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 |
|---|---|---|---|---|---|
Epistimio__orion-631 | [
{
"changes": {
"added_entities": [
"src/orion/client/experiment.py:ExperimentClient.fetch_pending_trials"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/orion/client/experiment.py:ExperimentClient"
]
},
"file": "src/orion/c... | Epistimio/orion | 0921b7fa265d9bbf13f90641e8f4916966fd587e | Experiment cannot reserve trial of parent experiment
This is very problematic as non-completed trials of parents cannot be execute anymore unless the environment state is reverted to the one used for parent experiment (ex: resetting code). It should look for executable trials across the EVC tree.
From @hbertrand | diff --git a/src/orion/client/experiment.py b/src/orion/client/experiment.py
index f0a17485..a7054104 100644
--- a/src/orion/client/experiment.py
+++ b/src/orion/client/experiment.py
@@ -294,6 +294,15 @@ class ExperimentClient:
status, with_evc_tree=with_evc_tree
)
+ def fetch_pending_trials(... |
Epistimio__orion-680 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/orion/algo/tpe.py:TPE.__init__",
"src/orion/algo/tpe.py:TPE.suggest",
"src/orion/algo/tpe.py:TPE._suggest"
],
"edited_modules": [
"src/orion/algo/tpe.py:TPE"
... | Epistimio/orion | da001535f4796ed0dbf683cd27e18dc46c4a901d | TPE stuck during suggest()
@mgermain reported 2 cases where TPE apparently got stuck after as few as 30 trials. Last log line was `DEBUG::orion.core.worker.producer::### Algorithm suggests new points.` and nothing else was logged for hours. The search space was small, limited to about 300 points:
```python
{
'x'... | diff --git a/src/orion/algo/tpe.py b/src/orion/algo/tpe.py
index a2f26526..46d5a0b5 100644
--- a/src/orion/algo/tpe.py
+++ b/src/orion/algo/tpe.py
@@ -142,31 +142,37 @@ class TPE(BaseAlgorithm):
----------
space: `orion.algo.space.Space`
Optimisation space with priors for each dimension.
- seed: N... |
Erotemic__ubelt-64 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ubelt/util_path.py:ensuredir"
],
"edited_modules": [
"ubelt/util_path.py:ensuredir"
]
},
"file": "ubelt/util_path.py"
}
] | Erotemic/ubelt | 89085f148ace79aa0dfdc17383423e3dfe138017 | Request: ensure director verbose mentions if it created a new directory
It would be nice if the verbose mode actually said something like
Ensuring directory ('...') status: existing
Ensuring directory ('...') status: creating
Maybe have a second verbose level if you want to maintain the original way. | diff --git a/ubelt/util_path.py b/ubelt/util_path.py
index c028ba2..5241209 100644
--- a/ubelt/util_path.py
+++ b/ubelt/util_path.py
@@ -291,9 +291,9 @@ def ensuredir(dpath, mode=0o1777, verbose=None, recreate=False):
>>> assert exists(dpath)
>>> os.rmdir(dpath)
"""
- if verbose is None: # no... |
European-XFEL__EXtra-data-104 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"extra_data/stacking.py:stack_detector_data"
],
"edited_modules": [
"extra_data/stacking.py:stack_detector_data"
]
},
"file": "extra_data/stacking.py"
}
] | European-XFEL/EXtra-data | 99e7c96643c1e31d09d71e4b63c21a7465a14755 | stack_detector_data has wrong default fill value for uint64 data
We've assumed that `np.nan` is universally converted to 0 for integer dtypes, but that doesn't hold for uint64:
```
In [4]: np.full(1, np.nan, dtype=np.uint32)
Out[4]: array([0], dtype=uint32)
In [5]: np.full(1, np.nan,... | diff --git a/extra_data/stacking.py b/extra_data/stacking.py
index 7b5f29e..a4878f6 100644
--- a/extra_data/stacking.py
+++ b/extra_data/stacking.py
@@ -53,7 +53,7 @@ def stack_data(train, data, axis=-3, xcept=()):
return np.stack(ordered_arrays, axis=axis)
-def stack_detector_data(train, data, axis=-3, module... |
European-XFEL__EXtra-data-128 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "extra_data/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"extra_data/re... | European-XFEL/EXtra-data | 76c30bf18529ed0c3eb9de9c3d1c15494f807ac5 | Selected keys can be overridden
`.select()` is meant to always make a narrower selection from the current one, but @daviddoji found a case where it can get broader again:
```python
source = 'FXE_DET_LPD1M-1/DET/2CH0:xtdf'
sel = run.select(source, "image.data")
print(sel.keys_for_source(source))
sel = sel.selec... | diff --git a/.github/dependabot/constraints.txt b/.github/dependabot/constraints.txt
index ff0884c..8ca9cb1 100644
--- a/.github/dependabot/constraints.txt
+++ b/.github/dependabot/constraints.txt
@@ -13,7 +13,7 @@ psutil==5.8.0
pyparsing==2.4.7
python-dateutil==2.8.1
pytz==2020.5
-pyzmq==21.0.1
-scipy<=1.5.4
+pyzmq... |
European-XFEL__EXtra-data-165 | [
{
"changes": {
"added_entities": [
"extra_data/reader.py:DataCollection.train_timestamps"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"extra_data/reader.py:DataCollection"
]
},
"file": "extra_data/reader.py"
}
] | European-XFEL/EXtra-data | 05de22b55fdc424473127335d2ca6b3a7026ab6d | Provide a means to get train timestamps
The new DAQ version adds a timestamp field in the INDEX section, with a timestamp matching each train ID. We should have a way to access these. | diff --git a/docs/reading_files.rst b/docs/reading_files.rst
index faabbfa..f8b6b4a 100644
--- a/docs/reading_files.rst
+++ b/docs/reading_files.rst
@@ -67,6 +67,8 @@ to refer to all data associated with that 0.1 second window.
.. automethod:: get_data_counts
+ .. automethod:: train_timestamps
+
.. autome... |
European-XFEL__EXtra-data-175 | [
{
"changes": {
"added_entities": [
"extra_data/file_access.py:FileAccess.metadata"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"extra_data/file_access.py:FileAccess"
]
},
"file": "extra_data/file_access.py"
},
{
"chan... | European-XFEL/EXtra-data | 13a2af8210d71d8a5e97d6e94a36091fc2ebd458 | Provide a means to access metadata fields
The new DAQ version records a few extra fields in the `METADATA` section of files, including start time and DAQ version. It should be possible to get this information through EXtra-data.
Complication: we allow combining data from more than one run. What should happen where t... | diff --git a/extra_data/file_access.py b/extra_data/file_access.py
index f70edb8..6ef8bea 100644
--- a/extra_data/file_access.py
+++ b/extra_data/file_access.py
@@ -292,6 +292,25 @@ class FileAccess:
counts = np.uint64((ix_group['last'][:ntrains] - firsts + 1) * status)
return firsts, counts
+ ... |
European-XFEL__EXtra-data-222 | [
{
"changes": {
"added_entities": [
"extra_data/keydata.py:KeyData._data_chunks_nonempty"
],
"added_modules": null,
"edited_entities": [
"extra_data/keydata.py:KeyData._data_chunks",
"extra_data/keydata.py:KeyData.data_counts",
"extra_data/keydata.py:KeyDat... | European-XFEL/EXtra-data | b738290e6dbb09ed2906f43f985cce9f16513ba3 | Can't instantiate multi-module detector access if any module has no data
This happens a lot with LPD data. It looks like the root cause is a problem with `.data_counts()`.
```python
run = open_run(2729, 44)
LPD1M(run.select_trains(np.s_[:100])
```
```
----------------------------------------------------------... | diff --git a/extra_data/keydata.py b/extra_data/keydata.py
index 86fc141..167b173 100644
--- a/extra_data/keydata.py
+++ b/extra_data/keydata.py
@@ -53,11 +53,14 @@ class KeyData:
"""An ordered list of chunks containing data"""
if self._cached_chunks is None:
self._cached_chunks = sorted(... |
European-XFEL__EXtra-data-257 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"extra_data/keydata.py:KeyData.data_counts"
],
"edited_modules": [
"extra_data/keydata.py:KeyData"
]
},
"file": "extra_data/keydata.py"
}
] | European-XFEL/EXtra-data | dac73a279511b033937bde2f1b239c0dd80b657b | AssertionError in .data_counts(labelled=False)
@yohey-uemura discovered this over the weekend. When writing this method, I had overlooked the possibility of having a selected train which doesn't correspond to any data for the given source. For instance, in this run, LPD08 starts from train 1232492275, but other sources... | diff --git a/.github/dependabot/constraints.txt b/.github/dependabot/constraints.txt
index ee3a594..7cfce9f 100644
--- a/.github/dependabot/constraints.txt
+++ b/.github/dependabot/constraints.txt
@@ -1,3 +1,4 @@
+coverage==6.1.2
cycler==0.11.0
h5py<3.7.0
karabo-bridge==0.6.1
diff --git a/extra_data/keydata.py b/ext... |
European-XFEL__EXtra-data-278 | [
{
"changes": {
"added_entities": [
"extra_data/components.py:MultimodDetectorBase.train_id_chunks",
"extra_data/components.py:MultimodDetectorBase.train_id_to_ix",
"extra_data/components.py:MultimodDetectorBase.select_trains",
"extra_data/components.py:MultimodDetectorBase.... | European-XFEL/EXtra-data | be509dcad9eee7bec008a8a1d6d6dd105ed16e4e | split_trains method for xtdf detector classes
Something I noticed while working on code for FXE - it would be useful to be able to split the `LPD1M` object into chunks, like we can with `DataCollection` and `KeyData`. In particular, a `frames_per_part` option would be useful when you want to limit how much data a chunk... | diff --git a/.github/dependabot/constraints.txt b/.github/dependabot/constraints.txt
index 20ca231..d5be32a 100644
--- a/.github/dependabot/constraints.txt
+++ b/.github/dependabot/constraints.txt
@@ -8,7 +8,7 @@ msgpack==1.0.3
msgpack-numpy==0.4.7.1
numpy<1.23.0
pandas<1.5.0
-Pillow==9.0.1
+Pillow==9.0.0
psutil==5... |
European-XFEL__EXtra-data-287 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"extra_data/writer.py:VirtualFileWriter._assemble_data",
"extra_data/writer.py:VirtualFileWriter.add_dataset"
],
"edited_modules": [
"extra_data/writer.py:VirtualFileWriter"
... | European-XFEL/EXtra-data | 5c2046f6385b3a3c767f2e85ab97765d8dbc2d4d | Virtual overview file missing instrument sources with no data
E.g. `MID_EXP_AGIPD1M1/REDU/LITFRM:output` is
- present in `/gpfs/exfel/exp/MID/202230/p900249/raw/r0198/RAW-R0198-DA05-S00000.h5`
- missing from `/gpfs/exfel/exp/MID/202230/p900249/usr/.extra_data/RAW-R0198-OVERVIEW.h5`
We haven't figured out why yet... | diff --git a/extra_data/writer.py b/extra_data/writer.py
index 89e540e..1d1678d 100644
--- a/extra_data/writer.py
+++ b/extra_data/writer.py
@@ -199,14 +199,10 @@ class VirtualFileWriter(FileWriter):
super().__init__(path, data)
- def _assemble_data(self, source, key):
+ def _assemble_data(self, key... |
European-XFEL__EXtra-data-290 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"extra_data/reader.py:RunDirectory"
],
"edited_modules": [
"extra_data/reader.py:RunDirectory"
]
},
"file": "extra_data/reader.py"
}
] | European-XFEL/EXtra-data | 5c2046f6385b3a3c767f2e85ab97765d8dbc2d4d | Run opened from virtual overview file is not considered a single run
Something we noticed today while debugging an issue in offline calibration.
