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 |
|---|---|---|---|---|---|
intake__intake-467 | [
{
"changes": {
"added_entities": [
"intake/catalog/local.py:UserParameter.__repr__"
],
"added_modules": null,
"edited_entities": [
"intake/catalog/local.py:UserParameter.__str__"
],
"edited_modules": [
"intake/catalog/local.py:UserParameter"
]
... | intake/intake | f3a28891f94b686bd500c368f7214d8f071693ae | Better repr for user parameters
Currently user parameters render like:
```python
[<intake.catalog.local.UserParameter at 0x7f7072960d90>,
<intake.catalog.local.UserParameter at 0x7f70723c7e80>]
```
It'd be nice if they were a dict, but if that is too hard, at least the repr for the object should contain the ... | diff --git a/intake/catalog/local.py b/intake/catalog/local.py
index 7525886..4ed102f 100644
--- a/intake/catalog/local.py
+++ b/intake/catalog/local.py
@@ -79,14 +79,10 @@ class UserParameter(DictSerialiseMixin):
self.allowed = [coerce(self.type, item)
for item in self.allowed... |
intake__intake-479 | [
{
"changes": {
"added_entities": [
"intake/__init__.py:__getattr__"
],
"added_modules": [
"intake/__init__.py:__getattr__"
],
"edited_entities": null,
"edited_modules": null
},
"file": "intake/__init__.py"
},
{
"changes": {
"added_entitie... | intake/intake | b12e06b23a7bd638301336e799284d30e75fe182 | Unify catalog read
At the moment there is a `intake.Catalog` alias for `intake.open_catalog` and there is also `intake.load_catalog`. It'd be nice to at least consolidate around one approach in the docs. Additionally, it'd be nice to get rid of the top level `Catalog` since it is confusing that it is not a class. | diff --git a/docs/source/glossary.rst b/docs/source/glossary.rst
index 857b617..cb73968 100644
--- a/docs/source/glossary.rst
+++ b/docs/source/glossary.rst
@@ -14,8 +14,8 @@ Glossary
format of the files is unchanged in this case, but may be decompressed.
Catalog
- A collection of entries, each o... |
intake__intake-493 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"intake/catalog/base.py:Catalog.serialize"
],
"edited_modules": [
"intake/catalog/base.py:Catalog"
]
},
"file": "intake/catalog/base.py"
}
] | intake/intake | bd3d02aa098ce396457414769b95e78f2b0bf124 | .save() functionality in Catalog for custom local catalog class
Found a number of errors in trying to save a catalog that was defined in a custom class. Source here: https://github.com/manfralab/intake-qcodes
Here's the solution I ended up with, including some comments about what errors needed to be fixed. Sorry, th... | diff --git a/intake/catalog/base.py b/intake/catalog/base.py
index 34c2e7c..9fd7087 100644
--- a/intake/catalog/base.py
+++ b/intake/catalog/base.py
@@ -273,7 +273,10 @@ class Catalog(DataSource):
output = {"metadata": self.metadata, "sources": {},
"name": self.name}
for key, entry ... |
intake__intake-522 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"intake/catalog/base.py:Catalog.__init__",
"intake/catalog/base.py:Catalog.force_reload",
"intake/catalog/base.py:Catalog.__getitem__"
],
"edited_modules": [
"intake/c... | intake/intake | 3c604f18a0c9e278bb5f4736402d45167ae778be | Make catalogs lazy by default
Currently, the Catalog base does the following on instantiation:
```
self._entries = self._make_entries_container() # gives {} by default
self.force_reload()
```
so that `_load()` is called at that time (and whenever the TTL runs out, which is on by default!). Now, we... | diff --git a/.travis.yml b/.travis.yml
index 0909fd5..2a472d4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,11 +8,6 @@ branches:
only:
- master
-env:
- global:
- # ANACONDA_TOKEN
- secure: XJ+hvBFtSNUy6xYQmpEFVoR1MTYdTtLIN9R46qfW5XhAOEzuA0mDBd4FL9mgaw4+hoB4+3B8ItHquGxRN/ugw8O/VRA5CuGBbmfbJfG2vLKAbe3Rr... |
intake__intake-547 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"intake/__init__.py:__getattr__"
],
"edited_modules": [
"intake/__init__.py:__getattr__"
]
},
"file": "intake/__init__.py"
},
{
"changes": {
"added_entitie... | intake/intake | 51b1a183d3ba9ee6693cbead667fbd2a3476b9ed | 'auth' attribute and __init__ parameter removed from Catalog
@martindurant Can you comment on the intent behind removing the `auth` attribute and `__init__` parameter from `Catalog`?
https://github.com/intake/intake/commit/bf5fb33d87914e004b29c792791ce208aee78313#diff-4e371ca3c37982987024b768df161ca8c8da696ff4a34590... | diff --git a/docs/source/api_other.rst b/docs/source/api_other.rst
index 28fa692..e0d578e 100644
--- a/docs/source/api_other.rst
+++ b/docs/source/api_other.rst
@@ -86,60 +86,60 @@ GUI
.. autosummary::
- intake.gui.base.Base
- intake.gui.base.BaseSelector
- intake.gui.base.BaseView
- intake.gui.catalog.add... |
intake__intake-548 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"intake/__init__.py:__getattr__"
],
"edited_modules": [
"intake/__init__.py:__getattr__"
]
},
"file": "intake/__init__.py"
},
{
"changes": {
"added_entitie... | intake/intake | 43242afe6cbbb8cc7fa74968f96b62a60a1d63c2 | Regression: internals require API that is not always defined
It seems as if not all Catalogs implement `_container`, and so this change
```diff
- return e(name=key)
+ if e._container == 'catalog':
+ return e(name=key)
+ return e()
```
in https://github.com/inta... | diff --git a/docs/source/api_other.rst b/docs/source/api_other.rst
index e0d578e..28fa692 100644
--- a/docs/source/api_other.rst
+++ b/docs/source/api_other.rst
@@ -86,60 +86,60 @@ GUI
.. autosummary::
- intake.interface.base.Base
- intake.interface.base.BaseSelector
- intake.interface.base.BaseView
- inta... |
intake__intake-567 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"intake/__init__.py:open_catalog"
],
"edited_modules": [
"intake/__init__.py:open_catalog"
]
},
"file": "intake/__init__.py"
},
{
"changes": {
"added_entit... | intake/intake | 32de95bcc4d5e3c6b214807f9409d4ad423e8d11 | Pass pathlib to open_catalog
Was trying to pass a `pathlib.Path` to `intake.open_catalog` and got the following error:
```
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-22-ceeaa41394e2> in <mod... | diff --git a/intake/__init__.py b/intake/__init__.py
index 799ad3e..6857987 100644
--- a/intake/__init__.py
+++ b/intake/__init__.py
@@ -8,6 +8,7 @@
import importlib
import re
import logging
+import os
import warnings
from ._version import get_versions
@@ -106,11 +107,11 @@ def open_catalog(uri=None, **kwargs):
... |
intake__intake-675 | [
{
"changes": {
"added_entities": [
"intake/source/jsonfiles.py:JSONFileSource._load_metadata",
"intake/source/jsonfiles.py:JSONFileSource._get_schema",
"intake/source/jsonfiles.py:JSONLinesFileSource._load_metadata",
"intake/source/jsonfiles.py:JSONLinesFileSource._get_sche... | intake/intake | fc2a5cbd63fbbfd0bd7163de24c366bb59db2361 | Implementation of `discover` method for JSON driver
### Problem
I'm trying to apply the `discover` method on a [JSON catalog entry](https://github.com/eurec4a/eurec4a-intake/blob/6bbfab8a59af878d7e8aedde9a4ce859da9dcedd/tests/test_catalog.py#L38-L43). However, the `discover`-method is not yet implemented.
### What ... | diff --git a/intake/source/jsonfiles.py b/intake/source/jsonfiles.py
index e7168c2..afa3272 100644
--- a/intake/source/jsonfiles.py
+++ b/intake/source/jsonfiles.py
@@ -80,6 +80,12 @@ class JSONFileSource(DataSource):
) as f:
return json.load(f)
+ def _load_metadata(self):
+ pass
+
+ ... |
intel__code-base-investigator-178 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"codebasin/coverage/__main__.py:_compute"
],
"edited_modules": [
"codebasin/coverage/__main__.py:_compute"
]
},
"file": "codebasin/coverage/__main__.py"
}
] | intel/code-base-investigator | a5c34b9548f1b020fede51479f2d3695048c6ce6 | Extend coverage format to support computing coverage
### Feature/behavior summary
The current coverage format (from the P3 Analysis Library) was designed to be sufficient for computing code divergence, which does not need to know anything about the number of unused lines of code. Now that we have true coverage-related... | diff --git a/codebasin/coverage/__main__.py b/codebasin/coverage/__main__.py
index fbfb20d..8c221c7 100755
--- a/codebasin/coverage/__main__.py
+++ b/codebasin/coverage/__main__.py
@@ -133,19 +133,22 @@ def _compute(args: argparse.Namespace):
with open(filename, "rb") as f:
digest = hashlib.file_d... |
intel__dffml-266 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "dffml/base.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dffml/util/cli/arg.py:... | intel/dffml | 85cd82379042d543fb280163fee68b0043cc94da | model: scikit: scikit model parameters not accepting negative values
While testing CLI usage of scikit this came up:
```console
$ dffml train -model scikitlr -features def:Years:int:1 -model-predict Salary -model-n_jobs -1 -sources f=csv -source-filename dataset.csv -source-readonly -log deb... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4ab77c481..29fd61599 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Fixed
- Correctly identify when functions decorated with `op` use `self` to reference
the `OperationI... |
intel__dffml-492 | [
{
"changes": {
"added_entities": [
"dffml/df/memory.py:MemoryOperationImplementationNetworkContext.dispatch_auto_starts"
],
"added_modules": null,
"edited_entities": [
"dffml/df/memory.py:MemoryOrchestratorContext.run_operations_for_ctx"
],
"edited_modules": [... | intel/dffml | 0607cb6f30bc1d9fd5348f7365f639759cb9d286 | df: memory: Dispatch operations without inputs as soon as DataFlow begins
We may have operations which need to be kicked off as soon as a dataflow starts, a good example would be something which is waiting for a message in a gitter channel, and the output it the message. This operation likely has no need for an input, ... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index a6b219868..bb6d643b1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Add python code for tensorflow DNNEstimator
- Ability to run a subflow as if it were an operation using ... |
intel__dffml-518 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "configloader/png/setup.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dffml/df/m... | intel/dffml | 73fa133e5179e5634a15f27d0f9bf87811f891ae | df: memory: async iterator operations
Functions which are async iterators (`async def` with `yield`) should be supported by `@op`, as well as `dffml/df/memory.py` needs to be able to run one of these kinds of operations. Everytime the operation `yield`s, whatever it `yield`'d should be added to the input network contex... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index d6506363d..7c6fd5cef 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added
- Python prompts `>>>` can now be enabled or disabled for easy copying of code into interactive se... |
intel__dffml-521 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dffml/base.py:is_config_dict",
"dffml/base.py:_fromdict"
],
"edited_modules": [
"dffml/base.py:is_config_dict",
"dffml/base.py:_fromdict"
]
},
"file": "... | intel/dffml | 9a6f403fd62792b40318251f881b784cfda4a9ce | configuration: Change "arg" to "plugin"
`dffml/base.py` and some other places interpret `dict`s with `"arg"` and `"config"` keys in a special way.
`"arg"` is the name of the plugin to load, and `"config"` is the config for that plugin.
Therefore, `"arg"` should really be `"plugin"`
https://github.com/intel/dff... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index b47e17809..48eb67680 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased]
+#... |
intel__dffml-617 | [
{
"changes": {
"added_entities": [
"dffml/source/file.py:FileSource.__init__"
],
"added_modules": null,
"edited_entities": [
"dffml/source/file.py:FileSource._open",
"dffml/source/file.py:FileSource._close"
],
"edited_modules": [
"dffml/source/... | intel/dffml | a6b8a42f1dbbbaf18e5bd431783f90cc976f3690 | sources: file: Should take a pathlib.Path as filename
Right now if we have a filesource and we pass it a `pathlib.Path` as the filename, it will throw errors.
