Merge pull request #38 from bbglab/develop

Release v1.0.1

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -0,0 +1,91 @@
+name: Bug report 
+title: OpenVariant Bug | 
+description: Create a bug report to help us improve OpenVariant.
+labels: ["bug"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Please fill out the sections below to help everyone identify and fix the bug
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the issue
+      placeholder: Describe your issue and its behaviour (you can add screenshots or videos). 
+    validations:
+      required: true
+  - type: textarea
+    id: steps
+    attributes:
+      label: Steps to reproduce the bug
+      placeholder: Describe the steps to reproduce the bug or the commands to run.
+    validations:
+      required: true
+  - type: textarea
+    id: error
+    attributes:
+      label: Error encountered or actual result
+      placeholder: Copy/paste the stderr output or describe the wrong result. 
+    validations:
+      required: true
+  - type: textarea
+    id: result
+    attributes:
+      label: Expected result
+      placeholder: Describe the result that OpenVariant should show. 
+    validations:
+      required: true
+  - type: input
+    id: version
+    attributes:
+      label: OpenVariant version
+      placeholder: X.Y.Z
+    validations:
+      required: true
+  - type: input
+    id: python
+    attributes:
+      label: Python version
+      placeholder: X.Y.Z
+    validations:
+      required: true
+  - type: input
+    id: installation
+    attributes:
+      label: Installation method
+      placeholder: e.g. pip, source code
+    validations:
+      required: true
+  - type: input
+    id: environment
+    attributes:
+      label: Environment
+      placeholder: e.g. Jupyter notebook, CLI, Nextflow, Docker/Singularity, Conda, script
+    validations:
+      required: true
+  - type: input
+    id: os
+    attributes:
+      label: OS
+      placeholder: e.g. Debian/Ubuntu, Arch Linux, macOS, Windows
+    validations:
+      required: true
+  - type: textarea
+    id: comment
+    attributes:
+      label: Other commentaries (optional)
+      placeholder: Add other commentaries that may be helpful to fix the bug. 
+    validations:
+      required: false
+  - type: input
+    id: contact
+    attributes:
+      label: Contact details (optional)
+      description: How can we get in touch with you if we need more info?
+      placeholder: e.g. [email protected]
+    validations:
+      required: false
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for reporting this bug!

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: true
+contact_links:
+  - name: Questions
+    url: https://github.com/bbglab/openvariant/discussions/categories/general
+    about: Ask general questions or get help from the community. 
+  - name: Email us
+    url: mailto:[email protected]
+    about: Email us for inquiries, collaborations, or more details on OpenVariant.

.github/ISSUE_TEMPLATE/new-feature.yml

@@ -0,0 +1,42 @@
+name: New feature
+title: OpenVariant New Feature | 
+description: Propose a new feature to improve OpenVariant
+labels: ["enhancement"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Please fill out the sections below to help us to build the new feature.
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the feature
+      placeholder: Describe the new feature and its behaviour.
+    validations:
+      required: true
+  - type: textarea
+    id: why
+    attributes:
+      label: Why it should be implemented?
+      placeholder: Give us the reasons why this new feature show be in OpenVariant.
+    validations:
+      required: true
+  - type: textarea
+    id: suggest
+    attributes:
+      label: The best way to implement the new feature (optional)
+      placeholder: Suggest how it should be implemented or give additional context.  
+    validations:
+      required: false
+  - type: input
+    id: contact
+    attributes:
+      label: Contact details (optional)
+      description: How can we get in touch with you if we need more info?
+      placeholder: e.g. [email protected]
+    validations:
+      required: false
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for your suggestion!

