From a3c444db870aefa07b7f172e22d5610237b09bf6 Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Thu, 4 Mar 2021 07:28:02 -0800 Subject: [PATCH 01/19] Update issue templates Remove issue reports for feature requests and documentation. These have been moved to discussions --- .github/ISSUE_TEMPLATE/bug-report.md | 10 +++++-- .../ISSUE_TEMPLATE/documentation-request.md | 30 ------------------- .github/ISSUE_TEMPLATE/feature-request.md | 24 --------------- 3 files changed, 7 insertions(+), 57 deletions(-) delete mode 100644 .github/ISSUE_TEMPLATE/documentation-request.md delete mode 100644 .github/ISSUE_TEMPLATE/feature-request.md diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-report.md index adc1b1c9..3dd48e19 100644 --- a/.github/ISSUE_TEMPLATE/bug-report.md +++ b/.github/ISSUE_TEMPLATE/bug-report.md @@ -7,7 +7,11 @@ 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 +26,13 @@ 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/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. From 968e4421ce7187a8ac7ea1cf6077412126876d5f Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Mon, 8 Mar 2021 07:24:15 -0800 Subject: [PATCH 02/19] Update issue templates --- .github/ISSUE_TEMPLATE/bug-report.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-report.md index 3dd48e19..d978275e 100644 --- a/.github/ISSUE_TEMPLATE/bug-report.md +++ b/.github/ISSUE_TEMPLATE/bug-report.md @@ -1,6 +1,7 @@ --- name: Bug Report -about: Create a bug report to help us improve ArchR +about: Create a bug report to help us improve ArchR. NOT to be used for questions + or feature requests! title: '' labels: bug assignees: '' From 28a17f7ee90e406fc061f1c1f7e0611a55ba8a3c Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Fri, 28 May 2021 20:41:31 -0700 Subject: [PATCH 03/19] Update issue templates --- ...s---feature-requests--use-discussions--.md | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/bug-report---no-questions---feature-requests--use-discussions--.md diff --git a/.github/ISSUE_TEMPLATE/bug-report---no-questions---feature-requests--use-discussions--.md b/.github/ISSUE_TEMPLATE/bug-report---no-questions---feature-requests--use-discussions--.md new file mode 100644 index 00000000..e89438b4 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug-report---no-questions---feature-requests--use-discussions--.md @@ -0,0 +1,42 @@ +--- +name: Bug Report - NO QUESTIONS / FEATURE REQUESTS (Use Discussions!) +about: Create a bug report to help us improve ArchR. NOT to be used for questions + or feature requests! +title: '' +labels: bug +assignees: '' + +--- + +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()) + +If your issue persists, then please submit this bug report. + +PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE. + +**Attach your log file** +ArchR has a built-in logging functionality for all complex functions. You MUST attach your log file (indicated in the console output) to this issue. Just drag and drop it here. + +**Describe the bug** +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. 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. 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. + +**Additional context** +Add any other context about the problem here. From e1482547873b6739e2c7c194062c5ea8b5924901 Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Fri, 28 May 2021 20:42:45 -0700 Subject: [PATCH 04/19] Update issue templates --- .github/ISSUE_TEMPLATE/bug-report.md | 42 ---------------------------- 1 file changed, 42 deletions(-) delete mode 100644 .github/ISSUE_TEMPLATE/bug-report.md diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-report.md deleted file mode 100644 index d978275e..00000000 --- a/.github/ISSUE_TEMPLATE/bug-report.md +++ /dev/null @@ -1,42 +0,0 @@ ---- -name: Bug Report -about: Create a bug report to help us improve ArchR. NOT to be used for questions - or feature requests! -title: '' -labels: bug -assignees: '' - ---- - -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()) - -If your issue persists, then please submit this bug report. - -PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE. - -**Attach your log file** -ArchR has a built-in logging functionality for all complex functions. You MUST attach your log file (indicated in the console output) to this issue. Just drag and drop it here. - -**Describe the bug** -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. 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. 