Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Adding in some more tests for save/reload #2235

Merged
merged 3 commits into from Oct 21, 2020
Merged

Adding in some more tests for save/reload #2235

merged 3 commits into from Oct 21, 2020

Conversation

rbharath
Copy link
Member

This PR continues work for #2217 and adds save/reload tests for a few more models following the fix @hsjang001205 introduced to make sure weights are initialized correctly.

As a notable omission, GraphConvModel is still broken. I'm seeing the same errors @nesanders reports in #2217 (comment).

@coveralls
Copy link

Coverage Status

Coverage increased (+0.6%) to 80.078% when pulling a01e688 on smiles2vec into 31c9b6b on master.

@rbharath
Copy link
Member Author

We have a failing test on windows test_gat_regression. None of the code in this PR should affect this test, so I'm going to go ahead and merge in since this is probably just a flaky test issue. If it's not, will fix in a future PR

@rbharath rbharath merged commit 02fce35 into master Oct 21, 2020
@rbharath rbharath deleted the smiles2vec branch October 21, 2020 04:27
nissy-dev added a commit to nissy-dev/deepchem that referenced this pull request Oct 21, 2020
@nissy-dev
Squashed commit of the following:
f0da848 
commit 02fce35
Merge: 31c9b6b a01e688
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Tue Oct 20 21:27:44 2020 -0700

    Merge pull request deepchem#2235 from deepchem/smiles2vec

    Adding in some more tests for save/reload

commit a01e688
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Tue Oct 20 19:39:38 2020 -0700

    Cleaning up

commit 8a01506
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Tue Oct 20 19:27:30 2020 -0700

    Getting some more tests in

commit 55e3df9
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Thu Oct 15 23:50:11 2020 -0700

    First steps to reload test

commit 31c9b6b
Merge: 19eeac1 9e6155f
Author: peastman <peastman@stanford.edu>
Date:   Tue Oct 20 13:49:47 2020 -0700

    Merge pull request deepchem#2213 from peastman/molnet

    [WIP] Updated API for MoleculeNet loader functions

commit 9e6155f
Author: peastman <peastman@stanford.edu>
Date:   Mon Oct 19 16:01:27 2020 -0700

    Attempt at fixing travis failures

commit 19eeac1
Merge: 29d01b5 8a06870
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Sun Oct 18 23:19:40 2020 -0700

    Merge pull request deepchem#2232 from hsjang001205/WEAVE_reload

    Fix weave bug

commit 8a06870
Author: hsjang001205 <71421490+hsjang001205@users.noreply.github.com>
Date:   Mon Oct 19 13:30:17 2020 +0900

    Update test_reload.py

commit 3b74cde
Author: hsjang001205 <71421490+hsjang001205@users.noreply.github.com>
Date:   Mon Oct 19 13:29:42 2020 +0900

    Update test_reload.py

commit 4123f02
Author: hsjang001205 <71421490+hsjang001205@users.noreply.github.com>
Date:   Mon Oct 19 13:27:03 2020 +0900

    Update test_reload.py

commit 2374713
Author: hsjang001205 <71421490+hsjang001205@users.noreply.github.com>
Date:   Mon Oct 19 13:22:52 2020 +0900

    Update layers.py

commit 669a311
Merge: 98ad20e 29d01b5
Author: hsjang001205 <71421490+hsjang001205@users.noreply.github.com>
Date:   Mon Oct 19 12:58:09 2020 +0900

    Merge branch 'master' into WEAVE_reload

commit 29d01b5
Merge: 2b792b4 e94b9db
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Sun Oct 18 20:53:45 2020 -0700

    Merge pull request deepchem#2228 from hsjang001205/DAG_reload

    Fix directed acyclic graph network bug

commit e94b9db
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Sat Oct 17 17:12:40 2020 +0900

    DAG_reload

commit 98ad20e
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Sat Oct 17 13:11:31 2020 +0900

    WEAVE_reload

commit 01a2b5f
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Sat Oct 17 13:01:40 2020 +0900