If you remove the `str` call here the failing test(s) will show you all the things that are wrong.
https://github.com/intel/dffml/blob/41d18ffea176dbec4922... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index fad2d825a..b81423268 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Classes now use `CONFIG` if it has a default for every field and `config` is `None`
- Models now dynamic... |
intel__dffml-862 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dffml/source/file.py:FileSource._close"
],
"edited_modules": [
"dffml/source/file.py:FileSource"
]
},
"file": "dffml/source/file.py"
}
] | intel/dffml | 4d0ca9f32f015bd429e74cf9e1788d3bd0cf25f1 | source: file: close does not use WRITEMODE
https://github.com/intel/dffml/blob/78f7ba8de290214919dc45de50800030bbe60f24/dffml/source/file.py#L108
does not use `self.WRITEMODE` (unlike `open`)
change the `"w+"` to be `self.WRITEMODE` and then fix the associated tests | diff --git a/dffml/source/file.py b/dffml/source/file.py
index a2e312787..e50f21319 100644
--- a/dffml/source/file.py
+++ b/dffml/source/file.py
@@ -105,7 +105,7 @@ class FileSource(BaseSource):
elif self.config.filename.suffix == ".zip":
close = self.zip_closer_helper()
else:... |
intel__dffml-863 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dffml/source/file.py:FileSource._close"
],
"edited_modules": [
"dffml/source/file.py:FileSource"
]
},
"file": "dffml/source/file.py"
},
{
"changes": {
"ad... | intel/dffml | b98b07f4fe9884b7e5f0edd03558adbc68295e2f | model: autosklearn: Incompatable with version 0.10.0
```
2020-09-26T21:08:58.5863710Z + cd /home/runner/work/dffml/dffml/model/autosklearn
2020-09-26T21:08:58.5864710Z + python3.7 -m pip install -U -e .
2020-09-26T21:08:59.0360700Z Obtaining file:///home/runner/work/dffml/dffml/model/autosklearn
2020-09-26T21:08:59.038... | diff --git a/dffml/source/file.py b/dffml/source/file.py
index a2e312787..e50f21319 100644
--- a/dffml/source/file.py
+++ b/dffml/source/file.py
@@ -105,7 +105,7 @@ class FileSource(BaseSource):
elif self.config.filename.suffix == ".zip":
close = self.zip_closer_helper()
else:... |
internap__python-hostsresolver-5 | [
{
"changes": {
"added_entities": [
"hostsresolver/cache.py:SocketType._use_host_cache"
],
"added_modules": null,
"edited_entities": [
"hostsresolver/cache.py:SocketType.connect",
"hostsresolver/cache.py:SocketType.connect_ex"
],
"edited_modules": [
... | internap/python-hostsresolver | d9e94459b05e323b9bf8e28b696ca8a7f920dc91 | gaierror when using docker-py
Hello!
I stumbled on a little problem while using the host resolver and docker-py at the same time:
```
ConnectionError: ('Connection aborted.', gaierror(8, 'nodename nor servname provided, or not known'))
```
Seems like docker-py speaks to the docker engine via unix socket and ha... | diff --git a/hostsresolver/cache.py b/hostsresolver/cache.py
index 1318ecb..45c6ad6 100644
--- a/hostsresolver/cache.py
+++ b/hostsresolver/cache.py
@@ -41,13 +41,19 @@ def create_connection(address, *args, **kwargs):
class SocketType(_SocketType):
+ def _use_host_cache(self, address):
+ try:
+ ... |
intezer__analyze-python-sdk-63 | [
{
"changes": {
"added_entities": [
"intezer_sdk/analysis.py:FileAnalysis.get_detections"
],
"added_modules": null,
"edited_entities": [
"intezer_sdk/analysis.py:FileAnalysis.__init__",
"intezer_sdk/analysis.py:UrlAnalysis.downloaded_file_analysis"
],
"... | intezer/analyze-python-sdk | fc02b6905a5a5221df6f7a203a2e51cecc72e0b1 | Unimplemented Endpoint: GET analyses/:analysis-id/detect
The Intezer API documentation has documentation for the endpoint `GET analyses/:analysis-id/detect` and hitting the API shows it is active, but the SDK does not have a specific function for this endpoint. Can a function for this endpoint please be added? Thanks! | diff --git a/CHANGES b/CHANGES
index b137073..d8c1de6 100644
--- a/CHANGES
+++ b/CHANGES
@@ -1,3 +1,7 @@
+Not released yet
+-------
+- Add detection report
+
1.12
-------
- Add file analysis by download url
diff --git a/intezer_sdk/analysis.py b/intezer_sdk/analysis.py
index 8c94a24..f4acb72 100644
--- a/intezer_sdk... |
invenia__TagBotGitLab-17 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tagbotgitlab/changelog.py:Changelog._issues",
"tagbotgitlab/changelog.py:Changelog._merge_requests",
"tagbotgitlab/changelog.py:Changelog._collect_data"
],
"edited_modules": ... | invenia/TagBotGitLab | d0390926003403215fae466bed374b1dc4572b42 | Backport releases have incorrect notes
I ran into a scenario where a package was preparing for a major release (4.0.0-DEV) on the `master` branch and I wanted to backport a bugfix to the last release (3.3.0 in this case). This new release of 3.3.1 included closed issues and merge-request links to changes that occurred ... | diff --git a/tagbotgitlab/changelog.py b/tagbotgitlab/changelog.py
index ac66336..9739b22 100644
--- a/tagbotgitlab/changelog.py
+++ b/tagbotgitlab/changelog.py
@@ -66,40 +66,49 @@ class Changelog:
prev_ver = ver
return prev_rel
- def _issues(self, start: datetime, end: datetime) -> List[... |
ionelmc__python-holdup-2 | [
{
"changes": {
"added_entities": [
"src/holdup/cli.py:HttpCheck.can_create_default_context"
],
"added_modules": null,
"edited_entities": [
"src/holdup/cli.py:Check.is_passing",
"src/holdup/cli.py:TcpCheck.run",
"src/holdup/cli.py:HttpCheck.__init__",
... | ionelmc/python-holdup | 01e29e2ee1348043caa29684f0b841dae95990ec | Add support for Insecure HTTPS
The current `HttpCheck` against a https service defaults to requiring SSL Certificate Validation. In certain cases, we would like to perform a check against an IP address instead of a hostname (for e.g., `holdup https://10.1.2.3`). In this case the certificate validation will always fail ... | diff --git a/.gitignore b/.gitignore
index a74475a..66ad3dd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -59,6 +59,8 @@ docs/_build
.env
.cache
.pytest
+.pytest_cache
.bootstrap
.appveyor.token
*.bak
+.venv/
diff --git a/AUTHORS.rst b/AUTHORS.rst
index d01607a..3268092 100644
--- a/AUTHORS.rst
+++ b/AUTHORS.rst
@@... |
ioos__erddapy-135 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"erddapy/erddapy.py:ERDDAP.to_ncCF",
"erddapy/erddapy.py:ERDDAP.to_xarray",
"erddapy/erddapy.py:ERDDAP.to_iris"
],
"edited_modules": [
"erddapy/erddapy.py:ERDDAP"
... | ioos/erddapy | 29b82922ad5293614745180e431638c89e2cd494 | erddapy with griddap .to_xarray() .to_netcdf() response forces .ncCF (not a griddap option)
I know griddap isn't officially supported but it previously had worked for the purposes I needed... seems the implementation of .ncCF response may be throwing it off (url building it forces .ncCF as the response type now but the... | diff --git a/.isort.cfg b/.isort.cfg
index 4fd1b03..47bb6f5 100644
--- a/.isort.cfg
+++ b/.isort.cfg
@@ -1,2 +1,2 @@
[settings]
-known_third_party = pandas,pendulum,pytest,pytz,requests,setuptools
+known_third_party = iris,pandas,pendulum,pytest,pytz,requests,setuptools,xarray
diff --git a/erddapy/erddapy.py b/erddapy... |
ioos__erddapy-155 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"erddapy/erddapy.py:ERDDAP.get_search_url"
],
"edited_modules": [
"erddapy/erddapy.py:ERDDAP"
]
},
"file": "erddapy/erddapy.py"
}
] | ioos/erddapy | aa166c1eaf9a233114bd5709c80195e426564554 | HTTP Error with erddap V2.10
seems a little something has changed and is throwing an error - I've not looked into the erddapy code but here is what I did (both on the swfsc erddap server and my own):
```
from erddapy import ERDDAP
import pandas as pd
e = ERDDAP(server="https://coastwatch.pfeg.noaa.gov/erddap")
... | diff --git a/erddapy/erddapy.py b/erddapy/erddapy.py
index a70a7b9..da76b21 100644
--- a/erddapy/erddapy.py
+++ b/erddapy/erddapy.py
@@ -258,7 +258,9 @@ class ERDDAP:
maxTime=kwargs.get("max_time", default),
searchFor=search_for,
)
-
+ # ERDDAP 2.10 no longer accepts strings pl... |
ioos__erddapy-311 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"erddapy/erddapy.py:ERDDAP.griddap_initialize"
],
"edited_modules": [
"erddapy/erddapy.py:ERDDAP"
]
},
"file": "erddapy/erddapy.py"
}
] | ioos/erddapy | 59ce5fbafb4e6f775ce25e03406923f215e42d73 | e.to_xarray falling for new erddapy version
Hi all,
I am developing a jupyternotebook utilizing the erddapy package. My simple code snippet which used to work doesn't seems to work anymore after I reinstall my entire conda environment that run the notebook yesterday. I think it might be related to the erddapy packag... | diff --git a/erddapy/erddapy.py b/erddapy/erddapy.py
index d1d0e8e..8ba9d3d 100644
--- a/erddapy/erddapy.py
+++ b/erddapy/erddapy.py
@@ -158,6 +158,10 @@ class ERDDAP:
)
if dataset_id is None:
raise ValueError(f"Must set a valid dataset_id, got {self.dataset_id}")
+ # Return th... |
iossifovlab__gpf-245 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dae/dae/gpf_instance/gpf_instance.py:GPFInstance.genomic_scores_db"
],
"edited_modules": [
"dae/dae/gpf_instance/gpf_instance.py:GPFInstance"
]
},
"file": "dae/dae/gpf_... | iossifovlab/gpf | 42bbea5f27e82759a23e697c2e2131f3ccd5e645 | [BUG] Genomic scores DB initialisation in GPF instance is broken
**What happened**:
When a GPFInstance has an annotation configuration the initialization of genomic scores DB throws an exception.
**What you expected to happen**:
Genomic scores DB should be initialized with scores configured in the annotation confi... | diff --git a/dae/dae/gpf_instance/gpf_instance.py b/dae/dae/gpf_instance/gpf_instance.py
index 2b4724a3f..5e57e4b0f 100644
--- a/dae/dae/gpf_instance/gpf_instance.py
+++ b/dae/dae/gpf_instance/gpf_instance.py
@@ -170,11 +170,9 @@ class GPFInstance:
continue
for field_name in sche... |
iossifovlab__gpf-253 | [
{
"changes": {
"added_entities": [
"dae/dae/gpf_instance/gpf_instance.py:GPFInstance.genotype_storages"
],
"added_modules": null,
"edited_entities": [
"dae/dae/gpf_instance/gpf_instance.py:GPFInstance.__init__",
"dae/dae/gpf_instance/gpf_instance.py:GPFInstance.lo... | iossifovlab/gpf | cc66c277f8270bffbeb9ce2944595c2d1215a125 | [ENH] Add internal in-memory genotype storage
**Is your feature request related to a problem? Please describe.**
Currently, each GPF instance has genotype storages that are described in the `genotype_storages` configuration section.
We would like to have a default `genotype_storages` configuration that configure... | diff --git a/dae/dae/gpf_instance/gpf_instance.py b/dae/dae/gpf_instance/gpf_instance.py
index 4e950071a..3fc166e7c 100644
--- a/dae/dae/gpf_instance/gpf_instance.py
+++ b/dae/dae/gpf_instance/gpf_instance.py
@@ -83,6 +83,7 @@ class GPFInstance:
self.dae_config = dae_config
self.dae_dir = str(dae_di... |
iossifovlab__gpf-254 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dae/dae/genotype_storage/genotype_storage_registry.py:GenotypeStorageRegistry.get_default_genotype_storage",
"dae/dae/genotype_storage/genotype_storage_registry.py:GenotypeStorageRegistry.get_ge... | iossifovlab/gpf | e4fc82c8303aa99af0d08ada61fcad0ddd6d709e | [BUG] `GenotypeStorageRegistry.get_genotype_storage(None)` should return default genotype storage
**What happened**:
When `GenotypeStorageRegistry.get_genotype_storage()` is called with storage id `None`, it throws `ValueError` execption.
