feat: create app for diffpy.cmi CLI #20

cadenmyers13 · 2025-07-01T20:43:24Z

closes #7

New CLI commands -V and -h. Also link to docs is presented.

codecov · 2025-07-01T20:45:05Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 75.67%. Comparing base (261ec9b) to head (b156607).
Report is 16 commits behind head on main.

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@@           Coverage Diff           @@
##             main      #20   +/-   ##
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  Coverage   75.67%   75.67%           
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  Files           3        3           
  Lines          37       37           
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  Hits           28       28           
  Misses          9        9

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cadenmyers13 · 2025-07-01T20:45:55Z

@sbillinge ready for review with no force pushes.

@bobleesj What do we think about the --version and -h being added to skpkg?

bobleesj · 2025-07-01T23:19:35Z

@cadenmyers13 i think package --version maybe. -h is automatically available as shown below:

package --version

Reduce effort for maintaining and developing packages.

positional arguments:
  {create,add,update,build}
    create              Create a new package
    add                 Add a new file like a news item
    update              Update existing package.
    build               Build API docs

options:
  -h, --help            show this help message and exit

sbillinge

please see comments. I think we want to use argparse (we may need it later anyway) and reuse our existing version.py, so most of this can be done without in that way.

sbillinge · 2025-07-01T23:44:20Z

pyproject.toml

@@ -48,6 +48,9 @@ include = ["*"]  # package names should match these glob patterns (["*"] by defa
 exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)

+[project.scripts]
+diffpy-cmi = "diffpy.cmi.app:main"


shall we also have one that is just cmi (for lazy people). It can run the same function.

Also, what happens if you just type diffpy-cmi or cmi without -v or -h? Let's test that and make sure it behaves in a nice friendly way.

@sbillinge just typing diffpy-cmi also returns the same thing as the -h command.

shall we also have one that is just cmi (for lazy people). It can run the same function.

Yeah we can do that!

sbillinge · 2025-07-01T23:49:48Z

src/diffpy/cmi/app.py

+    print(
+        """\
+
+DiffPy-CMI is our complex modeling framework. It is a highly flexible library


how about "is a complex modelling...."

Sadly, this terminology never got widely adopted. Many people call it "multi-modal analysis" so we could say something like: "Welcome to diffpy.cmi, a complex modeling infrastructurel for multi-modal analysis of scientific data form different sources.

It is a highly flexible....."

It is not for nanostructure analysis, it can be used for anything....even predicting stock prices. We can say something like that, but mention that modules currently exist for studies of structure from PDF and SAS data, with mroe to be added later. sthg like that?

@sbillinge Okay got it. I copy/pasted this from the current diffpy-cmi documentation fyi. I'll add these changes

sbillinge · 2025-07-01T23:50:51Z

src/diffpy/cmi/app.py

+    diffpy-cmi [--version] [--help]
+
+Options:
+    -V, --version     Show version and exit


why is the V capitalized? Is that some standard coming from Python? If not, let's lower-case it.

@sbillinge I capitalized because -v typically stands for verbose. I don't think it matters too much so we could change it to -v or simply remove the short-hand and require users to do --version. I feel like when I'm looking for a package version i always type --version anyways.

yes, let's remove the shortcut to remove confusion

sbillinge · 2025-07-01T23:51:25Z

src/diffpy/cmi/app.py

+
+
+def version():
+    from diffpy.cmi.version import __version__


why is this import not at the top of the file? Also, don't we have a version.py? Is there a reason we are defining a new one?

Yeah this should be fine at the top of the file as well. I'll move it.

Also, don't we have a version.py?

yeah in version.py, __version__ is defined and returns the version number. This just imports that version from the file so we aren't defining a new one.

so we aren't defining a new one.

but I see def version(): which seems to contradict your comment?

Oh I see what youre saying, I'll change the function name

src/diffpy/cmi/app.py

cadenmyers13 · 2025-07-02T16:02:19Z

@bobleesj What I mean when a package is created (ie diffpy.myproject) you can go into your terminal and run diffpy-myproject --version and it returns the version of the project you just created. That is what I did on this PR for diffpy.cmi

bobleesj · 2025-07-02T16:23:21Z

@cadenmyers13 yes, I understand. Feel free to make an issue an PR?

cadenmyers13 · 2025-07-02T16:24:24Z

@bobleesj will do, once this is merged I'll do that so we have a good idea of what we want.

cadenmyers13 · 2025-07-02T16:34:08Z

@sbillinge ready for review

cadenmyers13 · 2025-07-02T16:41:56Z

I had to change the requirements file name because of the change made to tests-on-pr here: https://github.com/scikit-package/release-scripts/blob/v0/.github/workflows/_tests-on-pr.yml

sbillinge

please see comments

sbillinge · 2025-07-02T17:17:59Z

src/diffpy/cmi/__init__.py

@@ -12,7 +12,8 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-"""Complex modeling infrastructure: a modulare framework for multi-modal modeling of scientific data."""
+"""Complex modeling infrastructure:
+a modulare framework for multi-modal modeling of scientific data."""