The fix is very easy, but ideally we can also add a test that would have caught this (e.g. load a virtual overview file and ensure we can use `.get_run_value()`. | diff --git a/extra_data/reader.py b/extra_data/reader.py
index f6bfe55..3803896 100644
--- a/extra_data/reader.py
+++ b/extra_data/reader.py
@@ -1419,7 +1419,7 @@ def RunDirectory(
if _use_voview and (sel_files == files):
voview_file_acc = voview.find_file_valid(path)
if voview_file_acc is not No... |
European-XFEL__EXtra-data-375 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"extra_data/reader.py:RunDirectory"
],
"edited_modules": [
"extra_data/reader.py:RunDirectory"
]
},
"file": "extra_data/reader.py"
},
{
"changes": {
"added... | European-XFEL/EXtra-data | 2ae9f5eafd9a7661c653cbb57eb6f25373fe519c | RunDirectory does not work as context manager when voview file present
[In the Jungfrau correction notebook, the raw run files are opened using a context manager](https://git.xfel.eu/detectors/pycalibration/-/blob/master/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb#L697).
This works fine when no v... | diff --git a/extra_data/reader.py b/extra_data/reader.py
index 21ad0f4..90643e5 100644
--- a/extra_data/reader.py
+++ b/extra_data/reader.py
@@ -1398,7 +1398,9 @@ def RunDirectory(
if _use_voview and (sel_files == files):
voview_file_acc = voview.find_file_valid(path)
if voview_file_acc is not No... |
European-XFEL__EXtra-data-92 | [
{
"changes": {
"added_entities": [
"extra_data/keydata.py:KeyData.data_counts"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"extra_data/keydata.py:KeyData"
]
},
"file": "extra_data/keydata.py"
},
{
"changes": {
"... | European-XFEL/EXtra-data | 2b3fe44a66e4cdf49323441add35bd633c8bc192 | train_ids in KeyData
the `train_ids` attribute of the `KeyData` object is a simple copy of the train ids contained in the `DataCollection`. That leads to some inconsistencies. For example calling `.shape` will return a shape where the trainId axis match the actual count of data available in the files for the source, bu... | diff --git a/extra_data/keydata.py b/extra_data/keydata.py
index 858fb96..5e5573e 100644
--- a/extra_data/keydata.py
+++ b/extra_data/keydata.py
@@ -95,6 +95,27 @@ class KeyData:
def __getitem__(self, item):
return self.select_trains(item)
+ def data_counts(self):
+ """Get a count of data poin... |
EvoluxBR__greenswitch-83 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"greenswitch/esl.py:ESLProtocol.stop"
],
"edited_modules": [
"greenswitch/esl.py:ESLProtocol"
]
},
"file": "greenswitch/esl.py"
}
] | EvoluxBR/greenswitch | eb210f31ff723bba75d83b09d898f7e1273eb63b | ESLProtocol.stop: Socket is not cleaned up if socket is closed
When `ESLProtocol.stop()` is called, it issues a `socket.send`, but it will raise an exception if socket is already closed
```ruby
mai 12 18:17:41: Traceback (most recent call last):
mai 12 18:17:41: File "src/gevent/_abstract_linkable.py", line 26... | diff --git a/greenswitch/esl.py b/greenswitch/esl.py
index ef9a397..6c25f29 100644
--- a/greenswitch/esl.py
+++ b/greenswitch/esl.py
@@ -217,7 +217,7 @@ class ESLProtocol(object):
if self.connected:
try:
self.send('exit')
- except (NotConnectedError, socket.error):
+ ... |
EvoluxBR__greenswitch-85 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"greenswitch/esl.py:OutboundSession.connect"
],
"edited_modules": [
"greenswitch/esl.py:OutboundSession"
]
},
"file": "greenswitch/esl.py"
}
] | EvoluxBR/greenswitch | 169a419103712c813f4b531480184a7e228bafe4 | ESLProtocol.connect: Socket is not cleaned up if socket is closed
This issue is very similar to #82
When `ESLProtocol.connect` is called, it issues a `socket.send`, but, in rare cases, it could raise an exception if socket is already closed, but the socket is not cleanup
```ruby
mai 22 16:18:14: Traceback (most... | diff --git a/greenswitch/esl.py b/greenswitch/esl.py
index 6c25f29..9f9bdaf 100644
--- a/greenswitch/esl.py
+++ b/greenswitch/esl.py
@@ -359,7 +359,12 @@ class OutboundSession(ESLProtocol):
if self._outbound_connected:
return self.session_data
- resp = self.send('connect')
+ try:
+... |
Eyepea__aiosip-111 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"aiosip/transaction.py:FutureTransaction._result"
],
"edited_modules": [
"aiosip/transaction.py:FutureTransaction"
]
},
"file": "aiosip/transaction.py"
}
] | Eyepea/aiosip | 3219ca46cdfd115a72101d92cd1f717f78d9f7b9 | Improper handling of 401 authentication failures
In a call flow such as
* send REGISTER
* get 401 response with auth challenge
* send REGISTER with valid authentication
* get 401 response with no challenge (ie: your credentials are fine, but still denied)
The client will continue to retransmit the request wit... | diff --git a/aiosip/transaction.py b/aiosip/transaction.py
index da61942..4f2b0ab 100644
--- a/aiosip/transaction.py
+++ b/aiosip/transaction.py
@@ -145,6 +145,9 @@ class FutureTransaction(BaseTransaction):
self.dialog.end_transaction(self)
def _result(self, msg):
+ if self.authentification:
+ ... |
F5Networks__f5-common-python-1485 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"f5/bigip/tm/sys/license.py:License.__init__"
],
"edited_modules": [
"f5/bigip/tm/sys/license.py:License"
]
},
"file": "f5/bigip/tm/sys/license.py"
}
] | F5Networks/f5-common-python | fb001e95cc16ddf84ba03c3193582c69cd8ce0df | Add license installation
Add license installation command similar to the revoking the license:
Code snippet for the revoking the license:
```python
mgnt = ManagementRoot(bigip_mgnt, user, pass)
mgnt.tm.sys.license.exec_cmd('revoke')`
```
Code snippet for the license installation:
```python
mgnt = ManagementR... | diff --git a/f5/bigip/tm/sys/license.py b/f5/bigip/tm/sys/license.py
index df150f9..c38d3d4 100644
--- a/f5/bigip/tm/sys/license.py
+++ b/f5/bigip/tm/sys/license.py
@@ -41,7 +41,7 @@ class License(UnnamedResource, CommandExecutionMixin):
super(License, self).__init__(sys)
self._meta_data['required_jso... |
F5Networks__f5-common-python-809 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"f5/bigip/resource.py:ResourceBase._update"
],
"edited_modules": [
"f5/bigip/resource.py:ResourceBase"
]
},
"file": "f5/bigip/resource.py"
}
] | F5Networks/f5-common-python | adde820d63f53295a322e093df4438b17c9eeae1 | factor other supported parameters and formats into iapp_parser
The iapp_parser util supports the common formats for iapps but does not support all of them, particularly those that are part of the iapp templates that F5 releases on downloads.f5.com | diff --git a/f5/bigip/resource.py b/f5/bigip/resource.py
index 3bfcfec..018bfe1 100644
--- a/f5/bigip/resource.py
+++ b/f5/bigip/resource.py
@@ -100,6 +100,7 @@ from f5.bigip.mixins import LazyAttributeMixin
from f5.bigip.mixins import ToDictMixin
from f5.sdk_exception import F5SDKError
from f5.sdk_exception import ... |
F5Networks__f5-common-python-819 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"f5/utils/iapp_parser.py:IappParser.__init__",
"f5/utils/iapp_parser.py:IappParser._get_section_end_index",
"f5/utils/iapp_parser.py:IappParser.parse_template"
],
"edited_modu... | F5Networks/f5-common-python | 7cb5a9e7e4121a64a2a00e768431d92a8e4d050b | make iapp_parser code python3 compat
as part of the py3 effort, make the iapp parser compatible. | diff --git a/f5/utils/iapp_parser.py b/f5/utils/iapp_parser.py
index 5418909..8b5abfc 100644
--- a/f5/utils/iapp_parser.py
+++ b/f5/utils/iapp_parser.py
@@ -21,48 +21,48 @@ from f5.sdk_exception import F5SDKError
class IappParser(object):
template_sections = [
- u'presentation',
- u'implementation... |
F5Networks__f5-common-python-967 | [
{
"changes": {
"added_entities": [
"f5/bigip/tm/asm/tasks.py:Import_Policy_s.__init__",
"f5/bigip/tm/asm/tasks.py:Import_Policy.__init__",
"f5/bigip/tm/asm/tasks.py:Import_Policy.modify"
],
"added_modules": [
"f5/bigip/tm/asm/tasks.py:Import_Policy"
],
... | F5Networks/f5-common-python | 52861aea481189c805419221bd8e98114c364ee6 | Create 3 missing endpoints at /mgmt/tm/asm/tasks/
Hello Devs!
Greatly enjoy using the SDK. Hopefully these endpoints can be added in the scope of next release :)
```
"reference": {
"link": "https://localhost/mgmt/tm/asm/tasks/import-policy"
}
"reference": {
"link": "https://... | diff --git a/f5/bigip/tm/asm/tasks.py b/f5/bigip/tm/asm/tasks.py
index f669107..2b05f57 100644
--- a/f5/bigip/tm/asm/tasks.py
+++ b/f5/bigip/tm/asm/tasks.py
@@ -91,8 +91,8 @@ class Export_Policy_s(Collection):
class Export_Policy(AsmResource):
"""BIG-IP® ASM Export Policy Resource."""
- def __init__(self, ap... |
FCP-INDI__cpac-43 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/cpac/__main__.py:_parser"
],
"edited_modules": [
"src/cpac/__main__.py:_parser"
]
},
"file": "src/cpac/__main__.py"
},
{
"changes": {
"added_entities"... | FCP-INDI/cpac | ff172c198b35d557cbf6fabbcbfb1651232064db | ✨ Call `ba-timeseries-gradients` and `tsconcat` from wrapper
<!-- ### User interface changes
_No response_ -->
### Project sub-parts and estimates
- [x] Call `ba_timeseries_gradients` from `cpac` ① (#42)
- [x] Call `tsconcat` from `cpac` ① (#43)
### Timeline notes
#### version management
* `ba_timeseri... | diff --git a/README.rst b/README.rst
index b3ae0590..deb6819a 100644
--- a/README.rst
+++ b/README.rst
@@ -33,7 +33,7 @@ Usage
usage: cpac [-h] [--version] [-o OPT] [-B CUSTOM_BINDING]
[--platform {docker,singularity}] [--image IMAGE] [--tag TAG]
[--working_dir PATH] [-v] [-vv]
- ... |
FZJ-IEK3-VSA__tsam-71 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tsam/periodAggregation.py:aggregatePeriods"
],
"edited_modules": [
"tsam/periodAggregation.py:aggregatePeriods"
]
},
"file": "tsam/periodAggregation.py"
},
{
"c... | FZJ-IEK3-VSA/tsam | 14f04dc8ab195129600ecbaa121b832dc8cbeecf | Error when creating typical periods which are longer than 24h (e.g. 48h or 72h)
I am using version 2.0.1 of Pandas. Unfortunately, as of version 1.4.0, DataFrame.append() has been deprecated. So now I get an error message when I try to create typical periods longer than 24h, for example, typical periods that are 48h lo... | diff --git a/tsam/periodAggregation.py b/tsam/periodAggregation.py
index 768d16f..52b1128 100644
--- a/tsam/periodAggregation.py
+++ b/tsam/periodAggregation.py
@@ -49,7 +49,7 @@ def aggregatePeriods(
clusterOrder.append(
[n_clusters - 1] * int(n_sets - cluster_size * n_clusters)
... |
FactoryBoy__factory_boy-1045 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"factory/django.py:mute_signals.__exit__"
],
"edited_modules": [
"factory/django.py:mute_signals"
]
},
"file": "factory/django.py"
}
] | FactoryBoy/factory_boy | 63c2df43ea640adb08d68c2b09c542667691f588 | Unusable password generator for Django
#### The problem
The recently added `Password` generator for Django is helpful, but it's not clear how to use it to create an unusable password (similar to calling `set_unusable_password` on the generated user).
#### Proposed solution
Django's `set_unusable_password` is a... | diff --git a/docs/orms.rst b/docs/orms.rst
index 3839707..5967e1b 100644
--- a/docs/orms.rst
+++ b/docs/orms.rst
@@ -128,7 +128,11 @@ Extra fields
.. method:: __init__(self, password)
- :param str password: Default password.
