test: `copy_examples` test #65

cadenmyers13 · 2025-10-20T18:17:28Z

cleaned up version of this PR: #60

closes: #56

cadenmyers13 · 2025-10-20T19:55:32Z

@sbillinge ready for review

sbillinge · 2025-10-20T22:42:21Z

Looks good as long as all the edits were brought over correctly!

cadenmyers13 · 2025-10-21T01:29:45Z

@sbillinge compared them side-by-side and the two PRs are the same

sbillinge · 2025-10-21T02:41:15Z

Let's then implement the method

…case

cadenmyers13 · 2025-10-22T21:36:13Z

@sbillinge ready for review. All tests pass except one that captures the bad output. Im still figuring out how to capture the statement, but wanted to make a push so you can leave comments on function styling and such

src/diffpy/cmi/packsmanager.py

cadenmyers13 · 2025-10-23T14:57:03Z

I've included a test for the forced overwrite copy of examples.

sbillinge · 2025-10-24T03:38:59Z

this still seems to be failing tests

src/diffpy/cmi/packsmanager.py

cadenmyers13 · 2025-10-28T15:34:39Z

@sbillinge Pytest is passing locally now but this is failing CI for some reason. I'm trying to debug on my fork cadenmyers13#8 and I can't quite figure out whats going on. There is a shell script that runs (requirements/packs/scripts/_pytest.sh) and it calls tar_url.txt which contains this

https://github.com/diffpy/diffpy.srreal/archive/refs/tags/1.4.0.tar.gz
https://github.com/diffpy/diffpy.srfit/archive/refs/tags/3.2.0.tar.gz
https://github.com/diffpy/pyobjcryst/archive/refs/tags/2025.1.0.tar.gz
https://github.com/diffpy/diffpy.structure/archive/refs/tags/3.3.1.tar.gz
https://github.com/Tieqiong/diffpy.utils/archive/refs/tags/3.6.2-rc.0.tar.gz

@Tieqiong Do you know what might be causing this?

FYI, I forgot to pull from upstream before creating this branch so i had to merge the python 3.14 support 🤦‍♂️

Tieqiong · 2025-10-29T14:10:35Z

@cadenmyers13 seems like tests for srreal and pyobjcryst didn't run, probably not compatible with python 3.14 resulting in installation issue. You can see the test env runs on 3.14, which roots from recent 3.14 update on release-scripts/.github/workflows/_tests-on-pr.yml.
Not quite sure about the ones that got successfully tested though, they are supposed to support only up to 3.13 ... Let's try to add python_version: 3.13 in the test-on-pr workflow for now and see if it passes for now!

sbillinge · 2025-10-29T17:05:26Z

We also are out of free credits. Even though CMI is open software, it turns out Mac and Windows builds are not free even then, and CMI running all it's examples burned through our allocation. This is also causing tests to fail, at least the merge to main tests

codecov · 2025-10-30T18:54:10Z

Codecov Report

❌ Patch coverage is 97.40260% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.27%. Comparing base (9f47832) to head (87c1f43).
⚠️ Report is 30 commits behind head on main.

Files with missing lines	Patch %	Lines
tests/test_packsmanager.py	96.29%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #65      +/-   ##
==========================================
+ Coverage   82.93%   83.27%   +0.33%     
==========================================
  Files          13       12       -1     
  Lines        1313     1351      +38     
==========================================
+ Hits         1089     1125      +36     
- Misses        224      226       +2

Files with missing lines	Coverage Δ
tests/conftest.py	`89.53% <100.00%> (+1.86%)`	⬆️
tests/test_packsmanager.py	`93.90% <96.29%> (+4.61%)`	⬆️

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

cadenmyers13 · 2025-10-30T18:58:03Z

@Tieqiong Okay, i added python_version: 3.13 and it looks like its working. Ive created an issue to remove this pin when we get the necessary packages up to python 3.14. As @sbillinge mentioned we are out of credits, but the tests pass:

@sbillinge On another note, is this how the warning message should be handled/captured for the case when the user tries to copy to a pre-existing directory?

sbillinge · 2025-10-30T21:32:53Z

warnings that are raised correctly should pass green in tests. We would like to write a test that tests that a warning is raised correctly.

sbillinge

This looks good now except hte warning. We should think a bit about this. Let's say there is one file that is duplicate. Do we want the code to crash and not copy anything? Or do we want it to copy everything it can, but just not copy the duplicate and throw a warning? Which is better behavior?

src/diffpy/cmi/packsmanager.py

cadenmyers13 · 2025-10-31T01:32:39Z

We should think a bit about this. Let's say there is one file that is duplicate. Do we want the code to crash and not copy anything? Or do we want it to copy everything it can, but just not copy the duplicate and throw a warning? Which is better behavior?

@sbillinge I like copying everything it can and throw the warning. I like this because if the user wants a restart on a specific file, they can remove this file then run cmi copy example_name. All other work on any other file will not be overwritten, but they can have a fresh start on the new file. Then, if they want a complete restart, the can run with --force and everything will be overwritten. Doing this the other way doesn't add this extra layer of flexibility. The user would have to completely start over with --force or copy to a different location then manually move whatever files they want over.

sbillinge · 2025-10-31T11:55:28Z

Ok, that is persuasive, I like it. Let's go with that. We just need all tests Green. We probably need a print instead of a warnings.warn I guess. The print can say "WARNING: This and that" but doesn't have to have the character of a python warning` that shows up on tests. That is for things like deprecations

cadenmyers13 · 2025-10-31T17:17:54Z

tests/test_packsmanager.py

+            False,
+        ),
+    ],
+)


Added an extra case to test if new files are copied and old files remain unchanged.

cadenmyers13 · 2025-10-31T17:19:59Z

src/diffpy/cmi/packsmanager.py

+                if example_name == name:
+                    return True
+        return False
+


Main update on recent push is the content below here.

