Permalink
Browse files

update various readme-like files with new docs link

  • Loading branch information...
1 parent 837a454 commit e83d049fbf7dd4bebcd94f7285a77fb6efdcbe1a @daler daler committed Dec 12, 2016
Showing with 4 additions and 785 deletions.
  1. +1 −5 CONTRIBUTING.md
  2. +1 −174 FAQs.md
  3. +1 −361 GUIDELINES.md
  4. +1 −245 README.md
View
@@ -1,7 +1,3 @@
# Contributing to bioconda
-Contibuting to bioconda is easy. Just create a pull request.
-When writing a recipe, ensure to read the [guidelines](GUIDELINES.md) before submitting a PR. If you don't have already, consider becoming part of our comminity by requesting access in [issue #1](https://github.com/bioconda/bioconda-recipes/issues/1).
-
-* If the PR adds a new recipe, please mention `@bioconda/core` to get a review.
-* If the PR just updates an existing recipe, feel free to merge without asking for review.
+Please visit https://bioconda.github.io/contributing.html for the updated docs.
View
175 FAQs.md
@@ -1,176 +1,3 @@
# FAQs
-
-
-## How do I get set up to test recipes locally?
-
-### One-time setup
-
-#### Install prerequisites
-
-- Install conda (use the Python 3 version).
-
-- Install conda-build in the root environment.
-
-- Install Docker (optional, but allows you to simulate most closely the Travis-CI tests).
-
-- Identify the branch of bioconda-utils currently used. It is indicated in
-`bioconda-recipes/.travis.yml` (look for the `BIOCONDA_UTILS_TAG` env var).
-Export that as an environment variable:
-
-```
-export BIOCONDA_UTILS_TAG=<PASTE TAG HERE>
-```
-
-- Install the requirements for that version of bioconda-utils:
-
-```
-conda install --file https://raw.githubusercontent.com/bioconda/bioconda-utils/${BIOCONDA_UTILS_TAG}/conda-requirements.txt
-```
-
-- Install that version of bioconda-utils:
-
-```
-pip install git+https://github.com/bioconda/bioconda-utils.git@${BIOCONDA_UTILS_TAG}
-```
-
-
-#### Git and GitHub setup
-
-- Create a fork of bioconda-recipes on GitHub and clone it locally. Even if you
-are a member of the bioconda team with push access, this will allow testing of
-your recipes on travis-ci without consuming resources allocated by travis-ci to
-the `bioconda` group:
-
-```
-git clone https://github.com/<USERNAME>/bioconda-recipes.git
-```
-
-- Add the main bioconda-recipes repo as an upstream remote:
-
-```
-git remote add upstream https://github.com/bioconda/bioconda-recipes.git
-```
-
-- Connect the fork to travis-ci, following steps 1 and 2 from the [travis-ci
-docs](https://docs.travis-ci.com/user/getting-started/#To-get-started-with-Travis-CI%3A)
-
-
-### Write a recipe
-
-Check out a new branch (e.g., `git checkout -b my-recipe`) and write one or
-more recipes.
-
-See the [conda docs](http://conda.pydata.org/docs/building/recipe.html) for
-writing recipes, and see `GUIDELINES.md` in the bioconda-recipes repo for more
-info.
-
-### Test locally
-The `simulate-travis.py` script reads the config files in the repo and sets
-things up as closely as possible to how the builds will be run on travis-ci. It
-should be run in the top-level dir of the repo. Any arguments are passed on to
-the `bioconda-utils build` command, so check `bioconda-utils build -h` for help
-and more options.
-
-Some example commands:
-
-This tests everything, using the installed conda-build. It will check all
-recipes to see what needs to be built and so it is the most comprehensive:
-
-```
-./simulate-travis.py
-```
-
-Same thing but using `--docker`. If you're on OSX and have docker installed,
-you can use this to test the recipe under Linux:
-
-```
-./simulate-travis.py --docker
-```
-
-Use the `--quick` option which will just check recipes that have changed since
-the last commit to master branch or that have been newly removed from any
-configured blacklists:
-
-```
-./simulate-travis.py --docker --quick
-```
-
