vsc-install 0.21.1

vsc-install provides shared setuptools functions and classes for python libraries developed by UGent's HPC group

Description

vsc-install provides shared setuptools functions and classes for python libraries developed by UGent's HPC group

Common pitfalls

bdist_rpm will fail if your install_requires = 'setuptools' because it will fail to find a setuptools rpm.

export VSC_RPM_PYTHON=1

will make sure the python- prefix is added to the packages in install_requires for building RPM's so python-setuptools will be used.

Add tests

Test are python modules in the test directory which have subclass of TestCase and at least one method that has a name starting with test_

You are advised to use

from vsc.install.testing import TestCase

(instead of basic TestCase from unittest).

And any __main__ or suite() is not needed (anymore).

Initialise the test directory with

mkdir -p test
echo '' > test/__init__.py
echo 'from vsc.install.commontest import CommonTest' > test/00-import.py

When the tests are run, test, lib and bin (if relevant) are added to sys.path, so no need to do so in the tets modules.

Run tests

python setup.py test

Filter tests with -F (test module names) and -f (test method names)

See also

python setup.py test --help

The dependencies are installed automatically in the .eggs directory. It will first try github.ugent.be and then github.com to install them. The same method is used as through which the original repository was cloned (http, ssh, ...). In case you need private dependencies, always clone with ssh.

In case following error occurs, it means there is a test module XYZ that cannot be imported.

File "setup.py", line 499, in loadTestsFromModule
    testsuites = ScanningLoader.loadTestsFromModule(self, module)
File "build/bdist.linux-x86_64/egg/setuptools/command/test.py", line 37, in loadTestsFromModule
File "/usr/lib64/python2.7/unittest/loader.py", line 100, in loadTestsFromName
    parent, obj = obj, getattr(obj, part)
AttributeError: 'module' object has no attribute 'XYZ'

You can try get the actual import error for fixing the issue with

python -c 'import sys;sys.path.insert(0, "test");import XYZ;'

Fix failing tests

• Missing / incorrect LICENSE

• Copy the appropirate license file under known_licenses in the project directory and name the file LICENSE

• Missing README.md

• Create a README.md file with at least a Description section

• Fix license headers as described in https://github.com/hpcugent/vsc-install/blob/master/lib/vsc/install/headers.py

  cd <project dir with .git folder>
  REPO_BASE_DIR=$PWD python -m vsc.install.headers path/to/file script_or_not
  

  Fix them all at once using find

  find ./{lib,test} -type f -name '*.py' | REPO_BASE_DIR=$PWD xargs -I '{}' python -m vsc.install.headers '{}'
  find ./bin -type f -name '*.py' | REPO_BASE_DIR=$PWD xargs -I '{}' python -m vsc.install.headers '{}' 1
  

  Do not forget to check the diff. Modules/scripts without docstring (or magic comment '### END OF HEADER') (incl. test modules) will get correct header appended to existing one. Add a docstring (or magic comment) to resolve this.

• Python scripts (i.e. with a python shebang and installed as scripts in setup) have to use #!/usr/bin/env python as shebang

• Remove any build_rpms_settings.sh leftovers

• The TARGET dict in setup.py should be minimal unless you really know what you are doing (i.e. if it is truly different from defaults)

• Remove name, scripts, ...

• Exception: vsc namespace packages do not allow non-shared namespace

• Add to the __init__.py

"""
Allow other packages to extend this namespace, zip safe setuptools style
"""
import pkg_resources
pkg_resources.declare_namespace(__name__)

bare-except

try:
   # something
except:

This is bad, because this except will also catch sys.exit() or Keyboardinterupts, something you typically do not want, if you catch these the program will be in a weird state and then continue on, whilst the person who just pressed ctrl+c is wondering what is going on and why it is not stopping.

so at the very least make this except Exception (which doesn't catch sys.exit and KeyboardInterupt) and it would be appreciated if you could actually figure out what exceptions to expect and only catch those and let your program crash if something you did not intend happens because it helps developers catch weird errors on their side better.

