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Actions #128

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merged 7 commits into from
May 10, 2022
Merged

Actions #128

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c3afa79
add workflow
jburel May 10, 2022
7b11a51
skip tests for now
jburel May 3, 2022
5bbc70b
check install only
jburel May 4, 2022
d69d478
run flake8
jburel May 4, 2022
2cf0e32
use ice action
jburel May 5, 2022
8a0bb7d
test with v1
jburel May 6, 2022
57fa0d2
use org repo
jburel May 6, 2022
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51 changes: 51 additions & 0 deletions .github/workflows/workflow.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,5 +18,56 @@ jobs:
- '3.8'
os:
- ubuntu-20.04
commands:
- 'install'
runs-on: ${{ matrix.os }}
services:
postgres:
image: postgres:11
env:
POSTGRES_DB: omero
POSTGRES_PASSWORD: omero
POSTGRES_USER: omero
ports:
- 5432:5432
# Set health checks to wait until postgres has started
options: >-
--health-cmd pg_isready
--health-interval 10s
--health-timeout 5s
--health-retries 5
steps:
- uses: actions/checkout@v2
- name: Install Ice Java and Python binding
uses: ome/action-ice@v1
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👍

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https://github.com/jburel/omego/actions/runs/2281780723 green

- name: Install Python dependencies
run: |
pip install flake8 tox wheel pytest
pip install omero-server[default]
- name: Run flake8
run: flake8 .
- name: Set up OMERO config
run: |
mkdir $HOME/OMERO
echo "config set omero.data.dir $HOME/OMERO" > $HOME/config.omero
echo "config set omero.db.name omero" >> $HOME/config.omero
echo "config set Ice.IPv6 0" >> $HOME/config.omero
- name: Get tox target
id: toxtarget
run: |
py=$(echo ${{ matrix.python-version }} | tr -d .)
echo "::set-output name=py::$py"
- name: Check Ice version
run: python -c 'import Ice; print(Ice.stringVersion())'
- name: Run tests
run:
tox -e py${{ steps.toxtarget.outputs.py }}
env:
# The hostname used to communicate with the PostgreSQL service container
POSTGRES_HOST: localhost
# The default PostgreSQL port
POSTGRES_PORT: 5432
POSTGRES_DB: omero
POSTGRES_PASSWORD: omero
POSTGRES_USER: omero
TEST: ${{ matrix.commands }}
3 changes: 2 additions & 1 deletion omego/artifacts.py
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Expand Up @@ -4,7 +4,7 @@
from __future__ import print_function
from __future__ import absolute_import
from future import standard_library
standard_library.install_aliases() # noqa

from builtins import str
from past.builtins import basestring
from builtins import object
Expand All @@ -27,6 +27,7 @@
except ImportError:
from elementtree.ElementTree import XML

standard_library.install_aliases() # noqa
log = logging.getLogger("omego.artifacts")


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20 changes: 10 additions & 10 deletions omego/convert.py
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Expand Up @@ -69,17 +69,17 @@ def parse(filename, MAX_TERM_COUNT=1000):
parents = []

termCount = 0
for l in f.readlines():
if l.startswith("id:"):
termId = l.strip()[4:]
if l.startswith("name:"):
name = l.strip()[6:]
elif l.startswith("def:"):
desc = l.strip()[5:]
elif l.startswith("is_a:"):
pid = l.strip()[6:].split(" ", 1)[0]
for line in f.readlines():
if line.startswith("id:"):
termId = line.strip()[4:]
if line.startswith("name:"):
name = line.strip()[6:]
elif line.startswith("def:"):
desc = line.strip()[5:]
elif line.startswith("is_a:"):
pid = line.strip()[6:].split(" ", 1)[0]
parents.append(pid)
if len(l) == 1: # newline
if len(line) == 1: # newline
# save
if termId is not None and name is not None:
terms[termId] = {'name': name, 'desc': desc,
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2 changes: 1 addition & 1 deletion omego/fileutils.py
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Expand Up @@ -4,7 +4,6 @@
from __future__ import division
from __future__ import print_function
from future import standard_library
standard_library.install_aliases() # noqa
from past.builtins import basestring
from builtins import object
from past.utils import old_div
Expand All @@ -20,6 +19,7 @@
import zipfile
from yaclifw.framework import Stop

standard_library.install_aliases() # noqa
log = logging.getLogger("omego.fileutils")


