diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..e756550 --- /dev/null +++ b/.github/CODE_OF_CONDUCT.md @@ -0,0 +1,41 @@ +## Our Pledge + +In the interest of fostering an open and welcoming environment, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities. We are committed to making participation in our projects and our community a harassment-free experience for everyone, regardless of level of experience, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project teams are obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct may be removed from the project team. + +## Attribution + +This Code of Conduct is adapted from the Contributor Covenant, version 1.4, available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 0000000..e69de29 diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md new file mode 100644 index 0000000..60e55f4 --- /dev/null +++ b/.github/ISSUE_TEMPLATE.md @@ -0,0 +1,25 @@ +### Description of the issue: +*Try to be as clear as possible: Is it something wrong/missing in the model? Is it a simulation issue? PLEASE DELETE THIS LINE.* + + +#### Expected feature/value/output: +*How the reaction/metabolite/gene/simulation result should look (cite literature if needed). PLEASE DELETE THIS LINE.* + + +#### Current feature/value/output: +*How the reaction/metabolite/gene/simulation actually looks in the `master` branch. PLEASE DELETE THIS LINE.* + + +#### Reproducing these results: +*Please attach any code used below (if it's python code replace the keyword "matlab" with "python". PLEASE DELETE THIS LINE.* +```matlab + +``` + +**I hereby confirm that I have:** +- [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---user) for running the model +- [ ] Done this analysis in the `master` branch of the repository +- [ ] Checked that a similar issue does not exist already +- [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about the issue + +*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE* diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..5c2d4ab --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,9 @@ +### Main improvements in this PR: +*Try to be as clear as possible: Is it fixing/adding something in the model? Is it an additional test/function/dataset? PLEASE DELETE THIS LINE.* + +**I hereby confirm that I have:** + +- [ ] Tested my code on my own computer for running the model +- [ ] Selected `devel` as a target branch + +*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE* diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9c92715 --- /dev/null +++ b/.gitignore @@ -0,0 +1,314 @@ +### Source https://github.com/github/gitignore/ + + +## R.gitignore +# History files +.Rhistory +.Rapp.history + +# Session Data files +.RData + +# User-specific files +.Ruserdata + +# Example code in package build process +*-Ex.R + +# Output files from R CMD build +/*.tar.gz + +# Output files from R CMD check +/*.Rcheck/ + +# RStudio files +.Rproj.user/ + +# produced vignettes +vignettes/*.html +vignettes/*.pdf + +# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 +.httr-oauth + +# knitr and R markdown default cache directories +*_cache/ +/cache/ + +# Temporary files created by R markdown +*.utf8.md +*.knit.md + +# R Environment Variables +.Renviron + + +## Julia.gitignore +# 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 +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 + + +## Python.gitignore +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + + +## Java.gitignore + +# Compiled class file +*.class + +# Log file +*.log + +# BlueJ files +*.ctxt + +# Mobile Tools for Java (J2ME) +.mtj.tmp/ + +# Package Files # +*.jar +*.war +*.nar +*.ear +*.zip +*.tar.gz +*.rar + +# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml +hs_err_pid* + + +### Source https://github.com/jupyter/notebook/blob/master/.gitignore +MANIFEST +build +dist +_build +docs/man/*.gz +docs/source/api/generated +docs/source/config.rst +docs/gh-pages +notebook/i18n/*/LC_MESSAGES/*.mo +notebook/i18n/*/LC_MESSAGES/nbjs.json +notebook/static/components +notebook/static/style/*.min.css* +notebook/static/*/js/built/ +notebook/static/*/built/ +notebook/static/built/ +notebook/static/*/js/main.min.js* +notebook/static/lab/*bundle.js +node_modules +*.py[co] +__pycache__ +*.egg-info +*~ +*.bak +.ipynb_checkpoints +.tox +.DS_Store +\#*# +.#* +.coverage +.pytest_cache +src + +*.swp +*.map +.idea/ +Read the Docs +config.rst +*.iml +/.project +/.pydevproject + +package-lock.json +geckodriver.log +*.iml + + +### Source https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore +# Windows default autosave extension +*.asv + +# OSX / *nix default autosave extension +*.m~ + +# Compiled MEX binaries (all platforms) +*.mex* + +# Packaged app and toolbox files +*.mlappinstall +*.mltbx + +# Generated helpsearch folders +helpsearch*/ + +# Simulink code generation folders +slprj/ +sccprj/ + +# Matlab code generation folders +codegen/ + +# Simulink autosave extension +*.autosave + +# Simulink cache files +*.slxc + +# Octave session info +octave-workspace + + +### Misc +.DS_Store diff --git a/.standard-GEM.md b/.standard-GEM.md new file mode 100644 index 