Merge pull request #2220 from GreenleafLab/master

Update release 1.0.2 to reflect Jeff's bug fixes

.github/ISSUE_TEMPLATE/bug-report.md → .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.

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/workflows/auto-comment.yml

@@ -0,0 +1,36 @@
+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! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other 
+            responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
+            a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
+            In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
+            Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.
+            
+#          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.<br />
+#            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, all of which are extremely challenging to troubleshoot. As such, we require [reproducible examples](https://reprex.tidyverse.org/articles/reprex-dos-and-donts.html) (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
+#            Before going through the work of making a reproducible example, 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 your post does not contain a reproducible example, it is unlikely to receive a response.<br />
+#            __In addition to a reproducible example, you must do the following things before we help you, 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.__ Did you post your log file? If not, add it now.
+#            __3.__ 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 vacation and will not be responding to any issues or discussion threads until 5/5.<br />
+#            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.<br />
+#            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, all of which are extremely challenging to troubleshoot. As such, we require [reproducible examples](https://reprex.tidyverse.org/articles/reprex-dos-and-donts.html) (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, how will we be able to help?
+#            Before going through the work of making a reproducible example, 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 your post does not contain a reproducible example, it is unlikely to receive a response.<br />
+#            __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.

R/CreateArrow.R

@@ -205,7 +205,7 @@ createArrowFiles <- function(
   if(subThreading){
     h5disableFileLocking()
   }else{
-    args$threads <- length(inputFiles)
+    args$threads <- min(length(inputFiles), threads)
   }
 
   args$minTSS <- NULL

R/MatrixGeneScores.R

@@ -125,7 +125,7 @@ addGeneScoreMatrix <- function(
   if(subThreading){
     h5disableFileLocking()
   }else{
-    args$threads <- length(ArrowFiles)
+    args$threads <- min(length(ArrowFiles), threads)
   }
 
   #Remove Input from args