+===================
+- [Variogram] :func:`bins <skgstat.Variogram.bins>` now cases manual setted bin edges au... |
mmaelicke__scikit-gstat-94 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "docs/conf.py"
},
{
"changes": {
"added_entities": [
"skgstat/Variogram.py:Variogram.to_gs_krige"
],
"added_modules": null,
... | mmaelicke/scikit-gstat | 1da3d79f6c134158838561cca3a45a8cefbd7120 | Export coordinates as cond_pos
I wrapped my whole day around the skgstat - gstools interface today. I tried to use the `gstools.krige.Krige` with one of `skgstat.Variogram`. This is what happened:
The sc... | diff --git a/docs/conf.py b/docs/conf.py
index 523d8f4..441f125 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -215,5 +215,6 @@ intersphinx_mapping = {
'python': ('https://docs.python.org/3.6', None),
'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
'numpy': ('https://docs.scipy.org/d... |
mmcdermott__MEDS_Tabular_AutoML-62 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/MEDS_tabular_automl/scripts/describe_codes.py:main"
],
"edited_modules": [
"src/MEDS_tabular_automl/scripts/describe_codes.py:main"
]
},
"file": "src/MEDS_tabular_a... | mmcdermott/MEDS_Tabular_AutoML | 2be13d9212ece27b1af08d1b6d136fb31ee5d720 | Updating path inputs and outputs to be consistent with MEDS v0.3 (`final_cohort` -> `data`, store all MEDS-Tab outputs in an output cohort directory instead of the input MEDS cohort directory so we don't overwrite MEDS cohort metadata). | diff --git a/src/MEDS_tabular_automl/configs/default.yaml b/src/MEDS_tabular_automl/configs/default.yaml
index 8f8513c..82a2164 100644
--- a/src/MEDS_tabular_automl/configs/default.yaml
+++ b/src/MEDS_tabular_automl/configs/default.yaml
@@ -1,11 +1,13 @@
MEDS_cohort_dir: ???
+output_cohort_dir: ???
do_overwrite: Fals... |
mmcdermott__MEDS_Tabular_AutoML-71 | [
{
"changes": {
"added_entities": [
"src/MEDS_tabular_automl/scripts/cache_task.py:write_lazyframe"
],
"added_modules": [
"src/MEDS_tabular_automl/scripts/cache_task.py:write_lazyframe"
],
"edited_entities": [
"src/MEDS_tabular_automl/scripts/cache_task.py:ma... | mmcdermott/MEDS_Tabular_AutoML | c9595f29bc62d82c9fd02efb842a3115def59b07 | Updating how we handle patient splits to use `metadata/patient_splits.parquet`
Note that, given our usage of shard files to make XGBoost iteration easier and faster, the right way to handle this is to re-shard the data for tasks and MEDS data on input into split-separated shards. This is annoying, but should be an easy... | diff --git a/pyproject.toml b/pyproject.toml
index e82db50..b7972f9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,8 @@ classifiers = [
]
dependencies = [
"polars", "pyarrow", "loguru", "hydra-core", "numpy", "scipy<1.14.0", "pandas", "tqdm", "xgboost",
- "scikit-learn", "hydra-optuna-sweeper", "hy... |
mmcdermott__MEDS_transforms-119 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "src/MEDS_transforms/extract/convert_to_sharded_events.py"
},
{
"changes": {
"added_entities": [
"src/MEDS_transforms/mapreduce/mapper.py... | mmcdermott/MEDS_transforms | d719ab46b6b46f8762c89d615d0e3e4ea262adf0 | Add match & revise syntax transformations
Suggested syntax / configuration.
Suppose a transformation has a `stage_cfg` that normally takes some arguments. As all `stage_cfg`s are dictionaries, we can do the following:
If (for transformations that support match & revise), the `stage_cfg` has a `_match_and_revise` ... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b188f48..98bc99d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -126,8 +126,4 @@ repos:
- id: nbqa-isort
args: ["--profile=black"]
- id: nbqa-flake8
- args:
- [
- "--extend-ignor... |
mmcdermott__MEDS_transforms-132 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/MEDS_transforms/extract/convert_to_sharded_events.py:main"
],
"edited_modules": [
"src/MEDS_transforms/extract/convert_to_sharded_events.py:main"
]
},
"file": "src/... | mmcdermott/MEDS_transforms | 36a172df3ceb88f3082bde58558a52b211b60c53 | Pipelines should automatically determine shards from the input directory rather than relying on the `splits.json` file.
This would allow pipelines to be used even on dataests not extracted with `MEDS-extract`. This entails:
- [x] Cleaning up the interface to not rely on this and automatically load shards.
- [x] E... | diff --git a/src/MEDS_transforms/configs/extract.yaml b/src/MEDS_transforms/configs/extract.yaml
index 377c39c..b0f2d50 100644
--- a/src/MEDS_transforms/configs/extract.yaml
+++ b/src/MEDS_transforms/configs/extract.yaml
@@ -30,7 +30,7 @@ event_conversion_config_fp: ???
# The code modifier columns are in this pipeline... |
mmcdermott__MEDS_transforms-154 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/MEDS_transforms/extract/extract_code_metadata.py:main"
],
"edited_modules": [
"src/MEDS_transforms/extract/extract_code_metadata.py:main"
]
},
"file": "src/MEDS_tra... | mmcdermott/MEDS_transforms | a27d361221689bde213c0665216ec3a662d7e935 | Extraction ETL crashes if you include the `extract_metadata` stage but you don't have any `_metadata` blocks in your configs.
Instead, this stage should just copy or symlink over any existing `metadata/codes.parquet` and terminate in this case.
**In case this issue is impacting anybody**, before it gets formally fix... | diff --git a/src/MEDS_transforms/extract/extract_code_metadata.py b/src/MEDS_transforms/extract/extract_code_metadata.py
index 1b8b394..e9133eb 100644
--- a/src/MEDS_transforms/extract/extract_code_metadata.py
+++ b/src/MEDS_transforms/extract/extract_code_metadata.py
@@ -364,6 +364,10 @@ def main(cfg: DictConfig):
... |
mmcdermott__MEDS_transforms-157 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/MEDS_transforms/aggregate_code_metadata.py:run_map_reduce"
],
"edited_modules": [
"src/MEDS_transforms/aggregate_code_metadata.py:run_map_reduce"
]
},
"file": "src/... | mmcdermott/MEDS_transforms | 66364281167aeaf567cec781bcadca6b4f525d8d | The default extraction ETL should likely not include an `aggregate_code_metadata.py` stage, unless anyone thinks it would be almost universally useful.
This means columns like `code/n_occurrences`, `value/sum`, etc. would not be computed during aggregation. Code metadata (e.g., `description`, `parent_codes`, etc.) woul... | diff --git a/src/MEDS_transforms/aggregate_code_metadata.py b/src/MEDS_transforms/aggregate_code_metadata.py
index 9290926..bcc056a 100755
--- a/src/MEDS_transforms/aggregate_code_metadata.py
+++ b/src/MEDS_transforms/aggregate_code_metadata.py
@@ -682,6 +682,15 @@ def run_map_reduce(cfg: DictConfig):
cs.numer... |
mmcdermott__MEDS_transforms-166 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/MEDS_transforms/aggregate_code_metadata.py:mapper_fntr"
],
"edited_modules": [
"src/MEDS_transforms/aggregate_code_metadata.py:mapper_fntr"
]
},
"file": "src/MEDS_t... | mmcdermott/MEDS_transforms | 3cab51260c104867fc026535ceb66c6ac3959454 | Aggregation integration test should cover all integrations | diff --git a/src/MEDS_transforms/aggregate_code_metadata.py b/src/MEDS_transforms/aggregate_code_metadata.py
index bcc056a..13e9b34 100755
--- a/src/MEDS_transforms/aggregate_code_metadata.py
+++ b/src/MEDS_transforms/aggregate_code_metadata.py
@@ -406,7 +406,9 @@ def mapper_fntr(
│ C ┆ 1 ┆ 81.25 ... |
mmcdermott__MEDS_transforms-242 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/MEDS_transforms/extract/shard_events.py:scan_with_row_idx",
"src/MEDS_transforms/extract/shard_events.py:main"
],
"edited_modules": [
"src/MEDS_transforms/extract/shard_e... | mmcdermott/MEDS_transforms | f54ea5ae6dc86bbbbdb15e3dbb68b4cd103e583d | `.par` files should also be recognized as `parquet` files during extraction.
This would warrant only a tiny change on this line: https://github.com/mmcdermott/MEDS_transforms/blob/main/src/MEDS_transforms/extract/shard_events.py#L145 | diff --git a/src/MEDS_transforms/extract/shard_events.py b/src/MEDS_transforms/extract/shard_events.py
index cd8e474..a11e1de 100755
--- a/src/MEDS_transforms/extract/shard_events.py
+++ b/src/MEDS_transforms/extract/shard_events.py
@@ -142,7 +142,7 @@ def scan_with_row_idx(fp: Path, columns: Sequence[str], **scan_kwar... |
mmcdermott__MEDS_transforms-287 | [
{
"changes": {
"added_entities": [
"src/MEDS_transforms/__main__.py:print_help_stage",
"src/MEDS_transforms/__main__.py:resolve_pipeline_yaml"
],
"added_modules": [
"src/MEDS_transforms/__main__.py:print_help_stage",
"src/MEDS_transforms/__main__.py:resolve_pipe... | mmcdermott/MEDS_transforms | bf236fdc2aa41d89d6a07f70572538a213821c48 | [Proposal] Consider having main entry run point explicitly take both the pipeline config yaml (or package) and the stage name, and register stages without a pipeline.