.github/ISSUE_TEMPLATE/test.yml

@@ -0,0 +1,49 @@
+name: Test suggestion
+title: "OpenVariant Test | " 
+description: Propose a new unit test or modify the actual ones.
+labels: ["test"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Please fill out the sections below to help us to build or modify unit tests.
+  - type: input
+    id: feature
+    attributes:
+      label: Which feature relates to this test?
+      placeholder: e.g. task, command, annotation
+    validations:
+      required: true
+  - type: textarea
+    id: description
+    attributes:
+      label: Describe the new unit test or the changes to apply
+      placeholder: Describe the new test to implement or the modifications to carry on. 
+    validations:
+      required: true
+  - type: textarea
+    id: why
+    attributes:
+      label: Why it should be implemented/changed?
+      placeholder: Give us the reasons why this unit test should be implemented or modified.
+    validations:
+      required: true
+  - type: textarea
+    id: suggest
+    attributes:
+      label: The best way to test the feature (optional)
+      placeholder: Suggest how the feature should be tested or give additional context.
+    validations:
+      required: false
+  - type: input
+    id: contact
+    attributes:
+      label: Contact details (optional)
+      description: How can we get in touch with you if we need more info?
+      placeholder: e.g. [email protected]
+    validations:
+      required: false
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for testing!

.github/workflows/openvariant_tester.yml

@@ -24,27 +24,30 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    env:
+      UV_LINK_MODE: copy
+      RUFF_FORMAT: github
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov
-        pip install -e .
-    - name: Lint with flake8
+        python-version-file: "pyproject.toml"
+
+    - uses: astral-sh/setup-uv@v4
+
+    - name: Lint with Ruff
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
+        uv sync --extra linting --frozen
+        uv run ruff check openvariant
+
+    - name: Test
       run: |
-        pytest --cov .
+        uv sync --extra tests --frozen
+        uv run pytest --cov . 
+
     - name: Upload coverage reports to Codecov with GitHub Action
       uses: codecov/codecov-action@v3
-        
+

.readthedocs.yaml

@@ -3,15 +3,18 @@ version: 2
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "3.7"
+    python: "3.10"
   apt_packages:
+    - build-essential
+    - libzmq3-dev 
     - gcc
-
-# Build from the docs/ directory with Sphinx
+    - g++
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv sync --extra docs --frozen
+    - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
+
 sphinx:
-  configuration: docs/conf.py
-
-# Explicitly set the version of Python and its requirements
-python:
-  install:
-    - requirements: requirements-docs.txt
+  configuration: docs/conf.py 

CITATION.cff

@@ -0,0 +1,73 @@
+cff-version: 1.2.0
+message: "If you use OpenVariant in your research, please cite it as below."
+title: "OpenVariant: a toolkit to parse and operate multiple input file formats"
+authors:
+  - family-names: "Martínez-Millán"
+    given-names: "David"
+    orcid: "https://orcid.org/0000-0002-4903-029X"
+  - family-names: "Brando"
+    given-names: "Federica"
+    orcid: "https://orcid.org/0000-0003-0537-0281"
+  - family-names: "L. Grau"
+    given-names: "Miguel"
+    orcid: "https://orcid.org/0000-0002-5137-9976"
+  - family-names: "Sánchez-Guixé"
+    given-names: "Mònica"
+    orcid: "https://orcid.org/0000-0002-9430-4413"
+  - family-names: "López-Elorduy"
+    given-names: "Carlos"
+    orcid: "https://orcid.org/0000-0001-8971-9051"
+  - family-names: "Reyes-Salazar"
+    given-names: "Iker"
+  - family-names: "Deu-Pons"
+    given-names: "Jordi"
+    orcid: "https://orcid.org/0000-0002-1150-1586"
+  - family-names: "López-Bigas"
+    given-names: "Núria"
+    orcid: "https://orcid.org/0000-0003-4925-8988"
+  - family-names: "González-Pérez"
+    given-names: "Abel"
+    orcid: "https://orcid.org/0000-0002-8582-4660"
+date-released: "2024-12-02"
+version: "1.0.0"
+doi: "10.1093/bioinformatics/btae714"
+url: "https://doi.org/10.1093/bioinformatics/btae714"
+journal: "Bioinformatics"
+volume: "40"
+issue: "12"
+license: "CC-BY-4.0"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Martínez-Millán"
+    given-names: "David"
+    orcid: "https://orcid.org/0000-0002-4903-029X"
+  - family-names: "Brando"
+    given-names: "Federica"
+    orcid: "https://orcid.org/0000-0003-0537-0281"
+  - family-names: "L. Grau"
+    given-names: "Miguel"
+    orcid: "https://orcid.org/0000-0002-5137-9976"
+  - family-names: "Sánchez-Guixé"
+    given-names: "Mònica"
+    orcid: "https://orcid.org/0000-0002-9430-4413"
+  - family-names: "López-Elorduy"
+    given-names: "Carlos"
+    orcid: "https://orcid.org/0000-0002-9430-4413"
+  - family-names: "Reyes-Salazar"
+    given-names: "Iker"
+  - family-names: "Deu-Pons"
+    given-names: "Jordi"
+    orcid: "https://orcid.org/0000-0002-1150-1586"
+  - family-names: "López-Bigas"
+    given-names: "Núria"
+    orcid: "https://orcid.org/0000-0003-4925-8988"
+  - family-names: "González-Pérez"
+    given-names: "Abel"
+    orcid: "https://orcid.org/0000-0002-8582-4660"
+  title: "OpenVariant: a toolkit to parse and operate multiple input file formats"
+  doi: "10.1093/bioinformatics/btae714"
+  journal: "Bioinformatics"
+  volume: "40"
+  issue: "12"
+  year: 2024

