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 |
|---|---|---|---|---|---|
peopledoc__vault-cli-48 | [
{
"changes": {
"added_entities": [
"vault_cli/cli.py:set_verbosity",
"vault_cli/cli.py:dump_config"
],
"added_modules": [
"vault_cli/cli.py:set_verbosity",
"vault_cli/cli.py:dump_config"
],
"edited_entities": [
"vault_cli/cli.py:cli"
],... | peopledoc/vault-cli | a7d15a7e0dfd713710ca6d472a37dd49a7e8c575 | Add details on where the settings are coming from
write in stderr the location of the settings file, if used.
(ping @tlehoux ) | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 24f56b7..8eea173 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,12 @@
CHANGELOG
=========
+0.4.0 (unreleased)
+------------------
+
+- Added vault dump-config
+- Added vault bootstrap-env
+
0.3.9
-----
diff --git a/README.md b/README.md
index cca31b1..ac7e... |
peopledoc__vault-cli-49 | [
{
"changes": {
"added_entities": [
"vault_cli/cli.py:delete_all"
],
"added_modules": [
"vault_cli/cli.py:delete_all"
],
"edited_entities": [
"vault_cli/cli.py:get_all",
"vault_cli/cli.py:env"
],
"edited_modules": [
"vault_cli/cli.... | peopledoc/vault-cli | 9f29b0eb5ea00ffa0fdb429a0c7e793d2c6a45d9 | Feature request: delete-all command
Same as `get-all` but for recursive deletion:
`vault -U https://myvault.test:8200 -b myapp -w delete-all db/` | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8eea173..9c36d05 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,8 @@ CHANGELOG
- Added vault dump-config
- Added vault bootstrap-env
+- API break : `client.get_all(paths)` becomes `client.get_all_secrets(*paths)`
+- Added vault delete-all
0.3.9
-----
diff ... |
peopledoc__vault-cli-91 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"vault_cli/cli.py:get"
],
"edited_modules": [
"vault_cli/cli.py:get"
]
},
"file": "vault_cli/cli.py"
}
] | peopledoc/vault-cli | 3d9b7015383e9b97f4b4c617cd7d1ad34acc0ef8 | vault get should be --text by default, --yaml if explicitely requested
This would make thing so much simpler.
@pilou- do you think it would change something to the role you developed ? (we can discuss this in a private space if you want) | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 33edc55..3eaf296 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,11 @@
CHANGELOG
=========
+0.8.0 (unreleased)
+------------------
+
+- vault get defaults to text for string secrets, yaml for complex types (#87)
+
0.7.0 (2019-07-04)
------------------
diff ... |
pepkit__eido-77 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "eido/_version.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"eido/conversion_plu... | pepkit/eido | 884ce1955cde7bec3861bed0e88697cbc8b65aea | eido convert filters for csv and yaml appear to be broken
I have a PEP project which appears to be functional when using it with peppy, and also the eido filters `yaml-samples` and `basic` run without error.
But when I try to convert it to yaml or csv, eido crashes with various error messages:
```python
eido ... | diff --git a/eido/_version.py b/eido/_version.py
index d31c31e..788da1f 100644
--- a/eido/_version.py
+++ b/eido/_version.py
@@ -1,1 +1,1 @@
-__version__ = "0.2.3"
+__version__ = "0.2.4"
diff --git a/eido/conversion_plugins.py b/eido/conversion_plugins.py
index 01dd550..fe45805 100644
--- a/eido/conversion_plugins.py
+... |
pepkit__peppy-450 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "peppy/_version.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules":... | pepkit/peppy | 8449635bb35e16748e693bdd2c4820502d7b448d | Add orient argument to `to_dict` method
It would be niece to add `orient` argument, that sets orientation of the output structure of the samples and subsamples
https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.to_dict.html
Related issue: https://github.com/pepkit/pephub/issues/186 | diff --git a/docs/changelog.md b/docs/changelog.md
index 22ea48b..3ecc382 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -2,6 +2,16 @@
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
+## [0.35.6] -- 2... |
pepkit__peppy-453 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "peppy/_version.py"
},
{
"changes": {
"added_entities": [
"peppy/project.py:Project._set_indexes"
],
"added_modules": null,
... | pepkit/peppy | f9845b12b60793d08fba6d9c9aee30a4de75ce23 | from_dict method does not set correctly sample and subsample indexes
Related issue: https://github.com/pepkit/pephub/issues/207 | diff --git a/docs/changelog.md b/docs/changelog.md
index 3ecc382..1351854 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -2,6 +2,11 @@
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
+## [0.35.7] -- 2... |
pepkit__peppy-488 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "peppy/_version.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules":... | pepkit/peppy | e71627d3483ed3256b9b3ce764b9a2e8e8b5c5e0 | String yaml representation of sample
Is there any way for me to get a straight-up yaml representation of a sample? I found `sample.to_yaml()` but this appears to only be able to output to a file.
I can also just `print(sample)`, but then I get all this extra stuff too:
```
Sample 'sample1' in Project (/home/nshe... | diff --git a/docs/changelog.md b/docs/changelog.md
index 4a96c87..4db79aa 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -2,6 +2,10 @@
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
+## [0.40.2] -- 2... |
pepkit__peppy-494 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "peppy/_version.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"peppy/project.py:P... | pepkit/peppy | 0f28c65e7cc95cce8aa0c4b318ddb2dfb809bd17 | Make PEP representations consistent
We currently have 3 ways of representing PEPs:
1. Schema representations -> see: https://schema.databio.org/?namespace=pep&schema=2.1.0
2. peppy.Project object -> this is a mutable mapping containing `_config` and `samples` attributes.
3. dict via peppy.Project.to_dict() -> this... | diff --git a/peppy/_version.py b/peppy/_version.py
index d6d6823..6e2b9ea 100644
--- a/peppy/_version.py
+++ b/peppy/_version.py
@@ -1,1 +1,1 @@
-__version__ = "0.40.5"
+__version__ = "0.40.6"
diff --git a/peppy/project.py b/peppy/project.py
index 9f46ccc..b7b58e0 100644
--- a/peppy/project.py
+++ b/peppy/project.py
@@... |
pepkit__ubiquerg-33 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"setup.py:read_reqs"
],
"edited_modules": [
"setup.py:read_reqs"
]
},
"file": "setup.py"
},
{
"changes": {
"added_entities": null,
"added_modules": n... | pepkit/ubiquerg | 771ffbf6a70929d2bc472c348f1f6677e28bd4cf | make is_url more strict?
Is the current implementation too lose?
```
In [1]: from ubiquerg import is_url
In [2]: is_url("description: 'this is a schema.'")
Out[2]: True
```
Here I also require no spaces:
```
def is_url(maybe_url):
from urllib.parse import urlparse
return ' ' not in maybe_url a... | diff --git a/docs/changelog.md b/docs/changelog.md
index 8fdc819..a0432ae 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -2,6 +2,11 @@
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
+## [0.6.2] - 20... |
permamodel__permamodel-79 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"permamodel/components/Ku_method.py:Ku_method.Extract_Soil_Texture2"
],
"edited_modules": [
"permamodel/components/Ku_method.py:Ku_method"
]
},
"file": "permamodel/compo... | permamodel/permamodel | a8b0014abb54bda682f275cf74e45bcabebf955c | Update use of int for numpy>=1.24
In NumPy 1.24, `numpy.int` is replaced with `int`. This causes the Ku model to fail:
```
File ~/anaconda3/envs/pymt/lib/python3.10/site-packages/permamodel/components/Ku_method.py:788, in Ku_method.Extract_Soil_Texture2(self)
784 lat = np.transpose(np.reshape(np.repeat(self.lat,... | diff --git a/permamodel/components/Ku_method.py b/permamodel/components/Ku_method.py
index feeb38a..5e5f174 100644
--- a/permamodel/components/Ku_method.py
+++ b/permamodel/components/Ku_method.py
@@ -844,8 +844,8 @@ class Ku_method(perma_base.PermafrostComponent):
x_coords, y_coords = ~aff * (lon, lat)
- ... |
peter-wangxu__persist-queue-115 | [
{
"changes": {
"added_entities": [
"persistqueue/queue.py:Queue.empty"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"persistqueue/queue.py:Queue"
]
},
"file": "persistqueue/queue.py"
},
{
"changes": {
"added_enti... | peter-wangxu/persist-queue | bff90abfae0011427de552bb0243d521d6fa79ce | Add #.empty
Hello @peter-wangxu, would you accept a PR adding the #.empty method to your queue implementations?
We could also add #.full but since the SQLite queue does not support `maxsize` I guess it would not make much sense. | diff --git a/persistqueue/queue.py b/persistqueue/queue.py
index dac8ec6..0a1e301 100644
--- a/persistqueue/queue.py
+++ b/persistqueue/queue.py
@@ -138,6 +138,9 @@ class Queue(object):
def _qsize(self):
return self.info['size']
+ def empty(self):
+ return self.qsize() == 0
+
def put(self... |
peter-wangxu__persist-queue-127 | [
{
"changes": {
"added_entities": [
"persistqueue/sqlackqueue.py:SQLiteAckQueue.shrink_disk_usage"
],
"added_modules": null,
"edited_entities": [
"persistqueue/sqlackqueue.py:SQLiteAckQueue.resume_unack_tasks",
"persistqueue/sqlackqueue.py:SQLiteAckQueue._count",
... | peter-wangxu/persist-queue | 7bdbcdeb03ca2e202a5a98a7be86783b778b6238 | ACK Queue: clear_acked_data() behavior
Playing around with the ```clear_acked_data()``` function, it seems to hang on to the last 1000 acked queue items. Why is that? I've already acked the data, yet disk space continued to be used.
Looking at the code in question:
```python
@sqlbase.with_conditional_transacti... | diff --git a/README.rst b/README.rst
index aaa6ae1..13ca369 100644
--- a/README.rst
+++ b/README.rst
@@ -31,6 +31,14 @@ and `Pickling Class Instances(Python3) <https://docs.python.org/3/library/pickle
This project is based on the achievements of `python-pqueue <https://github.com/balena/python-pqueue>`_
and `queuelib... |
peter-wangxu__persist-queue-153 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "persistqueue/__init__.py"
},
{
"changes": {
"added_entities": [
"persistqueue/sqlackqueue.py:SQLiteAckQueue._check_id",
"persist... | peter-wangxu/persist-queue | 1089921e7a626f05f5bf0a6f7a6d5d286f7b290d | qsize() reports negative value
Using the SQLiteAckQueue multithreaded and I'm trying to get a count on the queue size using qsize(), but sometimes I'll see negative numbers. I think that the issue is the `_unack_cache` is not included in the total queue size, which I think it probably should be as it hasn't yet receiv... | diff --git a/.circleci/config.yml b/.circleci/config.yml
index fdbf99b..629c232 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -3,7 +3,7 @@ jobs:
py27:
docker:
# Primary container image where all steps run.
- - image: circleci/python:2.7.15
+ - image: circleci/python:2.7.17
... |
peter-wangxu__persist-queue-170 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"persistqueue/sqlackqueue.py:FILOSQLiteAckQueue"
]
},
"file": "persistqueue/sqlackqueue.py"
}
] | peter-wangxu/persist-queue | cc974b1568b2358555352f85053c2cbdc090fa9c | FILOSQLiteAckQueue _SQL_SELECT broken
It seems that FILOSQLliteAckQueue's _SQL_SELECT is not formatted properly.
