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 |
|---|---|---|---|---|---|
Materials-Consortia__optimade-python-tools-547 | [
{
"changes": {
"added_entities": [
"optimade/models/structures.py:StructureResourceAttributes.check_ordered_formula",
"optimade/models/structures.py:StructureResourceAttributes.check_anonymous_formula"
],
"added_modules": null,
"edited_entities": [
"optimade/model... | Materials-Consortia/optimade-python-tools | 6f3439900630d71f6e23400e4a2aea11d8c5eefd | Chemical formulae are not properly validated on model creation
Currently, any rubbish can be placed in the chemical formula field when creating a model as we didn't write any validators (!) for them. This is not a massive deal as its an easy thing for implementations to get right, but e.g. `chemical_formula_anonymous` ... | diff --git a/openapi/openapi.json b/openapi/openapi.json
index ad33b329..98f07741 100644
--- a/openapi/openapi.json
+++ b/openapi/openapi.json
@@ -3050,16 +3050,19 @@
},
"chemical_formula_reduced": {
"title": "Chemical Formula Reduced",
+ "pattern": "^([A-Z][a-z]?\\d*)*$",
... |
Materials-Consortia__optimade-python-tools-582 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optimade/models/structures.py:StructureResourceAttributes.check_ordered_formula",
"optimade/models/structures.py:StructureResourceAttributes.check_anonymous_formula"
],
"edited_modul... | Materials-Consortia/optimade-python-tools | e7a8de9822da1edd8a2432e8d562982e27f00255 | Hill notation validation turning around C and H
In Hill notation the first element should be carbon, then hydrogen and the every other element in alphabetical order.
Currently, we are validating formulas wrongly, by expecting first hydrogen, then carbon, and finally (as it should be) every other element in alphabeti... | diff --git a/optimade/models/structures.py b/optimade/models/structures.py
index 4203824a..e1aebb19 100644
--- a/optimade/models/structures.py
+++ b/optimade/models/structures.py
@@ -774,7 +774,8 @@ The properties of the species are found in the property `species`.
expected_elements = sorted(elements)
... |
Materials-Consortia__optimade-python-tools-586 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optimade/models/structures.py:StructureResourceAttributes.check_ordered_formula"
],
"edited_modules": [
"optimade/models/structures.py:StructureResourceAttributes"
]
},
... | Materials-Consortia/optimade-python-tools | d48b7a80e24aad591857c386498774037bbec89c | Hill notation wrong (still)
Actual definition:
- If carbon is present, place it first, then hydrogen if present.
- Following hydrogen, sort elements alphabetically.
- If carbon is _not_ present, sort elements alphabetically, also if hydrogen is present.
Example of valid Hill notation formulas:
- C H<sub>4</sub> ... | diff --git a/optimade/models/structures.py b/optimade/models/structures.py
index e1aebb19..82ad7f1c 100644
--- a/optimade/models/structures.py
+++ b/optimade/models/structures.py
@@ -774,11 +774,12 @@ The properties of the species are found in the property `species`.
expected_elements = sorted(elements)
... |
Materials-Consortia__optimade-python-tools-590 | [
{
"changes": {
"added_entities": [
"optimade/filtertransformers/mongo.py:MongoTransformer._apply_mongo_date_filter"
],
"added_modules": null,
"edited_entities": [
"optimade/filtertransformers/mongo.py:MongoTransformer.postprocess",
"optimade/filtertransformers/mon... | Materials-Consortia/optimade-python-tools | 31818d4b6254360ee1b6cc6bf967bd9c28aef9e2 | Missing support for timestamps/datetime in grammar
The grammar is currently missing support for timestamps (or `datetime.datetime` in terms of Python types).
The relevant section in the spec may be found [here](https://github.com/Materials-Consortia/OPTiMaDe/blob/develop/optimade.rst#type-handling-and-conversions-in... | diff --git a/optimade/filtertransformers/mongo.py b/optimade/filtertransformers/mongo.py
index 9b09844a..eb806e7a 100755
--- a/optimade/filtertransformers/mongo.py
+++ b/optimade/filtertransformers/mongo.py
@@ -1,7 +1,8 @@
import copy
+import warnings
from lark import v_args, Token
from optimade.filtertransformers.b... |
Materials-Consortia__optimade-python-tools-670 | [
{
"changes": {
"added_entities": [
"optimade/validator/validator.py:ImplementationValidator._test_versions_headers"
],
"added_modules": null,
"edited_entities": [
"optimade/validator/validator.py:ImplementationValidator._test_versions_endpoint",
"optimade/validato... | Materials-Consortia/optimade-python-tools | 5fb7590db87866918745a7e9a67ecd1bdd7d7314 | Misleading error message from validator on failure from '/versions'
It seems from Materials-Consortia/providers#58 that the versioned `/versions`-endpoint's headers is checked, while it's not even present, and is afterwards correctly determined to return a `404 Not Found` response.
Essentially, if a `404 Not Found` ... | diff --git a/optimade/validator/validator.py b/optimade/validator/validator.py
index f67dd00c..4403af64 100644
--- a/optimade/validator/validator.py
+++ b/optimade/validator/validator.py
@@ -926,8 +926,10 @@ class ImplementationValidator:
# First, check that there is a versions endpoint in the appropriate plac... |
Materials-Consortia__optimade-python-tools-700 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optimade/validator/validator.py:ImplementationValidator.validate_implementation"
],
"edited_modules": [
"optimade/validator/validator.py:ImplementationValidator"
]
},
"... | Materials-Consortia/optimade-python-tools | f9d3b8a8fdf5e438f2b7c746bcdefb661de9c86c | When using `--as-type` in validator, one does not get a summary (`--json` doesn't work)
It's an issue that using `--as-type` for the validator doesn't properly print the summary, which would ensure the `--json` option can be used. | diff --git a/optimade/validator/validator.py b/optimade/validator/validator.py
index 959297e2..ff974674 100644
--- a/optimade/validator/validator.py
+++ b/optimade/validator/validator.py
@@ -252,6 +252,7 @@ class ImplementationValidator:
)
self._test_as_type()
self.valid = not boo... |
Materials-Consortia__optimade-python-tools-740 | [
{
"changes": {
"added_entities": [
"optimade/server/config.py:config_file_settings"
],
"added_modules": [
"optimade/server/config.py:config_file_settings"
],
"edited_entities": [
"optimade/server/config.py:ServerConfig.use_real_mongo_override",
"opti... | Materials-Consortia/optimade-python-tools | 216ee8177bf22cea6c3fad8e325c9ef2dc0b3367 | Custom configuration extensions & use standard pydantic way of loading config file
It would be nice to be able to extend the configuration class with custom configuration options, but this is currently not allowed (`extra` attribute in embedded `Config` class).
Furthermore, [pydantic](https://pydantic-docs.helpmanua... | diff --git a/.github/workflows/deps_lint.yml b/.github/workflows/deps_lint.yml
index ade14fc5..1f789fc0 100644
--- a/.github/workflows/deps_lint.yml
+++ b/.github/workflows/deps_lint.yml
@@ -204,6 +204,9 @@ jobs:
run: |
pip install -r requirements-client.txt
# AiiDA-specific
+ # sqlalche... |
Materials-Consortia__optimade-python-tools-796 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optimade/filtertransformers/elasticsearch.py:ElasticTransformer._query_op"
],
"edited_modules": [
"optimade/filtertransformers/elasticsearch.py:ElasticTransformer"
]
},
... | Materials-Consortia/optimade-python-tools | 44593e112de425d014b651e66dd7b9a156ec70e0 | Verify that missing values are not returned in comparisons
> (MongoDB's NOT will also return documents with missing values which is not allowed accoording the OPTMIADE standard. An alternative would be to add an extra expression to check wether a certain entry is present in a Document.
This is a good point that we m... | diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 52864936..af9d90a4 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -1,3 +1,3 @@
-* @CasperWA @ml-evs
-*mongo* @ml-evs @shyamd
-*elastic* @ml-evs @markus1978
+* @CasperWA @ml-evs @JPBergsma
+*mongo* @CasperWA @JPBergsma @ml-evs @shyamd
+*elastic* @Ca... |
Materials-Consortia__optimade-python-tools-797 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "optimade/filtertransformers/__init__.py"
},
{
"changes": {
"added_entities": [
"optimade/filtertransformers/base_transformer.py:Quantity... | Materials-Consortia/optimade-python-tools | 0f11919a7293c8370f77ad29f4a0a54f9b7661a4 | Missing optional fields are not returned as null when requested with response_fields
According to the specification, if an optional field is asked for using the `response_fields` query parameter, it must be returned as `null` if missing from the document. We currently don't do this (see e.g. `immutable_id` in the test ... | diff --git a/.github/workflows/deps_lint.yml b/.github/workflows/deps_lint.yml
index 67ae8818..342f3417 100644
--- a/.github/workflows/deps_lint.yml
+++ b/.github/workflows/deps_lint.yml
@@ -276,7 +276,7 @@ jobs:
- name: Build
run: |
invoke create-api-reference-docs
- mkdocs build --strict -... |
Materials-Consortia__optimade-python-tools-813 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optimade/filterparser/lark_parser.py:get_versions",
"optimade/filterparser/lark_parser.py:LarkParser.__init__",
"optimade/filterparser/lark_parser.py:LarkParser.parse"
],
"ed... | Materials-Consortia/optimade-python-tools | ce8b4ddd1dbdf2a11ab2d8f2457eb2cac6624009 | ParserError's should not return 500 HTTP status codes
When the Lark parser is unable to parse a filter in an unhandled way, we throw a `ParserError`, which inherits directly from `Exception` and thus the server treats it as a 500 Server Error.
Instead this should raise a 400 Bad Request and return the Lark error mes... | diff --git a/optimade/filterparser/lark_parser.py b/optimade/filterparser/lark_parser.py
index 9a6a5cd1..f1200ed0 100644
--- a/optimade/filterparser/lark_parser.py
+++ b/optimade/filterparser/lark_parser.py
@@ -1,13 +1,35 @@
+"""This submodule implements the [`LarkParser`][optimade.filterparser.LarkParser] class,
+whic... |
Materials-Consortia__optimade-python-tools-814 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optimade/filtertransformers/mongo.py:MongoTransformer._recursive_expression_phrase"
],
"edited_modules": [
"optimade/filtertransformers/mongo.py:MongoTransformer"
]
},
... | Materials-Consortia/optimade-python-tools | 00cb4e6872735e244123bef4acc74193118cf720 | NOT filter operation of mongo query for complex expressions
This implementation of [NOT operation](https://docs.mongodb.com/manual/reference/operator/query/not/) fails in the case when it has been applied for a "complex" expression. Here are some example for the inputs and outputs of a `Transformer`:
```
"NOT a>1" -... | diff --git a/INSTALL.md b/INSTALL.md
index 3097d25c..1e9060b9 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -38,6 +38,9 @@ conda activate optimade
# Install package and dependencies in editable mode (including "dev" requirements).
pip install -e ".[dev]"
+# Optional: Retrieve the list of OPTIMADE providers. (Without ... |
Materials-Consortia__optimade-python-tools-83 | [
{
"changes": {
"added_entities": [
"optimade/models/jsonapi.py:Relationships.check_illegal_relationships_fields",
"optimade/models/jsonapi.py:Attributes.check_illegal_attributes_fields"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"... | Materials-Consortia/optimade-python-tools | 7aa23880f41492f21f2eb2b6379cf78d807f60a3 | server.jsonapi has no patternProperties
In the current version of pydanitc patternProperties can only be added inside sub-elements of properties. If that is fixed then remove items from optimade.server.models.jsonapi.Attributes and optimade.server.models.jsonapi.Realationships and make it match that new formalism.
... | diff --git a/optimade/models/jsonapi.py b/optimade/models/jsonapi.py
index a6bbd197..80189d34 100644
--- a/optimade/models/jsonapi.py
+++ b/optimade/models/jsonapi.py
@@ -1,5 +1,5 @@
"""This module should reproduce JSON API v1.0 https://jsonapi.org/format/1.0/"""
-from typing import Optional, Set, Union
+from typing i... |
MatterMiners__cobald-46 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/cobald/controller/stepwise.py:UnboundStepwise.s"
],
"edited_modules": [
"src/cobald/controller/stepwise.py:UnboundStepwise"
]
},
"file": "src/cobald/controller/step... | MatterMiners/cobald | 79788e7e172089b88ecce4ffab7bbda27fcccb55 | Allow `.s` syntax for pools as well
Controller and decorator types both have a ``.s`` classmethod to allow binding them with ``>>``. Pools do not, as they are always concrete and mark the end of a binding chain.