> So, one additional challenge with this is that the intention for the generic stages in the MEDS-Transforms repo (or even in derived packages) is that t... | diff --git a/src/MEDS_transforms/__main__.py b/src/MEDS_transforms/__main__.py
index f01a619..6c60601 100644
--- a/src/MEDS_transforms/__main__.py
+++ b/src/MEDS_transforms/__main__.py
@@ -1,8 +1,18 @@
+import os
import sys
from importlib.metadata import entry_points
+from importlib.resources import files
+from pathl... |
mmcdermott__MEDS_transforms-83 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "src/MEDS_transforms/aggregate_code_metadata.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": ... | mmcdermott/MEDS_transforms | 4e2be4d96471520ac28d5060659a05c0b4f26ca3 | Switch codes from categorical to string column types
Experiments from both @prenc and @EthanSteinberg suggest that this has a minimal to positive impact on stored filesize on disk and file read/write time, and has better interoperability with other tools. As much as I don't like it aesthetically, we should switch to st... | diff --git a/src/MEDS_transforms/aggregate_code_metadata.py b/src/MEDS_transforms/aggregate_code_metadata.py
index 85ac23c..6550659 100755
--- a/src/MEDS_transforms/aggregate_code_metadata.py
+++ b/src/MEDS_transforms/aggregate_code_metadata.py
@@ -18,8 +18,6 @@ from MEDS_transforms import PREPROCESS_CONFIG_YAML
from ... |
mmerickel__pyramid_services-12 | [
{
"changes": {
"added_entities": [
"pyramid_services/__init__.py:ServiceInfo.__init__"
],
"added_modules": [
"pyramid_services/__init__.py:ServiceInfo"
],
"edited_entities": [
"pyramid_services/__init__.py:register_service_factory",
"pyramid_services... | mmerickel/pyramid_services | 85f423102ec14195698b1e44b12fccf30650679d | Singleton per request object
One issue I ran into with your **dbsession** service example (that uses a service factory) is the following:
When looking for the service different sessions are returned depending on the context. This is by design. Citing the documentation:
> The factory will be used at most once per ... | diff --git a/CHANGES.txt b/CHANGES.txt
index 8d05981..6240712 100644
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -1,8 +1,21 @@
unreleased
==========
+Backward Incompatibilities
+--------------------------
+
- Drop Python 3.2 support.
+- Use the original service context interface as the cache key instead
+ of the cur... |
mmerickel__wired-14 | [
{
"changes": {
"added_entities": [
"src/wired/container.py:ServiceCache.find",
"src/wired/container.py:ServiceContainer.register_factory",
"src/wired/container.py:ServiceContainer.register_singleton",
"src/wired/container.py:_register_factory",
"src/wired/container.... | mmerickel/wired | 966110141fc4c794e1f22ed9aa2a014cae4eac64 | Caching issue
Seems like a bug to me.
Set up code
```python
# registering two factories, one without context and another with a context
registry.register_factory(factory_a, DummyFactory)
registry.register_factory(factory_b, DummyFactory, context=ContextB)
```
Scenario 1, works fine:
```python
# getting fa... | diff --git a/CHANGES.rst b/CHANGES.rst
index d82b91f..9dcd454 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -1,6 +1,21 @@
Unreleased
==========
+Backward Incompatibilities
+--------------------------
+
+- ``wired.ServiceContainer.set`` has been redefined to set a service instance
+ for a specific context object in... |
mmerickel__wired-2 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/wired/container.py:_iface_for_type"
],
"edited_modules": [
"src/wired/container.py:_iface_for_type"
]
},
"file": "src/wired/container.py"
}
] | mmerickel/wired | f6367cc7c9566e4bf42ecefaa33f07fa5bef692c | Lookup by class (instead of name) doesn't use fully qualified name
I just did this in a test and was surprised it passed:
```python
# from wired.samples.simple_factory import Greeter
class Greeter:
pass
factory = registry.find_factory(Greeter)
```
I have a registry with wired.samples.simple_factory.Greet... | diff --git a/CHANGES.rst b/CHANGES.rst
index 8f65c20..971a172 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -3,6 +3,9 @@ unreleased
- Add support for Python 3.7.
+- Fix an issue where two different service classes with the same name would
+ be treated as the same service, defeating the type-based lookup.
+
0.1.1... |
mmgalushka__bootwrap-17 | [
{
"changes": {
"added_entities": [
"bootwrap/components/base.py:ClassMixin.m",
"bootwrap/components/base.py:ClassMixin.mt",
"bootwrap/components/base.py:ClassMixin.mb",
"bootwrap/components/base.py:ClassMixin.ml",
"bootwrap/components/base.py:ClassMixin.mr",
... | mmgalushka/bootwrap | 5e6a3b2287af852cf24f901a12848065d45dd314 | Make spacing more efficient
**Bootstrap** includes a wide range of shorthand responsive margin and padding utility classes to modify an element’s appearance which is presented [here](https://getbootstrap.com/docs/4.0/utilities/spacing/).
In the current implementation margin and padding utility classes can be introdu... | diff --git a/bootwrap/components/base.py b/bootwrap/components/base.py
index c56c3f6..693fc6a 100644
--- a/bootwrap/components/base.py
+++ b/bootwrap/components/base.py
@@ -107,6 +107,243 @@ class ClassMixin:
return ' '.join(self.__classes)
return None
+ def m(self, size):
+ """Sets ma... |
mmgalushka__bootwrap-54 | [
{
"changes": {
"added_entities": [
"bootwrap/components/button.py:Button.with_icon"
],
"added_modules": null,
"edited_entities": [
"bootwrap/components/button.py:Button.__init__",
"bootwrap/components/button.py:Button.__str__"
],
"edited_modules": [
... | mmgalushka/bootwrap | e93830324640fde0e6617b41108d396860a2202b | Add icon to button
Add icon beside the button name (on the left or right side). | diff --git a/bootwrap/components/button.py b/bootwrap/components/button.py
index d76cb57..c0fd902 100644
--- a/bootwrap/components/button.py
+++ b/bootwrap/components/button.py
@@ -13,6 +13,7 @@ from .base import (
)
from .panel import Panel
from .dialog import Dialog
+from .icon import Icon
from .utils import attr... |
mmgalushka__bootwrap-58 | [
{
"changes": {
"added_entities": [
"bootwrap/components/panel.py:Panel.align_items"
],
"added_modules": null,
"edited_entities": [
"bootwrap/components/panel.py:Panel.justify_content"
],
"edited_modules": [
"bootwrap/components/panel.py:Panel"
]
... | mmgalushka/bootwrap | 52ddc752621cd6d915deffd42b37a7a4a749e860 | Add align items option to panel
```html
<div class="d-flex align-items-start">...</div>
<div class="d-flex align-items-end">...</div>
<div class="d-flex align-items-center">...</div>
<div class="d-flex align-items-baseline">...</div>
<div class="d-flex align-items-stretch">...</div>
``` | diff --git a/bootwrap/components/panel.py b/bootwrap/components/panel.py
index e4bfa13..c401cfe 100644
--- a/bootwrap/components/panel.py
+++ b/bootwrap/components/panel.py
@@ -158,18 +158,67 @@ class Panel(WebComponent, ClassMixin, ):
self.__arrangement = None
if not isinstance(style, str):
... |
mmgalushka__bootwrap-60 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bootwrap/components/panel.py:Panel.background",
"bootwrap/components/panel.py:Panel.__str__"
],
"edited_modules": [
"bootwrap/components/panel.py:Panel"
]
},
"f... | mmgalushka/bootwrap | 4af7c6fdf597f47266912b6f98080039a6efb409 | Add outline mix to the panel and text web components. | diff --git a/bootwrap/components/panel.py b/bootwrap/components/panel.py
index c401cfe..72366d2 100644
--- a/bootwrap/components/panel.py
+++ b/bootwrap/components/panel.py
@@ -2,11 +2,11 @@
A panel.
"""
-from .base import WebComponent, ClassMixin
+from .base import WebComponent, ClassMixin, AppearanceMixin, Outlin... |
mmgalushka__bootwrap-62 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bootwrap/components/text.py:Text.__init__",
"bootwrap/components/text.py:Text.as_code",
"bootwrap/components/text.py:Text.__str__"
],
"edited_modules": [
"bootwrap/co... | mmgalushka/bootwrap | cad0548f586d6caf5689d7f41d34b19fce31fbcd | Add suppoert of code highlight for JSON and YAML. | diff --git a/bootwrap/components/text.py b/bootwrap/components/text.py
index bb3f429..771c43c 100644
--- a/bootwrap/components/text.py
+++ b/bootwrap/components/text.py
@@ -42,7 +42,7 @@ class Text(WebComponent, ClassMixin, AppearanceMixin, OutlineMixin):
self.__small = False
self.__strong = False
... |
mmgalushka__bootwrap-68 | [
{
"changes": {
"added_entities": [
"bootwrap/components/form.py:CheckboxInput.label_on_left"
],
"added_modules": null,
"edited_entities": [
"bootwrap/components/form.py:CheckboxInput.__init__",
"bootwrap/components/form.py:CheckboxInput.__str__",
"bootwrap... | mmgalushka/bootwrap | 1594cbab5af3f2bf45aae7d58db47b0bb96946d7 | Incorrect response of checkbox, json input and navtabs. | diff --git a/bootwrap/components/form.py b/bootwrap/components/form.py
index ae67d48..62821eb 100644
--- a/bootwrap/components/form.py
+++ b/bootwrap/components/form.py
@@ -5,6 +5,7 @@ A form with input elements.
from abc import ABC, abstractmethod
from textwrap import dedent
from html import escape
+from json impor... |
mmgalushka__bootwrap-70 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"bootwrap/components/form.py:Form.__str__",
"bootwrap/components/form.py:Input.__str__",
"bootwrap/components/form.py:CheckboxInput.__str__",
"bootwrap/components/form.py:Freehand... | mmgalushka/bootwrap | f74b641af088765cbd5baaf1a9fdd4d697424fa8 | Incorrect visualization if the check button group. | diff --git a/bootwrap/components/form.py b/bootwrap/components/form.py
index 62821eb..dc67516 100644
--- a/bootwrap/components/form.py
+++ b/bootwrap/components/form.py
@@ -7,9 +7,16 @@ from textwrap import dedent
from html import escape
from json import dumps
-from .base import WebComponent, ClassMixin, Availabili... |
mmngreco__IneqPy-17 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ineqpy/api.py:Convey.__init__",
"ineqpy/api.py:Survey.__init__",
"ineqpy/api.py:Survey._constructor",
"ineqpy/api.py:Survey.c_moment",
"ineqpy/api.py:Survey.percentile",
... | mmngreco/IneqPy | 0223d5fb125a6561633c9849817c1b299da84a4e | Can not retrieve DataFrame
Hello,
this works:
svy.lorenz('Reduced.Lunch').plot(legend=False,colors=['silver', 'black'])
BUT I can not get the data frame!!!
svy.lorenz('Reduced.Lunch') gives me:
AttributeError: 'numpy.ndarray' object has no attribute 'endswith'
Can you help me ? | diff --git a/ineqpy/api.py b/ineqpy/api.py
index 07167e1..fab2179 100644
--- a/ineqpy/api.py
+++ b/ineqpy/api.py
@@ -1,22 +1,18 @@
-"""This module extend pandas.DataFrames with the main functions from statistics and
-inequality modules.