Typo must've been made when package was created, Ive fixed that everywhere its found

sbillinge · 2025-07-02T17:19:20Z

src/diffpy/cmi/app.py

+
+
+def main():
+    try:


please do this work using argparse

cadenmyers13 · 2025-07-02T17:46:15Z

@sbillinge ready for review. I added a function that returns a shorter message if an unknown flag is given:

(cmi_test) → app-creation ~/billingelab/dev/diffpy.cmi $ cmi -a
Error: unrecognized arguments: -a
Usage: diffpy-cmi [--version] [--help]
Use --help to see more.

I've tested this with cmi and diffpy-cmi for --version, --help, and -h and all things behaved as expected

sbillinge

please see my comment

sbillinge · 2025-07-02T22:39:45Z

src/diffpy/cmi/app.py

+
+from diffpy.cmi.version import __version__
+
+


the reason to use argparse is that it does most of this work for you. It will print usage and help so you don't need those functions. Something like

parser = argparse.ArgumentParser( description="help/usage message" ) parser.add_argument( "--version", action="store_true" help="Show the program's version number and exit", ) args = parser.parse_args() if args.version: print("version message") else: print("help/intro message")

should do everything you want

cadenmyers13 · 2025-07-03T03:09:31Z

@sbillinge Ah i see, with some help from chatgpt, this is ready for review. After testing with cmi and diffpy-cmi it behaves as desired. Thanks for your patience on this

sbillinge

please see my questions about code style, but also, please could you paste what we wee when you type diffpy-cmi and also cmi. For one of them do all the options in the matrix:

cmi
cmi --version
cmi -h

for the other we are just testing that it works. I see it as an endpoint in the toml but does it have to be explicitly listed in the arg parser too? not sure. You may have to reinstall the package to get it to work. I expect it is installed as -e but if you change the package metadata I think all bets are off.....

sbillinge · 2025-07-03T11:01:33Z

src/diffpy/cmi/app.py

+        ),
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+


is pre-commit doing this or can we close up these blank lines? Currently,

this

is a

bit too

spread out for my liking....

precommit does a cr for the parenths but i removed the lines

cadenmyers13 · 2025-07-03T15:42:30Z

I see it as an endpoint in the toml but does it have to be explicitly listed in the arg parser too? not sure.

@sbillinge no you only need to mention it in the toml

(cmi_test) → 🌿app-creation ~/billingelab/dev/diffpy.cmi $ cmi
usage: diffpy-cmi [-h] [--version]

Welcome to diffpy-CMI, a complex modeling infrastructure for multi-modal analysis of scientific data.

Docs: https://www.diffpy.org/diffpy.cmi

options:
  -h, --help  show this help message and exit
  --version   Show the program's version number and exit

(cmi_test) → 🌿app-creation ~/billingelab/dev/diffpy.cmi $ cmi -h
usage: diffpy-cmi [-h] [--version]

Welcome to diffpy-CMI, a complex modeling infrastructure for multi-modal analysis of scientific data.

Docs: https://www.diffpy.org/diffpy.cmi

options:
  -h, --help  show this help message and exit
  --version   Show the program's version number and exit

(cmi_test) → 🌿app-creation ~/billingelab/dev/diffpy.cmi $ cmi --version
diffpy.cmi 0.0.1

test case for unexpected arg

(cmi_test) → 🌿app-creation ~/billingelab/dev/diffpy.cmi $ cmi -f
usage: diffpy-cmi [-h] [--version]
diffpy-cmi: error: unrecognized arguments: -f

similar commands work the same for diffpy-cmi

Ready for review

cadenmyers13 added 4 commits July 1, 2025 16:37

pre-commit: line length fix

31a0e67

feat: CLI in pyproject.toml

ce68bce

feat: add app file for CLI

8c8a09f

chore: news

540769b

sbillinge reviewed Jul 1, 2025

View reviewed changes

chore: move import to the top and edit description

2cd8244

change test.txt to tests.txt based on new skpkg syntax

7e6880c

cadenmyers13 added 2 commits July 2, 2025 13:16

doc: change test to tests in docs

79b4309

bug: change version() to print_version()

7efdf61

sbillinge reviewed Jul 2, 2025

View reviewed changes

cadenmyers13 added 2 commits July 2, 2025 13:25

feat: add cmi to pyproject.toml for CLI

2408c82

feat: add new function for invalid input and remove -V flag

ae124b4

cadenmyers13 mentioned this pull request Jul 2, 2025

feat: add app that returns version number and short description of created packages scikit-package/scikit-package#565

Closed

cadenmyers13 added 2 commits July 2, 2025 13:29

chore: fix modulare in short description across 3 files

7170b07

feat: migration main() to argparse

a247ec6

sbillinge reviewed Jul 2, 2025

View reviewed changes

feat: use argsparse description feature

89328df

change diffpy-cmi to diffpy.cmi

fd40eed

sbillinge reviewed Jul 3, 2025

View reviewed changes

style: remove extra lines

b156607

sbillinge merged commit 86b65e8 into diffpy:main Jul 3, 2025
5 checks passed

feat: create app for diffpy.cmi CLI #20

feat: create app for diffpy.cmi CLI #20

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