README.md

@@ -1,6 +1,4 @@
 <div align="center">
-    <br>
-    <br>
     <a href="https://openvariant.readthedocs.io/">
       <img src="https://github.com/bbglab/openvariant/raw/master/logo.png" width="590" height="350">
     </a>
@@ -68,16 +66,27 @@ For more details check our [Installation](https://openvariant.readthedocs.io/en/
 
 ## Examples
 
-We offer a bunch of [Examples](https://github.com/bbglab/openvariant/tree/master/examples) to we be able to understand how OpenVariant can be applied. Also, check 
-[Examples](https://openvariant.readthedocs.io/en/latest/examples.html) section in OpenVariant's documentation.
+We provide a variety of [examples](https://github.com/bbglab/openvariant/tree/master/examples) to help to understand how OpenVariant can be applied. Explore the 
+[Examples](https://openvariant.readthedocs.io/en/latest/examples.html) section in OpenVariant's documentation for more details.
+
+As well, we present a small dataset for hands-on use with OpenVariant, allowing users to test the tool's functionalities. It may be found at [Zenodo](https://zenodo.org/records/14215914) and it can be downloaded using the following commands:
+```bash
+pip install zenodo_get                      
+zenodo_get 14215914
+```
 
 ## Contributing
 
-Feel free to contribute as much as you want to the code.
+You're welcome to contribute to the code as much as you'd like!
 
-See [CONTRIBUTING](https://github.com/bbglab/openvariant/blob/master/CONTRIBUTING.md) for guidelines on contributing and respect your behaviour specified
-at [CODE OF CONDUCT](https://github.com/bbglab/openvariant/blob/master/CODE_OF_CONDUCT.md).
+Please review the guidelines outlined in the [Contributing](https://github.com/bbglab/openvariant/blob/master/CONTRIBUTING.md) document and adhere to the standards of conduct detailed in the [Code of Conduct](https://github.com/bbglab/openvariant/blob/master/CODE_OF_CONDUCT.md).
 
 ## License
 
-The software is licensed under [BSD-3-Clause](https://github.com/bbglab/openvariant/blob/master/LICENSE).
+The software is licensed under [BSD-3-Clause](https://github.com/bbglab/openvariant/blob/master/LICENSE).
+
+## Reference
+
+If you use OpenVariant in your research, please cite:
+
+> David Martínez-Millán, Federica Brando, Miguel L. Grau, Mònica Sánchez-Guixé, Carlos López-Elorduy, Iker Reyes-Salazar, Jordi Deu-Pons, Núria López-Bigas, Abel González-Pérez, OpenVariant: a toolkit to parse and operate multiple input file formats, Bioinformatics, Volume 40, Issue 12, December 2024, btae714, [https://doi.org/10.1093/bioinformatics/btae714](https://doi.org/10.1093/bioinformatics/btae714)