**What you expected to happen**:
It should return the default genotype stora... | diff --git a/dae/dae/genotype_storage/genotype_storage_registry.py b/dae/dae/genotype_storage/genotype_storage_registry.py
index d17d6e2a6..5d46b7094 100644
--- a/dae/dae/genotype_storage/genotype_storage_registry.py
+++ b/dae/dae/genotype_storage/genotype_storage_registry.py
@@ -1,5 +1,5 @@
import logging
-from typin... |
iossifovlab__gpf-295 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dae/dae/gene/gene_scores.py:GeneScoresDb.__init__",
"dae/dae/gene/gene_scores.py:GeneScoresDb.get_gene_score"
],
"edited_modules": [
"dae/dae/gene/gene_scores.py:GeneScoresDb... | iossifovlab/gpf | 4367b298b1116ada0511b90b413c4d4e3a3a62e5 | [BUG] Exception in gene scores with empty HG38 instance
**What happened**:
I am working with an empty instance prepared as described in https://www.iossifovlab.com/gpfuserdocs/administration/getting_started.html#create-an-empty-gpf-instance
I imported a study as described here: https://www.iossifovlab.com/gpfuserdo... | diff --git a/dae/dae/gene/gene_scores.py b/dae/dae/gene/gene_scores.py
index f94aa6bed..14dbe6d61 100644
--- a/dae/dae/gene/gene_scores.py
+++ b/dae/dae/gene/gene_scores.py
@@ -2,7 +2,6 @@ from __future__ import annotations
import itertools
import logging
-from collections import OrderedDict
from typing import Opt... |
iossifovlab__gpf-306 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dae/dae/genomic_resources/genomic_scores.py:GenomicScore.get_schema"
],
"edited_modules": [
"dae/dae/genomic_resources/genomic_scores.py:GenomicScore"
]
},
"file": "dae... | iossifovlab/gpf | 6f9a9c7d880c11f29851747932da2beb102a62ad | [BUG] Legacy snakemake based import system is broken
**What happened**:
The `gpf_validation_data` build is broken. The snakemake could not run on snakemake files produced by the GPF batch import command.
**What you expected to happen**:
I expect the `gpf_validation_data` build to pass.
**Minimal Complete Ve... | diff --git a/dae/dae/genomic_resources/genomic_scores.py b/dae/dae/genomic_resources/genomic_scores.py
index 47c96e10a..7322e11b6 100644
--- a/dae/dae/genomic_resources/genomic_scores.py
+++ b/dae/dae/genomic_resources/genomic_scores.py
@@ -419,7 +419,7 @@ class GenomicScore(GenomicResourceImplementation):
def get... |
iossifovlab__gpf-330 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dae/dae/import_tools/import_tools.py:ImportProject.get_pedigree_params"
],
"edited_modules": [
"dae/dae/import_tools/import_tools.py:ImportProject"
]
},
"file": "dae/da... | iossifovlab/gpf | 54a5ddf65febae362fbac0081d71b42412dbe3f2 | [BUG] Families from In-Memory genotype storage are without tags
**What happened**:
When loading families from in-memory genotype storage, they have no pedigree tags. This breaks functionality for filtering families by tags in the datasets statistics UI.
**What you expected to happen**:
The pedigree tags should... | diff --git a/dae/dae/impala_storage/schema1/impala_variants.py b/dae/dae/impala_storage/schema1/impala_variants.py
index b15ad6b3d..7b0368f07 100644
--- a/dae/dae/impala_storage/schema1/impala_variants.py
+++ b/dae/dae/impala_storage/schema1/impala_variants.py
@@ -197,6 +197,7 @@ class ImpalaVariants:
self.ped... |
iossifovlab__gpf-382 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "dae/dae/genomic_resources/genomic_position_table/__init__.py"
},
{
"changes": {
"added_entities": [
"dae/dae/genomic_resources/genomic_p... | iossifovlab/gpf | 2315b1125020220da482ccd825064c78f4e8b33e | Make VCF genome position table score configs "merge" with autodetected configs
So that we can specify a number of scores from the INFO field we wish to use, but also make use of the information that is provided by the VCF header such as type, number, etc. | diff --git a/dae/dae/genomic_resources/genomic_position_table/__init__.py b/dae/dae/genomic_resources/genomic_position_table/__init__.py
index 6c468e50a..856c10ce1 100644
--- a/dae/dae/genomic_resources/genomic_position_table/__init__.py
+++ b/dae/dae/genomic_resources/genomic_position_table/__init__.py
@@ -1,4 +1,4 @@... |
iossifovlab__gpf-443 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dae/dae/genomic_resources/cli.py:cli_browse"
],
"edited_modules": [
"dae/dae/genomic_resources/cli.py:cli_browse"
]
},
"file": "dae/dae/genomic_resources/cli.py"
}
] | iossifovlab/gpf | 98e719cca98768b808602d9d797c8f3e6adbb00b | [ENH] Imporvements in `grr_browse`
- [x] dump GRR configuration in YAML format
- [x] make `--print-grr` default behavior | diff --git a/dae/dae/genomic_resources/cli.py b/dae/dae/genomic_resources/cli.py
index a07e9a55c..adaef7470 100644
--- a/dae/dae/genomic_resources/cli.py
+++ b/dae/dae/genomic_resources/cli.py
@@ -5,7 +5,6 @@ import logging
import argparse
import pathlib
import copy
-import pprint
from typing import Dict, Union
... |
iossifovlab__gpf-446 | [
{
"changes": {
"added_entities": [
"dae/dae/annotation/annotate_vcf.py:get_chromosome_length"
],
"added_modules": [
"dae/dae/annotation/annotate_vcf.py:get_chromosome_length"
],
"edited_entities": [
"dae/dae/annotation/annotate_vcf.py:annotate",
"dae... | iossifovlab/gpf | e099357354c33e4eb0d77350f1da479dd5e69356 | [ENH] Improvements and small fixes in `annotate_vcf`
There are some small changes we need to fix in `annotate_vcf`:
- [x] should not use a reference genome for splitting the work into regions
- [x] create part flags inside the work dir
- [x] after successful merging remove the VCF chunks
- [x] ensure that the pip... | diff --git a/dae/dae/annotation/annotate_vcf.py b/dae/dae/annotation/annotate_vcf.py
index d87754cbc..b8c0659f7 100644
--- a/dae/dae/annotation/annotate_vcf.py
+++ b/dae/dae/annotation/annotate_vcf.py
@@ -16,7 +16,9 @@ from dae.annotation.annotation_factory import build_annotation_pipeline
from dae.utils.verbosity_c... |
iossifovlab__gpf-456 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dae/dae/genomic_resources/genomic_position_table/table.py:GenomicPositionTable.get_chromosome_length"
],
"edited_modules": [
"dae/dae/genomic_resources/genomic_position_table/table.p... | iossifovlab/gpf | 365ec4e1ba61e34209d34c64b23eabfcbd725207 | Extract region splitting functionality into a separate util
Region splitting functionality can be found in multiple places:
- genomic_scores
- reference_genome
- annotate_vcf
- import tools
We should extract all of this functionality into a set of utilities that cover all our cases.
NOTES:
- Try extracting g... | diff --git a/dae/dae/genomic_resources/genomic_position_table/table.py b/dae/dae/genomic_resources/genomic_position_table/table.py
index e53617d65..340d136fd 100644
--- a/dae/dae/genomic_resources/genomic_position_table/table.py
+++ b/dae/dae/genomic_resources/genomic_position_table/table.py
@@ -165,37 +165,3 @@ class ... |
iossifovlab__gpf-466 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"dae/dae/common_reports/common_report.py:CommonReport.build_report",
"dae/dae/common_reports/common_report.py:CommonReport.to_dict"
],
"edited_modules": [
"dae/dae/common_repo... | iossifovlab/gpf | 320ad2d67a0c2d4237947bb9d1024120b83f0098 | [BUG] Denovo report missing in representation when empty
**What happened**:
Generating a common report on a study without denovo variants results in a missing denovo report in the final output.
**What you expected to happen**:
The frontend expects the denovo report to be an empty list of tables instead of missing. | diff --git a/dae/dae/common_reports/common_report.py b/dae/dae/common_reports/common_report.py
index 49cc4d0eb..114c100fb 100644
--- a/dae/dae/common_reports/common_report.py
+++ b/dae/dae/common_reports/common_report.py
@@ -125,8 +125,6 @@ class CommonReport:
"families_report": families_report.to_dict(ful... |
iossifovlab__gpf-563 | [
{
"changes": {
"added_entities": [
"dae/dae/pheno/pheno_db.py:PhenotypeData.get_people_measure_values",
"dae/dae/pheno/pheno_db.py:PhenotypeStudy._build_measures_subquery",
"dae/dae/pheno/pheno_db.py:PhenotypeStudy._split_measures_into_groups",
"dae/dae/pheno/pheno_db.py:Ph... | iossifovlab/gpf | 3c7994ba90c58f3f5d861f16a8a6e59171ee8145 | [BUG] Pheno browser download measures uses too much memory
**What happened**:
Pheno browser download is complex and collects a bunch of data in memory. This is tedious and slow
**What you expected to happen**:
The request takes too long and should be more optimized
| diff --git a/dae/dae/pheno/pheno_db.py b/dae/dae/pheno/pheno_db.py
index fa7eacc0a..5ed234766 100644
--- a/dae/dae/pheno/pheno_db.py
+++ b/dae/dae/pheno/pheno_db.py
@@ -9,12 +9,9 @@ from abc import ABC, abstractmethod
from collections import defaultdict
from itertools import chain
-import csv
-from io import String... |
iotile__python_iotile_cloud-29 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"iotile_cloud/utils/mock_cloud.py:MockIOTileCloud.handle_report_api",
"iotile_cloud/utils/mock_cloud.py:MockIOTileCloud._get_streamer_ack",
"iotile_cloud/utils/mock_cloud.py:MockIOTileClo... | iotile/python_iotile_cloud | 4cd309944c3702a252e953cfcf199994c80aeab1 | KeyError on streamer
It seems this should be `last_id` instead of `highest_id`. @timburke can you confirm?
