mirror of
https://github.com/MillironX/SequenceVariation.jl.git
synced 2024-11-22 13:29:56 +00:00
Merge pull request #12 from MillironX/registration-prep
Prepare for package registration
This commit is contained in:
GitHub
commit
976d5b3a3d
20 changed files with 535 additions and 242 deletions
59
.github/ISSUE_TEMPLATE/bug.yml
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name: Bug
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description: Bug report
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body:
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||||||
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|
||||||
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- type: markdown
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||||||
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attributes:
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||||||
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value: "> _This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any section, leave it unchanged and a reviewer will help you_ :smile:."
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||||||
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||||||
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- type: textarea
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validations:
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required: true
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attributes:
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label: Expected behavior
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description: Tell us what you expect to happen
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||||||
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- type: textarea
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||||||
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validations:
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||||||
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required: true
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attributes:
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||||||
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label: Current behavior
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description: Tell us what happens instead of the expected behavior
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||||||
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||||||
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- type: textarea
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||||||
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attributes:
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label: Possible solution
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description: Suggest a fix/reason for the bug (optional)
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||||||
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||||||
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- type: textarea
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validations:
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required: true
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attributes:
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label: Steps to reproduce
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description: You may include copy-pasteable snippets or a list of steps to reproduce the bug
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- type: textarea
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||||||
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attributes:
|
||||||
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label: Context
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||||||
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description: How has this issue affected you? What are you trying to accomplish? Providing context helps us come up with a solution that is most useful in the real world.
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||||||
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- type: input
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||||||
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attributes:
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||||||
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label: Package version used
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- type: input
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attributes:
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label: Julia version used
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label: Operating system and version
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label: Link to your project
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- type: textarea
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attributes:
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label: Please list installed packages here
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||||||
38
.github/ISSUE_TEMPLATE/change.yml
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name: Change
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description: Change/improvement suggestion
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body:
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||||||
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||||||
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- type: markdown
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||||||
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attributes:
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||||||
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value: "> _This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any section, leave it unchanged and a reviewer will help you_ :smile:."
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||||||
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|
||||||
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- type: textarea
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||||||
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validations:
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||||||
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required: true
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||||||
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attributes:
|
||||||
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label: Expected behavior
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||||||
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description: Tell us how it should work
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||||||
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||||||
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- type: textarea
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||||||
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validations:
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||||||
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required: true
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||||||
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attributes:
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||||||
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label: Current behavior
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||||||
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description: Explain the difference from current behavior
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||||||
|
|
||||||
|
- type: textarea
|
||||||
|
validations:
|
||||||
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required: true
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||||||
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attributes:
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||||||
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label: Possible implementation
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||||||
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description: Suggest ideas how to implement the addition or change
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||||||
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- type: textarea
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||||||
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attributes:
|
||||||
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label: Context
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||||||
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description: How has this issue affected you? What are you trying to accomplish? Providing context helps us come up with a solution that is most useful in the real world.
|
||||||
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||||||
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- type: input
|
||||||
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attributes:
|
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label: Link to your project
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||||||
47
.github/PULL_REQUEST_TEMPLATE.md
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47
.github/PULL_REQUEST_TEMPLATE.md
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||||||
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# A clear and descriptive title (No issue numbers please)
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||||||
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|
||||||
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> _This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any section, leave it unchanged and a reviewer will help you_ :smile:. _This template is simply a tool to help everyone remember the BioJulia guidelines, if you feel anything in this template is not relevant, simply delete it._
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||||||
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||||||
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## Types of changes
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||||||
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||||||
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This PR implements the following changes:
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||||||
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_(Please tick any or all of the following that are applicable)_
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||||||
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||||||
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- [ ] :sparkles: New feature (A non-breaking change which adds functionality).
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- [ ] :bug: Bug fix (A non-breaking change, which fixes an issue).
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- [ ] :boom: Breaking change (fix or feature that would cause existing functionality to change).
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## :clipboard: Additional detail
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||||||
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||||||
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- If you have implemented new features or behaviour
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||||||
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- **Provide a description of the addition** in as many details as possible.
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||||||
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||||||
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- **Provide justification of the addition**.
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||||||
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- **Provide a runnable example of use of your addition**. This lets reviewers
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and others try out the feature before it is merged or makes it's way to release.
