Feature #15888

Update run-tests.sh to use python 3

Added by Eric Biagiotti about 1 year ago. Updated 3 months ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
-
Target version:
Start date:
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
-
Release relationship:
Auto

Description

run-tests.sh uses python in other places besides running the sdk/python tests (e.g. starting services, etc). Update these instances to use python 3. Specifically, change VENVDIR/bin/activate to VENV3DIR/bin/activate.

If py2 isn't installed, run-tests.sh should succeed (by skipping the py2 tests). If py2 is installed, run-tests.sh should not skip the py2 tests.

sdk/python/tests/run_test_server.py is being called with `python` from sdk/go/arvadostest/run_servers.go. Does run_test_server.py even support python 3? We should probably replace it with arvados-boot instead of spending more time on it.


Subtasks

Task #16768: ReviewNewPeter Amstutz


Related issues

Related to Arvados Epics - Story #14532: [Epic] Port to Python 3 to for Python 2 sunset in December 2019Resolved01/01/202009/16/2020

Related to Arvados - Bug #16795: [a-d-c] flaky testResolved09/02/2020

Associated revisions

Revision 62b3435f (diff)
Added by Nico Cesar 5 months ago

replacing all the py2 for py3 occurrences

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision add09f35 (diff)
Added by Nico Cesar 5 months ago

major search and replace from python to python3

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision 2b4eccc7 (diff)
Added by Nico Cesar 5 months ago

Installing extra python3 libraries

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision ddae1b57 (diff)
Added by Nico Cesar 5 months ago

Installing extra python3 libraries

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision ab00a0a4 (diff)
Added by Nico Cesar 5 months ago

Revert "Installing extra python3 libraries"

This reverts commit ddae1b57f077d8a7c091b3cdf9ecaa562703fb3c.

setuptools should be done outside pip

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision 0ea4bd88 (diff)
Added by Nico Cesar 5 months ago

Installing extra python3 libraries:dist_wheel has to go before PyYAML

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision 279388ea (diff)
Added by Nico Cesar 5 months ago

activate was deleted by mistake

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision 3e068db7 (diff)
Added by Nico Cesar 5 months ago

maybe all this should be re-done

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision 5aca4129 (diff)
Added by Nico Cesar 4 months ago

py3 argparse differs from py2 for action='version'

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision 4cfab58a (diff)
Added by Nico Cesar 4 months ago

Changes related to https://dev.arvados.org/issues/15888#note-25

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision bdeca909
Added by Nico Cesar 4 months ago

Merge branch '15888-remove-py2-from-test' into master

closes #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision c9bfe925 (diff)
Added by Nico Cesar 4 months ago

Addresses https://dev.arvados.org/issues/15888#note-27

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision c4bee0bd
Added by Nico Cesar 4 months ago

Merge branch '15888-pycurl' into master

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision bf8027f0 (diff)
Added by Nico Cesar 4 months ago

remove python2 packages from Dockerfile.base in arvbox

refs #15888

Arvados-DCO-1.1-Signed-off-by: Nico Cesar <>

Revision 86ed259e
Added by Ward Vandewege 4 months ago

Merge branch '15888-remove-more-python2-remnants'

refs #15888

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <>

Revision 9ebb1a7d (diff)
Added by Ward Vandewege about 2 months ago

Remove one more python2 remnant. This is a fix for the
python3-arvados-cwl-runner package, it now installs /usr/bin/cwltool
again.

refs #15888

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <>

Revision 56240e53 (diff)
Added by Ward Vandewege about 2 months ago

Remove one more python2 remnant. This is a fix for the
python3-arvados-cwl-runner package, it now installs /usr/bin/cwltool
again.

refs #15888

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <>

Revision 71f347dd (diff)
Added by Ward Vandewege about 2 months ago

Remove one more python2 remnant. This is a fix for the
python3-arvados-cwl-runner package, it now installs /usr/bin/cwltool
again.

refs #15888

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <>

Revision e643759e (diff)
Added by Ward Vandewege about 2 months ago

Move the handle_python_package() function from run-library.sh to
run-build-packages-python-and-ruby.sh, it is only used in the latter.
Update it to call python3 instead of just 'python'.

