Remove easily deprecated functions from project.py #574

atravitz · 2021-07-19T20:02:16Z

Description

There's a considerable amount of code that is scheduled to be removed ahead of the signac 2.0 release.

Motivation and Context

This removes deprecated content from project.py that I felt confident could be removed safely. I will follow this up with another PR that will require some discussion before we delete code.

There are still some tests dependent on deprecated code, and so I'm making sure that the tests are being updated accordingly and that we aren't losing code coverage.

Types of Changes

Documentation update
Bug fix
New feature
Breaking change¹

¹The change breaks (or has the potential to break) existing functionality.

Checklist:

I am familiar with the Contributing Guidelines.
I agree with the terms of the Contributor Agreement.
My name is on the list of contributors.
My code follows the code style guideline of this project.
The changes introduced by this pull request are covered by existing or newly introduced tests.

If necessary:

I have updated the API documentation as part of the package doc-strings.
I have created a separate pull request to update the framework documentation on signac-docs and linked it here.
I have updated the changelog and added all related issue and pull request numbers for future reference (if applicable). See example below.

vyasr · 2021-07-19T22:08:27Z

@atravitz I think we'll need to hold on this PR for at least one more thorough review of the code base. I can't think of them off the top of my head, but I'm quite sure that there are a number of functions scattered around that had not been deprecated yet but were considered for deprecation in 2.0. That means (unless I'm mistaken) that we'll need at least one more deprecation pass and one more minor release before 2.0.

I've been a bit swamped between work and lots of travel lately, but I will nominate myself to scope this out in the near future since I'm done traveling for about a month after this weekend and hopefully am wrapping up some major pushes at work.

atravitz · 2021-07-20T15:21:38Z

@atravitz I think we'll need to hold on this PR for at least one more thorough review of the code base. I can't think of them off the top of my head, but I'm quite sure that there are a number of functions scattered around that had not been deprecated yet but were considered for deprecation in 2.0. That means (unless I'm mistaken) that we'll need at least one more deprecation pass and one more minor release before 2.0.

I've been a bit swamped between work and lots of travel lately, but I will nominate myself to scope this out in the near future since I'm done traveling for about a month after this weekend and hopefully am wrapping up some major pushes at work.

Sounds good! I'm happy to help with that.

codecov · 2021-07-23T21:47:15Z

Codecov Report

❗ No coverage uploaded for pull request base (next@883f54f). Click here to learn what that means.
The diff coverage is n/a.

❗ Current head 348108c differs from pull request most recent head ae40887. Consider uploading reports for the commit ae40887 to get more accurate results

@@           Coverage Diff           @@
##             next     #574   +/-   ##
=======================================
  Coverage        ?   78.21%           
=======================================
  Files           ?       65           
  Lines           ?     7022           
  Branches        ?     1302           
=======================================
  Hits            ?     5492           
  Misses          ?     1230           
  Partials        ?      300

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 883f54f...ae40887. Read the comment docs.

bdice

I'm pushing some minor changes to tests. Otherwise this looks good.

bdice · 2021-07-24T22:02:37Z

tests/test_job.py

@@ -1535,20 +1531,18 @@ def test_reset_statepoint_project(self):
            src_job.data[key] = d
            assert key in src_job.data
            assert len(src_job.data) == 1
-        with pytest.deprecated_call():


This test is now an exact duplicate of test_reset_statepoint_job. I removed it.

bdice · 2021-07-24T22:02:48Z

tests/test_job.py

@@ -1064,8 +1064,7 @@ def test_reset_statepoint_project(self):
        src_job.data[key] = d
        assert key in src_job.data
        assert len(src_job.data) == 1
-        with pytest.deprecated_call():


This test is now an exact duplicate of test_reset_statepoint_job. I removed it.

bdice · 2021-07-24T22:04:45Z

tests/test_project.py

-        with pytest.deprecated_call():
-            assert self.project.get_id() == "testing_test_project"
-            assert str(self.project) == self.project.get_id()
+    def test_project_id(self):


This test is now an exact duplicate of test_property_id. I removed it.

bdice · 2021-07-24T22:06:36Z

tests/test_project.py

-            assert 1 == len(list(self.project.find_job_ids({"sp.a": 0, "doc.b": 0})))
-            assert 0 == len(list(self.project.find_job_ids({"sp.a": 0, "doc.b": 5})))
-            assert 0 == len(list(self.project.find_job_ids({"sp.a": 5, "doc.b": 0})))
-            assert 0 == len(list(self.project.find_job_ids({"sp.a": 5, "doc.b": 5})))


There are some test cases for unified queries like {"sp.a": 5, "doc.b": 5} shown in this function that are not in test_find_jobs below. I moved those test cases to test_find_jobs so that we retain coverage of those code paths.

bdice · 2021-07-24T22:21:39Z

This conversation about signac-flow support is somewhat relevant for this PR as well. I think signac-flow only calls project.get_id() in one location, which we can easily replace.
#578 (comment)

for more information, see https://pre-commit.ci

This reverts commit 4e52a01.

This reverts commit 5f30ef4.

…benchmark times).