https://github.com/iotile/python_iotile_cloud/blob/4cd309944c3702a252e953cfcf199994c80aeab1/iotile_cloud/utils/mock_cloud.py#L266 | diff --git a/CHANGELOG.md b/CHANGELOG.md
index fd79bda..8a6b6a6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,8 @@
-### 0.8.4
+### v0.8.5 (2018-02-23)
+
+ * Fix get stream acknowledgment to get the right dictionary field (Issue #28)
+
+### v0.8.4
* Add support for PATCH in API
diff --git a/iotile_cl... |
ipfs-shipyard__py-ipfs-http-client-278 | [
{
"changes": {
"added_entities": [
"ipfshttpclient/exceptions.py:MatcherSpecInvalidError.__init__"
],
"added_modules": [
"ipfshttpclient/exceptions.py:MatcherSpecInvalidError"
],
"edited_entities": [
"ipfshttpclient/exceptions.py:AddressError.__init__",
... | ipfs-shipyard/py-ipfs-http-client | 09cae7672a39ca3ff991684c1b31cfe7875174c3 | Move MatcherSpecInvalidError into `ipfshttpclient/exceptions.py`
https://github.com/ipfs-shipyard/py-ipfs-http-client/blob/09cae7672a39ca3ff991684c1b31cfe7875174c3/ipfshttpclient/filescanner.py#L416-L420
We currently expose all possible exceptions in the `ipfshttpclient/exceptions.py` module. Ideally this one should... | diff --git a/ipfshttpclient/exceptions.py b/ipfshttpclient/exceptions.py
index 22d03c2..02b773e 100644
--- a/ipfshttpclient/exceptions.py
+++ b/ipfshttpclient/exceptions.py
@@ -10,13 +10,14 @@ The class hierarchy for exceptions is:
│ ├── EncoderMissingError
│ ├── EncodingError
│ └── DecodingError
- └... |
ipython__ipykernel-1049 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ipykernel/comm/comm.py:Comm.__init__"
],
"edited_modules": [
"ipykernel/comm/comm.py:Comm"
]
},
"file": "ipykernel/comm/comm.py"
},
{
"changes": {
"added_... | ipython/ipykernel | 4dc303364ca73b5185685807de41c7fe4b4a4dc7 | Latest version break IPyWidgets
IPyKernel Version: 6.18.3
Install Jupyter and ipywidgets
Run a notebook with the following code
* Cell 1
```python
from ipywidgets import FloatSlider, IntSlider, Image, IntText, link
slider = IntSlider(description="Continuous Slider", continuous_update=True)
textbox = IntText(d... | diff --git a/ipykernel/comm/comm.py b/ipykernel/comm/comm.py
index f1fb0c8..c06d233 100644
--- a/ipykernel/comm/comm.py
+++ b/ipykernel/comm/comm.py
@@ -71,6 +71,9 @@ class Comm(traitlets.config.LoggingConfigurable, BaseComm):
def __init__(self, *args, **kwargs):
# Comm takes positional arguments, Logging... |
ipython__ipykernel-1051 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ipykernel/comm/comm.py:Comm.__init__"
],
"edited_modules": [
"ipykernel/comm/comm.py:Comm"
]
},
"file": "ipykernel/comm/comm.py"
}
] | ipython/ipykernel | b13c46ac5fa800359748386c64f89402ac0e204e | Latest version break IPyWidgets
IPyKernel Version: 6.19.0
Install Jupyter and ipywidgets
Run a notebook with the following code
```python
import ipywidgets as widgets
widgets.IntSlider()
```
Slider is not renderered
Here is the error message
```
A Jupyter widget could not be displayed because the widget ... | diff --git a/ipykernel/comm/comm.py b/ipykernel/comm/comm.py
index c06d233..295232e 100644
--- a/ipykernel/comm/comm.py
+++ b/ipykernel/comm/comm.py
@@ -71,9 +71,8 @@ class Comm(traitlets.config.LoggingConfigurable, BaseComm):
def __init__(self, *args, **kwargs):
# Comm takes positional arguments, Logging... |
ipython__ipykernel-1056 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ipykernel/comm/comm.py:Comm.__init__"
],
"edited_modules": [
"ipykernel/comm/comm.py:Comm"
]
},
"file": "ipykernel/comm/comm.py"
},
{
"changes": {
"added_... | ipython/ipykernel | 04e1d753e328194be391b62ffd22662f0fe6dc56 | Error opening new comm
With the `6.19.x` line, i'm seeing this in [this gist](https://gist.github.com/bollwyvl/543d7bc10705dd4006494f21aa48ca92).
Rolling back to `6.17.1` does not show this behavior.
T... | diff --git a/.github/workflows/downstream.yml b/.github/workflows/downstream.yml
index ab1f103..57c8561 100644
--- a/.github/workflows/downstream.yml
+++ b/.github/workflows/downstream.yml
@@ -84,6 +84,41 @@ jobs:
pip install -e ".[test]"
python test_ipykernel.py
+ qtconsole:
+ runs-on: ubun... |
ipython__ipykernel-1061 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ipykernel/comm/comm.py:Comm.__init__"
],
"edited_modules": [
"ipykernel/comm/comm.py:Comm"
]
},
"file": "ipykernel/comm/comm.py"
}
] | ipython/ipykernel | 2c66b2de835856b19b25c6a890d9665902dda907 | Can't update `children` trait after widget is displayed.
Akin to #1059, here's another [fun gist with binder](https://gist.github.com/bollwyvl/181eed3cda265e205310f829aa7cc600) that demonstrates some issues observed while try to upgrade to `6.19.x`.
Basically:
- Creating a `HBox` with `children` displays them immed... | diff --git a/ipykernel/comm/comm.py b/ipykernel/comm/comm.py
index 77f9f07..6ec6ff3 100644
--- a/ipykernel/comm/comm.py
+++ b/ipykernel/comm/comm.py
@@ -70,13 +70,16 @@ class Comm(BaseComm, traitlets.config.LoggingConfigurable):
def __init__(self, target_name='', data=None, metadata=None, buffers=None, **kwargs)... |
ipython__ipykernel-1076 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ipykernel/iostream.py:OutStream.__init__",
"ipykernel/iostream.py:OutStream.close"
],
"edited_modules": [
"ipykernel/iostream.py:OutStream"
]
},
"file": "ipyker... | ipython/ipykernel | b4ea598646b68d326da9e182fddaf67d0061d842 | OutStream.close raises if `watchfd=False`
Closing an `OutStream` instance via its `close` method fails if that `OutStream` instance is created with `watchfd=False`, with an exception `AttributeError: 'OutStream' object has no attribute 'watch_fd_thread'`.
Here's a full traceback from some Envisage tests. We're creat... | diff --git a/ipykernel/iostream.py b/ipykernel/iostream.py
index 92df61a..32829f6 100644
--- a/ipykernel/iostream.py
+++ b/ipykernel/iostream.py
@@ -401,6 +401,7 @@ class OutStream(TextIOBase):
self._buffer = StringIO()
self.echo = None
self._isatty = bool(isatty)
+ self._should_watch ... |
ipython__ipykernel-1271 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ipykernel/kernelapp.py:IPKernelApp.init_poller"
],
"edited_modules": [
"ipykernel/kernelapp.py:IPKernelApp"
]
},
"file": "ipykernel/kernelapp.py"
},
{
"changes"... | ipython/ipykernel | 3089438d84447bf859556b89f528ef59332803c5 | PPID is not necessarily 1 when parent frontend is killed
Hi, I have raised this issue separately on [jupyter-console](https://github.com/jupyter/jupyter_console/issues/221)
The problem I noticed is that when I directly close the frontend program that called "jupyter-console" (e.g. my terminal), it leaves the "ipyker... | diff --git a/ipykernel/kernelapp.py b/ipykernel/kernelapp.py
index 2f462af..394f52a 100644
--- a/ipykernel/kernelapp.py
+++ b/ipykernel/kernelapp.py
@@ -220,7 +220,7 @@ class IPKernelApp(BaseIPythonApplication, InteractiveShellApp, ConnectionFileMix
# PID 1 (init) is special and will never go away,
... |
ipython__ipykernel-188 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ipykernel/iostream.py:OutStream.__init__"
],
"edited_modules": [
"ipykernel/iostream.py:OutStream"
]
},
"file": "ipykernel/iostream.py"
},
{
"changes": {
... | ipython/ipykernel | 6c63f53000e07b7f4f8542501dc94b42578f1d15 | 'thread._local' object has no attribute 'hooks'
I just installed the newest versions of ipython and GraphLab and noticed this error. Here is the relevant code and the traceback.
# sales is an SFrame
graphlab.canvas.set_target('ipynb')
sales.show(view="Scatter Plot", x="CrimeRate", y="HousePrice")
Tr... | diff --git a/ipykernel/iostream.py b/ipykernel/iostream.py
index 5c7f96e..dae05af 100644
--- a/ipykernel/iostream.py
+++ b/ipykernel/iostream.py
@@ -205,8 +205,6 @@ class OutStream(object):
warnings.warn("pipe argument to OutStream is deprecated and ignored",
DeprecationWarning)
s... |
ipython__ipykernel-59 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ipykernel/kernelspec.py:InstallIPythonKernelSpecApp.start"
],
"edited_modules": [
"ipykernel/kernelspec.py:InstallIPythonKernelSpecApp"
]
},
"file": "ipykernel/kernelsp... | ipython/ipykernel | 4cda22a855a3e6833fac5ea1ee229eea0a444be6 | Typo in install_kernelspec causes to break
#57 causes
`The command "python -m ipykernel.kernelspec --user" failed and exited with 1 during .`
as reported in https://travis-ci.org/jupyter/nbconvert/jobs/81479990.
Working on a fix + test now. | diff --git a/ipykernel/kernelspec.py b/ipykernel/kernelspec.py
index 1d8541f..0203a87 100644
--- a/ipykernel/kernelspec.py
+++ b/ipykernel/kernelspec.py
@@ -153,7 +153,7 @@ class InstallIPythonKernelSpecApp(Application):
opts = parser.parse_args(self.argv)
try:
dest = install(user=opts.us... |
ipython__ipykernel-902 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ipykernel/ipkernel.py:IPythonKernel.do_execute"
],
"edited_modules": [
"ipykernel/ipkernel.py:IPythonKernel"
]
},
"file": "ipykernel/ipkernel.py"
},
{
"changes"... | ipython/ipykernel | e8ffc9e21d784de35ac02a2c121e35af16f37a6d | cell_id required in do_execute
Hi there,
Not exactly sure whether the issue is here or in spyder-kernels (reported there too as https://github.com/spyder-ide/spyder-kernels/issues/380), but running the spyder-kernels test suite with ipykernel 6.11 results in this:
```python
_______________________ ERROR at teardow... | diff --git a/ipykernel/ipkernel.py b/ipykernel/ipkernel.py
index 77ee7bf..3c69597 100644
--- a/ipykernel/ipkernel.py
+++ b/ipykernel/ipkernel.py
@@ -304,7 +304,7 @@ class IPythonKernel(KernelBase):
user_expressions=None,
allow_stdin=False,
*,
- cell_id,
+ cell_id=None,
):
... |
ipython__ipyparallel-457 | [
{
"changes": {
"added_entities": [
"ipyparallel/client/asyncresult.py:AsyncResult._iopub_streaming_output_callback",
"ipyparallel/client/asyncresult.py:AsyncResult.stream_output"
],
"added_modules": null,
"edited_entities": [
"ipyparallel/client/asyncresult.py:Asy... | ipython/ipyparallel | cb0d510c8731ddf6fe49cd06e563e98428aec711 | Real-time logging for parallel magics
I would like to be able to use the px magic with real-time logging when running parallel cells with blocking set to True. The current behavior of blocked cell is that it won’t print out stdout, stderr and exception output until all the workers finished. I would like to be able to... | diff --git a/ipyparallel/client/asyncresult.py b/ipyparallel/client/asyncresult.py
index e2ee8605..41ece2c5 100644
--- a/ipyparallel/client/asyncresult.py
+++ b/ipyparallel/client/asyncresult.py
@@ -7,7 +7,9 @@ import sys
import threading
import time
from concurrent.futures import Future
+from contextlib import cont... |
ipython__ipyparallel-465 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ipyparallel/serialize/canning.py:CannedFunction.__init__",
"ipyparallel/serialize/canning.py:CannedFunction.get_object"
],
"edited_modules": [
"ipyparallel/serialize/canning.... | ipython/ipyparallel | cc18e6a25e9779c15740bc64e6367921f5827e5b | Required Keyword defaults missing after serialization round trip
When using Keyword-Only arguments in a function definition, the defaults for those keywords are lost on a round trip through the `pack/unpack_apply_message` functions of the `serialize` module.
Minimal example in a file called "stest.py":
```python
... | diff --git a/ipyparallel/serialize/canning.py b/ipyparallel/serialize/canning.py
index f2ba4140..b83ef98e 100644
--- a/ipyparallel/serialize/canning.py
+++ b/ipyparallel/serialize/canning.py
@@ -193,6 +193,16 @@ class CannedFunction(CannedObject):
else:
self.defaults = None
+ if f.__kwdef... |
ipython__ipyparallel-479 | [
{
"changes": {
"added_entities": [
"ipyparallel/client/client.py:Client.wait_for_engines"
],
"added_modules": null,
"edited_entities": [
"ipyparallel/client/client.py:Client._register_engine"
],
"edited_modules": [
"ipyparallel/client/client.py:Client"... | ipython/ipyparallel | 854ff2e04470c569758f331fe40b439651a3d640 | Daemonize after engines start
Currently, `ipcluster` can be run in the foreground or in the background using the `--daemonize` option. However, this daemonizing appears to happen immediately at startup. So if I run something like:
```bash
#!/bin/bash
ipcluster-3 start -n 4 --daemonize
python3 <<EOF
from ipyparal... | diff --git a/ipyparallel/client/client.py b/ipyparallel/client/client.py
index 126ffc7a..d2d82c3f 100644
--- a/ipyparallel/client/client.py
+++ b/ipyparallel/client/client.py
@@ -3,8 +3,6 @@
# Distributed under the terms of the Modified BSD License.
from __future__ import print_function
-import threading
-
try:
... |
ipython__ipyparallel-504 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "docs/source/conf.py"
},
{
"changes": {
"added_entities": [
"ipyparallel/client/asyncresult.py:AsyncResult._collect_exceptions"
],
... | ipython/ipyparallel | 37da0fdecc2ad443ce9a6737a44460d1ee359dd3 | Unable to use AsyncMapResult when *some* of the tasks have raised an exception.