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9 changes: 9 additions & 0 deletions test/integration/test_download.py
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Expand Up @@ -45,19 +45,22 @@ def setup_class(self):
self.branch = 'OMERO-DEV-latest'
self.ice = '3.6'

@pytest.mark.skipif(True, reason='URL to be updated')
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What does "URL to be updated" mean?

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I meant: Change URL since it uses the old ci

def testDownloadNoUnzip(self, tmpdir):
with tmpdir.as_cwd():
self.download('--skipunzip', '--branch', self.branch,
'--ice', self.ice)
files = tmpdir.listdir()
assert len(files) == 1

@pytest.mark.skipif(True, reason='URL to be updated')
def testDownloadUnzip(self, tmpdir):
with tmpdir.as_cwd():
self.download('--branch', self.branch, '--ice', self.ice)
files = tmpdir.listdir()
assert len(files) == 2

@pytest.mark.skipif(True, reason='URL to be updated')
def testDownloadUnzipDir(self, tmpdir):
with tmpdir.as_cwd():
self.download('--unzipdir', 'OMERO.py', '--branch', self.branch,
Expand All @@ -66,6 +69,7 @@ def testDownloadUnzipDir(self, tmpdir):
assert expected.exists()
assert expected.isdir()

@pytest.mark.skipif(True, reason='URL to be updated')
def testDownloadSym(self, tmpdir):
with tmpdir.as_cwd():
self.download('--branch', self.branch, '--ice', self.ice,
Expand All @@ -88,6 +92,7 @@ def testDownloadSym(self, tmpdir):
assert sym2 == (old_div(tmpdir, 'custom.sym'))
assert sym2.isdir()

@pytest.mark.skipif(True, reason='URL to be updated')
def testDownloadRelease(self, tmpdir):
with tmpdir.as_cwd():
self.download('--release', 'latest', '--ice', self.ice)
Expand All @@ -98,6 +103,7 @@ def testDownloadNonExistingArtifact(self):
with pytest.raises(AttributeError):
self.download('-n', '--release', '5.3', '--ice', '3.3')

@pytest.mark.skipif(True, reason='URL to be updated')
def testDownloadBuildNumber(self):
# Old Jenkins artifacts are deleted so we can't download.
# Instead assert that an AttributeError is raised.
Expand All @@ -113,6 +119,7 @@ class TestDownloadBioFormats(Downloader):
def setup_class(self):
self.branch = 'BIOFORMATS-DEV-latest'

@pytest.mark.skipif(True, reason='URL to be updated')
def testDownloadJar(self, tmpdir):
self.artifact = 'formats-api'
with tmpdir.as_cwd():
Expand All @@ -121,6 +128,7 @@ def testDownloadJar(self, tmpdir):
assert len(files) == 1
assert files[0].basename == 'formats-api.jar'

@pytest.mark.skipif(True, reason='URL to be updated')
def testDownloadFullFilename(self, tmpdir):
self.artifact = 'formats-api'
with tmpdir.as_cwd():
Expand All @@ -136,6 +144,7 @@ def setup_class(self):
self.artifact = ''
self.branch = 'latest'

@pytest.mark.skipif(True, reason='URL to be updated')
def testDownloadList(self, tmpdir):
with tmpdir.as_cwd():
self.download('--branch', self.branch)
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5 changes: 2 additions & 3 deletions test/integration/test_upgrade.py
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Expand Up @@ -50,6 +50,7 @@ def testSkipunzip(self):
self.upgrade("--skipunzip")

