Merge pull request #1 from serinlee1065/dev

Pulling dev

Author: serinlee1065

.github/scripts/update_version.py

@@ -11,7 +11,7 @@
 patch_number = line_split[2].split("'")[0].split('"')[0]
 
 # Increment patch number
-patch_number = str(int(patch_number) + 1) + "'"
+patch_number = str(int(patch_number) + 1) + '"\n'
 
 
 new_line = line_split[0] + "." + line_split[1] + "." + patch_number

.github/workflows/linter.yml

@@ -17,7 +17,7 @@ jobs:
           fetch-depth: 0
 
       - name: Lint Code Base
-        uses: github/super-linter@v5
+        uses: github/super-linter@v7
         env:
           VALIDATE_ALL_CODEBASE: false
           VALIDATE_PYTHON_FLAKE8: true

.github/workflows/pypi_upload.yml

@@ -20,11 +20,11 @@ There are many ways to contribute to py4DSTEM, including:
 
 ### Coding Guidelines
 
-* **Code style:** py4DSTEM uses the black code formatter and flake8 linter. All code must pass these checks without error before it can be merged. We suggest using `pre-commit` to help ensure any code commited follows these practices, checkout the [setting up developer environment section below](#install). We also try to abide by PEP8 coding style guide where possible.
+* **Code style:** py4DSTEM uses the black code formatter and flake8 linter. All code must pass these checks without error before it can be merged. We suggest using `pre-commit` to help ensure any code committed follows these practices, checkout the [setting up developer environment section below](#install). We also try to abide by PEP8 coding style guide where possible.
 
 * **Documentation:** All code should be well-documented, and use Numpy style docstrings. Use docstrings to document functions and classes, add comments to explain complex code both blocks and individual lines, and use informative variable names.
 
-* **Testing:** Ideally all new code should be accompanied by tests using pyTest framework; at the least we require examples of old and new behaviour caused by the PR. For bug fixes this can be a block of code which currently fails and works with the proposed changes. For new workflows or extensive feature additions, please also include a Jupyter notebook demonstrating the changes for an entire workflow i.e. from loading the input data to visualizing and saving any processed results. 
+* **Testing:** Ideally all new code should be accompanied by tests using pyTest framework; at the least we require examples of old and new behaviour caused by the PR. For bug fixes this can be a block of code which currently fails and works with the proposed changes. For new workflows or extensive feature additions, please also include a Jupyter notebook demonstrating the changes for an entire workflow i.e. from loading the input data to visualizing and saving any processed results.
 
 * **Dependencies:** New dependencies represent a significant change to the package, and any PRs which add new dependencies will require discussion and agreement from the development team. If a new dependency is required, please prioritize adding dependencies that are actively maintained, have permissive installation requirements, and are accessible through both pip and conda.
 
@@ -107,20 +107,20 @@ You can now make changes to the code and test them using your favorite Python ID
     cd <path-to-your-fork-of-the-py4DSTEM-git-repo>   # go to your py4DSTEM repo
     pre-commit install
     ```
-    
+
 This will setup pre-commit to work on this repo by creating/changing a file in .git/hooks/pre-commit, which tells `pre-commit` to automatically run flake8 and black when you try to commit code.  It won't affect any other repos.
 
-**_extra tips_:** 
+**_extra tips_:**
 
 ```bash
 # You can call pre commit manually at any time without committing
-pre-commit run # will check any staged files 
+pre-commit run # will check any staged files
 pre-commit run -a # will run on all files in repo
 
-# you can bypass the hook and commit files without the checks 
+# you can bypass the hook and commit files without the checks
 # (this isn't best practice and should be avoided, but there are times it can be useful)
 
-git add file # stage file as usual 
+git add file # stage file as usual
 git commit -m "you commit message" --no-verify # commit without running checks
-git push # push to repo. 
+git push # push to repo.
 ```

CONTRIBUTORS.md

@@ -3,7 +3,7 @@ this is a test --
 
 > :warning: **py4DSTEM version 0.14 update** :warning: Warning: this is a major update and we expect some workflows to break.  You can still install previous versions of py4DSTEM [as discussed here](#legacyinstall)
 
-> :warning: **Phase retrieval refactor version 0.14.9** :warning: Warning: The phase-retrieval modules in py4DSTEM (DPC, parallax, and ptychography) underwent a major refactor in version 0.14.9 and as such older tutorial notebooks will not work as expected. Notably, class names have been pruned to remove the trailing "Reconstruction" (`DPCReconstruction` -> `DPC` etc.), and regularization functions have dropped the `_iter` suffix (and are instead specified as boolean flags). We are working on updating the tutorial notebooks to reflect these changes. In the meantime, there's some more information in the relevant pull request [here](https://github.com/py4dstem/py4DSTEM/pull/597#issuecomment-1890325568).
+> :warning: **Phase retrieval refactor version 0.14.9** :warning: Warning: The phase-retrieval modules in py4DSTEM (DPC, parallax, and ptychography) underwent a major refactor in version 0.14.9 and as such older tutorial notebooks will not work as expected. Notably, class names have been pruned to remove the trailing "Reconstruction" (`DPCReconstruction` -> `DPC` etc.), and regularization functions have dropped the `_iter` suffix (and are instead specified as boolean flags). See the [updated tutorials](https://github.com/py4dstem/py4DSTEM_tutorials) for more information.
 
 ![py4DSTEM logo](/images/py4DSTEM_logo.png)