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||||||
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||||||
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- If you have changed current behaviour...
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||||||
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- **Describe the behaviour prior to you changes**
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||||||
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- **Describe the behaviour after your changes** and justify why you have made the changes,
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Please describe any breakages you anticipate as a result of these changes.
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||||||
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- **Does your change alter APIs or existing exposed methods/types?**
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If so, this may cause dependency issues and breakages, so the maintainer
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will need to consider this when versioning the next release.
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- If you are implementing changes that are intended to increase performance, you
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should provide the results of a simple performance benchmark exercise
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demonstrating the improvement. Especially if the changes make code less legible.
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## :ballot_box_with_check: Checklist
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||||||
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- [ ] :art: The changes implemented is consistent with the [julia style guide](https://docs.julialang.org/en/v1/manual/style-guide/).
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- [ ] :blue_book: I have updated and added relevant docstrings, in a manner consistent with the [documentation styleguide](https://docs.julialang.org/en/v1/manual/documentation/).
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- [ ] :blue_book: I have added or updated relevant user and developer manuals/documentation in `docs/src/`.
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- [ ] :ok: There are unit tests that cover the code changes I have made.
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- [ ] :ok: The unit tests cover my code changes AND they pass.
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- [ ] :pencil: I have added an entry to the `[UNRELEASED]` section of the manually curated `CHANGELOG.md` file for this repository.
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- [ ] :ok: All changes should be compatible with the latest stable version of Julia.
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||||||
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- [ ] :thought_balloon: I have commented liberally for any complex pieces of internal code.
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16
.github/workflows/CompatHelper.yml
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name: CompatHelper
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on:
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schedule:
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- cron: 0 0 * * *
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workflow_dispatch:
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jobs:
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||||||
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CompatHelper:
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||||||
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runs-on: ubuntu-latest
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steps:
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- name: Pkg.add("CompatHelper")
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run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
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- name: CompatHelper.main()
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||||||
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env:
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||||||
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
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run: julia -e 'using CompatHelper; CompatHelper.main()'
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name: Documentation
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on:
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push:
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branches:
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- master
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- develop
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- release/.*
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tags: ['*']
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pull_request:
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jobs:
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docs:
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name: Documentation
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: julia-actions/setup-julia@v1
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with:
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version: '1'
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- run: julia --color=yes --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
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- run: julia --color=yes --project=docs docs/make.jl
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env:
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JULIA_PKG_SERVER: ""
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
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name: TagBot
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on:
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issue_comment:
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types:
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||||||
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- created
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workflow_dispatch:
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jobs:
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TagBot:
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if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
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runs-on: ubuntu-latest
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steps:
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- uses: JuliaRegistries/TagBot@v1
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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ssh: ${{ secrets.DOCUMENTER_KEY }}
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name: Unit Tests
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on:
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- push
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- pull_request
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jobs:
|
||||||
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test:
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name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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julia-version:
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- '1.6'
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- '1'
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- 'nightly'
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julia-arch:
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- x64
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- x86
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os:
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- ubuntu-latest
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- windows-latest
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- macOS-latest
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exclude:
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- os: macOS-latest
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julia-arch: x86
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||||||
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||||||
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steps:
|
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- name: Checkout repository
|
||||||
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uses: actions/checkout@v3
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- name: Setup Julia
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uses: julia-actions/setup-julia@v1
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with:
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version: ${{ matrix.julia-version }}
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arch: ${{ matrix.julia-arch }}
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- name: Cache artifacts
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uses: actions/cache@v3
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env:
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cache-name: cache-artifacts
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with:
|
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path: ~/.julia/artifacts
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key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
|
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restore-keys: |
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${{ runner.os }}-test-${{ env.cache-name }}-
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${{ runner.os }}-test-
|
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${{ runner.os }}-
|
||||||
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- name: Build package
|
||||||
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uses: julia-actions/julia-buildpkg@v1
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||||||
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- name: Run tests
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||||||
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uses: julia-actions/julia-runtest@v1
|
||||||
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- name: Create CodeCov
|
||||||
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uses: julia-actions/julia-processcoverage@v1
|
||||||
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- name: Upload CodeCov
|
||||||
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uses: codecov/codecov-action@v1
|
||||||
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with:
|
||||||
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file: lcov.info
|
||||||
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flags: unittests
|
||||||
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name: codecov-umbrella
|
||||||
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fail_ci_if_error: false
|
||||||
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token: ${{ secrets.CODECOV_TOKEN }}
|
||||||
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||||||
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name: Register Package
|
||||||
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on:
|
||||||
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workflow_dispatch:
|
||||||
|
inputs:
|
||||||
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version:
|
||||||
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description: Version to register or component to bump
|
||||||
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required: true
|
||||||
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jobs:
|
||||||
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register:
|
||||||
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runs-on: ubuntu-latest
|
||||||
|
steps:
|
||||||
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- uses: julia-actions/RegisterAction@latest
|
||||||
|
with:
|
||||||
|
token: ${{ secrets.GITHUB_TOKEN }}
|
||||||
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||||||
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# Files generated by invoking Julia with --code-coverage
|
||||||
|
*.jl.cov
|
||||||
|
*.jl.*.cov
|
||||||
|
|
||||||
|
# Files generated by invoking Julia with --track-allocation
|
||||||
|
*.jl.mem
|
||||||
|
|
||||||
|
# System-specific files and directories generated by the BinaryProvider and BinDeps packages
|
||||||
|
# They contain absolute paths specific to the host computer, and so should not be committed
|
||||||
|
deps/deps.jl
|
||||||
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deps/build.log
|
||||||
|
deps/downloads/
|
||||||
|
deps/usr/
|
||||||
|
deps/src/
|
||||||
|
|
||||||
|
# Build artifacts for creating documentation generated by the Documenter package
|
||||||
|
docs/build/
|
||||||
|
docs/site/
|
||||||
|
|
||||||
|
# File generated by Pkg, the package manager, based on a corresponding Project.toml
|
||||||
|
# It records a fixed state of all packages used by the project. As such, it should not be
|
||||||
|
# committed for packages, but should be committed for applications that require a static
|
||||||
|
# environment.
|
||||||
|
Manifest.toml
|
||||||
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CHANGELOG.md
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|
|
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|
||||||
|
# Changelog
|
||||||
|
|
||||||
|
All notable changes to this project will be documented in this file.
|
||||||
|
|
||||||
|
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0)
|
||||||
|
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
|
||||||
|
|
||||||
|
## [Unreleased]
|
||||||
|
|
||||||
|
### Added
|
||||||
|
|
||||||
|
- Mutation types (`Substitution`, `Deletion`, `Insertion`)
|
||||||
|
- `Variant` type to store groups of mutations together
|
||||||
|
- `Variation` type to store and compare individual mutations
|
||||||
|
- `reconstruct!` function to build mutated sequences from `Variant`s
|
||||||
|
- `Variant` constructor to automatically detect mutations from a `BioAlignments.PairwiseAlignment`
|
||||||
|
|
||||||
|
[unreleased]: https://github.com/BioJulia/SequenceVariation.jl
|
||||||
21
LICENSE
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21
LICENSE
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|
|
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|
||||||
|
MIT License
|
||||||
|
|
||||||
|
Copyright (c) 2022 Jakob Nybo Nissen, Thomas A. Christensen II and other contributors.
|
||||||
|
|
||||||
|
Permission is hereby granted, free of charge, to any person obtaining a copy
|
||||||
|
of this software and associated documentation files (the "Software"), to deal
|
||||||
|
in the Software without restriction, including without limitation the rights
|
||||||
|
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||||
|
copies of the Software, and to permit persons to whom the Software is
|
||||||
|
furnished to do so, subject to the following conditions:
|
||||||
|
|
||||||
|
The above copyright notice and this permission notice shall be included in all
|
||||||
|
copies or substantial portions of the Software.
|
||||||
|
|
||||||
|
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
||||||
|
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
||||||
|
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
||||||
|
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
||||||
|
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
||||||
|
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
||||||
|
SOFTWARE.