+ :param str or None password: Default password.
+
+ .. note:: When t... |
FactoryBoy__factory_boy-1067 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"factory/declarations.py:Maybe.evaluate_pre"
],
"edited_modules": [
"factory/declarations.py:Maybe"
]
},
"file": "factory/declarations.py"
}
] | FactoryBoy/factory_boy | 7ed1e5417e06c3d83e0495a67508b3868de53823 | KeyError: 'locale'
#### Description
KeyError: 'locale' generated when calling Faker.
factory/faker.py:46: KeyError
Seems that the `extra` dictionary is empty, but `locale` key is expected.
#### To Reproduce
running unit test with tox
python 3.10; factory-boy==3.2.1 faker==13.15.0
##### Model / Factory code
... | diff --git a/factory/declarations.py b/factory/declarations.py
index 70abe35..951b45f 100644
--- a/factory/declarations.py
+++ b/factory/declarations.py
@@ -536,7 +536,7 @@ class Maybe(BaseDeclaration):
return target
def evaluate_pre(self, instance, step, overrides):
- choice = self.decider.e... |
FactoryBoy__factory_boy-631 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"factory/declarations.py:Maybe.__init__"
],
"edited_modules": [
"factory/declarations.py:Maybe"
]
},
"file": "factory/declarations.py"
}
] | FactoryBoy/factory_boy | 4d2aca14723126adf47f1482c3c9f2f0e662debe | Maybe: Inconsistent phases TypeError masked by __repr__ AttributeError
#### Description
The TypeError check in `declarations.Maybe.__init__` is masked by an AttributeError because the TypeError error message uses `__repr__` which in turn uses `self` attributes that haven't yet be set in `__init__`.
#### To Reprodu... | diff --git a/factory/declarations.py b/factory/declarations.py
index bdb44ab..18c1fd5 100644
--- a/factory/declarations.py
+++ b/factory/declarations.py
@@ -444,6 +444,15 @@ SKIP = Skip()
class Maybe(BaseDeclaration):
def __init__(self, decider, yes_declaration=SKIP, no_declaration=SKIP):
super(Maybe, se... |
FactoryBoy__factory_boy-752 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"factory/base.py:FactoryOptions.__str__"
],
"edited_modules": [
"factory/base.py:FactoryOptions"
]
},
"file": "factory/base.py"
},
{
"changes": {
"added_en... | FactoryBoy/factory_boy | 85543a502eed7a3d5de17669a98e761e92a78add | 'Options' object has no attribute 'pre_declarations' is too ambiguous
#### The problem
Typo incorrectly specifying the Model for a Factory.
#### Proposed solution
Check if any specified factories are actually Models, in which case give a more clear error message.
#### Extra notes
Thanks for the good work on th... | diff --git a/docs/changelog.rst b/docs/changelog.rst
index 0c6043a..5e919bc 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -43,6 +43,10 @@ The following aliases were removed:
- :py:meth:`get_random_state()` now represents the state of Faker and ``factory_boy`` fuzzy attributes.
- Add SQLAlchemy `... |
FactoryBoy__factory_boy-841 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"factory/alchemy.py:SQLAlchemyModelFactory._get_or_create",
"factory/alchemy.py:SQLAlchemyModelFactory._create",
"factory/alchemy.py:SQLAlchemyModelFactory._save"
],
"edited_m... | FactoryBoy/factory_boy | b53b2be578a92b48934248ebeedb99d8215f17a1 | SQL Alchemy: TypeError: _save() got multiple values for argument 'session' when model has column named `session`
#### Description
We have a SQLAlchemy model which has a foreign key `session_id` and a relationship `session`. Whenever we try creating an instance with factory boy and pass in the session relationship to t... | diff --git a/CREDITS b/CREDITS
index caa7538..b7ba1ab 100644
--- a/CREDITS
+++ b/CREDITS
@@ -73,6 +73,7 @@ The project has received contributions from (in alphabetical order):
* Samuel Paccoud <samuel@sampaccoud.com>
* Saul Shanabrook <s.shanabrook@gmail.com>
* Sean Löfgren <SeanBE@users.noreply.github.com>
+* Shahr... |
Fatal1ty__mashumaro-116 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/core/meta/code/builder.py:CodeBuilder.field_types",
"mashumaro/core/meta/code/builder.py:CodeBuilder._add_pack_method_lines"
],
"edited_modules": [
"mashumaro/core/... | Fatal1ty/mashumaro | 8ec9c6e0d644209698f2446700fdebf1ed47e19d | Distinguishing annotated types from non-annotated ones in serialization_strategy
**Is your feature request related to a problem? Please describe.**
There are situations when we have multiple custom types derived from builtin ones which need to be handled differently. A `NewType` approach is not always suitable for a... | diff --git a/README.md b/README.md
index 423e8ed..19ab7a6 100644
--- a/README.md
+++ b/README.md
@@ -74,6 +74,7 @@ Table of contents
* [Subclasses without a common field](#subclasses-without-a-common-field)
* [Class level discriminator](#class-level-discriminator)
* [Working with union of classes](... |
Fatal1ty__mashumaro-122 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/jsonschema/schema.py:Instance.fields",
"mashumaro/jsonschema/schema.py:on_dataclass"
],
"edited_modules": [
"mashumaro/jsonschema/schema.py:Instance",
"mash... | Fatal1ty/mashumaro | 41b90d2a0505c2a5d463150d880df8cf917227a8 | JSON Schema generator doesn't honor `default_factory`
* mashumaro version: 3.7
* Python version: 3.11 (but 3.10 is the same)
* Operating System: macOS Ventura
### Description
See the full code and output below. When using default value, directly or via `field(default=...)` the schema correctly recognizes the fi... | diff --git a/mashumaro/jsonschema/schema.py b/mashumaro/jsonschema/schema.py
index 90fa19f..65c3ec3 100644
--- a/mashumaro/jsonschema/schema.py
+++ b/mashumaro/jsonschema/schema.py
@@ -154,7 +154,7 @@ class Instance:
self.__builder = CodeBuilder(self.origin_type, type_args)
self.__builder.rese... |
Fatal1ty__mashumaro-127 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/jsonschema/schema.py:on_dataclass"
],
"edited_modules": [
"mashumaro/jsonschema/schema.py:on_dataclass"
]
},
"file": "mashumaro/jsonschema/schema.py"
}
] | Fatal1ty/mashumaro | 73a937aebf8383da558cac3e71978cc1f8e6a0c7 | When generating a jsonschema, use "description" in field metadata
**Is your feature request related to a problem? Please describe.**
We've labeled our jsonschema objects with descriptions in field metadata:
```
project_name: Optional[str] = field(
default=None, ... | diff --git a/README.md b/README.md
index d1287b9..96a1ff2 100644
--- a/README.md
+++ b/README.md
@@ -2364,7 +2364,7 @@ For simple one-time cases it's recommended to start from using a configurable
serialized to json or to dict:
```python
-from dataclasses import dataclass
+from dataclasses import dataclass, field
... |
Fatal1ty__mashumaro-128 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/jsonschema/schema.py:on_dataclass"
],
"edited_modules": [
"mashumaro/jsonschema/schema.py:on_dataclass"
]
},
"file": "mashumaro/jsonschema/schema.py"
}
] | Fatal1ty/mashumaro | 73a937aebf8383da558cac3e71978cc1f8e6a0c7 | Allow customizing additionalProperties in jsonschemas
**Is your feature request related to a problem? Please describe.**
We have some classes for which we set additionalProperties=True in the jsonschema. Would it be possible to allow setting that in the embedded Config class?
**Describe the solution you'd like**
A... | diff --git a/README.md b/README.md
index d1287b9..f6e11e6 100644
--- a/README.md
+++ b/README.md
@@ -2698,7 +2698,9 @@ Object constraints:
### Extending JSON Schema
Using a `Config` class it is possible to override some parts of the schema.
-Currently, it works for dataclass fields via "properties" key:
+Currently,... |
Fatal1ty__mashumaro-130 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"mashumaro/jsonschema/dialects.py:JSONSchemaDraft202012Dialect"
]
},
"file": "mashumaro/jsonschema/dialects.py"
}
] | Fatal1ty/mashumaro | b1f5ab3284bdac682fc465e67d7c8f8b2ce44827 | When using "all_refs=True" to generate a jsonschema, validation fails because the top-level object has invalid reference url
* mashumaro version: latest
* Python version: 3.10
* Operating System: MacOS
### Description
I have the conversion from our old jsonschema generation app (hologram) to mashumaro working o... | diff --git a/README.md b/README.md
index ecc77a8..ac230a4 100644
--- a/README.md
+++ b/README.md
@@ -2519,7 +2519,7 @@ print(build_json_schema(List[User], all_refs=True).to_json())
}
},
"items": {
- "$ref": "#/defs/User"
+ "$ref": "#/$defs/User"
}
}
```
diff --git a/mashumaro/jso... |
Fatal1ty__mashumaro-140 | [
{
"changes": {
"added_entities": [
"mashumaro/jsonschema/schema.py:Instance._self_builder",
"mashumaro/jsonschema/schema.py:Instance.owner_class",
"mashumaro/jsonschema/schema.py:Instance.derive",
"mashumaro/jsonschema/schema.py:Instance.get_owner_config",
"mashumar... | Fatal1ty/mashumaro | c0a4cf8943de51a626bc30681c935a628565cecf | Overridden serialization methods doesn't work in JSON Schema for optional fields and inner dataclasses
* mashumaro version: 3.9
* Python version: 3.11
* Operating System: MacOS 13.3.1
### Description
When you override serialization method through `serialization_strategy` or field metadata as noted [here](https:... | diff --git a/mashumaro/jsonschema/schema.py b/mashumaro/jsonschema/schema.py
index 00bfe69..9dc6edc 100644
--- a/mashumaro/jsonschema/schema.py
+++ b/mashumaro/jsonschema/schema.py
@@ -14,7 +14,6 @@ from typing import (
Dict,
Iterable,
List,
- Mapping,
Optional,
Tuple,
Type,
@@ -104,36 ... |
Fatal1ty__mashumaro-142 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/jsonschema/schema.py:Instance.fields",
"mashumaro/jsonschema/schema.py:_default",
"mashumaro/jsonschema/schema.py:on_named_tuple"
],
"edited_modules": [
"ma... | Fatal1ty/mashumaro | 89f4b1ad2048877e72dc4c86a3c532683753ea8a | Third party default is not reflected in the generated JSON Schema
* mashumaro version: 3.9
* Python version: 3.11
* Operating System: MacOS 3.13.1
### Description
```python
from dataclasses import dataclass
from mashumaro.config import BaseConfig
from mashumaro.jsonschema import build_json_schema
def as_s... | diff --git a/mashumaro/jsonschema/schema.py b/mashumaro/jsonschema/schema.py
index 9dc6edc..34760e8 100644
--- a/mashumaro/jsonschema/schema.py
+++ b/mashumaro/jsonschema/schema.py
@@ -178,7 +178,7 @@ class Instance:
if f_default is MISSING:
f_default = self._self_builder.namespace.get(f_n... |
Fatal1ty__mashumaro-145 | [
{
"changes": {
"added_entities": [
"mashumaro/core/meta/code/builder.py:CodeBuilder.evaluate_forward_ref"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"mashumaro/core/meta/code/builder.py:CodeBuilder"
]
},
"file": "mashumaro/c... | Fatal1ty/mashumaro | a86eaf8e4a5f23a7e48644db230fc5a39beffc69 | Add support for ForwardRef
* mashumaro version: 3.9.1
* Python version: 3.10.12
* Operating System: Linux
### Description
I'm trying to use mashumaro to deserialize a `TypedDict`, got an exception like:
```python
Traceback (most recent call last):
File "/home/ubuntu/workspace/example/python/repro.py", li... | diff --git a/mashumaro/core/meta/code/builder.py b/mashumaro/core/meta/code/builder.py
index 00c16db..2c353a2 100644
--- a/mashumaro/core/meta/code/builder.py
+++ b/mashumaro/core/meta/code/builder.py
@@ -1,5 +1,6 @@
import importlib
import inspect
+import sys
import types
import typing
from contextlib import cont... |
Fatal1ty__mashumaro-146 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/core/meta/code/builder.py:CodeBuilder._add_unpack_method_lines"
],
"edited_modules": [
"mashumaro/core/meta/code/builder.py:CodeBuilder"
]
},
"file": "mashuma... | Fatal1ty/mashumaro | 8c32badea5a5005e2243fd8c0ec8aa0dcc6b8c5d | Allow discrimination based on a key that is not part of the model
**Is your feature request related to a problem? Please describe.**
I'am using mashumaro as (de)serialization backend of my [AST library](https://github.com/mishamsk/pyoak/)
What this means is that I (de)serialize huge (millions of nodes) nested datac... | diff --git a/mashumaro/core/meta/code/builder.py b/mashumaro/core/meta/code/builder.py
index 7ba9d0e..00c16db 100644
--- a/mashumaro/core/meta/code/builder.py
+++ b/mashumaro/core/meta/code/builder.py
@@ -330,6 +330,7 @@ class CodeBuilder:
# prevent RecursionError
field=discr.f... |
Fatal1ty__mashumaro-159 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/jsonschema/schema.py:on_type_with_overridden_serialization"
],
"edited_modules": [
"mashumaro/jsonschema/schema.py:on_type_with_overridden_serialization"
]
},
... | Fatal1ty/mashumaro | 7349f736c5d4b25f0c9ae3849f6daed1e7a6e06f | Allow basic types used as serialization methods to be reflected in the JSON schema
**Is your feature request related to a problem? Please describe.**
If we use basic types like `str`, `int`, `float`, `bool` as a serialization method, the generated JSON Schema will use `Any` because they don't have signature:
```p... | diff --git a/mashumaro/jsonschema/schema.py b/mashumaro/jsonschema/schema.py
index 35a82b0..44f29ae 100644
--- a/mashumaro/jsonschema/schema.py
+++ b/mashumaro/jsonschema/schema.py
@@ -282,6 +282,9 @@ Registry = InstanceSchemaCreatorRegistry()
register = Registry.register
+BASIC_TYPES = {str, int, float, bool}
+
+... |
Fatal1ty__mashumaro-162 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"mashumaro/config.py:BaseConfig"
]
},
"file": "mashumaro/config.py"
},
{
"changes": {
"added_entities": [
"mashumaro/core/meta/code/build... | Fatal1ty/mashumaro | 92d539cfde20c50d953730128441b951f60505cd | Add an option to omit values equal to defaults on serialization
**Is your feature request related to a problem? Please describe.**
There are cases when it's preferable to omit default values on serialization. It can potentially reduce the storage space used or the amount of data transferred.
