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* Migrate to precimed GH organization Fixes #17
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| Original file line number | Diff line number | Diff line change |
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@@ -6,10 +6,10 @@ Thanks for considering contributing! Please read this document to learn the vari | |
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| ### Did you find a bug? | ||
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| First, do [a quick search](https://github.com/espenhgn/container_template/issues) to see whether your issue has already been reported. | ||
| First, do [a quick search](https://github.com/precimed/container_template/issues) to see whether your issue has already been reported. | ||
| If your issue has already been reported, please comment on the existing issue. | ||
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| Otherwise, open [a new GitHub issue](https://github.com/espenhgn/container_template/issues). Be sure to include a clear title | ||
| Otherwise, open [a new GitHub issue](https://github.com/precimed/container_template/issues). Be sure to include a clear title | ||
| and description. The description should include as much relevant information as possible. The description should | ||
| explain how to reproduce the erroneous behavior as well as the behavior you expect to see. Ideally you would include a | ||
| code sample or an executable test case demonstrating the expected behavior. | ||
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@@ -21,7 +21,7 @@ We use GitHub issues to track feature requests. Before you create a feature requ | |
| * Make sure you have a clear idea of the enhancement you would like. If you have a vague idea, consider discussing | ||
| it first on a GitHub issue. | ||
| * Check the documentation to make sure your feature does not already exist. | ||
| * Do [a quick search](https://github.com/espenhgn/container_template/issues) to see whether your feature has already been suggested. | ||
| * Do [a quick search](https://github.com/precimed/container_template/issues) to see whether your feature has already been suggested. | ||
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| When creating your request, please: | ||
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@@ -47,7 +47,7 @@ When you're ready to contribute code to address an open issue, please follow the | |
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| git clone [email protected]:USERNAME/container_template.git | ||
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| At this point the local clone of your fork only knows that it came from *your* repo, github.com/USERNAME/container_template.git, but doesn't know anything the *main* repo, [https://github.com/espenhgn/container_template.git](https://github.com/espenhgn/container_template). You can see this by running | ||
| At this point the local clone of your fork only knows that it came from *your* repo, github.com/USERNAME/container_template.git, but doesn't know anything the *main* repo, [https://github.com/precimed/container_template.git](https://github.com/precimed/container_template). You can see this by running | ||
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| git remote -v | ||
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@@ -56,22 +56,22 @@ When you're ready to contribute code to address an open issue, please follow the | |
| origin https://github.com/USERNAME/container_template.git (fetch) | ||
| origin https://github.com/USERNAME/container_template.git (push) | ||
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| This means that your local clone can only track changes from your fork, but not from the main repo, and so you won't be able to keep your fork up-to-date with the main repo over time. Therefore you'll need to add another "remote" to your clone that points to [https://github.com/espenhgn/container_template.git](https://github.com/espenhgn/container_template). To do this, run the following: | ||
| This means that your local clone can only track changes from your fork, but not from the main repo, and so you won't be able to keep your fork up-to-date with the main repo over time. Therefore you'll need to add another "remote" to your clone that points to [https://github.com/precimed/container_template.git](https://github.com/precimed/container_template). To do this, run the following: | ||
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| git remote add upstream https://github.com/espenhgn/container_template.git | ||
| git remote add upstream https://github.com/precimed/container_template.git | ||
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| Now if you do `git remote -v` again, you'll see | ||
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| origin https://github.com/USERNAME/container_template.git (fetch) | ||
| origin https://github.com/USERNAME/container_template.git (push) | ||
| upstream https://github.com/espenhgn/container_template.git (fetch) | ||
| upstream https://github.com/espenhgn/container_template.git (push) | ||
| upstream https://github.com/precimed/container_template.git (fetch) | ||
| upstream https://github.com/precimed/container_template.git (push) | ||
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| 2. **Ensure your fork is up-to-date** | ||
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| <details><summary>Expand details 👇</summary><br/> | ||
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| Once you've added an "upstream" remote pointing to [https://github.com/espenhgn/container_template.git](https://github.com/espenhgn/container_template), keeping your fork up-to-date is easy: | ||
| Once you've added an "upstream" remote pointing to [https://github.com/precimed/container_template.git](https://github.com/precimed/container_template), keeping your fork up-to-date is easy: | ||
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| git checkout main # if not already on main | ||
| git pull --rebase upstream main | ||
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@@ -97,12 +97,12 @@ When you're ready to contribute code to address an open issue, please follow the | |
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| <details><summary>Expand details 👇</summary><br/> | ||
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| Our continuous integration (CI) testing runs [a number of checks](https://github.com/espenhgn/container_template/actions) for each pull request on [GitHub Actions](https://github.com/features/actions). | ||
| Our continuous integration (CI) testing runs [a number of checks](https://github.com/precimed/container_template/actions) for each pull request on [GitHub Actions](https://github.com/features/actions). | ||
| You can run most of these tests locally, which is something you should do *before* opening a PR to help speed up the review process and make it easier for us. | ||
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| And finally, please update the [CHANGELOG](https://github.com/espenhgn/container_template/blob/main/CHANGELOG.md) with notes on your contribution in the "Unreleased" section at the top. | ||
| And finally, please update the [CHANGELOG](https://github.com/precimed/container_template/blob/main/CHANGELOG.md) with notes on your contribution in the "Unreleased" section at the top. | ||
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| After all of the above checks have passed, you can now open [a new GitHub pull request](https://github.com/espenhgn/container_template/pulls). | ||
| After all of the above checks have passed, you can now open [a new GitHub pull request](https://github.com/precimed/container_template/pulls). | ||
| Make sure you have a clear description of the problem and the solution, and include a link to relevant issues. | ||
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| We look forward to reviewing your PR! | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -10,7 +10,7 @@ It only contains Python 3.10. | |
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| ## Getting Started | ||
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| * Download ``container_template.sif`` from [here](https://github.com/espenhgn/container_template/tree/main/containers) | ||
| * Download ``container_template.sif`` from [here](https://github.com/precimed/container_template/tree/main/containers) | ||
| * Import these files to your secure HPC environment | ||
| * Run ``singularity exec --no-home container_template.sif python3 --help``, to validate that you can run singularity. This command is expected to produce the standard python help message, starting like this: | ||
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@@ -53,7 +53,7 @@ There are several ways to give singularity container access to your data. Here a | |
| In this way in your python command you can refer to the files as if they are in your local folder without specifying the path. | ||
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| 2. Now, let's assume that instead of downloading the ``container_template.sif`` container file you've cloned the entire github repo | ||
| (``git clone [email protected]:espenhgn/container_template.git``), have built and pushed the container, and have transfered it to your HPC environment. | ||
| (``git clone [email protected]:precimed/container_template.git``), have built and pushed the container, and have transfered it to your HPC environment. | ||
| Then change your folder to the root of the ``container_template`` repository, and run these commands: | ||
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| ``` | ||
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@@ -91,4 +91,4 @@ There are several ways to give singularity container access to your data. Here a | |
| singularity exec --home $PWD:/home container_template.sif python -c "print('Hello Moon')" | ||
| ``` | ||
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| Please [let us know](https://github.com/espenhgn/container_template/issues/new) if you face any problems. | ||
| Please [let us know](https://github.com/precimed/container_template/issues/new) if you face any problems. | ||
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