I'm getting:
```
File "/home/*************/.venv/lib/python3.8/site-packages/persistqueue/sqlackqueue.py", line 290, in get
serialized = self._pop(
File "/home/*************/.venv/lib/python... | diff --git a/persistqueue/sqlackqueue.py b/persistqueue/sqlackqueue.py
index 6669895..e689a03 100644
--- a/persistqueue/sqlackqueue.py
+++ b/persistqueue/sqlackqueue.py
@@ -362,7 +362,7 @@ class FILOSQLiteAckQueue(SQLiteAckQueue):
_TABLE_NAME = 'ack_filo_queue'
# SQL to select a record
_SQL_SELECT = (
- ... |
peter-wangxu__persist-queue-182 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "persistqueue/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"persistqueu... | peter-wangxu/persist-queue | 464a82063f9421409491b9e099b0ea4c46fdb411 | File is not getting cleared after get() function
I entered data to file in file-based queue. But after performing get() the elements from the queue is deleted but if we open the file we can still see the data. So i think the file size will keep on increasing if we keep on increasing data. | diff --git a/README.rst b/README.rst
index 67ec6bf..111752f 100644
--- a/README.rst
+++ b/README.rst
@@ -180,6 +180,11 @@ Close the console, and then recreate the queue:
'str2'
>>>
+New functions:
+*Available since v0.8.0*
+
+- ``shrink_disk_usage`` perform a ``VACUUM`` against the sqlite, and rebuild the dat... |
peter-wangxu__persist-queue-25 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "persistqueue/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"persistqueu... | peter-wangxu/persist-queue | 10b8fa0e8bf5da6d44dbeb85f94a2b0779685d41 | FIFOSQLiteQueue: the get() method returns None instead of blocking
and if I specify get(block=True) it raises the empty exception | diff --git a/persistqueue/__init__.py b/persistqueue/__init__.py
index c066e10..ef321ef 100644
--- a/persistqueue/__init__.py
+++ b/persistqueue/__init__.py
@@ -1,7 +1,7 @@
# coding=utf-8
__author__ = 'Peter Wang'
__license__ = 'BSD License'
-__version__ = '0.3.0'
+__version__ = '0.3.1'
from .exceptions import Em... |
peter-wangxu__persist-queue-28 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"persistqueue/sqlbase.py:SQLiteBase._new_db_connection",
"persistqueue/sqlbase.py:SQLiteBase._init",
"persistqueue/sqlbase.py:SQLiteBase._count"
],
"edited_modules": [
... | peter-wangxu/persist-queue | 8cd900781aa449d2e921bf5db953d02815110646 | FIFOSQLiteQueue: the get() method returns None instead of blocking
and if I specify get(block=True) it raises the empty exception | diff --git a/persistqueue/sqlbase.py b/persistqueue/sqlbase.py
index 48955f7..e0a7672 100644
--- a/persistqueue/sqlbase.py
+++ b/persistqueue/sqlbase.py
@@ -79,6 +79,7 @@ class SQLiteBase(object):
def _init(self):
"""Initialize the tables in DB."""
+
if self.path == self._MEMORY:
s... |
peterbe__hashin-106 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:run"
],
"edited_modules": [
"hashin.py:run"
]
},
"file": "hashin.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
... | peterbe/hashin | a27c211bdab753f89530558397490a736cb73116 | Fails on pyup comments in requirements file
E.g.
```
▶ hashin --dry-run -u -r requirements/default.txt
Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/packaging/requirements.py", line 93, in __init__
req = REQUIREMENT.parseString(requirement_string)
File "/usr/local/lib/py... | diff --git a/README.rst b/README.rst
index 7a37972..a4f08b2 100644
--- a/README.rst
+++ b/README.rst
@@ -270,6 +270,11 @@ put it directly into ``pip``.
Version History
===============
+0.14.2
+ * When using ``--update-all`` and parsing requirements file it could be fooled
+ by comments that look like package sp... |
peterbe__hashin-109 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:run_packages",
"hashin.py:get_parser"
],
"edited_modules": [
"hashin.py:run_packages",
"hashin.py:get_parser"
]
},
"file": "hashin.py"
},
... | peterbe/hashin | ad75a2338bb1aa5ce6a56ac5288ad582fcbad65d | New --index-url option is broken
Shame on me for landing https://github.com/peterbe/hashin/pull/107 without properly testing it manually on the command line.
```
▶ python hashin.py -r /tmp/reqs.txt DJANGO -v
Traceback (most recent call last):
File "hashin.py", line 812, in <module>
sys.exit(main())
Fil... | diff --git a/README.rst b/README.rst
index 7f63630..3aefe28 100644
--- a/README.rst
+++ b/README.rst
@@ -270,8 +270,12 @@ put it directly into ``pip``.
Version History
===============
+0.14.4
+ * Bugfix for new ``--index-url`` option feature in version 0.14.3.
+ See https://github.com/peterbe/hashin/issues/108
... |
peterbe__hashin-110 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:run_packages"
],
"edited_modules": [
"hashin.py:run_packages"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | 90f2804dc624a52cd9283bd62fead99b837a3c1f | Order of hashes no longer canonical
Since version 0.14, the order of hashes does not seem to be deterministic.
Before 0.14, the hashes used to be lexicographically ordered.
I am guessing this was changed in https://github.com/peterbe/hashin/pull/95
What is the reason for this?
We use hashin in electrum for de... | diff --git a/hashin.py b/hashin.py
index cbc998c..a43390e 100755
--- a/hashin.py
+++ b/hashin.py
@@ -246,7 +246,7 @@ def run_packages(
maybe_restriction = "" if not restriction else "; {0}".format(restriction)
new_lines = "{0}=={1}{2} \\\n".format(req, data["version"], maybe_restriction)
padd... |
peterbe__hashin-111 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:main"
],
"edited_modules": [
"hashin.py:main"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | 23840376aaf09746264a99545526fe4bbec93e17 | Be kinder if the package is a requirements file
So many times I've typed something like this:
```bash
▶ hashin --dry-run -u requirements/default.txt
Can not combine the --update-all option with a list of packages.
```
when I meant to type `hashin --dry-run -u -r requirements/default.txt`
It reminds me of how ... | diff --git a/hashin.py b/hashin.py
index a43390e..427079f 100755
--- a/hashin.py
+++ b/hashin.py
@@ -773,6 +773,23 @@ def main():
parser = get_parser()
args = parser.parse_args()
+ if (
+ args.update_all
+ and args.packages
+ and len(args.packages) == 1
+ and os.path.isfile(ar... |
peterbe__hashin-114 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:amend_requirements_content"
],
"edited_modules": [
"hashin.py:amend_requirements_content"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | 10a7048202c27d05befd8c2391e3701069d467ef | Handle indentation
Would be nice if `hashin` could handle indented files like this one:
https://github.com/liberapay/liberapay.com/blob/master/requirements_base.txt
```
boto3==1.9.85 \
--hash=sha256:acfd27967cf1ba7f9d83ad6fc2011764541e4c295fe0d896ea7b495cc2f03336 \
--hash=sha256:96296871863e0245b04931d... | diff --git a/hashin.py b/hashin.py
index a053ca1..515e037 100755
--- a/hashin.py
+++ b/hashin.py
@@ -387,43 +387,45 @@ def amend_requirements_content(requirements, all_new_lines):
padding = " " * 4
- def is_different_lines(package, new_lines):
- # This assumes that for sure the package is already men... |
peterbe__hashin-117 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:amend_requirements_content"
],
"edited_modules": [
"hashin.py:amend_requirements_content"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | a9e2239bf46fcba12be9ecac272a806fc48bfe1e | Hashin support for not distinguishing between underscored/hyphenated
pypi appears to follow guidelines outlined in PEP8 around package names preferring to hyphenate them as opposed to underscore them
https://www.python.org/dev/peps/pep-0008/#package-and-module-names
"""
Modules should have short, all-lowercase n... | diff --git a/hashin.py b/hashin.py
index 515e037..df1a229 100755
--- a/hashin.py
+++ b/hashin.py
@@ -388,17 +388,39 @@ def amend_requirements_content(requirements, all_new_lines):
padding = " " * 4
def is_different_lines(old_lines, new_lines, indent):
+ # This regex is used to only temporarily normal... |
peterbe__hashin-125 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:amend_requirements_content"
],
"edited_modules": [
"hashin.py:amend_requirements_content"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | 5e81048ea69ddd07bb9a9a2e46a54fa11d6e3f1d | hashin removes # when hashes were generated with pip-compile
Looks like `hashin` removes `#` when hashes were generated with `pip-compile` originally. Example
```
-requests==2.25.1 \
- --hash=sha256:27973dd4a904a4f13b263a19c866c13b92a39ed1c964655f025f3f8d3d75b804 \
- --hash=sha256:c210084e36a42ae6b9219e00e... | diff --git a/README.rst b/README.rst
index 367570c..c2389f4 100644
--- a/README.rst
+++ b/README.rst
@@ -270,6 +270,9 @@ put it directly into ``pip``.
Version History
===============
+ * Preserve indented comments when updating requirements files.
+ See https://github.com/peterbe/hashin/issues/124
+
* Switch... |
peterbe__hashin-131 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:run_packages",
"hashin.py:get_package_hashes"
],
"edited_modules": [
"hashin.py:run_packages",
"hashin.py:get_package_hashes"
]
},
"file": "ha... | peterbe/hashin | 966ccf0bbfc24acc18d1c31a37b19b1bb5ace5cd | Order of hashes from `get_package_hashes`
As in #105 , I wonder if we could expect the output of `get_package_hashes` to have hashes in lexicographical order.
GitHub's dependabot is relying on that and is creating commits in my repo that are conflicting with other tools. Of course dependabot could fix it, but I beli... | diff --git a/README.rst b/README.rst
index 7715b8f..011cbde 100644
--- a/README.rst
+++ b/README.rst
@@ -272,6 +272,10 @@ Version History
* Add python 3.9 and 3.10 to the test matrix.
+ * Preserve lexigraphical order of hashes for the output of the
+ ``get_releases_hashes`` function.
+ See https://github.... |
peterbe__hashin-186 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:expand_python_version"
],
"edited_modules": [
"hashin.py:expand_python_version"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | 2bea4202782312b79a3857a3995305a1c0fcd62a | Running hashin with Python versions >= 3.10 raises PackageError('No releases can be found....')
The issue seems to stem from this piece of code.
```python
def expand_python_version(version):
if not re.match(r"^\d\.\d$", version):
return [version]
```
The above regular expression assumes the minor ... | diff --git a/hashin.py b/hashin.py
index 284af3b..ecef05f 100755
--- a/hashin.py
+++ b/hashin.py
@@ -459,9 +459,9 @@ def expand_python_version(version):
Expand Python versions to all identifiers used on PyPI.
>>> expand_python_version('3.5')
- ['3.5', 'py3', 'py2.py3', 'cp35']
+ ['3.5', 'cp35', 'py2.p... |
peterbe__hashin-22 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:amend_requirements_content"
],
"edited_modules": [
"hashin.py:amend_requirements_content"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | ce536a0cffac911124b9af4d14ec0ab79e32816a | Wrong package replaced when target name is found in existing package
For example, an attempt to add hashes for the `selenium` package replaces the `pytest-selenium` package. Another example would be `pytest-django` and `django`.
Before:
```ini
pytest-selenium==1.2.1 \
--hash=sha256:e82f0a265b0e238ac42ac275d79... | diff --git a/hashin.py b/hashin.py
index 510e9bf..d2d1fe6 100755
--- a/hashin.py
+++ b/hashin.py
@@ -120,7 +120,6 @@ def run(spec, file, algorithm, python_versions=None, verbose=False):
def amend_requirements_content(requirements, package, new_lines):
-
# if the package wasn't already there, add it to the bot... |
peterbe__hashin-33 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "hashin.py"
}
] | peterbe/hashin | 6549e7a0cf88f62c5c38a2ac3a5b3ea069415f34 | Unrecognizable url Error
This one works:
```
hashin turbine
```
This one doesn't:
```
hashin turbine --python-version 2.7
```
```
Traceback (most recent call last):
File "/Users/j/dev/.virtualenvs/hashin/bin/hashin", line 11, in <module>
sys.exit(main())
File "/Users/j/dev/.virtualenvs/hashin/li... | diff --git a/hashin.py b/hashin.py
index 8946bc7..bb3b378 100755
--- a/hashin.py
+++ b/hashin.py
@@ -234,6 +234,7 @@ CLASSIFY_EGG_RE = re.compile('''
CLASSIFY_ARCHIVE_RE = re.compile('''
^(?P<package>.+)-
(?P<version>\d[^-]*)
+ (-(?P<platform>[^\.]+))?
