Conda installation - Githubissues

ellasiera commented 1 year ago

Hi Linxing! I just wanted to recommend adding detailed installation instructions for a conda environment that users could just copy and paste. I know it's silly, but many users are not savvy in python but have conda available, and I think it would extend your user list if you just do this one small thing.

linxingchen commented 1 year ago

Thank you Ella for the suggestion (asked by one of the reviewers as well), I have been working on it but slowly.

linxingchen commented 1 year ago

Hi Ella, you could install it via pip install cobra-meta now, please let me know if it works for you.

rdenise commented 1 year ago

If you have a pip install already the bioconda package should not be complicated to do (https://bioconda.github.io/contributor/index.html):

Create a Fork of bioconda Recipes Repo -> https://github.com/bioconda/bioconda-recipes
git clone git@github.com:/bioconda-recipes.git
cd bioconda-recipes
git remote add upstream git@github.com:bioconda/bioconda-recipes.git
git checkout master
git pull upstream master
git push origin master
git checkout -b cobra-meta
cd recipes
conda skeleton pypi cobra-meta
Do the change inside the meta.yaml if specific package need to be download to work with cobra-meta (blast, biopython, pysam...)
Now head back to GitHub. Go to your fork of the bioconda-recipes repository and find the branch you have just created in the Branch: drop down. You should now see a message saying This branch is 1 commit ahead [...] bioconda:master. To the right of that line you will find a button Pull Request. Click this and follow the instructions to open a new Pull Request.

Now you just wait for someone to review the pull request and after you will have nothing to do ever as bioconda will automatically check if a new version of the package is on pypi

I did it recently and it was really easy to do their documentation is well done especially for python package

linxingchen commented 1 year ago

If you have a pip install already the bioconda package should not be complicated to do (https://bioconda.github.io/contributor/index.html):

Create a Fork of bioconda Recipes Repo -> https://github.com/bioconda/bioconda-recipes

git clone git@github.com:/bioconda-recipes.git

cd bioconda-recipes

git remote add upstream git@github.com:bioconda/bioconda-recipes.git

git checkout master

git pull upstream master

git push origin master

git checkout -b cobra-meta

cd recipes

conda skeleton pypi cobra-meta

Do the change inside the meta.yaml if specific package need to be download to work with cobra-meta (blast, biopython, pysam...)

Now head back to GitHub. Go to your fork of the bioconda-recipes repository and find the branch you have just created in the Branch: drop down. You should now see a message saying This branch is 1 commit ahead [...] bioconda:master. To the right of that line you will find a button Pull Request. Click this and follow the instructions to open a new Pull Request.

Now you just wait for someone to review the pull request and after you will have nothing to do ever as bioconda will automatically check if a new version of the package is on pypi

I did it recently and it was really easy to do their documentation is well done especially for python package

Hi Remi, thank you. I actually have started the process two months ago. The review is forever. I should ask them again.

rdenise commented 1 year ago

Yes you should probably. Also you can ask the bot to flag the pull request for review and merge. When I put my package on bioconda it took around a day to have it merge even less.

rdenise commented 1 year ago

Hi, I looked at you meta.yaml that you try to merge on bionconda.

There is multiple thing you can change that could be good to have a better maybe conda meta.yaml file to be merge on bioconda. First you don't need a build.sh put the build inside the meta.yaml.

Also I saw that you didn't put BLAST on the run dependencies while using it in COBRA. So maybe you should add it to have the environment self sufficient when install. (Best would also be to specify version for the dependencies to make sure the install never break)

source:
  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cobra-meta-{{ version }}.tar.gz
  sha256: 14dda04eb9732acc8f0385f9a0dffc8ee090100efc3d12c47471195aff7a4a9d

build:
  entry_points:
    - cobra-meta = cobra:main
  noarch: python
  script: "{{ PYTHON }} -m pip install . -vv"
  number: 0
  run_exports:
    - {{ pin_subpackage('cobra-meta', max_pin="x") }}

requirements:
  host:
    - python
    - pip
  run:
    - python
    - biopython
    - pysam
    - numpy
    - cython
    - blast >=2.14.0,<3.0.0

and at the end in the extra add:

extra:
  identifiers:
    - doi: https://doi.org/10.1101/2023.05.30.542503
  recipe-maintainers:
    - linxingchen

rdenise commented 1 year ago

Also when the check is done by their github action, ask the bot to flag the request with the flag that tell people to do the merge @BiocondaBot please add label

Hope all this help

ellasiera commented 1 year ago

Hi Linxing and Remi, Just to let you know I'm cc'd on these emails so avoid secret codes :) Cheers, Ella

On Thu, Nov 23, 2023 at 10:40 AM Remi Denise @.***> wrote:

Also when the check is done by their github action, ask the bot to flag the request with the flag that tell people to do the merge @BiocondaBot please add label

Hope all this help

— Reply to this email directly, view it on GitHub https://github.com/linxingchen/cobra/issues/8#issuecomment-1824075386, or unsubscribe https://github.com/notifications/unsubscribe-auth/AO5JAIKGTC2OXAUUZJQ5XO3YF4KYBAVCNFSM6AAAAAA3Q6LEBOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRUGA3TKMZYGY . You are receiving this because you authored the thread.Message ID: @.***>

rdenise commented 1 year ago

It is not secret at all. Also this issue is visible by anyone that has access to GitHub. So you are not the only one that could see whatever is written here

linxingchen commented 11 months ago

Also when the check is done by their github action, ask the bot to flag the request with the flag that tell people to do the merge @BiocondaBot please add label

Hope all this help

Hi Remi, Thank you so much, I have modified the meta.yaml file as you suggested (mostly). Please have a look if you want and have time.

linxingchen commented 11 months ago

@ellasiera I am glad to let you know that the Conda installation is finally live.

ellasiera commented 11 months ago

Great! Thank you! I'll install it now. Looking forward to using it!

On Sun, Dec 17, 2023 at 5:16 AM LinXing Chen @.***> wrote:

@ellasiera https://github.com/ellasiera I am glad to let you know that the Conda installation is finally live.

— Reply to this email directly, view it on GitHub https://github.com/linxingchen/cobra/issues/8#issuecomment-1859033403, or unsubscribe https://github.com/notifications/unsubscribe-auth/AO5JAILGDO5OL3SW7VTGZQ3YJZWZ7AVCNFSM6AAAAAA3Q6LEBOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJZGAZTGNBQGM . You are receiving this because you were mentioned.Message ID: @.***>

linxingchen commented 11 months ago

Great! Thank you! I'll install it now. Looking forward to using it! … On Sun, Dec 17, 2023 at 5:16 AM LinXing Chen @.> wrote: @ellasiera https://github.com/ellasiera I am glad to let you know that the Conda installation is finally live. — Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AO5JAILGDO5OL3SW7VTGZQ3YJZWZ7AVCNFSM6AAAAAA3Q6LEBOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJZGAZTGNBQGM . You are receiving this because you were mentioned.Message ID: @.>

Great. Let me know if it does not work for you. :)

linxingchen / cobra

Conda installation #8