    WEAVE_reload

commit 438b956
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Sat Oct 17 10:25:48 2020 +0900

    DAG_reload

commit a1480a3
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Sat Oct 17 09:39:17 2020 +0900

    DAG_reload

commit 1894509
Author: peastman <peastman@stanford.edu>
Date:   Fri Oct 16 16:41:39 2020 -0700

    Changed how molnet handles Transformers

commit 2b792b4
Merge: 51a76d9 c7f0cec
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Fri Oct 16 10:46:37 2020 -0700

    Merge pull request deepchem#2223 from deepchem/chembl

    Fixing chembl example

commit d792c5b
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Fri Oct 16 21:31:59 2020 +0900

    DAG_reload

commit 032ac8b
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Fri Oct 16 21:05:14 2020 +0900

    DAG_reload

commit 95d32df
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Fri Oct 16 20:58:43 2020 +0900

    DAG_reload

commit e5827cc
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Fri Oct 16 18:22:54 2020 +0900

    DAG_reload

commit ba3455b
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Fri Oct 16 17:43:02 2020 +0900

    DAG_reload_fix

commit 51a76d9
Merge: 6eb5f18 64c3fbf
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Thu Oct 15 23:40:06 2020 -0700

    Merge pull request deepchem#2221 from vincentweisser/patch-1

    Wrong link corrected

commit 6eb5f18
Merge: cc7e2ec c3d9ef1
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Thu Oct 15 23:39:10 2020 -0700

    Merge pull request deepchem#2222 from vincentweisser/patch-2

    Wrong Link Corrected

commit cc7e2ec
Merge: cd7d2c1 55bdc19
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Thu Oct 15 23:38:07 2020 -0700

    Merge pull request deepchem#2224 from deepchem/chemception

    Adding chemception save/reload tests

commit c7f0cec
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Thu Oct 15 22:49:20 2020 -0700

    Fixing example

commit 55bdc19
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Thu Oct 15 22:17:52 2020 -0700

    Fixing chemception tests

commit 76ed80e
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Thu Oct 15 16:29:22 2020 -0700

    Fixing chembl example

commit c3d9ef1
Author: Vincent Weisser <32839303+vincentweisser@users.noreply.github.com>
Date:   Thu Oct 15 22:32:07 2020 +0200

    Wrong Link Corrected

commit 64c3fbf
Author: Vincent Weisser <32839303+vincentweisser@users.noreply.github.com>
Date:   Thu Oct 15 22:29:16 2020 +0200

    Wrong link corrected

commit 5c55f23
Author: peastman <peastman@stanford.edu>
Date:   Wed Oct 14 14:33:05 2020 -0700

    Bug fix

commit 407db0e
Author: peastman <peastman@stanford.edu>
Date:   Wed Oct 14 14:29:32 2020 -0700

    Refactored molnet loader

commit 47006c5
Author: peastman <peastman@stanford.edu>
Date:   Wed Oct 14 10:59:46 2020 -0700

    Minor improvements to molnet loader functions

commit 413c6a4
Merge: bd52b89 ae12a7e
Author: peastman <peastman@stanford.edu>
Date:   Wed Oct 14 10:11:26 2020 -0700

    Merge branch 'master' into molnet

commit bd52b89
Author: peastman <peastman@stanford.edu>
Date:   Tue Oct 13 14:28:58 2020 -0700

    Updated API for load_delaney()
nissy-dev added a commit to nissy-dev/deepchem that referenced this pull request Oct 21, 2020
@nissy-dev
Squashed commit of the following:
0479788 
commit f272f7c
Merge: 02fce35 09828fb
Author: Daiki Nishikawa <nd.12021218@gmail.com>
Date:   Wed Oct 21 16:44:50 2020 +0900

    Merge pull request deepchem#2215 from nd-02110114/sklearn-model

    Generalize XGBoostModel to GBDTModel (support LightGBM)

commit 09828fb
Author: nd-02110114 <nd.12021218@gmail.com>
Date:   Wed Oct 21 15:12:35 2020 +0900