0000000..154a857 --- /dev/null +++ b/.standard-GEM.md @@ -0,0 +1,109 @@ +standard-GEM 0.5 +================= + +For details about the [aims](https://github.com/MetabolicAtlas/standard-GEM/wiki/Aims,-scope-and-terminology#aims), [scope](https://github.com/MetabolicAtlas/standard-GEM/wiki/Aims,-scope-and-terminology#scope), and [use case](https://github.com/MetabolicAtlas/standard-GEM/wiki/Use-case) of this standard see the [wiki pages of the `standard-GEM` repository](https://github.com/MetabolicAtlas/standard-GEM/wiki). + +### Terminology +To facilitate understanding, the definitions used throughout this guide are copied below [from the wiki](https://github.com/MetabolicAtlas/standard-GEM/wiki/Aims,-scope-and-terminology#terminology). For easier differentiation, we have associated colors to each of them. +``` +Based on the ISO guidelines, tweaked for easy understanding. +🟥 Requirements: must, must not +🟧 Recommendations: should, should not +🟨 Possibility and capability: can +``` + +### Instructions +This document serves as a checklist for creating an open source genome-scale metabolic model (GEM) on GitHub. + +- [ ] 🟥 All GEMs that follow the `standard-GEM` must contain this file. +This serves as a traceable adherence to the standard, manually confirmed by the original authors. This file must be edited only with [checkmarks](https://help.github.com/en/github/managing-your-work-on-github/about-task-lists), in order to support automatic parsing and validation of this file. Some of the checkmarks are pre-applied based on the contents of the `standard-GEM` template repository. GEM authors have the responsibility of checking that their model repository does follow the guidelines entirely. +With further updates to `standard-GEM`, one should paste over the new version of this file, and see that the changes in the new guidelines are met. + +Repository creation +------------------- +- [ ] 🟨 Navigate to [standard-GEM](https://github.com/MetabolicAtlas/standard-GEM/) and click on the button `Use this template` +The `standard-GEM` template can be used to initiate a repository. This will copy the contents of the _master_ branch into the new repository, which can be either private or public. + +- [ ] 🟥 Pick a repository name +The name must be either a common name, KEGG organism, or taxonomy-derived short name, followed by the extension `-GEM` or `-GSMM`. The `-GEM` extension is preferred to ease pronunciation. The name can be prefixed by an abbreviation, eg `ec` (enzyme constrained), `sec` (with secretory pathways), `mito` (with mitochondrion pathways), `pro` (with protein structures). +Example: `ecYeast-GEM` + +- [ ] 🟥 Pick a repository description +The description must include the taxonomic classification in full. +Example: `The consensus GEM for Saccharomyces cerevisiae` + +- [ ] 🟥 Add repository topic +The topic `standard-GEM` must be added. Other topics like `genome-scale-models`, `systems-biology` can be added. Having this topic on your repository enables automatic finding using the GitHub API, and automatic validation of the standard. +Topics are not copied from `standard-GEM`, so they need to be added manually. + +- [ ] 🟨 Add a repository URL +The URL can be the link to the publication/pre-print/website where the model is introduced, for example via an identifier system (doi/EuropePMC/PubMed). + + +Repository workflow +------------------- +- [ ] 🟥 Git branches +The GEM repository must have at least two branches: _master_ and _develop_. + +- [ ] 🟥 Releases +Releases must use the tag format `X.X.X` where X are numbers, according to [semantic versioning principles](https://semver.org/). The last field, also called “patch”, can also be used to indicate changes to the repository that do not actually change the GEM itself. The use of a `v` before the version number (`v1.0`) [is discouraged](https://semver.org/#is-v123-a-semantic-version). For more information about releases see the [documentation at GitHub](https://docs.github.com/en/github/administering-a-repository/managing-releases-in-a-repository). + +- [ ] 🟨 Commits +Commit messages can follow the style of semantic commits. + + +File tree +--------- +`/` signifies the root of the repository. +`.keep` files are used to indicate that the empty folder should not be ignored by _git_ - without it _git_ would simply not want to version empty directories. Once folders are not empty, it is okay to remove these files. + +- [x] 🟥 `/.gitignore` +The repository must contain a `/.gitignore` file. This generic [.gitignore](https://git-scm.com/docs/gitignore) was prepared for multiple programming languages. While it does not require modification, it can be further adapted to the needs of the repository. + +- [x] 🟥 `/.github` +The repository must contain a `/.github` folder, in which the contributing guidelines, code of conduct, issue templates and pull request templates must be placed. Defaults are provided and they do not require any modification. + +- [ ] 🟥 `/.github/CONTRIBUTING.md` +This file is provided by the template, but it is empty. It must be filled in with the adequate contributing guideline instructions; a good example