allow additional image extensions by andrewGhazi · Pull Request #160 · drighelli/SpatialExperiment

andrewGhazi · 2024-11-07T22:20:13Z

As first brought up here #159 , this PR makes a small change to the pattern used in the .path_validity() function to allows additional image file extensions and their capitalized variants. It increases the "long lines" note from BiocCheck::BiocCheck() from 25 to 26 but doesn't affect the check or test results otherwise.

 * NOTE: Consider shorter lines; 26 lines (1%) are > 80 characters
long.

I tried to follow the contributor guidelines here as best as I could, please let me know if you'd like something changed.

LiNk-NY · 2025-05-12T18:39:14Z

please allow the maintainer to perform the version bumps at their discretion

I have "Allow edits by maintainers" checked on the PR menu, is there something else that I need to change to allow maintainers to version bump?

I meant to say that I usually leave the version bumping up to the maintainer so to avoid conflicts with the main branch. That means that I wouldn't commit any changes to the version in the DESCRIPTION file. You may also consider reverting the change to the DESCRIPTION and using git commit --amend and then force pushing to your branch git push -f aghazi addl_img_exts where aghazi is the name of the remote for your fork.

Ah okay. I saw a version bump in a different PR that I was imitating so I thought that was required. I'll try the fix you suggest.

I made the change you suggested 👍

Looks good!

LiNk-NY · 2025-05-12T18:42:03Z

It may be better to use tools::file_ext() and tolower() to check the extension with vector of allowed extensions.

Consider doing something like:
## [... outside the function].ALLOWED_FORMATS<- c("png", "jpg", "jpeg", "tif", "tiff") ## [... inside the function]ext<-tools::file_ext(x) |> tolower() ext%in%.ALLOWED_FORMATS

Okay, I also made this change as well 👍

…zed variants. Amended earlier changes that directly bumped the version number. Also changed the pattern detection to use tolower() as suggested.

LiNk-NY

Great, thanks!

andrewGhazi · 2024-11-07T22:20:13Z

As first brought up here #159 , this PR makes a small change to the pattern used in the .path_validity() function to allows additional image file extensions and their capitalized variants. It increases the "long lines" note from BiocCheck::BiocCheck() from 25 to 26 but doesn't affect the check or test results otherwise.

 * NOTE: Consider shorter lines; 26 lines (1%) are > 80 characters
long.

I tried to follow the contributor guidelines here as best as I could, please let me know if you'd like something changed.

LiNk-NY · 2025-05-12T18:39:14Z

please allow the maintainer to perform the version bumps at their discretion

I have "Allow edits by maintainers" checked on the PR menu, is there something else that I need to change to allow maintainers to version bump?

I meant to say that I usually leave the version bumping up to the maintainer so to avoid conflicts with the main branch. That means that I wouldn't commit any changes to the version in the DESCRIPTION file. You may also consider reverting the change to the DESCRIPTION and using git commit --amend and then force pushing to your branch git push -f aghazi addl_img_exts where aghazi is the name of the remote for your fork.

Ah okay. I saw a version bump in a different PR that I was imitating so I thought that was required. I'll try the fix you suggest.

I made the change you suggested 👍

Looks good!

LiNk-NY · 2025-05-12T18:42:03Z

It may be better to use tools::file_ext() and tolower() to check the extension with vector of allowed extensions.

Consider doing something like:
## [... outside the function].ALLOWED_FORMATS<- c("png", "jpg", "jpeg", "tif", "tiff") ## [... inside the function]ext<-tools::file_ext(x) |> tolower() ext%in%.ALLOWED_FORMATS

Okay, I also made this change as well 👍

…zed variants. Amended earlier changes that directly bumped the version number. Also changed the pattern detection to use tolower() as suggested.

LiNk-NY

Great, thanks!

andrewGhazi · 2024-11-07T22:20:13Z

As first brought up here #159 , this PR makes a small change to the pattern used in the .path_validity() function to allows additional image file extensions and their capitalized variants. It increases the "long lines" note from BiocCheck::BiocCheck() from 25 to 26 but doesn't affect the check or test results otherwise.

 * NOTE: Consider shorter lines; 26 lines (1%) are > 80 characters
long.

I tried to follow the contributor guidelines here as best as I could, please let me know if you'd like something changed.

LiNk-NY · 2025-05-12T18:39:14Z

please allow the maintainer to perform the version bumps at their discretion

I have "Allow edits by maintainers" checked on the PR menu, is there something else that I need to change to allow maintainers to version bump?

