GitHub PullRequestReviewCommentEvent at 2014-12-03 02:04:44
Repository: timestreamlib
Actor: kdmurray91
Payload: {"action":"created","comment":{"url":"https://api.github.com/repos/borevitzlab/timestreamlib/pulls/comments/21208501","id":21208501,"diff_hunk":"@@ -0,0 +1,136 @@\n+# Copyright 2015 Joel Granados joel.granados@gmail.com\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program.  If not, see <http://www.gnu.org/licenses/>.\n+\n+import imghdr\n+import sys\n+import os\n+import os.path\n+import warnings\n+import pickle\n+import numpy\n+\n+from unittest import TestCase\n+from tests import helpers\n+sys.path.insert(0, \"./scripts\")\n+from run_pipeline import maincli\n+from timestream import TimeStreamImage\n+from timestream.manipulate.pot import ImagePotMatrix\n+\n+\n+class TestSimplePipelineRun(TestCase):\n+\n+    \"\"\" Test a simple run of pipeline.\n+\n+    We produce:\n+            1. Output Color corrected images\n+            2. Segemented images\n+            3. Feature files (csv files)\n+    Not really testing the results. Just makings sure that everything is\n+    produced as expected.\n+\n+    \"\"\"\n+\n+    def setUp(self):\n+        self.simple_opts = {'--comp': False, '--conf': False, '--doc': False,\n+                            '--gui': False, '--help': False, '--logfile': None,\n+                            '--recalculate': False, '--set': None,\n+                            '-i': helpers.FILES[\"timestream_good_images\"],","path":"tests/test_pipeline.py","position":49,"original_position":49,"commit_id":"21f78de69fbeedfedf7b44a7264153470cb083fc","original_commit_id":"21f78de69fbeedfedf7b44a7264153470cb083fc","user":{"login":"kdmurray91","id":1560490,"avatar_url":"https://avatars.githubusercontent.com/u/1560490?v=3","gravatar_id":"","url":"https://api.github.com/users/kdmurray91","html_url":"https://github.com/kdmurray91","followers_url":"https://api.github.com/users/kdmurray91/followers","following_url":"https://api.github.com/users/kdmurray91/following{/other_user}","gists_url":"https://api.github.com/users/kdmurray91/gists{/gist_id}","starred_url":"https://api.github.com/users/kdmurray91/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kdmurray91/subscriptions","organizations_url":"https://api.github.com/users/kdmurray91/orgs","repos_url":"https://api.github.com/users/kdmurray91/repos","events_url":"https://api.github.com/users/kdmurray91/events{/privacy}","received_events_url":"https://api.github.com/users/kdmurray91/received_events","type":"User","site_admin":false},"body":"Is it possible to re-factor this such that we have a function that takes the timestream to test as an argument and does this setup? That way we can run this with (the as-yet imaginary) \"timestream_bad_images\" ts, and check for graceful failure?","created_at":"2014-12-03T02:04:44Z","updated_at":"2014-12-03T02:04:44Z","html_url":"https://github.com/borevitzlab/timestreamlib/pull/150#discussion_r21208501","pull_request_url":"https://api.github.com/repos/borevitzlab/timestreamlib/pulls/150","_links":{"self":{"href":"https://api.github.com/repos/borevitzlab/timestreamlib/pulls/comments/21208501"},"html":{"href":"https://github.com/borevitzlab/timestreamlib/pull/150#discussion_r21208501"},"pull_request":{"href":"https://api.github.com/repos/borevitzlab/timestreamlib/pulls/150"}}},"pull_request":{"url":"https://api.github.com/repos/borevitzlab/timestreamlib/pulls/150","id":25349185,"html_url":"https://github.com/borevitzlab/timestreamlib/pull/150","diff_url":"https://github.com/borevitzlab/timestreamlib/pull/150.diff","patch_url":"https://github.com/borevitzlab/timestreamlib/pull/150.patch","issue_url":"https://api.github.com/repos/borevitzlab/timestreamlib/issues/150","number":150,"state":"open","locked":false,"title":"Pipeline test and Misc fixes","user":{"login":"Joelgranados","id":356364,"avatar_url":"https://avatars.githubusercontent.com/u/356364?v=3","gravatar_id":"","url":"https://api.github.com/users/Joelgranados","html_url":"https://github.com/Joelgranados","followers_url":"https://api.github.com/users/Joelgranados/followers","following_url":"https://api.github.com/users/Joelgranados/following{/other_user}","gists_url":"https://api.github.com/users/Joelgranados/gists{/gist_id}","starred_url":"https://api.github.com/users/Joelgranados/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Joelgranados/subscriptions","organizations_url":"https://api.github.com/users/Joelgranados/orgs","repos_url":"https://api.github.com/users/Joelgranados/repos","events_url":"https://api.github.com/users/Joelgranados/events{/privacy}","received_events_url":"https://api.github.com/users/Joelgranados/received_events","type":"User","site_admin":false},"body":"Main push is for pipeline test cases. Pretty self explanatory in the commit messages. We still need to address the fact that we can't push to tests/data because its another git repository.\r\n\r\nI suggest we put all the stuff in tests/data in this (timestreamlib) repo. The work-flow for pushing a commit that has to do with these two repositories is just crazy: I have to fork the data repo, create a PR, get it reviewed (separately though they are linked), then merge in data. Only when that happens can I really finish the PR in timestreamlib by updating the data submodule pointer. Additionally the reviews (of the same logic) will happen in two different places making it difficult to keep track of what is going 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