.(?P<format>tar.(gz|bz2)|zip)
(\#md5=.*)?
... |
peterbe__hashin-42 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:get_latest_version"
],
"edited_modules": [
"hashin.py:get_latest_version"
]
},
"file": "hashin.py"
},
{
"changes": {
"added_entities": null,
... | peterbe/hashin | 150daa03f4ec17544d93aa9e66a06d1adc45bf26 | hashin cannot handle leading zeros in package version numbers
Pip can install packages with a missing leading zero in the version number e.g. `Unidecode==0.04.20`:
I was passing the output of `pip freeze` into `hashin` and encountered this problem.
```
/tmp > bin/pip install Unidecode==0.4.20 # or Unidecode==0.... | diff --git a/README.rst b/README.rst
index 965e63c..984d968 100644
--- a/README.rst
+++ b/README.rst
@@ -185,6 +185,11 @@ put it directly into ``pip``.
Version History
===============
+0.11.0
+ * Cope with leading zeros in version numbers when figuring out what
+ the latest version is.
+ See https://github.c... |
peterbe__hashin-43 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:main"
],
"edited_modules": [
"hashin.py:main"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | 469e16c992dd8952871254a64355335a72afe35c | hashin --version should say what version hashin is
Title says it all. | diff --git a/README.rst b/README.rst
index 984d968..15310ff 100644
--- a/README.rst
+++ b/README.rst
@@ -185,6 +185,11 @@ put it directly into ``pip``.
Version History
===============
+0.11.1
+ * Ability to run ``hashin --version`` to see what version of hashin is
+ installed.
+ See https://github.com/peterb... |
peterbe__hashin-50 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:main"
],
"edited_modules": [
"hashin.py:main"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | ac3f43043a3de7e9b87c731d2aeccf7713c1d465 | Python version typos generate messy exception
Currently, if I specify the python version improperly, or there is no package for that version, I get an exception thrown:
```
$ hashin -p python2.8 -v -r requirements.txt pyasn1==0.2.3
https://pypi.python.org/pypi/pyasn1/json
Traceback (most recent call last):
File ... | diff --git a/hashin.py b/hashin.py
index 6856bcb..f2b3c1e 100755
--- a/hashin.py
+++ b/hashin.py
@@ -430,13 +430,17 @@ def main():
args = parser.parse_args()
- return run(
- args.packages,
- args.requirements_file,
- args.algorithm,
- args.python_version,
- verbose=args.ve... |
peterbe__hashin-65 | [
{
"changes": {
"added_entities": null,
"added_modules": [
"hashin.py:NoVersionsError"
],
"edited_entities": [
"hashin.py:run_single_package",
"hashin.py:get_latest_version",
"hashin.py:get_package_hashes",
"hashin.py:main"
],
"edited_mo... | peterbe/hashin | bbe0b6c379e25fbd8d3e702473e8e29677ccd9c0 | `hashin black` fails
```
▶ hashin black
Traceback (most recent call last):
File "/usr/local/bin/hashin", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python3.6/site-packages/hashin.py", line 474, in main
verbose=args.verbose,
File "/usr/local/lib/python3.6/site-packages/hashin.py", li... | diff --git a/hashin.py b/hashin.py
index c1bb79b..1590560 100755
--- a/hashin.py
+++ b/hashin.py
@@ -58,6 +58,11 @@ parser.add_argument(
help='Verbose output',
action='store_true',
)
+parser.add_argument(
+ '--include-prereleases',
+ help='Include pre-releases (off by default)',
+ action='store_true... |
peterbe__hashin-74 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:get_releases_hashes"
],
"edited_modules": [
"hashin.py:get_releases_hashes"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | a80c5efbb1630f75a9cfd4492627e9aff051c3e1 | Verbose option doesn't make sense any more when the algorithm is in the release
When we [started using pypi.org instead](https://github.com/peterbe/hashin/commit/66aa748a6d80e436283f26526b5af2b3b9a0d62f) one important change was that now we can (almost) always get the digests as part of the JSON payload. Before we had ... | diff --git a/README.rst b/README.rst
index 91b83ea..4be9060 100644
--- a/README.rst
+++ b/README.rst
@@ -221,6 +221,11 @@ put it directly into ``pip``.
Version History
===============
+0.13.x
+
+ * Don't show URLs when using ``--verbose`` if files don't need to be
+ downloaded. See https://github.com/peterbe/ha... |
peterbe__hashin-83 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:run_single_package",
"hashin.py:amend_requirements_content"
],
"edited_modules": [
"hashin.py:run_single_package",
"hashin.py:amend_requirements_content"
... | peterbe/hashin | ffe6115cceef588f6e559710d9ce2fdb3e07f4eb | fails on extras syntax
example:
```
$ hashin 'python-language-server[yapf]'
Traceback (most recent call last):
File "/home/user/go/src/github.com/user/flaskexp/ve/bin/hashin", line 11, in <module>
sys.exit(main())
File "/home/user/go/src/github.com/user/flaskexp/ve/lib/python3.6/site-packages/hashin.py"... | diff --git a/README.rst b/README.rst
index 6380fff..e22dd09 100644
--- a/README.rst
+++ b/README.rst
@@ -252,7 +252,12 @@ put it directly into ``pip``.
Version History
===============
-0.13.x
+next
+
+ * Support for "extras syntax". E.g. ``hashin "requests[security]"``. Doesn't
+ actually get hashes for ``secur... |
peterbe__hashin-88 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:run",
"hashin.py:main"
],
"edited_modules": [
"hashin.py:run",
"hashin.py:main"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | ccb661bd6548db78a0520b051f24a1dbba502065 | Add `--update-all` option and update all dependencies with their hashes?
Hey @peterbe!
I work with a lot of legacy projects that don't add hashes to their dependencies and I'd like to improve their security.
What do you think about an option which would just scan through all entries and add hashes to them?
Currently... | diff --git a/README.rst b/README.rst
index e22dd09..d7d6ae3 100644
--- a/README.rst
+++ b/README.rst
@@ -254,6 +254,10 @@ Version History
next
+ * New flag ``--update-all`` (alias ``-u``) will parse the requirements file,
+ ignore the version, and update all packages that have new versions.
+ See https://gi... |
peterbe__hashin-89 | [
{
"changes": {
"added_entities": null,
"added_modules": [
"hashin.py:PackageNotFoundError"
],
"edited_entities": [
"hashin.py:_download"
],
"edited_modules": [
"hashin.py:_download"
]
},
"file": "hashin.py"
}
] | peterbe/hashin | 8c0de876224632d30415e064c2bee9b3315d4466 | Rewrap 404 errors from pypi.org
E.g.:
```bash
▶ python hashin.py -r /tmp/r.txt requests djangu
Traceback (most recent call last):
File "hashin.py", line 544, in <module>
sys.exit(main())
File "hashin.py", line 536, in main
dry_run=args.dry_run,
File "hashin.py", line 142, in run
run_single_... | diff --git a/README.rst b/README.rst
index d7d6ae3..e8684f3 100644
--- a/README.rst
+++ b/README.rst
@@ -254,6 +254,10 @@ Version History
next
+ * In Python 3, if the package can't be found you get a more explicit exception
+ pointing out which package (URL) that failed.
+ See https://github.com/peterbe/has... |
peterbe__hashin-92 | [
{
"changes": {
"added_entities": [
"hashin.py:run_packages"
],
"added_modules": [
"hashin.py:run_packages"
],
"edited_entities": [
"hashin.py:run",
"hashin.py:run_single_package",
"hashin.py:amend_requirements_content"
],
"edited_... | peterbe/hashin | 85d3e5f3798236eb61312bf3dc9d8fc6f244cbb4 | Make it atomic
At the moment if you run `hashin` with more than one package, it deals with it one package at a time. See https://github.com/peterbe/hashin/blob/ccb661bd6548db78a0520b051f24a1dbba502065/hashin.py#L126-L127
Basically, it means, that it's the same thing doing:
```bash
$ hashin foo bar
```
as doing
... | diff --git a/hashin.py b/hashin.py
index 98d5c44..3ed9677 100755
--- a/hashin.py
+++ b/hashin.py
@@ -152,13 +152,12 @@ def run(specs, requirements_file, *args, **kwargs):
if isinstance(specs, str):
specs = [specs]
- for spec in specs:
- run_single_package(spec, requirements_file, *args, **kwar... |
peterbe__hashin-95 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hashin.py:amend_requirements_content",
"hashin.py:get_package_hashes"
],
"edited_modules": [
"hashin.py:amend_requirements_content",
"hashin.py:get_package_hashes"
... | peterbe/hashin | fefd565a57d1b465f7112e6ac09181c2c9eb81ca | Order of hashes shouldn't matter
Consider this example:
```bash
▶ python hashin.py -r ~/songsearch/requirements.txt --dry-run --update-all
--- Old
+++ New
...
xmltodict==0.11.0 \
- --hash=sha256:add07d92089ff611badec526912747cf87afd4f9447af6661aca074eeaf32615 \
- --hash=sha256:8f8d7d40aa28d83f4109a7e8aa8... | diff --git a/README.rst b/README.rst
index 7cddf5e..45e29eb 100644
--- a/README.rst
+++ b/README.rst
@@ -254,6 +254,10 @@ Version History
next
+ * Order of hashes should not affect if a package in the requirements file
+ should be replaced or not.
+ See https://github.com/peterbe/hashin/issues/93
+
* (In... |
peterbe__premailer-124 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"premailer/premailer.py:Premailer.transform"
],
"edited_modules": [
"premailer/premailer.py:Premailer"
]
},
"file": "premailer/premailer.py"
}
] | peterbe/premailer | f211f3f1bcfc87dc0318f056d319bb5575f62a72 | Replacement of urls beginning with //
When using a link whose href starts with "//", Premailer should just add http or https depending on the base url it uses. Currently, it replaces it with the full host, so ``//another.host/`` becomes ``http://my.base.host/another.host/`` | diff --git a/premailer/premailer.py b/premailer/premailer.py
index b53fc23..2d3a221 100644
--- a/premailer/premailer.py
+++ b/premailer/premailer.py
@@ -17,7 +17,7 @@ if sys.version_info >= (3,): # pragma: no cover
# As in, Python 3
from io import StringIO
from urllib.request import urlopen
- from ur... |
peterbe__premailer-128 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"premailer/premailer.py:Premailer.__init__"
],
"edited_modules": [
"premailer/premailer.py:Premailer"
]
},
"file": "premailer/premailer.py"
}
] | peterbe/premailer | d2a2a4afdd06e5931545bc76b9ee940fdefdb543 | Unknown property names
Property: Unknown Property name. [31:17: -ms-interpolation-mode]
Property: Unknown Property name. [4:17: mso-line-height-rule]
Property: Unknown Property name. [106:17: -webkit-text-size-adjust]
Property: Unknown Property name. [107:17: -ms-text-size-adjust]
Property: Unknown Property name. [... | diff --git a/README.rst b/README.rst
index 272a0b9..a3af844 100644
--- a/README.rst
+++ b/README.rst
@@ -221,7 +221,38 @@ attribute ``bgcolor="#eee"``.
