Package: pyctdev
pyctdev: python packaging common tasks for developersTools (and documentation) to support common tasks across many similar
projects, focusing on those making upHoloViz.org.Note: documentation is draft/currently being writtenWhat is pyctdev?The main part of pyctdev is a cross-platform, make-like tool plus library
of common tasks to allow project admin tasks to be run equally well
locally or on various CI systems, on different platforms, or to support
different python package 'ecosystems' (pip and conda):$ doit list
build_docs        build docs
develop_install   python develop install with specified optional groups of dependencies.
ecosystem_setup   Common pip setup
env_capture       Report all information required to recreate current environment.
env_create        TODO: create named environment if it doesn't already exist.
env_export        TODO
list_envs
package_build     Build pip package, then install and test all_quick (or other
package_upload    Upload pip packages to pypi
test_all          Run "all" tests
test_examples     Run "examples" tests
test_flakes       Run "flakes" tests
test_unit         Run "unit" tests

$ doit ecosystem=conda list
build_docs           build docs
develop_install      python develop install, with specified optional groups of dependencies (installed by conda only).
ecosystem_setup      Common conda setup (must be run in base env).
env_capture          Report all information required to recreate current conda environment
env_create           Create named environment if it doesn't already exist
env_export           Generate a pinned environment.yaml from specified env, filtering against specified groups of deps.
list_envs
miniconda_download   Download Miniconda3-latest
miniconda_install    Install Miniconda3-latest to location if not already present
package_build        Build and then test conda.recipe/ (or specified alternative).
package_upload       Upload package built from conda.recipe/ (or specified alternative).
test_all             Run "all" tests
test_examples        Run "examples" tests
test_flakes          Run "flakes" tests
test_unit            Run "unit" testsAlthough doit+pyctdev must be installed to run these tasks, the approach
is trying to call standard python and/or conda tools where possible,
so that people can run commands independently without installing
doit+pyctdev. This means pyctdev can be viewed as:documentation of what all the common tasks aredocumentation of the commands necessary to perform those tasksa way to expose gaps in underlying tools that we might like to
fill (or exposes our lack of knowledge of how to use them, so we
can be corrected :) )a way to map relatively unchanging "high level tasks" (e.g. "run
the unit tests") to underlying specific commands that might change over
time (e.g. as the python packaging ecosystem changes) or that vary
between projects (e.g. run tests with nose or with pytest).our current best understanding of how to perform the various tasks
(balancing the best possible way with what's practically possible
in general, given what tools are currently widely available).The accompanyingbackgrounddocument (even more draft
than this one!) contains more details, along with explanations for
choices. It's broken into the same sections, so can be read alongside
this document.There's also aninstructionsdocument for setting
up a new project (but it's only a placeholder right now...).If you have a question, please feel free to open an issue (after first
checking theFAQ.What does pyctdev cover?pyctdev is a work in progress, and when it stabilizes we will need to
expand this description to include a clear mission statement about
what is intended to be covered by pyctdev and which aspects of package
management are out of scope.0. What are all the tasks? How to run a task?pyctdev shows what tasks there are, e.g. "run unit tests", "build conda
package", "upload conda package", "install as a developer", and so on.pyctdev also documents how to perform those tasks, i.e. what the
necessary command(s) are for a task, or what tasks should be run
before others.To see all the tasks, you can typedoit listin a project using pyctdev
to get a list of the tasks with descriptions.doit infogives more
detail on any particular task. Alternatively, you can read the pyctdev
source code; most tasks are straightforward commands.1. Can run project admin tasks locally, on CI, and across platformsdoit/pyctdev are written in python so should work everywhere python's
available (not just on Unix-like systems, unlike many project
configuration files). (And once any python's available, doit can be
used to install other pythons if necessary - currently miniconda and
anaconda.) Having the same command to run on each platform helps ensure
that testing, package building, and related tasks are done consistently
across platforms, which is particularly important when developers use
one platform but users will download packages for another.Other suggested tools used by pyctdev are also cross platform: tox,
conda, pip, etc.2. support python and conda ecosystemspyctdev supports performing most tasks with either the python/pip or the
conda ecosystem. E.g.doit develop_installwill typically runpip install -e .[tests], which installs the dependencies using pip and
then does an editable install. Alternatively,doit ecosystem=conda develop installwill install dependencies using conda, followed by an
editable install. Projects can set a default ecosystem.The ability to install with pip or conda, create reproducible/isolated