-Or specify exactly which packages you want to try building. Note that the
-arguments to `--package` can be globs and are of package *names* rather than
-*paths* to recipe directories. For example, to consider all R and Bioconductor
-packages:
-
-```
-./simulate-travis.py --docker --package r-* bioconductor-*
-```
-
-
-### Push to fork, wait for Travis-CI, submit pull request.
-
-Push your changes to your fork on github, and watch the Travis-CI logs. Keep
-making changes on your fork and pushing them until the travis-ci builds pass.
-
-Open a [pull request](https://help.github.com/articles/about-pull-requests/) on
-the bioconda-recipes repo. If it's your first recipe or the recipe is doing
-something non-standard, please ask `@bioconda/core` for a review.
-
-### Use your new recipe
-
-When the PR is merged with the master branch, travis-ci will again do the
-builds but at the end will upload the packages to anaconda.org. Once the merge
-build completes, your new package is installable by anyone using:
-
-```
-conda install my-package-name -c bioconda
-```
-
-
-## How is Travis-CI set up and configured?
-
-- `.travis.yml` is read by the Travis-CI worker.
-
-- the worker runs `scripts/travis-setup.sh`, which installs conda, adds channels, and installs `bioconda-utils`
-
-- the worker runs `scripts/travis-run.sh`. If the system is Linux, then the
-build is performed in a docker container (the one listed in `.travis.yml`). If
-OSX, then the build is performed without docker.
-
-- Only if the build is on the master branch will it be uploaded to anaconda.org
-## What does "SUBDAG" mean on Travis-CI?
-
-We have limited resources on Travis-CI on which to build packages. In an
-attempt to speed up builds, we split the full DAG of recipes that need to be
-built in to multiple independent sub-DAGs. These are named `SUBDAG 0` and
-`SUBDAG 1`. Each sub-DAG is considered an independent build and they are built
-in parallel. If you submit a single recipe, which sub-DAG it is built on is
-nondeterministic so if you don't see log output for the recipe in one sub-DAG,
-check the other.
-
-## How are environmental variables defined and used?
-
-It is possible to use jinja2 templating in recipes to use a uniform set of
-versions for core packages used by bioconda packages, for example see [this
-`meta.yaml`](https://github.com/bioconda/bioconda-recipes/blob/f5eb63e30a76fd13c28663786d219c9f7750267c/recipes/gfold/meta.yaml).
-
-This works by the following:
-
-- [`config.yml` indicates an
-`env_matrix`](https://github.com/bioconda/bioconda-recipes/blob/0be2881ef95be68feb09fae7814e0217aca57285/config.yml#L1)
-in which CONDA_GSL is defined
-
-- when figuring out which recipes need to be built, the filtering step attaches
-each [unique env to a Target
-object](https://github.com/bioconda/bioconda-utils/blob/63aacdedf583b6cda770c84f241120d48dfb77f5/bioconda_utils/utils.py#L511)
-(e.g., `CONDA_GSL=1.6; CONDA_PY=27, CONDA_R=3.3.1;` etc}
-- that [env is provided to the build
-function](https://github.com/bioconda/bioconda-utils/blob/63aacdedf583b6cda770c84f241120d48dfb77f5/bioconda_utils/build.py#L312)
-which is either
- - sent [directly to
- docker](https://github.com/bioconda/bioconda-utils/blob/63aacdedf583b6cda770c84f241120d48dfb77f5/bioconda_utils/build.py#L81)
- - or used to [temporarily update
- os.environ](https://github.com/bioconda/bioconda-utils/blob/63aacdedf583b6cda770c84f241120d48dfb77f5/bioconda_utils/build.py#L94)
- so that conda-build sees it.
-- These environmental variables are then [used over in
-conda-build](https://github.com/conda/conda-build/blob/9ace97969e77a10afc3c03022f8a1d0f47c2a043/conda_build/jinja_context.py#L205)
-to fill in the templated variables via jinja2.
+Please visit https://bioconda.github.io/faqs.html for the new FAQs page.
Oops, something went wrong.

0 comments on commit e83d049

Please sign in to comment.