+"""This module extend pandas.DataFrames with the main functions from statistics
+... |
mmngreco__IneqPy-19 | [
{
"changes": {
"added_entities": [
"src/ineqpy/inequality.py:hoover"
],
"added_modules": [
"src/ineqpy/inequality.py:hoover"
],
"edited_entities": null,
"edited_modules": null
},
"file": "src/ineqpy/inequality.py"
}
] | mmngreco/IneqPy | 5b4d40b9b77304da1e7a883701b21b655d8bb4d4 | Hoover index
Hi, do you plan to add this index to your nice project?
The project is very useful, thanks! | diff --git a/src/ineqpy/inequality.py b/src/ineqpy/inequality.py
index edffbaf..b11348c 100644
--- a/src/ineqpy/inequality.py
+++ b/src/ineqpy/inequality.py
@@ -28,6 +28,7 @@ __all__ = [
"reynolds_smolensky",
"theil",
"ratio_top_rest",
+ "hoover",
]
@@ -516,3 +517,55 @@ def ratio_top_rest(income,... |
mne-tools__mne-bids-1312 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne_bids/read.py:_handle_participants_reading"
],
"edited_modules": [
"mne_bids/read.py:_handle_participants_reading"
]
},
"file": "mne_bids/read.py"
}
] | mne-tools/mne-bids | 9575eabd893002819a54d3128d923fcc69db1dca | We are misusing info["subject_info"]
As revealed by:
- https://github.com/mne-tools/mne-python/pull/12875
And this CI failure: https://github.com/mne-tools/mne-bids/actions/runs/11081048651/job/30792323679#step:16:327
We are adding some keys to `info["subject_info"]` that should not be added:
https://github... | diff --git a/mne_bids/read.py b/mne_bids/read.py
index e0281899..b216b03c 100644
--- a/mne_bids/read.py
+++ b/mne_bids/read.py
@@ -7,7 +7,7 @@ import json
import os
import os.path as op
import re
-from datetime import datetime, timezone
+from datetime import datetime, timedelta, timezone
from difflib import get_clo... |
mne-tools__mne-bids-1357 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne_bids/utils.py:_write_json"
],
"edited_modules": [
"mne_bids/utils.py:_write_json"
]
},
"file": "mne_bids/utils.py"
}
] | mne-tools/mne-bids | 3492fa01157d921f77b93ea31a4db192c47d3bb0 | UTF-8 Encoding is not respected by make_dataset_description
### Description of the problem
Given the wide use of `encoding=utf-8-sig` in mne-bids, I assume that the example below is a bug, and `mne-bids` does want to support characters like ł ([latin small letter with stroke](https://www.compart.com/en/unicode/U+01... | diff --git a/doc/whats_new.rst b/doc/whats_new.rst
index b685cd3c..456af029 100644
--- a/doc/whats_new.rst
+++ b/doc/whats_new.rst
@@ -23,6 +23,7 @@ The following authors had contributed before. Thank you for sticking around!
* `Stefan Appelhoff`_
* `Daniel McCloy`_
+* `Scott Huberty`_
Detailed list of changes
... |
mne-tools__mne-bids-1359 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "mne_bids/config.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne_bids/path.py:... | mne-tools/mne-bids | 3f59b0e0ee835549d068ad4ad85936ddf0ed04cb | rec vs recording?
Is there a reason why mne-bids shortens the recording field to 'rec', while all examples in the specification writes the full 'recording?
see for instance the examples in:
https://bids-specification.readthedocs.io/en/stable/modality-specific-files/physiological-recordings.html
I only just rea... | diff --git a/doc/whats_new.rst b/doc/whats_new.rst
index 456af029..d4ad39cb 100644
--- a/doc/whats_new.rst
+++ b/doc/whats_new.rst
@@ -48,6 +48,7 @@ Detailed list of changes
^^^^^^^^^^^^
- :func:`mne_bids.read_raw_bids` can optionally return an ``event_id`` dictionary suitable for use with :func:`mne.events_from_an... |
mne-tools__mne-bids-1388 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne_bids/path.py:_get_matching_bidspaths_from_filesystem"
],
"edited_modules": [
"mne_bids/path.py:_get_matching_bidspaths_from_filesystem"
]
},
"file": "mne_bids/path.... | mne-tools/mne-bids | 4ac800537776b63b8fde1f8ad97bdbfcdeb50389 | Is zero-padding mandatory in indices?
### Description of the problem
Hi, I have a dataset in which the runs are NOT zero-padded. Something like this:
```bash
mkdir -p test_bids/sub-1/eeg/
touch test_bids/sub-1/eeg/sub-1_run-1_raw.fif
touch test_bids/sub-1/eeg/sub-1_run-10_raw.fif
```
[This BIDS validator](https://bi... | diff --git a/doc/whats_new.rst b/doc/whats_new.rst
index da93f569..b9db98f7 100644
--- a/doc/whats_new.rst
+++ b/doc/whats_new.rst
@@ -26,6 +26,7 @@ The following authors had contributed before. Thank you for sticking around!
* `Stefan Appelhoff`_
* `Daniel McCloy`_
* `Scott Huberty`_
+* `Pierre Guetschel`_
Deta... |
mne-tools__mne-connectivity-104 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "doc/conf.py"
},
{
"changes": {
"added_entities": [
"mne_connectivity/spectral/time.py:_pli",
"mne_connectivity/spectral/time.py:... | mne-tools/mne-connectivity | 53b6b162ee0e04d24e7014d750eadd2fe27df21d | Issues with time-resolved spectral connectivity
"Hello everyone,
I’m currently using MNE connectivity to perform a functional connectivity analysis in a single epoch. With this said, I’ve read some threads where concerns were raised about using spectral_connectivity/spectral_connectivity_epochs on a single epoch.In ... | diff --git a/doc/authors.inc b/doc/authors.inc
index a4caeb5c..096e5d55 100644
--- a/doc/authors.inc
+++ b/doc/authors.inc
@@ -7,3 +7,4 @@
.. _Szonja Weigl: https://github.com/weiglszonja
.. _Kenji Marshall: https://github.com/kenjimarshall
.. _Sezan Mert: https://github.com/SezanMert
+.. _Santeri Ruuskanen: https:/... |
mne-tools__mne-python-10880 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/decoding/decoding_rsa_sgskip.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | mne-tools/mne-python | f0948f862c82159781ce822b2bd7614298f924be | plot_topomap()'s cnorm param should accept a CenteredNorm
Plotting T statistics on topographic maps with @SophieHerbst, I discovered that `mne.viz.plot_topomap()` only accepts `TwoSlopeNorm` as `cnorm` paramter.
However, I believe for our purpose, [`TwoSlopeNorm`](https://matplotlib.org/stable/api/_as_gen/matplotlib... | diff --git a/examples/decoding/decoding_rsa_sgskip.py b/examples/decoding/decoding_rsa_sgskip.py
index bf6cea810..6edd4f4ee 100644
--- a/examples/decoding/decoding_rsa_sgskip.py
+++ b/examples/decoding/decoding_rsa_sgskip.py
@@ -78,9 +78,8 @@ event_id['0/human bodypart/human/not-face/animal/natural']
#################... |
mne-tools__mne-python-11178 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/time_frequency/spectrum.py:BaseSpectrum.__init__",
"mne/time_frequency/spectrum.py:Spectrum.__init__",
"mne/time_frequency/spectrum.py:EpochsSpectrum.__init__"
],
"edited... | mne-tools/mne-python | 1f19c0fcf89d2cfa6b2702c9d9f5a485797d4ec6 | compute_psd does not apply projs correctly
I tested it for `compute_psd()`. It shows the exact same behavior as `psd_welch()`: The projection is not applied during plotting, even if the projection kwarg is set to True `raw_CAR.compute_psd(proj=True)`.
_Originally posted by @moritz-gerster in https://github.com/mne-t... | diff --git a/mne/time_frequency/spectrum.py b/mne/time_frequency/spectrum.py
index e4597834e..f3b23c140 100644
--- a/mne/time_frequency/spectrum.py
+++ b/mne/time_frequency/spectrum.py
@@ -279,6 +279,7 @@ class BaseSpectrum(ContainsMixin, UpdateChannelsMixin):
# apply proj if desired
if proj:
... |
mne-tools__mne-python-11577 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "mne/utils/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/utils/conf... | mne-tools/mne-python | 2bd0c3ee25606fc1e755fe589b0cc6bf409d3f84 | sys_info fails to find mne-qt-browser
It runs on my laptop but it took about a minute to print.