Having these extra attributes basically as a "back up" for really shit
email clients that can't even take the style attributes. A lot of
professional HTML newsletter... |
peterbe__premailer-138 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"premailer/merge_style.py:csstext_to_pairs"
],
"edited_modules": [
"premailer/merge_style.py:csstext_to_pairs"
]
},
"file": "premailer/merge_style.py"
}
] | peterbe/premailer | e5e1feb7d63fc7499702d70e3197ad3d293e90bf | SyntaxErr on <h1> with !important
Feeding the following into ```transform()``` results in a ```SyntaxErr```:
```
<style type="text/css">
h1 { border:1px solid black }
p { color:red;}
</style>
<p>Hey</p>
<h1 style="display: block;font-family: Helvetica;font-size: 26px;font-style: normal;font-weight: bold;line-h... | diff --git a/premailer/merge_style.py b/premailer/merge_style.py
index 0fe93f7..9842e63 100644
--- a/premailer/merge_style.py
+++ b/premailer/merge_style.py
@@ -1,5 +1,6 @@
import cssutils
import threading
+from operator import itemgetter
def csstext_to_pairs(csstext):
@@ -10,11 +11,10 @@ def csstext_to_pairs(cs... |
peterbe__premailer-167 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "premailer/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"premailer/prem... | peterbe/premailer | cc18022e334d5336e48f75bd4e0a73c98cc5942a | keep class attributes
the transform() function replaces the "class" attribute with the appropriate styling, but it also removes the class from the html elements. I need the styling added inline, but the classes to be left within their elements so that my @media (!important) styling can be inserted in after and still ha... | diff --git a/premailer/__init__.py b/premailer/__init__.py
index e831baa..570b55c 100644
--- a/premailer/__init__.py
+++ b/premailer/__init__.py
@@ -1,4 +1,4 @@
from __future__ import absolute_import, unicode_literals
from .premailer import Premailer, transform
-__version__ = '2.11.0'
+__version__ = '3.0.0'
diff --... |
peterbe__premailer-185 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"premailer/premailer.py:Premailer._parse_style_rules",
"premailer/premailer.py:Premailer.transform"
],
"edited_modules": [
"premailer/premailer.py:Premailer"
]
},
... | peterbe/premailer | 597b57740c661df8b3f4f5bdec7c495afe955275 | Crashing when using on Semantic with exclude_pseudoclasses=False
Tried running this script:
```
# Just a test script for premailer
import premailer
html = """
<html>
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/semantic-ui/2.2.9/semantic.min.css"/>
<style>
h1{ bord... | diff --git a/premailer/premailer.py b/premailer/premailer.py
index 7cfb186..0a8c40d 100644
--- a/premailer/premailer.py
+++ b/premailer/premailer.py
@@ -250,6 +250,9 @@ class Premailer(object):
continue
elif '*' in selector and not self.include_star_selectors:
... |
peterbe__premailer-208 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"premailer/premailer.py:Premailer._css_rules_to_string"
],
"edited_modules": [
"premailer/premailer.py:Premailer"
]
},
"file": "premailer/premailer.py"
}
] | peterbe/premailer | 63f350d4477da71b8b9721e22b78f81afc83e1fb | AttributeError: 'CSSUnknownRule' object has no attribute 'style' in _css_rules_to_string
Exception on complicated style sheet:
>> from premailer import Premailer; import requests; url='https://www.smashingmagazine.com'; Premailer(html=requests.get(url).content.decode('utf-8'), base_url=url).transform()
Tracebac... | diff --git a/README.rst b/README.rst
index 5fc563c..f8445af 100644
--- a/README.rst
+++ b/README.rst
@@ -10,7 +10,7 @@ Looking for sponsors
This project is actively looking for corporate sponsorship. If you want
to help making this an active project consider `pinging
-Peter <http://www.peterbe.com/contact>`__ and w... |
peterbe__premailer-218 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"premailer/premailer.py:Premailer.transform"
],
"edited_modules": [
"premailer/premailer.py:Premailer"
]
},
"file": "premailer/premailer.py"
}
] | peterbe/premailer | 350af2440ccc9598d01841d1a22a8e5236da85a1 | Reusing premailer instances does not work
The README contains a [nice section](https://github.com/peterbe/premailer#if-execution-speed-is-on-your-mind) on speeding up premailer by reusing premailer instances. This, however, [throws an exception](https://github.com/peterbe/premailer/blob/master/premailer/premailer.py#L3... | diff --git a/premailer/premailer.py b/premailer/premailer.py
index 344a6ad..37fd743 100644
--- a/premailer/premailer.py
+++ b/premailer/premailer.py
@@ -311,18 +311,18 @@ class Premailer(object):
return rules, leftover
def transform(self, html=None, pretty_print=True, **kwargs):
- """change the s... |
peterbe__premailer-258 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"premailer/premailer.py:Premailer.__init__",
"premailer/premailer.py:Premailer._load_external_url"
],
"edited_modules": [
"premailer/premailer.py:Premailer"
]
},
... | peterbe/premailer | 7dcee9e68756442effb087c97823b444dde74a0a | Add cache support for _load_external_url
It would be handy if one could use `allow_network` to fetch styles and also rely on a cache for speedy results
It might be simple enough to just expose the session creation used for requests. Then something like [CacheControl](https://2.python-requests.org/en/master/communit... | diff --git a/CHANGES.rst b/CHANGES.rst
index 85c1be6..debbd61 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -4,6 +4,10 @@ premailer Changes
Peter's note: Unfortunately, ``premailer`` didn't use to keep a change log. But it's
never too late to start, so let's start here and now.
+Unreleased
+----------
+* New option... |
peterbe__premailer-261 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"premailer/merge_style.py:csstext_to_pairs"
],
"edited_modules": [
"premailer/merge_style.py:csstext_to_pairs"
]
},
"file": "premailer/merge_style.py"
}
] | peterbe/premailer | b5c543248c104cb04f7441721113ebfe8ae97177 | Style sorting breaking proper precedence
For the following styles:
```
.foo {
padding-left: 6px;
padding-right: 6px;
padding-top: 8px;
padding-bottom: 8px;
padding: 4px;
}
```
The browser should see the padding rules as all having the same precedence. As a tie-breaker, whichever appears last in the ... | diff --git a/CHANGES.rst b/CHANGES.rst
index debbd61..1c6fa58 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -7,6 +7,25 @@ never too late to start, so let's start here and now.
Unreleased
----------
* New option ``session=None`` to provide the session used for making http requests.
+* Bug fix: inlined styles are no l... |
petl-developers__petl-580 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"petl/transform/conversions.py:convertall"
],
"edited_modules": [
"petl/transform/conversions.py:convertall"
]
},
"file": "petl/transform/conversions.py"
}
] | petl-developers/petl | 012cc7faf79d2fa8147a2cfe3a8b39b110f77051 | `convertall` does not work when table header has non-string elements
#### Minimal, reproducible code sample, a copy-pastable example if possible
```python
t = [['foo', 11, 22], [2, 2, 2]]
petl.convertall(t, lambda x: x**2)
```
#### Problem description
`convertall()` uses `head()` to access the field names, bu... | diff --git a/petl/transform/conversions.py b/petl/transform/conversions.py
index 5328e2d..c699a79 100644
--- a/petl/transform/conversions.py
+++ b/petl/transform/conversions.py
@@ -6,7 +6,7 @@ from petl.compat import next, integer_types, string_types, text_type
import petl.config as config
from petl.errors import A... |
petl-developers__petl-634 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"petl/io/sources.py:_resolve_source_from_arg",
"petl/io/sources.py:read_source_from_arg",
"petl/io/sources.py:write_source_from_arg"
],
"edited_modules": [
"petl/io/so... | petl-developers/petl | 9f065ba647a86b8fcc183ed7c752d347382a8707 | tocsv(source=None) does not output to stdout
#### Minimal, reproducible code sample, a copy-pastable example if possible
```python
petl.wrap([...]).tocsv()
```
#### Problem description
The documentation says
```
Load - writing tables to files and databases
The following functions write data from a t... | diff --git a/docs/contributing.rst b/docs/contributing.rst
index d1952bf..c604472 100644
--- a/docs/contributing.rst
+++ b/docs/contributing.rst
@@ -29,7 +29,7 @@ suite with::
$ pip install -r requirements-tests.txt
$ pytest -v petl
-Currently :mod:`petl` supports Python 2.7, 3.6 up to 3.10
+Currently :mod:... |
petrobras__ross-1141 | [
{
"changes": {
"added_entities": [
"ross/coupling_element.py:CouplingElement.save",
"ross/coupling_element.py:CouplingElement.read_toml_data"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"ross/coupling_element.py:CouplingElement"
... | petrobras/ross | 19cdae938d0885a220b17168b583b15fb58408e7 | Error when trying to save rotor with coupling element
As mentioned in #1134, an error was encountered when saving a rotor with coupling element:
```
File d:\ProgramData\Anaconda3\Lib\site-packages\spyder_kernels\py3compat.py:356 in compat_exec
exec(code, globals, locals) File ..\wvc_insideshafting\ross10v01_inside_c... | diff --git a/docs/user_guide/tutorial_part_1.ipynb b/docs/user_guide/tutorial_part_1.ipynb
index 111580e8..37bc71ee 100644
--- a/docs/user_guide/tutorial_part_1.ipynb
+++ b/docs/user_guide/tutorial_part_1.ipynb
@@ -630,6 +630,195 @@
"```"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "sourc... |
pganssle__zoneinfo-45 | [
{
"changes": {
"added_entities": [
"src/zoneinfo/_zoneinfo.py:_ttinfo.__eq__"
],
"added_modules": null,
"edited_entities": [
"src/zoneinfo/_zoneinfo.py:ZoneInfo._find_trans",
"src/zoneinfo/_zoneinfo.py:ZoneInfo._load_file"
],
"edited_modules": [
... | pganssle/zoneinfo | ded22b8d6fc7b2470e75fe41349f9d42e04b3e27 | Add support for fixed offset time zones
Zones like `UTC` are always one time zone and have no DST. I think traditionally zones with no DST return `None` instead of `timedelta(0)`, so we can do the same thing.
Not sure what to do about time zones like `Africa/Abidjan` that have been using `GMT` since 1912, and do hav... | diff --git a/lib/zoneinfo_module.c b/lib/zoneinfo_module.c
index d438a64..3647143 100644
--- a/lib/zoneinfo_module.c
+++ b/lib/zoneinfo_module.c
@@ -43,6 +43,7 @@ typedef struct {
_ttinfo *ttinfo_before;
_tzrule tzrule_after;
_ttinfo *_ttinfos; // Unique array of ttinfos for ease of deallocation
+ un... |
pganssle__zoneinfo-46 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "src/zoneinfo/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": [
"src/zoneinfo/_common.py:ZoneInfoNotFoundEr... | pganssle/zoneinfo | 0b41c027aac4b69cb5eb9ca599ff78ea5826701c | Enforce that all inputs are relative directories
To avoid path traversal attacks, the PEP requires that inputs be relative and not absolute paths. | diff --git a/src/zoneinfo/__init__.py b/src/zoneinfo/__init__.py
index 82f855b..da6e5a6 100644
--- a/src/zoneinfo/__init__.py
+++ b/src/zoneinfo/__init__.py
@@ -1,6 +1,7 @@
-__all__ = ["ZoneInfo", "reset_tzpath", "TZPATH"]
+__all__ = ["ZoneInfo", "reset_tzpath", "TZPATH", "ZoneInfoNotFoundError"]
from . import _tzpa... |
pgmpy__pgmpy-1059 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/readwrite/BIF.py:BIFReader.get_probability_grammar",
"pgmpy/readwrite/BIF.py:BIFReader.get_values"
],
"edited_modules": [
"pgmpy/readwrite/BIF.py:BIFReader"
]
... | pgmpy/pgmpy | c5ba23a8f7891c0f32df56b24fa2dc5fc0ddbc85 | Bug in BIFReader function
### Subject of the issue
There is a bug in the BIFReader function. I think while reading the CPD only the order in which the states are specified is taken into account , not the actual values of the state.