|
||||||
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|
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|
||||||
# This file is machine-generated - editing it directly is not advised
|
|
||||||
|
|
||||||
[[ArgTools]]
|
|
||||||
uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
|
|
||||||
|
|
||||||
[[Artifacts]]
|
|
||||||
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
|
|
||||||
|
|
||||||
[[Automa]]
|
|
||||||
deps = ["DataStructures", "Printf", "Random", "Test", "TranscodingStreams"]
|
|
||||||
git-tree-sha1 = "c81526bf5f6fb4616b4e22a3cd62ac20e255fd3c"
|
|
||||||
uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
|
|
||||||
version = "0.8.0"
|
|
||||||
|
|
||||||
[[Base64]]
|
|
||||||
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
|
|
||||||
|
|
||||||
[[BioAlignments]]
|
|
||||||
deps = ["BioGenerics", "BioSequences", "BioSymbols", "IntervalTrees", "LinearAlgebra"]
|
|
||||||
git-tree-sha1 = "f610a3a965f187890edb0b1fdef4f30d77852edd"
|
|
||||||
uuid = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
|
|
||||||
version = "2.0.0"
|
|
||||||
|
|
||||||
[[BioGenerics]]
|
|
||||||
deps = ["TranscodingStreams"]
|
|
||||||
git-tree-sha1 = "6d3f3b474b3df2e83dc67ad12ec63aee4eb5241b"
|
|
||||||
uuid = "47718e42-2ac5-11e9-14af-e5595289c2ea"
|
|
||||||
version = "0.1.1"
|
|
||||||
|
|
||||||
[[BioSequences]]
|
|
||||||
deps = ["BioGenerics", "BioSymbols", "Combinatorics", "IndexableBitVectors", "Printf", "Random", "StableRNGs", "Twiddle"]
|
|
||||||
git-tree-sha1 = "093ccb9211bdc71924abf8e74a0790af11da35a7"
|
|
||||||
uuid = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
|
|
||||||
version = "2.0.5"
|
|
||||||
|
|
||||||
[[BioSymbols]]
|
|
||||||
deps = ["Automa"]
|
|
||||||
git-tree-sha1 = "ec77888ac3e78f9d372c2b533bdb52668f9e2b09"
|
|
||||||
uuid = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
|
|
||||||
version = "4.0.4"
|
|
||||||
|
|
||||||
[[Combinatorics]]
|
|
||||||
git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860"
|
|
||||||
uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
|
|
||||||
version = "1.0.2"
|
|
||||||
|
|
||||||
[[Compat]]
|
|
||||||
deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
|
|
||||||
git-tree-sha1 = "8cd7b7d1c7f6fcbe7e8743a58adf57788ec7f787"
|
|
||||||
uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
|
|
||||||
version = "3.18.0"
|
|
||||||
|
|
||||||
[[CompilerSupportLibraries_jll]]
|
|
||||||
deps = ["Artifacts", "Libdl"]
|
|
||||||
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
|
|
||||||
|
|
||||||
[[DataStructures]]
|
|
||||||
deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
|
|
||||||
git-tree-sha1 = "0347f23484a96d56e7096eb1f55c6975be34b11a"
|
|
||||||
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|
|
||||||
version = "0.18.6"
|
|
||||||
|
|
||||||
[[Dates]]
|
|
||||||
deps = ["Printf"]
|
|
||||||
uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
|
|
||||||
|
|
||||||
[[DelimitedFiles]]
|
|
||||||
deps = ["Mmap"]
|
|
||||||
uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
|
|
||||||
|
|
||||||
[[Distributed]]
|
|
||||||
deps = ["Random", "Serialization", "Sockets"]
|
|
||||||
uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
|
|
||||||
|
|
||||||
[[Downloads]]
|
|
||||||
deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
|
|
||||||
uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
|
|
||||||
|
|
||||||
[[FileWatching]]
|
|
||||||
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
|
|
||||||
|
|
||||||
[[IndexableBitVectors]]
|
|
||||||
deps = ["Random", "Test"]
|
|
||||||
git-tree-sha1 = "b7f5e42dc867b8a8654a5f899064632dac05bc82"
|
|
||||||
uuid = "1cb3b9ac-1ffd-5777-9e6b-a3d42300664d"
|
|
||||||
version = "1.0.0"
|
|
||||||
|
|
||||||
[[InteractiveUtils]]
|
|
||||||
deps = ["Markdown"]
|
|
||||||
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
|
|
||||||
|
|
||||||
[[IntervalTrees]]
|
|
||||||
deps = ["InteractiveUtils", "Profile", "Random", "Test"]
|
|
||||||
git-tree-sha1 = "6c9fcd87677231ae293f6806fad928c216ab6658"
|
|
||||||