is https://github.com/SysBioChalmers/yeast-GEM/blob/master/.github/CONTRIBUTING.md. + +- [ ] 🟥 `/code/README.md` +The repository must contain a `/code` folder. This folder must contain all the code used in generating the model. It must also include a `README.md` file that describes how the folder is organized. + +- [ ] 🟥 `/data/README.md` +The repository must contain a `/data` folder. This folder contains the data used in generating the model. It must also include a `README.md` file that describes how the folder is organized. + +- [ ] 🟥 `/model` +The repository must contain `/model` folder. +This folder must contain the model files, in multiple formats, according to the table below. As a general guideline, binary formats (`.mat`, `.xlsx`) must not exist on any other branches than _master_. The main reason for this is that binary files cannot be diff'ed, which means changes cannot be compared to previous versions, thus increasing the chance of errors. Moreover, with time, the size of the repository can create difficulties, and we cannot yet recommend storing these files with Git LFS, as it introducs complexity. +For more information on the `sbtab` file format, see [sbtab.net](https://sbtab.net). +All model files must be named the same as the repository, and with the appropriate extension. +Example: `yeast-GEM.mat` + +| Model file format | _master_ branch | _develop_ and other branches | +| ----------------- | --------------- | ---------------------------- | +| JSON `.json` | can || +| Matlab `.mat` | should | must not | +| sbtab `.tsv` | can || +| Text file `.txt` | must || +| Excel `.xlsx` | must | must not | +| SBML `.xml` | must || +| YAML `.yml` | must || + + +- [x] 🟥 `/LICENSE.md` +The repository must contain a license file. The default license is [CC-BY 4.0 International](https://creativecommons.org/licenses/by/4.0/). Unless a different license is desired, the file does not require modification. + +- [ ] 🟥 `/README.md` +The repository must contain a `README.md` file. A default file is provided, and the adequate contents must be filled in. +The `/README.md` file must include a version badge. A default is provided in the file. +Additionally, the `/README.md` file should contain the [Zenodo](https://zenodo.org) badge. As soon as the first public release is in made, the repository [should be archived via Zenodo](https://github.com/MetabolicAtlas/standard-GEM/wiki/FAQ#zenodo), and the corresponding badge be updated. A default is provided in the file. +The `/README.md` can contain a contact badge, for example [Gitter](https://gitter.io). When setting up the Gitter chat room, the GitHub activity should be synced with Gitter in order to see the latest updates of the repository in the chat room. A default for this badge is provided in the file. + +- [x] 🟥 `/version.txt` +The repository must contain this file, which is required for the version badge in the `/README.md`. The value refers to the version of the GEM, not of the `standard-GEM`. The value must be updated with each release. + +- [ ] 🟨 Files for continuous integration testing +The repository can be set up for continuous integration testing using memote with eg. Travis CI (`.travis.yml`), Jenkins (`Jenkinsfile`), GitHub Actions (under `.github/workflows`). + +- [ ] 🟨 _MEMOTE_ report +The repository could contain a [MEMOTE](https://www.nature.com/articles/s41587-020-0446-y) report on the _master_ branch, in `.html` format. diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..a7ba38e --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,159 @@ +## Creative Commons + +# Attribution 4.0 International + +Creative Commons Corporation (“Creative Commons”) is not a law firm and does not provide legal services or legal advice. Distribution of Creative Commons public licenses does not create a lawyer-client or other relationship. Creative Commons makes its licenses and related information available on an “as-is” basis. Creative Commons gives no warranties regarding its licenses, any material licensed under their terms and conditions, or any related information. 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If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions. + +c. No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor. + +d. Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority. + +> Creative Commons is not a party to its public licenses. Notwithstanding, Creative Commons may elect to apply one of its public licenses to material it publishes and in those instances will be considered the “Licensor.” Except for the limited purpose of indicating that material is shared under a Creative Commons public license or as otherwise permitted by the Creative Commons policies published at [creativecommons.org/policies](http://creativecommons.org/policies), Creative Commons does not authorize the use of the trademark “Creative Commons” or any other trademark or logo of Creative Commons without its prior written consent including, without limitation, in connection with any unauthorized modifications to any of its public licenses or any other arrangements, understandings, or agreements concerning use of licensed