e.g. variable Pollution {low high} **high - 1 low - 0**
variable Smoker {True Fals... | diff --git a/pgmpy/readwrite/BIF.py b/pgmpy/readwrite/BIF.py
index affdcf8d..af0bbbf2 100644
--- a/pgmpy/readwrite/BIF.py
+++ b/pgmpy/readwrite/BIF.py
@@ -95,7 +95,7 @@ class BIFReader(object):
# 1.00 or 1 or 1.00. 0.00 or 9.8e-5 etc
num_expr = Word(nums + '-' + '+' + 'e' + 'E' + '.') + Suppress(Optio... |
pgmpy__pgmpy-1215 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/factors/discrete/CPD.py:TabularCPD.__init__",
"pgmpy/factors/discrete/CPD.py:TabularCPD.get_values"
],
"edited_modules": [
"pgmpy/factors/discrete/CPD.py:TabularCPD"
... | pgmpy/pgmpy | a3a544694f55105208ae5edc1decd64be9ea913a | XML Belief Network writer class hardcoded for variables with cardinality 2
The current implementation seems to be hardcoded to work only for the CPDs of variables having a cardinality of 2. The lines at: https://github.com/pgmpy/pgmpy/blob/dev/pgmpy/readwrite/XMLBeliefNetwork.py#L451. The `range` here makes the assumpt... | diff --git a/pgmpy/factors/discrete/CPD.py b/pgmpy/factors/discrete/CPD.py
index 3f51d365..5c1de436 100644
--- a/pgmpy/factors/discrete/CPD.py
+++ b/pgmpy/factors/discrete/CPD.py
@@ -125,6 +125,15 @@ class TabularCPD(DiscreteFactor):
if values.ndim != 2:
raise TypeError("Values must be a 2D list/a... |
pgmpy__pgmpy-1216 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/estimators/BayesianEstimator.py:BayesianEstimator.estimate_cpd"
],
"edited_modules": [
"pgmpy/estimators/BayesianEstimator.py:BayesianEstimator"
]
},
"file": "pgm... | pgmpy/pgmpy | c37dda4401f23ec73fc5d17d957867cd62e588d3 | writing Bayesian model in a file and read it later
### Subject of the issue
I am using pgmpy package for learning Bayesian Network from data and predicting using it.
I want to save learned Bayesian Network in a file and use it for predicting in another time.
I saw your example on pgmpy_notebook but i understood tha... | diff --git a/pgmpy/estimators/BayesianEstimator.py b/pgmpy/estimators/BayesianEstimator.py
index 7e4fbcf2..ac085bb6 100644
--- a/pgmpy/estimators/BayesianEstimator.py
+++ b/pgmpy/estimators/BayesianEstimator.py
@@ -1,5 +1,7 @@
# -*- coding: utf-8 -*-
+from itertools import chain
+
import numpy as np
from pgmpy.e... |
pgmpy__pgmpy-1235 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/factors/discrete/DiscreteFactor.py:DiscreteFactor.reduce"
],
"edited_modules": [
"pgmpy/factors/discrete/DiscreteFactor.py:DiscreteFactor"
]
},
"file": "pgmpy/fac... | pgmpy/pgmpy | 88ad46b1643fb50ffedef366563a60f9f4beafab | state_name and state_no in reduce()
### Subject of the issue
The value argument in reduce() function for TabularCPD and DiscreteFactor. It looks like right now the argument should be (var_name, var_state_name), but previously it's (var_name, var_state_no). However, in pre_compute_reduce() of Sampling.py, this for loop... | diff --git a/pgmpy/factors/discrete/DiscreteFactor.py b/pgmpy/factors/discrete/DiscreteFactor.py
index 7a8cc62d..dab8fbc3 100644
--- a/pgmpy/factors/discrete/DiscreteFactor.py
+++ b/pgmpy/factors/discrete/DiscreteFactor.py
@@ -2,6 +2,7 @@ from __future__ import division
from itertools import product
from collection... |
pgmpy__pgmpy-1264 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/estimators/BayesianEstimator.py:BayesianEstimator.get_parameters",
"pgmpy/estimators/BayesianEstimator.py:BayesianEstimator.estimate_cpd"
],
"edited_modules": [
"pgmpy/... | pgmpy/pgmpy | b7dec2aef3d660d3d53be379f17953810cfc045d | VariableElimination ignores identical factors
### Subject of the issue
When VariableElimination generates several identical factors (same variables, same values) only one is considered and the rest are discarded. This is due to the use of sets (see e.g. "final_distribution = set()" in ExactInference.py), which do not ... | diff --git a/Contributing.md b/Contributing.md
index 37cc4166..3a8a5c6d 100644
--- a/Contributing.md
+++ b/Contributing.md
@@ -1,48 +1,50 @@
# Contributing to pgmpy
-Hi! Thanks for your interest in contributing to [pgmpy](https://pgmpy.org).
-In this document we'll try to summarize everything that you need to know t... |
pgmpy__pgmpy-1285 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/readwrite/BIF.py:BIFReader.get_model"
],
"edited_modules": [
"pgmpy/readwrite/BIF.py:BIFReader"
]
},
"file": "pgmpy/readwrite/BIF.py"
},
{
"changes": {
... | pgmpy/pgmpy | f379c8c3ca58651f4309b20289a09e7636fc0157 | Inconsistent reading and writing from files because of state names
By default, pgmpy assigns an `int` type state name to variables if no state names are explicitly specified. This creates a problem when these models are written to a file and read back. Since there is no way to differentiate between an `int` type state ... | diff --git a/pgmpy/readwrite/BIF.py b/pgmpy/readwrite/BIF.py
index 5d0c7e22..3095dc5c 100644
--- a/pgmpy/readwrite/BIF.py
+++ b/pgmpy/readwrite/BIF.py
@@ -345,9 +345,14 @@ class BIFReader(object):
]
return edges
- def get_model(self):
+ def get_model(self, state_name_type=str):
"""
- ... |
pgmpy__pgmpy-1312 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/estimators/ExhaustiveSearch.py:ExhaustiveSearch.all_dags"
],
"edited_modules": [
"pgmpy/estimators/ExhaustiveSearch.py:ExhaustiveSearch"
]
},
"file": "pgmpy/estim... | pgmpy/pgmpy | 45a769eb8338eec6740781ab46e74376d680c515 | An empty whitelist produces different results than no whitelist for HillClimbSearch
@ankurankan --- Posting as a new issue since the other issue got closed. I pulled dev/latest and ran some tests. Something is off with the whitelist functionality in the HillClimbSearch for Bayesian Networks. I have a fix locally, ha... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2503d0ff..e186fddc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
1. PC estimator with original, stable, and parallel variants.
2. PDAG class to represent partially directed D... |
pgmpy__pgmpy-1330 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "pgmpy/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/factors/cont... | pgmpy/pgmpy | 1499f2cfe7e416364b671d3650599edf9f556138 | Variable naming inconsistency?
### Subject of the issue
In line 54, 55 of pgmpy/pgmpy/models/LinearGaussianBayesianNetwork.py, cpd.variables has been checked for, whereas, line 66 of pgmpy/pgmpy/factors/continuous/LinearGaussianCPD.py has self.variable specified and not variables. Hence, I think that this error is be... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index e186fddc..f229f139 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,10 +13,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
5. Adds a global `SHOW_PROGRESS` variable.
6. Adds Chow-Liu structure learning algorithm.
7. Add `pgmpy.u... |
pgmpy__pgmpy-1341 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/estimators/MmhcEstimator.py:MmhcEstimator.mmpc"
],
"edited_modules": [
"pgmpy/estimators/MmhcEstimator.py:MmhcEstimator"
]
},
"file": "pgmpy/estimators/MmhcEstima... | pgmpy/pgmpy | 6b74695ecdb464480ab35d70c839964c7a4e7bee | Unable to run MMPC function in MMHC estimator
### Subject of the issue
`estimators.mmhc.mmpc()` crashes regardless of dataset used.
### Your environment
* pgmpy version 0.1.11.dev0
* Python version 3.6.9
* Operating System macOS catalina
### Steps to reproduce
Tell us how to reproduce this issue. Please prov... | diff --git a/pgmpy/estimators/MmhcEstimator.py b/pgmpy/estimators/MmhcEstimator.py
index 56f5c4f0..a67708c1 100644
--- a/pgmpy/estimators/MmhcEstimator.py
+++ b/pgmpy/estimators/MmhcEstimator.py
@@ -156,7 +156,7 @@ class MmhcEstimator(StructureEstimator):
"""Measure for (conditional) association between va... |
pgmpy__pgmpy-1349 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/estimators/HillClimbSearch.py:HillClimbSearch.estimate"
],
"edited_modules": [
"pgmpy/estimators/HillClimbSearch.py:HillClimbSearch"
]
},
"file": "pgmpy/estimator... | pgmpy/pgmpy | 84046ca382bff08944e05f5d3f30c262bbbd372e | ValueError in HillClimbSearch().estimate()
### Subject of the issue
It raises ValueError when estimating the graph with the HillClimbSearch model.