uuid = "524e6230-43b7-53ae-be76-1e9e4d08d11b"
|
|
||||||
version = "1.0.0"
|
|
||||||
|
|
||||||
[[LibCURL]]
|
|
||||||
deps = ["LibCURL_jll", "MozillaCACerts_jll"]
|
|
||||||
uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
|
|
||||||
|
|
||||||
[[LibCURL_jll]]
|
|
||||||
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
|
|
||||||
uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
|
|
||||||
|
|
||||||
[[LibGit2]]
|
|
||||||
deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
|
|
||||||
uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
|
|
||||||
|
|
||||||
[[LibSSH2_jll]]
|
|
||||||
deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
|
|
||||||
uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
|
|
||||||
|
|
||||||
[[Libdl]]
|
|
||||||
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
|
|
||||||
|
|
||||||
[[LinearAlgebra]]
|
|
||||||
deps = ["Libdl", "libblastrampoline_jll"]
|
|
||||||
uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
|
|
||||||
|
|
||||||
[[Logging]]
|
|
||||||
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
|
|
||||||
|
|
||||||
[[Markdown]]
|
|
||||||
deps = ["Base64"]
|
|
||||||
uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
|
|
||||||
|
|
||||||
[[MbedTLS_jll]]
|
|
||||||
deps = ["Artifacts", "Libdl"]
|
|
||||||
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
|
|
||||||
|
|
||||||
[[Mmap]]
|
|
||||||
uuid = "a63ad114-7e13-5084-954f-fe012c677804"
|
|
||||||
|
|
||||||
[[MozillaCACerts_jll]]
|
|
||||||
uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
|
|
||||||
|
|
||||||
[[NetworkOptions]]
|
|
||||||
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
|
|
||||||
|
|
||||||
[[OpenBLAS_jll]]
|
|
||||||
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
|
|
||||||
uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
|
|
||||||
|
|
||||||
[[OrderedCollections]]
|
|
||||||
git-tree-sha1 = "16c08bf5dba06609fe45e30860092d6fa41fde7b"
|
|
||||||
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
|
|
||||||
version = "1.3.1"
|
|
||||||
|
|
||||||
[[Pkg]]
|
|
||||||
deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
|
|
||||||
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
|
|
||||||
|
|
||||||
[[Printf]]
|
|
||||||
deps = ["Unicode"]
|
|
||||||
uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
|
|
||||||
|
|
||||||
[[Profile]]
|
|
||||||
deps = ["Printf"]
|
|
||||||
uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
|
|
||||||
|
|
||||||
[[REPL]]
|
|
||||||
deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
|
|
||||||
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
|
|
||||||
|
|
||||||
[[Random]]
|
|
||||||
deps = ["SHA", "Serialization"]
|
|
||||||
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
|
|
||||||
|
|
||||||
[[SHA]]
|
|
||||||
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
|
|
||||||
|
|
||||||
[[Serialization]]
|
|
||||||
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
|
|
||||||
|
|
||||||
[[SharedArrays]]
|
|
||||||
deps = ["Distributed", "Mmap", "Random", "Serialization"]
|
|
||||||
uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
|
|
||||||
|
|
||||||
[[Sockets]]
|
|
||||||
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
|
|
||||||
|
|
||||||
[[SparseArrays]]
|
|
||||||
deps = ["LinearAlgebra", "Random"]
|
|
||||||
uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
|
|
||||||
|
|
||||||
[[StableRNGs]]
|
|
||||||
deps = ["Random", "Test"]
|
|
||||||
git-tree-sha1 = "b57c4216b6c163a3a9d674f6b9f7b99cdccdb959"
|
|
||||||
uuid = "860ef19b-820b-49d6-a774-d7a799459cd3"
|
|
||||||
version = "0.1.2"
|
|
||||||
|
|
||||||
[[Statistics]]
|
|
||||||
deps = ["LinearAlgebra", "SparseArrays"]
|
|
||||||
uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
|
|
||||||
|
|
||||||
[[TOML]]
|
|
||||||
deps = ["Dates"]
|
|
||||||
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
|
|
||||||
|
|
||||||
[[Tar]]
|
|
||||||
deps = ["ArgTools", "SHA"]
|
|
||||||
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
|
|
||||||
|
|
||||||
[[Test]]
|
