From 3647b6a417e8ed2a9214ec32b2e44d3709e5fb51 Mon Sep 17 00:00:00 2001 From: Nitesh Turaga Date: Mon, 6 Jul 2020 08:56:35 -0400 Subject: [PATCH 1/2] Update new-package-workflow.md These changes are for the new-package-workflow, where the package is added directly to the Bioconductor git server. --- .../how-to/git/new-package-workflow.md | 55 ++++++++++++++----- 1 file changed, 40 insertions(+), 15 deletions(-) diff --git a/content/developers/how-to/git/new-package-workflow.md b/content/developers/how-to/git/new-package-workflow.md index b1bc6c10c..ef6f5c29b 100644 --- a/content/developers/how-to/git/new-package-workflow.md +++ b/content/developers/how-to/git/new-package-workflow.md @@ -1,37 +1,60 @@ # New package workflow -__Goal__: You have developed a package in GitHub, following the -_Bioconductor_ new package [Contributions README][] and other -guidelines, and your package has been accepted! The accepted package -has been added to the _Bioconductor_ git repository. Now what? +__Goal__: You developed a package in GitHub, following the +_Bioconductor_ new package [Contributions README][] guidelines, +[submitted it to _Bioconductor_][], and your package has been +moderated. As part of moderation process, the package to be +reviewed has been added to the _Bioconductor_ git repository. +Package authors will learn to push to the _Bioconductor_ git +repository, from the time a package has been submitted to +_Bioconductor_. -After your package has been accepted, it is visible on the -[_Bioconductor_ git server][]. +After your package has been moderated and assigned a reviewer, +it is available on the [_Bioconductor_ git server][]. - __SSH (developer) read / write access:__ `git@git.bioconductor.org` - __HTTPS (public) read only access:__ `https://git.bioconductor.org` - ## Steps: 1. _Bioconductor_ needs to know your SSH 'public key'. _Bioconductor_ - will use keys in `https://github.com/.keys`. + will use keys in `https://github.com/.keys`. This step + is now mandated by the package submission process, so it should have been + completed if you have gone through the first step of the submission process. Alternatively, [submit your SSH public key][submit-keys] or github - id to _Bioconductor_. + id to _Bioconductor_ via the [BiocCredentials application][]. 1. Configure the "remotes" of your local git repository. You will need - to push any future changes to your package to the _Bioconductor_ - repository, and pull changes the _Bioconductor_ core team will make - (e.g., bug fixes or bumping a version number for a new - release). Add a remote to your machine's local git repository - using: + to push any future changes to your package to the _Bioconductor_ git + repository to issue a new build of your package. + + Once the package is accepted, you pull changes the _Bioconductor_ core + team will make (e.g., bug fixes or bumping a version number for a new + release). + + Add a remote to your package's local git repository using: git remote add upstream git@git.bioconductor.org:packages/.git +1. **Start a new build**: Your package version number is in the format + 'major.minor.patch'. To start a new build on our server, you must only + update the 'patch' version. Newly submitted packages will have versions + similar to `0.99.0`. Then, push to the _Bioconductor_ git repository. + + To push, + + git add + + git commit -m "" + + git push upstream master + 1. [Pull upstream changes][] made by the _Bioconductor_ core team - during addition of your repository. + during addition of your repository. This step is relevant once you + package is accepted by Bioconductor. You will need to pull the changes + made by the Bioconductor team. 1. See other scenarios for working with _Bioconductor_ and GitHub repositories, in particular: @@ -44,3 +67,5 @@ After your package has been accepted, it is visible on the [Fix bugs in devel and release]: ../bug-fix-in-release-and-devel [Contributions README]: https://github.com/Bioconductor/Contributions [_Bioconductor_ git server]: https://git.bioconductor.org +[submitted it to _Bioconductor_]: http://bioconductor.org/developers/package-submission/ +[BiocCredentials application]: https://git.bioconductor.org/BiocCredentials/ From 2c46089f8c5ca702d1c2310527349086761a328b Mon Sep 17 00:00:00 2001 From: Nitesh Turaga Date: Mon, 6 Jul 2020 09:00:13 -0400 Subject: [PATCH 2/2] Update new-package-workflow.md Add note about SSH protocol. --- content/developers/how-to/git/new-package-workflow.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/content/developers/how-to/git/new-package-workflow.md b/content/developers/how-to/git/new-package-workflow.md index ef6f5c29b..d87b19e5b 100644 --- a/content/developers/how-to/git/new-package-workflow.md +++ b/content/developers/how-to/git/new-package-workflow.md @@ -37,6 +37,10 @@ it is available on the [_Bioconductor_ git server][]. Add a remote to your package's local git repository using: git remote add upstream git@git.bioconductor.org:packages/.git + + NOTE: As a package developer, you must only use the SSH protocol to + gain read/write access to your package in the _Bioconductor_ git + repository. 1. **Start a new build**: Your package version number is in the format 'major.minor.patch'. To start a new build on our server, you must only