refs #15888

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <>

Revision df6a4694 (diff)
Added by Ward Vandewege about 2 months ago

Move the handle_python_package() function from run-library.sh to
run-build-packages-python-and-ruby.sh, it is only used in the latter.
Update it to call python3 instead of just 'python'.

refs #15888

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <>

Revision e6c3e65f (diff)
Added by Ward Vandewege about 1 month ago

Remove one more python2 remnant. This is a fix for the
python3-arvados-cwl-runner package, it now installs /usr/bin/cwltool
again.

refs #15888

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <>

Revision 076d6df6 (diff)
Added by Ward Vandewege about 1 month ago

Move the handle_python_package() function from run-library.sh to
run-build-packages-python-and-ruby.sh, it is only used in the latter.
Update it to call python3 instead of just 'python'.

refs #15888

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <>

History

#1 Updated by Eric Biagiotti about 1 year ago

  • Description updated (diff)

#2 Updated by Eric Biagiotti about 1 year ago

  • Parent task deleted (#14532)

#3 Updated by Eric Biagiotti about 1 year ago

  • Related to Story #14532: [Epic] Port to Python 3 to for Python 2 sunset in December 2019 added

#4 Updated by Peter Amstutz 5 months ago

  • Target version changed from Arvados Future Sprints to 2020-08-26 Sprint
  • Assigned To set to Nico César

#5 Updated by Peter Amstutz 5 months ago

  • Description updated (diff)

#6 Updated by Ward Vandewege 5 months ago

  • Tracker changed from Task to Feature

#7 Updated by Nico César 5 months ago

  • Description updated (diff)

#8 Updated by Nico César 5 months ago

During standup we agreed (Peter/Tom/Lucas/me) that this ticket has not aged well since we don't support py2 anymore. Migrating all python tooling to py3 is the best idea we have.