|
||||||
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
|
|
||||||
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
|
|
||||||
|
|
||||||
[[TranscodingStreams]]
|
|
||||||
deps = ["Random", "Test"]
|
|
||||||
git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c"
|
|
||||||
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
|
|
||||||
version = "0.9.5"
|
|
||||||
|
|
||||||
[[Twiddle]]
|
|
||||||
git-tree-sha1 = "29509c4862bfb5da9e76eb6937125ab93986270a"
|
|
||||||
uuid = "7200193e-83a8-5a55-b20d-5d36d44a0795"
|
|
||||||
version = "1.1.2"
|
|
||||||
|
|
||||||
[[UUIDs]]
|
|
||||||
deps = ["Random", "SHA"]
|
|
||||||
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
|
|
||||||
|
|
||||||
[[Unicode]]
|
|
||||||
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
|
|
||||||
|
|
||||||
[[Zlib_jll]]
|
|
||||||
deps = ["Libdl"]
|
|
||||||
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
|
|
||||||
|
|
||||||
[[libblastrampoline_jll]]
|
|
||||||
deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
|
|
||||||
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
|
|
||||||
|
|
||||||
[[nghttp2_jll]]
|
|
||||||
deps = ["Artifacts", "Libdl"]
|
|
||||||
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
|
|
||||||
|
|
||||||
[[p7zip_jll]]
|
|
||||||
deps = ["Artifacts", "Libdl"]
|
|
||||||
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
|
|
||||||
|
|
@ -1,6 +1,6 @@
|
||||||
name = "SequenceVariation"
|
name = "SequenceVariation"
|
||||||
uuid = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
|
uuid = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
|
||||||
authors = ["Jakob Nybo Nissen <jakobnybonissen@gmail.com>"]
|
authors = ["Jakob Nybo Nissen <jakobnybonissen@gmail.com>", "Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>"]
|
||||||
version = "0.1.0"
|
version = "0.1.0"
|
||||||
|
|
||||||
[deps]
|
[deps]
|
||||||
|
|
@ -9,6 +9,13 @@ BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
|
||||||
BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
|
BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
|
||||||
BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
|
BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
|
||||||
|
|
||||||
|
[compat]
|
||||||
|
BioAlignments = "2.0.0"
|
||||||
|
BioGenerics = "0.1"
|
||||||
|
BioSequences = "2"
|
||||||
|
BioSymbols = "4"
|
||||||
|
julia = "1.6"
|
||||||
|
|
||||||
[extras]
|
[extras]
|
||||||
BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
|
BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
|
||||||
BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
|
BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
|
||||||
|
|
|
||||||
73
README.md
Normal file
73
README.md
Normal file
|
|
@ -0,0 +1,73 @@
|
||||||
|
# <img src="docs/src/assets/logo.png" width="30%" align="right" /> SequenceVariation
|
||||||
|
|
||||||
|
[](https://www.repostatus.org/#wip)
|
||||||
|
[](https://github.com/BioJulia/SequenceVariation.jl/releases/latest)
|
||||||
|
[](https://github.com/BioJulia/SequenceVariation.jl/blob/master/LICENSE)
|
||||||
|
[](https://biojulia.github.io/SequenceVariation.jl/stable)
|
||||||
|
[](https://biojulia.github.io/SequenceVariation.jl/dev/)
|
||||||
|
|
||||||
|
> This project follows the [semver](https://semver.org) _pro forma_ and uses the [OneFlow branching model](https://www.endoflineblog.com/oneflow-a-git-branching-model-and-workflow).
|
||||||
|
|
||||||
|
## Description
|
||||||
|
|
||||||
|
SequenceVariation provides a Julia vocabulary for comparing genetic mutations within biological sequences.
|
||||||
|
|
||||||
|
## Installation
|
||||||
|
|
||||||
|
You can install SequenceVariation from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
|
||||||
|
Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), and enter the following:
|
||||||
|
|
||||||
|
```julia
|
||||||
|
add https://github.com/SequenceVariation.jl
|
||||||
|
```
|
||||||
|
|
||||||
|
## Testing
|
||||||
|
|
||||||
|
SequenceVariation is tested against Julia `1.X` on Linux, OS X, and Windows.
