Merge branch 'main' into sjspielman/12-clone

.github/DISCUSSION_TEMPLATE/troubleshooting.yml

@@ -0,0 +1,32 @@
+body:
+- type: textarea
+  attributes:
+    label: Summary
+    description: What problem or error do you need help with?
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Code or step
+    description: What code or step did you try?
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Desired outcome
+    description: What was the desired outcome?
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Observed outcome or error message
+    description: What was the observed outcome and/or error message? Include screenshots as needed. 
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Example
+    description: Please provide any example code or links that will help reproduce the problem. For example, link the code in your branch that caused the error. 
+  validations:
+    required: true
+

.github/components/dictionary.txt

@@ -0,0 +1,37 @@
+ableist
+ALSF
+bioinformatics
+Carpentries
+conda
+config
+DM
+doxxing
+formatters
+GitHub
+GitKraken
+JSON
+LGBTQ
+LinkedIn
+linter
+linter's
+linters
+LSfR
+macOS
+Miniconda
+nonconsensual
+OpenScPCA
+openscpca
+pre
+precommit
+README
+renv
+reproducibility
+ScPCA
+socio
+Stumptown
+trainings
+transphobic
+triaged
+WisCon
+WSL
+

.github/cron-issue-templates/spellcheck-issue-template.md

@@ -0,0 +1,11 @@
+This issue tracks the results from running the scheduled spellcheck workflow.
+This issue is filed whether there are errors or not.
+Please see the issue comment for specific errors.
+
+If there are no errors, this issue can be closed.
+
+## Issue checklist
+
+- [ ] Assign an OpenScPCA admin
+- [ ] Spell check errors have been fixed via a PR
+- [ ] Spell check workflow has been manually run to confirm spelling errors are fixed

.github/workflows/spellcheck.yml

@@ -0,0 +1,89 @@
+name: Check Spelling
+on:
+  pull_request: # TEMPORARY
+    branches:
+     - main
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 * * 1" # every Monday at midnight
+
+# From https://medium.com/@VeselyCodes/bi-weekly-github-actions-7bea6be7bd96
+env:
+  # The date of the first run of the action.
+  FIRST_RUN_DATE: 2024-03-25
+
+concurrency:
+  # only one run per branch at a time
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  weekindex:
+    if: ${{ github.event_name == 'schedule' }}
+    runs-on: ubuntu-latest
+    outputs:
+      weekindex: ${{ steps.calculate.outputs.weekindex }}
+    steps:
+      - name: Calculate weekdiff
+        id: calculate
+        run: |
+          current_date=$(date +%Y-%m-%d)
+          start=$(date -d ${{ env.FIRST_RUN_DATE }} +%s)
+          end=$(date -d $current_date +%s)
+          weekdiff=$(((end-start) / 60 / 60 / 24 / 7))
+          weekindex=$((weekdiff % 4))  ##################### We want to run every 4 weeks!
+          echo "weekindex=$weekindex" >> "$GITHUB_OUTPUT"
+
+  spellcheck:
+    if: ${{ needs.weekindex.outputs.weekindex == 0 || github.event_name != 'schedule' }}
+    runs-on: ubuntu-latest
+    name: Spell check files
+    permissions:
+      contents: read
+      issues: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Spell check action
+        uses: alexslemonade/spellcheck@v0
+        id: spell
+        with:
+          dictionary: .github/components/dictionary.txt
+
+      - name: Upload spell check errors
+        uses: actions/upload-artifact@v4
+        id: artifact-upload-step
+        with:
+          name: spell_check_errors
+          path: spell_check_errors.tsv
+
+#      # Uncomment this job at OpenScPCA Launch
+#      - name: Post issue with spellcheck results
+#        id: spellissue
+#        uses: peter-evans/create-issue-from-file@v5
+#        with:
+#          title: Monthly spellcheck results
+#          content-filepath: .github/cron-issue-templates/spellcheck-issue-template.md
+#          labels: |
+#            OpenScPCA admin
+#            spelling
+#
+#      # Uncomment this job at OpenScPCA Launch
+#      - name: Comment artifact on issue
+#        uses: peter-evans/create-or-update-comment@v4
+#        with:
+#          issue-number: ${{ steps.spellissue.outputs.issue-number }}
+#          body: |
+#            The spellchecker found **${{ steps.spell.outputs.error_count }} errors**.
+#
+#            [Click to download the spelling errors TSV.](${{ steps.artifact-upload-step.outputs.artifact-url }})
+
+
+      - name: Fail if there are spelling errors
+        if: steps.spell.outputs.error_count > 0
+        run: |
+          echo "There were ${{ steps.spell.outputs.error_count }} errors"
+          column -t spell_check_errors.tsv
+          exit 1

README.md

@@ -1 +1,2 @@
-# OpenScPCA-analysis
+# OpenScPCA-analysis
+

docs/contributing.md

@@ -26,11 +26,11 @@ To serve the documentation during local development, run `mkdocs serve` from the
 
 Documentation is written as a series of markdown files nested by topic in directories.
 
-- All directories at the top-level inside `docs` will represent navbar sections.
+- All directories at the top-level inside `docs` will represent `navbar` sections.
   - Each top-level directory should contain an `index.md` file with an overall description of what that section contains.
-  - The `index.md` should have an L1 header with the same title as the navbar section.
+  - The `index.md` should have an L1 header with the same title as the `navbar` section.
   - Markdown files in each directory represent sections shown along the left sidebar.
-- Nested directories within each navbar section should be used to add an additional bold (gray) header on the left sidebar.
+- Nested directories within each `navbar` section should be used to add an additional bold (gray) header on the left sidebar.
   - Markdown files within each nested directory will fall under this additional bold (gray) header.
 - Any visual aids used in the docs should be placed in `docs/img`.
 

docs/general-style-guide.md

@@ -53,7 +53,7 @@ Use it for describing:
 
 ## Using buttons
 
-Use [Github buttons](https://gist.github.com/apaskulin/1ad686e42c7165cb9c22f9fe1e389558#buttons) to draw attention to important links.
+Use [GitHub buttons](https://gist.github.com/apaskulin/1ad686e42c7165cb9c22f9fe1e389558#buttons) to draw attention to important links.
 Use buttons sparingly.
 
 Use the buttons for links critical for users to continue on to the next stage like:

docs/technical-setup/install-a-github-client.md

@@ -41,7 +41,7 @@ After installing Git, you will also need take these steps:
 - [Set up an SSH key](https://docs.github.com/en/authentication/connecting-to-github-with-ssh) to interact with `GitHub`
 - [Set up your Git config file](https://git-scm.com/book/en/v2/Getting-Started-First-Time-Git-Setup)
 
-### Install Git on MacOS
+### Install Git on macOS
 
 We recommend installing Git via Apple's developer command line tools.
 For this, launch a Terminal window, enter the command shown below, and follow the instructions.