### Your environment
* pgmpy version : 0.1.12
* Python version : 3.7.7
* Operating System : Ubuntu 18.04.2 LTS
### Steps to reproduce
```python3
data = pd.DataFr... | diff --git a/pgmpy/estimators/HillClimbSearch.py b/pgmpy/estimators/HillClimbSearch.py
index 66b942d9..c19cd865 100644
--- a/pgmpy/estimators/HillClimbSearch.py
+++ b/pgmpy/estimators/HillClimbSearch.py
@@ -284,7 +284,8 @@ class HillClimbSearch(StructureEstimator):
iteration = range(int(max_iter))
... |
pgmpy__pgmpy-1360 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/estimators/PC.py:PC.skeleton_to_pdag"
],
"edited_modules": [
"pgmpy/estimators/PC.py:PC"
]
},
"file": "pgmpy/estimators/PC.py"
}
] | pgmpy/pgmpy | fd657ed91778459280bcdf103acf9282c876c1af | Some bugs in PC -> skeleton_to_pdag
### Some bugs in PC -> skeleton_to_pdag
When I debug the module `PC`, I found that `node_pairs` in `skeleton_to_pdag` is defined as a `combination` iterator. So after first iteration, it will not yield any more. Check this answer:
https://stackoverflow.com/a/25336739
In anothe... | diff --git a/README.md b/README.md
index d1a909f9..e7477581 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
pgmpy
=====
-[](https://travis-ci.org/pgmpy/pgmpy)
+[](https://travis... |
pgmpy__pgmpy-1398 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/inference/ExactInference.py:VariableElimination.query",
"pgmpy/inference/ExactInference.py:VariableElimination.max_marginal",
"pgmpy/inference/ExactInference.py:VariableElimination... | pgmpy/pgmpy | 2ae8c904ee59ffffe2ff7bbc794a075cc37646ae | Implement Network Pruning for optimizing Inference
### Subject of the issue
In some cases, some of the variables in the model do not effect the results of inference. The network can, therefore, be pruned before any inference is run on it. And since pruning would reduce the size of the network, it should make inference... | diff --git a/pgmpy/base/DAG.py b/pgmpy/base/DAG.py
index 46775525..1868d7fb 100644
--- a/pgmpy/base/DAG.py
+++ b/pgmpy/base/DAG.py
@@ -586,12 +586,15 @@ class DAG(nx.DiGraph):
"""
Returns a dictionary with the given variables as keys and all the nodes reachable
from that respective variable a... |
pgmpy__pgmpy-1402 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/inference/ExactInference.py:VariableElimination._get_elimination_order"
],
"edited_modules": [
"pgmpy/inference/ExactInference.py:VariableElimination"
]
},
"file"... | pgmpy/pgmpy | 843f7222686d2299cbe288dfb170d60aef945be8 | Manually specified elimination order throws an error
Since network pruning has now been added, if the elimination order is specified over all the variables in the model, it throws an error as some of the variables don't exist in the model anymore as a result of pruning. To fix this, add a check for manually specified e... | diff --git a/pgmpy/inference/ExactInference.py b/pgmpy/inference/ExactInference.py
index a9a3612b..c26da331 100644
--- a/pgmpy/inference/ExactInference.py
+++ b/pgmpy/inference/ExactInference.py
@@ -74,6 +74,7 @@ class VariableElimination(Inference):
)
# Step 1: If elimination_order is a list, verif... |
pgmpy__pgmpy-1416 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/models/DynamicBayesianNetwork.py:DynamicBayesianNetwork.initialize_initial_state"
],
"edited_modules": [
"pgmpy/models/DynamicBayesianNetwork.py:DynamicBayesianNetwork"
]... | pgmpy/pgmpy | a92ad86c662ee0253ac3f244d5c40575e9d46e87 | Dimensionality error when initializing DynamicBayesianNetwork
### Subject of the issue
Dimensionality error when initializing DynamicBayesianNetwork
### Your environment
* pgmpy_1617178903326
* Python 3.8.2
* Operating System OS X 11.3.1
### Steps to reproduce
```
from pgmpy.models import DynamicBayesianNet... | diff --git a/pgmpy/models/DynamicBayesianNetwork.py b/pgmpy/models/DynamicBayesianNetwork.py
index 4be5d4e4..c9a0c244 100644
--- a/pgmpy/models/DynamicBayesianNetwork.py
+++ b/pgmpy/models/DynamicBayesianNetwork.py
@@ -564,13 +564,13 @@ class DynamicBayesianNetwork(DAG):
new_cpd = TabularCP... |
pgmpy__pgmpy-1423 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/estimators/BayesianEstimator.py:BayesianEstimator.estimate_cpd"
],
"edited_modules": [
"pgmpy/estimators/BayesianEstimator.py:BayesianEstimator"
]
},
"file": "pgm... | pgmpy/pgmpy | 748c6390f79a9ca588ee8f4ce777a82de5f9740e | ValueError using BayesianEstimation with pseudo_counts after updating to 0.1.14
### ValueError using BayesianEstimation with pseudo_counts after updating to 0.1.14
Passing pseudo_counts to BayesianEstimator.estimate_cpd() leads to an ValueError:
> ValueError: The truth value of an array with more than one element ... | diff --git a/pgmpy/estimators/BayesianEstimator.py b/pgmpy/estimators/BayesianEstimator.py
index ba52255d..8af808ca 100644
--- a/pgmpy/estimators/BayesianEstimator.py
+++ b/pgmpy/estimators/BayesianEstimator.py
@@ -161,7 +161,9 @@ class BayesianEstimator(ParameterEstimator):
prior_type = prior_type.lower()
... |
pgmpy__pgmpy-1434 | [
{
"changes": {
"added_entities": [
"pgmpy/models/BayesianModel.py:BayesianModel.fit_update"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"pgmpy/models/BayesianModel.py:BayesianModel"
]
},
"file": "pgmpy/models/BayesianModel.py... | pgmpy/pgmpy | 564cd7ce1f4c42918b36365ecf6cdf60dd7ec7a0 | About BN's Incremental update’
### Subject of the issue
If we had an established Bayesian Network, Now we have some datas about it, Can we use this datas update the established Bayesian Network, instead of re-learning all the datas(the original datas and the datas we just mentiond) to Caculate the Bayesian Network's ... | diff --git a/pgmpy/models/BayesianModel.py b/pgmpy/models/BayesianModel.py
index b89c2f31..4b3232c7 100644
--- a/pgmpy/models/BayesianModel.py
+++ b/pgmpy/models/BayesianModel.py
@@ -506,6 +506,10 @@ class BayesianModel(DAG):
for large networks (>100 nodes). For smaller networks might reduce
p... |
pgmpy__pgmpy-1438 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/base/DAG.py:DAG.get_markov_blanket"
],
"edited_modules": [
"pgmpy/base/DAG.py:DAG"
]
},
"file": "pgmpy/base/DAG.py"
},
{
"changes": {
"added_entitie... | pgmpy/pgmpy | f2d1b8a60e8a7f6d1913bbf97ba90fde65a47e34 | KeyError in DynamicBayesianNetwork.active_trail_nodes()
### Subject of the issue
Invoking the `active_trail_nodes()` method of `DynamicBayesianNetwork` (inherited from `DAG`) raises a KeyError.
### Your environment
* pgmpy version 0.1.11dev
* Python version 3.8.5
* Operating System Manjaro x86_64
### Steps to... | diff --git a/pgmpy/base/DAG.py b/pgmpy/base/DAG.py
index 7dedca39..e0f6f489 100644
--- a/pgmpy/base/DAG.py
+++ b/pgmpy/base/DAG.py
@@ -667,7 +667,7 @@ class DAG(nx.DiGraph):
for child_node in children:
blanket_nodes.extend(self.get_parents(child_node))
blanket_nodes = set(blanket_nodes)
-... |
pgmpy__pgmpy-1441 | [
{
"changes": {
"added_entities": [
"pgmpy/factors/discrete/CPD.py:TabularCPD._truncate_strtable"
],
"added_modules": null,
"edited_entities": [
"pgmpy/factors/discrete/CPD.py:TabularCPD._make_table_str"
],
"edited_modules": [
"pgmpy/factors/discrete/CP... | pgmpy/pgmpy | e4efd1c1d3067b40da611f79aa3f6243dfd35177 | Don't print the complete Tabular CPD when the table is too large
Try with this CPD to see what happens when table is too large:
``` python3
meeting_cpd = TabularCPD('meetingtype', 2, [[0.75], [0.25]])
bottle_cpd = TabularCPD('levelbottle', 5, [[0.2], [0.2], [0.2], [0.2], [0.2]])
obstacle_cpd = TabularCPD('obstacle',... | diff --git a/pgmpy/factors/discrete/CPD.py b/pgmpy/factors/discrete/CPD.py
index ca456a23..65dd6c8e 100644
--- a/pgmpy/factors/discrete/CPD.py
+++ b/pgmpy/factors/discrete/CPD.py
@@ -9,6 +9,8 @@ import numpy as np
from pgmpy.factors.discrete import DiscreteFactor
from pgmpy.extern import tabulate
+from shutil impor... |
pgmpy__pgmpy-1447 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/models/DynamicBayesianNetwork.py:DynamicBayesianNetwork.get_interface_nodes"
],
"edited_modules": [
"pgmpy/models/DynamicBayesianNetwork.py:DynamicBayesianNetwork"
]
... | pgmpy/pgmpy | f4f6fc22fcd8cb2fdb18ab14722d7dbee35fbb6b | DBNInference ValueError: Self loops are not allowed
Hi!
when I try to construct model with DBN like this:
`from pgmpy.models import DynamicBayesianNetwork as DBN`
`from pgmpy.factors.discre... | diff --git a/pgmpy/models/DynamicBayesianNetwork.py b/pgmpy/models/DynamicBayesianNetwork.py
index 3cacc633..d12e610b 100644
--- a/pgmpy/models/DynamicBayesianNetwork.py
+++ b/pgmpy/models/DynamicBayesianNetwork.py
@@ -373,10 +373,13 @@ class DynamicBayesianNetwork(DAG):
"""
if not isinstance(time_sli... |
pgmpy__pgmpy-1450 | [
{
"changes": {
"added_entities": [
"pgmpy/models/DynamicBayesianNetwork.py:DynamicBayesianNetwork._timeslices"
],
"added_modules": null,
"edited_entities": [
"pgmpy/models/DynamicBayesianNetwork.py:DynamicNode.__repr__",
"pgmpy/models/DynamicBayesianNetwork.py:Dyn... | pgmpy/pgmpy | 7b691d27f0dc39999db1a44a186813e42c515f7c | DynamicBayesianNetwork model function get_cdps does not gets all TabularCDPs
### Subject of the issue
Apparently, the model `pgmpy.models.DynamicBayesianNetwork` function `get_cpds(*)` ignores all `TabularCDP` with time index 1, for example:
`cdp_T = TabularCPD(('s', 1), 1000, T.T, [('s', 0)], [1000])`
### Y... | diff --git a/pgmpy/models/DynamicBayesianNetwork.py b/pgmpy/models/DynamicBayesianNetwork.py
index 2c66813b..b9451614 100644
--- a/pgmpy/models/DynamicBayesianNetwork.py
+++ b/pgmpy/models/DynamicBayesianNetwork.py
@@ -32,7 +32,7 @@ class DynamicNode:
return f"({self.node}, {self.time_slice})"
def __rep... |
pgmpy__pgmpy-1454 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/inference/dbn_inference.py:DBNInference.__init__"
],
"edited_modules": [
"pgmpy/inference/dbn_inference.py:DBNInference"
]
},
"file": "pgmpy/inference/dbn_inferen... | pgmpy/pgmpy | d0542730c7a6368fb4bca8f393f39586879d3779 | DBNInference ValueError: Self loops are not allowed
Hi!
when I try to construct model with DBN like this:
`from pgmpy.models import DynamicBayesianNetwork as DBN`
`from pgmpy.factors.discre... | diff --git a/pgmpy/inference/dbn_inference.py b/pgmpy/inference/dbn_inference.py
index 72540d1a..c0c4854e 100644
--- a/pgmpy/inference/dbn_inference.py
+++ b/pgmpy/inference/dbn_inference.py
@@ -64,8 +64,8 @@ class DBNInference(Inference):
start_markov_model = self.start_bayesian_model.to_markov_model()
... |
pgmpy__pgmpy-1461 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/inference/CausalInference.py:CausalInference.query"
],
"edited_modules": [
"pgmpy/inference/CausalInference.py:CausalInference"
]
},
"file": "pgmpy/inference/Caus... | pgmpy/pgmpy | 0af6feac332c66fa79f422e88397073366575ff4 | CausalInference: Same Variables in Variables/Evidence Error when not the same?
### Subject of the issue
Hi, I seem to be running into a bug where the CausalInference.query method complains that the variables in the "variables" and evidence arg are the same when they actually aren't. Below is the code:
### Your e... | diff --git a/pgmpy/inference/CausalInference.py b/pgmpy/inference/CausalInference.py
index b85f9dce..15dede64 100644
--- a/pgmpy/inference/CausalInference.py
+++ b/pgmpy/inference/CausalInference.py
@@ -6,6 +6,7 @@ import networkx as nx
from tqdm.auto import tqdm
from pgmpy.models import BayesianNetwork
+from pgmpy... |
pgmpy__pgmpy-1470 | [
{
"changes": {
"added_entities": [
"pgmpy/models/BayesianNetwork.py:BayesianNetwork.states"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"pgmpy/models/BayesianNetwork.py:BayesianNetwork"
]
},
"file": "pgmpy/models/BayesianNetw... | pgmpy/pgmpy | 4a0c160626d703ea7ae9cd4ed40119ecc7df25b6 | Adding a dictionary of node:states to models
I often find myself needing to iterate over the states of a node.
For this, it would be useful to have a dictionary that maps the names of the nodes of a model to
I have resorted to the workaround of initializing this myself when loading a model.
```
from pgmpy.util... | diff --git a/pgmpy/models/BayesianNetwork.py b/pgmpy/models/BayesianNetwork.py
index 77987214..0da60ffe 100644
--- a/pgmpy/models/BayesianNetwork.py
+++ b/pgmpy/models/BayesianNetwork.py
@@ -371,6 +371,22 @@ class BayesianNetwork(DAG):
cardinalities[cpd.variable] = cpd.cardinality[0]
retur... |
pgmpy__pgmpy-1488 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/factors/continuous/LinearGaussianCPD.py:LinearGaussianCPD.__str__"
],
"edited_modules": [
"pgmpy/factors/continuous/LinearGaussianCPD.py:LinearGaussianCPD"
]
},
"... | pgmpy/pgmpy | caea6ef7c914464736818fb185a1d395937ed52f | Bug in printing LinearGaussianCPD
### Subject of the issue
Calling print on an instance of LinearGaussian CPD gives the wrong result.
