diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md similarity index 51% rename from .github/ISSUE_TEMPLATE/bug-report.md rename to .github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md index adc1b1c9..dfa6fd79 100644 --- a/.github/ISSUE_TEMPLATE/bug-report.md +++ b/.github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md @@ -1,13 +1,18 @@ --- -name: Bug Report -about: Create a bug report to help us improve ArchR +name: Bug/Error Report - NO USAGE QUESTIONS / FEATURE REQUESTS (Use Discussions!) +about: Create a bug/error report to help us improve ArchR. NOT to be used for usage + questions or feature requests! title: '' labels: bug assignees: '' --- -Before you submit this issue please update ArchR to the latest version and make sure that this issue has not already been fixed in the latest release. ArchR is in *beta* and we will fix problems as they arise. To update ArchR: +This is an issue template made by the developers of ArchR. You MUST follow these instructions. + +Questions related to how to use ArchR or requests for new features should be posted in the Discussions forum (https://github.com/GreenleafLab/ArchR/discussions). + +Before you submit this Bug Report please update ArchR to the latest stable version and make sure that this issue has not already been fixed in the latest release. ArchR is still in active development and we will fix problems as they arise. To update ArchR: devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories()) @@ -22,13 +27,13 @@ ArchR has a built-in logging functionality for all complex functions. You MUST a A clear and concise description of what the bug is. **To Reproduce** -To help us optimally address your issue, please try to reproduce this issue using the tutorial hematopoiesis dataset and provide us the command(s) to reproduce your bug. +To help us optimally address your issue, please try to reproduce this issue using the tutorial hematopoiesis dataset and provide us the command(s) to reproduce your bug. Our first question to you will be "can you reproduce this with the tutorial dataset" so please do this. **Expected behavior** A clear and concise description of what you expected to happen. **Screenshots** -If applicable, add screenshots to help explain your problem. +If applicable, add screenshots to help explain your problem. Do not screenshot code or text but embed this in markdown using triple-backticks. **Session Info** If you do not have a log file because the function that caused the error does not produce one, please paste the output of "sessionInfo()" here. diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 00000000..3ba13e0c --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1 @@ +blank_issues_enabled: false diff --git a/.github/ISSUE_TEMPLATE/documentation-request.md b/.github/ISSUE_TEMPLATE/documentation-request.md deleted file mode 100644 index 31511d14..00000000 --- a/.github/ISSUE_TEMPLATE/documentation-request.md +++ /dev/null @@ -1,30 +0,0 @@ ---- -name: Documentation Request -about: Help us improve ArchR's documentation -title: '' -labels: documentation -assignees: '' - ---- - -Before you submit this issue, go to the ArchR user manual (https://www.archrproject.com/bookdown/index.html) and use the search function (magnifying glass in the top navbar) to search the manual for the content you are looking for! - -PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE. - -### If this is an issue with an existing explanation: - -**Where is the problematic documentation?** -For example: The explanation of [...] in Section 4.3 of the user manual - -**Describe what is unclear or confusing** -A concise and clear explanation of what documentation could be improved - -### If this is an issue with documentation that is absent/missing: - -**Describe what material you feel should be explained** -A concise and clear explanation of what documentation could be improved - -**Where do you think this documentation would belong?** -For example: This would belong in Section 4.3 of the user manual. -OR -You should create a new section in the user manual in Chapter 4. diff --git a/.github/ISSUE_TEMPLATE/feature-request.md b/.github/ISSUE_TEMPLATE/feature-request.md deleted file mode 100644 index c414496e..00000000 --- a/.github/ISSUE_TEMPLATE/feature-request.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -name: Feature Request -about: Suggest an idea to enhance ArchR -title: '' -labels: enhancement -assignees: '' - ---- - -Do not use this form to report a bug in ArchR! Instead, use the "Bug report" option. - -PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE. - -**Describe the problem that your feature request would address.** -A clear and concise description of what the problem is. Ex. A common analysis that is performed but not currently supported is [...] - -**Describe the solution you'd like** -A clear and concise description of what you want to happen. - -**Describe alternatives you've considered** -A clear and concise description of any alternative solutions or features you've considered. - -**Additional context** -Add any other context or screenshots about the feature request here. diff --git a/.github/auto-comment.yml b/.github/auto-comment.yml deleted file mode 100644 index 53fd071d..00000000 --- a/.github/auto-comment.yml +++ /dev/null @@ -1,6 +0,0 @@ -# Comment to a new issue. -issueOpened: > - Thank your for raising a issue. We will try and get back to you as soon as possible. - - Please make sure you have given us as much context as possible. - diff --git a/.github/workflows/auto-comment.yml b/.github/workflows/auto-comment.yml new file mode 100644 index 00000000..3ae4ec02 --- /dev/null +++ b/.github/workflows/auto-comment.yml @@ -0,0 +1,25 @@ +name: Auto Comment +on: [issues] +jobs: + run: + runs-on: ubuntu-latest + steps: + - uses: wow-actions/auto-comment@v1 + with: + GITHUB_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }} + issuesOpened: | + Hi @{{ author }}! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the [Discussions](https://github.com/GreenleafLab/ArchR/discussions) section, not in Issues.
+ __Before we help you, you must respond to the following questions__ unless your original post already contained this information: + __1.__ If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? + __2.__ Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example. + __3.__ Did you post your log file? If not, add it now. + __4.__ Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post. + +# issuesOpened: | +# Hi @{{ author }}! Thanks for using ArchR! I am currently on paternity leave and will not be responding to any issues or discussion threads. I plan to be back in late January and will do my best to address your issue then.
+# In the meantime, it is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment. Search the previous [Issues](https://github.com/GreenleafLab/ArchR/issues), [Discussions](https://github.com/GreenleafLab/ArchR/discussions), [function definitions](https://www.archrproject.com/reference/index.html), or the [ArchR manual](https://www.archrproject.com/bookdown/index.html) and you will likely find the answers you are looking for.
+# If you are able to solve your issue, please post the solution and close this issue post.
+# Otherwise __if you would like my help when I return, you must respond to the following questions__ unless your original post already contained this information: +# __1.__ If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? +# __2.__ Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example. +# __3.__ Did you post your log file? If not, add it now. diff --git a/R/ReproduciblePeakSet.R b/R/ReproduciblePeakSet.R index 8699e748..0fabcf97 100644 --- a/R/ReproduciblePeakSet.R +++ b/R/ReproduciblePeakSet.R @@ -788,8 +788,8 @@ addReproduciblePeakSet <- function( run <- system2(pathToMacs2, cmd, wait=TRUE, stdout=NULL, stderr=NULL) #Read Summits! - out <- data.table::fread(summitsFile, select = c(1,2,3,5)) - out <- GRanges(out$V1, IRanges(out$V2 + 1, out$V3), score = out$V5) + out <- data.table::fread(narrowPeaksFile, select = c(1,2,5,7,10)) + out <- GRanges(out$V1, IRanges(out$V2 + out$V10 + 1, out$V2 + out$V10 + 1), score = out$V5/10, signalValue = out$V7) #Remove Files r2 <- suppressWarnings(file.remove(summitsFile, narrowPeaksFile, xlsFile))