I'm running into some problem when using ipyparallel: when *some* of the tasks raise an exception, there seems no way to get at the successful task results in the AsyncMapResult.
I have posted the same question on StackOverflow, along wi... | diff --git a/docs/source/conf.py b/docs/source/conf.py
index f2a38b68..56813b7a 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -117,7 +117,7 @@ exclude_patterns = ['winhpc.rst']
# The reST default role (used for this markup: `text`) to use for all
# documents.
-# default_role = None
+default_role = '... |
ipython__ipyparallel-545 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ipyparallel/util.py:_push",
"ipyparallel/util.py:_pull",
"ipyparallel/util.py:_execute"
],
"edited_modules": [
"ipyparallel/util.py:_push",
"ipyparallel/util.... | ipython/ipyparallel | 061bcb15d15fd3f152981dd8cc1c266446341369 | dview.push breaks when using dill or cloudpickle
```python
import ipyparallel
client = ipyparallel.Client()
dview = client[:]
dview.use_dill()
def bar(x):
return x * x
dview.push(dict(foo=foo))
%px foo
```
traceback:
```
[0:execute]:
-----------------------------------------------------------... | diff --git a/ipyparallel/util.py b/ipyparallel/util.py
index 7ef03e5f..387e53a8 100644
--- a/ipyparallel/util.py
+++ b/ipyparallel/util.py
@@ -309,10 +309,9 @@ def interactive(f):
return f
-@interactive
def _push(**ns):
"""helper method for implementing `client.push` via `client.apply`"""
- user_ns = ... |
ipython__ipython-10157 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/inputtransformer.py:TokenInputTransformer.__init__",
"IPython/core/inputtransformer.py:TokenInputTransformer.reset_tokenizer",
"IPython/core/inputtransformer.py:TokenInputTr... | ipython/ipython | ee0571bd401ef1bd296c728b5436ff219097846f | End of multiline string that contains a backslash-terminated line is not recognized
IPython 5.0/PTK1.0.5 does not recognize that
```
"""
foo\
bar
"""
```
is a full string and that it should execute the typed-in string after that point.
| diff --git a/IPython/core/inputtransformer.py b/IPython/core/inputtransformer.py
index 9036add8a..3fdc64160 100644
--- a/IPython/core/inputtransformer.py
+++ b/IPython/core/inputtransformer.py
@@ -120,25 +120,18 @@ class TokenInputTransformer(InputTransformer):
"""
def __init__(self, func):
self.func... |
ipython__ipython-10263 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/completer.py:match_dict_keys"
],
"edited_modules": [
"IPython/core/completer.py:match_dict_keys"
]
},
"file": "IPython/core/completer.py"
}
] | ipython/ipython | 06e6b58e0f7878296ee655c825e8a764999a5cc8 | Dict key completion with bytes keys raises
Dict key tab completion raises when trying to complete a prefix of a bytes literal that is a valid key in the dict, as below. This issue persists after `pip install --upgrade ipython`.
``` python
Python 3.4.3 (default, Mar 3 2015, 10:49:33)
Type "copyright", "credits" or "... | diff --git a/IPython/core/completer.py b/IPython/core/completer.py
index d2637c4bb..80aafee41 100644
--- a/IPython/core/completer.py
+++ b/IPython/core/completer.py
@@ -622,8 +622,27 @@ def get__all__entries(obj):
return [cast_unicode_py2(w) for w in words if isinstance(w, str)]
-def match_dict_keys(keys, pref... |
ipython__ipython-10959 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/lib/pretty.py:RepresentationPrinter.pretty",
"IPython/lib/pretty.py:_seq_pprinter_factory",
"IPython/lib/pretty.py:_set_pprinter_factory",
"IPython/lib/pretty.py:_dict_pp... | ipython/ipython | 38e0033a6cf59136208b998c394ac5472b9c1849 | OrderedDict output differs in ipython from python (and official documentation)
[collections — Container datatypes](https://docs.python.org/3/library/collections.html#collections.OrderedDict)
An ordered dictionary can be combined with the Counter class so that the counter remembers the order elements are first encoun... | diff --git a/IPython/lib/pretty.py b/IPython/lib/pretty.py
index cbbb72600..9181113e3 100644
--- a/IPython/lib/pretty.py
+++ b/IPython/lib/pretty.py
@@ -392,6 +392,10 @@ def pretty(self, obj):
meth = cls._repr_pretty_
if callable(meth):
... |
ipython__ipython-11350 | [
{
"changes": {
"added_entities": [
"IPython/core/display.py:HTML.__init__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"IPython/core/display.py:HTML"
]
},
"file": "IPython/core/display.py"
}
] | ipython/ipython | 194d1d7fe2fcc8547205bd7f54fcf63bee9df4e3 | HTML vs Iframe
I was again the witness of people miss-using HTML to display IFrames, and having issues.
Could we detect in HTML the usage of `<iframe>....</iframe>` and warn user that there is an iframe object ?
| diff --git a/IPython/core/display.py b/IPython/core/display.py
index ca5c3aa5b..4a2e28179 100644
--- a/IPython/core/display.py
+++ b/IPython/core/display.py
@@ -666,6 +666,11 @@ def _repr_pretty_(self, pp, cycle):
class HTML(TextDisplayObject):
+ def __init__(self, data=None, url=None, filename=None, metadata=N... |
ipython__ipython-11358 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/inputtransformer2.py:SystemAssign.find",
"IPython/core/inputtransformer2.py:EscapedCommand.transform",
"IPython/core/inputtransformer2.py:TransformerManager.check_complete"
... | ipython/ipython | b3edf6c1ddbae4e8f6ed59947afc883861165d5d | Cannot make multi-line code blocks in ipython
I just did a `pip install ipython` while teaching a class today and typed an if statement and then hit enter after the first line and the code executed.
This seems like a bug.
I did a `pip install ipython==6.5.0` and hitting Enter in a code block properly showed me th... | diff --git a/.travis.yml b/.travis.yml
index 09e161464..cf184a9d9 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -34,6 +34,7 @@ after_success:
matrix:
include:
+ - { python: "3.6-dev", dist: xenial, sudo: true }
- { python: "3.7", dist: xenial, sudo: true }
- { python: "3.7-dev", dist: x... |
ipython__ipython-11398 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/inputtransformer2.py:EscapedCommand.find"
],
"edited_modules": [
"IPython/core/inputtransformer2.py:EscapedCommand"
]
},
"file": "IPython/core/inputtransfo... | ipython/ipython | 8ed6e67ed9d7662222542d9f4c4bd92bd68d5adb | Cannot enter docstring in IPython
Type the following snippet and then hit `C-m` or `C-j` or `C-o` then IPython produces "Exception list index out of range" from `IPython/core/inputtransformer2.py`
```
In [1]: def f():
...: """
```
Traceback:
```pytb
Unhandled exception in event loop:
File "/home/... | diff --git a/IPython/core/inputtransformer2.py b/IPython/core/inputtransformer2.py
index 5777559fb..e2dd2d087 100644
--- a/IPython/core/inputtransformer2.py
+++ b/IPython/core/inputtransformer2.py
@@ -355,9 +355,14 @@ def find(cls, tokens_by_line):
"""Find the first escaped command (%foo, !foo, etc.) in the ce... |
ipython__ipython-11418 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/inputtransformer2.py:_find_assign_op",
"IPython/core/inputtransformer2.py:make_tokens_by_line"
],
"edited_modules": [
"IPython/core/inputtransformer2.py:_find_as... | ipython/ipython | 4b3baed67bceb4a10f6189d87580d7fcfe5ef079 | Capturing shell command output after indentation causes SyntaxError in IPython console.
To reproduce, type this in console:
```python
def test():
for i in range(1):
print(i)
res =! ls
```
But if something is put above the line, everything will seem to be fine.
```python
def test():
for i in rang... | diff --git a/IPython/core/inputtransformer2.py b/IPython/core/inputtransformer2.py
index e2dd2d087..b73d70121 100644
--- a/IPython/core/inputtransformer2.py
+++ b/IPython/core/inputtransformer2.py
@@ -13,7 +13,7 @@
from codeop import compile_command
import re
import tokenize
-from typing import List, Tuple
+from typ... |
ipython__ipython-11718 | [
{
"changes": {
"added_entities": [
"IPython/core/inputtransformer2.py:leading_empty_lines"
],
"added_modules": [
"IPython/core/inputtransformer2.py:leading_empty_lines"
],
"edited_entities": [
"IPython/core/inputtransformer2.py:TransformerManager.__init__"
... | ipython/ipython | 380db0d7241372f9c12d5d5aaaa8e7e4c70575d5 | Problem with indentation in the `run_cell` method
Hi,
When using the InteractiveShell method `run_cell`, there is a problem when the string to execute begins with a line that contains only 4 spaces. It then does not handle properly the indentations of the subsequent loops.
+def leading_empty_lines(lines):
+ """Remove leading empty l... |
ipython__ipython-12130 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/completer.py:Completer.__init__",
"IPython/core/completer.py:IPCompleter.matchers"
],
"edited_modules": [
"IPython/core/completer.py:Completer",
"IPython... | ipython/ipython | 201acc865abb92a6184b3c01d21c577e1ff07139 | set_custom_completer seems to be a no-op
In [interactive_shell.py](https://github.com/ipython/ipython/blob/a2685d78f2403f84e6cb915ae11a4f6033ccc5f6/IPython/core/interactiveshell.py#L2034), `set_custom_completer` does
self.Completer.matchers.insert(pos,newcomp)
Looking at the source code of IPCompleter, though... | diff --git a/.travis.yml b/.travis.yml
index def0d930b..4139cc2b6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -72,7 +72,7 @@ matrix:
- arch: arm64
python: "3.7"
dist: xenial
- env: ARM64=True
+ env: ARM64=True IPYTHON_TESTING_TIMEOUT_SCALE=2
sudo: true
- arch: amd64
pyt... |
ipython__ipython-12144 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/completer.py:Completer.__init__",
"IPython/core/completer.py:IPCompleter.matchers"
],
"edited_modules": [
"IPython/core/completer.py:Completer",
"IPython... | ipython/ipython | 5b0df90efaa7fe99abb4d92b0acffc1051ec5549 | set_custom_completer seems to be a no-op
In [interactive_shell.py](https://github.com/ipython/ipython/blob/a2685d78f2403f84e6cb915ae11a4f6033ccc5f6/IPython/core/interactiveshell.py#L2034), `set_custom_completer` does
self.Completer.matchers.insert(pos,newcomp)
Looking at the source code of IPCompleter, though... | diff --git a/.travis.yml b/.travis.yml
index a70f00a22..9bb3a9bb0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -72,7 +72,7 @@ matrix:
- arch: arm64
python: "3.7"
dist: xenial
- env: ARM64=True
+ env: ARM64=True IPYTHON_TESTING_TIMEOUT_SCALE=2
sudo: true
- arch: amd64
pyt... |
ipython__ipython-12171 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/magics/execution.py:ExecutionMagics.run"
],
"edited_modules": [
"IPython/core/magics/execution.py:ExecutionMagics"
]
},
"file": "IPython/core/magics/execut... | ipython/ipython | 34327182a1578d76e17a9fd1843052994f4dca45 | %run does not work with import hooks
Hi,
I ran into an issue where the use of `imp` vs `__import__` matters. `imp` is bypassing some things that import statements do, such as calling custom [import hooks](https://docs.python.org/3/reference/import.html#import-hooks). Is there are reason `imp` is being used? If not, ... | diff --git a/IPython/core/magics/execution.py b/IPython/core/magics/execution.py
index 2b26ebe96..fb2df90b5 100644
--- a/IPython/core/magics/execution.py
+++ b/IPython/core/magics/execution.py
@@ -692,6 +692,11 @@ def run(self, parameter_s='', runner=None,
warn('For Windows, use double quotes to wrap a... |
ipython__ipython-12280 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/completer.py:IPCompleter.latex_matches"
],
"edited_modules": [
"IPython/core/completer.py:IPCompleter"
]
},
"file": "IPython/core/completer.py"
}
] | ipython/ipython | e1082955d6560ebc313e8af7257e74ea143df812 | completer latex_matches no respecting API
It return matched text even if it return no completions. | diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index fbe0daac7..b8f093569 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -12,4 +12,3 @@
#
# <full commit hash> # initial black-format
# <full commit hash> # rename something internal
-6e748726282d1acb9a4f9f264ee679c474c4b8f5 # App... |
ipython__ipython-12954 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/interactiveshell.py:InteractiveShell.system_raw"
],
"edited_modules": [
"IPython/core/interactiveshell.py:InteractiveShell"
]
},
"file": "IPython/core/inte... | ipython/ipython | 322f2fe50d9dccb6134d3d61df7d90772ecf2751 | Suggest %pip or %conda when user types !pip or !conda
To guide users towards doing things right, could we suggest they use the magics instead of the shell invocations? Possibly with a short explanation why. Was also mentioned in <https://github.com/ipython/ipython/pull/11524#issuecomment-444875270>. | diff --git a/IPython/core/interactiveshell.py b/IPython/core/interactiveshell.py
index 22b531ec1..47db3fe2b 100644
--- a/IPython/core/interactiveshell.py
+++ b/IPython/core/interactiveshell.py
@@ -2521,6 +2521,23 @@ def system_raw(self, cmd):
Command to execute.