### Your environment
* pgmpy version 0.1.16
* Python version 3.7.1
* Operating System Windows 10
### Steps to reproduce
Taken right from https://pgmpy.org/detailed_notebooks/7... | diff --git a/pgmpy/factors/continuous/LinearGaussianCPD.py b/pgmpy/factors/continuous/LinearGaussianCPD.py
index aa45b670..c8b7414a 100644
--- a/pgmpy/factors/continuous/LinearGaussianCPD.py
+++ b/pgmpy/factors/continuous/LinearGaussianCPD.py
@@ -232,7 +232,7 @@ class LinearGaussianCPD(BaseFactor):
mu=... |
pgmpy__pgmpy-1512 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/inference/CausalInference.py:CausalInference.is_valid_backdoor_adjustment_set"
],
"edited_modules": [
"pgmpy/inference/CausalInference.py:CausalInference"
]
},
"f... | pgmpy/pgmpy | 578a839ed9a5d6603d5fc9dd4411aa2d1304c712 | Z on is_valid_backdoor_adjustment_set does not accept str type.
### Subject of the issue
When Z on is_valid_backdoor_adjustment_set is str type, it fails and throw ValueError exception.
### Your environment
* pgmpy version 0.1.17
* Python version 3.9.6
* Operating System OS X 12.2.1
### Steps to reproduce
Te... | diff --git a/pgmpy/inference/CausalInference.py b/pgmpy/inference/CausalInference.py
index 6e2fd46f..6f83c49d 100644
--- a/pgmpy/inference/CausalInference.py
+++ b/pgmpy/inference/CausalInference.py
@@ -97,7 +97,8 @@ class CausalInference(object):
>>> inference.is_valid_backdoor_adjustment_set("X", "Y")
... |
pgmpy__pgmpy-1566 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/factors/base.py:factor_product"
],
"edited_modules": [
"pgmpy/factors/base.py:factor_product"
]
},
"file": "pgmpy/factors/base.py"
}
] | pgmpy/pgmpy | 923754ba36facee9c050a684f3f6264cd81dbece | `factor_product` returns same object as input for single argument
### Subject of the issue
`pgmpy.factors.base.factor_product` returns the same object as input. No copy is made
### Your environment
* pgmpy version - 0.1.18
* Python version - 3.8.10
* Operating System - WSL 2 on Windows 10 Enterprise
### Steps... | diff --git a/pgmpy/factors/base.py b/pgmpy/factors/base.py
index bd55c64e..0ad6ddd4 100644
--- a/pgmpy/factors/base.py
+++ b/pgmpy/factors/base.py
@@ -70,7 +70,10 @@ def factor_product(*args):
"All the args are expected to be instances of the same factor class."
)
- return reduce(lambda phi1,... |
pgmpy__pgmpy-1899 | [
{
"changes": {
"added_entities": [
"pgmpy/estimators/PC.py:PC._check_incoming_edges"
],
"added_modules": null,
"edited_entities": [
"pgmpy/estimators/PC.py:PC.apply_orientation_rules"
],
"edited_modules": [
"pgmpy/estimators/PC.py:PC"
]
},
... | pgmpy/pgmpy | b09372dd9405c770b8eb6be3fc543e2f2e3d5b1b | PC algorithm orientation rules throw error
Code to reproduce:
```python
In [1]: from pgmpy.estimators import PC
... | diff --git a/pgmpy/base/DAG.py b/pgmpy/base/DAG.py
index 676c471a..eee7807e 100644
--- a/pgmpy/base/DAG.py
+++ b/pgmpy/base/DAG.py
@@ -405,7 +405,7 @@ class DAG(nx.DiGraph):
>>> from pgmpy.base import DAG
>>> chain = DAG([('X', 'Y'), ('Y', 'Z')])
>>> chain.get_independencies()
- (X \u2... |
pgmpy__pgmpy-1905 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/sampling/base.py:BayesianModelInference._reduce_marg",
"pgmpy/sampling/base.py:BayesianModelInference.pre_compute_reduce_maps"
],
"edited_modules": [
"pgmpy/sampling/ba... | pgmpy/pgmpy | 4b1743dfefcc2b749517df68887ec783f009e5e7 | Incorrect sampling when the state names of a variable overlap with the state numbers
### Subject of the issue
The short explanation is to take a look at https://github.com/pgmpy/pgmpy/blob/f303886ff5b0979e13ca665dab8f476a1a49758c/pgmpy/sampling/Sampling.py#L316 and https://github.com/pgmpy/pgmpy/blob/f303886ff5b0979e1... | diff --git a/pgmpy/sampling/base.py b/pgmpy/sampling/base.py
index c5fe81aa..9d7a23b9 100644
--- a/pgmpy/sampling/base.py
+++ b/pgmpy/sampling/base.py
@@ -65,7 +65,7 @@ class BayesianModelInference(Inference):
return cached_values
@staticmethod
- def _reduce_marg(variable_cpd, variable_evid, reduce_i... |
pgmpy__pgmpy-1906 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/models/SEM.py:SEMGraph.to_lisrel"
],
"edited_modules": [
"pgmpy/models/SEM.py:SEMGraph"
]
},
"file": "pgmpy/models/SEM.py"
},
{
"changes": {
"added_... | pgmpy/pgmpy | 4b1743dfefcc2b749517df68887ec783f009e5e7 | A Bug in SEMEstimator.py
The masks are being used in different ways in SEM.py and SEMEstimator.py
in [SEM.py](https://github.com/pgmpy/pgmpy/blob/f4a0485668f437182d08abdf4b33d5be1b7c42d1/pgmpy/models/SEM.py#L882C1-L886C10)
```
# Masks represent the parameters which need to be learnt while training.
self.B_mask = np.mu... | diff --git a/pgmpy/models/SEM.py b/pgmpy/models/SEM.py
index bf1591ff..0ff03d8a 100644
--- a/pgmpy/models/SEM.py
+++ b/pgmpy/models/SEM.py
@@ -589,20 +589,20 @@ class SEMGraph(DAG):
"""
nodelist = list(self.observed) + list(self.latents)
graph_adj = nx.to_numpy_array(self.graph, nodelist=node... |
pgmpy__pgmpy-1945 | [
{
"changes": {
"added_entities": [
"pgmpy/base/DAG.py:DAG._variable_name_contains_non_string"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"pgmpy/base/DAG.py:DAG"
]
},
"file": "pgmpy/base/DAG.py"
},
{
"changes": {
... | pgmpy/pgmpy | 6fe2f55fceea4f068cb7d99406782326d36b7474 | CausalInference misbehaves when state_name is integer.
get_all_backdoor_adjustment_sets is behaving inconsistently when state_name is integer.
```
BN1 = BayesianNetwork([(1,2),(1,3),(2,4),(1,4),(1,5)])
CI1 = CausalInference(BN1)
CI1.get_all_backdoor_adjustment_sets(2,4)
```
gives an error as below:
```
--------------... | diff --git a/pgmpy/base/DAG.py b/pgmpy/base/DAG.py
index 8ab2af63..2218c071 100644
--- a/pgmpy/base/DAG.py
+++ b/pgmpy/base/DAG.py
@@ -1244,6 +1244,15 @@ class DAG(nx.DiGraph):
bn.add_cpds(*cpds_list)
return bn
+ def _variable_name_contains_non_string(self):
+ """
+ Checks if the va... |
pgmpy__pgmpy-1963 | [
{
"changes": {
"added_entities": [
"pgmpy/models/DynamicBayesianNetwork.py:DynamicBayesianNetwork.states"
],
"added_modules": null,
"edited_entities": [
"pgmpy/models/DynamicBayesianNetwork.py:DynamicBayesianNetwork.initialize_initial_state"
],
"edited_modules... | pgmpy/pgmpy | 9c1ce70d8bc426f195dce10a395c59b439ae1d4d | state_names not handled in DBN initialize_initial_state
When I take an example from tutorial and pass `state_names` parameter, I get inconsistent result after `initialize_initial_state`.
```
from pgmpy.models import DynamicBayesianNetwork as DBN
from pgmpy.factors.discrete import TabularCPD
# Initialize a simple DBN ... | diff --git a/pgmpy/models/DynamicBayesianNetwork.py b/pgmpy/models/DynamicBayesianNetwork.py
index 05a92c65..df2dafb9 100644
--- a/pgmpy/models/DynamicBayesianNetwork.py
+++ b/pgmpy/models/DynamicBayesianNetwork.py
@@ -640,6 +640,8 @@ class DynamicBayesianNetwork(DAG):
for cpd in self.cpds:
temp_v... |
pgmpy__pgmpy-937 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/readwrite/BIF.py:BIFReader.get_model"
],
"edited_modules": [
"pgmpy/readwrite/BIF.py:BIFReader"
]
},
"file": "pgmpy/readwrite/BIF.py"
},
{
"changes": {
... | pgmpy/pgmpy | 110b4c1e8ef8c24da83931d87298b96c196c9462 | Reading a XML BIF with isolated nodes
The XMLBIFReader class doesn't allow to return the model from a BIF XML file where there are isolated nodes.
I can create the XMLBIFReader:
`bif = pgmpy.readwrite.XMLBIF.XMLBIFReader('diabetes.xml')`
but when trying to return the model:
`bif_model = bif.get_model()`
It ... | diff --git a/pgmpy/readwrite/BIF.py b/pgmpy/readwrite/BIF.py
index fac86ab9..98c11d39 100644
--- a/pgmpy/readwrite/BIF.py
+++ b/pgmpy/readwrite/BIF.py
@@ -284,9 +284,10 @@ class BIFReader(object):
<pgmpy.models.BayesianModel.BayesianModel object at 0x7f20af154320>
"""
try:
- model ... |
pgmpy__pgmpy-973 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pgmpy/estimators/BayesianEstimator.py:BayesianEstimator.get_parameters",
"pgmpy/estimators/BayesianEstimator.py:BayesianEstimator.estimate_cpd"
],
"edited_modules": [
"pgmpy/... | pgmpy/pgmpy | b85e9ca3b20296925dd4b5686356031dc1f80fec | Issue with dirichlet prior for bayesian learning
The issue is with Bayesian Estimator.
http://pgmpy.org/estimators.html#bayesian-estimator
The prior type can be one of the following: ‘dirichlet’, ‘BDeu’, ‘K2’
My issue is with the dirichlet, and the parameter: "pseudo_counts". It seems like pgmpy only allows for ONE... | diff --git a/pgmpy/estimators/BayesianEstimator.py b/pgmpy/estimators/BayesianEstimator.py
index 01689a50..4326ef35 100644
--- a/pgmpy/estimators/BayesianEstimator.py
+++ b/pgmpy/estimators/BayesianEstimator.py
@@ -27,8 +27,9 @@ class BayesianEstimator(ParameterEstimator):
prior_type: 'dirichlet', 'BDeu', or '... |
phac-nml__irida-uploader-142 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "iridauploader/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"iridauploa... | phac-nml/irida-uploader | e1f0974e68be93a2a69b11bb1cb569d95191e499 | GUI: partially uploaded runs resulting in error are not being detected as partial
This means the user cannot continue an upload if their upload stops halfway through do to a server error
| diff --git a/CHANGELOG.md b/CHANGELOG.md
index cef3b7d..8ee2cf4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,14 @@
Changes
=======
+Beta 0.8.3
+----------
+Changes:
+* [GUI] Partial uploads now display the reason (error) that caused the run to stop.