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. - -**Additional context** -Add any other context about the problem here. From 52e7011e26703aad4d9f62d12a7a79492980c09f Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Fri, 23 Jul 2021 08:49:11 -0700 Subject: [PATCH 05/19] Update issue templates --- ...s---feature-requests--use-discussions--.md | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md diff --git a/.github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md b/.github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md new file mode 100644 index 00000000..dfa6fd79 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md @@ -0,0 +1,42 @@ +--- +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: '' + +--- + +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()) + +If your issue persists, then please submit this bug report. + +PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE. + +**Attach your log file** +ArchR has a built-in logging functionality for all complex functions. You MUST attach your log file (indicated in the console output) to this issue. Just drag and drop it here. + +**Describe the bug** +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. 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. 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. + +**Additional context** +Add any other context about the problem here. From 2be1294eb1fbff364fb538d71f4f545ee4384d09 Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Fri, 23 Jul 2021 08:49:35 -0700 Subject: [PATCH 06/19] Update issue templates --- ...s---feature-requests--use-discussions--.md | 42 ------------------- 1 file changed, 42 deletions(-) delete mode 100644 .github/ISSUE_TEMPLATE/bug-report---no-questions---feature-requests--use-discussions--.md diff --git a/.github/ISSUE_TEMPLATE/bug-report---no-questions---feature-requests--use-discussions--.md b/.github/ISSUE_TEMPLATE/bug-report---no-questions---feature-requests--use-discussions--.md deleted file mode 100644 index e89438b4..00000000 --- a/.github/ISSUE_TEMPLATE/bug-report---no-questions---feature-requests--use-discussions--.md +++ /dev/null @@ -1,42 +0,0 @@ ---- -name: Bug Report - NO QUESTIONS / FEATURE REQUESTS (Use Discussions!) -about: Create a bug report to help us improve ArchR. NOT to be used for questions - or feature requests! -title: '' -labels: bug -assignees: '' - ---- - -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()) - -If your issue persists, then please submit this bug report. - -PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE. - -**Attach your log file** -ArchR has a built-in logging functionality for all complex functions. You MUST attach your log file (indicated in the console output) to this issue. Just drag and drop it here. - -**Describe the bug** -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. 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. 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. - -**Additional context** -Add any other context about the problem here. From 6765ad962d4d8dcb292a326071c9b5c30c25918e Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Mon, 11 Oct 2021 12:40:21 -0700 Subject: [PATCH 07/19] Create config.yml --- .github/ISSUE_TEMPLATE/config.yml | 1 + 1 file changed, 1 insertion(+) create mode 100644 .github/ISSUE_TEMPLATE/config.yml 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 From 75544172bc1962fd0050bb190450ee826ce1aba0 Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Mon, 1 Nov 2021 21:24:43 -0700 Subject: [PATCH 08/19] fix logic of if statement after partial matrix sampling in response to https://github.com/GreenleafLab/ArchR/issues/1130 --- R/ArrowRead.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/ArrowRead.R b/R/ArrowRead.R index 20bbdb6c..d1124772 100644 --- a/R/ArrowRead.R +++ b/R/ArrowRead.R @@ -783,10 +783,10 @@ getMatrixFromArrow <- function( matFiles <- lapply(mat, function(x) x[[2]]) %>% Reduce("c", .) mat <- lapply(mat, function(x) x[[1]]) %>% Reduce("cbind", .) - if(!all(cellNames %in% colnames(mat))){ + if(!all(colnames(mat) %in% cellNames)){ .logThis(sampledCellNames, "cellNames supplied", logFile = logFile) .logThis(colnames(mat), "cellNames from matrix", logFile = logFile) - stop("Error not all cellNames found in partialMatrix") + stop("Error - some colnames in partialMatrix do not match cellNames") } mat <- mat[,sampledCellNames, drop = FALSE] mat <- .checkSparseMatrix(mat, length(sampledCellNames)) From 422f0ffcfebfd061e38665efddaa4844d1fa0a82 Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Mon, 1 Nov 2021 21:35:28 -0700 Subject: [PATCH 09/19] revert changes mistakenly made to master --- R/ArrowRead.