Recookiecut #85

bobleesj · 2024-09-24T04:28:27Z

No description provided.

Move test directory and remove -e install (Testing)

bobleesj · 2024-09-24T04:51:48Z

src/diffpy/pdffit2/__init__.py

-from diffpy.pdffit2.version import __version__, __date__
-from diffpy.pdffit2.pdffit import PdfFit
-from diffpy.pdffit2.pdffit2 import is_element
+from diffpy.pdffit2.version import __date__, __version__


I finally found one origin of "import" problem.

The C++ extension below pdffit2.pdffit2 uses the __verison__ global variable.

from diffpy.pdffit2.pdffit2 import is_element

But when we apply isort via pre-commit, the C++ module is imported first before __version__ variable is initialized, causing the import issue.

Good work @bobleesj . I guess we need a fix? Is it to disable isort for this case? Or change how the imports are done? It is a bit brittle if it can be broken by isort, but that fix is ok if we document it carefully so we don't break it again in the first when we try and do better linting....

(thinking about a solution)

@sbillinge Indeed there are two options. First, we can disable isort for this file using .flake8 (the previous solution), but this approach is brittle since the .flake8 file can be overwritten when reapplying the cookiecutter template, as you mentioned.

The second option is to disable isort at the file level using the isort: off/on directives, as shown here. I've also made the comments more explicit to ensure that these directives shall not be removed.

bobleesj · 2024-09-24T04:53:17Z

Ready for review @sbillinge !

sbillinge

Please see inline

sbillinge · 2024-09-24T11:18:07Z

.coveragerc

-omit =
-    # exclude debug.py from codecov report
-    */tests/debug.py
+    diffpy.structure


Should be diffpy.pdffit2?

sbillinge · 2024-09-24T11:19:45Z

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

+    uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    with:
+      project: diffpy.structure
+      c_extension: false


Please check. I think this maybe should be yes

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

sbillinge · 2024-09-24T11:20:40Z

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

+    types:
+      - prereleased
+      - published
+  workflow_dispatch: null


Still this null bug.

README.rst

sbillinge · 2024-09-24T11:23:21Z

README.rst

 http://www.diffpy.org/doc/pdffit2.

+For more information about the diffpy.pdffit2 library, please consult our `online documentation <https://diffpy.github.io/diffpy.pdffit2>`_.
+


Please look for a rogue slash in the curation below.

Also, please replace the installation instructions with the cookie cutter version. If there are special instructions for installing it from sources we can add them, but use the cookie cutter as a starting point with minimal updates and delete the old instructions.

Please look for a rogue slash in the curation below.

Removed

Also, please replace the installation instructions with the cookie cutter version

Indeed the starting point was the cookiecutter. It was further populated from the prior readme.rst (confirmed since all the matrix yml links above modified automatically)

Perhaps we can make an issue for now to improve the installation instructions in reaadme once we have a PyPI/conda version available?

No, do it now. We won't release until we have a puppy/cons version and then the instructions will work

Instructions added.

Done - rendered readme: https://github.com/bobleesj/diffpy.pdffit2/tree/recookiecut

doc/source/license.rst

sbillinge · 2024-09-24T11:30:09Z

src/diffpy/pdffit2/__init__.py

-from diffpy.pdffit2.version import __version__, __date__
-from diffpy.pdffit2.pdffit import PdfFit
-from diffpy.pdffit2.pdffit2 import is_element
+from diffpy.pdffit2.version import __date__, __version__


Good work @bobleesj . I guess we need a fix? Is it to disable isort for this case? Or change how the imports are done? It is a bit brittle if it can be broken by isort, but that fix is ok if we document it carefully so we don't break it again in the first when we try and do better linting....

README.rst

bobleesj · 2024-09-24T12:49:35Z

doc/source/index.rst

+we ask that you acknowledge use of the program by citing the following paper
 in your publication:

   C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch, Th. Proffen


rogue slash removed.