```python3
LinearController.s() >> Pool()
```
The use of ``.s`` or not might be confusing without un... | diff --git a/src/cobald/controller/stepwise.py b/src/cobald/controller/stepwise.py
index 3b4241a..1e79f09 100644
--- a/src/cobald/controller/stepwise.py
+++ b/src/cobald/controller/stepwise.py
@@ -187,7 +187,7 @@ class UnboundStepwise(object):
:note: The partial rules are sealed, and :py:meth:`~.UnboundStepwis... |
MatterMiners__cobald-87 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "setup.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/cobald/daemon/config/py... | MatterMiners/cobald | 93c8f8d89a70a557888388390edb3d7821df09a3 | Drop dependency on include package
The ``include`` package is currently used to load Python configuration files. Since it is not compatible with Py3.9 it limits ``cobald`` as well.
The package is no longer maintained. We should just [use the builtin ``importlib`` instead](https://stackoverflow.com/questions/67631/ho... | diff --git a/setup.py b/setup.py
index 9abe2b8..80c85bb 100644
--- a/setup.py
+++ b/setup.py
@@ -55,7 +55,6 @@ if __name__ == "__main__":
install_requires=[
"pyyaml",
"trio>=0.4.0",
- "include",
"entrypoints",
"toposort",
"typing_exten... |
MatterMiners__lapis-45 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lapis/drone.py:Drone.run",
"lapis/drone.py:Drone.shutdown",
"lapis/drone.py:Drone.start_job"
],
"edited_modules": [
"lapis/drone.py:Drone"
]
},
"file": ... | MatterMiners/lapis | 0c602a7ede7cab77f692b51a15da2cf9c2578ed0 | Improve logging scheme
The logging scheme should be improved, including
* [ ] generation of log messages from the job itself
* [ ] parameters being logged to be put on next lines as mentioned in #23 | diff --git a/lapis/drone.py b/lapis/drone.py
index d217993..9b33dde 100644
--- a/lapis/drone.py
+++ b/lapis/drone.py
@@ -1,5 +1,3 @@
-import logging
-
from cobald import interfaces
from usim import time, Scope, instant, Capacities, ResourcesUnavailable
@@ -55,7 +53,7 @@ class Drone(interfaces.Pool):
await ... |
MatterMiners__lapis-63 | [
{
"changes": {
"added_entities": [
"lapis/drone.py:Drone.schedule_job",
"lapis/drone.py:Drone._run_job"
],
"added_modules": null,
"edited_entities": [
"lapis/drone.py:Drone.__init__",
"lapis/drone.py:Drone.run",
"lapis/drone.py:Drone.start_job"
... | MatterMiners/lapis | a698820f4ee6700157aafb511206c39e51a85cae | Job transfers seem to interrupt scheduling cycle
@tfesenbecker reported there seems to be an issue with the scheduling cycle when files are transferred from within jobs. As jobs should be absolutely independent from the scheduler itself, this should not happen at all. So we should ensure that file transfer can last lon... | diff --git a/lapis/drone.py b/lapis/drone.py
index b6d9cab..9826c78 100644
--- a/lapis/drone.py
+++ b/lapis/drone.py
@@ -1,5 +1,5 @@
from cobald import interfaces
-from usim import time, Scope, instant, Capacities, ResourcesUnavailable
+from usim import time, Scope, instant, Capacities, ResourcesUnavailable, Queue
... |
MatterMiners__lapis-66 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lapis/drone.py:Drone._run_job"
],
"edited_modules": [
"lapis/drone.py:Drone"
]
},
"file": "lapis/drone.py"
},
{
"changes": {
"added_entities": [
"... | MatterMiners/lapis | 213a69da5c554bfadec160ed5246ba726d880760 | Simulation doesn't await job execution after last scheduling cycle
I am under the impression that after the last update the simulation finishes after when the job queue is empty and all jobs are scheduled to drones but does not await the execution of all jobs in the drones job queue.
You can reproduce this by runnin... | diff --git a/lapis/drone.py b/lapis/drone.py
index 9826c78..7126242 100644
--- a/lapis/drone.py
+++ b/lapis/drone.py
@@ -154,9 +154,8 @@ class Drone(interfaces.Pool):
await instant
job_execution.cancel()
self.jobs -= 1
- if not job.successful:
- j... |
MatterMiners__lapis-69 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lapis/drone.py:Drone._run_job"
],
"edited_modules": [
"lapis/drone.py:Drone"
]
},
"file": "lapis/drone.py"
},
{
"changes": {
"added_entities": null,
... | MatterMiners/lapis | 5e10d37d054ff87da91010260ab8ab8da52614c0 | Jobs can run without a drone being assigned
Apparently jobs can run although not being properly assigned to a drone. We should take care that this cannot happen.
See:
> This happens in the unit tests... Same with the fileprovider in
> https://github.com/tfesenbecker/lapis/blob/53ebec5ea004e4f031a0f70102276fe010... | diff --git a/lapis/drone.py b/lapis/drone.py
index 7126242..0e6845a 100644
--- a/lapis/drone.py
+++ b/lapis/drone.py
@@ -127,7 +127,7 @@ class Drone(interfaces.Pool):
self._utilisation = self._allocation = None
- job_execution = scope.do(job.run())
+ job_execution = scope.do(job.r... |
MatterMiners__tardis-112 | [
{
"changes": {
"added_entities": [
"tardis/adapters/batchsystems/fakebatchsystem.py:FakeBatchSystemAdapter.get_utilisation"
],
"added_modules": null,
"edited_entities": [
"tardis/adapters/batchsystems/fakebatchsystem.py:FakeBatchSystemAdapter.get_utilization"
],
... | MatterMiners/tardis | a93c0b2cfa4ea132c843595bc6ba30e768634036 | Inconsistent spelling of utilization/utilisation
COBalD consistenly uses `utilisation` but in TARDIS both [utili**s**ation](https://github.com/MatterMiners/tardis/search?q=utilisation&unscoped_q=utilisation) and [utili**z**ation](https://github.com/MatterMiners/tardis/search?q=utilization&unscoped_q=utilization) are us... | diff --git a/docs/source/adapters/batchsystem.rst b/docs/source/adapters/batchsystem.rst
index e12431a..e9041b7 100644
--- a/docs/source/adapters/batchsystem.rst
+++ b/docs/source/adapters/batchsystem.rst
@@ -7,7 +7,7 @@ Batch System Adapters
Fake Batch System Adapter
-------------------------
-.. |FakeBatchSystemA... |
MatterMiners__tardis-116 | [
{
"changes": {
"added_entities": [
"tardis/agents/siteagent.py:SiteAgent.drone_minimum_lifetime"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"tardis/agents/siteagent.py:SiteAgent"
]
},
"file": "tardis/agents/siteagent.py"
}... | MatterMiners/tardis | 36b2ce08c563afef5175b6e82be50225b4203f72 | Add configurable drone lifetime
To allow for a more flexible response to demands in the local batch system, it would be nice to add a configurable drone lifetime. The idea is that after the drone lifetime has been reached, the drone is drained such that the resources are released more quickly and in a smooth way. For t... | diff --git a/docs/source/adapters/site.rst b/docs/source/adapters/site.rst
index 2cda19b..c1a12c5 100644
--- a/docs/source/adapters/site.rst
+++ b/docs/source/adapters/site.rst
@@ -10,8 +10,15 @@ Site Adapter
of resources and a dynamic orchestration of pre-built VM images and containers.
Sites are generally... |
MatterMiners__tardis-119 | [
{
"changes": {
"added_entities": [
"tardis/configuration/configuration.py:translate_config"
],
"added_modules": [
"tardis/configuration/configuration.py:translate_config"
],
"edited_entities": [
"tardis/configuration/configuration.py:encode_user_data",
... | MatterMiners/tardis | 60d00ae8a6adc720903632ef823941418210ccd7 | AttributeError: 'str' object has no attribute 'run_command'
Trying out a site with `Slurm` adapter and `SSHExecutor`I always receive the following error:
```
File "/opt/cobald/lib64/python3.6/site-packages/tardis/adapters/sites/slurm.py", line 156, in handle_exceptions
yield
File "/opt/cobald/lib64/python3.6/site-p... | diff --git a/docs/source/executors/executors.rst b/docs/source/executors/executors.rst
index 2bb46bb..711d444 100644
--- a/docs/source/executors/executors.rst
+++ b/docs/source/executors/executors.rst
@@ -7,9 +7,13 @@ Executors
.. container:: left-col
All executors can be loaded using YAML tags using the (`!Tag... |
MatterMiners__tardis-141 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tardis/adapters/sites/moab.py:MoabAdapter.__init__"
],
"edited_modules": [
"tardis/adapters/sites/moab.py:MoabAdapter"
]
},
"file": "tardis/adapters/sites/moab.py"
}
... | MatterMiners/tardis | d1a436ebdb48d7f415b9a26526d8f5e0f68e564a | Missing resource status in moab site adapter
Because of the lack of some job status and their translations in the moab site adapter, an exception is thrown e.g. for drones in state "Removed". | diff --git a/tardis/adapters/sites/moab.py b/tardis/adapters/sites/moab.py
index 3ab110a..cec43d0 100644
--- a/tardis/adapters/sites/moab.py
+++ b/tardis/adapters/sites/moab.py
@@ -72,15 +72,41 @@ class MoabAdapter(SiteAdapter):
remote_resource_uuid="JobID", resource_status="State"
)
+ # ... |
MatterMiners__tardis-197 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tardis/adapters/sites/slurm.py:SlurmAdapter.sbatch_cmdline_options"
],
"edited_modules": [
"tardis/adapters/sites/slurm.py:SlurmAdapter"
]
},
"file": "tardis/adapters/s... | MatterMiners/tardis | b3ea6fa926048c7812632a43663f0a5b005ee443 | Slurm siteadapter fails with fractional GB of memory
@wiene and I found that trying to define drones with non-integer `Memory` in their `MachineMetaData` works fine with most siteadapters (e.g. HTCondor), but breaks with Slurm:
```
2021-07-11 03:32:12 [WARNING][cobald.runtime.tardis.adapters.sites.slurm]: Execute com... | diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
index 0fa911c..2d008be 100644
--- a/docs/source/changelog.rst
+++ b/docs/source/changelog.rst
@@ -1,4 +1,4 @@
-.. Created by changelog.py at 2021-07-12, command
+.. Created by changelog.py at 2021-07-15, command
'/Users/giffler/.cache/pre-commit/rep... |
MatterMiners__tardis-238 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"tardis/resources/dronestates.py:AvailableState"
]
},
"file": "tardis/resources/dronestates.py"
},
{
"changes": {
"added_entities": null,
"... | MatterMiners/tardis | f89d96a5bb6cf519cf8c93218b8477d04a353d8a | Missing task done call in AsyncBulkCall
It seems that `AsyncBulkCall` is missing one `task_done` call. The simplify the logic, we can assume that `size` is set to 1.