#9 Updated by Nico César 5 months ago

apt-get  remove $(COLUMNS=160 dpkg -l | grep -E 'python[^3]'| awk '{ print $2 }' | grep -v 'dh-python' )
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages will be REMOVED:
  cython libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal
  libpython2.7-stdlib linkchecker python python-chardet python-epydoc python-minimal
  python-pip python-pip-whl python-pkg-resources python-pycurl python-requests
  python-setuptools python-six python-urllib3 python-virtualenv python-yaml python2.7
  python2.7-minimal python3-pip python3-virtualenv virtualenv
0 upgraded, 0 newly installed, 27 to remove and 1 not upgraded.
After this operation, 79.7 MB disk space will be freed.
Do you want to continue? [Y/n] 
(Reading database ... 38304 files and directories currently installed.)
Removing cython (0.25.2-1) ...
Removing libpython-dev:amd64 (2.7.13-2) ...
Removing python-yaml (3.12-1) ...
Removing linkchecker (9.3-4) ...
Removing python-requests (2.12.4-1) ...
Removing python-urllib3 (1.19.1-1) ...
Removing python-six (1.10.0-3) ...
Removing python-virtualenv (15.1.0+ds-1) ...
Removing python-setuptools (33.1.1-1) ...
Removing libpython2.7-dev:amd64 (2.7.13-2+deb9u3) ...
Removing libpython2.7:amd64 (2.7.13-2+deb9u3) ...
Removing python-chardet (2.3.0-2) ...
Removing python-epydoc (3.0.1+dfsg-14) ...
Removing python-pip (9.0.1-2+deb9u1) ...
Removing virtualenv (15.1.0+ds-1) ...
Removing python3-virtualenv (15.1.0+ds-1) ...
Removing python-pkg-resources (33.1.1-1) ...
Removing python-pycurl (7.43.0-2) ...
Removing python3-pip (9.0.1-2+deb9u1) ...
Removing python (2.7.13-2) ...
Removing libpython-stdlib:amd64 (2.7.13-2) ...
Removing python2.7 (2.7.13-2+deb9u3) ...
Removing libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ...
Removing python-minimal (2.7.13-2) ...
Removing python2.7-minimal (2.7.13-2+deb9u3) ...
Removing libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ...
Removing python-pip-whl (9.0.1-2+deb9u1) ...
Processing triggers for mime-support (3.60) ...
Processing triggers for libc-bin (2.24-11+deb9u4) ...
root@4e513ebf867f:/usr/src/arvados# apt-get install python3-pip python3-virtualenv
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  dbus python-pip-whl python3-cffi-backend python3-crypto python3-cryptography python3-dbus
  python3-gi python3-idna python3-keyring python3-keyrings.alt python3-pyasn1
  python3-secretstorage python3-six python3-wheel python3-xdg
Suggested packages:
  default-dbus-session-bus | dbus-session-bus python3-crypto-dbg python-crypto-doc
  python-cryptography-doc python3-cryptography-vectors python-dbus-doc python3-dbus-dbg
  gnome-keyring libkf5wallet-bin gir1.2-gnomekeyring-1.0 python3-pykde4 doc-base
  python-secretstorage-doc
The following NEW packages will be installed:
  dbus python-pip-whl python3-cffi-backend python3-crypto python3-cryptography python3-dbus
  python3-gi python3-idna python3-keyring python3-keyrings.alt python3-pip python3-pyasn1
  python3-secretstorage python3-six python3-virtualenv python3-wheel python3-xdg
0 upgraded, 17 newly installed, 0 to remove and 1 not upgraded.
Need to get 3,245 kB of archives.
After this operation, 8,668 kB of additional disk space will be used.
Do you want to continue? [Y/n] 
Get:1 http://deb.debian.org/debian stretch/main amd64 dbus amd64 1.10.32-0+deb9u1 [213 kB]
Get:2 http://deb.debian.org/debian stretch/main amd64 python-pip-whl all 9.0.1-2+deb9u1 [1,399 kB]
Get:3 http://deb.debian.org/debian stretch/main amd64 python3-cffi-backend amd64 1.9.1-2 [70.1 kB]
Get:4 http://deb.debian.org/debian stretch/main amd64 python3-crypto amd64 2.6.1-7 [259 kB]
Get:5 http://deb.debian.org/debian stretch/main amd64 python3-idna all 2.2-1 [32.7 kB]
Get:6 http://deb.debian.org/debian stretch/main amd64 python3-pyasn1 all 0.1.9-2 [34.5 kB]
Get:7 http://deb.debian.org/debian stretch/main amd64 python3-six all 1.10.0-3 [14.4 kB]
Get:8 http://deb.debian.org/debian stretch/main amd64 python3-cryptography amd64 1.7.1-3+deb9u2 [211 kB]
Get:9 http://deb.debian.org/debian stretch/main amd64 python3-dbus amd64 1.2.4-1+b1 [184 kB]
Get:10 http://deb.debian.org/debian stretch/main amd64 python3-gi amd64 3.22.0-2 [473 kB]
Get:11 http://deb.debian.org/debian stretch/main amd64 python3-secretstorage all 2.3.1-2 [14.2 kB]
Get:12 http://deb.debian.org/debian stretch/main amd64 python3-keyring all 10.1-1 [36.8 kB]
Get:13 http://deb.debian.org/debian stretch/main amd64 python3-keyrings.alt all 1.3-1 [16.2 kB]
Get:14 http://deb.debian.org/debian stretch/main amd64 python3-pip all 9.0.1-2+deb9u1 [142 kB]
Get:15 http://deb.debian.org/debian stretch/main amd64 python3-virtualenv all 15.1.0+ds-1 [57.7 kB]
Get:16 http://deb.debian.org/debian stretch/main amd64 python3-wheel all 0.29.0-2 [51.8 kB]
Get:17 http://deb.debian.org/debian stretch/main amd64 python3-xdg all 0.25-4 [35.7 kB]
Fetched 3,245 kB in 1s (1,949 kB/s)     
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package dbus.
(Reading database ... 36214 files and directories currently installed.)
Preparing to unpack .../00-dbus_1.10.32-0+deb9u1_amd64.deb ...
Unpacking dbus (1.10.32-0+deb9u1) ...
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invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
Setting up python3-cryptography (1.7.1-3+deb9u2) ...
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#10 Updated by Nico César 5 months ago