README.rst

bobleesj · 2024-09-24T13:13:32Z

@sbillinge Ready for review

sbillinge

Please see inline

bobleesj · 2024-09-24T13:43:25Z

README.rst


+To confirm that the installation was successful, run the following in a terminal ::
+                
+        python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"


Added a quick version test for the user.

bobleesj · 2024-09-24T13:52:59Z

@sbillinge ready for review - primarily pip install instruction

sbillinge

one small last tweak

sbillinge · 2024-09-24T16:55:06Z

README.rst

-To install using ``pip`` into your ``diffpy.pdffit2_env`` environment, we will also have to install dependencies ::

-        pip install -r https://github.com/raw/diffpy/diffpy.pdffit2/main/requirements/run.txt
+To install the C++ compiler and required dependencies in your ``diffpy.pdffit2_env`` environment, type ::


The less preferred approach is the install using ``pip`` to download and install the latest release from `Python Package Index <https://pypi.python.org>`_. In this case you currently have to build the codes on your computer from the sources and you will have to have a C++ installer available. To install the C++ ..... ``

bobleesj · 2024-09-24T17:18:20Z

@sbillinge Ready for review - just modified the pip source install instruction suggested by you.

bobleesj added 14 commits September 22, 2024 15:51

Remove -e build

f89dcc0

Merge pull request #3 from bobleesj/tests-dir-import

2ae3fd6

Move test directory and remove -e install (Testing)

Merge branch 'main' of https://github.com/diffpy/diffpy.pdffit2

3a5bf39

Merge branch 'main' of https://github.com/diffpy/diffpy.pdffit2

025af2b

Add github workflows

4492220

Add .codecov, coverage, gitignore, remove gitattributes

12d0c5a

Add news

031809b

Add version test

f8827b8

Add pytest-cov test

f644142

Add readme, doc, project.toml

90658de

meta.yml to meta.txt

3987b18

Apply precomit

05b15ce

Ensure ordering of import in __init__.py

304f0d6

Fix typo

43b31a5

bobleesj commented Sep 24, 2024

View reviewed changes

bobleesj mentioned this pull request Sep 24, 2024

Re-cookiecut #84

Closed

sbillinge reviewed Sep 24, 2024

View reviewed changes

bobleesj added 4 commits September 24, 2024 08:41

rm mention of diffpy.structure, add c extensions

47fd5a7

rm rogue dash

226fef0

Fix contributing typo

3016fc5

remove rogue slash in citation

b953041

bobleesj commented Sep 24, 2024

View reviewed changes

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bobleesj commented Sep 24, 2024

View reviewed changes

Remove avoid flake8 in __init__ and add clear directions with isort tags

1ba7042

bobleesj commented Sep 24, 2024

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sbillinge reviewed Sep 24, 2024

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bobleesj added 2 commits September 24, 2024 09:26

Add pip source install step in readme

1b091b5

Fix Ubuntu command for g++

a225c8b

bobleesj added 3 commits September 24, 2024 09:34

Add compiler download for pip install

a9aa591

Use conda to download dependencies

9fabfc4

add testing for version prompt

693414d

bobleesj commented Sep 24, 2024

View reviewed changes

bobleesj added 5 commits September 24, 2024 09:46

Fix indention for conda install

3ba006e

you to your

dd71f7f

Add double quote for pre

d0ea0b9

Remove the next to env

9d5fad5

Improve instruction for conda install

39be2ba

Add double quote for pre

e040739

sbillinge reviewed Sep 24, 2024

View reviewed changes

Include Billinge's recommended instruction for pip source install

8eba008

sbillinge merged commit f04c782 into diffpy:main Sep 24, 2024
2 checks passed

bobleesj deleted the recookiecut branch September 24, 2024 20:00

		http://www.diffpy.org/doc/pdffit2.

		For more information about the diffpy.pdffit2 library, please consult our `online documentation <https://diffpy.github.io/diffpy.pdffit2>`_.


		To confirm that the installation was successful, run the following in a terminal ::

		python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"

Recookiecut #85

Recookiecut #85

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bobleesj commented Sep 24, 2024

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bobleesj commented Sep 24, 2024

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bobleesj commented Sep 24, 2024

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