Also I get this
```
❯ mne sys_info
Platform: macOS-13.2.1-arm64-arm-64bit
Python: 3.10.8 | packaged by conda-forge | (main, Nov 22 2022, 08:25:29) [Clang 14.0.6 ]
Executable: /Users/agramfor... | diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 51a65fc0d..bedd00825 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -123,7 +123,7 @@ stages:
- bash: |
set -e
mne sys_info -pd
- mne sys_info -pd | grep "qtpy: .*(PySide6=.*)$"
+ mne sys_info -pd | grep "qtp... |
mne-tools__mne-python-11640 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "mne/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": n... | mne-tools/mne-python | 909e45821bd004b6072a6426e4e8ea88e51b72ad | mne.concatenate_raws(raws) wrongly concatenates raws if the order of the channel names varies across raws
### Description of the problem
[For a description of the problem check this pdf.](https://github.com/mne-tools/mne-python/files/11248385/mne_concatenate_channels_order.pdf)
`mne.concatenate_raws(raws)` wrongly ... | diff --git a/doc/sensor_space.rst b/doc/sensor_space.rst
index a1c72b3aa..b4bbda600 100644
--- a/doc/sensor_space.rst
+++ b/doc/sensor_space.rst
@@ -11,6 +11,7 @@ Sensor Space Data
concatenate_raws
equalize_channels
grand_average
+ match_channel_orders
pick_channels
pick_channels_cov
pick_chan... |
mne-tools__mne-python-11939 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "mne/preprocessing/maxfilter.py"
}
] | mne-tools/mne-python | 82b2e82e42c5167f30df371f3ca7e18b86a2313a | MAINT: deprecate mne maxfilter command line tool
I'm actually inclined to deprecate this instead and remove it after 1.6. We have had `mne.preprocessing.maxwell_filter` for some time which should be more fully featured and it's what we want to support going forward. If people want to use the command-line `maxfilter` fr... | diff --git a/doc/changes/devel.rst b/doc/changes/devel.rst
index 191e057a4..424f32a2a 100644
--- a/doc/changes/devel.rst
+++ b/doc/changes/devel.rst
@@ -41,4 +41,4 @@ Bugs
API changes
~~~~~~~~~~~
-- None yet
+- ``mne.preprocessing.apply_maxfilter`` and ``mne maxfilter`` have been deprecated and will be removed in 1... |
mne-tools__mne-python-12027 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/channels/channels.py:InterpolationMixin.interpolate_bads"
],
"edited_modules": [
"mne/channels/channels.py:InterpolationMixin"
]
},
"file": "mne/channels/channels.p... | mne-tools/mne-python | 04e05d4d323b26af483dde38664cb817f7df8e8a | Enable mne.concatenate_raws(raws) to handle varying bad channels in raws
### Describe the new feature or enhancement
Maximization of available data is very important for many machine learning tasks. Therefore it is better to concatenate three similar recordings instead of using only one. However, what if the bad chann... | diff --git a/mne/channels/channels.py b/mne/channels/channels.py
index 7c3de44fd..b6c82f27b 100644
--- a/mne/channels/channels.py
+++ b/mne/channels/channels.py
@@ -830,7 +830,8 @@ class InterpolationMixin:
.. versionadded:: 0.17
method : dict | None
Method to use for each channel typ... |
mne-tools__mne-python-12033 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/channels/channels.py:InterpolationMixin.interpolate_bads"
],
"edited_modules": [
"mne/channels/channels.py:InterpolationMixin"
]
},
"file": "mne/channels/channels.p... | mne-tools/mne-python | 04e05d4d323b26af483dde38664cb817f7df8e8a | [DOC] Improve tutorials for generating `-trans.fif`
In the process of setting up a source-space-analysis, it took me a really long time to realize all the steps necessary to create a `-trans.fif`. As I am new to these type of analyses, it could be just me not knowing the terminology and what to look for, but I think th... | diff --git a/mne/channels/channels.py b/mne/channels/channels.py
index 7c3de44fd..b6c82f27b 100644
--- a/mne/channels/channels.py
+++ b/mne/channels/channels.py
@@ -830,7 +830,8 @@ class InterpolationMixin:
.. versionadded:: 0.17
method : dict | None
Method to use for each channel typ... |
mne-tools__mne-python-12080 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/_fiff/tag.py:_read_string"
],
"edited_modules": [
"mne/_fiff/tag.py:_read_string"
]
},
"file": "mne/_fiff/tag.py"
},
{
"changes": {
"added_entities": ... | mne-tools/mne-python | 643580122691d58e855f5f25124e78615fbcd933 | Annotations do not support Unicode characters during I/O roundtrip
### Description of the problem
Raw data (and possibly epochs, which I haven't tested) with Annotations that contain Unicode descriptions cannot be saved.
This was initially reported at https://mne.discourse.group/t/saving-filtered-data-and-epochs/... | diff --git a/doc/changes/devel.rst b/doc/changes/devel.rst
index ff753de08..8fc12edc6 100644
--- a/doc/changes/devel.rst
+++ b/doc/changes/devel.rst
@@ -65,6 +65,7 @@ Bugs
- Fix parsing of eye-link :class:`~mne.Annotations` when ``apply_offsets=False`` is provided to :func:`~mne.io.read_raw_eyelink` (:gh:`12003` by `M... |
mne-tools__mne-python-12128 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "mne/utils/check.py"
}
] | mne-tools/mne-python | 8c003e843717e316ba85008eff2298917489bbd1 | "array-like" check incorrectly accepts strings
### Description of the problem
`_validate_type()` accepts a string parameter value "array-like" to allow checking for array-like input. However, the implementation of this recent addition is incorrect by considering any `Sequence` as `array-like`
https://github.com/mne... | diff --git a/mne/utils/check.py b/mne/utils/check.py
index a26495106..2faa364b7 100644
--- a/mne/utils/check.py
+++ b/mne/utils/check.py
@@ -8,7 +8,6 @@ import operator
import os
import re
from builtins import input # no-op here but facilitates testing
-from collections.abc import Sequence
from difflib import get_... |
mne-tools__mne-python-12142 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/viz/evoked.py:_plot_lines"
],
"edited_modules": [
"mne/viz/evoked.py:_plot_lines"
]
},
"file": "mne/viz/evoked.py"
},
{
"changes": {
"added_entities":... | mne-tools/mne-python | debc275b795ea4cf4da72a74ee586c82b2e154fc | Should PSD plots in the report contain bad channels by default?
Since we switched from plot_psd() to compute_psd().plot(), PSD plots in the Report contain bad channels. Is this a default we want to keep? I was using MNE-BIDS-Pipeline and triple-checked my data until I realized what's going on. (I thought something was ... | diff --git a/doc/changes/devel.rst b/doc/changes/devel.rst
index 5457e844f..c52705a9a 100644
--- a/doc/changes/devel.rst
+++ b/doc/changes/devel.rst
@@ -38,6 +38,7 @@ Enhancements
- Add support for writing forward solutions to HDF5 and convenience function :meth:`mne.Forward.save` (:gh:`12036` by `Eric Larson`_)
- Re... |
mne-tools__mne-python-12186 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/epochs.py:BaseEpochs.plot"
],
"edited_modules": [
"mne/epochs.py:BaseEpochs"
]
},
"file": "mne/epochs.py"
},
{
"changes": {
"added_entities": null,
... | mne-tools/mne-python | bb93c0a20cc936f7cdfbadc8aa5ee40a974a6e80 | BUG: Spectrum should only warn on zero spectrum for non-bads
CircleCI just [hit](https://app.circleci.com/pipelines/github/mne-tools/mne-python/21221/workflows/00fe92c1-8ad8-46c3-b797-d8fda6ab4fce/jobs/60092) this:
```
/home/circleci/project/tutorials/preprocessing/50_artifact_correction_ssp.py failed leaving traceba... | diff --git a/doc/changes/devel.rst b/doc/changes/devel.rst
index d11bb3ad6..d5089fd95 100644
--- a/doc/changes/devel.rst
+++ b/doc/changes/devel.rst
@@ -47,17 +47,20 @@ Enhancements
- :func:`~mne.epochs.make_metadata` now accepts ``tmin=None`` and ``tmax=None``, which will bound the time window used for metadata gener... |
mne-tools__mne-python-12218 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/export/_edf.py:_try_to_set_value",
"mne/export/_edf.py:_auto_close",
"mne/export/_edf.py:_export_raw"
],
"edited_modules": [
"mne/export/_edf.py:_try_to_set_value... | mne-tools/mne-python | 44c787fd4cffa3453ffbc7b6735a5d09f47eed44 | Support STIM channels in EDF export
I found some issues with our recently added EDF export that we might want to fix before the next release:
1. The error if `EDFlib-Python` is not installed is misleading, because it says `RuntimeError: For exporting to EDF to work, the EDFlib module is needed, but it could not be i... | diff --git a/doc/changes/devel.rst b/doc/changes/devel.rst
index b30353407..e3738f86b 100644
--- a/doc/changes/devel.rst
+++ b/doc/changes/devel.rst
@@ -23,7 +23,8 @@ Version 1.7.dev0 (development)
Enhancements
~~~~~~~~~~~~
-- None yet
+- Speed up export to .edf in :func:`mne.export.export_raw` by using ``edfio`` i... |
mne-tools__mne-python-12289 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/annotations.py:Annotations.to_data_frame"
],
"edited_modules": [
"mne/annotations.py:Annotations"
]
},
"file": "mne/annotations.py"
},
{
"changes": {
... | mne-tools/mne-python | 5df4cd6506ca2fb244070865a92bdbba8dabc1c4 | ENH: make use of time-stamps optional in `mne.Annotations.to_data_frame()`
### Describe the new feature or enhancement
Hi folks!
I find the `.to_data_frame()` method for annotations very practical but I realize that the default behavior of having onsets in timestamps is not always what is practical from a perspecti... | diff --git a/doc/changes/devel.rst b/doc/changes/devel.rst
index 3fd579ad4..feae12dcb 100644
--- a/doc/changes/devel.rst
+++ b/doc/changes/devel.rst
@@ -39,6 +39,7 @@ Enhancements
- We added type hints for the return values of :func:`mne.read_evokeds` and :func:`mne.io.read_raw`. Development environments like VS Code ... |
mne-tools__mne-python-12514 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/time_frequency/tfr.py:read_tfrs"
],
"edited_modules": [
"mne/time_frequency/tfr.py:read_tfrs"
]
},
"file": "mne/time_frequency/tfr.py"
}
] | mne-tools/mne-python | 169372da67dc243b817f024820b349495a5aa109 | BUG: EpochsTFR bug popping up in MNE-BIDS-Pipeline
@drammock see https://app.circleci.com/pipelines/github/mne-tools/mne-bids-pipeline/4395/workflows/4c871947-2971-4fca-8d92-b7a2892c91db/jobs/62041
To reproduce you can `pip install -e .` mne-bids-pipeline and do (it will download some GB of data to `~/mne_data`):
`... | diff --git a/mne/time_frequency/tfr.py b/mne/time_frequency/tfr.py
index 97df892ad..5a16cac80 100644
--- a/mne/time_frequency/tfr.py
+++ b/mne/time_frequency/tfr.py
@@ -4222,8 +4222,12 @@ def read_tfrs(fname, condition=None, *, verbose=None):
hdf5_dict = read_hdf5(fname, title="mnepython", slash="replace")
# ... |
mne-tools__mne-python-2018 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/report.py:Report._validate_input"
],
"edited_modules": [
"mne/report.py:Report"
]
},
"file": "mne/report.py"
}
] | mne-tools/mne-python | 0bf2f433842c26436fc8f1ee168dfa49b07c45c3 | BUG: Adding more than one figure to Report is broken
If a call to `add_figs_to_section` is made with a list of figures, only the first one is added.
In this example, only the first figure appears on the report.
```Python
import numpy as np
import matplotlib.pyplot as plt
from mne.report import Report
r = Re... | diff --git a/mne/report.py b/mne/report.py
index a8e0d21a6..892aab074 100644
--- a/mne/report.py
+++ b/mne/report.py
@@ -554,7 +554,12 @@ image_template = Template(u"""
{{if comment is not None}}
<br><br>
<div style="text-align:center;">
- {{comment}}
+ <style>
+ ... |
mne-tools__mne-python-2023 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/io/brainvision/brainvision.py:_get_eeg_info"
],
"edited_modules": [
"mne/io/brainvision/brainvision.py:_get_eeg_info"
]
},
"file": "mne/io/brainvision/brainvision.p... | mne-tools/mne-python | acf8364f01f98233613f7574cac7d533c35183bf | check extension of brainvision file
I mistakenly tried:
raw = mne.io.read_raw_brainvision('test.vmrk')
instead of
raw = mne.io.read_raw_brainvision('test.vhdr')
and got this error, which is not super explicit:
--> 402 assert l == 'Brain Vision Data Exchange Header File Version 1.0'
to help her... | diff --git a/mne/io/brainvision/brainvision.py b/mne/io/brainvision/brainvision.py
index 35fd057a2..81b41fa78 100644
--- a/mne/io/brainvision/brainvision.py
+++ b/mne/io/brainvision/brainvision.py
@@ -396,6 +396,10 @@ def _get_eeg_info(vhdr_fname, eog, misc):
info['filename'] = vhdr_fname
eeg_info = {}
+ ... |
mne-tools__mne-python-2053 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "mne/io/meas_info.py"
}
] | mne-tools/mne-python | 1164d58d954f4dae9266b551d9d3efb979c3f597 | Initialise coil types
How to initialize coil types in info object?