Intalled python-venv

this will allow to do

python3 -m venv /DIR

#11 Updated by Nico César 5 months ago

python3-httplib2 is needed

++ python3 sdk/python/tests/run_test_server.py setup_config
Traceback (most recent call last):
  File "sdk/python/tests/run_test_server.py", line 13, in <module>
    import httplib2
ImportError: No module named 'httplib2'
+ eval

#12 Updated by Nico César 5 months ago

  • Target version changed from 2020-08-26 Sprint to 2020-09-09 Sprint

#13 Updated by Nico César 5 months ago

62b3435fc45adff01541c508be22e10be83427ce

There are still some issues with importing arvados in the py3 environment

TestArvKeepGet#test_help = Traceback (most recent call last):
  File "./bin/arv-put", line 6, in <module>
    from arvados.commands.put import main
ImportError: No module named 'arvados'
Traceback (most recent call last):
  File "./bin/arv-put", line 6, in <module>
    from arvados.commands.put import main
ImportError: No module named 'arvados'
Traceback (most recent call last):
  File "./bin/arv-put", line 6, in <module>
    from arvados.commands.put import main
ImportError: No module named 'arvados'
0.11 s = F

#14 Updated by Nico César 5 months ago

  • Target version deleted (2020-09-09 Sprint)
  • Assigned To deleted (Nico César)

cd /usr/src/arvados/build ; bash ./run-tests.sh WORKSPACE=/usr/src/arvados ARVADOS_CONFIG=/etc/arvados/config.yml --temp ~/.cache/arvados-build --leave-temp

#15 Updated by Nico César 5 months ago

  • Target version set to 2020-09-09 Sprint
  • Assigned To set to Nico César

#16 Updated by Ward Vandewege 5 months ago

#17 Updated by Ward Vandewege 5 months ago

Before merging into master, will need to remove the pycurl pin added here: https://dev.arvados.org/issues/16795#note-3

#18 Updated by Nico César 5 months ago

  • Status changed from New to In Progress

#20 Updated by Nico César 4 months ago

If we use the python2.7 "own python" from package this is the behaviour:

nico@shell:~$ arv-get --version
/usr/bin/arv-get 2.0.3
nico@shell:~$ head --lines=1 /usr/bin/arv-get
#!/usr/share/python2.7/dist/python-arvados-python-client/bin/python
nico@shell:~$ arv-get --version 2> /dev/null
nico@shell:~$ 
1) Failure:
TestArvKeepGet#test_get_version [/tmp/workspace/developer-run-tests-remainder/sdk/cli/test/test_arv-keep-get.rb:31]:
STDOUT not expected: './bin/arv-get 2.1.0.dev20200826203407
'.
Expected "./bin/arv-get 2.1.0.dev20200826203407\n" to be empty.

this is the test from sdk/cli/test/test_arv-keep-get.rb

  def test_get_version
    out, err = capture_subprocess_io do
      assert_arv_get '--version'
    end
    assert_empty(out, "STDOUT not expected: '#{out}'")
    assert_match(/[0-9]+\.[0-9]+\.[0-9]+/, err, "Version information incorrect: '#{err}'")
  end

#21 Updated by Nico César 4 months ago

nico@shell:~$ python3 /usr/bin/arv-get --version
Traceback (most recent call last):
  File "/usr/bin/arv-get", line 8, in <module>
    from arvados.commands.get import main
ModuleNotFoundError: No module named 'arvados'

because of the lack of that library installed:

nico@shell:~$ dpkg -l | grep python3-arvados-python-client 
nico@shell:~$ 

So here we have to make sure that when we change our packages to have the right dependency when deploying

#22 Updated by Nico César 4 months ago

after installing:

nico@shell:~$ dpkg -l | grep python3-arvados-python-client 
ii  python3-arvados-python-client    2.0.4-1                      amd64        Arvados client library
nico@shell:~$ head /usr/bin/arv-get
#!/usr/share/python3/dist/python3-arvados-python-client/bin/python
nico@shell:~$ /usr/share/python3/dist/python3-arvados-python-client/bin/python /usr/bin/arv-get --version 2> /dev/null
/usr/bin/arv-get 2.0.4

#25 Updated by Ward Vandewege 4 months ago

A few comments:

  • shouldn't commit the go.sum and go.mod changes

noted

  • trailing space added in run-tests.sh line 657
  • run-tests.sh:
@@ -558,7 +555,7 @@ setup_ruby_environment() {
                 fi
             done
             "$bundle" version | tee /dev/stderr | grep -q 'version 2'
-        ) || fatal 'install bundler'
+        ) #|| fatal 'install bundler' ## This is needed for now.
     fi
 }

This seems like it should not be part of the patch?