if you do something like

try:
    Path(int(somestring)).write_text('important data')
except Exception:
    pass # if somestring is not an integer, we didn't need to write anyway, but otherwise we do

because you know sometimes this string does not contain an integer, so the int() call can fail you should really only catch ValueError, because this will also fail when your disk is full, or you don't have permissions or xxx other reasons, and the important data will not be written out and nobody will notice anything!

if not 'a' in somelist -> if 'a' not in somelist

this isn't that big of a deal, but if everyone is consistent it's less likely to introduce bugs when a not is added or removed where it didn't need to. Also helps code review, not in reads better, like english.

arguments-differ

this will give you errors if you override a function of a superclass but don't use the same amount of arguments, using less will surely give you errors, so the linter catches this for you now

unused-argument

if you have a function definition witch accepts an argument that is never used in the function body this will now give an error. clean up your function definition, or fix the error where you actually do need to take this argument into account

unused-variable

defining a variable and then not using it anymore smells bad, why did you do that? sometimes you do things like

out, exit_code = run_command(something)

but you are not interested in the out, only in the exit code, in this case, write

_, exit_code = run_command(something)

using _ as a variable name lets pylint and other readers know you do not intend to use that output in the first place.

reimported

when you re import a name somewhere else, usually this is just an import to much, or 2 imports with the same name, pay attention.

import six
from django import six

=>

import six
from django import six as django_six

redefinition of unused name

this usually also points to something you did not expect

from vsc.accountpageclient import VscGroup
<snip>

class VscGroup(object):
    pass

=> do you need the import? use import as did you mean to use the same name? ...

Redefined builtin

use different name, for example change

def filter(b_b):
    """Function filter"""
    return b_b

=>

def new_filter(b_b):
    """Function filter"""
    return b_b

logging-not-lazy

Don't use string interpolation when logging if not needed:

import logging
name = 'world'
program ='python'
logging.info('Hello %s! This is %s.' % (name, program))

=>

import logging
name = 'world'
program ='python'
logging.info('Hello %s! This is %s.', name, program)

Fix Python 3 failing tests

• We try to follow https://docs.python.org/3/howto/pyporting.html
• some useful info can be found here as well https://portingguide.readthedocs.io/en/latest/index.html

unpacking-in-except / redefine-in-handler

Multiple exception have to be grouped in a tuple like

    ...
except (ExceptionOne, ExceptionTwo) ...
    ...

(espcially when used like except A, B: which should be except (A, B):.

Old raise syntax

Python 2’s raise statement was designed at a time when exceptions weren’t classes, and an exception’s type, value, and traceback components were three separate objects. In Python 3, one single object includes all information about an exception.

raise NameError, "Error"

=>

raise NameError("Error")

or change

raise NameError, "Error", some_traceback

=>

raise NameError("Error")

e = NameError("Error")
e.__traceback__ = some_traceback

backtick

A = 2
B = `A`

=>

A = 2
B = str(A)

Old ne operator

if 2 <> 3:

=>

if 2 != 3:

Octal literal

os.chmod(foo, 0700)

=>

os.chmod(foo, 0o700)

Import star module level

Do not import *, be more specific. If it is impossible, import it in the top level (and suppress the pyflakes error F403.)

def coords(angle, distance):
    """Function coords"""
    from math import *
    return distance * cos(angle), distance * sin(angle)

=>

from math import *  # noqa: F403
def coords(angle, distance):
    """Function coords"""
    return distance * cos(angle), distance * sin(angle)

Raising string

raise ValueError, 'message'

=>

raise ValueError('message')

Indexing exception

except IndexError as err:
    err[0]

=>

except IndexError as err:
    IndexError.args[0]

turning off these errors

If in any of these cases you think: yes, I really needed to do this, I'm monkeypatching things, I'm adding extra functionality that does indeed have an extra(default) paramenter, etc, etc you can let pylint know to ignore this error in this one specific block of code by adding e.g. the comment # pylint: disable=<name or numeric id of pylint code>

class Something(object):
    def dosomething(self, some, thing):
        # do something

class MyFancyThing(SomeThing):
    # pylint: disable=arguments-differ
    def dosomething(self, some, thing, fancy=None):
         # do something fancy

Full list with all codes is available at http://pylint-messages.wikidot.com/all-codes

Auto-generated Jenkinsfile / tox.ini

vsc-install has support for auto-generating the Jenkinsfile (and accompanying tox.ini), via:

python -m vsc.install.ci

Failing check on (contents of) Jenkinsfile or tox.ini

There are dedicated tests that check whether the Jenkinsfile and tox.ini files were auto-generated by vsc-install.