**Describe the solution... | diff --git a/README.md b/README.md
index 9694aa6..dc24b42 100644
--- a/README.md
+++ b/README.md
@@ -59,6 +59,7 @@ Table of contents
* [`aliases` config option](#aliases-config-option)
* [`serialize_by_alias` config option](#serialize_by_alias-config-option)
* [`omit_none` config option](#omi... |
Fatal1ty__mashumaro-164 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/core/meta/code/builder.py:CodeBuilder._get_field_packer"
],
"edited_modules": [
"mashumaro/core/meta/code/builder.py:CodeBuilder"
]
},
"file": "mashumaro/core... | Fatal1ty/mashumaro | 711705f2d0e799f8215d13da7ceb84228d1c4acc | Add an option to avoid collection data types copying
**Is your feature request related to a problem? Please describe.**
Currently, all collection data types are serialized as copies to prevent mutation, but for mixins like `DataClassORJSONMixin` we can avoid that and improve serialization performance. The list of mixi... | diff --git a/README.md b/README.md
index e748d83..5ab18b4 100644
--- a/README.md
+++ b/README.md
@@ -72,6 +72,7 @@ Table of contents
* [`serialization_strategy` dialect option](#serialization_strategy-dialect-option)
* [`omit_none` dialect option](#omit_none-dialect-option)
* [`omit_default` dialec... |
Fatal1ty__mashumaro-178 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/core/meta/code/builder.py:CodeBuilder.evaluate_forward_ref"
],
"edited_modules": [
"mashumaro/core/meta/code/builder.py:CodeBuilder"
]
},
"file": "mashumaro/c... | Fatal1ty/mashumaro | b7d6435a96ede5cef7d1915a3817e3e1f14df6e7 | "`dict[str, T]` as a field type is not supported"
* mashumaro version: 3.10
* Python version: 3.11.5
In a seemingly simple example with generics, close to the one presented in the docs, mashumaro seems to stumble on `dict[str, T]` annotation; wonder if this is intended, or a bug, or some misunderstanding on my side... | diff --git a/mashumaro/core/meta/code/builder.py b/mashumaro/core/meta/code/builder.py
index 27e0b1e..ec8587d 100644
--- a/mashumaro/core/meta/code/builder.py
+++ b/mashumaro/core/meta/code/builder.py
@@ -293,7 +293,8 @@ class CodeBuilder:
typ: typing.ForwardRef,
owner: typing.Optional[typing.Type],
... |
Fatal1ty__mashumaro-180 | [
{
"changes": {
"added_entities": [
"mashumaro/core/meta/code/builder.py:CodeBuilder.get_type_name_identifier"
],
"added_modules": null,
"edited_entities": [
"mashumaro/core/meta/code/builder.py:FieldUnpackerCodeBlockBuilder.build"
],
"edited_modules": [
... | Fatal1ty/mashumaro | d70c5c5606bca8854ce9ad309bdb637309d590cb | The types defined inside the function result in syntactically invalid generated code
* mashumaro version: 3.11
* Python version: 3.12
* Operating System: macOS 14.1
### Description
If someone puts dataclasses or other types inside a function, a syntax error will occur. This problem first reported in the followi... | diff --git a/mashumaro/core/meta/code/builder.py b/mashumaro/core/meta/code/builder.py
index a3daba2..4e65ae5 100644
--- a/mashumaro/core/meta/code/builder.py
+++ b/mashumaro/core/meta/code/builder.py
@@ -45,6 +45,7 @@ from mashumaro.core.meta.helpers import (
is_hashable,
is_init_var,
is_literal,
+ i... |
Fatal1ty__mashumaro-185 | [
{
"changes": {
"added_entities": [
"mashumaro/core/meta/types/unpack.py:DiscriminatedUnionUnpackerBuilder._add_register_variant_tags"
],
"added_modules": null,
"edited_entities": [
"mashumaro/core/meta/types/unpack.py:DiscriminatedUnionUnpackerBuilder._add_body"
],
... | Fatal1ty/mashumaro | 6cd3924476872a913faf68b5165e2620c645abbd | Allow for more complex logic for subclass Discrimnator field matching
**Is your feature request related to a problem? Please describe.**
In building a deserializer for a large complex configuration file, some subclasses have identical shapes, but it would still be useful to distinguish by a `type` field. Unfortunately... | diff --git a/README.md b/README.md
index e224048..3dc602a 100644
--- a/README.md
+++ b/README.md
@@ -2020,7 +2020,7 @@ It has the following parameters that affects class selection rules:
by which all the variants can be distinguished
* `include_subtypes` — allow to deserialize subclasses
* `include_supertypes` — a... |
Fatal1ty__mashumaro-189 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/core/meta/types/unpack.py:DiscriminatedUnionUnpackerBuilder._get_variants_map",
"mashumaro/core/meta/types/unpack.py:DiscriminatedUnionUnpackerBuilder._get_variant_names"
],
... | Fatal1ty/mashumaro | ab8242448631ab7a1ad2e437561377cd698a99e9 | The types defined inside the function result in syntactically invalid generated code
* mashumaro version: 3.11
* Python version: 3.12
* Operating System: macOS 14.1
### Description
If someone puts dataclasses or other types inside a function, a syntax error will occur. This problem first reported in the followi... | diff --git a/mashumaro/core/meta/types/unpack.py b/mashumaro/core/meta/types/unpack.py
index 3de5ee8..5900f91 100644
--- a/mashumaro/core/meta/types/unpack.py
+++ b/mashumaro/core/meta/types/unpack.py
@@ -256,7 +256,8 @@ class DiscriminatedUnionUnpackerBuilder(AbstractUnpackerBuilder):
def _get_variants_map(self, ... |
Fatal1ty__mashumaro-191 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/core/meta/code/builder.py:CodeBuilder.evaluate_forward_ref"
],
"edited_modules": [
"mashumaro/core/meta/code/builder.py:CodeBuilder"
]
},
"file": "mashumaro/c... | Fatal1ty/mashumaro | c3c6739640533426ac08b231b747607aeb596c9c | TypedDicts not working with `from __future__ import annotations`
* mashumaro version: 3.11
* Python version: 3.10.13
* Operating System: Ubuntu
### What I Did
```py
from __future__ import annotations
from mashumaro.jsonschema import build_json_schema
from typing import TypedDict
class TypedDictRequiredK... | diff --git a/mashumaro/core/meta/code/builder.py b/mashumaro/core/meta/code/builder.py
index e4fbb27..8d361ad 100644
--- a/mashumaro/core/meta/code/builder.py
+++ b/mashumaro/core/meta/code/builder.py
@@ -1,7 +1,6 @@
import importlib
import inspect
import math
-import sys
import types
import typing
import uuid
@@... |
Fatal1ty__mashumaro-220 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mashumaro/core/meta/types/pack.py:_pack_with_annotated_serialization_strategy"
],
"edited_modules": [
"mashumaro/core/meta/types/pack.py:_pack_with_annotated_serialization_strategy"
... | Fatal1ty/mashumaro | c076075516af07c0bb552b1a388019380f8d76ae | Annotated SerializationStrategy used as a field serialization strategy leads to RecursionError
* mashumaro version: 3.12
* Python version: 3.12.2
* Operating System: macOS 14.4
### Description
Minimap reproducible example:
```python
from typing import Any
from dataclasses import dataclass, field
from ma... | diff --git a/mashumaro/core/meta/types/pack.py b/mashumaro/core/meta/types/pack.py
index f03181d..e8b4637 100644
--- a/mashumaro/core/meta/types/pack.py
+++ b/mashumaro/core/meta/types/pack.py
@@ -110,6 +110,19 @@ def _pack_with_annotated_serialization_strategy(
)
overridden_fn = f"__{spec.field_ctx.name}_ser... |
Fatal1ty__mashumaro-94 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"mashumaro/core/meta/code/builder.py:CodeBuilder"
]
},
"file": "mashumaro/core/meta/code/builder.py"
}
] | Fatal1ty/mashumaro | 76381804fe0ddd6eec7b9aabb7dddb950eca2b47 | Inconsistent Application of serialization_strategy
* mashumaro version: 3.2 and 3.3
* Python version: 3.10
* Operating System: macOS
### Description
There is an apparent regression in serialization behavior when the serialization_strategy object is being used and there are multiple properties of the same type o... | diff --git a/mashumaro/core/meta/code/builder.py b/mashumaro/core/meta/code/builder.py
index 453da7f..be2b69a 100644
--- a/mashumaro/core/meta/code/builder.py
+++ b/mashumaro/core/meta/code/builder.py
@@ -899,7 +899,6 @@ class CodeBuilder:
yield metadata.get("serialization_strategy")
yield from self._... |
FlorianLudwig__rueckenwind-9 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rw/event.py:EventException.__init__",
"rw/event.py:Event.__call__"
],
"edited_modules": [
"rw/event.py:EventException",
"rw/event.py:Event"
]
},
"file":... | FlorianLudwig/rueckenwind | a9856bf3b640562310eda0953c921054b7a050ef | exceptions thrown in events
Exceptions thrown in events are caught and wrapped into an EventException (https://github.com/FlorianLudwig/rueckenwind/blob/master/rw/event.py#L75). As the EventException is not an HTTPError, it results in tornado not responding at all to the request.