```
chans = mne.channels.read_montage('BrainAmpMRIPlus_32sfp', ch_names=None, path= datapath, unit='mm', transform=False)
chanNames = chans.ch_names
info = mne.create_info(chanNames, 250.0, ch_types='eeg')
layout = mne.channels.find_layout(info... | diff --git a/mne/io/meas_info.py b/mne/io/meas_info.py
index 6e850b71a..b55a983b6 100644
--- a/mne/io/meas_info.py
+++ b/mne/io/meas_info.py
@@ -31,7 +31,7 @@ from ..externals.six import b, BytesIO, string_types, text_type
_kind_dict = dict(
- eeg=(FIFF.FIFFV_EEG_CH, FIFF.FIFFV_COIL_NONE, FIFF.FIFF_UNIT_V),
+ ... |
mne-tools__mne-python-2076 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "mne/datasets/sample/__init__.py"
},
{
"changes": {
"added_entities": [
"mne/datasets/sample/sample.py:get_version"
],
"added... | mne-tools/mne-python | 7f8071891d7a8c2fdaa61ea3a8819394fcd86de2 | Q: Dataset versions
Have we gotten any useful information from embedding dataset versions in our tarballs? As far as I can tell it has just led to a bunch of warnings when doing imports (see e.g. Mainak's recent notebook examples). I propose we get rid of them for now, and replace them with a new system in the future i... | diff --git a/mne/datasets/sample/__init__.py b/mne/datasets/sample/__init__.py
index 1a278cfcc..3e4de83f4 100644
--- a/mne/datasets/sample/__init__.py
+++ b/mne/datasets/sample/__init__.py
@@ -1,4 +1,4 @@
"""MNE sample dataset
"""
-from .sample import data_path, has_sample_data
+from .sample import data_path, has_s... |
mne-tools__mne-python-2080 | [
{
"changes": {
"added_entities": [
"mne/io/base.py:_BaseRaw.preload_data",
"mne/io/base.py:_BaseRaw._preload_data"
],
"added_modules": null,
"edited_entities": [
"mne/io/base.py:_BaseRaw.__init__",
"mne/io/base.py:_BaseRaw._read_segment"
],
"ed... | mne-tools/mne-python | f2ab0641f087c63beab715ff5fdaa9399c0807fe | preload_data is only for RawFIF
I was just working with a RawEDF and I went to call `raw.preload_data`, but I noticed that this method didn't exist for this Raw class. It's currently only implemented for RawFIF. I also saw that there is a new (to me at least) parameter in `_read_segment` called `data_buffer` that is be... | diff --git a/mne/io/base.py b/mne/io/base.py
index 9a3c83be2..578109de7 100644
--- a/mne/io/base.py
+++ b/mne/io/base.py
@@ -215,22 +215,39 @@ class _BaseRaw(ProjMixin, ContainsMixin, PickDropChannelsMixin,
Subclasses must provide the following methods:
- * _read_segment(start, stop, sel, projector, ver... |
mne-tools__mne-python-2193 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "mne/__init__.py"
},
{
"changes": {
"added_entities": [
"mne/bem.py:_calc_beta",
"mne/bem.py:_lin_pot_coeff",
"mne/bem.py... | mne-tools/mne-python | 6ccf41c6295760dcf36e2a1062132e5b319a4812 | implement bem-sol.fif code in python
for @Eric89GXL ... | diff --git a/doc/source/python_reference.rst b/doc/source/python_reference.rst
index dc0967bcd..8ac585031 100644
--- a/doc/source/python_reference.rst
+++ b/doc/source/python_reference.rst
@@ -159,7 +159,8 @@ Functions:
read_trans
save_stc_as_volume
write_labels_to_annot
- write_bem_surface
+ write_bem_... |
mne-tools__mne-python-2228 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/stats/multi_comp.py:bonferroni_correction"
],
"edited_modules": [
"mne/stats/multi_comp.py:bonferroni_correction"
]
},
"file": "mne/stats/multi_comp.py"
}
] | mne-tools/mne-python | b143c6df244dca2e6121048fae99cb6e1cfa84ab | BUG/API issue with multi_comp.bonferroni_correction
Do people agree that this is a bug, at least a very unexpected output:
https://github.com/mne-tools/mne-python/blob/master/mne/stats/multi_comp.py#L101
`pval_corrected` should instead be used for creating the output mask.
@agramfort @Eric89GXL @mainakjas | diff --git a/doc/source/whats_new.rst b/doc/source/whats_new.rst
index 5ff2f77d1..3c7c0a5fd 100644
--- a/doc/source/whats_new.rst
+++ b/doc/source/whats_new.rst
@@ -14,6 +14,8 @@ BUG
- Fix ``mne.io.add_reference_channels`` not setting ``info[nchan]`` correctly by `Federico Raimondo`_
+ - Fix ``mne.stats.bon... |
mne-tools__mne-python-2495 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/preprocessing/plot_estimate_covariance_matrix_raw.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edi... | mne-tools/mne-python | a9cc9c9b5e9433fd06258e05e41cc7edacfe4391 | rename compute_raw_data_covariance to compute_raw_covariance
any objection to rename compute_raw_data_covariance to compute_raw_covariance ?
the _data is not consistent. See eg compute_raw_psd etc... | diff --git a/doc/manual/cookbook.rst b/doc/manual/cookbook.rst
index ac96a2780..17a256d13 100644
--- a/doc/manual/cookbook.rst
+++ b/doc/manual/cookbook.rst
@@ -347,9 +347,9 @@ ways:
- Employ empty room data (collected without the subject) to
calculate the full noise covariance matrix. This is recommended
for an... |
mne-tools__mne-python-5394 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/cuda.py:fft_resample"
],
"edited_modules": [
"mne/cuda.py:fft_resample"
]
},
"file": "mne/cuda.py"
},
{
"changes": {
"added_entities": null,
"ad... | mne-tools/mne-python | 3d08007b755931bcd0955b6aacc6d3fb424ff7e6 | BUG: sklearn cross_val_predict changed, now incompatible with SlidingEstimator with predict proba
sklearn `cross_val_predict` has recently changed, and is now incompatible with SlidingEstimator with classification estimators, as it requires `n_classes`
```python
import numpy as np
from mne.decoding import SlidingE... | diff --git a/.gitignore b/.gitignore
index bb2f48639..3f14a575e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -68,3 +68,8 @@ examples/visualization/foobar.html
# Visual Studio Code
.vscode
+
+# Emacs
+*.py#
+*.rst#
+
diff --git a/doc/whats_new.rst b/doc/whats_new.rst
index 6735b45cd..75797cfdb 100644
--- a/doc/whats_... |
mne-tools__mne-python-5971 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/channels/channels.py:UpdateChannelsMixin.drop_channels"
],
"edited_modules": [
"mne/channels/channels.py:UpdateChannelsMixin"
]
},
"file": "mne/channels/channels.py... | mne-tools/mne-python | 5537ba206f101bd2c191a6a63d9575b858f74dd3 | [VIZ] Rendering bug in plot_evoked_field()
#### Describe the bug
Rendering bug introduced by the migration to the renderer backend.
Current result:
Correct result:
![image](https://user-images.githubu... | diff --git a/doc/whats_new.rst b/doc/whats_new.rst
index 1fc8a2446..0312eb299 100644
--- a/doc/whats_new.rst
+++ b/doc/whats_new.rst
@@ -69,6 +69,8 @@ Changelog
- Add ``channel_wise`` argument to :func:`mne.io.Raw.apply_function` to allow applying a function on multiple channels at once by `Hubert Banville`_
+- Al... |
mne-tools__mne-python-6184 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mne/annotations.py:_read_annotations_csv"
],
"edited_modules": [
"mne/annotations.py:_read_annotations_csv"
]
},
"file": "mne/annotations.py"
},
{
"changes": {
... | mne-tools/mne-python | 8ac51be3e8eeaeb25adaafd8d580fee4dff0f558 | BUG: "mne.read_annotations"
#### Describe the bug
When I used the command '**mne.read_annotations'** to read .csv file. The **onset** always is 0. However, the **duration** and **description** work well. If I change the file into .txt, it works correctly.
| diff --git a/doc/contributing.rst b/doc/contributing.rst
index e4f0c9e7d..15faa7e05 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -33,10 +33,12 @@ you can follow those steps:
$ git clone git@github.com:mne-tools/mne-python.git
$ cd mne-python
- $ conda env create -f environment.yml
-... |
mne-tools__mne-python-6879 | [
{
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"edited_modules": null
},
"file": "examples/inverse/plot_compute_mne_inverse_raw_in_label.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_... | mne-tools/mne-python | f59d54ef3632fa7bde410d8550a6276b4311895b | BUG, VIZ: raw.plot_psd fmax param ignored when plotting
the `fmax` parameter should be used to set the right-hand xlim of the plot, but it is not. In the plots below, the right-hand xlim is determined by the `sfreq` even though `fmax=350` is specified for both plots.
```
import os
import mne
sample_data_folder = ... | diff --git a/doc/glossary.rst b/doc/glossary.rst
index 4de71fe51..de7a7704a 100644
--- a/doc/glossary.rst
+++ b/doc/glossary.rst
@@ -25,7 +25,9 @@ general neuroimaging concepts. If you think a term is missing, please consider
for a tutorial on how to manipulate such objects.
Beamformer
- Beamfor... |
moble__quaternionic-30 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"quaternionic/converters.py:mixin.from_axis_angle",
"quaternionic/converters.py:mixin.from_euler_angles",
"quaternionic/converters.py:mixin.from_spherical_coordinates",
"quaternio... | moble/quaternionic | ae3dd085d68588552f785de8244800babd9ab31f | Unexpected result when give int spherical coordinates
Hi, I'm not sure if this is a bug, but it's very confusing.
When I enter int theta and phi, it gives zeros.