* beginning to pull out deprecated from project.py * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Revert "[pre-commit.ci] auto fixes from pre-commit.com hooks" This reverts commit 4e52a01. * Revert "beginning to pull out deprecated from project.py" This reverts commit 5f30ef4. * removing deprecated get_id() * removing deprecated get_id() from project.py * updating more instances of project.get_id() * removing index building methods * removing access module and reset/update statepoint from project.py * Simplify benchmark setup code for readability (no observed impact on benchmark times). * Remove tests that are exact duplicates. * Add missing test cases for test_find_jobs from the removed function test_find_job_ids. Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Bradley Dice <bdice@bradleydice.com>

atravitz changed the title ~~removing deprecated code for signac 2.0~~ removing deprecated functions from project.py for signac 2.0 Jul 23, 2021

atravitz changed the title ~~removing deprecated functions from project.py for signac 2.0~~ Removing deprecated functions from project.py for signac 2.0 Jul 23, 2021

atravitz changed the title ~~Removing deprecated functions from project.py for signac 2.0~~ Remove deprecated functions from project.py for signac 2.0 Jul 23, 2021

atravitz changed the title ~~Remove deprecated functions from project.py for signac 2.0~~ Remove easily deprecated functions from project.py for signac 2.0 Jul 23, 2021

atravitz changed the title ~~Remove easily deprecated functions from project.py for signac 2.0~~ Remove easily deprecated functions from project.py Jul 23, 2021

atravitz requested review from bdice and vyasr July 23, 2021 23:26

atravitz marked this pull request as ready for review July 23, 2021 23:41

atravitz requested review from a team as code owners July 23, 2021 23:41

atravitz requested review from pepak13 and removed request for a team July 23, 2021 23:41

bdice approved these changes Jul 24, 2021

View reviewed changes

bdice added this to the v2.0.0 milestone Jul 24, 2021

bdice assigned atravitz Jul 24, 2021

bdice mentioned this pull request Jul 26, 2021

Remove public API of indexing module. #580

Merged

14 tasks

atravitz and others added 10 commits July 28, 2021 16:15

beginning to pull out deprecated from project.py

5234d12

[pre-commit.ci] auto fixes from pre-commit.com hooks

8f75e5b

for more information, see https://pre-commit.ci

Revert "[pre-commit.ci] auto fixes from pre-commit.com hooks"

061b167

This reverts commit 4e52a01.

Revert "beginning to pull out deprecated from project.py"

9090a99

This reverts commit 5f30ef4.

removing deprecated get_id()

affaa63

removing deprecated get_id() from project.py

184a310

updating more instances of project.get_id()

d628fbc

removing index building methods

43a67df

removing access module and reset/update statepoint from project.py

0ebf48a

Simplify benchmark setup code for readability (no observed impact on …

a4f4fed

…benchmark times).

bdice added a commit that referenced this pull request Dec 5, 2021

Remove Project.update_statepoint from docs (missed in PR #574).

6123507

vyasr pushed a commit that referenced this pull request Dec 25, 2021

Remove Project.update_statepoint from docs (missed in PR #574).

69b53cb

vyasr pushed a commit that referenced this pull request Jan 4, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

c19faf7

vyasr pushed a commit that referenced this pull request Jan 27, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

b72777e

vyasr pushed a commit that referenced this pull request Feb 4, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

1aa985a

vyasr pushed a commit that referenced this pull request Feb 21, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

058e7e8

vyasr pushed a commit that referenced this pull request Feb 21, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

4a47e36

vyasr pushed a commit that referenced this pull request Mar 14, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

fba1c0e

vyasr pushed a commit that referenced this pull request Apr 19, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

3b2115c

vyasr pushed a commit that referenced this pull request Apr 21, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

998fb29

vyasr pushed a commit that referenced this pull request May 2, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

e5e0e02

bdice added a commit that referenced this pull request Jun 14, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

b85aac5

bdice added a commit that referenced this pull request Aug 1, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

5490304

bdice added a commit that referenced this pull request Oct 7, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

b461761

bdice added a commit that referenced this pull request Oct 27, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

cc7a8ea

vyasr pushed a commit that referenced this pull request Oct 30, 2022

Remove Project.update_statepoint from docs (missed in PR #574).

a68a231

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Remove easily deprecated functions from project.py #574

Remove easily deprecated functions from project.py #574

atravitz commented Jul 19, 2021 •

edited by bdice

Loading

vyasr commented Jul 19, 2021

atravitz commented Jul 20, 2021

codecov bot commented Jul 23, 2021 •

edited

Loading

bdice left a comment

bdice Jul 24, 2021

bdice Jul 24, 2021

bdice Jul 24, 2021

bdice Jul 24, 2021

bdice commented Jul 24, 2021

Remove easily deprecated functions from project.py #574

Remove easily deprecated functions from project.py #574

Conversation

atravitz commented Jul 19, 2021 • edited by bdice Loading

Description

Motivation and Context

Types of Changes

Checklist:

vyasr commented Jul 19, 2021

atravitz commented Jul 20, 2021

codecov bot commented Jul 23, 2021 • edited Loading

Codecov Report

bdice left a comment

Choose a reason for hiding this comment

bdice Jul 24, 2021

Choose a reason for hiding this comment

bdice Jul 24, 2021

Choose a reason for hiding this comment

bdice Jul 24, 2021

Choose a reason for hiding this comment

bdice Jul 24, 2021

Choose a reason for hiding this comment

bdice commented Jul 24, 2021

atravitz commented Jul 19, 2021 •

edited by bdice

Loading

codecov bot commented Jul 23, 2021 •

edited

Loading