In that case the first task is fetched in
https://github.com/MatterMiners/tardis/blob/75b60e3a6c91caf4774d6638b2faf26cc8b6b3a7/tardis/utilities/as... | diff --git a/.flake8 b/.flake8
index d461ede..d098624 100644
--- a/.flake8
+++ b/.flake8
@@ -1,6 +1,6 @@
[flake8]
statistics = True
max-line-length = 80
-ignore = E501, B008, B011, W503
+ignore = E501, B008, B011, B019, W503
select = C,E,F,W,B,B9
exclude = docs,.svn,CVS,.bzr,.hg,.git,__pycache__,.tox,.eggs,*.egg
d... |
MatterMiners__tardis-241 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tardis/adapters/sites/slurm.py:SlurmAdapter.__init__"
],
"edited_modules": [
"tardis/adapters/sites/slurm.py:SlurmAdapter"
]
},
"file": "tardis/adapters/sites/slurm.py"... | MatterMiners/tardis | 8f1cd47fc7610ec7cd10de3379084cae9d10c480 | Drones go into `Error` state when a slurm batch job times out
If a slurm batch job runs out of walltime it will report status `TIMEOUT` in `squeue`. This is not properly recognized by tardis which puts the corresponding VM into `Error` state and repeatedly tries to `scancel` the job (which reports success, since from a... | diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
index a09a9a3..70c6322 100644
--- a/docs/source/changelog.rst
+++ b/docs/source/changelog.rst
@@ -1,4 +1,4 @@
-.. Created by changelog.py at 2022-03-09, command
+.. Created by changelog.py at 2022-04-13, command
'/Users/giffler/.cache/pre-commit/rep... |
MatterMiners__tardis-301 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tardis/resources/drone.py:Drone.__init__",
"tardis/resources/drone.py:Drone.run"
],
"edited_modules": [
"tardis/resources/drone.py:Drone"
]
},
"file": "tardis/r... | MatterMiners/tardis | 35bfe1762fc99e53737ad55b41e9a8fe2ad56212 | Missing resource_status results is crashing Prometheus plugin
Dear all,
we are currently migrating our C/T to the newest image (the old image is from September 2022 with a custom auditor plugin) and are seeing some crashes related to the Prometheus monitoring plugin. We are running the following image:
```
docke... | diff --git a/tardis/resources/drone.py b/tardis/resources/drone.py
index 4d0322b..a5b3c13 100644
--- a/tardis/resources/drone.py
+++ b/tardis/resources/drone.py
@@ -3,9 +3,9 @@ from typing import List, Union, Optional, Type
from tardis.agents.batchsystemagent import BatchSystemAgent
from tardis.agents.siteagent impor... |
MatterMiners__tardis-306 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tardis/plugins/auditor.py:Auditor.notify"
],
"edited_modules": [
"tardis/plugins/auditor.py:Auditor"
]
},
"file": "tardis/plugins/auditor.py"
}
] | MatterMiners/tardis | 2bf9dcbeeeb548da01161a26c83d0809ecd165d6 | Auditor plugin crashes when drone does not reach AvailableState
In some cases, it can happen that a drone is started but never reaches the `AvailableState`. However, during clean-up, it reaches the `DownState`. This case is currently not handled correctly in the auditor plugin, see
https://github.com/MatterMiners/ta... | diff --git a/tardis/plugins/auditor.py b/tardis/plugins/auditor.py
index b2d120e..0976a39 100644
--- a/tardis/plugins/auditor.py
+++ b/tardis/plugins/auditor.py
@@ -85,7 +85,18 @@ class Auditor(Plugin):
.replace(tzinfo=self._local_timezone)
.astimezone(pytz.utc)
)
- ... |
MatterMiners__tardis-307 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tardis/adapters/sites/cloudstack.py:CloudStackAdapter.__init__"
],
"edited_modules": [
"tardis/adapters/sites/cloudstack.py:CloudStackAdapter"
]
},
"file": "tardis/adap... | MatterMiners/tardis | 886255e0ae081198b23d63a895d40d1719301632 | drone_minimum_lifetime ignored
Hi,
the `drone_minimum_lifetime` setting seems to be ignored. I am not completely sure what the intended behaviour is, but here is what puzzles me.
From `resources/dronestates.py` we have
```python
async def check_minimum_lifetime(
state_transition, drone: "Drone", current_stat... | diff --git a/.gitignore b/.gitignore
index 8b76bbe..d1c9b65 100644
--- a/.gitignore
+++ b/.gitignore
@@ -116,8 +116,11 @@ test_scripts/
cobald*.yml
*tardis.yml
-#Ignore cloudinit files
+# Ignore cloudinit files
cloudinit/
-#Ignore logs
-*.log*
+# Ignore logs
+*.log
+
+# Igonre vscode
+.vscode*
diff --git a/docs/... |
MatterMiners__tardis-317 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tardis/plugins/sqliteregistry.py:SqliteRegistry._deploy_db_schema"
],
"edited_modules": [
"tardis/plugins/sqliteregistry.py:SqliteRegistry"
]
},
"file": "tardis/plugins... | MatterMiners/tardis | 0348c6740664f4809b1b05f32df04d74ae56985f | Fix code scanning alert - Implicit string concatenation in a list
This seems to be a bug in the SqliteRegistry.
Tracking issue for:
- [ ] https://github.com/MatterMiners/tardis/security/code-scanning/5
| diff --git a/tardis/plugins/sqliteregistry.py b/tardis/plugins/sqliteregistry.py
index 99b2ad6..5e931b0 100644
--- a/tardis/plugins/sqliteregistry.py
+++ b/tardis/plugins/sqliteregistry.py
@@ -96,7 +96,7 @@ class SqliteRegistry(Plugin):
"CONSTRAINT unique_machine_type_per_site UNIQUE (machine_type, sit... |
MatterMiners__tardis-77 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"tardis/plugins/telegrafmonitoring.py:TelegrafMonitoring.__init__"
],
"edited_modules": [
"tardis/plugins/telegrafmonitoring.py:TelegrafMonitoring"
]
},
"file": "tardis/... | MatterMiners/tardis | 06d67fbbd6e3a4cf6cee51f871f86f3fdc25405a | Add information about hostname to logging config
The logging configuration should include information about the *hostname*. Currently it works implicitly via the global configuration for telegraf but this can be disabled by the user.
To ensure the availability of information about the host and reduce external depend... | diff --git a/docs/source/plugins/plugins.rst b/docs/source/plugins/plugins.rst
index ab4d881..bf26cec 100644
--- a/docs/source/plugins/plugins.rst
+++ b/docs/source/plugins/plugins.rst
@@ -2,7 +2,7 @@
Plugins
=======
-All plugins are configured within the `plugins` section of the TARDIS configuration. Using multipl... |
MatthewFlamm__pynws-208 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/pynws/simple_nws.py:parse_icon"
],
"edited_modules": [
"src/pynws/simple_nws.py:parse_icon"
]
},
"file": "src/pynws/simple_nws.py"
}
] | MatthewFlamm/pynws | aae2aeefc87bd422c532fc2adeeffac2755dd8ce | Icon format in forecast change
API used to return something like:
```
"icon": "https://api.weather.gov/icons/land/night/sct?size=small",
```
now it returns something like
```
"icon": "/icons/land/night/sct?size=small",
``` | diff --git a/pyproject.toml b/pyproject.toml
index dd36143..1ff17fd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,8 @@ name = "pynws"
requires-python = ">=3.8"
dependencies = [
"aiohttp",
- "metar"
+ "metar",
+ "yarl"
]
description = "Python library to retrieve observations and forecasts... |
MatthewFlamm__pynws-94 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pynws/raw_data.py:raw_stations_observations"
],
"edited_modules": [
"pynws/raw_data.py:raw_stations_observations"
]
},
"file": "pynws/raw_data.py"
}
] | MatthewFlamm/pynws | fff40aa8ab373e834bb55a1d8dce31b17708f78f | oberservation start time parameter not formed correctly
When passing `start_time=datetime.datetime.utcnow()` to `SimpleNWS.update_observations`, the following error message is returned:
```txt
Invalid date-time \"2023-03-22T11:43:40\", expected format YYYY-MM-DDThh:mm:ssZ or YYYY-MM-DDThh:mm:ss+hh:mm
``` | diff --git a/pynws/raw_data.py b/pynws/raw_data.py
index db0578b..985e5b7 100644
--- a/pynws/raw_data.py
+++ b/pynws/raw_data.py
@@ -51,7 +51,11 @@ async def raw_stations_observations(
if start:
if not isinstance(start, datetime):
- raise ValueError
+ raise ValueError(
+ ... |
MatthieuDartiailh__bytecode-102 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/bytecode/instr.py:Compare"
]
},
"file": "src/bytecode/instr.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
... | MatthieuDartiailh/bytecode | 30d6adbda1e3a4333d656248036adb9eff1591d3 | The `Compare` enum is broken starting from Python 3.9
~~~
Python 3.9.7 (default, Sep 3 2021, 12:37:55)
[Clang 12.0.5 (clang-1205.0.22.9)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from dis import cmp_op
>>> len(cmp_op)
6
>>> cmp_op
('<', '<=', '==', '!=', '>', '>=')
... | diff --git a/doc/changelog.rst b/doc/changelog.rst
index 4016453..cf4b604 100644
--- a/doc/changelog.rst
+++ b/doc/changelog.rst
@@ -12,6 +12,10 @@ Bugfixes:
- Removed ``EXC_MATCH`` from the ``Compare`` enumeration starting with Python
3.9. The new ``JUMP_IF_NOT_EXC_MATCH`` opcode should be used instead.
+- Remov... |
MaxGhenis__microdf-80 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"microdf/weighted.py:quantile_chg"
],
"edited_modules": [
"microdf/weighted.py:quantile_chg"
]
},
"file": "microdf/weighted.py"
}
] | MaxGhenis/microdf | ec6209573968caeadc043abd18306fb88e33b4d8 | name 'ordinal_label' is not defined in quantile_chg_plot
```
mdf.quantile_chg_plot(v1=df_1986.inc_2018, v2=df_2019.inc_2018,
w1=df_1986.asecwt, w2=df_2019.asecwt)
```
produces
```
NameError Traceback (most recent call last)
<ipython-input-17-ef85fa8bbfb4> in ... | diff --git a/ROADMAP.md b/ROADMAP.md
index a25fc16..5797082 100644
--- a/ROADMAP.md
+++ b/ROADMAP.md
@@ -6,4 +6,4 @@
* Presets for working with common datasets, e.g. suggesting the appropriate weight for SCF and CPS
* Standard error calculations for surveys with replicate weight files
-See the [issues page](https:/... |
MaxGhenis__synthimpute-31 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"synthimpute/rf_impute.py:rf_impute"
],
"edited_modules": [
"synthimpute/rf_impute.py:rf_impute"
]
},
"file": "synthimpute/rf_impute.py"
}
] | MaxGhenis/synthimpute | f668c4ab967e2a42bc0bed668d59efc681bf2485 | Add observation weights to rf_impute
`sample_weight` in `fit` should do it: https://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestRegressor.html#sklearn.ensemble.RandomForestRegressor.fit | diff --git a/synthimpute/rf_impute.py b/synthimpute/rf_impute.py
index bdec8fc..06b22a4 100644
--- a/synthimpute/rf_impute.py
+++ b/synthimpute/rf_impute.py
@@ -45,7 +45,7 @@ def rf_quantile(m, X, q):
def rf_impute(x_train, y_train, x_new, x_cols=None, random_state=None,
- **kwargs):
+ sa... |
MechanicalSoup__MechanicalSoup-140 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mechanicalsoup/form.py:Form.set_select"
],
"edited_modules": [
"mechanicalsoup/form.py:Form"
]
},
"file": "mechanicalsoup/form.py"
}
] | MechanicalSoup/MechanicalSoup | 6e45a67591ec9bf204eb1323477fb40289d615ae | Manage <select multiple>
`<select multiple>` should behave essentially like multiple checkboxes with the same name. For now, they don't: selecting one option deselects the previous ones.
@hemberger: while you're working on form, you may want to fix this too. | diff --git a/docs/ChangeLog.rst b/docs/ChangeLog.rst
index 63d2685..7ba5011 100644
--- a/docs/ChangeLog.rst
+++ b/docs/ChangeLog.rst
@@ -40,6 +40,9 @@ Main changes:
``browser.get_current_form().print_summary()`` to get a summary of the
fields you need to fill-in (and which ones are already filled-in).
+* The ``... |
MechanicalSoup__MechanicalSoup-152 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mechanicalsoup/stateful_browser.py:StatefulBrowser.select_form"
],
"edited_modules": [
"mechanicalsoup/stateful_browser.py:StatefulBrowser"
]
},
"file": "mechanicalsoup... | MechanicalSoup/MechanicalSoup | 0d147eb88b3bffb4853b841b418924cbb569c4ea | Implement nr option?
In MechanicalSoup, almost all of our methods that find some element return or operate on the first one that is found (`Form.choose_submit` appears to be the recently-modified exception). If, for example, you have a page with two `<form>...</form>` with no unique attributes, then you cannot select t... | diff --git a/docs/ChangeLog.rst b/docs/ChangeLog.rst
index 1fd119d..cbaa569 100644
--- a/docs/ChangeLog.rst
+++ b/docs/ChangeLog.rst
@@ -23,7 +23,9 @@ Main changes:
* We now have a documentation: https://mechanicalsoup.readthedocs.io/
* ``StatefulBrowser.select_form`` can now be called without argument,
- and defa... |
MechanicalSoup__MechanicalSoup-166 | [
{
"changes": {
"added_entities": [
"mechanicalsoup/browser.py:Browser._request"
],
"added_modules": null,
"edited_entities": [
"mechanicalsoup/browser.py:Browser._build_request",
"mechanicalsoup/browser.py:Browser._prepare_request",
"mechanicalsoup/browser... | MechanicalSoup/MechanicalSoup | 8c149d6baeb012ce44b1d7ece85dccfed7cc5c71 | Unexpected keyword argument 'proxies'
The use of requests.Request base class does not include a proxies keyword like the requests.request class.