```python
import quaternionic
quaternionic.array.from_spherical_coordinates(1, 2)
# --> quaternionic.array([0., 0., 0., 0.])
```
Only when I expl... | diff --git a/quaternionic/converters.py b/quaternionic/converters.py
index 8a3b4c6..a9db14f 100644
--- a/quaternionic/converters.py
+++ b/quaternionic/converters.py
@@ -394,8 +394,9 @@ def QuaternionConvertersMixin(jit=jit):
"""
vec = np.asarray(vec)
- quats = np.zeros(vec.shape[:... |
moble__spherical-10 | [
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"edited_entities": [
"spherical/utilities/indexing.py:WignerHsize"
],
"edited_modules": [
"spherical/utilities/indexing.py:WignerHsize"
]
},
"file": "spherical/utilities/indexing.py"
},
... | moble/spherical | 1f006a9ccdfa86b7f8798ad22ab8b38156997dc5 | The problem of calculating the spherical harmonics
When I use this program to calculate the spherical harmonics(s=0), the results are obviously problematic (compared to [scipy](https://docs.scipy.org/doc/scipy/reference/generated/scipy.special.sph_harm.html)), is there something wrong with my code?
```python
import... | diff --git a/poetry.lock b/poetry.lock
index 5ede578..2bbb3ff 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -96,7 +96,7 @@ python-versions = "*"
[[package]]
name = "cffi"
-version = "1.14.4"
+version = "1.14.5"
description = "Foreign Function Interface for Python calling C code."
category = "dev"
optional = fals... |
model-bakers__model_bakery-253 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"model_bakery/baker.py:Baker._make",
"model_bakery/baker.py:Baker._skip_field"
],
"edited_modules": [
"model_bakery/baker.py:Baker"
]
},
"file": "model_bakery/ba... | model-bakers/model_bakery | 1b04e23b2d11f9bec8914d5229088eae59d9d934 | Use of itertools.count to generate record ids in Recipe
Hi,
`itertools.count` does not seem to be working in recipe or in a direct make statement
when I declare:
```
import itertools as it
baker.make('Play', puzzle_id=it.count(start=1), _quantity=7)
```
or
`fake_play = Recipe(Play, puzzle_id=it.count(st... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index f55041b..d0eacf0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
### Changed
- Validate `increment_by` parameter of `seq` helper when `value` is an instance of `datetime` [PR #247](http... |
model-bakers__model_bakery-301 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"model_bakery/baker.py:Baker.generate_value"
],
"edited_modules": [
"model_bakery/baker.py:Baker"
]
},
"file": "model_bakery/baker.py"
}
] | model-bakers/model_bakery | 64d7709cd2ee91271394360e0c7c618234a7db45 | Better exception message for non supported fields
## Expected behavior
To add the field name to the exception that's raised when bakery can't handle a specific field type. Not having the field name in the exception forces the developer to inspect the model definition to figure out what's the name of the field they m... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4c64159..499ba3c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
- Extend type hints in `model_bakery.recipe` module, make `Recipe` class generic [PR #292](https://github.com/model-baker... |
model-bakers__model_bakery-353 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"model_bakery/utils.py:seq"
],
"edited_modules": [
"model_bakery/utils.py:seq"
]
},
"file": "model_bakery/utils.py"
}
] | model-bakers/model_bakery | 370406f487fa692be93eacbfab678cf2f316bbee | seq doesn't work for timezone aware datetime objects
## Expected behavior
I expect to get a generator of datetimes.
## Actual behavior
I got an exception.
## Reproduction Steps
```pycon
>>> from model_bakery.recipe import seq
>>> from datetime import datetime, timedelta, timezone
>>> dt = datetime(202... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3313c2b..9e30a2b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
### Added
### Changed
+- Fixed a bug with `seq` being passed a tz-aware start value [PR #353](https://github.com/model... |
model-bakers__model_bakery-354 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"model_bakery/baker.py:bulk_create"
],
"edited_modules": [
"model_bakery/baker.py:bulk_create"
]
},
"file": "model_bakery/baker.py"
}
] | model-bakers/model_bakery | cc08b58d4ee919e1efa1833c2c0ac03d30c38cbc | _bulk_create=True silently and undocumentedly does not create M2M-entries
Probably related to #202, as it is the same issue applied to ManyToManyField.
When using `baker.make` with `_bulk_create=True`, it will silently ignore arguments that should be used to fill many-to-many fields.
## Expected behavior
with
`... | diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index 6a06232..dfc3c77 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -4,7 +4,7 @@ on: pull_request
jobs:
remind:
- runs-on: ubuntu-latest
+ runs-on: ubuntu-22.04
if: |
!contains... |
model-bakers__model_bakery-417 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"model_bakery/utils.py:seq"
],
"edited_modules": [
"model_bakery/utils.py:seq"
]
},
"file": "model_bakery/utils.py"
}
] | model-bakers/model_bakery | 75735ff68341e2a030d1381b25907e3a4377a76f | utils.seq does not start from 0
**Describe the issue**
seq function does not work properly with start=0 due to there is [wrong check for None](https://github.com/model-bakers/model_bakery/blob/75735ff68341e2a030d1381b25907e3a4377a76f/model_bakery/utils.py#L97) (default) value.
```
for i in seq(0, start=0):
prin... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index e85d6d7..7ee2199 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
### Added
### Changed
+- Fix utils.seq with start=0
### Removed
diff --git a/model_bakery/utils.py b/model_bakery... |
model-bakers__model_bakery-480 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"model_bakery/baker.py:Baker._handle_one_to_many",
"model_bakery/baker.py:Baker._handle_m2m"
],
"edited_modules": [
"model_bakery/baker.py:Baker"
]
},
"file": "m... | model-bakers/model_bakery | a9ae541e9775690d536ad814fe4360d85fff7ca7 | Using make_recipe with _quantity together with related key only applies to last item created
Using make_recipe with _quantity together with related key only applies to last item created
Given this setup code:
mommy_recipes.py:
```python
dog1 = recipe.Recipe(
Dog
)
dog2 = recipe.Recipe(
Dog
)
... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index c7c6c91..1c0dc75 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
### Added
### Changed
+- Fix `make_recipe` to work with `_quantity` (#28)
### Removed
diff --git a/model_bakery/b... |
model-bakers__model_bakery-486 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"model_bakery/baker.py:bulk_create"
],
"edited_modules": [
"model_bakery/baker.py:bulk_create"
]
},
"file": "model_bakery/baker.py"
}
] | model-bakers/model_bakery | 5aa3070e72c27b91e13989da9429a7c9e6a98995 | `make()` with `_bulk_create=True` does not create M2M-entries that are specified using the reverse/related name.
When using `baker.make` with `_bulk_create=True`, it will silently ignore arguments that should be used to fill many-to-many fields if the arguments use the reverve/related name.
Follow up to #298, where ... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index c9862b1..b4d09e0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
### Added
### Changed
+- Handle bulk creation when using reverse related name
### Removed
diff --git a/model_bake... |
model-bakers__model_bakery-520 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"model_bakery/baker.py:Baker._skip_field",
"model_bakery/baker.py:Baker._handle_auto_now"
],
"edited_modules": [
"model_bakery/baker.py:Baker"
]
},
"file": "mode... | model-bakers/model_bakery | 8051e3f5bcc1c9cae96e0cc54d98e695d6701051 | Regression for DateField/DateTimeField in 1.20.3
**Describe the issue**
This is a regression introduced in #507. Version 1.20.3 is affected, the 1.20.2 and above are fine.
**To Reproduce**
```py
# test_baker.py
...
class TestAutoNowFields:
@pytest.mark.django_db
def test_make_with_datetime_generator(self):
... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8277cd6..fb82e2a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
### Added
### Changed
+- Fix regression introduced in 1.20.3 that prevented using `auto_now` and `auto_now_add` fields... |
model-bakers__model_bakery-76 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "model_bakery/baker.py"
}
] | model-bakers/model_bakery | 0256cf6607c5d8ba24576c2e0290060c1a203a88 | Enable seq to be imported from baker
I think it would be useful to also enable the seq() function to be imported from the baker module like it is in the recipe module so that it can be used as baker.seq() if preferred or to avoid namespace issues.
The current import can be left in place for backwards compatibility o... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 18fc8a1..ccebfea 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
### Added
### Changed
+- Enable `seq` to be imported from `baker` [PR #76](https://github.com/model-bakers/model_baker... |
modelcontextprotocol__python-sdk-167 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/mcp/client/session.py:ClientSession.list_resource_templates"
],
"edited_modules": [
"src/mcp/client/session.py:ClientSession"
]
},
"file": "src/mcp/client/session.p... | modelcontextprotocol/python-sdk | 08042c3307bdd0d4a66b0dd3200f38222f447b1e | Random error thrown on response
**Describe the bug**
Sometimes, I see a stacktrace printed in the logs of my mcp server. Claude eventually succeeds to response but I think its good to investigate it.
