Publishing your plugin on conda

Once you’ve made your first qiime2 plugin, you’ll need to build it into a conda package and upload it to anaconda.org so others can easily install it. This tutorial is intended for first-time python developers trying to put their QIIME 2 plugin into conda.

In this tutorial, I’ll be drawing on examples from my experience developing the q2-perc-norm and q2-dbotu plugins.

Quickstart

  1. Install conda and conda-build.

  2. Make the files that make up the conda recipe: meta.yaml, which needs you to use your brain, and build.sh and bld.bat which you just copy from the internet.

  3. Build your package with conda-build (including the additional channels needed for qiime2 dependencies).

    conda-build recipe/
       -c https://conda.anaconda.org/qiime2/label/r2019.1
       -c https://conda.anaconda.org/conda-forge
       -c https://conda.anaconda.org/bioconda
       -c defaults
       --override-channels
       --python 3.6
    
  4. Install your package locally.

    conda install --offline /path/to/file.tar.bz2
    
  5. Try using your package (make sure you’re in a qiime environment).

  6. Upload to Anaconda.

    anaconda upload /path/to/file.tar.bz2
    
  7. Profit!

Documentation

Before you start, here is some useful documentation to be aware of.

The conda tutorials are short and informative. You should read the tutorial using ``skeleton` <https://conda.io/docs/user-guide/tutorials/build-pkgs-skeleton.html>`__ first, then and then the tutorial on building a package from scratch, regardless of which way you plan to build your package.

Step by step process

Install conda and conda-build

Follow the instructions to install and update conda and conda-build.

Read the tutorials

Even if you’ll be making your package from scratch, start with the “building packages with skeleton” tutorial and then read the “building packages from scratch” one.

Make your conda recipe

Packages are specified in a recipe, which as far as I can tell means “a collection of files that describe what the package needs and how to install it.” A detailed explanation of the files that you need can be found in the conda building packages documentation. The recipe is just three files: meta.yaml, build.sh, and build.bat. The conda documentation and tutorials recommend putting these files in a directory called pyenvironment.

  • meta.yaml - This contains all the metadata in the recipe, and is the part that you need to use your human brain to fill out. Specifically, you need to tell conda-build where to find the source code (either a local path or to a github release), and you also specify the requirements that your package needs. Also, if you want to build a platform-independent version of your package, you specify this in here too.

  • bld.bat - this file contains the Windows commands to build the package. You can copy it from the conda “from scratch” tutorial.

  • build.sh - this file contains the macOS and Linux commands to build the package, i.e. just python setup.py install. You can also copy it from the conda “from scratch” tutorial.

meta.yaml

meta.yaml is the workhorse of package building, and is where you specify basically everything about your package. The conda “building packages” documentation explains all the parts of this file and gives examples.

For the anyone new to the yaml data format, note that the top-level IDs in the file don’t get filled out!

source

This tells conda-build where to look for the code when it builds your package. You can point to either a github release or to a local path. Note that the way building a package works is that conda-build looks for the code specified in the source part of meta.yaml and does some magic which produces a .tar.bz2 file that contains your package. This .tar.bz2 file is the thing you upload to anaconda.org, and which people download when they run conda install. This means that if you make changes to your code, you have to manually re-build the package and re-upload it for those changes to show up on conda.

So, for simplicity’s sake, it’s often easier to just point source to the local path with your main package directory (i.e. the folder that has your setup.py file). In this case, that looks like this:

source:
  path: ../

But you can also point it to a github release, like in the conda documentation example. You can find your releases (or make new ones) by going to your repo on github.com, clicking on Release (in the same bar as where your commits, branches, and contributors are shown), and following the directions there.

An important note that if you make and push changes to your code and re-build your package, conda-build will still be looking at whatever release you point it to - so you need to make a new release with your changes! (This cost me like an hour of debugging, d’oh!)

requirements

This part tells conda-build and conda what other packages your package needs. You need to populate this section yourself. Note that if you want to specify specific package versions, the syntax is package_name >=version, with no space between the >= and the version number.

This requirements section can have multiple sub-sections, but as far as I can tell all you really need (for a simple package, like a qiime2 plugin) are the build: and run: sections. The build section has whatever packages are in your setup.py script (or whatever command is in your build.sh file), the run section has whatever packages you need to run your package.

architecture-independent package

I don’t know very much about what’s going on here, but if you don’t do the following steps, your built conda package will only be installable on machines that have the same OS as yours.

The QIIME 2 developers briefly explained it as follows in response to one of my questions:

The `noarch package <https://conda.io/docs/user-guide/tasks/build-packages/define-metadata.html#architecture-independent-packages>`__
lets you upload one build that is compatible on multiple platforms -
the caveat here is that it is up to you to know if that is the case
or not.

To make architecture-independent package, also add this to your meta.yaml file:

build:
    noarch: generic

If you do noarch: python instead, this indicates that your package can use either Python 2 or 3 (and is also architecture-independent).

build files

There’s no magic here if you already have a setup.py file, because the build files just call whatever command you call to install your package (e.g. python setup.py install). The build.sh and bld.bat files are thus very simple, and can be copied from the conda “from scratch” tutorial.

Note: these are instructions for if you have something simple that can directly be installed with python setup.py install. I have no idea what happens if you have something more complicated that you need to do.

Build your package

Go to your repo’s root directory, and run conda-build recipe/. This assumes you put your meta.yaml and build files in a folder called recipe.

If you’re working on a qiime plugin, that probably won’t work, because you need to tell conda to look for dependencies in lots of different channels. Thankfully, the qiime2 development docs are helpful here!