```python
import requests
import mechanicalsoup
self.Session = requests.Session()
self.browser = mechanicalsoup.StatefulBrowser(session=self.Session)
self.browser.get(... | diff --git a/docs/ChangeLog.rst b/docs/ChangeLog.rst
index 9b61e30..472b8e1 100644
--- a/docs/ChangeLog.rst
+++ b/docs/ChangeLog.rst
@@ -5,6 +5,19 @@ Release Notes
Version 1.0 (in development)
============================
+Main changes:
+-------------
+* ``Browser.submit`` and ``StatefulBrowser.submit_selected`` ac... |
MechanicalSoup__MechanicalSoup-181 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mechanicalsoup/form.py:Form.choose_submit"
],
"edited_modules": [
"mechanicalsoup/form.py:Form"
]
},
"file": "mechanicalsoup/form.py"
}
] | MechanicalSoup/MechanicalSoup | 736083562d4cc03efdf08f7be16ced8fb1460ee5 | Crash on input without name in form
I am currently dealing with a form containing a submit button without a name. When submitting this form (with multiple submit buttons) via
```
browser.submit_selected(btnName='name')
```
this causes a crash in `Form.choose_submit()` since the attribute `name` is not present, [her... | diff --git a/mechanicalsoup/form.py b/mechanicalsoup/form.py
index 7819535..285fac6 100644
--- a/mechanicalsoup/form.py
+++ b/mechanicalsoup/form.py
@@ -307,7 +307,8 @@ class Form(object):
found = False
inps = self.form.select('input[type="submit"], button[type="submit"]')
for inp in inps:
- ... |
MechanicalSoup__MechanicalSoup-192 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mechanicalsoup/stateful_browser.py:StatefulBrowser.select_form"
],
"edited_modules": [
"mechanicalsoup/stateful_browser.py:StatefulBrowser"
]
},
"file": "mechanicalsoup... | MechanicalSoup/MechanicalSoup | 7171e2b79ba0fbe02a7245066cb5536ddb2fe94e | Allow passing a Tag object to StatefulBrowser.select_form
Hi,
I've recently had to select a form based on its children and the only way I found to do that is:
```py
buttons = browser.get_current_page().select("form > button[name=apply]")
browser._StatefulBrowser__current_form = mechanicalsoup.Form(buttons[0].parent... | diff --git a/mechanicalsoup/stateful_browser.py b/mechanicalsoup/stateful_browser.py
index a233f6d..b96dc1b 100644
--- a/mechanicalsoup/stateful_browser.py
+++ b/mechanicalsoup/stateful_browser.py
@@ -177,7 +177,8 @@ class StatefulBrowser(Browser):
def select_form(self, selector="form", nr=0):
"""Select a... |
MechanicalSoup__MechanicalSoup-212 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"mechanicalsoup/utils.py:LinkNotFoundError"
]
},
"file": "mechanicalsoup/utils.py"
}
] | MechanicalSoup/MechanicalSoup | 7d9ee675f465b0e6596b5fcb9f9c9cb7ce8ded74 | LinkNotFoundError should not inherit from BaseException
Hello,
I have code that performs many tests, reporting which tests failed. We therefore implement a try-catch such as
```python
try:
run_test()
except Exception:
msg = traceback.format_exc()
report_failure()
```
LinkNotFoundError is not... | diff --git a/docs/ChangeLog.rst b/docs/ChangeLog.rst
index 787e4bb..faa9109 100644
--- a/docs/ChangeLog.rst
+++ b/docs/ChangeLog.rst
@@ -5,6 +5,16 @@ Release Notes
Version 1.0 (in development)
============================
+Bug fixes
+---------
+
+* **Breaking Change:** :class:`~mechanicalsoup.LinkNotFoundError` now... |
MechanicalSoup__MechanicalSoup-290 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mechanicalsoup/browser.py:Browser._request"
],
"edited_modules": [
"mechanicalsoup/browser.py:Browser"
]
},
"file": "mechanicalsoup/browser.py"
}
] | MechanicalSoup/MechanicalSoup | 0b04e8b9aed3a3e5160ac89081e2c270598c2f09 | Respect enctype specified in forms
MechanicalSoup currently ignores the enctype specified for a form when submitting it, instead using the default used by requests (which is application/x-www-form-urlencoded unless you specify "files" to upload). I'd like it to behave more like a browser by respecting the given enctyp... | diff --git a/mechanicalsoup/browser.py b/mechanicalsoup/browser.py
index 35e4047..3979c64 100644
--- a/mechanicalsoup/browser.py
+++ b/mechanicalsoup/browser.py
@@ -155,6 +155,8 @@ class Browser(object):
# Requests also retains order when encoding form data in 2-tuple lists.
data = [(k, v) for k, v in... |
MetOffice__stylist-22 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "setup.py"
},
{
"changes": {
"added_entities": [
"source/stylist/fortran.py:MissingPointerInit.__init__",
"source/stylist/fortran... | MetOffice/stylist | a5ddd993648b5f9c88e162aae8d9b21cee0d87b1 | Rule for trapping uninitialised pointers
Initialising a Fortran pointer is syntactically optional but not doing so is a bad idea. Why? Because the `associated(...)` intrinsic returns a boolean based on the tri-state of a pointer. A pointer may be associated, unassociated or undefined. The intrinsic will return `.true.`... | diff --git a/setup.py b/setup.py
index 2699d2a..5b65503 100644
--- a/setup.py
+++ b/setup.py
@@ -44,7 +44,7 @@ setup(
package_dir={'': 'source'},
packages=find_packages(where='source'),
python_requires='>=3.6, <4',
- install_requires=['fparser'],
+ install_requires=['fparser > 0.0.10'],
extras... |
MicroPyramid__forex-python-27 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"forex_python/converter.py:CurrencyRates.get_rate"
],
"edited_modules": [
"forex_python/converter.py:CurrencyRates"
]
},
"file": "forex_python/converter.py"
}
] | MicroPyramid/forex-python | 1ebd8dda32503ca63d52b8a55f5647804fd1d1dd | identity get_rate
It would be nice that the conversion from one currency to itself also work
```
>>> c.get_rate("CHF", "CHF")
Traceback (most recent call last):
File "<input>", line 1, in <module>
File "/home/user/.virtualenvs/tool/local/lib/python2.7/site-packages/forex_python/converter.py", line 67, in get_r... | diff --git a/forex_python/converter.py b/forex_python/converter.py
index bcc8348..316f0cf 100644
--- a/forex_python/converter.py
+++ b/forex_python/converter.py
@@ -56,6 +56,8 @@ class CurrencyRates(Common):
raise RatesNotAvailableError("Currency Rates Source Not Ready")
def get_rate(self, base_cur, des... |
Midnighter__dependency-info-6 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/depinfo/info.py:_get_package_version"
],
"edited_modules": [
"src/depinfo/info.py:_get_package_version"
]
},
"file": "src/depinfo/info.py"
}
] | Midnighter/dependency-info | aaee24bce878624d739a195936a534e416938108 | Parsing of packages fails for most package strings (requirement)
<!--
Before you create a new problem report, please look through the list of existing open
and closed issues to see if there are similar ones.
https://github.com/Midnighter/dependency-info/issues
-->
#### Problem description
Most package s... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 432ff96..8e22715 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -4,6 +4,7 @@ Change Log
Next Release
------------
+* Improved parsing of package information
1.6.0 (2020-10-11)
------------------
diff --git a/README.rst b/README.rst
index 69fba35..9db8039 10064... |
MindscapeHQ__raygun4py-82 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "python2/raygun4py/version.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"python3... | MindscapeHQ/raygun4py | 16d2e7a3ebcca16548e5ec806c85b3edfda95930 | AttributeError: 'NoneType' object has no attribute 'set_user'
Recently upgraded from 3.1.6 to 4.1.0 and it looks like `RaygunMessageBuilder.set_request_details` is returning `None` in some situations, causing exception sending to fail with an `AttributeError: 'NoneType' object has no attribute 'set_user'`
https://gi... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9a8e114..d80a3f8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,7 @@
+## 4.2.2 (23/01/2019):
+Bugfixes
+ - Fix `set_request_details` builder method not returning self causing it to be unchainable
+
## 4.2.1 (18/12/2018):
Bugfixes
- Set version correctly in c... |
ModellingWebLab__cellmlmanip-186 | [
{
"changes": {
"added_entities": [
"cellmlmanip/model.py:Model.get_derived_quantities"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"cellmlmanip/model.py:Model"
]
},
"file": "cellmlmanip/model.py"
}
] | ModellingWebLab/cellmlmanip | dadacbbae97fe5180f5843333ff7feb752618338 | Determine derived quantities
I need to be able to determine derived quantities for chaste codegen.
@maurice I was replying to your last comment when it disappeared!
Anyway, you can use `get_symbols_by_rdf` to find things annotated explicitly as d-q and also everything with an oxmeta name. Then use something like:
... | diff --git a/cellmlmanip/model.py b/cellmlmanip/model.py
index 98057c1..55d6d09 100644
--- a/cellmlmanip/model.py
+++ b/cellmlmanip/model.py
@@ -267,6 +267,14 @@ class Model(object):
derivative_symbols = [v for v in self.graph if isinstance(v, sympy.Derivative)]
return sorted(derivative_symbols, key=l... |
ModellingWebLab__cellmlmanip-20 | [
{
"changes": {
"added_entities": [
"cellmlmanip/mathml2sympy/transpiler.py:degree_handler",
"cellmlmanip/mathml2sympy/transpiler.py:logbase_handler",
"cellmlmanip/mathml2sympy/transpiler.py:get_nary_relation_callback",
"cellmlmanip/mathml2sympy/transpiler.py:simple_operator... | ModellingWebLab/cellmlmanip | a71fa61adf7bf1cf3a3bf30a9392a2b8d949fa93 | Expand the range of supported MathML
We should probably support the [CellML subset](https://www.cellml.org/specifications/cellml_1.1/#sec_math_cellml_subset) eventually (see also in [CellML 2](https://docs.google.com/document/d/1MleZJF6DYp4FO4vxslAHInrRFMqrSpARa1s_dPhwYU0/edit#heading=h.zegia3mrify8)). Not urgent thoug... | diff --git a/cellmlmanip/mathml2sympy/transpiler.py b/cellmlmanip/mathml2sympy/transpiler.py
index 4a20482..e0d7ad5 100644
--- a/cellmlmanip/mathml2sympy/transpiler.py
+++ b/cellmlmanip/mathml2sympy/transpiler.py
@@ -3,6 +3,7 @@ Parses Content MathML and returns equivalent SymPy expressions
Content Markup specificat... |
ModellingWebLab__cellmlmanip-209 | [
{
"changes": {
"added_entities": [
"cellmlmanip/model.py:Model._check_duplicate_definitions",
"cellmlmanip/model.py:Model.transform_constants"
],
"added_modules": null,
"edited_entities": [
"cellmlmanip/model.py:Model.__init__",
"cellmlmanip/model.py:Model... | ModellingWebLab/cellmlmanip | 86f74a0a354e23036197aea019fb8574bb39d536 | Improve how initial values and parameters are handled
Basically, once parsing is done, initial values should only appear for state variables, and everything else should be represented as actual assignment equations. To support this, we can adapt how we store equations internally to the `Model` so we have some extra loo... | diff --git a/cellmlmanip/model.py b/cellmlmanip/model.py
index feb8bf6..25a40d6 100644
--- a/cellmlmanip/model.py
+++ b/cellmlmanip/model.py
@@ -63,6 +63,12 @@ class Model(object):
# An RDF graph containing further meta data
self.rdf = rdflib.Graph()
+ # Map from VariableDummy to defining equ... |
ModellingWebLab__cellmlmanip-224 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cellmlmanip/model.py:Model.check_left_right_units_equal"
],
"edited_modules": [
"cellmlmanip/model.py:Model"
]
},
"file": "cellmlmanip/model.py"
},
{
"changes":... | ModellingWebLab/cellmlmanip | b55a11ecbaa653350dd1c686cadaeec6005aee9c | Add method to obtain unit name
Given a `pint.unit` we'd like to know its name. This used to be possible with `str(unit)` but that now adds a prefix we need to strip | diff --git a/cellmlmanip/model.py b/cellmlmanip/model.py
index de9aec1..fae9c45 100644
--- a/cellmlmanip/model.py
+++ b/cellmlmanip/model.py
@@ -278,8 +278,8 @@ class Model(object):
lhs_units = self.units.evaluate_units(equality.lhs)
rhs_units = self.units.evaluate_units(equality.rhs)
assert ... |
ModellingWebLab__cellmlmanip-258 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cellmlmanip/model.py:Model._convert_variable_instance"
],
"edited_modules": [
"cellmlmanip/model.py:Model"
]
},
"file": "cellmlmanip/model.py"
}
] | ModellingWebLab/cellmlmanip | fd7465f18e0cb8b288a6d1949deafb6f712102d2 | Initial values aren't copied in unit conversion
If they're 0 | diff --git a/cellmlmanip/model.py b/cellmlmanip/model.py
index d0882a0..90b458b 100644
--- a/cellmlmanip/model.py
+++ b/cellmlmanip/model.py
@@ -968,7 +968,7 @@ class Model(object):
# If original has initial_value calculate new initial value (only needed for INPUT case)
new_value = None
- if ... |
ModellingWebLab__cellmlmanip-268 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cellmlmanip/units.py:UnitStore.get_conversion_factor",
"cellmlmanip/units.py:UnitCalculator.convert_expression_recursively"
],
"edited_modules": [
"cellmlmanip/units.py:UnitS... | ModellingWebLab/cellmlmanip | 681131c93572c6685c694b8f371dac0558ba4c6b | Use consistent argument ordering for unit conversions?