|
||||||
|
|
||||||
|
**Latest build status:**
|
||||||
|
|
||||||
|
[](https://github.com/BioJulia/SequenceVariation.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
|
||||||
|
[](https://github.com/BioJulia/SequenceVariation.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
|
||||||
|
[](https://codecov.io/gh/BioJulia/SequenceVariation.jl)
|
||||||
|
|
||||||
|
## Contributing
|
||||||
|
|
||||||
|
We appreciate [contributions](https://github.com/BioJulia/SequenceVariation.jl/graphs/contributors) from users including reporting bugs, fixing issues, improving performance and adding new features.
|
||||||
|
|
||||||
|
Take a look at the [contributing files](https://github.com/BioJulia/Contributing) for detailed contributor and maintainer guidelines, and code of conduct.
|
||||||
|
|
||||||
|
### Financial contributions
|
||||||
|
|
||||||
|
We also welcome financial contributions in full transparency on our [open collective](https://opencollective.com/biojulia).
|
||||||
|
Anyone can file an expense.
|
||||||
|
If the expense makes sense for the development the core contributors and the person who filed the expense will be reimbursed.
|
||||||
|
|
||||||
|
|
||||||
|
## Backers & Sponsors
|
||||||
|
|
||||||
|
Thank you to all our backers and sponsors!
|
||||||
|
|
||||||
|
Love our work and community? [Become a backer](https://opencollective.com/biojulia#backer).
|
||||||
|
|
||||||
|
[](https://opencollective.com/biojulia#backers)
|
||||||
|
|
||||||
|
Does your company use BioJulia?
|
||||||
|
Help keep BioJulia feature rich and healthy by [sponsoring the project](https://opencollective.com/biojulia#sponsor).
|
||||||
|
Your logo will show up here with a link to your website.
|
||||||
|
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/0/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/1/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/2/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/3/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/4/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/5/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/6/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/7/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/8/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/9/website)
|
||||||
|
|
||||||
|
|
||||||
|
## Questions?
|
||||||
|
|
||||||
|
If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack/), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
|
||||||
2
docs/.gitignore
vendored
Normal file
2
docs/.gitignore
vendored
Normal file
|
|
@ -0,0 +1,2 @@
|
||||||
|
build/
|
||||||
|
site/
|
||||||
6
docs/Project.toml
Normal file
6
docs/Project.toml
Normal file
|
|
@ -0,0 +1,6 @@
|
||||||
|
[deps]
|
||||||
|
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
|
||||||
|
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
|
||||||
|
|
||||||
|
[compat]
|
||||||
|
Documenter = "0.27"
|
||||||
22
docs/make.jl
Normal file
22
docs/make.jl
Normal file
|
|
@ -0,0 +1,22 @@
|
||||||
|
using Pkg
|
||||||
|
using Documenter
|
||||||
|
using SequenceVariation
|
||||||
|
|
||||||
|
makedocs(;
|
||||||
|
checkdocs = :exports,
|
||||||
|
linkcheck = true,
|
||||||
|
sitename = "SequenceVariation.jl",
|
||||||
|
format = Documenter.HTML(),
|
||||||
|
modules = [SequenceVariation],
|
||||||
|
pages = [
|
||||||
|
"Home" => "index.md",
|
||||||
|
"API Reference" => "api.md",
|
||||||
|
],
|
||||||
|
authors = replace(join(Pkg.TOML.parsefile("Project.toml")["authors"], ", "), r" <.*?>" => "" ) * ", The BioJulia Organisation, and other contributors."