To fix the tests, simply run python -m vsc.install.ci using the latest version of vsc-install to re-generate Jenkinsfile and tox.ini, and then commit & push the changes.

If the contents of the file that is auto-generated by the latest version of vsc-install is incorrect for whatever reason, you can temporarily bypass the failing test by adding an a file named Jenkinsfile.NOT_AUTOGENERATED_YET or tox.ini.NOT_AUTOGENERATED_YET.

The file must contain the URL of a vsc-install issue, created via via https://github.com/hpcugent/vsc-install/issues/new, where the incorrectly generated file is reported.

Example:

echo "see https://github.com/hpcugent/vsc-install/issues/1234 for more info" > Jenkinsfile.NOT_AUTOGENERATED_YET

Requiring JIRA issue ref in PR title

To also include a check in the Jenkinsfile for having a JIRA issue ref (like [HPC-1234]) in the pull request title, add a configuration file for python -m vsc.install.ci named vsc-ci.ini like this into the repository:

[vsc-ci]
jira_issue_id_in_pr_title=1

Running shellcheck

To also run shellcheck in the generated Jenkinsfile, specify this via a vsc-ci.ini configuration file:

[vsc-ci]
run_shellcheck=1

Adding additional test commands to Jenkinsfile

If additional custom test commands (other than shellcheck) need to be run by the Jenkinsfile, you can speicfy this in vsc-ci.ini via additional_test_commands.

To add a single custom test command:

[vsc-ci]
additional_test_commands=./more_test.sh

To add multiple test commands:

[vsc-ci]
additional_test_commands=
  first-test-cmd
  second-test-cmd
  third-test-cmd

Overriding install location of scripts

In some repositories we specify a system-wide install location for scripts via setup.cfg (see for example the icinga-checks repository), which causes problems when installing vsc-install in the tox environment.

To override the installation prefix for scripts (only in the tox environment where the tests are run), specify this via a vsc-ci.ini configuration file:

[vsc-ci]
install_scripts_prefix_override=1

Use 'easy_install' to install tox

For legacy reasons easy_install is still supported. If you still need it you can enable it (not recommended):

[vsc-ci]
easy_install_tox=1

Avoid running pip install in repo checkout

For some repositories, running pip install to install tox from the checked out repository is problematic, because of the setup.cfg containing things that should not be picked up by pip.

For those repositories, you can specify that the installation commands in the Jenkinsfile should be run from $HOME, via:

[vsc-ci]
home_install=1

Leveraging system (Python) packages

If a repository requires Python packages as dependencies that are installed as OS packages (for example, pyslurm), tox must be configured to inherit these packages in the test environment. This can be enabled via:

[vsc-ci]
inherit_site_packages=1

Pre-installing dependencies before running tests

Although vsc-install will automatically install all dependencies listed in setup.py prior to running the tests, there are cases where this doesn't work out as expected. Some Python packages only support being installed with pip install (for example because they use a namespace that is spread across multiple different Python packages, like fs and fs.sshfs).

You can specify Python packages that should be installed (with pip install) before running the tests via pip_install_test_deps in vsc-ci.ini:

[vsc-ci]
pip_install_test_deps=
    foo
    bar<1.0

This results in corresponding pip install commands being added to the commands_pre section in tox.ini:

[testenv]
commands_pre =
    pip install 'foo'
    pip install 'bar<1.0'
    pip install 'setuptools<42.0'
    python -m easy_install -U vsc-install