    :ok_hand: fix test by review

commit 02fce35
Merge: 31c9b6b a01e688
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Tue Oct 20 21:27:44 2020 -0700

    Merge pull request deepchem#2235 from deepchem/smiles2vec

    Adding in some more tests for save/reload

commit a01e688
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Tue Oct 20 19:39:38 2020 -0700

    Cleaning up

commit 8a01506
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Tue Oct 20 19:27:30 2020 -0700

    Getting some more tests in

commit 55e3df9
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Thu Oct 15 23:50:11 2020 -0700

    First steps to reload test

commit 31c9b6b
Merge: 19eeac1 9e6155f
Author: peastman <peastman@stanford.edu>
Date:   Tue Oct 20 13:49:47 2020 -0700

    Merge pull request deepchem#2213 from peastman/molnet

    [WIP] Updated API for MoleculeNet loader functions

commit 9e6155f
Author: peastman <peastman@stanford.edu>
Date:   Mon Oct 19 16:01:27 2020 -0700

    Attempt at fixing travis failures

commit 19eeac1
Merge: 29d01b5 8a06870
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Sun Oct 18 23:19:40 2020 -0700

    Merge pull request deepchem#2232 from hsjang001205/WEAVE_reload

    Fix weave bug

commit 8a06870
Author: hsjang001205 <71421490+hsjang001205@users.noreply.github.com>
Date:   Mon Oct 19 13:30:17 2020 +0900

    Update test_reload.py

commit 3b74cde
Author: hsjang001205 <71421490+hsjang001205@users.noreply.github.com>
Date:   Mon Oct 19 13:29:42 2020 +0900

    Update test_reload.py

commit 4123f02
Author: hsjang001205 <71421490+hsjang001205@users.noreply.github.com>
Date:   Mon Oct 19 13:27:03 2020 +0900

    Update test_reload.py

commit 2374713
Author: hsjang001205 <71421490+hsjang001205@users.noreply.github.com>
Date:   Mon Oct 19 13:22:52 2020 +0900

    Update layers.py

commit 669a311
Merge: 98ad20e 29d01b5
Author: hsjang001205 <71421490+hsjang001205@users.noreply.github.com>
Date:   Mon Oct 19 12:58:09 2020 +0900

    Merge branch 'master' into WEAVE_reload

commit 29d01b5
Merge: 2b792b4 e94b9db
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Sun Oct 18 20:53:45 2020 -0700

    Merge pull request deepchem#2228 from hsjang001205/DAG_reload

    Fix directed acyclic graph network bug

commit e94b9db
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Sat Oct 17 17:12:40 2020 +0900

    DAG_reload

commit 98ad20e
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Sat Oct 17 13:11:31 2020 +0900

    WEAVE_reload

commit 01a2b5f
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Sat Oct 17 13:01:40 2020 +0900

    WEAVE_reload

commit 438b956
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Sat Oct 17 10:25:48 2020 +0900

    DAG_reload

commit a1480a3
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Sat Oct 17 09:39:17 2020 +0900

    DAG_reload

commit 1894509
Author: peastman <peastman@stanford.edu>
Date:   Fri Oct 16 16:41:39 2020 -0700

    Changed how molnet handles Transformers

commit 2b792b4
Merge: 51a76d9 c7f0cec
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Fri Oct 16 10:46:37 2020 -0700

    Merge pull request deepchem#2223 from deepchem/chembl

    Fixing chembl example

commit d104fd7
Author: nd-02110114 <nd.12021218@gmail.com>
Date:   Fri Oct 16 21:33:37 2020 +0900

    :bug: fix comment

commit d792c5b
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Fri Oct 16 21:31:59 2020 +0900

    DAG_reload

commit 032ac8b
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Fri Oct 16 21:05:14 2020 +0900

    DAG_reload

commit 95d32df
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Fri Oct 16 20:58:43 2020 +0900

    DAG_reload

commit e5827cc
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Fri Oct 16 18:22:54 2020 +0900