"""
cmd = self.var_expand(cm... |
ipython__ipython-13021 | [
{
"changes": {
"added_entities": [
"IPython/core/debugger.py:Pdb._get_frame_locals"
],
"added_modules": null,
"edited_entities": [
"IPython/core/debugger.py:Pdb._hidden_predicate",
"IPython/core/debugger.py:Pdb.format_stack_entry",
"IPython/core/debugger.p... | ipython/ipython | 90c12972758f46732e445414198cbbca7d96b833 | accessing f_locals in debugger resets namespace
This is the pendant of https://github.com/deshaw/pyflyby/pull/144, see there for a longer explanation.
We do access `current_frame.f_locals` in a couple of place which reset the namespace changes. | diff --git a/IPython/core/debugger.py b/IPython/core/debugger.py
index 36f0e71a6..e2676a61d 100644
--- a/IPython/core/debugger.py
+++ b/IPython/core/debugger.py
@@ -331,7 +331,7 @@ def _hidden_predicate(self, frame):
if frame in (self.curframe, getattr(self, "initial_frame", None)):
return... |
ipython__ipython-13625 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/inputtransformer.py:_make_help_call",
"IPython/core/inputtransformer.py:help_end"
],
"edited_modules": [
"IPython/core/inputtransformer.py:_make_help_call",
... | ipython/ipython | 4d73f5c6919c1140b0f908595728beddf97bb1df | Transformer for `pinfo` line magic incorrectly sets next input when the line contains parentheses
In JupyterLab we experience an annoyance with pinfo magic which results in some expressions creating a new cell instead of providing help (https://github.com/jupyterlab/jupyterlab/issues/12269). The following example creat... | diff --git a/IPython/core/inputtransformer.py b/IPython/core/inputtransformer.py
index f668f466a..77f69f388 100644
--- a/IPython/core/inputtransformer.py
+++ b/IPython/core/inputtransformer.py
@@ -193,7 +193,7 @@ def assemble_logical_lines():
line = ''.join(parts)
# Utilities
-def _make_help_call(target, es... |
ipython__ipython-13730 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/terminal/shortcuts.py:_apply_autosuggest",
"IPython/terminal/shortcuts.py:create_ipython_shortcuts"
],
"edited_modules": [
"IPython/terminal/shortcuts.py:_apply_autos... | ipython/ipython | b9c796a6a3a32f510c235041813ccb904888f14a | END key inserts autosuggestion in the middle of a line
Hitting END in the middle of a line inserts an autosuggestion at the cursor instead of the end of the line.
From a new IPython profile (hence ensuring no history), type these keystrokes:
```
123456789<Enter>
123456<End><Enter>
123456<Left arrow><Left arrow... | diff --git a/IPython/terminal/shortcuts.py b/IPython/terminal/shortcuts.py
index 615397abc..6c1ba0418 100644
--- a/IPython/terminal/shortcuts.py
+++ b/IPython/terminal/shortcuts.py
@@ -32,6 +32,22 @@ def cursor_in_leading_ws():
return (not before) or before.isspace()
+# Needed for to accept autosuggestions in ... |
ipython__ipython-13768 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/compilerop.py:CachingCompiler.__init__",
"IPython/core/compilerop.py:CachingCompiler.cache",
"IPython/core/compilerop.py:check_linecache_ipython"
],
"edited_modu... | ipython/ipython | 1b5674ca8bbac62daa42eb460848173c0542cf2e | Incorrect call to `open` function not handled correctly.
<!-- This is the repository for IPython command line, if you can try to make sure this question/bug/feature belong here and not on one of the Jupyter repositories.
If it's a generic Python/Jupyter question, try other forums or discourse.jupyter.org.
If you... | diff --git a/IPython/core/compilerop.py b/IPython/core/compilerop.py
index 228f70566..b43e570b3 100644
--- a/IPython/core/compilerop.py
+++ b/IPython/core/compilerop.py
@@ -73,6 +73,25 @@ class CachingCompiler(codeop.Compile):
def __init__(self):
codeop.Compile.__init__(self)
+ # This is ugly, bu... |
ipython__ipython-13943 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/completer.py:Completer.attr_matches"
],
"edited_modules": [
"IPython/core/completer.py:Completer"
]
},
"file": "IPython/core/completer.py"
}
] | ipython/ipython | 2a5fdf9dab8e5fa50a03ce686aaf11cb38844587 | ipython==8.8.0 has weird tab completion bug
<!-- This is the repository for IPython command line, if you can try to make sure this question/bug/feature belong here and not on one of the Jupyter repositories.
If it's a generic Python/Jupyter question, try other forums or discourse.jupyter.org.
If you are unsure, ... | diff --git a/IPython/core/completer.py b/IPython/core/completer.py
index f0bbb4e56..a41f492b0 100644
--- a/IPython/core/completer.py
+++ b/IPython/core/completer.py
@@ -1162,11 +1162,36 @@ def attr_matches(self, text):
raise
except Exception:
# Silence errors from completion function
... |
ipython__ipython-13991 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "IPython/terminal/shortcuts/__init__.py"
},
{
"changes": {
"added_entities": [
"IPython/terminal/shortcuts/auto_suggest.py:accept_or_jump... | ipython/ipython | 4db24c349d2e211b5cfb51f3b1485c6d7f037290 | Auto suggestions cannot be completed when in the middle of multi-line input
<!-- This is the repository for IPython command line, if you can try to make sure this question/bug/feature belong here and not on one of the Jupyter repositories.
If it's a generic Python/Jupyter question, try other forums or discourse.jup... | diff --git a/IPython/terminal/shortcuts/__init__.py b/IPython/terminal/shortcuts/__init__.py
index 41533c807..f71ce498f 100644
--- a/IPython/terminal/shortcuts/__init__.py
+++ b/IPython/terminal/shortcuts/__init__.py
@@ -181,30 +181,45 @@ def create_identifier(handler: Callable):
]
AUTO_SUGGEST_BINDINGS = [
+ # ... |
ipython__ipython-14185 | [
{
"changes": {
"added_entities": null,
"added_modules": [
"IPython/core/guarded_eval.py:Duck"
],
"edited_entities": [
"IPython/core/guarded_eval.py:eval_node"
],
"edited_modules": [
"IPython/core/guarded_eval.py:eval_node"
]
},
"file": "I... | ipython/ipython | 6004e9b0bb0c702b840dfec54df8284234720817 | Tab complete for class __call__ not working
<!-- This is the repository for IPython command line, if you can try to make sure this question/bug/feature belong here and not on one of the Jupyter repositories.
If it's a generic Python/Jupyter question, try other forums or discourse.jupyter.org.
If you are unsure, ... | diff --git a/IPython/core/guarded_eval.py b/IPython/core/guarded_eval.py
index 5d405b220..a304affc3 100644
--- a/IPython/core/guarded_eval.py
+++ b/IPython/core/guarded_eval.py
@@ -1,3 +1,4 @@
+from inspect import signature, Signature
from typing import (
Any,
Callable,
@@ -335,6 +336,7 @@ def __getitem__(se... |
ipython__ipython-14231 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/events.py:EventManager.trigger"
],
"edited_modules": [
"IPython/core/events.py:EventManager"
]
},
"file": "IPython/core/events.py"
},
{
"changes": ... | ipython/ipython | 4977b5d92b4b46327e78fc60ae9aa45db8db24b1 | Using autoreload magic fails with the latest version
<!-- This is the repository for IPython command line, if you can try to make sure this question/bug/feature belong here and not on one of the Jupyter repositories.
If it's a generic Python/Jupyter question, try other forums or discourse.jupyter.org.
If you are... | diff --git a/IPython/core/events.py b/IPython/core/events.py
index 90ff8f746..ef39c4fd0 100644
--- a/IPython/core/events.py
+++ b/IPython/core/events.py
@@ -82,7 +82,11 @@ def trigger(self, event, *args, **kwargs):
func(*args, **kwargs)
except (Exception, KeyboardInterrupt):
... |
ipython__ipython-14371 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/debugger.py:Pdb.__init__"
],
"edited_modules": [
"IPython/core/debugger.py:Pdb"
]
},
"file": "IPython/core/debugger.py"
},
{
"changes": {
"ad... | ipython/ipython | 38aa68c305c58017bfa4074fba9c391439147290 | Move backend mapping to Matplotlib
I wanted to draw your attention to matplotlib/matplotlib#27663, about moving the Matplotlib backend mappings out of IPython and into Matplotlib.