environments with python tools (virtualenv+pip, or pipenv) or with
conda tools (conda env), package for pip or conda, helps developers
using primarily one ecosystem to still support the other (e.g. via CI
systems).3. support multiple versions of pythonSimilarly to allowing developers to support both pip and conda
ecosystems, pyctdev allows developers to support multiple versions of
python. For python, doit uses tox to run same tests over multiple
environments using tox. For conda, pyctdev runs conda build over multiple
versions of python.4. dependencies in one placepyctdev allows developers to express their project's "abstract"
dependencies in one place. Currently this place is setup.py, as it's
widely supported by both python and conda tools. The dependencies
listed in setup.py are used for:end-user pip packagesend-user conda packagesdevelopers using condadevelopers using pipgenerating environment files (e.g. examples environment.yml)The abstract dependencies may be transformed to more concrete ones,
e.g. for a tutorial examples environment, versions of all dependencies
may be pinned to ensure reproducibility (see 10/environment files,
below).pyctdev supports transforming dependencies and generating environment.yml
(and possibly pipenv or similar).5. dependencies labelled for different purposespyctdev supports expressing build and install/runtime dependencies, plus
various optional groups of dependencies (e.g. for running examples,
building docs, etc).pyctdev uses standard/generally supported python/pip/setuptools setup.py
arguments to do this (install_requiresandextras_require). pip
understands these, so the same optional dependency groups are
available to users (e.g. a user can runpip install package[examples]to get package and the dependencies necessary to
run its examples.To support 'options' in the conda ecosystem, multiple packages are
generated - though typically our projects just have "base" and
"examples" packages.package-examplesdepends on a specific pinnedpackage(pinned at build time).6. testing of what users installpyctdev encourages testing of the packages that users will install,
rather than focusing only on testing what developers work with.In the python ecosystem, tox is used to build a package, create a
clean virtual environment, installs the package, and then run the
tests. tox additionally supports running the same tests over multiple
versions of python, in multiple environments (e.g. with different sets
of dependencies installed), etc.In the conda ecosystem, conda build is called multiple times to
achieve the same.7. testing of what developers doIt's often difficult to contribute to a project, because setting it up
to the point of being able to run the tests is difficult. Seasoned
project developers know what they are doing, but it's less obvious to
occasional developers.pyctdev ensures the dependencies required to develop a project are
obvious, and encourages developers to keep them up to date (e.g. by
testingdoit develop_installon neutral CI machines).pyctdev also tries to capture how developers set up their environment.
E.g. dependencies installed by conda, with apython setup.py develop --no-depson top.8. Testing in different environmentsE.g.doit package_build --test-python=py36 --test_requires=with_xarray --test-group=unitwill build a package then install it into a python 3.6 environment,
and will then further installwith_xarraydependencies, and then
will run the unit tests. The dependencies forwith_xarrayare
specified in tox.ini (as are the unit test commands). This works with
ecosystem=pip and ecosystem=conda. It's also possible to have extra
test commands that only run in a particular test environment
(e.g.with_xarray).doit test_unitwill run the unit tests in your current environment.
If there are extra commands for a particular environment, they will be
run if you select it. E.g.doit test_unit --test-group with_xarray. However, your current environment is not altered by test
commands, so you would need to have installedwith_xarraydependencies if necessary.9. packages on demand? simplify packaging recipes?As well as specifying dependencies once, pyct attempts to express other
package metadata only once. Currently this is in setup.py. Templating
is then used for conda build. This prevents the common situation where
descriptions, URLs, licenses, etc, are mismatched.pyctdev expects project is being released first on pypi and on an
anaconda.org channel. From these sources, conda-forge can be updated, followed by
anaconda defaults (but we are not necessarily the maintainers of those
channels).pyctdev is currently primarily supporting pure Python packages. While
they may often have complex, platform specific dependencies, the
packages controlled by pyct are so far all pure Python. Therefore
we build noarch:python conda packages where possible.  If we start
maintaining packages with binary code, pyct will be extended
to support platform-specific packages, but for now none of our
packages require that.10. Channels/sources of dependenciesFor python/pip: typically just pypi.org. But other 'channels' can be
specified. E.g. test.pypi.org, or a private server.The conda packages we maintain for HoloViz.org can usually be installed
on top of either anaconda defaults or conda-forge. We currently put
them on anaconda.org pyviz (releases) and pyviz/label/dev (dev
versions), and only our specific packages are on this channel. For a
variety of reasons we recommend that any one install should not mix
conda-forge and defaults. For a project with tricky requirements, we
recommend one above the other. Or if a project suffers in