Example:
```python
@plugin.init
... | diff --git a/rw/event.py b/rw/event.py
index 103a14b..4cf69f3 100644
--- a/rw/event.py
+++ b/rw/event.py
@@ -20,22 +20,16 @@ Signal
"""
from __future__ import absolute_import, division, print_function, with_statement
-import traceback
-
from tornado import gen
-import rw.scope
-
-
-class EventException(Exception):... |
Fortnite-API__py-wrapper-26 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "fortnite_api/__init__.py"
},
{
"changes": {
"added_entities": [
"fortnite_api/client.py:Client.beta_fetch_new_display_assets",
"... | Fortnite-API/py-wrapper | ea1032f5e393470ddfeac9f4bebe3b2a44c1f618 | [BETA] Add new display asset endpoint
The wrapper currently doesn't support [beta/newdisplayassets](https://fortnite-api.com/beta/newdisplayassets). Support should be added as a beta endpoint.
This may require a breaking change to prevent duplicated `NewDisplayAsset` objects, since there is already a `ShopEntryNewDi... | diff --git a/docs/api/objects.rst b/docs/api/objects.rst
index 64f7d85..1707084 100644
--- a/docs/api/objects.rst
+++ b/docs/api/objects.rst
@@ -47,6 +47,15 @@ The API has many objects that represent different parts of the Fortnite API. Bel
.. autoclass:: fortnite_api.POILocation
:members:
+.. autoclass:: fortn... |
FundersClub__bai-lockbox-2 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"lockbox/exceptions.py:LockboxParseError"
]
},
"file": "lockbox/exceptions.py"
},
{
"changes": {
"added_entities": [
"lockbox/parser.py:L... | FundersClub/bai-lockbox | c7e4fbc207b21953e4741ba55f787eaa108e55fb | Code review
* [x] https://github.com/FundersClub/bai-lockbox/blob/master/setup.py#L12 - are all of these used?
* [x] https://github.com/FundersClub/bai-lockbox/blob/master/setup.py#L20 - incorrect
* [x] https://github.com/FundersClub/bai-lockbox/blob/master/lockbox/exceptions.py#L32 - what is this?
* [x] https://git... | diff --git a/.gitignore b/.gitignore
index 9bec050..87bf718 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,6 +11,7 @@
__pycache__/
*.py[cod]
*$py.class
+*.egg
*.egg-info/
.eggs/
.tox/
diff --git a/LICENSE.txt b/LICENSE.txt
index 65c5ca8..11b3d94 100644
--- a/LICENSE.txt
+++ b/LICENSE.txt
@@ -1,165 +1,201 @@
- ... |
Future-House__aviary-142 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "src/aviary/core.py"
},
{
"changes": {
"added_entities": [
"src/aviary/env.py:maybe_wait_for"
],
"added_modules": [
"... | Future-House/aviary | dcb34e07f47f77b9cc78b65670200467e69f5e17 | Move `eval_answer` from `tools`
Should not live in `tools`, since it's more of an environment function | diff --git a/src/aviary/core.py b/src/aviary/core.py
index 8c3369d..587e76b 100644
--- a/src/aviary/core.py
+++ b/src/aviary/core.py
@@ -20,7 +20,6 @@ from aviary.message import EnvStateMessage, MalformedMessageError, Message, join
from aviary.render import Renderer
from aviary.tools import (
INVALID_TOOL_NAME,
... |
G-Node__nix-odML-converter-28 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nixodmlconverter/convert.py:infer_dtype",
"nixodmlconverter/convert.py:non_binary_value",
"nixodmlconverter/convert.py:odml_to_nix_property",
"nixodmlconverter/convert.py:nix_to_... | G-Node/nix-odML-converter | 8847b9ade2c8fb5949abf6bf98890e831a8d3185 | Add more test covering empty/None attributes
I noticed some irregularities when using the converter on files, which do not have entries for all attributes. E.g. the following test fails:
```python
def test_empty(self):
odml.Property(name='empty property', value=[],
parent=self.od... | diff --git a/nixodmlconverter/convert.py b/nixodmlconverter/convert.py
index 3a75a14..accb945 100644
--- a/nixodmlconverter/convert.py
+++ b/nixodmlconverter/convert.py
@@ -93,11 +93,9 @@ def user_input(prompt):
def infer_dtype(values):
"""
- PROTOTYPE
+ Tests, whether values with dtype "string" are maybe... |
G-Node__nix-odML-converter-30 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nixodmlconverter/convert.py:user_input",
"nixodmlconverter/convert.py:infer_dtype",
"nixodmlconverter/convert.py:odml_to_nix_property",
"nixodmlconverter/convert.py:nixwrite",
... | G-Node/nix-odML-converter | 738b3fac61af7aa163c937bba06d2f2981a45dde | [odml-nix-conversion] Cannot specify target NIX file
Currently content from an odML file will only be appended to a NIX file, if both files have the same filename.
It would be useful to specify a NIX file to which the content of an odML file will be appended. | diff --git a/nixodmlconverter/convert.py b/nixodmlconverter/convert.py
index accb945..60702ad 100644
--- a/nixodmlconverter/convert.py
+++ b/nixodmlconverter/convert.py
@@ -9,10 +9,10 @@ Furthermore, the converter b) exports odML content from a NIX file and saves it
to an XML formatted odML file. If an odML file of th... |
G-Node__python-odml-195 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"odml/section.py:BaseSection.__init__"
],
"edited_modules": [
"odml/section.py:BaseSection"
]
},
"file": "odml/section.py"
},
{
"changes": {
"added_entitie... | G-Node/python-odml | e618e125963abd2bd214274861ae7636f3fdfae5 | fileio/odmlparser error when loading JSON or YAML
When loading a JSON odML file via `fileio.py` the following error occurs:
odml.load('f.json', 'json')
... odmlparser.py#246 : AttributeError: 'str' object has no attribute 'close'
When loading a YAML odML file via `fileio.py` the following error occurs:... | diff --git a/odml/section.py b/odml/section.py
index 407bf31..2086b0b 100644
--- a/odml/section.py
+++ b/odml/section.py
@@ -26,13 +26,16 @@ class BaseSection(base.sectionable, Section):
_format = format.Section
- def __init__(self, name, type=None, parent=None,
- definition=None, reference=... |
G-Node__python-odml-237 | [
{
"changes": {
"added_entities": [
"odml/property.py:BaseProperty._convert_value_input",
"odml/property.py:BaseProperty.__setitem__",
"odml/property.py:BaseProperty.extend",
"odml/property.py:BaseProperty.append"
],
"added_modules": null,
"edited_entities"... | G-Node/python-odml | 2830914c8b5b67290d891d89aa28df344c5cacc7 | Usage of python list as odml value circumvents dtype checks
Since we removed the odml.Value class and simply replaced it with a python `list`, this `list` provides of course methods like `append` which in turn ignores all the nice `dtype` checks we would like to have in place to keep odML values consistent.
As an ex... | diff --git a/.travis.yml b/.travis.yml
index 64226cd..ba6c228 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -25,28 +25,44 @@ matrix:
# env:
# - OSXENV=2.7
-before_install:
- - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then bash resources/install_osx_virtualenv.sh; fi
-
install:
- export PYVER=${TRAVIS_P... |
G-Node__python-odml-251 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"odml/doc.py:BaseDocument.__init__"
],
"edited_modules": [
"odml/doc.py:BaseDocument"
]
},
"file": "odml/doc.py"
},
{
"changes": {
"added_entities": null,
... | G-Node/python-odml | 8953343f0f4616c0a71087d406b5f6d4a2036748 | [dtype] Return defined default values
Currently the "get" methods in `dtype.py` return magic numbers as default values. Make them return the already defined default values instead. | diff --git a/odml/doc.py b/odml/doc.py
index 8d75f2b..ea15912 100644
--- a/odml/doc.py
+++ b/odml/doc.py
@@ -34,10 +34,13 @@ class BaseDocument(base.sectionable, Document):
print(e)
self._id = str(uuid.uuid4())
self._author = author
- self._date = date # date must be a datetim... |
G-Node__python-odml-269 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"odml/property.py:BaseProperty._convert_value_input",
"odml/property.py:BaseProperty.value",
"odml/property.py:BaseProperty.uncertainty",
"odml/property.py:BaseProperty.merge",
... | G-Node/python-odml | c16f9891c4363dfcf907fd7daa076acba4cbe5eb | Property.append returns dtype error on unset dtype
When using `Property.append` of a Property where neither value nor dtype are set, a dtype mismatch related ValueError is raised. | diff --git a/odml/property.py b/odml/property.py
index 74e31f7..894296d 100644
--- a/odml/property.py
+++ b/odml/property.py
@@ -22,9 +22,9 @@ class BaseProperty(base.baseobject, Property):
dependency=None, dependency_value=None, dtype=None,
value_origin=None, id=None):
"""
... |
G-Node__python-odml-275 | [
{
"changes": {
"added_entities": [
"odml/base.py:SmartList.__init__",
"odml/base.py:SmartList.__setitem__",
"odml/base.py:SmartList.index",
"odml/base.py:SmartList.remove"
],
"added_modules": null,
"edited_entities": [
"odml/base.py:SafeList.index"... | G-Node/python-odml | a66ecdf4c0d2ad3fbd098b72ad3d8705a43ccd3d | Property handling
Currently it is possible to add anything to the ```properties``` list of a section without any check being performed.
This way
- non ```odml.Property``` objects can be inserted into the odml structure (eg ```sec.properties[0] = 'blaa'```)
- inserted ```odml.Property``` objects are not linked pr... | diff --git a/odml/base.py b/odml/base.py
index e145c8c..3940880 100644
--- a/odml/base.py
+++ b/odml/base.py
@@ -84,34 +84,18 @@ class baseobject(_baseobj):
return id(self)
-class SafeList(list):
+class SmartList(list):
- def index(self, obj):
+ def __init__(self, content_type):
"""
- ... |
G-Node__python-odml-284 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"odml/format.py:Section"
]
},
"file": "odml/format.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entit... | G-Node/python-odml | bc4bade4c93e0d5cb3ab8c0fb427fcf3c0ed96e1 | odML Format update
Define Section `name` and `type` as well as Property `name` as required in `format.py`. | diff --git a/odml/format.py b/odml/format.py
index bae2d68..7a0a796 100644
--- a/odml/format.py
+++ b/odml/format.py
@@ -130,7 +130,7 @@ class Section(Format):
_args = {
'id': 0,
'type': 1,
- 'name': 0,
+ 'name': 1,
'definition': 0,
'reference': 0,
'link':... |
G-Node__python-odml-296 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"odml/tools/version_converter.py:VersionConverter._parse_xml",
"odml/tools/version_converter.py:VersionConverter._handle_properties"
],
"edited_modules": [
"odml/tools/version... | G-Node/python-odml | a75d1db5ddb02cf7414b17ed41ef97a80c6245fb | VersionConverter encoding problem
With Python3, the VersionConverter encounters a `ValueError: Unicode strings with encoding declaration are not supported` when the xml tag of the to be converted file contains the `encoding="UTF-8"` attribute. | diff --git a/.travis.yml b/.travis.yml
index 6c8e347..9b80df5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -15,10 +15,6 @@ matrix:
- os: linux
python: "3.6"
- - os: osx
- language: generic
- env:
- - OSXENV=3.5.0
- os: osx
language: generic
env:
diff --git a/odml/to... |
G-Node__python-odml-304 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"odml/base.py:Sectionable.clone"
],
"edited_modules": [
"odml/base.py:Sectionable"
]
},
"file": "odml/base.py"
},
{
"changes": {
"added_entities": null,
... | G-Node/python-odml | 040fe230166c642810a991d801207090fe01382a | Clone id handling
Currently the `id` of a Property, Section or a Document (and their children) remains the same if the object is cloned.
- Since these ids should be used only once in a Document, by default the id of the clone and all potentially cloned children should be set to new UUIDs.
- The id attribute has to be... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9e7f4ae..845c973 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,19 @@ XML files via lxml. See #301.
The `odmlconversion` convenience console script has been added to convert multiple
previous odML version files to the latest odML version.