Currently we have a mix of `to_units, from_units` (e.g. `UnitStore.get_conversion_factor`) and `from_units, to_units` (e.g. `UnitStore.convert`). We should pick one!
@MichaelClerx and @jonc125 prefer `from, to`. However the main method used by external code is p... | diff --git a/cellmlmanip/units.py b/cellmlmanip/units.py
index b68b197..8091249 100644
--- a/cellmlmanip/units.py
+++ b/cellmlmanip/units.py
@@ -369,11 +369,11 @@ class UnitStore(object):
logger.debug('evaluate_units(%s) ⟶ %s', expr, found)
return found
- def get_conversion_factor(self, to_unit, ... |
ModellingWebLab__cellmlmanip-272 | [
{
"changes": {
"added_entities": [
"cellmlmanip/model.py:Model.is_constant",
"cellmlmanip/model.py:VariableDummy.model"
],
"added_modules": null,
"edited_entities": [
"cellmlmanip/model.py:Model.add_variable",
"cellmlmanip/model.py:Model.remove_variable",
... | ModellingWebLab/cellmlmanip | 971d4264f95acb2f39a50f902b6171542f11947f | Add model property to VariableDummy
- A variable dummy is tied to a model: it's not possible to re-use a variable dummy with a different model (e.g. a model stores all variable dummies it has when creating them, and they have a model-specific order_added property)
- I've got some use cases where we pass dummies around... | diff --git a/cellmlmanip/main.py b/cellmlmanip/main.py
index a9fefb7..42764f1 100644
--- a/cellmlmanip/main.py
+++ b/cellmlmanip/main.py
@@ -9,4 +9,3 @@ def load_model(path, unit_store=None):
underlying registry so that conversions between model units and those from the provided store work.
"""
retur... |
ModellingWebLab__cellmlmanip-276 | [
{
"changes": {
"added_entities": null,
"added_modules": [
"cellmlmanip/model.py:VariableType"
],
"edited_entities": [
"cellmlmanip/model.py:Model.add_equation",
"cellmlmanip/model.py:Model.transform_constants",
"cellmlmanip/model.py:Model.connect_variables... | ModellingWebLab/cellmlmanip | 1fea0028068efab78385b6d0889fecd2c1b42221 | Rename/move some Model functions
1. Model. add_number()
This function merely creates a NumberDummy object. It is completely independent of the Model and adds nothing to anything. I think the name could be misleading.
I would prefer: create_number_symbol
2. Model.check_left_right_units_equal(sympy.Equality)
Thi... | diff --git a/cellmlmanip/main.py b/cellmlmanip/main.py
index 42764f1..f7e907b 100644
--- a/cellmlmanip/main.py
+++ b/cellmlmanip/main.py
@@ -3,7 +3,7 @@ from cellmlmanip.parser import Parser
def load_model(path, unit_store=None):
- """Parses a CellML file and returns a :class:`cellmlmanip.Model`.
+ """Parses... |
ModellingWebLab__cellmlmanip-281 | [
{
"changes": {
"added_entities": [
"cellmlmanip/model.py:Model.create_quantity",
"cellmlmanip/model.py:Quantity.__new__"
],
"added_modules": [
"cellmlmanip/model.py:Quantity",
"cellmlmanip/model.py:Variable"
],
"edited_entities": [
"cellmlman... | ModellingWebLab/cellmlmanip | 39797e08160cdfb723321e29e26d2bdff0aa69c5 | Rename/move some Model functions
1. Model. add_number()
This function merely creates a NumberDummy object. It is completely independent of the Model and adds nothing to anything. I think the name could be misleading.
I would prefer: create_number_symbol
2. Model.check_left_right_units_equal(sympy.Equality)
Thi... | diff --git a/cellmlmanip/model.py b/cellmlmanip/model.py
index 743e0fe..cdfc23c 100644
--- a/cellmlmanip/model.py
+++ b/cellmlmanip/model.py
@@ -32,7 +32,7 @@ class Model(object):
graph that stores further meta data about the model.
Equations are stored as :class:`sympy.Eq` objects, but with the caveat that... |
MongoEngine__mongoengine-2858 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"mongoengine/base/datastructures.py:BaseList"
]
},
"file": "mongoengine/base/datastructures.py"
}
] | MongoEngine/mongoengine | 9aab9d20c068854e7ec6c11dc04d79d2c3de7389 | Changes from clear() on ListField are not saved
```python
class MyDoc(Document):
things = ListField(StringField())
```
If I get hold of a document with some things and do
```python
doc.things.clear()
doc.save()
```
`things` will not be emptied. If I do
```python
doc.things = []
doc.save()
```
`thing... | diff --git a/mongoengine/base/datastructures.py b/mongoengine/base/datastructures.py
index a175cd11..dcb8438c 100644
--- a/mongoengine/base/datastructures.py
+++ b/mongoengine/base/datastructures.py
@@ -177,6 +177,7 @@ class BaseList(list):
remove = mark_as_changed_wrapper(list.remove)
reverse = mark_as_chang... |
MontrealCorpusTools__Montreal-Forced-Aligner-624 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"montreal_forced_aligner/alignment/base.py:CorpusAligner.export_textgrids",
"montreal_forced_aligner/alignment/base.py:CorpusAligner.evaluate_alignments"
],
"edited_modules": [
... | MontrealCorpusTools/Montreal-Forced-Aligner | 9012a5e260690f6d608102287b9483ac048e1691 | [BUG] mfa diarize will fail with error missing attribute
**Debugging checklist**
[x] Have you updated to latest MFA version? Yes, v 2.2.9
[x] Have you tried rerunning the command with the `--clean` flag? Yes running from fresh docker.
**Describe the issue**
When trying to use `mfa diarize` on corpus, it fails... | diff --git a/docs/source/changelog/changelog_2.2.rst b/docs/source/changelog/changelog_2.2.rst
index d7e762e..6a52400 100644
--- a/docs/source/changelog/changelog_2.2.rst
+++ b/docs/source/changelog/changelog_2.2.rst
@@ -5,6 +5,12 @@
2.2 Changelog
*************
+2.2.10
+======
+
+- Fix crash in speaker diarization
... |
MoshiBin__ssdpy-17 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ssdpy/protocol.py:create_msearch_payload"
],
"edited_modules": [
"ssdpy/protocol.py:create_msearch_payload"
]
},
"file": "ssdpy/protocol.py"
}
] | MoshiBin/ssdpy | c3a5dd90e12ca38a02ef2d35318d947aaa5f3c9d | M-SEARCH has unescaped "Man" field
According to the official docs, the "Man" field's value should be wrapped in quotes.
Wrong:
```python
data = (
"M-SEARCH * HTTP/1.1\r\n"
"HOST:{}\r\n"
"MAN: ssdp:discover\r\n"
"ST:{}\r\n"
"MX:{}\r\n" ... | diff --git a/ssdpy/protocol.py b/ssdpy/protocol.py
index 50a1be6..ba2a2ff 100644
--- a/ssdpy/protocol.py
+++ b/ssdpy/protocol.py
@@ -18,7 +18,7 @@ def create_msearch_payload(host, st, mx=1):
data = (
"M-SEARCH * HTTP/1.1\r\n"
"HOST:{}\r\n"
- "MAN:ssdp:discover\r\n"
+ 'MAN: "ssdp:dis... |
MoshiBin__ssdpy-54 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ssdpy/cli/server.py:parse_args",
"ssdpy/cli/server.py:main"
],
"edited_modules": [
"ssdpy/cli/server.py:parse_args",
"ssdpy/cli/server.py:main"
]
},
"fi... | MoshiBin/ssdpy | f26ca358867467a58e79c65c4813f47431a5a627 | No support for custom fields
SSDP allows custom fields to be send by the server. However ssdpy does not support them.
See https://web.archive.org/web/20150905102426/http://upnp.org/specs/arch/UPnP-arch-DeviceArchitecture-v1.1.pdf chapter 1.1.3, SSDP header field extensions. | diff --git a/CHANGES.md b/CHANGES.md
index 6617b09..3583296 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -4,6 +4,7 @@
- Fixed an issue where `ssdpy.client.discover()` was using wrong syntax.
- Changed the exception raised by `ssdpy.compat.if_nametoindex()` to be the same as in Python 3 (OSError).
- Added tests for `s... |
MoshiBin__ssdpy-58 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ssdpy/client.py:SSDPClient.__init__"
],
"edited_modules": [
"ssdpy/client.py:SSDPClient"
]
},
"file": "ssdpy/client.py"
},
{
"changes": {
"added_entities"... | MoshiBin/ssdpy | 9f67a5f9fba13a7918418cf2e1c53f61dac6ee6e | Windows support
This issue tracks the work needed for supporting ssdpy on Windows.
- `socket.if_nametoindex` only exists in Windows since Python 3.8 - check how to bind to interface in Windows prior to that.
- TBD | diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 86c6fbf..a3cefc8 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -44,7 +44,7 @@ jobs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
- os: [ubuntu-latest]
+ os: [ubuntu-latest, windows-... |
MushroomMaula__fastapi_login-48 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fastapi_login/fastapi_login.py:LoginManager.has_scopes"
],
"edited_modules": [
"fastapi_login/fastapi_login.py:LoginManager"
]
},
"file": "fastapi_login/fastapi_login.p... | MushroomMaula/fastapi_login | f50e980dd0be40946109077d5f40c6c3a2702aca | TypeError: catching classes that do not inherit from BaseException is not allowed
It happens when the token is not correct, for example, a random string token.
```python
INFO: 127.0.0.1:51577 - "POST /auth/refresh HTTP/1.1" 500 Internal Server Error
ERROR: Exception in ASGI application
Traceback (most rece... | diff --git a/fastapi_login/fastapi_login.py b/fastapi_login/fastapi_login.py
index ed75a80..ea07735 100644
--- a/fastapi_login/fastapi_login.py
+++ b/fastapi_login/fastapi_login.py
@@ -308,7 +308,7 @@ class LoginManager(OAuth2PasswordBearer):
"""
try:
payload = self._get_payload(token)
- ... |
MushroomMaula__fastapi_login-59 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "docs_src/setup/setup_005.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fastapi_... | MushroomMaula/fastapi_login | d8387589304ee85e80f8adae09dd31a67db2ac75 | TypeError: the first argument must be callable
My program was developed based on fastapi_login==1.6.2
Today, I upgrade fastapi_login to the latest version: 1.7.0. When I login, it raises error.
some of the error code:
```
2021-09-23 14:58:04 | TypeError: the first argument must be callable
-- | --
| | ... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8aa667a..caac8d4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,25 @@
+# 1.7.1
+Fixes backwards compatibility ([#58](https://github.com/MushroomMaula/fastapi_login/issues/58)) of the ``LoginManager.user_loader`` decorator.