The primary use case it so support Matplotlib widgets (`ipympl` and `matplotlib-inline`) registering themselves as Matplotlib backends wi... | diff --git a/IPython/core/debugger.py b/IPython/core/debugger.py
index 4e4b17a94..a5d6431ca 100644
--- a/IPython/core/debugger.py
+++ b/IPython/core/debugger.py
@@ -253,6 +253,21 @@ def __init__(self, completekey=None, stdin=None, stdout=None, context=5, **kwarg
C = coloransi.TermColors
cst = self.col... |
ipython__ipython-14404 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/debugger.py:BdbQuit_excepthook"
],
"edited_modules": [
"IPython/core/debugger.py:BdbQuit_excepthook"
]
},
"file": "IPython/core/debugger.py"
},
{
"... | ipython/ipython | 8ff4109a184d242bbc8cdd08750d9a192b854784 | Default value in docs for TerminalInteractiveShell.simple_prompt is incorrect
The default value for `TerminalInteractiveShell.simple_prompt` per the [docs](https://ipython.readthedocs.io/en/stable/config/options/terminal.html#configtrait-TerminalInteractiveShell.simple_prompt) is `True` yet when one produces the defaul... | diff --git a/IPython/core/debugger.py b/IPython/core/debugger.py
index 59cf24c6a..4e4b17a94 100644
--- a/IPython/core/debugger.py
+++ b/IPython/core/debugger.py
@@ -149,17 +149,6 @@ def make_arrow(pad):
return ''
-def BdbQuit_excepthook(et, ev, tb, excepthook=None):
- """Exception hook which handles `BdbQui... |
ipython__ipython-14466 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/lib/pretty.py:RepresentationPrinter.pretty"
],
"edited_modules": [
"IPython/lib/pretty.py:RepresentationPrinter"
]
},
"file": "IPython/lib/pretty.py"
}
] | ipython/ipython | 1454013b8b615ce75d30d38b7710e3fccca16263 | `display` does not honor custom `__repr__` for `NamedTuple` when defined by `partialmethod`
The issue occurs when the custom `__repr__` is defined via `partialmethod`:
```python
from functools import partialmethod
from typing import NamedTuple
def my_pprint(obj, **options):
return "Hello World"
def add_... | diff --git a/IPython/lib/pretty.py b/IPython/lib/pretty.py
index 631445b24..8a24632d6 100644
--- a/IPython/lib/pretty.py
+++ b/IPython/lib/pretty.py
@@ -406,8 +406,16 @@ def pretty(self, obj):
meth = cls._repr_pretty_
if callable(meth):
... |
ipython__ipython-14486 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/prefilter.py:PythonOpsChecker.check",
"IPython/core/prefilter.py:AutocallChecker.check"
],
"edited_modules": [
"IPython/core/prefilter.py:PythonOpsChecker",
... | ipython/ipython | ad07901d8cf6fb874262c6387bd24d9e5a284144 | Bug with autocall
Hi,
We are seeing the following bug with autocall (where below is showing valid code for a type hint):
```
$ ipython
Python 3.11.8 (main, Mar 15 2024, 12:37:54) [GCC 10.3.1 20210422 (Red Hat 10.3.1-1)]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.22.2 -- An enhanced... | diff --git a/IPython/core/prefilter.py b/IPython/core/prefilter.py
index e611b4b83..a29df0c27 100644
--- a/IPython/core/prefilter.py
+++ b/IPython/core/prefilter.py
@@ -476,8 +476,8 @@ def check(self, line_info):
any python operator, we should simply execute the line (regardless of
whether or not ther... |
ipython__ipython-14503 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/ultratb.py:ListTB.structured_traceback"
],
"edited_modules": [
"IPython/core/ultratb.py:ListTB"
]
},
"file": "IPython/core/ultratb.py"
}
] | ipython/ipython | 78fea5f8d7bf6ca55796e82ed341e7fd291878f0 | Raising SystemExit leads to internal inspect module error
I recently noticed the following error now occurs in IPython and consequently Jupyter notebooks. Raising `SystemExit` in a `try/except` clause gives (possibly related to #11960):
```python
try:
5 / 0
except Exception as e:
raise SystemExit
```
... | diff --git a/IPython/core/ultratb.py b/IPython/core/ultratb.py
index cc139b1e2..66c9ce910 100644
--- a/IPython/core/ultratb.py
+++ b/IPython/core/ultratb.py
@@ -552,28 +552,31 @@ def structured_traceback(
lines = ''.join(self._format_exception_only(etype, evalue))
out_list.append(lines)
- exc... |
ipython__ipython-14693 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/magics/execution.py:ExecutionMagics._run_with_debugger"
],
"edited_modules": [
"IPython/core/magics/execution.py:ExecutionMagics"
]
},
"file": "IPython/cor... | ipython/ipython | 637e037d668db7aebe61ae04261ebfc5cb7f32c5 | Jupyter shebang cells ignore exit code on SIGINT
When a shebang cell (i.e., %%sh, %%bash, etc.) in a Jupyter notebook is manually interrupted, the cell promptly completes successfully, regardless of the exit code of the program. In the attached screenshot, I interrupted the kernel while the first cell was running, yet ... | diff --git a/IPython/core/magics/execution.py b/IPython/core/magics/execution.py
index 7387e212f..dd745249d 100644
--- a/IPython/core/magics/execution.py
+++ b/IPython/core/magics/execution.py
@@ -977,7 +977,21 @@ def _run_with_debugger(
break
finally:
sys.sett... |
ipython__ipython-14695 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/core/magics/script.py:ScriptMagics.shebang"
],
"edited_modules": [
"IPython/core/magics/script.py:ScriptMagics"
]
},
"file": "IPython/core/magics/script.py"
}... | ipython/ipython | b8220b5b975e3f4e19d078033aa1e68da28e2c9b | Jupyter shebang cells won't show partially written lines
When a shebang cell (i.e., %%sh, %%bash, etc.) in a Jupyter notebook writes/flushes output, the output doesn't show up until the script ends or a newline is written. This hurts the usability of programs that indicate progress by writing periodically on the same l... | diff --git a/IPython/core/magics/script.py b/IPython/core/magics/script.py
index 8abc22efe..3bfc4d8d6 100644
--- a/IPython/core/magics/script.py
+++ b/IPython/core/magics/script.py
@@ -220,7 +220,7 @@ def in_thread(coro):
async def _readchunk(stream):
try:
- return await stream.re... |
ipython__ipython-7469 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/utils/io.py:atomic_writing"
],
"edited_modules": [
"IPython/utils/io.py:atomic_writing"
]
},
"file": "IPython/utils/io.py"
}
] | ipython/ipython | 296f56bf70643d1d19ae0c1ab2a9d86b326d5559 | atomic write umask
Reported on gitter.im/ipython/ipython by @bigzachattack
Sadly no one was on the chat at that time, too busy with a big bearded men
dressed in red trying to smuggle things in our houses through the cheminee.
```
I noticed today working in master, that any new notebook I create or copy has p... | diff --git a/IPython/utils/io.py b/IPython/utils/io.py
index df1e39e60..3d236eb4d 100644
--- a/IPython/utils/io.py
+++ b/IPython/utils/io.py
@@ -267,17 +267,18 @@ def atomic_writing(path, text=True, encoding='utf-8', **kwargs):
path = os.path.join(os.path.dirname(path), os.readlink(path))
dirname, basen... |
ipython__ipython-7819 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/utils/tokenutil.py:token_at_cursor"
],
"edited_modules": [
"IPython/utils/tokenutil.py:token_at_cursor"
]
},
"file": "IPython/utils/tokenutil.py"
}
] | ipython/ipython | 92333e1084ea0d6ff91b55434555e741d2274dc7 | Inspect requests inside a function call should be smarter about what they inspect.
Previously, `func(a, b, <shift-tab>` would give information on `func`, now it gives information on `b`, which is not especially helpful.
This is because we removed logic from the frontend to make it more language agnostic, and we have... | diff --git a/IPython/html/static/notebook/js/actions.js b/IPython/html/static/notebook/js/actions.js
index 828b724e7..40816144e 100644
--- a/IPython/html/static/notebook/js/actions.js
+++ b/IPython/html/static/notebook/js/actions.js
@@ -79,7 +79,6 @@ define(function(require){
}
},
'select... |
ipython__ipython-7872 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/config/manager.py:BaseJSONConfigManager.set"
],
"edited_modules": [
"IPython/config/manager.py:BaseJSONConfigManager"
]
},
"file": "IPython/config/manager.py"
... | ipython/ipython | cbcf741896140953195ea9cd3de0f10c3f28bef1 | Default DOMWidget Padding should be 0px, and Button styling issue
@jdfreder
| diff --git a/IPython/config/manager.py b/IPython/config/manager.py
index 429bfaa97..0628a6afa 100644
--- a/IPython/config/manager.py
+++ b/IPython/config/manager.py
@@ -86,7 +86,7 @@ def set(self, section_name, data):
else:
f = open(filename, 'wb')
with f:
- json.dump(data, f, ... |
ipython__ipython-8030 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/config/loader.py:CommandLineConfigLoader._exec_config_str"
],
"edited_modules": [
"IPython/config/loader.py:CommandLineConfigLoader"
]
},
"file": "IPython/confi... | ipython/ipython | d4e786e20631074a8713f78c7103dcab0c72b840 | commandline parser can't handle --something="all"
It seems that parsing `all` will convert it to the `all()` function and an error is shown:
```python
knitpy_aliases.update({
'to' : 'KnitpyApp.export_format',
[...]
})
class KnitpyApp(BaseIPythonApplication):
# '--to' ends up here
export_form... | diff --git a/IPython/config/loader.py b/IPython/config/loader.py
index 12752d000..196ed4932 100644
--- a/IPython/config/loader.py
+++ b/IPython/config/loader.py
@@ -11,6 +11,7 @@
import re
import sys
import json
+from ast import literal_eval
from IPython.utils.path import filefind, get_ipython_dir
from IPython.u... |
ipython__ipython-8111 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"IPython/config/application.py:Application._log_datefmt_changed"
],
"edited_modules": [
"IPython/config/application.py:Application"
]
},
"file": "IPython/config/applicat... | ipython/ipython | 2af39462d92d3834d5780a87f44d5e6cee7ecb81 | `_log_format_changed()` missing 3 required positional arguments
In `IPython.config.application`, the `_log_datefmt_changed` handler calls `_log_format_changed` but does not pass it the required arguments. My guess would be that this is the correct implementation:
```
def _log_datefmt_changed(self, name, old, new):
... | diff --git a/IPython/config/application.py b/IPython/config/application.py
index ef97162b3..264d3793a 100644
--- a/IPython/config/application.py
+++ b/IPython/config/application.py
@@ -159,7 +159,7 @@ def _log_level_changed(self, name, old, new):
help="The date format used by logging formatters for %(asctime)s... |
iris-hep__func_adl-100 | [
{
"changes": {
"added_entities": [
"func_adl/util_ast.py:_rewrite_captured_vars.visit_Lambda",
"func_adl/util_ast.py:_rewrite_captured_vars.is_arg"
],
"added_modules": null,
"edited_entities": [
"func_adl/util_ast.py:_rewrite_captured_vars.__init__",
"func... | iris-hep/func_adl | a8b3e1ff5e397f4dcd156e255bd3f26e819f53d0 | Lambda closure prefers global over local arg name
In the following code:
```python
sys_muon = (calib_tools.query_sys_error(ds, 'MUON_ID__1up')
.Select(lambda e: e.Muons())
.Select(lambda l_muons: [m for m in l_muons if m.pt() > 30000.0])
.Select(lambda l_muons: {
... | diff --git a/func_adl/util_ast.py b/func_adl/util_ast.py
index 868029d..7b65cef 100644
--- a/func_adl/util_ast.py
+++ b/func_adl/util_ast.py
@@ -322,14 +322,28 @@ class _rewrite_captured_vars(ast.NodeTransformer):
def __init__(self, cv: inspect.ClosureVars):
self._lookup_dict: Dict[str, Any] = dict(cv.non... |
iris-hep__func_adl-106 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"func_adl/object_stream.py:ObjectStream"
]
},
"file": "func_adl/object_stream.py"
}
] | iris-hep/func_adl | 9df94767c64bf0d6a4e5762f533f60756f248017 | Add `as_awkward` and `as_pandas`, etc
These would do both `AsAwkwardArray` and `value` - just short hand to make it easier for the user. | diff --git a/func_adl/object_stream.py b/func_adl/object_stream.py
index 7c7ee4c..f25cec0 100644
--- a/func_adl/object_stream.py
+++ b/func_adl/object_stream.py
@@ -238,6 +238,8 @@ class ObjectStream(Generic[T]):
function_call("ResultPandasDF", [self._q_ast, as_ast(columns)])
)
+ as_pandas = ... |
iris-hep__func_adl-114 | [
{
"changes": {
"added_entities": [
"func_adl/util_ast.py:_line_string_reader.__init__",
"func_adl/util_ast.py:_line_string_reader.readline",
"func_adl/util_ast.py:_token_runner.__init__",
"func_adl/util_ast.py:_token_runner.init_tokenizer",
"func_adl/util_ast.py:_to... | iris-hep/func_adl | e32868c2b6094606b62ecd87cadf0cf7af0e9b9b | Bad parsing of a lambda in the ttbar analysis notebook
The below code (which is a test case) cauess an `assert` failure - no lambda is found.
