Dear Bioconductor team, we would like to submit two R packages (software and accompanying data package) that are located in a git repository jointly with a Python package that one of them depends upon. These two R packages are located at - https://github.com/bioFAM/MOFA/tree/master/MOFA - https://github.com/bioFAM/MOFA/tree/master/MOFAdata within the repository https://github.com/bioFAM/MOFA. However, the submission via the git submission system fails as it requires the package to sit at https://github.com/yourusername/yourpackagename <https://github.com/yourusername/yourpackagename>. We would like to avoid breaking up the repository https://github.com/bioFAM/MOFA into separate repositories for each package as they are inter-dependent and new developments or fixes often involve changes to both the python package (mofapy) and the R package (MOFA) (e.g. having common branches for the two packages is very useful). Is there a way to submit the packages at their current paths, i.e. make the submission system look at https://github.com/bioFAM/MOFA/tree/master/MOFA and /MOFAdata instead of https://github.com/bioFAM/MOFA? If not, do you have other suggestions how to solve this without breaking up the repository? Thanks for your help! Best, Britta Velten
[Bioc-devel] Submission of packages located at within a repository
2 messages · Britta Velten, Turaga, Nitesh
2 days later
Hi Britta, You could use submodules in git. I took some time to create an example use case for you, at https://github.com/nturaga/main_repository The ?main_repository? contains a README.md file which you might find useful to go about creating the submodule for your packages/ The example there, shows, main_repository, (parent repo) located at https://github.com/nturaga/main_repository submodule_one (as submodule) located at https://github.com/nturaga/submodule_one To give you a gist of what you could do: Main repository is ?MOFA_main?, located at https://github.com/bioFAM/MOFA_main submodule 1: MOFA software package located at https://github.com/bioFAM/MOFA submodule 2: MOFA data package located at https://github.com/bioFAM/MOFAdata They would both live in the MOFA_main repository but would act as submodules within their own independent repos. This will allow you to submit from their separate repos. https://github.com/nturaga/main_repository/blob/master/README.md gives you details on how to create submodules, if you need any assistance. But, I?ll highlight some steps, Step 0: Rename the main MOFA directory which already exists to MOFA_main. Step 1: Create two new repos in the bioFAM username, with MOFA, and MOFAdata. Step 2: Create submodules in MOFA_main, git submodule init git submodule add git at github.com:bioFAM/MOFA MOFA git submodule add git at github.com:bioFAM/MOFAdata MOFAdata Step 3: Add the submodules to MOFA_main git commit -m ?Add MOFA and MOFAdata as submodules?. The ?.gitmodules? should show, $ cat .gitmodules [submodule ?MOFA"] path = MOFA url = git at github.com:bioFAM/MOFA [submodule ?MOFAdata?] path = MOFAdata url = git at github.com:bioFAM/MOFAdata But to answer your question, bioconductor doesn?t have a way to submit multiple packages from within one repository. I can assist you in creating submodules, and submitting the repos as required to Bioconductor. Please let me know if you have any questions. Please check the example and the documentation I wrote up in the README.md at https://github.com/nturaga/main_repository. Best, Nitesh
On Feb 4, 2019, at 11:24 AM, Britta Velten <britta.velten at embl.de> wrote: Dear Bioconductor team, we would like to submit two R packages (software and accompanying data package) that are located in a git repository jointly with a Python package that one of them depends upon. These two R packages are located at - https://github.com/bioFAM/MOFA/tree/master/MOFA - https://github.com/bioFAM/MOFA/tree/master/MOFAdata within the repository https://github.com/bioFAM/MOFA. However, the submission via the git submission system fails as it requires the package to sit at https://github.com/yourusername/yourpackagename <https://github.com/yourusername/yourpackagename>. We would like to avoid breaking up the repository https://github.com/bioFAM/MOFA into separate repositories for each package as they are inter-dependent and new developments or fixes often involve changes to both the python package (mofapy) and the R package (MOFA) (e.g. having common branches for the two packages is very useful). Is there a way to submit the packages at their current paths, i.e. make the submission system look at https://github.com/bioFAM/MOFA/tree/master/MOFA and /MOFAdata instead of https://github.com/bioFAM/MOFA? If not, do you have other suggestions how to solve this without breaking up the repository? Thanks for your help! Best, Britta Velten [[alternative HTML version deleted]]
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