+In version 1.7.0 it was not possible to ... |
MushroomMaula__fastapi_login-81 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"fastapi_login/fastapi_login.py:LoginManager.__init__",
"fastapi_login/fastapi_login.py:LoginManager._get_token",
"fastapi_login/fastapi_login.py:LoginManager.has_scopes",
"fastap... | MushroomMaula/fastapi_login | 5cd5a08255a1f285e7de926457befb4bb66c9509 | Exception handling
When I use the example code from https://fastapi-login.readthedocs.io/advanced_usage/ and there is no, or an invalid token present in the request I get an error:
```
INFO: 127.0.0.1:5898 - "GET /proteced HTTP/1.1" 500 Internal Server Error
ERROR: Exception in ASGI application
Traceback (... | diff --git a/fastapi_login/fastapi_login.py b/fastapi_login/fastapi_login.py
index b4c4864..7e217f1 100644
--- a/fastapi_login/fastapi_login.py
+++ b/fastapi_login/fastapi_login.py
@@ -58,6 +58,7 @@ class LoginManager(OAuth2PasswordBearer):
"""
if use_cookie is False and use_header is False:
+ ... |
MycroftAI__lingua-franca-118 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lingua_franca/lang/parse_da.py:extract_datetime_da"
],
"edited_modules": [
"lingua_franca/lang/parse_da.py:extract_datetime_da"
]
},
"file": "lingua_franca/lang/parse_d... | MycroftAI/lingua-franca | d726b0562400769577e724c6fcb12307934435b6 | extract_datetime() returns 8 AM results in utterance where no time specification was made
forslund has backtracked this to lingua franca in [mycroft-core issue #2647](https://github.com/MycroftAI/mycroft-core/issues/2647)
> Found this while reworking the skill-reminder. While processing non timed reminder there is a... | diff --git a/lingua_franca/lang/parse_da.py b/lingua_franca/lang/parse_da.py
index 76bca9c..e513b47 100644
--- a/lingua_franca/lang/parse_da.py
+++ b/lingua_franca/lang/parse_da.py
@@ -733,7 +733,7 @@ def extract_datetime_da(string, currentDate, default_time):
found = True
# check that we found a da... |
MycroftAI__lingua-franca-226 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lingua_franca/lang/parse_en.py:extract_datetime_en"
],
"edited_modules": [
"lingua_franca/lang/parse_en.py:extract_datetime_en"
]
},
"file": "lingua_franca/lang/parse_e... | MycroftAI/lingua-franca | eb6d677d4f8d201e1bcf645382eb262c7d0688f1 | "In 2007" should be parsed as year
**Describe the bug**
I know for Mycroft it reasonable to parse 2007 as 20:07. But this is a separate library, and for 2007 should be a year.
**To Reproduce**
```python
from lingua_franca.parse import *
lingua_franca.load_language('en')
print(lingua_franca.parse.extract_datetim... | diff --git a/lingua_franca/lang/parse_en.py b/lingua_franca/lang/parse_en.py
index 0a8b8e1..3075715 100644
--- a/lingua_franca/lang/parse_en.py
+++ b/lingua_franca/lang/parse_en.py
@@ -694,7 +694,8 @@ def extract_datetime_en(text, anchorDate=None, default_time=None):
timeQualifiersAM = ['morning']
timeQualifi... |
MycroftAI__lingua-franca-23 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lingua_franca/lang/parse_en.py:extract_datetime_en"
],
"edited_modules": [
"lingua_franca/lang/parse_en.py:extract_datetime_en"
]
},
"file": "lingua_franca/lang/parse_e... | MycroftAI/lingua-franca | 4c66a5ec87113842519b5f6166695b75ed01a46f | extract_datetime(" ") returns today not None
Clearly this is my favourite method looking at the issues list :yum:
An empty string passed to `extract_datetime("")` correctly returns `None`.
However a non-empty string that does not contain a date eg `extract_datetime(" ")` returns a datetime of the current day at mi... | diff --git a/lingua_franca/lang/parse_en.py b/lingua_franca/lang/parse_en.py
index 872c478..2136423 100644
--- a/lingua_franca/lang/parse_en.py
+++ b/lingua_franca/lang/parse_en.py
@@ -1363,7 +1363,7 @@ def extract_datetime_en(string, dateNow, default_time):
idx += used - 1
found = True
#... |
MycroftAI__lingua-franca-230 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lingua_franca/lang/parse_en.py:extract_datetime_en"
],
"edited_modules": [
"lingua_franca/lang/parse_en.py:extract_datetime_en"
]
},
"file": "lingua_franca/lang/parse_e... | MycroftAI/lingua-franca | b76bc51a65e558a8cc214f28f62d3db680132ac0 | Using default_time arg on extract_datetime skews results
**Describe the bug**
The Reminder Skill uses the `default_time` argument of `extract_datetime` and the extracted datetime is being returned 8 hours later than it should.
Originally reported
https://github.com/MycroftAI/skill-reminder/issues/50
**To Reprod... | diff --git a/lingua_franca/lang/parse_en.py b/lingua_franca/lang/parse_en.py
index 3075715..e5e9ed2 100644
--- a/lingua_franca/lang/parse_en.py
+++ b/lingua_franca/lang/parse_en.py
@@ -13,7 +13,7 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-from datetim... |
MycroftAI__lingua-franca-32 | [
{
"changes": {
"added_entities": [
"lingua_franca/lang/parse_es.py:extract_numbers_es"
],
"added_modules": [
"lingua_franca/lang/parse_es.py:extract_numbers_es"
],
"edited_entities": [
"lingua_franca/lang/parse_es.py:extractnumber_es"
],
"edited_... | MycroftAI/lingua-franca | 6c43ca67438f14891930ec14e56572f2c2815427 | PR#2347 Fix extractnumber_es, add extract_numbers_es
https://github.com/MycroftAI/mycroft-core/pull/2347
- Fix bug causing extractnumber_es to return a sum instead of a list
- Add Spanish parser to extract_numbers and extract_number
| diff --git a/lingua_franca/lang/parse_es.py b/lingua_franca/lang/parse_es.py
index bebda23..d2ebea9 100644
--- a/lingua_franca/lang/parse_es.py
+++ b/lingua_franca/lang/parse_es.py
@@ -20,7 +20,8 @@
"""
from datetime import datetime
from dateutil.relativedelta import relativedelta
-from lingua_franca.lang.parse_comm... |
MycroftAI__lingua-franca-76 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lingua_franca/lang/format_en.py:pronounce_number_en"
],
"edited_modules": [
"lingua_franca/lang/format_en.py:pronounce_number_en"
]
},
"file": "lingua_franca/lang/forma... | MycroftAI/lingua-franca | a45b9d12a2a8adace210055a38f432dd51e7456d | Fails with 0.0x numbers
```
$ python3
Python 3.7.6 (default, Dec 19 2019, 22:52:49)
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
@>>> from lingua_franca.format import pronounce_number
@>>> pronounce_number(0.05)
' point'
@>>> pronounce_n... | diff --git a/lingua_franca/lang/format_en.py b/lingua_franca/lang/format_en.py
index 5634a95..bba9bc1 100644
--- a/lingua_franca/lang/format_en.py
+++ b/lingua_franca/lang/format_en.py
@@ -97,19 +97,20 @@ def pronounce_number_en(num, places=2, short_scale=True, scientific=False,
# handling since each c... |
MycroftAI__lingua-franca-85 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lingua_franca/lang/parse_da.py:extractnumber_da",
"lingua_franca/lang/parse_da.py:extract_datetime_da"
],
"edited_modules": [
"lingua_franca/lang/parse_da.py:extractnumber_da... | MycroftAI/lingua-franca | 5ac3a86f1b5d1f2f97722ecb14408411a0fc663f | Capitals break number parsing
"Ninety four" returns "4" unlike "ninety four" which returns "94". It doesn't recognize the number when the capital is anywhere else in a word as well. | diff --git a/lingua_franca/lang/parse_da.py b/lingua_franca/lang/parse_da.py
index 405a7f6..76bca9c 100644
--- a/lingua_franca/lang/parse_da.py
+++ b/lingua_franca/lang/parse_da.py
@@ -75,6 +75,8 @@ da_numbers = {
# TODO: short_scale and ordinals don't do anything here.
# The parameters are present in the function si... |
MycroftAI__lingua-franca-87 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lingua_franca/lang/parse_en.py:_extract_whole_number_with_text_en"
],
"edited_modules": [
"lingua_franca/lang/parse_en.py:_extract_whole_number_with_text_en"
]
},
"file... | MycroftAI/lingua-franca | 5ac3a86f1b5d1f2f97722ecb14408411a0fc663f | Multiples of ten describing other multiples of ten require an intermediary number. I.e "twenty thousand" doesn't work
"twenty thousand" returns "20". The only way I have found to get this sort of situation to work is to add an extra number. "twenty four thousand" properly returns "24000". | diff --git a/lingua_franca/lang/parse_en.py b/lingua_franca/lang/parse_en.py
index 58207de..ef0f93d 100644
--- a/lingua_franca/lang/parse_en.py
+++ b/lingua_franca/lang/parse_en.py
@@ -444,7 +444,11 @@ def _extract_whole_number_with_text_en(tokens, short_scale, ordinals):
current_val = val
e... |
MycroftAI__lingua-franca-90 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"lingua_franca/lang/parse_en.py:_extract_whole_number_with_text_en"
],
"edited_modules": [
"lingua_franca/lang/parse_en.py:_extract_whole_number_with_text_en"
]
},
"file... | MycroftAI/lingua-franca | e6837eb2f8fabb72af3a8389c4a85cbcdae5e40b | extractnumber_en() summing "leading hundreds"
```python
>>> extract_number("ninety nine million")
99000000
>>> extract_number("nine hundred ninety nine million")
99000900
| diff --git a/lingua_franca/lang/parse_en.py b/lingua_franca/lang/parse_en.py
index cf316d9..8054bf0 100644
--- a/lingua_franca/lang/parse_en.py
+++ b/lingua_franca/lang/parse_en.py
@@ -406,7 +406,9 @@ def _extract_whole_number_with_text_en(tokens, short_scale, ordinals):
# is the prev word a number and shoul... |
MycroftAI__mycroft-messagebus-client-30 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mycroft_bus_client/message.py:Message.response"
],
"edited_modules": [
"mycroft_bus_client/message.py:Message"
]
},
"file": "mycroft_bus_client/message.py"
}
] | MycroftAI/mycroft-messagebus-client | 24ca33ae96af0be14ec575c26582aee666233d85 | message.response should use message.reply internally
to account for proper message routing https://github.com/JarbasHiveMind/HiveMind-core/wiki/Mycroft-Messages + https://github.com/MycroftAI/mycroft-core/pull/2461 | diff --git a/mycroft_bus_client/message.py b/mycroft_bus_client/message.py
index 48351ca..037e3e3 100644
--- a/mycroft_bus_client/message.py
+++ b/mycroft_bus_client/message.py
@@ -146,9 +146,7 @@ class Message:
Returns
(Message) message with the type modified to match default response
""... |
Mykrobe-tools__mykrobe-104 | [
{
"changes": {
"added_entities": [
"src/mykrobe/cmds/amr.py:fix_X_amino_acid_variants"
],
"added_modules": [
"src/mykrobe/cmds/amr.py:fix_X_amino_acid_variants"
],
"edited_entities": [
"src/mykrobe/cmds/amr.py:ref_data_from_args",
"src/mykrobe/cmds/a... | Mykrobe-tools/mykrobe | 98befa765550e9b0aeb80d0f4f01cf765ca44bdb | X mutations in 201901 panel
Dear mykrobe team,
In the 201901 probe set, many (most?) putative mutations are annotated as "X". For example, all resistance mutations at position 445 in the rpoB gene is now annotated as H445X.