  • The patch is adding a few "FIXME" lines, do we need additional changes there?
  • Any reason you're removing the '-x' from the bash invocation (2 places)?

#26 Updated by Nico César 4 months ago

Did most of the changes.

about $pythonstuff...

install_all tries to do a pip install of the packages in $pythonstuff. as of 5aca41295

all of them have the suffix ":py3"

pythonstuff=(
    sdk/python:py3
    sdk/cwl:py3
    services/dockercleaner:py3
    services/fuse:py3
    tools/crunchstat-summary:py3
)

and I've seen some code that tries to remove the ones ending in ":py3"[1] by doing:

    for p in "${pythonstuff[@]}" 
    do
            dir=${p%:py3}

so I think we should remove this part.

My proposal is 4cfab58ae and running https://ci.arvados.org/job/developer-run-tests/2073/ now

[1] man bash
${parameter%word}
${parameter%%word}
    Remove matching suffix pattern. The word is expanded to produce a pattern just as in pathname expansion. If the pattern matches a trailing portion of the expanded value of parameter, then the result of the expansion is the expanded value of parameter with the shortest matching pattern (the ''%'' case) or the longest matching pattern (the ''%%'' case) deleted. If parameter is @ or *, the pattern removal operation is applied to each positional parameter in turn, and the expansion is the resultant list. If parameter is an array variable subscripted with @ or *, the pattern removal operation is applied to each member of the array in turn, and the expansion is the resultant list. 

#27 Updated by Ward Vandewege 4 months ago

Nico César wrote:

Did most of the changes.

about $pythonstuff...

install_all tries to do a pip install of the packages in $pythonstuff. as of 5aca41295

all of them have the suffix ":py3"
[...]

and I've seen some code that tries to remove the ones ending in ":py3"[1] by doing:
[...]

so I think we should remove this part.

My proposal is 4cfab58ae and running https://ci.arvados.org/job/developer-run-tests/2073/ now

[...]

Tests passed, LGTM. Just make sure after you merge master into your branch that you then change this line in sdk/python/setup.py:

'pycurl >=7.19.5.1, &lt;7.43.0.4', # 7.43.0.4 removes support for python2

to remove the '<7.43.0.4' part, which should no longer be needed after you purged python2. It was introduced in master after you forked.

Could also do that as a separate commit, of course.

#28 Updated by Nico César 4 months ago

https://ci.arvados.org/job/developer-run-tests/2073/ passed and ward said LGTM.

I'll go ahead and merge it

#29 Updated by Anonymous 4 months ago

  • % Done changed from 0 to 100
  • Status changed from In Progress to Resolved

#32 Updated by Ward Vandewege 4 months ago

Another remnant in arados-server, cf. 94a7479527652cd513a35f75e1da1798d9fdc213 on branch 15888-remove-more-python2-remnants.

#33 Updated by Nico César 4 months ago

94a7479527652cd513a35f75e1da1798d9fdc213 LGTM,

I noticed https://ci.arvados.org/view/Developer/job/developer-run-tests/2083/
with commit 94a7479527652cd513a35f75e1da1798d9fdc213, but it seems to be a flaky test.

#34 Updated by Ward Vandewege 4 months ago

Nico César wrote:

94a7479527652cd513a35f75e1da1798d9fdc213 LGTM,

I noticed https://ci.arvados.org/view/Developer/job/developer-run-tests/2083/
with commit 94a7479527652cd513a35f75e1da1798d9fdc213, but it seems to be a flaky test.

Thanks, merged it. It's a flaky test indeed.

#35 Updated by Peter Amstutz 3 months ago

  • Release set to 25

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