+## Changes in clo... |
G-Node__python-odml-307 | [
{
"changes": {
"added_entities": [
"odml/base.py:Sectionable.create_section"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"odml/base.py:Sectionable"
]
},
"file": "odml/base.py"
},
{
"changes": {
"added_entities":... | G-Node/python-odml | 4ce2e1b0e247334d949982abc8c275da3a661320 | harmonize attribute naming with nix
Accessing properties in nixpy and odml uses different attribute names, i.e. `props` and `properties`. | diff --git a/.gitignore b/.gitignore
index 6248f48..06a20fa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,6 +6,7 @@
dist
build
eggs
+.eggs
parts
# odml files
diff --git a/odml/base.py b/odml/base.py
index 1c64e5b..4cb674a 100644
--- a/odml/base.py
+++ b/odml/base.py
@@ -615,3 +615,19 @@ class Sectionable(BaseOb... |
G-Node__python-odml-313 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"odml/base.py:Sectionable.itervalues"
],
"edited_modules": [
"odml/base.py:Sectionable"
]
},
"file": "odml/base.py"
},
{
"changes": {
"added_entities": nul... | G-Node/python-odml | 25330dfc22ccf770a203483b56a6d8f891865351 | Value attribute differently named in odml and nixpy
The `Property.value` accessor is differently named in odml (`Property.value`) and nixpy (`Property.values`).
Should we unify this to either of the attribute names? This would be a breaking change. | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 845c973..e34a19f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,26 @@ until the next release.
# Latest changes in master
+...
+
+# Version 1.4.2
+
+## Print methods
+
+`pprint` methods have been added to both `Section` and `Property`
+to print whole Section t... |
G-Node__python-odml-321 | [
{
"changes": {
"added_entities": [
"odml/doc.py:pprint"
],
"added_modules": [
"odml/doc.py:pprint"
],
"edited_entities": null,
"edited_modules": null
},
"file": "odml/doc.py"
},
{
"changes": {
"added_entities": null,
"added_modules"... | G-Node/python-odml | ed8c0feee642fa2353b62b28491ba0f91fb745e0 | Add 'Document.pprint' method
Section and Property already feature a pprint method, it would be nice to have one for Document as well. | diff --git a/odml/doc.py b/odml/doc.py
index 279a9b2..4a33cce 100644
--- a/odml/doc.py
+++ b/odml/doc.py
@@ -141,3 +141,21 @@ class BaseDocument(base.Sectionable):
return None
term = terminology.load(self.repository)
return term
+def pprint(self, indent=2, max_depth=1, max_length=80, curr... |
G-Node__python-odml-346 | [
{
"changes": {
"added_entities": [
"odml/property.py:BaseProperty.export_leaf"
],
"added_modules": null,
"edited_entities": [
"odml/property.py:BaseProperty.values"
],
"edited_modules": [
"odml/property.py:BaseProperty"
]
},
"file": "odml... | G-Node/python-odml | 3ebada59ce95a5fbc54da08a47322f0d5857a607 | Leaf export feature
During a workshop a feature request came up: leaf export.
When working with a large, deeply nested odml file, that documents a whole experiment, it might be interesting to export only the path from a single leaf in an odml tree all the way to the root and hand this reduced odml file to a collabor... | diff --git a/odml/property.py b/odml/property.py
index a120ab3..8801325 100644
--- a/odml/property.py
+++ b/odml/property.py
@@ -328,8 +328,13 @@ class BaseProperty(base.BaseObject):
self._dtype = dtypes.infer_dtype(new_value[0])
if not self._validate_values(new_value):
- raise ValueE... |
G-Node__python-odml-356 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "odml/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"odml/dtypes.py:tupl... | G-Node/python-odml | 92e5781fbd8db0b2ac490abad7ce5e0fc0ce8d84 | Error when trying to save lists of odML style tuples
Currently saving a document which contains lists of custom odML tuples will abort with an error.
The two obvious choices are to:
- disallow lists of tuples on assignment.
- support saving and loading of odML style tuple lists.
| diff --git a/MANIFEST.in b/MANIFEST.in
index 610ff1b..070d3b5 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,5 +1,4 @@
-include LICENSE
-include README.rst
+include LICENSE README.md CHANGELOG.md
include odml/info.json
-include odml/resources/section_subclasses.yaml
-include odml/resources/odml-ontology.ttl
+recursi... |
G-Node__python-odml-372 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"odml/property.py:BaseProperty.extend",
"odml/property.py:BaseProperty.append"
],
"edited_modules": [
"odml/property.py:BaseProperty"
]
},
"file": "odml/property... | G-Node/python-odml | 7e9299e3a35f05fa87abe83c25715ead698fccda | [Property] Exception on x-tuple Property extend or append
When trying to append or extend an x-tuple Property value, a ValueError occurs.
e.g.
```
prop = odml.Property(name="tuple-test")
prop.dtype = "3-tuple"
prop.values = "(7; 8; 9)"
prop.values = ["(1; 2; 3)", "(4; 5; 6)"] # reassignment works
prop.... | diff --git a/odml/property.py b/odml/property.py
index 761375d..6c5caf0 100644
--- a/odml/property.py
+++ b/odml/property.py
@@ -688,7 +688,8 @@ class BaseProperty(base.BaseObject):
dtypes.infer_dtype(new_value[0]) != self.dtype:
type_check = dtypes.infer_dtype(new_value[0])
- ... |
G-Node__python-odml-375 | [
{
"changes": {
"added_entities": [
"odml/terminology.py:Terminologies.refresh"
],
"added_modules": null,
"edited_entities": [
"odml/terminology.py:cache_load",
"odml/terminology.py:Terminologies._load"
],
"edited_modules": [
"odml/terminology.p... | G-Node/python-odml | 01fb08abb62e8ab4fd4b0390e280e05ec150cc4c | [1.4] Terminology cache cannot be refreshed
Currently the Terminology cache cannot be refreshed. | diff --git a/odml/terminology.py b/odml/terminology.py
index 2076fa2..35d2140 100644
--- a/odml/terminology.py
+++ b/odml/terminology.py
@@ -24,12 +24,13 @@ REPOSITORY = '/'.join([REPOSITORY_BASE, 'v1.1', 'terminologies.xml'])
CACHE_AGE = datetime.timedelta(days=1)
-def cache_load(url):
+def cache_load(url, replac... |
G-Node__python-odml-393 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"odml/property.py:odml_tuple_import",
"odml/property.py:BaseProperty.extend",
"odml/property.py:BaseProperty.append"
],
"edited_modules": [
"odml/property.py:odml_tupl... | G-Node/python-odml | 441432bbf7368fa2a2ccac0348ce8b221266d2d2 | List-Style Tuple Integration
As the editor sends tuples in a list and this might be useful for some users, processing of tuples given in such a format would be helpful. | diff --git a/odml/property.py b/odml/property.py
index 4526045..e708422 100644
--- a/odml/property.py
+++ b/odml/property.py
@@ -34,19 +34,39 @@ def odml_tuple_import(t_count, new_value):
except NameError:
unicode = str
- if len(new_value) != 1 and not isinstance(new_value[0], unicode):
- retu... |
GAA-UAM__scikit-fda-142 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"skfda/representation/_functional_data.py:FData.plot",
"skfda/representation/_functional_data.py:FData._from_sequence",
"skfda/representation/_functional_data.py:FData._from_factorized",
... | GAA-UAM/scikit-fda | 2e5f88a3ba9c97696fabcf44b86579d879a851d3 | Problem with pandas methods
After update the neighbors brach (#112), I have an error on this line:
https://github.com/GAA-UAM/scikit-fda/blob/91d96eceee49400962515b8b10ee21d842fdc97f/examples/plot_k_neighbors_classification.py#L61
> Traceback (most recent call last):
File "plot_k_neighbors_classification.py", ... | diff --git a/skfda/representation/_functional_data.py b/skfda/representation/_functional_data.py
index a1458587..e423b205 100644
--- a/skfda/representation/_functional_data.py
+++ b/skfda/representation/_functional_data.py
@@ -6,16 +6,15 @@ objects of the package and contains some commons methods.
from abc import AB... |
GAA-UAM__scikit-fda-161 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/plot_k_neighbors_classification.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": nul... | GAA-UAM/scikit-fda | d7a522d4763566d50809a2f9cfaa7ea5725af7bb | Unify scalar and functional regressors
I was mentioned in a meeting that it makes no sense to differentiate between scalar and functional regressors. First, because there are not scalar, but multivariate, and second, because there is no confusion: the output of `predict` depends on the input to `fit`.
I forgot to m... | diff --git a/docs/modules/ml/classification.rst b/docs/modules/ml/classification.rst
index fb4e15f3..9524a4ae 100644
--- a/docs/modules/ml/classification.rst
+++ b/docs/modules/ml/classification.rst
@@ -11,10 +11,9 @@ Nearest Neighbors
This module contains `nearest neighbors
<https://en.wikipedia.org/wiki/K-nearest... |
GAA-UAM__scikit-fda-197 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/plot_oneway.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_mod... | GAA-UAM/scikit-fda | 6727106eca0f51d1fd8142495e1c722adf50f2dc | Concatenate function for FData objects of the same type
In this moment to concatenate `FData` objects it is necessary to call the `concatenate()` method. For example, let `fd_list`be a list of `FDataGrid` objects. To get the concatenation of the items in the list is necessary to execute:
```python
fd_c = fd_list[0].c... | diff --git a/.gitignore b/.gitignore
index 741aff5c..53f5bcc2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -107,3 +107,6 @@ ENV/
.idea/
pip-wheel-metadata/
+
+# macOS DS_Store
+.DS_Store
diff --git a/examples/plot_oneway.py b/examples/plot_oneway.py
index 40ca6e47..06d8b68b 100644
--- a/examples/plot_oneway.py
+++ b... |
GAA-UAM__scikit-fda-214 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/plot_composition.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edite... | GAA-UAM/scikit-fda | c3c24faf4d6fa912bba3f392c7b71488bab20ffc | Rename interpolator to interpolation, or extrapolation to extrapolator
The naming should be consistent between these properties. | diff --git a/docs/modules/representation.rst b/docs/modules/representation.rst
index f5c8719a..50d25b35 100644
--- a/docs/modules/representation.rst
+++ b/docs/modules/representation.rst
@@ -30,7 +30,7 @@ following class allows interpolation with different splines.
.. autosummary::
:toctree: autosummary
- skfd... |
GEOS-ESM__mepo-338 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/mepo/cmdline/parser.py:MepoArgParser.__status",
"src/mepo/cmdline/parser.py:MepoArgParser.__restore_state"
],
"edited_modules": [
"src/mepo/cmdline/parser.py:MepoArgParse... | GEOS-ESM/mepo | 6cf68b53bbd86e1c0ca3d1b2d60a48615e6c5516 | Move to mepo status as serial by default
As described in #336, the parallel/starmap path of `mepo status` seems to cause fork-bomb-like behavior at NAS. Indeed, I believe @pchakraborty also saw similar issues on an Intel Mac. This led him to add the `--serial` flag to `mepo status` for this case.