material. For the avoidance of doubt, this paragraph does not form part of the public licenses. +> +> Creative Commons may be contacted at creativecommons.org diff --git a/README.md b/README.md new file mode 100644 index 0000000..41866cd --- /dev/null +++ b/README.md @@ -0,0 +1,69 @@ +> Introduction (please delete after reading): +[standard-GEM](https://github.com/MetabolicAtlas/standard-GEM) is a template repository that aims to standardize the format of genome-scale metabolic models (GEMs) versioned with git. In addition to encouraging the open-sourcing of GEMs, it facilitates the import of GEMs into databases and online websites. Moreover, it provides the community with a familiar structure that is easy to adopt through this repository itself. The template comes with a set of requirements and recommendations, packaged as to-do items in a hidden Markdown file in this repository `.standard-GEM.md`. After downloading this repository, or using it as a template, those to-do items provide guidance to how adherence to the standard can be obtained. + +> Instructions for this `README` (please delete after reading): +This is the `README.md` template provided by [standard-GEM](https://github.com/MetabolicAtlas/standard-GEM) and was crafted to cover most use-cases. +Feel free to edit this template `README`. Blanks are indicated by `{{ test }}`. One may use a search function to find these `{{`. Here are some examples of blanks used throughout this file: `{{organization or username}}` is the organization name or username for this GitHub repository, eg. `SysBioChalmers`; `{{repository name}}` is the name of this GitHub repository, eg. `yeast-GEM`. +If you find this template does not fit your needs, we would appreciate if you could report this by creating a new issue on [standard-GEM](https://github.com/MetabolicAtlas/standard-GEM/issues). + + +## {{repository name}}: {{repository description}} + +[![Version](https://badge.fury.io/gh/{{organization or username}}%2F{{repository name}}.svg)](https://badge.fury.io/gh/sysbiochalmers/yeast-gem) +[![Zenodo](https://zenodo.org/badge/{{Zenodo ID}}.svg)](https://zenodo.org/badge/latestdoi/{{Zenodo ID}}) +[![Gitter chat](https://badges.gitter.im/{{organization or username}}/{{repository name}}.svg)](https://gitter.im/{{organization or username}}/{{repository name}}) + + +#### Description + +{{ fill in a short description or the paper abstract }} + + +#### Citation + +{{ provide the citation once available, for example: + > Lu, H., Li, F., Sánchez, B.J. et al (2019). A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nat Commun 10, 3586 [doi:10.1038/s41467-019-11581-3](https://doi.org/10.1038/s41467-019-11581-3) + +}} + + +#### Keywords + +> Keywords are be separated by semicolons. +> The `Model source` field contains the source(s) of the current model, eg existing GEMs. If possible, use the Markdown format to add the URL with the DOI. The (NCBI) taxonomy ID should be provided in the [format from identifiers.org](https://registry.identifiers.org/registry/taxonomy). For the genome identifier, please provide the ENA/GenBank/RefSeq identifier via *identifiers.org*, or from other sources such as PATRIC or KBase. + +**Utilisation:** {{ experimental data reconstruction; multi-omics integrative analysis;, _in silico_ strain design; model template }} +**Field:** {{ metabolic-network reconstruction }} +**Type of model:** {{ reconstruction; curated }} +**Model source:** {{ [YeastMetabolicNetwork](http://doi.org/10.1038/nbt1492) }} +**Omic source:** {{ genomics; metabolomics }} +**Taxonomic name:** {{ _Saccharomyces cerevisiae_ }} +**Taxonomy ID:** {{ [taxonomy:559292](https://identifiers.org/taxonomy:559292) }} +**Genome ID:** {{ [insdc.gca:GCA_000146045.2](https://identifiers.org/insdc.gca:GCA_000146045.2) }} +**Metabolic system:** {{ general metabolism }} +**Tissue:** +**Bioreactor:** +**Cell type:** +**Cell line:** +**Strain:** {{ S288C }} +**Condition:** {{ aerobic; glucose-limited; defined media }} + + +### Installation + +{{ Be mindful of users who do not have a typical background - provide a clear overview of the required software. Also, there might be different requirements for users and collaborators. }} + + +### Usage + +{{ Describe how to load and save the model. }} + + +### Contributing + +Contributions are always welcome! Please read the [contributing guideline](.github/CONTRIBUTING.md) to get started. + + +### Contributors + +Code contributors are reported automatically by GitHub under [Contributors](https://github.com/{{organization or username}}/{{repository name}}/graphs/contributors), while other contributions come in as [Issues](https://github.com/{{organization or username}}/{{repository name}}/issues). \ No newline at end of file diff --git a/code/README.md b/code/README.md new file mode 100644 index 0000000..e69de29 diff --git a/data/README.md b/data/README.md new file mode 100644 index 0000000..e69de29 diff --git a/model/.keep b/model/.keep new file mode 100644 index 0000000..e69de29 diff --git a/version.txt b/version.txt new file mode 100644 index 0000000..77d6f4c --- /dev/null +++ b/version.txt @@ -0,0 +1 @@ +0.0.0