Our clinicians are very interested in the actual amino acid change, so at the moment I am ... | diff --git a/src/mykrobe/cmds/amr.py b/src/mykrobe/cmds/amr.py
index 8901564..fce6c0b 100755
--- a/src/mykrobe/cmds/amr.py
+++ b/src/mykrobe/cmds/amr.py
@@ -25,6 +25,7 @@ from mykrobe.predict import MykrobePredictorSusceptibilityResult
from mykrobe.metagenomics import AMRSpeciesPredictor
from mykrobe.species_data imp... |
Mykrobe-tools__mykrobe-129 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/mykrobe/utils.py:_x_mutation_fixed_var_name"
],
"edited_modules": [
"src/mykrobe/utils.py:_x_mutation_fixed_var_name"
]
},
"file": "src/mykrobe/utils.py"
}
] | Mykrobe-tools/mykrobe | 854abaeaaf11bf7ebcc5c0f9d7c01c4acd950afd | mykrobe calls the wrong amino acid change for first drug resistance SNP on a bottom strand gene
I ran Mykrobe on the FASTQ data for BioProject PRJEB5280 Run ERR751367 from NCBI. Mykrobe identifies a SNP conferring isoniazid resistance, katG_S315G-GCT2155167GGT. The resulting amino acid, in this case the G in S315G, is ... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 86b3c90..a2cc13b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -32,10 +32,15 @@ this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
- Bug where the `--ont` flag resulted in mykrobe predict crashing if the panel
contained any presence/ab... |
N-Wouda__ALNS-21 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"alns/Result.py:Result._plot_operator_counts"
],
"edited_modules": [
"alns/Result.py:Result"
]
},
"file": "alns/Result.py"
},
{
"changes": {
"added_entitie... | N-Wouda/ALNS | c669e907808fa02138a55a68877d02021272af30 | Fix Result.plot_operator_counts plot looking 'weird'
E.g. when not plotting all possible outcome types, the axes are still fixed as if one did. Like so:
| diff --git a/alns/Result.py b/alns/Result.py
index a788279..beec688 100644
--- a/alns/Result.py
+++ b/alns/Result.py
@@ -165,9 +165,9 @@ class Result:
operator_names = list(operator_counts.keys())
operator_counts = np.array(list(operator_counts.values()))
- cumulative_counts = operator_counts... |
N3PDF__vegasflow-82 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/simgauss_tf.py"
},
{
"changes": {
"added_entities": [
"src/vegasflow/monte_carlo.py:MonteCarloFlow._digest_random_generation",
... | N3PDF/vegasflow | a11868282dc9cf3ed00488d783b24bac62826a49 | Specifying integration limits
Hi vegasflow developers!
Can I specify integration (upper and lower) limits in vegasflow? I searched the documentation but didn't found a way. | diff --git a/doc/source/how_to.rst b/doc/source/how_to.rst
index 488d6cc..3bc787d 100644
--- a/doc/source/how_to.rst
+++ b/doc/source/how_to.rst
@@ -189,6 +189,22 @@ The full list of integration algorithms and wrappers can be consulted at: :ref:`
Tips and Tricks
===============
+Changing the integration limits
+^^^... |
NASA-NAVO__servicemon-38 | [
{
"changes": {
"added_entities": [
"servicemon/query.py:compute_user_agent"
],
"added_modules": [
"servicemon/query.py:compute_user_agent"
],
"edited_entities": [
"servicemon/query.py:Query.__init__"
],
"edited_modules": [
"servicemon/que... | NASA-NAVO/servicemon | 1b9aa4c5779c98806fe71133a1ef4feb50dd7e6e | Adjust User-Agent to follow IVOA guidance
The User-Agent included in monitoring requests should be adjusted to conform to the IVOA recommendations specified at https://wiki.ivoa.net/twiki/bin/view/IVOA/UserAgentUsage
By default, we'll make the User-Agent be
`servicemon/[sm-version] (IVOA-monitor https://github.com/... | diff --git a/.travis.yml b/.travis.yml
index de7c7ac..a5b0f93 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -103,11 +103,12 @@ matrix:
env: TOXENV=py38-test-devdeps
# Try on Windows.
- - os: windows
- language: c
- name: Python 3.8 with required dependencies
- sta... |
NCAR__geocat-comp-315 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/geocat/comp/climatologies.py:_calculate_center_of_time_bounds",
"src/geocat/comp/climatologies.py:climatology",
"src/geocat/comp/climatologies.py:month_to_season",
"src/geoca... | NCAR/geocat-comp | cf5fdba0307533b69ae9a1774f14ea28f06fcc45 | Add `keep_attrs` kwarg to all `climatology.py` functions
Changes in xarray have resulted in an error when passing numpy objects into some `meteorology.py` functions. It has been determined in https://github.com/NCAR/geocat-comp/pull/312 that this arose from the global xarray option `keep_attrs` being set to `True` at t... | diff --git a/src/geocat/comp/climatologies.py b/src/geocat/comp/climatologies.py
index 264351b..db7a6d8 100644
--- a/src/geocat/comp/climatologies.py
+++ b/src/geocat/comp/climatologies.py
@@ -60,12 +60,13 @@ def _setup_clim_anom_input(dset, freq, time_coord_name):
def _calculate_center_of_time_bounds(
- dset: ... |
NCAR__geocat-comp-319 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/geocat/comp/meteorology.py:showalter_index"
],
"edited_modules": [
"src/geocat/comp/meteorology.py:showalter_index"
]
},
"file": "src/geocat/comp/meteorology.py"
... | NCAR/geocat-comp | 521f168263ef345ff3603a878610dd987a901055 | Upstream CI: Pint
In the most recent releases of geocat-comp, we've opted for pinning pint to >0.20, but we'll need to update our codebase to reflect the most recent update.
See [failing upstream CI tests](https://github.com/NCAR/geocat-comp/actions/runs/3560640392/jobs/5980811808#step:6:152) | diff --git a/build_envs/docs.yml b/build_envs/docs.yml
index ff1762e..436bd62 100644
--- a/build_envs/docs.yml
+++ b/build_envs/docs.yml
@@ -9,7 +9,7 @@ dependencies:
- geocat-viz
- xarray
- netcdf4
- - pint<0.20
+ - pint
- ipykernel
- ipython
- jupyter_client
diff --git a/build_envs... |
NCAR__geocat-comp-411 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"geocat/comp/climatologies.py:climate_anomaly",
"geocat/comp/climatologies.py:month_to_season",
"geocat/comp/climatologies.py:calendar_average",
"geocat/comp/climatologies.py:clim... | NCAR/geocat-comp | 42897c140bb350c7ef425580ab679a494e45f942 | Allow user to define seasonal boundaries for climatology_average
**Describe the feature you'd like added to this project**
Currently `climatology_average` does not allow the user to select the seasonal boundaries. Seasonal climatologies are only calculated for the meteorological seasons, which are defined as follows:
... | diff --git a/docs/release-notes.rst b/docs/release-notes.rst
index 572c233..47116cb 100644
--- a/docs/release-notes.rst
+++ b/docs/release-notes.rst
@@ -5,6 +5,15 @@
Release Notes
=============
+v2023.07.0 (Jul X, 2023)
+-----------------------
+[Plain text summary here]
+
+New Features
+^^^^^^^^^^^^
+* User-define... |
NCAR__geocat-comp-571 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"geocat/comp/meteorology.py:_delta_pressure1D"
],
"edited_modules": [
"geocat/comp/meteorology.py:_delta_pressure1D"
]
},
"file": "geocat/comp/meteorology.py"
}
] | NCAR/geocat-comp | 9ccf3e0cb4575c11f41288cdc95a0a8f6f3875ac | geocat.comp.meteorology.delta_pressure is different with dpres_plev
###this is the ncl code
plev = (/ 1000.,950.,900.,850.,800.,750.,700.,650.,600., \
550.,500.,450.,400.,350.,300.,250.,200., \
175.,150.,125.,100., 80., 70., 60., 50., \
40., 30., 25., 20. /)
plev = plev*100.
plev@u... | diff --git a/docs/release-notes.rst b/docs/release-notes.rst
index b28bdc2..474f355 100644
--- a/docs/release-notes.rst
+++ b/docs/release-notes.rst
@@ -5,7 +5,7 @@
Release Notes
=============
-v2024.03.0 (Unreleased)
+v2024.04.0 (Unreleased)
-----------------------
Internal Changes
@@ -15,6 +15,11 @@ Internal ... |
NCAR__geocat-comp-691 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"geocat/comp/climatologies.py:_infer_calendar_name"
],
"edited_modules": [
"geocat/comp/climatologies.py:_infer_calendar_name"
]
},
"file": "geocat/comp/climatologies.py... | NCAR/geocat-comp | 791fd0b4c53dfcaddd1eae27c51e75ac2eca81b3 | Support for non-nanosecond datetime
In short, the broader ecosystem is working to support non-nanosecond datetime objects (see: https://github.com/pydata/xarray/issues/7493) in Pandas 2+ and Xarray's release last month. This topic was brought to my attention by the recent upstream dev issues w/ Xarray (#681).
As I ... | diff --git a/docs/release-notes.rst b/docs/release-notes.rst
index 5de2681..6720d30 100644
--- a/docs/release-notes.rst
+++ b/docs/release-notes.rst
@@ -11,9 +11,13 @@ Release Notes
vYYYY.MM.## (unreleased)
------------------------
+Enhancements
+^^^^^^^^^^^^
+* Add tests and support for non-nanosecond datetime obj... |
NCAS-CMS__cf-python-284 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cf/aggregate.py:_Meta.__init__",
"cf/aggregate.py:aggregate"
],
"edited_modules": [
"cf/aggregate.py:_Meta",
"cf/aggregate.py:aggregate"
]
},
"file": "c... | NCAS-CMS/cf-python | 6475a87cb462763722ce1143b704392e040d58b7 | `cf.aggregate` fails when creating new axes with the `dimension` keyword
At v3.11.0 (and all other versions since 3.0.0) , `cf.aggregate` fails when creating new axes for each input field from one or more given properties, using the `dimension` keyword argument:
```python
>>> import cf
>>> print (cf.__version__)
... | diff --git a/Changelog.rst b/Changelog.rst
index 807c8ffd0..0ef1437a7 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -1,3 +1,13 @@
+version NEXT
+------------
+
+**????-??-??**
+
+* Fix `cf.aggregate` failures when using the ``dimension`` keyword
+ parameter (https://github.com/NCAS-CMS/cf-python/issues/283)
+
+---... |
NCAS-CMS__cf-python-288 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cf/timeduration.py:TimeDuration.__sub__",
"cf/timeduration.py:TimeDuration.__rsub__"
],
"edited_modules": [
"cf/timeduration.py:TimeDuration"
]
},
"file": "cf/t... | NCAS-CMS/cf-python | 98541d8e55c703eca9bfba4168fb3d42755267da | subtraction of cf.TimeDuration fails
Hi Both!
Having a bit of trouble with cf.TimeDuration() - looking at the code `def __sub__` appears to be missing[ this section](https://github.com/NCAS-CMS/cf-python/blob/master/cf/timeduration.py#L526) that appears in `def __add__`
Is that why it fails? (I should test this!)... | diff --git a/Changelog.rst b/Changelog.rst
index 0ef1437a7..f223372b3 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -5,6 +5,8 @@ version NEXT
* Fix `cf.aggregate` failures when using the ``dimension`` keyword
parameter (https://github.com/NCAS-CMS/cf-python/issues/283)
+* Fix bug that raised error with subtra... |
NCAS-CMS__cf-python-418 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "cf/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cf/mixin/propertiesda... | NCAS-CMS/cf-python | 57a7f104f2fe4c142b816749696225ebd5f1a5b6 | Creating time bounds - differing time units causes uncaptured error when collapsing
Hi Both!
Another minor issue - it arose when working with some datasets that use an auxiliary time axis, I have a work-around but I thought it was worth highlighting as it causes errors in `collapse` that are not captured.