    DAG_reload

commit ba3455b
Author: hsjang001205 <hsjang1205@naver.com>
Date:   Fri Oct 16 17:43:02 2020 +0900

    DAG_reload_fix

commit 51a76d9
Merge: 6eb5f18 64c3fbf
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Thu Oct 15 23:40:06 2020 -0700

    Merge pull request deepchem#2221 from vincentweisser/patch-1

    Wrong link corrected

commit 6eb5f18
Merge: cc7e2ec c3d9ef1
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Thu Oct 15 23:39:10 2020 -0700

    Merge pull request deepchem#2222 from vincentweisser/patch-2

    Wrong Link Corrected

commit cc7e2ec
Merge: cd7d2c1 55bdc19
Author: Bharath Ramsundar <rbharath@stanford.edu>
Date:   Thu Oct 15 23:38:07 2020 -0700

    Merge pull request deepchem#2224 from deepchem/chemception

    Adding chemception save/reload tests

commit 9a74887
Author: nd-02110114 <nd.12021218@gmail.com>
Date:   Fri Oct 16 15:20:46 2020 +0900

    fix lint

commit 05fb2bd
Author: nd-02110114 <nd.12021218@gmail.com>
Date:   Fri Oct 16 15:01:04 2020 +0900

    add reload test

commit c7f0cec
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Thu Oct 15 22:49:20 2020 -0700

    Fixing example

commit 55bdc19
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Thu Oct 15 22:17:52 2020 -0700

    Fixing chemception tests

commit 9829acd
Merge: d4d7470 cd7d2c1
Author: nd-02110114 <nd.12021218@gmail.com>
Date:   Fri Oct 16 12:11:56 2020 +0900

    Merge branch 'master' into sklearn-model

commit 76ed80e
Author: Bharath Ramsundar <bharath@Bharaths-MBP.zyxel.com>
Date:   Thu Oct 15 16:29:22 2020 -0700

    Fixing chembl example

commit c3d9ef1
Author: Vincent Weisser <32839303+vincentweisser@users.noreply.github.com>
Date:   Thu Oct 15 22:32:07 2020 +0200

    Wrong Link Corrected

commit 64c3fbf
Author: Vincent Weisser <32839303+vincentweisser@users.noreply.github.com>
Date:   Thu Oct 15 22:29:16 2020 +0200

    Wrong link corrected

commit d4d7470
Author: nd-02110114 <nd.12021218@gmail.com>
Date:   Thu Oct 15 11:36:21 2020 +0900

    :recycle: fix job name for travis.yml

commit 5c55f23
Author: peastman <peastman@stanford.edu>
Date:   Wed Oct 14 14:33:05 2020 -0700

    Bug fix

commit 407db0e
Author: peastman <peastman@stanford.edu>
Date:   Wed Oct 14 14:29:32 2020 -0700

    Refactored molnet loader

commit 47006c5
Author: peastman <peastman@stanford.edu>
Date:   Wed Oct 14 10:59:46 2020 -0700

    Minor improvements to molnet loader functions

commit 413c6a4
Merge: bd52b89 ae12a7e
Author: peastman <peastman@stanford.edu>
Date:   Wed Oct 14 10:11:26 2020 -0700

    Merge branch 'master' into molnet

commit 0d906cf
Author: nd-02110114 <nd.12021218@gmail.com>
Date:   Wed Oct 14 20:57:11 2020 +0900

    :fire: remove .python_version

commit 72ab577
Author: nd-02110114 <nd.12021218@gmail.com>
Date:   Wed Oct 14 20:56:10 2020 +0900

    :recycle: gdbt -> gbdt

commit 84a135d
Author: nd-02110114 <nd.12021218@gmail.com>
Date:   Wed Oct 14 18:39:53 2020 +0900

    :sparkles: generalize XGBoostModel to GDBTModel (support LightGBM)

commit bd52b89
Author: peastman <peastman@stanford.edu>
Date:   Tue Oct 13 14:28:58 2020 -0700

    Updated API for load_delaney()
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@rbharath @coveralls