https://github.com/databio/yacman

YAML configuration manager

Science Score: 26.0%

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Low similarity (15.0%) to scientific vocabulary

Keywords from Contributors

bioinformatics bioinformatics-pipeline ngs pipeline-submission-engine

Last synced: 10 months ago · JSON representation

Repository

YAML configuration manager

Basic Info

Host: GitHub
Owner: databio
License: bsd-2-clause
Language: Python
Default Branch: master
Homepage: https://pypi.org/project/yacman
Size: 352 KB

Statistics

Stars: 6
Watchers: 15
Forks: 2
Open Issues: 10
Releases: 29

Created about 7 years ago · Last pushed almost 2 years ago

Metadata Files

Readme License

README.md

yacman

Yacman is a YAML configuration manager. It provides some convenience tools for dealing with YAML configuration files.

Please see this Python notebook for features and usage instructions and this document for API documentation.

Upgrading guide

How to upgrade to yacman v1.0.0. Yacman v1 provides 2 feature upgrades:

Constructors take the form of yacman.YAMLConfigManager.from_x(...) functions, to make it clearer how to create a new ym object.
It separates locks into read locks and write locks, to allow mutliple simultaneous readers.

The v0.9.3 transition release has 3 versions of the basic yacman object, namely: - attmap-based version (YacAttMap) - non-attmap-but-mostly-compatible (YAMLConfigManager) - new future object (FutureYAMLConfigManager...), which is explicitly not backwards compatible with the attmap version.

In v1.0.0, FutureYAMLConfigManager will be renamed to YAMLConfigManager and the old stuff will be removed. Here's how to transition your code:

Use the FutureYAMLConfigManager in 0.9.3

Import the FutureYAMLConfigManager

Change from:

python from yacman import YAMLConfigManager

python from yacman import FutureYAMLConfigManager as YAMLConfigManager

Once we switch from v0.9.3 to v1.X.X, you will need to switch back.

Update any context managers to use write_lock or read_lock

python from yacman import write_lock, read_lock

Change

python with ym as locked_ym: locked_ym.write()

python with write_lock(ym) as locked_ym: locked_ym.rebase() locked_ym.write()

In the new system, you must use rebase() before write() if you want to allow for multiple processes to possibly have written the file since you read it in.

More examples:

```python

from yacman import FutureYAMLConfigManager as YAMLConfigManager from yacman import readlock, writelock

data = {"mylist": [1,2,3], "myint": 8, "mystr": "hello world!", "mydict": {"nested_val": 15}}

ym = YAMLConfigManager(data)

ym["mylist"] ym["myint"] ym["my_dict"]

Use in a context manager to write to the file

ym["new_var"] = 15

Use a write-lock, and rebase before writing to ensure you capture any changes since you loaded the file

with write(ym) as lockedym: lockedym.rebase() locked_ym.write()

use a read lock to rebase -- this will replay any in-memory updates on top of whatever is re-read from the file

with readlock(ym) as lockedym: locked_ym.rebase()

use a read lock to reset the in-memory object to whatever is on disk

with readlock(ym) as lockedym: locked_ym.reset()

```

Update any constructors to use the from_{x} functions

You can no longer just create a YAMLConfigManager object directly; now you need to use the constructor helpers.

Examples:

```python from yacman import FutureYAMLConfigManager as YAMLConfigManager

data = {"mylist": [1,2,3], "myint": 8, "mystr": "hello world!", "mydict": {"nestedval": 15}} filepath = "tests/data/full.yaml" yaml_data = "myvar: myval"

yacman.YAMLConfigManager.fromyamlfile(filepath) yacman.YAMLConfigManager.fromyamldata(yamldata) yacman.YAMLConfigManager.from_obj(data)

```

In the past, you could load from a file and overwrite some attributes with a dict of variables, all from the constructor. Now it would is more explicit:

python ym = yacman.YacMan.from_yaml_file(file_path) ym.update_from_obj(data)

To exppand environment variables in values, use .exp.

python ym.exp["text_expand_home_dir"]

From v0.9.3 (using future) to v1.X.X:

Switch back to:

from yacman import YAMLConfigManager

Demos

Some interactive demos

```python from yacman import FutureYAMLConfigManager as YAMLConfigManager ym = yacman.YAMLConfigManager(entries=["a", "b", "c"]) ym.to_dict() ym

print(ym.to_yaml())

ym = YAMLConfigManager(entries={"top": {"bottom": ["a", "b"], "bottom2": "a"}, "b": "c"}) ym print(ym.to_yaml())

ym = YAMLConfigManager(filepath="tests/data/confschema.yaml") print(ym.toyaml()) ym

ym = YAMLConfigManager(filepath="tests/data/empty.yaml") print(ym.to_yaml())

ym = YAMLConfigManager(filepath="tests/data/list.yaml") print(ym.to_yaml())

ym = YAMLConfigManager(YAMLConfigManager(filepath="tests/data/full.yaml").exp) print(ym.to_yaml())

ym = YAMLConfigManager(filepath="tests/data/full.yaml") print(ym.to_yaml(expand=True))