Since both v1 and v... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index a1c2a00..6831467 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,21 +13,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed
+- Moved `mepo status` and `mepo restore-state` to default to their serial variants rather th... |
GIScience__openrouteservice-py-17 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openrouteservice/isochrones.py:isochrones"
],
"edited_modules": [
"openrouteservice/isochrones.py:isochrones"
]
},
"file": "openrouteservice/isochrones.py"
}
] | GIScience/openrouteservice-py | 0d3a56f242f668429f91f87dc9b4e7baf4fc581c | Implement smoothing parameter for isochrone endpoint | diff --git a/openrouteservice/isochrones.py b/openrouteservice/isochrones.py
index 5e6850c..14a8d73 100644
--- a/openrouteservice/isochrones.py
+++ b/openrouteservice/isochrones.py
@@ -20,16 +20,17 @@ from openrouteservice import convert
def isochrones(client, locations,
- profile='driving-car',... |
GIScience__openrouteservice-py-31 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "openrouteservice/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openrou... | GIScience/openrouteservice-py | a93c3ac62f31de39e92901598e779dde5ad7a306 | 'Country' restriction has wrong parameter
`boundary.country` instead of `country` for `/search` and `/reverse`, `/autocomplete` is fine. | diff --git a/openrouteservice/__init__.py b/openrouteservice/__init__.py
index 6f697ff..d88a857 100644
--- a/openrouteservice/__init__.py
+++ b/openrouteservice/__init__.py
@@ -17,7 +17,7 @@
# the License.
#
-__version__ = "1.1.6"
+__version__ = "1.1.7"
# Make sure QGIS plugin can import openrouteservice-py
di... |
GIScience__openrouteservice-py-67 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openrouteservice/client.py:Client._get_body"
],
"edited_modules": [
"openrouteservice/client.py:Client"
]
},
"file": "openrouteservice/client.py"
}
] | GIScience/openrouteservice-py | ed5e5cd8ec406fad05381bf7bda64a77ce4bfe89 | JSONDecodeError when requesting directions in gpx format
<!-- If you have a question rather than an actual issue, pls use our forum:-->
<!-- https://ask.openrouteservice.org/c/sdks-->
#### Here's what I did
<!-- best paste the results of 'dry_run' (see README.md), so we can see your configuration -->
```coord... | diff --git a/openrouteservice/client.py b/openrouteservice/client.py
index ea763c4..3711d80 100644
--- a/openrouteservice/client.py
+++ b/openrouteservice/client.py
@@ -20,6 +20,7 @@
from datetime import datetime
from datetime import timedelta
+import cgi
import functools
import requests
import json
@@ -257,10 +... |
GSTT-CSC__hazen-204 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hazenlib/relaxometry.py:t2_function",
"hazenlib/relaxometry.py:t2_jacobian",
"hazenlib/relaxometry.py:T2ImageStack.__init__",
"hazenlib/relaxometry.py:T2ImageStack.initialise_fit... | GSTT-CSC/hazen | 7f10989301a976630e171bb5b552ed7cff4870ca | [HZN-105] Fit T2 relaxometry model with Rician PDF
Transferred by @LaurenceJackson on Apr 23, 2021, 16:56
:::Issue recreated from Jira issue [HZN-105](https://gsttmri.atlassian.net/browse/HZN-105):::
The current relaxometry method assumes Gaussian noise distribution. For magnitude images a Rician distribution is a b... | diff --git a/hazenlib/relaxometry.py b/hazenlib/relaxometry.py
index 71b9236..3ec4948 100644
--- a/hazenlib/relaxometry.py
+++ b/hazenlib/relaxometry.py
@@ -93,14 +93,19 @@ Algorithm overview
measurements.
6. Determine relaxation time (T1 or T2) by fitting the decay equation to
the ROI data for each sphere. ... |
GSTT-CSC__hazen-363 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hazenlib/__init__.py:main"
],
"edited_modules": [
"hazenlib/__init__.py:main"
]
},
"file": "hazenlib/__init__.py"
},
{
"changes": {
"added_entities": null... | GSTT-CSC/hazen | 5d9e4d747ccd1c908ac5cc0bfbbdb60c470e9bfb | Improve displaying results on terminal
PrettyPrinter could be replaced with `json.dumps()` that can format and display the result dictionary in a simple structured way with less configuration needed.
currently with PrettyPrint: (more compact)
<img width="759" alt="Screenshot 2023-07-15 at 18 27 16" src="https://git... | diff --git a/hazenlib/__init__.py b/hazenlib/__init__.py
index dafcf1a..309c585 100644
--- a/hazenlib/__init__.py
+++ b/hazenlib/__init__.py
@@ -112,7 +112,7 @@ import importlib
import inspect
import logging
import sys
-import pprint
+import json
import os
from docopt import docopt
@@ -156,7 +156,6 @@ def init_t... |
Galarzaa90__tibia.py-17 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "tibiapy/__init__.py"
},
{
"changes": {
"added_entities": [
"tibiapy/character.py:AccountBadge.__init__",
"tibiapy/character.py:A... | Galarzaa90/tibia.py | 7ebadf48e6d6869f9c799e72a8b9a26a2f6d08f5 | Parse character titles and main character information
Summer update 2019 introduced character titles, as well as a small icon that indicates which is the main character of the account in the other characters section. | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index a2f4d71..26d19fd 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -6,6 +6,14 @@ Changelog
Due to this library relying on external content, older versions are not guaranteed to work.
Try to always use the latest version.
+
+.. _v2.2.0:
+
+2.2.0 (2019-08-08)
+... |
Galarzaa90__tibia.py-27 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "tibiapy/__init__.py"
},
{
"changes": {
"added_entities": [
"tibiapy/bazaar.py:DisplayFamiliar.__init__",
"tibiapy/bazaar.py:Disp... | Galarzaa90/tibia.py | 509b7fe7672799f9e60342e7d5e7e33347706636 | DisplayItems attribute name is returning None
I was querying the items of a character at the bazaar and the DisplayItem attribute name is returning None
Here is my code snippet:
```
response : TibiaResponse = self.client.loop.run_until_complete(self.client.fetch_auction(character_auction_id,
fetch_item... | diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 630022b..4b968f8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,17 +1,14 @@
-image: python:3.6
+image: python:3.8
variables:
PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
SONAR_USER_HOME: "${CI_PROJECT_DIR}/.sonar" # Defines the location of the analysis... |
Galarzaa90__tibia.py-39 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tibiapy/urls.py:get_highscores_url"
],
"edited_modules": [
"tibiapy/urls.py:get_highscores_url"
]
},
"file": "tibiapy/urls.py"
}
] | Galarzaa90/tibia.py | c95c4094f3eefb0754c368b19069aeacf18d2c2e | get_highscores_url does not work as documented and breaks when no vocation is sent
Sending no vocation will default it to None.
But method's documentation says it would just consider all vocations instead
`{AttributeError}'NoneType' object has no attribute 'value'` is thrown
![image](https://github.com/Galarzaa9... | diff --git a/tibiapy/urls.py b/tibiapy/urls.py
index fd5d1e0..b0e0582 100644
--- a/tibiapy/urls.py
+++ b/tibiapy/urls.py
@@ -414,9 +414,13 @@ def get_highscores_url(
"""
pvp_types = pvp_types or []
pvp_params = [("worldtypes[]", p.value) for p in pvp_types]
- return get_tibia_url("community", "highsco... |
GazzolaLab__PyElastica-249 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "elastica/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"elastica/restar... | GazzolaLab/PyElastica | b271ad41fbeaa78fbd03887573b9a364c949ef5b | Possible Bug: Test restart functionality and applying constrains
We should test the below line in the restart code. We suspect it creates incorrect results, when we load and time-step.
https://github.com/GazzolaLab/PyElastica/blob/7b3fe2d0204a175c9e5e64265c70b9577b4ca8c9/elastica/restart.py#L92-L93 | diff --git a/elastica/__init__.py b/elastica/__init__.py
index 7622bf2..f60bc90 100644
--- a/elastica/__init__.py
+++ b/elastica/__init__.py
@@ -71,3 +71,4 @@ from elastica.timestepper import (
)
from elastica.memory_block.memory_block_rigid_body import MemoryBlockRigidBody
from elastica.memory_block.memory_block_ro... |
GazzolaLab__PyElastica-47 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"elastica/timestepper/symplectic_steppers.py:_SystemCollectionStepper.do_step"
],
"edited_modules": [
"elastica/timestepper/symplectic_steppers.py:_SystemCollectionStepper"
]
... | GazzolaLab/PyElastica | 0bcbb4427160a2e2404f795119ed61871424d21e | Current-step passed to callback is determined by floating point division.
<a href="https://github.com/skim0119"><img src="https://avatars.githubusercontent.com/u/3798023?v=4" align="left" width="96" height="96" hspace="10"></img></a> **Issue by [skim0119](https://github.com/skim0119)**
_Friday Dec 31, 2021 at 21:31 GM... | diff --git a/elastica/timestepper/symplectic_steppers.py b/elastica/timestepper/symplectic_steppers.py
index c268abe..b87483b 100644
--- a/elastica/timestepper/symplectic_steppers.py
+++ b/elastica/timestepper/symplectic_steppers.py
@@ -1,6 +1,7 @@
__doc__ = """Symplectic time steppers and concepts for integrating the... |
GeneralMills__pytrends-518 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pytrends/request.py:TrendReq.trending_searches",
"pytrends/request.py:TrendReq.today_searches",
"pytrends/request.py:TrendReq.top_charts",
"pytrends/request.py:TrendReq.suggestio... | GeneralMills/pytrends | 0e887b8510c3023fb57796cb253fef03d688b2f7 | Bug on "suggestions" when "requests_args" is not empty
If requests_args is not empty, then in line 453 of the requests.py, the "self.requests_args" is included as kwargs and line 126 of the _get_data method includes it again. So it causes an error. | diff --git a/pytrends/request.py b/pytrends/request.py
index 446cf41..4644102 100644
--- a/pytrends/request.py
+++ b/pytrends/request.py
@@ -428,8 +428,7 @@ class TrendReq(object):
# forms = {'ajax': 1, 'pn': pn, 'htd': '', 'htv': 'l'}
req_json = self._get_data(
url=TrendReq.TRENDING_SEAR... |
GenericMappingTools__pygmt-1258 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/gallery/3d_plots/scatter3d.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | GenericMappingTools/pygmt | 53b4e7416989e76be4ae2b19d352b076c4dd4fa1 | Rename the sizes parameter in plot/plot3d to be size
**Description of the problem**
Both [plot](https://www.pygmt.org/latest/api/generated/pygmt.Figure.plot.html#pygmt.Figure.plot) and [plot3d](https://www.pygmt.org/latest/api/generated/pygmt.Figure.plot3d.html#pygmt.Figure.plot3d) have the `sizes` parameter that ar... | diff --git a/examples/gallery/3d_plots/scatter3d.py b/examples/gallery/3d_plots/scatter3d.py
index 568c2de7..0c70581f 100644
--- a/examples/gallery/3d_plots/scatter3d.py
+++ b/examples/gallery/3d_plots/scatter3d.py
@@ -47,7 +47,7 @@ fig.plot3d(
y=df.sepal_length,
z=df.petal_length,
# Vary each symbol siz... |
GenericMappingTools__pygmt-1307 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/figure.py:Figure.savefig"
],
"edited_modules": [
"pygmt/figure.py:Figure"
]
},
"file": "pygmt/figure.py"
}
] | GenericMappingTools/pygmt | ec73ea42428da74fca505cf6c14e71c5c667a6f3 | Figure.savefig should support postscript format
**Description of the problem**
Screen Errors when I try a fig.savefig when using filenames with a ".ps" extension ; same savefig works fine with 'eps' extension or 'png' extension
**Full code that generated the error**
```python
#!/usr/bin/python3
import p... | diff --git a/pygmt/figure.py b/pygmt/figure.py
index e2b9089c..043f5617 100644
--- a/pygmt/figure.py
+++ b/pygmt/figure.py
@@ -237,12 +237,17 @@ class Figure:
prefix, ext = os.path.splitext(fname)
ext = ext[1:] # Remove the .