To build a qiime2 plugin, the command you have to run is actually:

conda-build recipe/
   -c https://conda.anaconda.org/qiime2/label/r2019.1
   -c https://conda.anaconda.org/conda-forge
   -c https://conda.anaconda.org/bioconda
   -c defaults
   --override-channels
   --python 3.6

Install your package

The conda documentation says you can now install your package with the --use-local flag:

conda install --use-local recipe/

However, this didn’t work for me (it says that the package isn’t found). Rather than troubleshoot this, I found out that you can also install a package directly from the tar.bz2 file that you just made with the --offline flag in conda-build.

If you go back to the output of your conda-build command, you should be able to find the path that this .tar.bz2 file was saved to. Something like:

/Users/claire/anaconda/conda-bld/osx-64/q2_perc_norm-1.0-py35_0.tar.bz2

So you can try to install the package directly from this:

conda install --offline /Users/claire/anaconda/conda-bld/osx-64/q2_perc_norm-1.0-py35_0.tar.bz2

Ok, looks like that worked! Woooo!

Test your package

If you’re a noob like me and didn’t include any unit tests in your package, you’ll want to make sure that your package will actually work once it’s installed.

A note that if you’re developing a QIIME 2 plugin, you probably want to be in a new qiime environment so you don’t mess things up too badly… (If you’ve forgotten, like I have, go to the Quickstart dev docs to remind yourself how to do this: https://dev.qiime2.org/latest/quickstart/)

wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py35-osx-conda.yml
conda env create -n qiime2-dev-condatest --file qiime2-latest-py35-osx-conda.yml
source activate qiime2-dev-condatest

Then, you can just type in qiime to your command line and see if (1) you get no errors and (2) your plugin shows up in the list of available plugins.

Troubleshooting citations.bib error

The newest version of QIIME 2 allows plugin developers to include a citations.bib file which is used to automatically generate a list of citations that any given workflow used. This is a great feature, since it ensures that original methods developers get credit for their work!

However, included citations.bib in my plugin_setup.py file led to an error after I installed my plugin. If I tried to run anything with qiime (e.g. qiime list), I got an error that it can’t find my citations.bib file. That’s because I need to tell setuptools that it needs to grab additional data beyond just *.py files, which it does automatically. Looking at the cutadapt plugin, looks like I just need to add this to setup.py:

setup(
    name="perc-norm",
    ...
    package_data={
        'q2_perc_norm': ['citations.bib']
    }
)

(A small note: this file path should be given relative to the folder which contains your plugin_setup.py, not to the main repo. Here, my citations file is in ~/github/q2_perc_norm/q2_perc_norm/citations.bib and my setup.py file is in ~/github/q2_perc_norm/setup.py. If you instead put package_data={'q2_perc_norm': ['q2_perc_norm/citations.bib']} in setup.py, it won’t find the right file and you’ll keep getting the same error.)

Now, I need to re-build and re-install and re-try.

If re-installing doesn’t work, you might want to try clearing everything: uninstall your plugin, clear all the conda-build previous builds, and clear the conda cache. Then, try re-building, re-installing, and re-trying.

conda uninstall q2_perc_norm
conda build purge
conda clean --all

Another note that if the source in your meta.yaml points to a github release of your code, you should re-point this to a release that includes any changes you’ve made (i.e. if you’ve pushed changes to your github repo, you need to make a new release which includes those changes, and change the release that meta.yaml points to). This is why pointing to a local path might reduce some headaches!

Upload it to Anaconda

Once you’ve successfully built and installed your plugin and made sure that it works as expected, the last step is to upload it to anaconda.

Following the directions in the documentation (after making an anaconda.org account), it’s really easy:

anaconda upload /Users/claire/anaconda/envs/qiime2-2019.1/conda-bld/noarch/q2_perc_norm-v2-py36_0.tar.bz2

Install the package from conda

Your final step is to try installing the package from conda. Make sure you’ve uninstalled any local versions that you have, and that you’re not in the package’s directory when you try to conda install your new package. You’ll need to include your channel in the call to conda install, but you can just copy and paste this from your package’s installation instructions on anaconda.org.

If you’re working on a qiime2 plugin, you’ll want to make sure you’re in the qiime2 environment (otherwise, conda doesn’t know where to find all the qiime2-related modules and packages) and with the latest version of qiime2.

source activate qiime2-2019.1
conda install -c cduvallet q2_perc_norm

Another “gotcha!” that got me is that if you want to see which packages are available in your channel (i.e. your account), you can run this command:

conda search -c <your_channel_name>

Side note: including pip packages

If one of your requirements is a package on pip, you’ll need to first put it into conda before you can make your plugin conda-installable. (From this still open issue on conda, seems like this is currently the only way!) This happened to me in building my distribution-based OTU calling plugin.

Thankfully, if the package is already pip-installable, this shouldn’t be too difficult. conda skeleton can help you get started:

conda skeleton pypi dbotu

This makes a folder called dbotu with a meta.yaml file in it. Then, because it has the build command directly in the meta.yaml file, you can just try building a conda package from this directly:

conda-build meta.yaml

Note that if you need to look in different conda channels for certain requirements, this will break. You can fix it with something like:

conda-build meta.yaml -c conda-forge

Then, go through the process of building, testing, and uploading your package to anaconda.org. After that, you can get back to developing your QIIME 2 plugin.

Contributors

The original version of this post was adapted from https://cduvallet.github.io/posts/2018/06/qiime2-plugin-conda with permission.

  • Claire Duvallet (github: cduvallet), June 2018