@pytest.mark.slowtest
@pytest.mark.skipif(True, reason='URL to be updated')
def testUpgrade(self):
args = ["--branch=OMERO-DEV-latest"]
# Python 3.6 on Travis: Force OMERO to run with 2.7 instead
Expand All @@ -58,9 +59,7 @@ def testUpgrade(self):
self.upgrade(*args)

@pytest.mark.slowtest
@pytest.mark.skipif(
getenv('TRAVIS_PYTHON_VERSION') == '3.6',
reason='OMERO not supported on Python 3.6')
@pytest.mark.skipif(True, reason='OMERO not supported on Python 3.6')
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Does this still hold if you've bumped to Py38?

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I have not re-activated the tests in this PR. I have actually skipped a good number due to URL.
This will be a second body of work

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I have not re-activated the tests in this PR

Fair enough. The comment might just be slightly confusing.

def testUpgradePython3(self):
self.upgrade("--branch=OMERO-DEV-latest")

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12 changes: 6 additions & 6 deletions tox.ini
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Expand Up @@ -4,7 +4,7 @@
# and then run "tox" from this directory.

[tox]
envlist = py27, py36
envlist = py27, py38
# https://tox.readthedocs.io/en/latest/config.html#conf-requires
# Ensure pip is new so we can install manylinux wheel
requires = pip >= 19.0.0
Expand All @@ -24,15 +24,15 @@ deps =
setuptools>=40.0
https://github.com/ome/zeroc-ice-py-manylinux/releases/download/0.1.0/zeroc_ice-3.6.5-cp27-cp27mu-manylinux2010_x86_64.whl

[testenv:py36travis]
basepython = python3.6
[testenv:py38travis]
basepython = python3.8
platform = linux.*
deps =
setuptools>=40.0
https://github.com/ome/zeroc-ice-py-manylinux/releases/download/0.1.0/zeroc_ice-3.6.5-cp36-cp36m-manylinux2010_x86_64.whl
https://github.com/ome/zeroc-ice-ubuntu2004/releases/download/0.2.0/zeroc_ice-3.6.5-cp38-cp38-linux_x86_64.whl

; [testenv:py27]
; basepython = /CONDA/envs/tox-py27/bin/python

; [testenv:py36]
; basepython = /CONDA/envs/tox-py36/bin/python
; [testenv:py38]
; basepython = /CONDA/envs/tox-py38/bin/python
10 changes: 6 additions & 4 deletions travis-build
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Expand Up @@ -24,16 +24,18 @@ fi
#Install a new server without web
#Tests rely on a non-zero error code being returned on failure
if [ $TEST = install ]; then
omego install --initdb --dbhost localhost --dbname omero --prestartfile $HOME/config.omero -v --release 5.3.5 --ice 3.6 --no-web $OMEGO_OMERO_PYTHON
export OMERODIR='./OMERO.server-5.6.4-ice36-b232'
omego install --initdb --dbhost localhost --dbname omero --prestartfile $HOME/config.omero -v --release 5.6.4 --ice 3.6 --no-web --no-start

ls OMERO.server
# Should return 0 DB_UPTODATE
omego db upgrade -n --dbhost localhost --dbname omero --serverdir OMERO.server-5.3.5-ice36-b73 $OMEGO_OMERO_PYTHON
omego db upgrade -n --dbhost localhost --dbname omero --serverdir OMERO.server

# Check the expected server version was downloaded
test $(readlink OMERO.server) = './OMERO.server-5.3.5-ice36-b73'
test $(readlink OMERO.server) = $OMERODIR

# Check db dump file
omego db dump --serverdir OMERO.server --dumpfile travis-omero.pgdump $OMEGO_OMERO_PYTHON
omego db dump --serverdir OMERO.server --dumpfile travis-omero.pgdump

pg_restore -l travis-omero.pgdump | grep 'dbpatch_versions_trigger'
fi
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