```python
def test_parse_multiline_lambda_with_comment():
"Comment in the middle of things"
found = []
class my_obj:
def Where(self, x: Callable):
... | diff --git a/.flake8 b/.flake8
index 0f51b36..44724dd 100644
--- a/.flake8
+++ b/.flake8
@@ -1,3 +1,3 @@
[flake8]
max-line-length=99
-ignore=E203
\ No newline at end of file
+ignore=E203, W503
\ No newline at end of file
diff --git a/func_adl/util_ast.py b/func_adl/util_ast.py
index 614daca..f4afa12 100644
--- a/func... |
iris-hep__func_adl-116 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"func_adl/object_stream.py:ObjectStream.SelectMany",
"func_adl/object_stream.py:ObjectStream.Select",
"func_adl/object_stream.py:ObjectStream.Where"
],
"edited_modules": [
... | iris-hep/func_adl | ace1464b8ed0ecc88297e1ef2a769167a0face02 | Variables in lambdas with identical names in a query
Using `func-adl` version `3.2.2`, the following query works:
```python
ds.Where(lambda e: e.met_e > 25).Select(lambda event: event.jet_pt)
```
but the same query does no longer work when the variables in both lambdas have the same name:
```python
ds.Where(lambd... | diff --git a/func_adl/object_stream.py b/func_adl/object_stream.py
index f25cec0..09a4410 100644
--- a/func_adl/object_stream.py
+++ b/func_adl/object_stream.py
@@ -110,7 +110,7 @@ class ObjectStream(Generic[T]):
from func_adl.type_based_replacement import remap_from_lambda
n_stream, n_ast, rtn_type... |
iris-hep__func_adl-131 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"func_adl/util_ast.py:_rewrite_captured_vars.visit_Name"
],
"edited_modules": [
"func_adl/util_ast.py:_rewrite_captured_vars"
]
},
"file": "func_adl/util_ast.py"
},
... | iris-hep/func_adl | 7295efc5dfee9c731fc21665abc54eb1c95e380b | Cannot use imported module names in lambdas
These lines don't check that a variable actually represents a constant before replacing a `Name` node with a `Constant` node:
https://github.com/iris-hep/func_adl/blob/89713708d8d1dc7234a38d78a6961170f4d26dca/func_adl/util_ast.py#L12-L15
For Python versions before 3.8, ... | diff --git a/func_adl/util_ast.py b/func_adl/util_ast.py
index 5c5f8a4..ab43f47 100644
--- a/func_adl/util_ast.py
+++ b/func_adl/util_ast.py
@@ -5,6 +5,7 @@ import inspect
import sys
import tokenize
from collections import defaultdict
+from types import ModuleType
from typing import Any, Callable, Dict, Generator, ... |
iris-hep__func_adl-140 | [
{
"changes": {
"added_entities": [
"func_adl/type_based_replacement.py:type_transformer.visit_Attribute"
],
"added_modules": null,
"edited_entities": [
"func_adl/type_based_replacement.py:type_transformer.lookup_type",
"func_adl/type_based_replacement.py:type_tran... | iris-hep/func_adl | 2891ca1695c01750fc3d5f1d34cab058d03bceee | Typing is not followed through dictionaries
It would seem that type checking is not followed through dictionaries:
```python
query = (ds
.Select(lambda e: {
'evt': e.EventInfo("EventInfo"),
'jet': e.Jets()
})
.Select(lambda ei: {
'event_num... | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 98869bd..180aa69 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -12,9 +12,9 @@ jobs:
flake8:
runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
- name: Set... |
iris-hep__func_adl-149 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"func_adl/ast/function_simplifier.py:simplify_chained_calls.visit_SelectMany_of_SelectMany",
"func_adl/ast/function_simplifier.py:simplify_chained_calls.visit_Subscript_Tuple",
"func_adl/... | iris-hep/func_adl | 95b14c9b3986201236d4f812dd4499185e99721e | Zip lookup for function types is causing a type tracing failure
This is from @ponyisi.
You get this error:
```text
File "/home/onyisi/servicex/analysis-grand-challenge/analyses/cms-open-data-ttbar/venv/lib64/python3.9/site-packages/func_adl/type_based_replacement.py", line 971, in visit_Attribute
raise V... | diff --git a/func_adl/ast/function_simplifier.py b/func_adl/ast/function_simplifier.py
index a476799..c6f63c6 100644
--- a/func_adl/ast/function_simplifier.py
+++ b/func_adl/ast/function_simplifier.py
@@ -244,8 +244,8 @@ class simplify_chained_calls(FuncADLNodeTransformer):
"SelectMany", [cast(ast.AST, cap... |
iris-hep__func_adl-151 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"func_adl/type_based_replacement.py:_load_default_global_functions"
],
"edited_modules": [
"func_adl/type_based_replacement.py:_load_default_global_functions"
]
},
"file... | iris-hep/func_adl | 29a3406bb2207b1433ec0e5ed9d13ccbc9b9c434 | The `len` call generates a type error
`len` is assumed to be float... Ops... Should not be.
First seen [here](https://github.com/iris-hep/idap-200gbps-atlas/issues/129) | diff --git a/func_adl/type_based_replacement.py b/func_adl/type_based_replacement.py
index cfc7563..e8d94e5 100644
--- a/func_adl/type_based_replacement.py
+++ b/func_adl/type_based_replacement.py
@@ -61,8 +61,10 @@ def _load_default_global_functions():
# TODO: Add in other functions
def my_abs(x: float) ->... |
iris-hep__func_adl-176 | [
{
"changes": {
"added_entities": [
"func_adl/ast/syntatic_sugar.py:syntax_transformer.convert_call_to_dict",
"func_adl/ast/syntatic_sugar.py:syntax_transformer.visit_Call"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"func_adl/ast/s... | iris-hep/func_adl | 2b6a6a82042349a29e0463439145f1ca9fbf934b | Named Tuples and data classes
Data classes are very useful as typed objects to be passed around.
As a way to avoid problems with dictionaries, allow typed data classes (or if untyped, then untyped!).
This is being done in part to help with the [idap test](https://github.com/iris-hep/idap-200gbps-atlas/issues/47). | diff --git a/func_adl/ast/syntatic_sugar.py b/func_adl/ast/syntatic_sugar.py
index fc2658d..1e788db 100644
--- a/func_adl/ast/syntatic_sugar.py
+++ b/func_adl/ast/syntatic_sugar.py
@@ -1,4 +1,6 @@
import ast
+import inspect
+from dataclasses import is_dataclass
from typing import Any, List
from func_adl.util_ast i... |
iris-hep__func_adl-184 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"func_adl/ast/function_simplifier.py:simplify_chained_calls.visit_Subscript_Tuple",
"func_adl/ast/function_simplifier.py:simplify_chained_calls.visit_Subscript_List",
"func_adl/ast/functi... | iris-hep/func_adl | 6f98f02049ccb7207e35c032c614ec80e70b57e1 | Function simiplification should not return the ast as-is, but a copy for multiple references
When we do a dict reference twice, we should not return the same AST. This is because there are cases where we attach other information to the ast, and then we evaulate things in multiple contexts, which turns sour very vast in... | diff --git a/func_adl/ast/function_simplifier.py b/func_adl/ast/function_simplifier.py
index a86f704..9a409a7 100644
--- a/func_adl/ast/function_simplifier.py
+++ b/func_adl/ast/function_simplifier.py
@@ -453,7 +453,7 @@ class simplify_chained_calls(FuncADLNodeTransformer):
f" {len(v.elts)} values long... |
iris-hep__func_adl-185 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"func_adl/type_based_replacement.py:_fill_in_default_arguments"
],
"edited_modules": [
"func_adl/type_based_replacement.py:_fill_in_default_arguments"
]
},
"file": "func... | iris-hep/func_adl | 8f97702a86ea6d8c725e2c8105d0b342eaf517b3 | Error message when missing [] on method is not helpful.
When compiling this code:
```python
from func_adl_servicex_xaodr22 import FuncADLQueryPHYSLITE, cpp_float
query = (
FuncADLQueryPHYSLITE()
.Select(lambda e: e.Vertices("BPHY4Quads"))
.Select(
lambda vtxs: {
"x": vtxs.Select(lambda... | diff --git a/func_adl/type_based_replacement.py b/func_adl/type_based_replacement.py
index 93eb8f6..e3a7e6c 100644
--- a/func_adl/type_based_replacement.py
+++ b/func_adl/type_based_replacement.py
@@ -329,6 +329,13 @@ def _fill_in_default_arguments(func: Callable, call: ast.Call) -> Tuple[ast.Call
Returns:
... |
iris-hep__func_adl-186 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"func_adl/type_based_replacement.py:type_transformer.visit_Name"
],
"edited_modules": [
"func_adl/type_based_replacement.py:type_transformer"
]
},
"file": "func_adl/type... | iris-hep/func_adl | ed624ca912e6ad70ff32acc14a6cb8a52a321492 | Support class enums when doing resolution
When we are working with a class like `VxType.VertexType.PriVtx` the problem is that `VxType` is a class, and so it is a class ctor (function), and doesn' thave `VertexType` directly in there. So we have to do another level of indirection.
```python
if hasattr(value, "... | diff --git a/func_adl/type_based_replacement.py b/func_adl/type_based_replacement.py
index e3a7e6c..d6eb09e 100644
--- a/func_adl/type_based_replacement.py
+++ b/func_adl/type_based_replacement.py
@@ -906,7 +906,8 @@ def remap_by_types(
elif node.id in _global_functions:
self._found_types[... |
iris-hep__func_adl-41 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"func_adl/event_dataset.py:_extract_dataset_info"
],
"edited_modules": [
"func_adl/event_dataset.py:_extract_dataset_info"
]
},
"file": "func_adl/event_dataset.py"
}
] | iris-hep/func_adl | 67fde5a39038ebee59f8ea6e8cf34139a3de5c2f | EventDataset can have as many arguments as it wants
Others might want to change the meaning (like uproot) of the arguments. Make sure that is possible in the EventDataset AST. The current `_extract_dataset_info` restricts the requirements to one. | diff --git a/func_adl/event_dataset.py b/func_adl/event_dataset.py
index 8915d4c..34d7a69 100644
--- a/func_adl/event_dataset.py
+++ b/func_adl/event_dataset.py
@@ -83,7 +83,6 @@ def _extract_dataset_info(ds_call: ast.Call) -> EventDataset:
args = cast(List[ast.AST], ds_call.args)
# List should be strings
-... |
iris-hep__func_adl-46 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "func_adl/__init__.py"
},
{
"changes": {
"added_entities": [
"func_adl/object_stream.py:ObjectStream.AsParquetFiles"
],
"adde... | iris-hep/func_adl | 98aecdd3c10ef7a37b4fafe021afea756eee243b | Add AsParqetFiles
Make sure there is an end-point in `ObjectStream` that will render parquet files
<!-- Edit the body of your new issue then click the ✓ "Create Issue" button in the top right of the editor. The first line will be the issue title. Assignees and Labels follow after a blank line. Leave an empty line bef... | diff --git a/.vscode/settings.json b/.vscode/settings.json
index 14a1a78..1ac2548 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -9,10 +9,13 @@
"Jupyter",
"LINQ",
"ROOTT",
+ "Topo",
"asts",
"astunparse",
"asyncio",
"codecov",
+ ... |
iris-hep__func_adl-47 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"func_adl/event_dataset.py:EventDataset.__init__"
],
"edited_modules": [
"func_adl/event_dataset.py:EventDataset"
]
},
"file": "func_adl/event_dataset.py"
},
{
"... | iris-hep/func_adl | b2ba083ca9e0bb70918ec0b8802eb9ce849380c7 | add a ast property to ObjectStream for access. | diff --git a/func_adl/event_dataset.py b/func_adl/event_dataset.py
index 34d7a69..15ccd8f 100644
--- a/func_adl/event_dataset.py
+++ b/func_adl/event_dataset.py
@@ -20,7 +20,7 @@ class EventDataset(ObjectStream, ABC):
# We participate in the AST parsing - as a node. This argument is used in a lookup
#... |
iris-hep__func_adl-74 | [
{
"changes": {
"added_entities": [
"func_adl/ast/function_simplifier.py:_is_method_call_on_first",
"func_adl/ast/function_simplifier.py:simplify_chained_calls.select_method_call_on_first",
"func_adl/ast/function_simplifier.py:simplify_chained_calls.visit_Subscript_Dict",
"f... | iris-hep/func_adl | bf37b298a79a0429ad2e411857524ecbe4591b5a | Allow dictionary semantics in expressions
If it follows python semantics, what dictionary operatiosn are allowed that make functional sense?
- Create a new dictionary that is a copy of the old one plus new items {'hi': 10, **d} (or whatever the syntax is, where d is the old dictionary.
- Addition, etc.?
- Update p... | diff --git a/func_adl/ast/function_simplifier.py b/func_adl/ast/function_simplifier.py
index 5a4cb17..2ca4b51 100644
--- a/func_adl/ast/function_simplifier.py
+++ b/func_adl/ast/function_simplifier.py
@@ -95,6 +95,19 @@ class FuncADLIndexError(Exception):
Exception.__init__(self, msg)
+def _is_method_call_... |
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