```

Owner

Name: Databio
Login: databio
Kind: organization
Location: University of Virginia

Website: https://databio.org
Repositories: 88
Profile: https://github.com/databio

Solving problems in computational biology

GitHub Events

Total

Last Year

Committers

Last synced: about 3 years ago

All Time

Total Commits: 264
Total Committers: 5
Avg Commits per committer: 52.8
Development Distribution Score (DDS): 0.367

Past Year

Commits: 18
Committers: 1
Avg Commits per committer: 18.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Michal Stolarczyk	s**3@g**m	167
nsheff	n**f@u**m	74
Vince	v**r@g**m	13
nsheff	n**n@c**g	9
Nicola Soranzo	n**o@g**m	1

Committer Domains (Top 20 + Academic)

code.databio.org: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time

Total issues: 34
Total pull requests: 31
Average time to close issues: 6 months
Average time to close pull requests: 4 days
Total issue authors: 6
Total pull request authors: 4
Average comments per issue: 2.68
Average comments per pull request: 0.61
Merged pull requests: 31
Bot issues: 0
Bot pull requests: 0

Past Year

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Pull requests: 0
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Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

nsheff (24)
vreuter (4)
stolarczyk (3)
rcorces (1)
afrendeiro (1)
zz1874 (1)

Pull Request Authors

nsheff (18)
stolarczyk (12)
vreuter (2)
nsoranzo (1)

Top Labels

Issue Labels

likely-solved (8) bug (6) enhancement (3) question (2) docs (1) version-specific (1)

Pull Request Labels

Packages

Total packages: 4
Total downloads:
- pypi 48,703 last-month
Total docker downloads: 30,558

Total dependent packages: 16
(may contain duplicates)
Total dependent repositories: 47
(may contain duplicates)
Total versions: 70
Total maintainers: 5

proxy.golang.org: github.com/databio/yacman

Documentation: https://pkg.go.dev/github.com/databio/yacman#section-documentation
License: bsd-2-clause
Latest release: v0.9.3
published over 2 years ago

Versions: 29
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.3%

Average: 5.5%

Dependent repos count: 5.7%

Last synced: 11 months ago

pypi.org: yacman

A standardized configuration object for reference genome assemblies

Homepage: https://github.com/databio/yacman
Documentation: https://yacman.readthedocs.io/
License: BSD2
Latest release: 0.9.3
published over 2 years ago

Versions: 30
Dependent Packages: 10
Dependent Repositories: 47
Downloads: 48,703 Last month
Docker Downloads: 30,558

Rankings

Dependent packages count: 1.1%

Docker downloads count: 1.3%

Downloads: 1.6%

Dependent repos count: 2.1%

Average: 7.8%

Forks count: 19.2%

Stargazers count: 21.6%

Maintainers (4)

nsheff vreuter databio michalstolarczyk

Last synced: 10 months ago

spack.io: py-yacman

A YAML configuration manager.

Homepage: https://github.com/databio/yacman
License: []
Latest release: 0.8.4
published over 3 years ago

Versions: 1
Dependent Packages: 4
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Dependent packages count: 14.2%

Average: 18.6%

Forks count: 30.1%

Stargazers count: 30.2%

Maintainers (1)

adamjstewart

Last synced: 10 months ago

conda-forge.org: yacman

Homepage: https://github.com/databio/yacman/
License: BSD-2-Clause
Latest release: 0.8.4
published over 4 years ago

Versions: 10
Dependent Packages: 2
Dependent Repositories: 0

Rankings

Dependent packages count: 19.5%

Dependent repos count: 34.0%

Average: 41.2%

Forks count: 54.2%

Stargazers count: 57.0%

Last synced: 11 months ago

Dependencies

.github/workflows/black.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
psf/black stable composite

.github/workflows/python-publish.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/run-locking-tests.yaml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/run-pytest.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
codecov/codecov-action v1 composite

requirements/requirements-all.txt pypi

attmap >=0.13.0
jsonschema >=3.2.0
oyaml *
pyyaml >=3.13
ubiquerg >=0.6.1

requirements/requirements-test.txt pypi

pytest * test
pytest-cov * test