**To Reproduce**
Its hard to reproduce as it does not always happen. The code in my codebase that caused it to happ... | diff --git a/.gitignore b/.gitignore
index bb25f9e..f27f895 100644
--- a/.gitignore
+++ b/.gitignore
@@ -162,6 +162,3 @@ cython_debug/
# and can be added to the global gitignore or merged into this file. For a more nuclear
# option (not recommended) you can uncomment the following to ignore the entire idea folder.... |
modelcontextprotocol__python-sdk-222 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/mcp/server/fastmcp/server.py:FastMCP.read_resource",
"src/mcp/server/fastmcp/server.py:Context.read_resource"
],
"edited_modules": [
"src/mcp/server/fastmcp/server.py:Fas... | modelcontextprotocol/python-sdk | 2628e01f4b892b9c59f3bdd2abbad718c121c87a | Returning multiple Resource and Tool results from FastMCP and Lowlevel
We currently do not support returning multiple values from resources and tools despite the spec explicitly allowing for it. | diff --git a/src/mcp/server/fastmcp/server.py b/src/mcp/server/fastmcp/server.py
index e08a161..122aceb 100644
--- a/src/mcp/server/fastmcp/server.py
+++ b/src/mcp/server/fastmcp/server.py
@@ -3,7 +3,7 @@
import inspect
import json
import re
-from collections.abc import AsyncIterator
+from collections.abc import Asy... |
modelcontextprotocol__python-sdk-384 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/mcp/server/fastmcp/utilities/func_metadata.py:FuncMetadata.pre_parse_json"
],
"edited_modules": [
"src/mcp/server/fastmcp/utilities/func_metadata.py:FuncMetadata"
]
},
... | modelcontextprotocol/python-sdk | 689c54c5915dda3ba484e55a59c126cb46dfc739 | Input should be a valid string [type=string_type, input_value=123, input_type=int]
MCP Server tools code:
`@mcp.tool(description="查询物流信息")
async def query_logistics(order_id: str) -> str:
"""查询物流信息。当用户需要根据订单号查询物流信息时，调用此工具
Args:
order_id: 订单号
Returns:
物流信息的字符串描述
"""
# 统一的物流信息数据
tracking_info = [... | diff --git a/src/mcp/server/fastmcp/utilities/func_metadata.py b/src/mcp/server/fastmcp/utilities/func_metadata.py
index cf93049..629580e 100644
--- a/src/mcp/server/fastmcp/utilities/func_metadata.py
+++ b/src/mcp/server/fastmcp/utilities/func_metadata.py
@@ -88,7 +88,7 @@ class FuncMetadata(BaseModel):
... |
modern-python__that-depends-118 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"that_depends/providers/object.py:Object.async_resolve",
"that_depends/providers/object.py:Object.sync_resolve"
],
"edited_modules": [
"that_depends/providers/object.py:Object... | modern-python/that-depends | 3657c23eb199b49e2e535a109c82fd57c4f4d6ee | Allow overriding Object provider
Currently, it's not possible to override the `Object` provider. For example:
```python
class DIContainer(BaseContainer):
object = providers.Object(42)
with DIContainer.override_providers({"object": 123}):
assert DIContainer.object.sync_resolve() == 123 # Raises Assertion... | diff --git a/that_depends/providers/object.py b/that_depends/providers/object.py
index a0095c7..2b218a3 100644
--- a/that_depends/providers/object.py
+++ b/that_depends/providers/object.py
@@ -15,7 +15,9 @@ class Object(AbstractProvider[T_co]):
self._obj: typing.Final = obj
async def async_resolve(self)... |
modernatx__seqlike-21 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"seqlike/SeqLike.py:SeqLike.translate"
],
"edited_modules": [
"seqlike/SeqLike.py:SeqLike"
]
},
"file": "seqlike/SeqLike.py"
}
] | modernatx/seqlike | 55e9820075842906c59caa72621e5845cf5f434f | SeqLike.translate() does not generate seqnum letter_annotations
When calling SeqLike.translate(), the new SeqRecord _aa_record does not have the seqnum letter_annotations that would exist if a new SeqLike were initialized. Instead, letter_annotations is an empty dict. | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6cf7b81..daa7036 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,8 @@
## [Unreleased]
+- Ensure that `.translate()` generates a SeqLike with "seqnum" letter annotations (@ndousis)
+
## [v1.1.3] - 2021-11-03
- First public release of SeqLike h/t @andrewgi... |
modernatx__seqlike-26 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"seqlike/SeqLike.py:SeqLike.aa"
],
"edited_modules": [
"seqlike/SeqLike.py:SeqLike"
]
},
"file": "seqlike/SeqLike.py"
}
] | modernatx/seqlike | cda0da37121c380113277e777ae8e8070445bf68 | Standard keyword arguments for translate in .aa()
As implemented currently, the SeqLike method `aa` passes kwargs to `SeqRecord.translate`, and so the default call to `.aa()` loses SeqRecord attributes like `id` and `name`. I propose that we keep `SeqLike.translate(**kwargs)`, but remove these optional arguments from ... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 075e878..f95a2df 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,8 @@
## [Unreleased]
+- Simplify `.aa()` interface, return original SeqRecord attributes (@ndousis)
+
## [v1.1.5] - 2021-11-15
- Ensure that `python-codon-tables` is listed as an explicit... |
modernatx__seqlike-76 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "seqlike/codon_tables.py"
}
] | modernatx/seqlike | 1859afc419b6f530d37ff849f4b76cd8576b8bd8 | fix codons_table bug
Adding entries to a codon table generated by `python_codon_tables.get_codons_table()` has the insidious effect of adding these entries to codon tables generated by subsequent calls to `get_codons_table()`. For example:
```python
import python_codon_tables as pct
# generate a codon table; a... | diff --git a/seqlike/codon_tables.py b/seqlike/codon_tables.py
index 349b764..0849d4e 100644
--- a/seqlike/codon_tables.py
+++ b/seqlike/codon_tables.py
@@ -79,13 +79,13 @@ CODON_TABLE = {
}
# https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables/blob/master/codon_usage_data/tables/h_sapiens_9606.csv
-huma... |
modflowpy__flopy-1136 | [
{
"changes": {
"added_entities": [
"flopy/discretization/grid.py:Grid.thick",
"flopy/discretization/grid.py:Grid.saturated_thick"
],
"added_modules": null,
"edited_entities": [
"flopy/discretization/grid.py:Grid.top_botm"
],
"edited_modules": [
... | modflowpy/flopy | e566845172380e3eae06981ca180923d2362ee56 | Reading data from PathlineFile is slow
Hi,
I'm using MODPATH 6 and encountering performance issues with data reading.
I can't provide a minimal working example easily, but my model has 40401 pathlines and 926690 points (that makes 23 points per pathline on average), and I use `PathlineFile.get_alldata()` to extract... | diff --git a/examples/Notebooks/flopy3_Modflow_postprocessing_example.ipynb b/examples/Notebooks/flopy3_Modflow_postprocessing_example.ipynb
index fb5b2831..dbe88833 100644
--- a/examples/Notebooks/flopy3_Modflow_postprocessing_example.ipynb
+++ b/examples/Notebooks/flopy3_Modflow_postprocessing_example.ipynb
@@ -9,21 ... |
modflowpy__flopy-1748 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"flopy/mf6/mfbase.py:MFFileMgmt.strip_model_relative_path"
],
"edited_modules": [
"flopy/mf6/mfbase.py:MFFileMgmt"
]
},
"file": "flopy/mf6/mfbase.py"
},
{
"chang... | modflowpy/flopy | 604183550e4a2a6b2d19cc38528e4de0686e58be | Load simulation error "list index out of range"
### Discussed in https://github.com/modflowpy/flopy/discussions/1383
<div type='discussions-op-text'>
<sup>Originally posted by **TIPJhonTellez** March 23, 2022</sup>
thanks for reading. I am currently trying to load a MODFLOW6 simulation with the FloPy library and... | diff --git a/flopy/mf6/mfbase.py b/flopy/mf6/mfbase.py
index 514a8871..0a9b7a33 100644
--- a/flopy/mf6/mfbase.py
+++ b/flopy/mf6/mfbase.py
@@ -10,6 +10,7 @@ from enum import Enum
from pathlib import Path
from shutil import copyfile
from typing import Union
+from warnings import warn
# internal handled exception... |
modflowpy__flopy-2179 | [
{
"changes": {
"added_entities": [
"flopy/utils/util_list.py:MfList.__cast_tabular"
],
"added_modules": null,
"edited_entities": [
"flopy/utils/util_list.py:MfList.__cast_data"
],
"edited_modules": [
"flopy/utils/util_list.py:MfList"
]
},
... | modflowpy/flopy | 8e16aab76b6e4f892fcf7031488324c3d490b75b | feat: support kper column in stress period recarray/dataframe input data
I like the idea of a kper column in the dataframe/recarray. We have been kicking that idea around for a while now and should see what it would take to support.
_Originally posted by @langevin-usgs in https://github.com/modflowpy/flopy/discussi... | diff --git a/flopy/utils/util_list.py b/flopy/utils/util_list.py
index 62fdb5ef..66d2baf3 100644
--- a/flopy/utils/util_list.py
+++ b/flopy/utils/util_list.py
@@ -296,6 +296,16 @@ class MfList(DataInterface, DataListInterface):
fmt_string = "".join(fmts)
return fmt_string
+ def __cast_tabular... |
modin-project__modin-1842 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"modin/pandas/dataframe.py:DataFrame.groupby"
],
"edited_modules": [
"modin/pandas/dataframe.py:DataFrame"
]
},
"file": "modin/pandas/dataframe.py"
}
] | modin-project/modin | 9ed8e06960cb610680763039a44ae211ea82931c | Simple groupby causes TypeError
Here is a failing test:
```
import pandas as pd
import modin.pandas as mpd
data = {
"a": [1, 1, 2],
"b": [11, 11, 22],
"c": [111, 111, 222]
}
df = pd.DataFrame(data)
df = pd.concat([df])
ref = df.groupby(["a", "b", df["c"]]).size()
print(ref)
df = mpd.DataFrame(data)
df =... | diff --git a/modin/pandas/dataframe.py b/modin/pandas/dataframe.py
index 68a9f05e..8cb7e2fc 100644
--- a/modin/pandas/dataframe.py
+++ b/modin/pandas/dataframe.py
@@ -440,7 +440,21 @@ class DataFrame(BasePandasDataset):
by = by._query_compiler
elif is_list_like(by):
# fastpath for mul... |
modin-project__modin-2036 | [
{
"changes": {
"added_entities": [
"modin/backends/base/query_compiler.py:BaseQueryCompiler.getitem_array"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"modin/backends/base/query_compiler.py:BaseQueryCompiler"
]
},
"file": "mo... | modin-project/modin | 2ca3f34b2c3c22bf285c0349d35a5099de3a2e78 | [REFACTOR] Avoid API level index access in getitem for bool indexer
Currently using the subscription operator for bool Series causes index access in API level. This operation is used in Census and we need it to be lazy.
