Merge branch 'main' of github.com:openproblems-bio/openproblems into main

Author: scottgigante-immunai

.github/ISSUE_TEMPLATE/bug_report.md

@@ -8,12 +8,13 @@ assignees: ''
 ---
 
 - [ ] I have checked that this issue has not already been reported.
-- [ ] I have confirmed this bug exists on the master branch of openproblems.
+- [ ] I have confirmed this bug exists on the `main` branch of openproblems.
 
 ---
 
-**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) detailing how to provide the necessary information for us to reproduce your bug.
-
+**Note**: Please read [this
+guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) detailing
+how to provide the necessary information for us to reproduce your bug.
 
 ### Minimal code sample (that we can copy&paste without having any data)
 
@@ -29,6 +30,7 @@ assignees: ''
 
 <details>
 
-[Paste the output of scanpy.logging.print_versions() leaving a blank line after the details tag]
+<!-- Paste the output of scanpy.logging.print_versions() leaving a blank line after the
+details tag -->
 
 </details>

.github/ISSUE_TEMPLATE/propose-a-new-dataset.md

@@ -4,7 +4,6 @@ about: Suggest new data for one or more tasks
 title: ''
 labels: enhancement, dataset
 assignees: ''
-
 ---
 
 **What is the dataset?**
@@ -14,4 +13,5 @@ Describe it briefly and include a citation.
 Include a link to the publicly available data.
 
 **Which tasks could it be used for?**
-If the dataset is to be used for a task that is not yet included in the code base, use the issue template *propose a new task* instead.
+If the dataset is to be used for a task that is not yet included in the code base, use
+the issue template *propose a new task* instead.

.github/ISSUE_TEMPLATE/propose-a-new-method.md

@@ -14,4 +14,5 @@ Describe it briefly and include a citation.
 Include a link to the publicly available codebase.
 
 **Which task(s) could it be used for?**
-If the method is to be used for a task that is not yet included in the code base, use the issue template *propose a new task* instead.
+If the method is to be used for a task that is not yet included in the code base, use
+the issue template *propose a new task* instead.

.github/ISSUE_TEMPLATE/propose-a-new-metric.md

@@ -14,4 +14,5 @@ Describe it briefly and include a citation if applicable.
 Include a link to the publicly available codebase if available.
 
 **Which task(s) could it be used for?**
-If the method is to be used for a task that is not yet included in the code base, use the issue template *propose a new task* instead.
+If the method is to be used for a task that is not yet included in the code base, use
+the issue template *propose a new task* instead.

.github/ISSUE_TEMPLATE/propose-a-new-task.md

@@ -17,4 +17,5 @@ Include links to at least one publicly available dataset that could be used.
 Include links to codebases of at least two methods that perform the task.
 
 **Propose metrics**
-Describe at least one metric by which to measure success on the task. It must be able to be applied to the proposed datasets.
+Describe at least one metric by which to measure success on the task. It must be able to
+be applied to the proposed datasets.

.github/pull_request_template.md

@@ -13,13 +13,18 @@
 ### Testing
 
 * [ ] This submission was written on a forked copy of SingleCellOpenProblems
-* [ ] GitHub Actions "Run Benchmark" tests are passing on this base branch of this pull request (include link to passed test: )
-* [ ] If this pull request is not ready for review (including passing the "Run Benchmark" tests), I will open this PR as a draft (click on the down arrow next to the "Create Pull Request" button)
+* [ ] GitHub Actions "Run Benchmark" tests are passing on this base branch of this pull
+  request (include link to passed test: )
+* [ ] If this pull request is not ready for review (including passing the "Run
+  Benchmark" tests), I will open this PR as a draft (click on the down arrow next to the
+  "Create Pull Request" button)
 
 ### Submission guidelines
 
-* [ ] This submission follows the guidelines in our [Contributing](../blob/master/CONTRIBUTING.md) document
-* [ ] I have checked to ensure there aren't other open [Pull Requests](../pulls) for the same update/change
+* [ ] This submission follows the guidelines in our
+  [Contributing](../blob/master/CONTRIBUTING.md) document
+* [ ] I have checked to ensure there aren't other open [Pull Requests](../pulls) for the
+  same update/change
 
 ### PR review checklist
 
@@ -28,7 +33,9 @@ This PR will be evaluated on the basis of the following checks:
 * [ ] The task addresses a valid open problem in single-cell analysis
 * [ ] The latest version of master is merged and tested
 * [ ] The methods/metrics are imported to `__init__.py` and were tested in the pipeline
-* [ ] Method and metric decorators are annotated with paper title, year, author, code version, and date
+* [ ] Method and metric decorators are annotated with paper title, year, author, code
+  version, and date
 * [ ] The README gives an outline of the methods, metrics and datasets in the folder
 * [ ] The README provides a satisfactory task explanation (for new tasks)
-* [ ] The sample test data is appropriate to test implementation of all methods and metrics (for new tasks)
+* [ ] The sample test data is appropriate to test implementation of all methods and
+  metrics (for new tasks)

.pre-commit-config.yaml

@@ -34,3 +34,8 @@ repos:
     -   id: style-files
     -   id: lintr
         verbose: true
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.32.0
+    hooks:
+      - id: markdownlint-fix
+        exclude: (SAGEMAKER.md|.github/ISSUE_TEMPLATE/bug_report.md|.github/pull_request_template.md)

CODE_OF_CONDUCT.md

@@ -68,9 +68,9 @@ members of the project's leadership.
 ## Attribution
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
-available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+available at <https://www.contributor-covenant.org/version/1/4/code-of-conduct.html>
 
 [homepage]: https://www.contributor-covenant.org
 
 For answers to common questions about this code of conduct, see
-https://www.contributor-covenant.org/faq
+<https://www.contributor-covenant.org/faq>