|
||||||
|
)
|
||||||
|
|
||||||
|
deploydocs(
|
||||||
|
repo = "github.com/BioJulia/SequenceVariation.jl.git",
|
||||||
|
devbranch = "master",
|
||||||
|
push_preview = true,
|
||||||
|
)
|
||||||
12
docs/src/api.md
Normal file
12
docs/src/api.md
Normal file
|
|
@ -0,0 +1,12 @@
|
||||||
|
```@meta
|
||||||
|
CurrentModule = SequenceVariation
|
||||||
|
DocTestSetup = quote
|
||||||
|
using SequenceVariation
|
||||||
|
end
|
||||||
|
```
|
||||||
|
|
||||||
|
# API Reference
|
||||||
|
|
||||||
|
```@autodocs
|
||||||
|
Modules = SequenceVariation
|
||||||
|
```
|
||||||
BIN
docs/src/assets/logo.png
Normal file
BIN
docs/src/assets/logo.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 18 KiB |
73
docs/src/index.md
Normal file
73
docs/src/index.md
Normal file
|
|
@ -0,0 +1,73 @@
|
||||||
|
# SequenceVariation.jl
|
||||||
|
|
||||||
|
[](https://www.repostatus.org/#wip)
|
||||||
|
[](https://github.com/BioJulia/SequenceVariation.jl/releases/latest)
|
||||||
|
[](https://github.com/BioJulia/SequenceVariation.jl/blob/master/LICENSE)
|
||||||
|
[](https://biojulia.github.io/SequenceVariation.jl/stable)
|
||||||
|
[](https://biojulia.github.io/SequenceVariation.jl/dev/)
|
||||||
|
|
||||||
|
> This project follows the [semver](https://semver.org) _pro forma_ and uses the [OneFlow branching model](https://www.endoflineblog.com/oneflow-a-git-branching-model-and-workflow).
|
||||||
|
|
||||||
|
## Description
|
||||||
|
|
||||||
|
SequenceVariation provides a Julia vocabulary for comparing genetic mutations within biological sequences.
|
||||||
|
|
||||||
|
## Installation
|
||||||
|
|
||||||
|
You can install SequenceVariation from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
|
||||||
|
Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), and enter the following:
|
||||||
|
|
||||||
|
```julia
|
||||||
|
add https://github.com/SequenceVariation.jl
|
||||||
|
```
|
||||||
|
|
||||||
|
## Testing
|
||||||
|
|
||||||
|
SequenceVariation is tested against Julia `1.X` on Linux, OS X, and Windows.
|
||||||
|
|
||||||
|
**Latest build status:**
|
||||||
|
|
||||||
|
[](https://github.com/BioJulia/SequenceVariation.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
|
||||||
|
[](https://github.com/BioJulia/SequenceVariation.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
|
||||||
|
[](https://codecov.io/gh/BioJulia/SequenceVariation.jl)
|
||||||
|
|
||||||
|
## Contributing
|
||||||
|
|
||||||
|
We appreciate [contributions](https://github.com/BioJulia/SequenceVariation.jl/graphs/contributors) from users including reporting bugs, fixing issues, improving performance and adding new features.
|
||||||
|
|
||||||
|
Take a look at the [contributing files](https://github.com/BioJulia/Contributing) for detailed contributor and maintainer guidelines, and code of conduct.
|
||||||
|
|
||||||
|
### Financial contributions
|
||||||
|
|
||||||
|
We also welcome financial contributions in full transparency on our [open collective](https://opencollective.com/biojulia).
|
||||||
|
Anyone can file an expense.
|
||||||
|
If the expense makes sense for the development the core contributors and the person who filed the expense will be reimbursed.
|
||||||
|
|
||||||
|
|
||||||
|
## Backers & Sponsors
|
||||||
|
|
||||||
|
Thank you to all our backers and sponsors!
|
||||||
|
|
||||||
|
Love our work and community? [Become a backer](https://opencollective.com/biojulia#backer).
|
||||||
|
|
||||||
|
[](https://opencollective.com/biojulia#backers)
|
||||||
|
|
||||||
|
Does your company use BioJulia?
|
||||||
|
Help keep BioJulia feature rich and healthy by [sponsoring the project](https://opencollective.com/biojulia#sponsor).
|
||||||
|
Your logo will show up here with a link to your website.
|
||||||
|
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/0/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/1/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/2/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/3/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/4/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/5/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/6/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/7/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/8/website)
|
||||||
|
[](https://opencollective.com/biojulia/sponsor/9/website)
|
||||||
|
|
||||||
|
|
||||||
|
## Questions?
|
||||||
|
|
||||||
|
If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack/), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
|
||||||
Loading…
Reference in a new issue