if ext not in fmts:
- raise GMTInvalidInput("Unknown ex... |
GenericMappingTools__pygmt-1329 | [
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"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/clib/session.py:Session.virtualfile_from_data"
],
"edited_modules": [
"pygmt/clib/session.py:Session"
]
},
"file": "pygmt/clib/session.py"
}
] | GenericMappingTools/pygmt | 7f37e1ca5b14a4064447304a5bf3936489cf933f | Histogram doesn't work for pandas.Series
**Description of the problem**
<!-- Please be as detailed as you can when describing an issue. The more information we have, the easier it will be for us to track this down. -->
**Full code that generated the error**
```python
import pygmt
import pandas as pd
import ... | diff --git a/pygmt/clib/session.py b/pygmt/clib/session.py
index 8172dbdb..89026a71 100644
--- a/pygmt/clib/session.py
+++ b/pygmt/clib/session.py
@@ -1449,9 +1449,11 @@ class Session:
_data.extend(extra_arrays)
elif kind == "matrix": # turn 2D arrays into list of vectors
try:
+ ... |
GenericMappingTools__pygmt-1382 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/clib/session.py:Session.virtualfile_from_data"
],
"edited_modules": [
"pygmt/clib/session.py:Session"
]
},
"file": "pygmt/clib/session.py"
},
{
"changes":... | GenericMappingTools/pygmt | b69fd0c36d872a57a3a9ca14232e366193e96fb7 | Support passing in pathlib.Path into pygmt modules
**Description of the desired feature**
_Originally posted by @liamtoney in https://github.com/GenericMappingTools/pygmt/issues/949#issuecomment-790796932_
> I'd add `Path` objects if they're not already supported. :)
The [`pathlib.Path`](https://docs.python.or... | diff --git a/pygmt/clib/session.py b/pygmt/clib/session.py
index 89026a71..a775a119 100644
--- a/pygmt/clib/session.py
+++ b/pygmt/clib/session.py
@@ -1376,9 +1376,10 @@ class Session:
check_kind : str
Used to validate the type of data that can be passed in. Choose
from 'raster', 'vec... |
GenericMappingTools__pygmt-1458 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/src/surface.py:surface"
],
"edited_modules": [
"pygmt/src/surface.py:surface"
]
},
"file": "pygmt/src/surface.py"
}
] | GenericMappingTools/pygmt | 2e74fa117e9cbd8f830b9120041b6766b041c008 | Rename outfile parameter in surface to be outgrid
**Description of the desired feature**
As mentioned at https://github.com/GenericMappingTools/pygmt/pull/1439#discussion_r687251597, most PyGMT functions which return a grid output have a parameter called `outgrid`, but the `surface` function uses `outfile`. It would... | diff --git a/pygmt/src/surface.py b/pygmt/src/surface.py
index 1d24a438..857f8602 100644
--- a/pygmt/src/surface.py
+++ b/pygmt/src/surface.py
@@ -9,6 +9,7 @@ from pygmt.helpers import (
GMTTempFile,
build_arg_string,
data_kind,
+ deprecate_parameter,
dummy_context,
fmt_docstring,
kwarg... |
GenericMappingTools__pygmt-1478 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/clib/session.py:Session.virtualfile_from_data"
],
"edited_modules": [
"pygmt/clib/session.py:Session"
]
},
"file": "pygmt/clib/session.py"
},
{
"changes":... | GenericMappingTools/pygmt | a99533ff30cffaaf5b6da84244ba5d773276c256 | Raise a GMTInvalidInput exception for only x,y input to blockmedian and blockmean
**Description of the desired feature**
Currently, no exception is raised in the `blockmedian` and `blockmean` functions if the `x` and `y` parameters are used but not the `z` parameter. This should be disallowed because these functions... | diff --git a/pygmt/clib/session.py b/pygmt/clib/session.py
index a775a119..39977287 100644
--- a/pygmt/clib/session.py
+++ b/pygmt/clib/session.py
@@ -1362,7 +1362,14 @@ class Session:
@fmt_docstring
def virtualfile_from_data(
- self, check_kind=None, data=None, x=None, y=None, z=None, extra_arrays=N... |
GenericMappingTools__pygmt-1484 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/clib/conversion.py:dataarray_to_matrix"
],
"edited_modules": [
"pygmt/clib/conversion.py:dataarray_to_matrix"
]
},
"file": "pygmt/clib/conversion.py"
}
] | GenericMappingTools/pygmt | 4163497b9a12bcfc35b337ced20dde9afae10ce7 | Segmentation fault if a grid has zero increments
`grdimage` throwing a segmentation fault insted of some proper error when mistakenly swapping `xarray` y and x coordination.
**Full code that generated the error**
```python
X, Y = np.meshgrid(np.arange(10), np.arange(10))
Z = X ** 2 + Y ** 2
da = xr.DataAr... | diff --git a/pygmt/clib/conversion.py b/pygmt/clib/conversion.py
index 24c6c447..57b2f92c 100644
--- a/pygmt/clib/conversion.py
+++ b/pygmt/clib/conversion.py
@@ -82,7 +82,7 @@ def dataarray_to_matrix(grid):
"""
if len(grid.dims) != 2:
raise GMTInvalidInput(
- "Invalid number of grid dimen... |
GenericMappingTools__pygmt-1530 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/clib/conversion.py:dataarray_to_matrix"
],
"edited_modules": [
"pygmt/clib/conversion.py:dataarray_to_matrix"
]
},
"file": "pygmt/clib/conversion.py"
}
] | GenericMappingTools/pygmt | 6aba9aea0484b1c9038a3ee63c3360d596401acb | PyGMT is too strict when checking for irregular grids
**Description of the problem**
<!-- Please be as detailed as you can when describing an issue. The more information we have, the easier it will be for us to track this down. -->
Since GMT only supports regular grids, PyGMT has a check to make sure all point sp... | diff --git a/pygmt/clib/conversion.py b/pygmt/clib/conversion.py
index 57b2f92c..7c94b788 100644
--- a/pygmt/clib/conversion.py
+++ b/pygmt/clib/conversion.py
@@ -1,6 +1,8 @@
"""
Functions to convert data types into ctypes friendly formats.
"""
+import warnings
+
import numpy as np
import pandas as pd
from pygmt.... |
GenericMappingTools__pygmt-1565 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/clib/conversion.py:dataarray_to_matrix"
],
"edited_modules": [
"pygmt/clib/conversion.py:dataarray_to_matrix"
]
},
"file": "pygmt/clib/conversion.py"
},
{
... | GenericMappingTools/pygmt | 6aba9aea0484b1c9038a3ee63c3360d596401acb | Standardize parameter name for table data inputs
**Description of the desired feature**
_Originally posted by @meghanrjones in https://github.com/GenericMappingTools/pygmt/issues/1441#issuecomment-901303058_
> This is somewhat related - I am not sure if it's worth a deprecation but I think we should decide on whe... | diff --git a/pygmt/clib/conversion.py b/pygmt/clib/conversion.py
index 57b2f92c..7c94b788 100644
--- a/pygmt/clib/conversion.py
+++ b/pygmt/clib/conversion.py
@@ -1,6 +1,8 @@
"""
Functions to convert data types into ctypes friendly formats.
"""
+import warnings
+
import numpy as np
import pandas as pd
from pygmt.... |
GenericMappingTools__pygmt-1857 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/src/grd2cpt.py:grd2cpt"
],
"edited_modules": [
"pygmt/src/grd2cpt.py:grd2cpt"
]
},
"file": "pygmt/src/grd2cpt.py"
},
{
"changes": {
"added_entities"... | GenericMappingTools/pygmt | 61781e433986d02825c7d553bd7b9bced9de3c76 | Figure.grdimage does not respect shading=None
**Description of the problem**
Figure.grdimage() crashes when specifying the option `shading=None`. According to the docstring, `shading=None` is the default value, so this is weird. For the script I am using, I need to always specify something for shading (either nothin... | diff --git a/pygmt/src/grd2cpt.py b/pygmt/src/grd2cpt.py
index 3c20e8c8..13d45b90 100644
--- a/pygmt/src/grd2cpt.py
+++ b/pygmt/src/grd2cpt.py
@@ -160,14 +160,14 @@ def grd2cpt(grid, **kwargs):
``categorical=True``.
{V}
"""
- if "W" in kwargs and "Ww" in kwargs:
+ if kwargs.get("W") is not None... |
GenericMappingTools__pygmt-1934 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "doc/conf.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
... | GenericMappingTools/pygmt | 8ddd11ce7314e1dba34fbfa428204b54e6fd15c3 | Suggestion for improvement of gallery examples regarding categorical colormaps
In two gallery examples categorical data (without order) is displayed by using color-coding for the categories:
- [Color points by categories](https://www.pygmt.org/dev/gallery/symbols/points_categorical.html#sphx-glr-gallery-symbols-points... | diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml
index 697b6b57..0a886cc5 100644
--- a/.github/workflows/check-links.yml
+++ b/.github/workflows/check-links.yml
@@ -26,7 +26,7 @@ jobs:
path: documentation
- name: Link Checker
- uses: lycheeverse/lychee-action@v1.4.... |
GenericMappingTools__pygmt-1963 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "pygmt/clib/session.py"
}
] | GenericMappingTools/pygmt | 1067fa316b214d470f26f4affba743a4835a53c8 | uint8 datatype issue
**Description of the problem**
I read an image of uint8 datatype with `rioxarray.open_rasterio` and plot with pygmt raise errors.
If I convert datatype to float, my script runs fluently.
**Full error message**
```
Traceback (most recent call last):
File "C:\ProgramData\Anaconda3\... | diff --git a/pygmt/clib/session.py b/pygmt/clib/session.py
index 7b48f0a0..03902233 100644
--- a/pygmt/clib/session.py
+++ b/pygmt/clib/session.py
@@ -53,14 +53,18 @@ MODES = ["GMT_CONTAINER_ONLY", "GMT_IS_OUTPUT"]
REGISTRATIONS = ["GMT_GRID_PIXEL_REG", "GMT_GRID_NODE_REG"]
DTYPES = {
- np.float64: "GMT_DOUBLE",... |
GenericMappingTools__pygmt-3326 | [
{
"changes": {
"added_entities": [
"pygmt/clib/session.py:Session.virtualfile_from_stringio"
],
"added_modules": null,
"edited_entities": [
"pygmt/clib/session.py:Session.create_data",
"pygmt/clib/session.py:Session.virtualfile_in"
],
"edited_modules":... | GenericMappingTools/pygmt | a592ade71244ec839f4350be7e431db9fdd15896 | Allow Figure.legend to read from StringIO
I need to display a legend of symbols for the magnitude of earthquakes. Currently the legend specification must be a file on disk. The Pythonic implementation should allow **Figure.legend(spec=**_<buffer|file>_**,...)**. My preference is to write the legend specification to io.... | diff --git a/doc/api/index.rst b/doc/api/index.rst
index cff460ce..1c80d8d1 100644
--- a/doc/api/index.rst
+++ b/doc/api/index.rst
@@ -317,5 +317,6 @@ Low level access (these are mostly used by the :mod:`pygmt.clib` package):
clib.Session.get_libgmt_func
clib.Session.virtualfile_from_data
clib.Session.vi... |
GenericMappingTools__pygmt-3418 | [
{
"changes": {
"added_entities": [
"pygmt/figure.py:_get_default_display_method"
],
"added_modules": [
"pygmt/figure.py:_get_default_display_method"
],
"edited_entities": null,
"edited_modules": null
},
"file": "pygmt/figure.py"
}
] | GenericMappingTools/pygmt | 2157333f4ed9341c592bb6d22d9e710f3216db0c | The dynamically generated images are not shown in the documentation
In https://github.com/GenericMappingTools/pygmt/pull/3379, we enabled the `myst-nb` extension to generate images dynamically from codes in Markdown files.
In the RTD preview (https://pygmt-dev--3379.org.readthedocs.build/en/3379/install.html#testing... | diff --git a/pygmt/figure.py b/pygmt/figure.py
index 0509e765..05cba50e 100644
--- a/pygmt/figure.py
+++ b/pygmt/figure.py
@@ -6,6 +6,7 @@ import base64
import os
from pathlib import Path, PurePath
from tempfile import TemporaryDirectory
+from typing import Literal
try:
import IPython
@@ -26,27 +27,49 @@ fro... |
GenericMappingTools__pygmt-529 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "pygmt/__init__.py"
},
{
"changes": {
"added_entities": [
"pygmt/figure.py:set_display"
],
"added_modules": [
"pygmt/... | GenericMappingTools/pygmt | 9c6a0f620b0ee58703b59b25707b5fc34a2108ce | Rethink the display mechanisms
**Description of the desired feature**
Currently, there many ways of displaying a PyGMT figure:
* Calling `Figure.show()` in the notebook returns an IPython PNG display object for the jupyter notebook
* Putting the `Figure` object at the end of a notebook cell displays the figure a... | diff --git a/Makefile b/Makefile
index e5cae667..a5342aa8 100644
--- a/Makefile
+++ b/Makefile
@@ -36,7 +36,7 @@ test:
@echo ""
@cd $(TESTDIR); python -c "import $(PROJECT); $(PROJECT).show_versions()"
@echo ""
- cd $(TESTDIR); pytest $(PYTEST_COV_ARGS) $(PROJECT)
+ cd $(TESTDIR); PYGMT_USE_EXTERNAL_DISPLAY="fals... |
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