If I ... | diff --git a/Changelog.rst b/Changelog.rst
index 94db42567..e62e85d31 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -1,3 +1,13 @@
+version 3.13.1
+--------------
+
+**2022-??-??**
+
+* Fix bug when setting coordinate bounds with different units to their
+ parent coordinates
+ (https://github.com/NCAS-CMS/cf-pytho... |
NCAS-CMS__cf-python-500 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cf/aggregate.py:_Meta.__init__"
],
"edited_modules": [
"cf/aggregate.py:_Meta"
]
},
"file": "cf/aggregate.py"
}
] | NCAS-CMS/cf-python | 5fbaee202f56a8eab7b2b732416ae843b71f0021 | `TypeError` is raised when using the `equal` or `exist` keyword to `cf.aggregate`
`TypeError` is raised when using the `equal` or `exist` keyword to `cf.aggregate`:
```python
>>> import cf
>>> f = cf.example_field(0)
>>> g = cf.aggregate([f[:2], f[2:]], equal=["standard_name"])
----------------------------------... | diff --git a/Changelog.rst b/Changelog.rst
index a55394508..c274a182c 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -6,6 +6,9 @@ version 3.14.0
* New method: `cf.Field.get_original_filenames`
(https://github.com/NCAS-CMS/cf-python/issues/448)
* New method: `cf.Field.to_dask_array`
+* Fixed bug that raised an e... |
NCAS-CMS__cf-python-548 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cf/data/data.py:Data.datetime_array"
],
"edited_modules": [
"cf/data/data.py:Data"
]
},
"file": "cf/data/data.py"
}
] | NCAS-CMS/cf-python | 2332322f8cce52edba248f232c1920ca4cd801eb | Investigate `'has_year_zero'` differences | diff --git a/cf/data/data.py b/cf/data/data.py
index bb113debf..76272595d 100644
--- a/cf/data/data.py
+++ b/cf/data/data.py
@@ -4515,11 +4515,11 @@ class Data(DataClassDeprecationsMixin, Container, cfdm.Data):
"because calendar is 'none'"
)
- units, reftime = units.units.split(" ... |
NCAS-CMS__cf-python-551 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cf/data/data.py:Data.__init__",
"cf/data/data.py:Data.to_dask_array"
],
"edited_modules": [
"cf/data/data.py:Data"
]
},
"file": "cf/data/data.py"
}
] | NCAS-CMS/cf-python | a7403282daea58e911fd4fdaf9a97991fb08c863 | LAMA to Dask: managing default(-argument) `Data` instance
(Opening as a general issue since `__init__` isn't listed under our table of methods in #295, so I am not sure of the migration status of `Data` initialisation.) Whilst I was trying to create diverse cases of instances of `Data` (in the context of https://github... | diff --git a/cf/data/data.py b/cf/data/data.py
index 97baabafd..402fc7e78 100644
--- a/cf/data/data.py
+++ b/cf/data/data.py
@@ -336,12 +336,6 @@ class Data(DataClassDeprecationsMixin, Container, cfdm.Data):
>>> d = cf.Data(tuple('fly'))
"""
- if array is None and source is None: # don't cre... |
NCAS-CMS__cf-python-603 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cf/aggregate.py:_Meta.__init__",
"cf/aggregate.py:_Meta.canonical_units",
"cf/aggregate.py:_Meta.structural_signature",
"cf/aggregate.py:aggregate",
"cf/aggregate.py:_agg... | NCAS-CMS/cf-python | 7b9e6b3bfcd24bacb4464b0b9988f2fe0732a501 | Allow `relaxed_units` in `cf.aggregate` to cope with invalid (in addition to missing) units
Currently, the `relaxed_units` keyword to `cf.aggregate` copes with missing units (i.e. `cf.units()`), but not invalid but otherwise equal units:
```python
>>> # 3.14.0 behaviour
>>> f = cf.example_field(0)
>>> bad_units = ... | diff --git a/Changelog.rst b/Changelog.rst
index f6345b30b..aae2752d8 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -3,6 +3,8 @@ version 3.14.1
**2023-??-??**
+* New keyword parameter to `cf.Data.concatenate`: ``relaxed_units``
+ (https://github.com/NCAS-CMS/cf-python/issues/602)
* New method: `cf.Field.del_... |
NCAS-CMS__cf-python-627 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cf/field.py:Field.compute_vertical_coordinates"
],
"edited_modules": [
"cf/field.py:Field"
]
},
"file": "cf/field.py"
}
] | NCAS-CMS/cf-python | d88872beaf423c57c6631f03ed891ad7c5591e0c | Bounds of computed vertical coordinates retain incorrect properties
When computing non-parametric vertical coordinates with `cf.Field.compute_vertical_coordinates`, the computed bounds can inherit properties from the parametric coordinates, which is incorrect. Here's an example of incorrect retained bounds that shows t... | diff --git a/Changelog.rst b/Changelog.rst
index 90f0c77f9..e761a3c0a 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -5,6 +5,9 @@ version 3.14.2
* Fixed bug in `cf.Field.read` when reading UM/PP data that are
runlength encoded (https://github.com/NCAS-CMS/cf-python/issues/621)
+* Fixed bug in `cf.Field.compute... |
NCAS-CMS__cfdm-114 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "cfdm/core/__init__.py"
},
{
"changes": {
"added_entities": [
"cfdm/read_write/netcdf/netcdfread.py:NetCDFRead._netCDF4_group"
],
... | NCAS-CMS/cfdm | d5222488853a0ffc0b444f2892f94840acc1c853 | Zero-sized unlimited dimension when read from a grouped netCDF file
The file `cm4twc_dump_file.nc` contains subgroups and has an unlimited dimension, currently of size 13. However, when read it gives the unlimited dimension as size 0:
```python
>>> cfdm.read('cm4twc_dump_file.nc')[0]
<Field: transfer_i(time(0), ... | diff --git a/Changelog.rst b/Changelog.rst
index ca53e24bb..09a754780 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -1,3 +1,12 @@
+version NEXT
+------------
+----
+
+**2021-??-??**
+
+* Fix for zero-sized unlimited dimensions when read from a grouped
+ netCDF file (https://github.com/NCAS-CMS/cfdm/issues/113)
+
... |
NCAS-CMS__cfdm-158 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfdm/read_write/netcdf/netcdfwrite.py:NetCDFWrite.write"
],
"edited_modules": [
"cfdm/read_write/netcdf/netcdfwrite.py:NetCDFWrite"
]
},
"file": "cfdm/read_write/netcdf... | NCAS-CMS/cfdm | 8d34bc31740c38f1137822c1857b3621576de125 | File name expansions do not work in `cfdm.write`
At cfdm 1.8.9.0, tilde and environment variable file name expansions no longer work in `cfdm.write`:
```python
>>> import cfdm
>>> f = cfdm.example_field(0)
>>> cfdm.write(f, 'test_file.nc') # OK
>>> cfdm.write(f, '~/test_file.nc') # Not OK
...
Permission... | diff --git a/Changelog.rst b/Changelog.rst
index 166631ac5..dda759411 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -25,7 +25,9 @@ version 1.9.0.0
reference parameters (https://github.com/NCAS-CMS/cfdm/issues/148)
* Interpret format specifiers for size 1 `cfdm.Data` arrays
(https://github.com/NCAS-CMS/cfdm/i... |
NCAS-CMS__cfdm-175 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfdm/domain.py:Domain.__str__"
],
"edited_modules": [
"cfdm/domain.py:Domain"
]
},
"file": "cfdm/domain.py"
}
] | NCAS-CMS/cfdm | 140dc1bc519a3ba990ea2e1ce46db8d84efc77f4 | Field/domain print fails when dimension corodinate has no data
(First reported over at https://github.com/NCAS-CMS/cf-python/issues/326 - see there for full details)
When a field has a construct which can have data, e.g. a coordinate, but that construct doesn't have data, the `str()` representation hits a `ValueErro... | diff --git a/Changelog.rst b/Changelog.rst
index 0125dce49..01e43ed93 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -1,3 +1,14 @@
+Version 1.9.?.?
+---------------
+
+**2022-0?-??**
+
+* Fixed bug that caused `cf.Domain.__str__` to fail when a dimension
+ coordinate construct does not have data
+ (https://github.... |
NCAS-CMS__cfdm-178 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "cfdm/core/__init__.py"
},
{
"changes": {
"added_entities": [
"cfdm/read_write/netcdf/netcdfwrite.py:NetCDFWrite._dimension_in_subgroup"
... | NCAS-CMS/cfdm | bb23013c4660b8329e44bb29b71aa6495d2ae60e | Failure from `cfdm.write` when writing identical (auxiliary) coordinates to different data variables in different groups
It should be possible to write to disk fields with identical dimension or auxiliary coordinates to different groups, but this causes a failure from `cfdm.write`, which complains that the netCDF data... | diff --git a/Changelog.rst b/Changelog.rst
index 01e43ed93..9c6d6fbfc 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -1,8 +1,11 @@
-Version 1.9.?.?
+Version 1.9.0.3
---------------
-**2022-0?-??**
+**2022-03-??**
+* Fixed bug that caused a failure from `cfdm.write` when writing
+ identical (auxiliary) coordina... |
NCAS-CMS__cfdm-203 | [
{
"changes": {
"added_entities": [
"cfdm/field.py:Field.indices"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"cfdm/field.py:Field"
]
},
"file": "cfdm/field.py"
}
] | NCAS-CMS/cfdm | eed0a764c3bc12716449aebeec7003ade9b43eb2 | Create indices for Field constructs from metadata values
@JonathanGregory suggested that it would be natural in cfdm to be able to subspace field constructs based on metadata constructs values, rather than just by indices. An excellent idea.
For instance, with
```python
>>> import cfdm
>>> f = cfdm.example_field(... | diff --git a/Changelog.rst b/Changelog.rst
index 95e4edffa..8732b1f6a 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -12,6 +12,7 @@ Version 1.9.1.0
* New method: `cfdm.Field.domain_ancillary`
* New method: `cfdm.Field.domain_axis`
* New method: `cfdm.Field.field_ancillary`
+* New method: `cfdm.Field.indices`
* N... |
NCAS-CMS__cfdm-205 | [
{
"changes": {
"added_entities": [
"cfdm/mixin/propertiesdata.py:PropertiesData.array",
"cfdm/mixin/propertiesdata.py:PropertiesData.datetime_array"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"cfdm/mixin/propertiesdata.py:Properti... | NCAS-CMS/cfdm | 2b4cfd47c0f48b244242ce6d37f6a5bc08ad7d55 | Allow `array` and `datetime_array` attributes on data-bearing contructs
Currently, the only way to access an array of a construct that has data is `f.data.array`. Experience indicates that this is needlessly verbose, and `f.array` should also work. Similarly for `datetime_array`. | diff --git a/Changelog.rst b/Changelog.rst
index d171c57a6..95e4edffa 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -12,6 +12,8 @@ Version 1.9.1.0
* New method: `cfdm.Field.domain_ancillary`
* New method: `cfdm.Field.domain_axis`
* New method: `cfdm.Field.field_ancillary`
+* New attribute: `cfdm.Field.array`
+* ... |
NCAS-CMS__cfdm-210 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfdm/field.py:Field.__getitem__"
],
"edited_modules": [
"cfdm/field.py:Field"
]
},
"file": "cfdm/field.py"
},
{
"changes": {
"added_entities": null,
... | NCAS-CMS/cfdm | 0c6f140dc8229d41530d2b9f439f740a28645a33 | Subspaces of constructs can currently have one or more size 0 axes
`numpy` (and similar data objects that share its API, such as `dask`, `cfdm.Data`) reasonably allow subspaces to have size 0 axes:
```python
>>> import numpy as np
>>> a = np.arange(9)
>>> a[[False] * 9]
array([], dtype=int64)
```
At cfdm `v1.10.... | diff --git a/cfdm/field.py b/cfdm/field.py
index 00ee583fd..8414a356d 100644
--- a/cfdm/field.py
+++ b/cfdm/field.py
@@ -297,6 +297,13 @@ class Field(
# ------------------------------------------------------------
new_data = data[tuple(indices)]
+ if 0 in new_data.shape:
+ raise In... |
NCAS-CMS__cfdm-212 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfdm/data/data.py:Data.__str__"
],
"edited_modules": [
"cfdm/data/data.py:Data"
]
},
"file": "cfdm/data/data.py"
}
] | NCAS-CMS/cfdm | 223b74bd0cf858870bd29810f51f74712a9980b5 | `Data.__str__` fails when the data contains date-times with the first element masked
At cfdm v1.10.0.0 we have:
```python
>>> # v1.10.0.0
>>> import cfdm
>>> import numpy as
>>> dt = np.ma.array([10, 20], mask=[True, False])
>>> d = cfdm.Data(dt, units='days since 2000-01-01')
>>> str(d)
Traceback
...
... | diff --git a/Changelog.rst b/Changelog.rst
index f16852e30..5f750fc13 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -1,3 +1,12 @@
+Version 1.10.0.1
+----------------
+
+**2022-??-??**
+
+* Fixed bug that caused a failure when printing date-time data with
+ the first element masked
+ (https://github.com/NCAS-CMS/c... |
NCAS-CMS__cfdm-220 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cfdm/cfdmimplementation.py:CFDMImplementation.get_original_filenames"
],
"edited_modules": [
"cfdm/cfdmimplementation.py:CFDMImplementation"
]
},
"file": "cfdm/cfdmimpl... | NCAS-CMS/cfdm | 525682552c236b95a2cc8706d3c9f05c152f5a5a | Incorrect data assignment with some multiple list indices
When multiple list indices are provided to a data assignment (i.e. `Data.__setitem__`), the assignment works if all of the lists are strictly monotonically increasing, but only for some cases cases where they are not:
```python
>>> import cfdm
>>> d = cfdm.... | diff --git a/Changelog.rst b/Changelog.rst
index 4c24fc3aa..232c07d6e 100644
--- a/Changelog.rst
+++ b/Changelog.rst
@@ -10,6 +10,8 @@ Version 1.10.0.1
(https://github.com/NCAS-CMS/cfdm/issues/215)
* New method: `cfdm.Field.get_original_filenames`
* New method: `cfdm.Data.get_original_filenames`
+* Fixed bug that ... |
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