I meant to say that I usually leave the version bumping up to the maintainer so to avoid conflicts with the main branch. That means that I wouldn't commit any changes to the version in the DESCRIPTION file. You may also consider reverting the change to the DESCRIPTION and using git commit --amend and then force pushing to your branch git push -f aghazi addl_img_exts where aghazi is the name of the remote for your fork.

Ah okay. I saw a version bump in a different PR that I was imitating so I thought that was required. I'll try the fix you suggest.

I made the change you suggested 👍

Looks good!

LiNk-NY · 2025-05-12T18:42:03Z

It may be better to use tools::file_ext() and tolower() to check the extension with vector of allowed extensions.

Consider doing something like:
## [... outside the function].ALLOWED_FORMATS<- c("png", "jpg", "jpeg", "tif", "tiff") ## [... inside the function]ext<-tools::file_ext(x) |> tolower() ext%in%.ALLOWED_FORMATS

Okay, I also made this change as well 👍

…zed variants. Amended earlier changes that directly bumped the version number. Also changed the pattern detection to use tolower() as suggested.

LiNk-NY

Great, thanks!

andrewGhazi · 2024-11-07T22:20:13Z

As first brought up here #159 , this PR makes a small change to the pattern used in the .path_validity() function to allows additional image file extensions and their capitalized variants. It increases the "long lines" note from BiocCheck::BiocCheck() from 25 to 26 but doesn't affect the check or test results otherwise.

 * NOTE: Consider shorter lines; 26 lines (1%) are > 80 characters
long.

I tried to follow the contributor guidelines here as best as I could, please let me know if you'd like something changed.

LiNk-NY · 2025-05-12T18:39:14Z

please allow the maintainer to perform the version bumps at their discretion

I have "Allow edits by maintainers" checked on the PR menu, is there something else that I need to change to allow maintainers to version bump?

I meant to say that I usually leave the version bumping up to the maintainer so to avoid conflicts with the main branch. That means that I wouldn't commit any changes to the version in the DESCRIPTION file. You may also consider reverting the change to the DESCRIPTION and using git commit --amend and then force pushing to your branch git push -f aghazi addl_img_exts where aghazi is the name of the remote for your fork.

Ah okay. I saw a version bump in a different PR that I was imitating so I thought that was required. I'll try the fix you suggest.

I made the change you suggested 👍

Looks good!

LiNk-NY · 2025-05-12T18:42:03Z

It may be better to use tools::file_ext() and tolower() to check the extension with vector of allowed extensions.

Consider doing something like:
## [... outside the function].ALLOWED_FORMATS<- c("png", "jpg", "jpeg", "tif", "tiff") ## [... inside the function]ext<-tools::file_ext(x) |> tolower() ext%in%.ALLOWED_FORMATS

Okay, I also made this change as well 👍

…zed variants. Amended earlier changes that directly bumped the version number. Also changed the pattern detection to use tolower() as suggested.

LiNk-NY

Great, thanks!

andrewGhazi · 2024-11-07T22:20:13Z

As first brought up here #159 , this PR makes a small change to the pattern used in the .path_validity() function to allows additional image file extensions and their capitalized variants. It increases the "long lines" note from BiocCheck::BiocCheck() from 25 to 26 but doesn't affect the check or test results otherwise.

 * NOTE: Consider shorter lines; 26 lines (1%) are > 80 characters
long.

I tried to follow the contributor guidelines here as best as I could, please let me know if you'd like something changed.

LiNk-NY · 2025-05-12T18:39:14Z

please allow the maintainer to perform the version bumps at their discretion

I have "Allow edits by maintainers" checked on the PR menu, is there something else that I need to change to allow maintainers to version bump?

I meant to say that I usually leave the version bumping up to the maintainer so to avoid conflicts with the main branch. That means that I wouldn't commit any changes to the version in the DESCRIPTION file. You may also consider reverting the change to the DESCRIPTION and using git commit --amend and then force pushing to your branch git push -f aghazi addl_img_exts where aghazi is the name of the remote for your fork.

Ah okay. I saw a version bump in a different PR that I was imitating so I thought that was required. I'll try the fix you suggest.

I made the change you suggested 👍

Looks good!

LiNk-NY · 2025-05-12T18:42:03Z

It may be better to use tools::file_ext() and tolower() to check the extension with vector of allowed extensions.

Consider doing something like:
## [... outside the function].ALLOWED_FORMATS<- c("png", "jpg", "jpeg", "tif", "tiff") ## [... inside the function]ext<-tools::file_ext(x) |> tolower() ext%in%.ALLOWED_FORMATS

Okay, I also made this change as well 👍

…zed variants. Amended earlier changes that directly bumped the version number. Also changed the pattern detection to use tolower() as suggested.