I've also found this package called rich that allows you to print console outputs in color which is nice. This will be good for pretty printing for cmi print info because that will output a lot of text. Color will help separate the content.

cadenmyers13 · 2025-10-31T17:25:16Z

@sbillinge ready for review. I've left some inline to highlight whats new on this recent push.

sbillinge

looking good. Just a few comments.

sbillinge · 2025-10-31T18:21:27Z

tests/test_packsmanager.py

+@pytest.mark.parametrize(
+    "expected_paths,force",
+    [
+        (


please can you put comment lines here as # case 1: input is such and such. Expect so and so behavior

sbillinge · 2025-10-31T18:21:50Z

tests/test_packsmanager.py

-        Path("packA/ex2/solutions/script2.py"),
-        Path("packA/ex2/script3.py"),
-    ]
+    pm.copy_examples(["packA"], target_dir=case5dir, force=force)


this test looks good now.

sbillinge · 2025-10-31T18:23:50Z

src/diffpy/cmi/packsmanager.py

 from pathlib import Path
 from typing import List, Union

+from rich.console import Console


this seems to be introducing a new dependency. Is it worth adding the bloat for this? Why not just print? If we can be convinced it is worth it we probably have to add rich to all the dependencies.

@sbillinge I was planning on using it for the print_info function (see image). it helps with separation. On second thought, I think we could also add it using ANSI color codes and get rid of the dependency. I'll do that.

we could use rich if it is a nice package, but it is a bit like using pathlib.Path, if we like it, we may want to kind of start using it as a group standard. We could even choose nice colors!

@sbillinge I agree! here's examples of what the syntax would look like with and without rich.

with rich:

from rich.console import Console console=Console() console.print("[bold green]This text prints in bold green[/]")

without rich:

print("\033[32m This text prints in green \033[0m")

There's probably a way to print in bold with ANSI code too. I think rich has preset colors that are commonly used/are nice but we could probably add a config file to change these if we wanted. what do you think?

I don't mind about the syntax, it is more whether we want to go there at all. Let's just do a print without any colors for now and merge the PR. We can make an issue to add rich formatting and have a discussion about it in the broader group.

cadenmyers13 · 2025-10-31T19:29:34Z

@sbillinge ready for review. I removed rich for now just so we can get this moving. This is what the print statements look like with ANSI color code.

cadenmyers13 · 2025-11-01T00:02:55Z

@sbillinge ready for review. removed colors

cadenmyers13 added 6 commits October 20, 2025 13:33

rm api from cli.py

17e3747

add copy_examples api to packsmanager

82f7394

add tests for copy_examples

d973c83

add additional dirs to temp structure

375606c

rm old tests

711c24e

add news

987c3e3

glob only files and not dirs

9e65a27

cadenmyers13 added 3 commits October 22, 2025 17:20

fix target dir location to be under cwd and change name for new test …

5354831

…case

Add additional test case, fix how copy location is tested

47d87fb

copy_examples function

0a490b9

cadenmyers13 added 3 commits October 23, 2025 10:20

rm error message function

6e2695d

add test for forced overwrite of copied files

e96988f

Add 'force' param to copy_examples

abfba68

cadenmyers13 commented Oct 23, 2025

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src/diffpy/cmi/packsmanager.py Show resolved Hide resolved

cadenmyers13 added 2 commits October 27, 2025 14:37

fix copy_tree to handle warnings and errors properly

d4cddf5

Merge branch 'main' of github.com:diffpy/diffpy.cmi into copy-func-test

38881b8

cadenmyers13 commented Oct 28, 2025

View reviewed changes

src/diffpy/cmi/packsmanager.py Show resolved Hide resolved

pin workflow to python 3.13

f4fe605

cadenmyers13 mentioned this pull request Oct 30, 2025

remove python 3.13 workflow pin when pyobjcryst and diffpy.srreal support python 3.14 #67

Open

sbillinge reviewed Oct 30, 2025

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src/diffpy/cmi/packsmanager.py Show resolved Hide resolved

cadenmyers13 added 3 commits October 31, 2025 12:37

add test for force and non-force to make sure files are copied correctly

07cbcd7

update copy_tree_to_target to handle different copying cases

078b13c

capture warning output in print statement

e7444d7

cadenmyers13 commented Oct 31, 2025

View reviewed changes

add rich to conda.txt

c792c0b

sbillinge reviewed Oct 31, 2025

View reviewed changes

cadenmyers13 added 3 commits October 31, 2025 14:48

add UC comments

7d7a2a3

use ANSI color code for now

52a6752

rm rich from reqs

611bdf5

cadenmyers13 and others added 3 commits October 31, 2025 19:58

Rm colors from print

d6f34e0

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

087851b

rm color from test

87c1f43

sbillinge merged commit 5f7f605 into diffpy:main Nov 1, 2025
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test: copy_examples test #65

test: copy_examples test #65

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test: `copy_examples` test #65

test: `copy_examples` test #65

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