| diff --git a/modin/backends/base/query_compiler.py b/modin/backends/base/query_compiler.py
index adc00814..c5800831 100644
--- a/modin/backends/base/query_compiler.py
+++ b/modin/backends/base/query_compiler.py
@@ -833,6 +833,23 @@ class BaseQueryCompiler(abc.ABC):
# END Abstract map across rows/columns
# A... |
modin-project__modin-2082 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "modin/apply_license_header.py"
}
] | modin-project/modin | 51ed0ae345cb19b1bb5ea23f73ce9b9ef9fb392f | Rename LISCENSE_HEADER to LICENSE_HEADER | diff --git a/LISCENSE_HEADER b/LICENSE_HEADER
similarity index 100%
rename from LISCENSE_HEADER
rename to LICENSE_HEADER
diff --git a/modin/apply_license_header.py b/modin/apply_license_header.py
index 7f9f94d1..997ee933 100644
--- a/modin/apply_license_header.py
+++ b/modin/apply_license_header.py
@@ -19,7 +19,7 @@ fr... |
modin-project__modin-2107 | [
{
"changes": {
"added_entities": [
"modin/experimental/cloud/rayscale.py:RayCluster._conda_requirements",
"modin/experimental/cloud/rayscale.py:RayCluster._update_conda_requirements",
"modin/experimental/cloud/rayscale.py:RayCluster._get_python_version"
],
"added_module... | modin-project/modin | f46382c31d2bea7706e6242143817f955e1eac52 | Synchronize the python version in the local context with the python version in the remote context. | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b7aac1e6..c739a346 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -166,7 +166,7 @@ jobs:
conda list
- name: Internals tests
shell: bash -l {0}
- run: python -m pytest modin/test/test_publish... |
modin-project__modin-2111 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"modin/experimental/backends/omnisci/query_compiler.py:DFAlgQueryCompiler._set_index",
"modin/experimental/backends/omnisci/query_compiler.py:DFAlgQueryCompiler._bin_op",
"modin/experimen... | modin-project/modin | ca8e7b5955527abbe0c7927febbe29d205d7daff | test_io.py::test_from_csv fails in remote context
### Describe the problem
<!-- Describe the problem clearly here. -->
When running `python -m pytest --simulate-cloud=normal modin\pandas\test\test_io.py::test_from_csv[123]` the following errors happen:
1. Bug in `__array__`
```
make_csv_file = <function make_csv... | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b7aac1e6..3645496b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -166,7 +166,7 @@ jobs:
conda list
- name: Internals tests
shell: bash -l {0}
- run: python -m pytest modin/test/test_publish... |
modin-project__modin-2117 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "modin/backends/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"modin/exp... | modin-project/modin | f82fc67c70f4fbc99b0f82a2729bae93d22486f5 | Add a mechanism that allows to install additional packages in a remote environment. | diff --git a/docs/supported_apis/dataframe_supported.rst b/docs/supported_apis/dataframe_supported.rst
index 45dc27ea..54704dbb 100644
--- a/docs/supported_apis/dataframe_supported.rst
+++ b/docs/supported_apis/dataframe_supported.rst
@@ -438,6 +438,8 @@ default to pandas.
+----------------------------+---------------... |
modin-project__modin-2146 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"modin/experimental/cloud/omnisci.py:RemoteOmnisci.__init__"
],
"edited_modules": [
"modin/experimental/cloud/omnisci.py:RemoteOmnisci"
]
},
"file": "modin/experimental/... | modin-project/modin | fe0afedd051f9aa721d27a63fcb8c67df32d9768 | "conda install python==3.7.9 -c conda-forge" failed when the cluster is created
### System information
- **OS Platform and Distribution (e.g., Linux Ubuntu 16.04)**:
- **Modin version** (`modin.__version__`):
- **Python version**:
- **Code we can use to reproduce**:
<!--
You can obtain the Modin version with
... | diff --git a/examples/cluster/h2o-runner.py b/examples/cluster/h2o-runner.py
index 56bffcfe..eb5fbbef 100644
--- a/examples/cluster/h2o-runner.py
+++ b/examples/cluster/h2o-runner.py
@@ -12,9 +12,10 @@
# governing permissions and limitations under the License.
-# pip install git+https://github.com/intel-go/ibis.gi... |
modin-project__modin-2977 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"modin/backends/base/query_compiler.py:BaseQueryCompiler.prod",
"modin/backends/base/query_compiler.py:BaseQueryCompiler.sum"
],
"edited_modules": [
"modin/backends/base/query... | modin-project/modin | 9a6108b69f8cda6b762d880addcc1e7c0cad352f | Update pandas to 1.2.4 | diff --git a/environment-dev.yml b/environment-dev.yml
index 12a389fb..2b60e4df 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -2,7 +2,7 @@ name: modin
channels:
- conda-forge
dependencies:
- - pandas==1.2.3
+ - pandas==1.2.4
- numpy>=1.16.5,<1.20 # pandas gh-39513
- pyarrow>=1.0.0
- lib... |
modin-project__modin-3034 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"modin/utils.py:_inherit_docstrings"
],
"edited_modules": [
"modin/utils.py:_inherit_docstrings"
]
},
"file": "modin/utils.py"
}
] | modin-project/modin | 1fd5eee3c76f78390c1a9947b147cb1d20caf0b6 | _inherit_docstrings does not wrap classmethods and own attributes
> Another problem with `doc_checker` is that for file `modin/pandas/accessor.py` from PR #3022 I get errors about functions `from_spmatrix` and `from_coo` although docstrings for these functions should be inherited.
The problem has to do with how `_in... | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9a68449c..88e5c7a0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -260,7 +260,15 @@ jobs:
- run: python -m pytest -n 2 modin/pandas/test/test_groupby.py --backend=${{ matrix.backend }}
- run: python -m pytest -... |
modin-project__modin-5058 | [
{
"changes": {
"added_entities": [
"modin/core/execution/ray/common/utils.py:wait"
],
"added_modules": [
"modin/core/execution/ray/common/utils.py:wait"
],
"edited_entities": null,
"edited_modules": null
},
"file": "modin/core/execution/ray/common/util... | modin-project/modin | 3ee4fa02ee69272aebf4fea005fe77268b166fbc | BUG: `virtual_partition.wait` failed if there are duplicate refs
### Modin version checks
- [X] I have checked that this issue has not already been reported.
- [X] I have confirmed this bug exists on the latest released version of Modin.
- [X] I have confirmed this bug exists on the main branch of Modin. (In order t... | diff --git a/docs/release_notes/release_notes-0.16.0.rst b/docs/release_notes/release_notes-0.16.0.rst
index 978b3650..5adac7b2 100644
--- a/docs/release_notes/release_notes-0.16.0.rst
+++ b/docs/release_notes/release_notes-0.16.0.rst
@@ -57,6 +57,7 @@ Key Features and Updates
* FIX-#4090: Fixed check if the index i... |
modin-project__modin-5075 | [
{
"changes": {
"added_entities": [
"modin/core/execution/ray/common/utils.py:wait"
],
"added_modules": [
"modin/core/execution/ray/common/utils.py:wait"
],
"edited_entities": null,
"edited_modules": null
},
"file": "modin/core/execution/ray/common/util... | modin-project/modin | 3ee4fa02ee69272aebf4fea005fe77268b166fbc | TEST: Rewrite --extra-test-parameters parsing so we can collect pytests
If I go to the modin root and run `pytest --collect-only`, I get an error because `config.option` has no attribute `extra_test_parameters`: https://github.com/modin-project/modin/blob/3ee4fa02ee69272aebf4fea005fe77268b166fbc/modin/conftest.py#L315
... | diff --git a/docs/release_notes/release_notes-0.16.0.rst b/docs/release_notes/release_notes-0.16.0.rst
index 978b3650..91159468 100644
--- a/docs/release_notes/release_notes-0.16.0.rst
+++ b/docs/release_notes/release_notes-0.16.0.rst
@@ -55,8 +55,10 @@ Key Features and Updates
* FIX-#4996: Evaluate BenchmarkMode at... |
modin-project__modin-6526 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"modin/core/dataframe/pandas/interchange/dataframe_protocol/column.py:PandasProtocolColumn.null_count"
],
"edited_modules": [
"modin/core/dataframe/pandas/interchange/dataframe_protoc... | modin-project/modin | 8f6e00378e095817deccd25f4140406c5ee6c992 | Interchange `Column.null_count` is a NumPy scalar, not a builtin `int`
A `PandasProtocolColumn` returns a `null_count` as a 0d integer array (specifically a NumPy scalar), as opposed to [`int` as specified in the interchange protocol](https://github.com/data-apis/dataframe-api/blob/4f7c1e0c425643d57120c5b73434d992b3e83... | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b20b6ab2..a7edbf65 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -234,11 +234,7 @@ jobs:
miniforge-version: latest
use-mamba: true
- name: ASV installation
- run: |
- # FIXME: us... |
modin-project__modin-6547 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"modin/core/dataframe/pandas/dataframe/dataframe.py:PandasDataframe.apply_select_indices"
],
"edited_modules": [
"modin/core/dataframe/pandas/dataframe/dataframe.py:PandasDataframe"
... | modin-project/modin | abe20a57b82ae366b2394171d1a7dd50ca1b9cb9 | `df[existing_cols] = df` should compute result dtypes where possible
Example:
```python
import modin.pandas as pd
df = pd.DataFrame([[1,2,3,4], [5,6,7,8]])
print(df._query_compiler._modin_frame.has_materialized_dtypes) # True
df2 = pd.DataFrame([[9,9], [5,5]])
print(df2._query_compiler._modin_frame.has_mater... | diff --git a/modin/core/dataframe/pandas/dataframe/dataframe.py b/modin/core/dataframe/pandas/dataframe/dataframe.py
index a5edd031..d81d2b26 100644
--- a/modin/core/dataframe/pandas/dataframe/dataframe.py
+++ b/modin/core/dataframe/pandas/dataframe/dataframe.py
@@ -2804,6 +2804,7 @@ class PandasDataframe(ClassLogger):... |
modin-project__modin-6678 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"modin/core/dataframe/pandas/dataframe/dataframe.py:PandasDataframe._set_columns"
],
"edited_modules": [
"modin/core/dataframe/pandas/dataframe/dataframe.py:PandasDataframe"
]
... | modin-project/modin | 324099d8737ead092e4acacfe03b1caa82e01986 | Update Modin on cluster documentation | diff --git a/docs/getting_started/using_modin/using_modin_cluster.rst b/docs/getting_started/using_modin/using_modin_cluster.rst
index 1dfc39d3..5393bb89 100644
--- a/docs/getting_started/using_modin/using_modin_cluster.rst
+++ b/docs/getting_started/using_modin/using_modin_cluster.rst
@@ -4,7 +4,7 @@ Using Modin in a ... |
modin-project__modin-6759 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"modin/core/dataframe/base/dataframe/utils.py:join_columns"
],
"edited_modules": [
"modin/core/dataframe/base/dataframe/utils.py:join_columns"
]
},
"file": "modin/core/d... | modin-project/modin | 0ba2a46218ecbc6f4b7d0d9e54c25e437e5e0b23 | Merge partial dtype caches on `concat(axis=0)`
we could have merged 'known_dtypes':
```python
import modin.pandas as pd
import numpy as np
from modin.core.dataframe.pandas.metadata import ModinDtypes, DtypesDescriptor
df1 = pd.DataFrame({"a": [1, 2, 3], "b": [3, 4, 5]})
df2 = pd.DataFrame({"a": [3.0, 4.0, 5.4],... | diff --git a/modin/core/dataframe/base/dataframe/utils.py b/modin/core/dataframe/base/dataframe/utils.py
index 7a1d5d98..75c1c999 100644
--- a/modin/core/dataframe/base/dataframe/utils.py
+++ b/modin/core/dataframe/base/dataframe/utils.py
@@ -96,6 +96,19 @@ def join_columns(
Sequence[IndexLabel], [right_on] if... |
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