+
+Bug Fixes:
+* Fixed Error's setting run to ERROR whe... |
phac-nml__irida-uploader-44 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"parsers/directory/sample_parser.py:_parse_sample_list"
],
"edited_modules": [
"parsers/directory/sample_parser.py:_parse_sample_list"
]
},
"file": "parsers/directory/sa... | phac-nml/irida-uploader | d3317233fe371df4e9dfc45288014ee1593cd464 | Allow Directory Parser to use full file paths, in addition to file names.
Suggested by @happykhan
Use case: Reads can sometimes be scattered around, so it would be nice to be able to just give the path directly in the SampleList.csv file.
Related code: `/parsers/directory/sample_parser.py` in `_parse_sample_list... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4443c81..8b5d251 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ Added functionality:
* Added config option overrides for the command line
* Can define in command line `--option parameter` or without a parameter `--option` for a user prompt
* Use th... |
phac-nml__irida-uploader-47 | [
{
"changes": {
"added_entities": [
"api/api_calls.py:ApiCalls._get_irida_exception"
],
"added_modules": null,
"edited_entities": [
"api/api_calls.py:ApiCalls.send_project",
"api/api_calls.py:ApiCalls.send_sample",
"api/api_calls.py:ApiCalls.send_sequence_f... | phac-nml/irida-uploader | 8b2f66ba7284d442595a4c7013f84cb5e0dd7b2b | Update response text to include 400 bad request
if response.status_code == HTTPStatus.CREATED:
json_res = json.loads(response.text)
else:
e = exceptions.IridaConnectionError("Error {status_code}: {err_msg}\n".format(
status_code... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8b5d251..a351c66 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,9 @@ Bug Fixes:
* Fixed hard crash that sometimes occurred when valid url's were given as the base_url
* Fixed hard crash when running the miniseq parser on a miseq run directory
+API Changes:
+... |
phac-nml__irida-uploader-67 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"config/config.py:setup"
],
"edited_modules": [
"config/config.py:setup"
]
},
"file": "config/config.py"
},
{
"changes": {
"added_entities": null,
"a... | phac-nml/irida-uploader | 2604f2709a1082445d691fdefec1f8929a172e58 | Optional global configuration file
## Describe your idea for a new feature
Nice to have an optional global configuration file for sequencer that may have dozen of local users. It is time consuming for each individual user to create the same configuration file.
## Additional information
Add any other context, file... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 736ba39..1a57bbc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,14 @@
Changes
=======
+Beta 0.3.2
+----------
+Added functionality:
+* Default config file can now be overridden across a system by adding a config.conf file to the source directory. Specifying co... |
phac-nml__irida-uploader-88 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "iridauploader/core/cli_entry.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"irid... | phac-nml/irida-uploader | 8993030a65046034e03fe87d77635b920d5a1c2e | Full file path support for directory uploader
## Describe your idea for a new feature
Currently the directory uploader only supports file names listed in specified directory, like so
```
[Data]
Sample_Name,Project_ID,File_Forward,File_Reverse
my-sample-1,5,file_1.fastq.gz,
my-sample-2,5,samp_F.fastq.gz,
```
It ... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index c2b20ad..682c1eb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,9 @@ Changes
Beta 0.4.3
----------
+Added functionality:
+* `directory` parsers now support full file paths for upload.
+
Developer changes:
* Added method `get_metadata(self, sample_name, proje... |
phac-nml__staramr-150 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "staramr/__init__.py"
},
{
"changes": {
"added_entities": [
"staramr/blast/pointfinder/PointfinderBlastDatabase.py:PointfinderBlastDataba... | phac-nml/staramr | 1925f188764f42e054d5982a2fe299e1a868cf82 | Change strict restriction on PointFinder organisms to be a warning
Currently, running with `--pointfinder-organism ORGANISM` with anything other than `salmonella` or `campylobacter` will result in an error due to a check I perform against a list of acceptable organisms here:
https://github.com/phac-nml/staramr/blob/... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index c9bd308..6e6bce0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,7 @@
* Fixed up some Python warnings related to pandas (0.8.0.dev0).
* Adjusted `mlst` tests to account for differences in results for newer versions (0.8.0.dev0).
* Drop support for Python 3.5 as ... |
phanrahan__magma-1018 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "magma/backend/blif.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"magma/bitutils... | phanrahan/magma | d509c918a3bfff6255d96699e5d342c7039060bd | Unify math.py:* and bitutils.py:*
- [x] fix the bitutils implementation to match the math one more closely
- [x] deprecate (warning) math one
- [ ] kill math one once we upgrade to magma3.0 | diff --git a/docs/cheat_sheet.md b/docs/cheat_sheet.md
index a925329c..cfd6053a 100644
--- a/docs/cheat_sheet.md
+++ b/docs/cheat_sheet.md
@@ -65,12 +65,6 @@ inout respectively.
* `m.sint(value, n=None)`: convert `value` to an `SInt` (same rules as
`m.bits`, except will not convert `m.UInt` to `m.SInt`)
-# Math H... |
phanrahan__magma-1076 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"magma/find_unconnected_ports.py:find_and_log_unconnected_ports"
],
"edited_modules": [
"magma/find_unconnected_ports.py:find_and_log_unconnected_ports"
]
},
"file": "ma... | phanrahan/magma | 24edb1c1ee051aa9a97f68c5c6f548ab15133255 | Undriven port bug
Mamga reports errors of undriven ports even though it's connected.
How to reproduce:
Uinsg `magma-lang==2.2.18`
Remove this hack here:
https://github.com/StanfordAHA/canal/blob/37799cb4db4e5260ea538b8650c5446759e7892c/canal/circuit.py#L1090
Then run `python tests/test_circuit.py` to see the err... | diff --git a/magma/find_unconnected_ports.py b/magma/find_unconnected_ports.py
index fd98acb2..0a57d5c5 100644
--- a/magma/find_unconnected_ports.py
+++ b/magma/find_unconnected_ports.py
@@ -133,4 +133,4 @@ def find_and_log_unconnected_ports(ckt):
visitor = _make_unconnected_port_diagnostic_visitor_cls()()
... |
phanrahan__magma-980 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"magma/bit.py:Bit.ite"
],
"edited_modules": [
"magma/bit.py:Bit"
]
},
"file": "magma/bit.py"
}
] | phanrahan/magma | 35d8ebfa311fe53bb538004c8ed6222cd83f7764 | Magma protocol losing type under ite
Bit.ite does not "cast" protocols back to their protocol type
Specifically:
```Python
assert type(proto0) == type(proto1)
v = Bit().ite(proto0, proto1)
assert type(v) == type(proto0)._to_magma_
```
where I would expect:
```Python
assert type(proto0) == type(proto1)
v = B... | diff --git a/magma/bit.py b/magma/bit.py
index 6e3cbd73..e67cef11 100644
--- a/magma/bit.py
+++ b/magma/bit.py
@@ -20,7 +20,7 @@ from magma.debug import debug_wire
from magma.family import get_family
from magma.interface import IO
from magma.language_utils import primitive_to_python
-from magma.protocol_type import ... |
phenology__cgc-65 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cgc/coclustering.py:Coclustering.__init__",
"cgc/coclustering.py:Coclustering.run_with_threads",
"cgc/coclustering.py:Coclustering._dask_runs_memory",
"cgc/coclustering.py:Coclus... | phenology/cgc | d3c79201513d1b84307a11250d5f009f7f6b138d | Remove non-Numba-accelerated low-memory version
It does not work with thread parallelism
| diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 7dad99c..7082963 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -8,6 +8,10 @@ This project adheres to `Semantic Versioning <http://semver.org/>`_.
[Unreleased]
************
+Changed
+-------
+* Numerical parameter epsilon is removed, which should lead to some impr... |
phenology__cgc-73 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cgc/kmeans.py:Kmeans.compute",
"cgc/kmeans.py:Kmeans._compute_statistic_measures"
],
"edited_modules": [
"cgc/kmeans.py:KmeansResults",
"cgc/kmeans.py:Kmeans"
]... | phenology/cgc | 6da0522a909ec0344ed3506d9cbc5457c2823e62 | k-means centroids
Centroids returned by the k-means refinement step are averages of the cluster averages. Should one instead return averages computed over all elements of the clusters that are being merged? | diff --git a/cgc/kmeans.py b/cgc/kmeans.py
index 5ba801f..400feb3 100644
--- a/cgc/kmeans.py
+++ b/cgc/kmeans.py
@@ -15,23 +15,23 @@ class KmeansResults(Results):
:var k_value: Optimal K value (value with maximum Silhouette score).
:type k_value: int
- :var km_labels: Refined clusters labels. It is a 2D-... |
phobson__paramnormal-24 | [
{
"changes": {
"added_entities": [
"paramnormal/paramnormal.py:exponential._process_args",
"paramnormal/paramnormal.py:exponential.fit"
],
"added_modules": [
"paramnormal/paramnormal.py:exponential"
],
"edited_entities": null,
"edited_modules": null
... | phobson/paramnormal | 9e0395b03e042d0ad4f0d6be12c768103233dc27 | add exponential distribution
seems pretty critical | diff --git a/docs/tutorial/fitting.ipynb b/docs/tutorial/fitting.ipynb
index b5434fa..364bccb 100644
--- a/docs/tutorial/fitting.ipynb
+++ b/docs/tutorial/fitting.ipynb
@@ -11,6 +11,17 @@
"Again, we'll demonstrate with a lognormal distribution and compare parameter estimatation with scipy."
]
},
+ {
+ "c... |
physiopy__phys2bids-189 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"phys2bids/phys2bids.py:phys2bids"
],
"edited_modules": [
"phys2bids/phys2bids.py:phys2bids"
]
},
"file": "phys2bids/phys2bids.py"
},
{
"changes": {
"added... | physiopy/phys2bids | 9ec9c33da2e7c3adf7653a79cb024ffcc130bf42 | Output files are not BIDS compliant
<!--- Provide a general summary of the issue in the Title above -->
## Expected Behavior
<!--- NECESSARY -->
<!--- Describe what one would expect from the buggy code -->
Following [BIDS 1.2.2](https://bids-specification.readthedocs.io/en/v1.2.2/), the `.tsv.gz` files should hav... | diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index bed7050..573bc64 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -348,7 +348,7 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
outfile = f'{outfile}_{uniq_freq}'
LGR.info(f'Ex... |
physiopy__phys2bids-193 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"phys2bids/phys2bids.py:phys2bids"
],
"edited_modules": [
"phys2bids/phys2bids.py:phys2bids"
]
},
"file": "phys2bids/phys2bids.py"
},
{
"changes": {
"added... | physiopy/phys2bids | 07bec6aa41d2cc1a2da4383b8dcf112bf9775734 | Update docstrings in viz.py
<!--- Provide a general summary of the issue in the Title above -->
## Detailed Description
<!--- Provide a detailed description of the change or addition you are proposing -->
At the moment, the docstring of the functions in `viz.py` are either outdated (after #153) or missing (for `pl... | diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 4bf09d1..c3b3ec7 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -254,7 +254,8 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
phys_in.print_info(filename)
# #!# Here the function viz.plot_chan... |
physiopy__phys2bids-212 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"phys2bids/phys2bids.py:print_summary",
"phys2bids/phys2bids.py:print_json"
],
"edited_modules": [
"phys2bids/phys2bids.py:print_summary",
"phys2bids/phys2bids.py:prin... | physiopy/phys2bids | f294930242820b541e67b153c6344b10938b7668 | Change floats print format
Currently, any print of a float in a file has a format with many decimals.
It would be better to have a formatted print with max 4 decimals.
This doesn't affect the data, only the information in the json and in the log. | diff --git a/phys2bids/phys2bids.py b/phys2bids/phys2bids.py
index 138a512..593b0e4 100644
--- a/phys2bids/phys2bids.py
+++ b/phys2bids/phys2bids.py
@@ -76,7 +76,7 @@ def print_summary(filename, ntp_expected, ntp_found, samp_freq, time_offset, out
f'Timepoints expected: {ntp_expected}\n'
... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.