LiNk-NY

Great, thanks!

andrewGhazi · 2024-11-07T22:20:13Z

As first brought up here #159 , this PR makes a small change to the pattern used in the .path_validity() function to allows additional image file extensions and their capitalized variants. It increases the "long lines" note from BiocCheck::BiocCheck() from 25 to 26 but doesn't affect the check or test results otherwise.

 * NOTE: Consider shorter lines; 26 lines (1%) are > 80 characters
long.

I tried to follow the contributor guidelines here as best as I could, please let me know if you'd like something changed.

LiNk-NY · 2025-05-12T18:39:14Z

please allow the maintainer to perform the version bumps at their discretion

I have "Allow edits by maintainers" checked on the PR menu, is there something else that I need to change to allow maintainers to version bump?

I meant to say that I usually leave the version bumping up to the maintainer so to avoid conflicts with the main branch. That means that I wouldn't commit any changes to the version in the DESCRIPTION file. You may also consider reverting the change to the DESCRIPTION and using git commit --amend and then force pushing to your branch git push -f aghazi addl_img_exts where aghazi is the name of the remote for your fork.

Ah okay. I saw a version bump in a different PR that I was imitating so I thought that was required. I'll try the fix you suggest.

I made the change you suggested 👍

Looks good!

LiNk-NY · 2025-05-12T18:42:03Z

It may be better to use tools::file_ext() and tolower() to check the extension with vector of allowed extensions.

Consider doing something like:
## [... outside the function].ALLOWED_FORMATS<- c("png", "jpg", "jpeg", "tif", "tiff") ## [... inside the function]ext<-tools::file_ext(x) |> tolower() ext%in%.ALLOWED_FORMATS

Okay, I also made this change as well 👍

…zed variants. Amended earlier changes that directly bumped the version number. Also changed the pattern detection to use tolower() as suggested.

LiNk-NY

Great, thanks!

andrewGhazi · 2024-11-07T22:20:13Z

As first brought up here #159 , this PR makes a small change to the pattern used in the .path_validity() function to allows additional image file extensions and their capitalized variants. It increases the "long lines" note from BiocCheck::BiocCheck() from 25 to 26 but doesn't affect the check or test results otherwise.

 * NOTE: Consider shorter lines; 26 lines (1%) are > 80 characters
long.

I tried to follow the contributor guidelines here as best as I could, please let me know if you'd like something changed.

LiNk-NY · 2025-05-12T18:39:14Z

please allow the maintainer to perform the version bumps at their discretion

I have "Allow edits by maintainers" checked on the PR menu, is there something else that I need to change to allow maintainers to version bump?

I meant to say that I usually leave the version bumping up to the maintainer so to avoid conflicts with the main branch. That means that I wouldn't commit any changes to the version in the DESCRIPTION file. You may also consider reverting the change to the DESCRIPTION and using git commit --amend and then force pushing to your branch git push -f aghazi addl_img_exts where aghazi is the name of the remote for your fork.

Ah okay. I saw a version bump in a different PR that I was imitating so I thought that was required. I'll try the fix you suggest.

I made the change you suggested 👍

Looks good!

LiNk-NY · 2025-05-12T18:42:03Z

It may be better to use tools::file_ext() and tolower() to check the extension with vector of allowed extensions.

Consider doing something like:
## [... outside the function].ALLOWED_FORMATS<- c("png", "jpg", "jpeg", "tif", "tiff") ## [... inside the function]ext<-tools::file_ext(x) |> tolower() ext%in%.ALLOWED_FORMATS

Okay, I also made this change as well 👍

…zed variants. Amended earlier changes that directly bumped the version number. Also changed the pattern detection to use tolower() as suggested.

LiNk-NY

Great, thanks!

andrewGhazi mentioned this pull request Nov 7, 2024
Allow additional SpatialImage file extensions #159
Open

LiNk-NY suggested changes May 12, 2025
View reviewed changes

andrewGhazi force-pushed the addl_img_exts branch from 66970df to 849a6dfCompare May 13, 2025 20:06

allow additional image extensions (jpeg and tiff) as well as capitali…
3f972d4
…zed variants. Amended earlier changes that directly bumped the version number. Also changed the pattern detection to use tolower() as suggested.

andrewGhazi force-pushed the addl_img_exts branch from 849a6df to 3f972d4Compare May 14, 2025 13:42

LiNk-NY approved these changes May 14, 2025
View reviewed changes