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/ArrowRead.R b/R/ArrowRead.R index d1124772..20bbdb6c 100644 --- a/R/ArrowRead.R +++ b/R/ArrowRead.R @@ -783,10 +783,10 @@ getMatrixFromArrow <- function( matFiles <- lapply(mat, function(x) x[[2]]) %>% Reduce("c", .) mat <- lapply(mat, function(x) x[[1]]) %>% Reduce("cbind", .) - if(!all(colnames(mat) %in% cellNames)){ + if(!all(cellNames %in% colnames(mat))){ .logThis(sampledCellNames, "cellNames supplied", logFile = logFile) .logThis(colnames(mat), "cellNames from matrix", logFile = logFile) - stop("Error - some colnames in partialMatrix do not match cellNames") + stop("Error not all cellNames found in partialMatrix") } mat <- mat[,sampledCellNames, drop = FALSE] mat <- .checkSparseMatrix(mat, length(sampledCellNames)) From 939dd9ec39caf349e59cd7a17151795cfa5578f3 Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Wed, 1 Dec 2021 16:20:08 -0800 Subject: [PATCH 10/19] Create label-actions.yml --- .github/label-actions.yml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 .github/label-actions.yml diff --git a/.github/label-actions.yml b/.github/label-actions.yml new file mode 100644 index 00000000..543023f6 --- /dev/null +++ b/.github/label-actions.yml @@ -0,0 +1,20 @@ +# Configuration for Label Actions - https://github.com/dessant/label-actions + +# When the `bug` label is added to issues +bug: + issues: + # Post a comment + comment: > + Thanks for using ArchR! Please make sure that your post belongs in the Issues section! This is where bugs and error reports belong.
+ 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.__ Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example.
+ __2.__ If you've encountered an error, have you already searched the full manual and previous Issues to make sure that this hasn't already been solved?
+ __3.__ Did you post your log file? If not, add it now.
+ +# When the `new_discussion` label is added to discussions +#new_discussion: +# discussions: +# # Post a comment +# comment: > +# Thanks for using ArchR! This is a discussion post From 442a6a2960966b572ee2f4ad93fc68b98032500b Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Wed, 1 Dec 2021 16:21:59 -0800 Subject: [PATCH 11/19] Delete label-actions.yml --- .github/label-actions.yml | 20 -------------------- 1 file changed, 20 deletions(-) delete mode 100644 .github/label-actions.yml diff --git a/.github/label-actions.yml b/.github/label-actions.yml deleted file mode 100644 index 543023f6..00000000 --- a/.github/label-actions.yml +++ /dev/null @@ -1,20 +0,0 @@ -# Configuration for Label Actions - https://github.com/dessant/label-actions - -# When the `bug` label is added to issues -bug: - issues: - # Post a comment - comment: > - Thanks for using ArchR! Please make sure that your post belongs in the Issues section! This is where bugs and error reports belong.
- 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.__ Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example.
- __2.__ If you've encountered an error, have you already searched the full manual and previous Issues to make sure that this hasn't already been solved?
- __3.__ Did you post your log file? If not, add it now.
- -# When the `new_discussion` label is added to discussions -#new_discussion: -# discussions: -# # Post a comment -# comment: > -# Thanks for using ArchR! This is a discussion post From 99a094381434d2b3d72f45d8309363cb7eb5f395 Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Thu, 2 Dec 2021 10:56:12 -0800 Subject: [PATCH 12/19] Delete auto-comment.yml --- .github/auto-comment.yml | 6 ------ 1 file changed, 6 deletions(-) delete mode 100644 .github/auto-comment.yml 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. - From 5a09694112345f5b4e65126f90e40316fb63ffcb Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Thu, 2 Dec 2021 11:33:56 -0800 Subject: [PATCH 13/19] Create auto-comment.yml --- .github/workflows/auto-comment.yml | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 .github/workflows/auto-comment.yml diff --git a/.github/workflows/auto-comment.yml b/.github/workflows/auto-comment.yml new file mode 100644 index 00000000..1853bb0d --- /dev/null +++ b/.github/workflows/auto-comment.yml @@ -0,0 +1,24 @@ +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. + +# 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. From 92ab814f86be0cea75c661f9827a9549c2cf47f5 Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Sat, 4 Dec 2021 10:21:51 -0800 Subject: [PATCH 14/19] Update auto-comment.yml --- .github/workflows/auto-comment.