performance on one or the other, we make a recommendation.Our dev builds and dev package releases of projects on Travis CI use
pyviz/label/dev to get other packages, while release package builds
just use pyviz. And then if devs are happy with those packages,
conda-forge and defaults should be updated.11. How to structure projectAlthough it's not necessary, a common structure simplifies things
across multiple similar projects. HoloViz projects typically have
repositories that look like:package/
package/tests
package/tests/data
package/examples/
package/examples/data
package/examples/assets
examples -> package/examples

doc/       # minimal nbsite skeleton only
doc/assets # e.g. favicon - not relevant to notebooksWe try to limit differences between what's in the repository and
what's in the package shipped to users, to avoid creating custom
package building code.12. Unify how various tools are runOften, it's not clear how to run the tests for a project. Pyct already
helps with this by having high level tasks such as "run unit
tests". However, pyctdev also encourages internal command definitions to
appear only once.Currently, setup.cfg is used to store global options for commands
(e.g. flake8 rules), while tox.ini is used to store the various actual
commands used for different things (e.g. running unit tests, running
tests in different environments, etc). (TODO: what is shared across
projects, and how? Would rather not have a config file for pyctdev...)13. What's tested, and how.There are various tools for running tests (e.g. pytest, nose). An aim
of pyctdev is for our HoloViz projects to all end up using the same
developer tools where possible. And to configure those tools in the
same kind of way.unit tests: pytestflakes: pyflakesexamples:notebooks run without error: pytest plugin nbsmokenotebooks flakes: pytest plugin nbsmokenotebooks "data tests": pytest plugin nbvaperformance/benchmark tests: (pytest-benchmark, custom stuff,
airspeed velocity, ??)...?pytest has features for defining ("marking") and then selecting groups
of tests to run. So pyctdev expects there to be:"slow tests" (pytest -m slow)...?14. docswebsitenbsite for examples -> websitelive docsLive/browser way for users to try examples: mybinder15. versioningVersion via git tag. Version is stored only in one place in the
repository (a git tag), and is written into packages. Every place that
needs to know version (__init__.py; packaging:setup.py,meta.yaml; docs) reads it from the single source.Storing in one place, and it being the tag rather than in the git repo
source code, makes it easier to automate various other 'release time'
tasks. Our projects generally useautover(via param).Versioning scheme:we usevX.Y.Zpost 1.0, (TODO: copy hv's scheme?)16. automate release type tasks on travisAs far as possible, just by running one or a couple of doit commands,
we avoid CI-provided magic except where it's truly unavoidable or very
useful (e.g. parallelizing builds, etc), because we need to support
multiple CI systems (Travis CI for Linux and Mac, plus Appveyor for
Windows).automatically generated packagesEvery (dev) release:conda packages are built and uploaded to anaconda.org
(pyviz/label/dev) pyviz/label/mainpip packages (sdist zip, universal wheel) are built and uploaded
to (test.pypi.org) pypi.orgA release happens when avX.Y.Ztag is pushed. Dev releases can
either be defined as "every merge to master" (e.g. for a mature
project), or "every time avX.Y.ZaNstyle tag is pushed (for a
rapidly changing project).Note: "package build" means generate package, install package into
clean environment, run tests.automatically generated websiteTwo main options:for young, fast-moving projects: a single main website (default:https://package.github.io/) updated on releases (plus maybe also
special post-release tags where we're fixing minor docs issues
without changing code, which presumably must be tagged
specially), with a separate dev website (default:https://pyviz-docs.github.io/package-master) updated on every
push to master (or every time an alpha/beta/rc format tag is
pushed ?).Same as 1, but also archiving websites for each major release
(i.e. one copy for X.Y, updated for each new .Z) over time until
we eventually delete them.  Presumably could actually just make 2
the default, with the definition that only versions 1.0 or
greater count as a major release, in which case it would follow
policy 1 until reaching 1.0, then policy 2, thereby acting as
appropriate for a young, fast-moving project until release 1.0,
then archiving each x.y version.Note: for e.g. datashader, using Travis CI isn't currently feasible
(build takes too long/uses too much memory/requires too-large
data). But Travis is just using doit commands, so same can be run
locally at release time.17. Extra CI thingsplatformsUbuntu (Travis CI)MacOS (Travis CI)Windows (appveyor)cachingInstalling miniconda and dependencies from scratch every time takes up
quite a lot of build time for some projects.Caching of miniconda/conda environments is therefore
supported. (Supported also for python/pip, although speed is not an
issue there).In many ways, this could be a better test than installing from
scratch, since many devs/users will be updating existing conda
installations/environments rather than starting from scratch.build stages/parallelization of buildsRather than running tasks sequentially (wall clock time consuming; a
task might affect subsequent ones), tasks can be run independently in
parallel.To add to docsgenerating pinned conda packagegenerating environment.yml