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/auto-comment.yml b/.github/workflows/auto-comment.yml index 1853bb0d..4337e0ac 100644 --- a/.github/workflows/auto-comment.yml +++ b/.github/workflows/auto-comment.yml @@ -7,18 +7,18 @@ jobs: - 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. - # 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: +# 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. + + 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. From 2ec4b9a7eb218c2d89f760e0112b1a559d8fada5 Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Fri, 28 Jan 2022 11:28:00 -0800 Subject: [PATCH 15/19] Update auto-comment.yml --- .github/workflows/auto-comment.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/auto-comment.yml b/.github/workflows/auto-comment.yml index 4337e0ac..1853bb0d 100644 --- a/.github/workflows/auto-comment.yml +++ b/.github/workflows/auto-comment.yml @@ -7,18 +7,18 @@ jobs: - 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. - 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: + 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. + +# 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. From 041882c7d123ab6288aa37fa33fa6add54ca833e Mon Sep 17 00:00:00 2001 From: Ryan Corces Date: Mon, 4 Apr 2022 08:37:47 -0700 Subject: [PATCH 16/19] ask users to not paste screenshots --- .github/workflows/auto-comment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/auto-comment.yml b/.github/workflows/auto-comment.yml index 1853bb0d..3ae4ec02 100644 --- a/.github/workflows/auto-comment.yml +++ b/.github/workflows/auto-comment.yml @@ -13,6 +13,7 @@ jobs: __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.
From 717956cc23ad1c5ce1724b6c319e590ac98b2b82 Mon Sep 17 00:00:00 2001 From: BaDoi Phan Date: Sat, 25 Jun 2022 13:36:38 -0400 Subject: [PATCH 17/19] save macs2 fold enrichment signal value in summits --- R/ReproduciblePeakSet.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/ReproduciblePeakSet.R b/R/ReproduciblePeakSet.R index 8699e748..17ce9790 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$V5) + out <- data.table::fread(summitsFile, select = c(1,2,3,5,7)) + out <- GRanges(out$V1, IRanges(out$V2 + 1, out$V3), score = out$V5, signalValue = out$V7) #Remove Files r2 <- suppressWarnings(file.remove(summitsFile, narrowPeaksFile, xlsFile)) From 783898ba5b11759fc63f39af56fd797e8a975a2e Mon Sep 17 00:00:00 2001 From: BaDoi Phan Date: Sat, 25 Jun 2022 16:53:49 -0400 Subject: [PATCH 18/19] summits bed file doesn't have signalValue change which file to read, grab from narrowPeak file and get equivalent columns of what otherwise would be the summits file, Summits score is 1/10th of narrowPeak score, based on macs2 documentation. To get summits from narrowPeak, add the summit offset in column 10 to the start and end coordinates. --- R/ReproduciblePeakSet.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/ReproduciblePeakSet.R b/R/ReproduciblePeakSet.R index 17ce9790..c9f8e946 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(1,2,3,5,7)) - out <- GRanges(out$V1, IRanges(out$V2 + 1, out$V3), score = out$V5, signalValue = out$V7) + out <- data.table::fread(narrowPeaksFile, select = c(1,2,3,5,7,10)) + out <- GRanges(out$V1, IRanges(out$V2 + out$V10 + 1, out$V3 + out$V10), score = out$V5/10, signalValue = out$V7) #Remove Files r2 <- suppressWarnings(file.remove(summitsFile, narrowPeaksFile, xlsFile)) From 652dc4ba5d0c11ac73656ffe86dee16166c1f887 Mon Sep 17 00:00:00 2001 From: BaDoi Phan Date: Sun, 26 Jun 2022 17:24:32 -0400 Subject: [PATCH 19/19] summits from narrow peak doesn't need end --- R/ReproduciblePeakSet.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/ReproduciblePeakSet.R b/R/ReproduciblePeakSet.R index c9f8e946..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(narrowPeaksFile, select = c(1,2,3,5,7,10)) - out <- GRanges(out$V1, IRanges(out$V2 + out$V10 + 1, out$V3 + out$V10), score = out$V5/10, signalValue = out$V7) + out <- data.table::fread(narrowPeaksFile, select = c(1,2,5,7,10)) + out <- GRanges(out$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))