Dev

.Rbuildignore

@@ -5,16 +5,15 @@
 ^CRAN-SUBMISSION$
 ^cran-comments\.md$
 ^inst/extdata/testing
-^TODO.md$
 ^.*\.DS_Store$
 .DS_Store
 .venv_altdoc
 ^docs$
 ^altdoc$
 ^_pkgdown\.yml$
 ^pkgdown$
-(^|/)wip-.*$
 ^.venv_altdoc$
 ^edit-bench$
 ^immdata-test$
 ^immundata-quick-start$
+^dev$

.github/ISSUE_TEMPLATE/2-enhancement.yml

@@ -3,17 +3,6 @@ description: "Propose a new feature or an improvement."
 labels:
 - enhancement
 body:
-- type: dropdown
-  id: kind
-  attributes:
-    label: What kind of feature would you like to request?
-    options:
-    - 'New data processing, filtering, wrangling methods you are missing'
-    - 'Request enhancement to input/output - format processing, reading data, writing data to the disk'
-    - 'Improve existing functions, e.g., add additional function parameters, change how a function works, change default values'
-    - 'Other - please describe it in the ticket body'
-  validations:
-    required: true
 - type: textarea
   id: description
   attributes:

.github/ISSUE_TEMPLATE/3-documentation.yml

@@ -3,19 +3,10 @@ description: "Propose a tutorial for a specific use case or new documentation."
 labels:
 - documentation
 body:
-- type: dropdown
-  id: kind
-  attributes:
-    label: What kind of documentation would you like to request?
-    options:
-    - 'New tutorial for a specific use case'
-    - 'Improved documentation or error message'
-    - 'Other - please describe it in the ticket body'
-  validations:
-    required: true
 - type: textarea
   id: description
   attributes:
-    label: Please describe your idea or what you want to achieve
+    label: What type of documentation would you like to see on the website?
+    description: Interested in a tutorial? More details on how a specific method works? More examples? Something else entirely?
   validations:
     required: true

.github/ISSUE_TEMPLATE/4-question.yml

@@ -6,7 +6,7 @@ body:
 - type: textarea
   id: description
   attributes:
-    label: Question
-    description: Describe what you want to know.
+    label: Your question
+    description: Describe what you want to know. E.g., how to analyse a specific data, how to do X, when a method will be available, etc.
   validations:
     required: true

.github/workflows/altdoc-dev.yaml

@@ -0,0 +1,66 @@
+name: Build development documentation
+
+on:
+  push:
+    branches: [dev]
+  workflow_dispatch:
+
+concurrency:
+  group: altdoc-pages
+  cancel-in-progress: false
+
+permissions: read-all
+
+jobs:
+  altdoc-dev:
+    if: github.ref == 'refs/heads/dev'
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: quarto-dev/quarto-actions/setup@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+          cache-dependency-path: altdoc/requirements.txt
+
+      - name: Install MkDocs
+        run: |
+          python -m venv .venv_altdoc
+          .venv_altdoc/bin/python -m pip install --requirement altdoc/requirements.txt
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: local::.
+          needs: website
+
+      - name: Configure development preview
+        run: |
+          sed -i 's#https://immunomind.github.io/immundata/#https://immunomind.github.io/immundata/dev/#g' altdoc/mkdocs.yml altdoc/pkgdown.yml README.md
+          sed -i 's/^site_name: immundata$/site_name: immundata dev/' altdoc/mkdocs.yml
+
+      - name: Build site
+        run: altdoc::render_docs(freeze = FALSE, parallel = FALSE, verbose = TRUE)
+        shell: Rscript {0}
+
+      - name: Deploy development preview
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          clean: true
+          branch: gh-pages
+          folder: docs
+          target-folder: dev

.github/workflows/altdoc.yaml

@@ -0,0 +1,68 @@
+name: Build documentation
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.event_name == 'pull_request' && format('altdoc-pr-{0}', github.event.pull_request.number) || 'altdoc-pages' }}
+  cancel-in-progress: false
+
+permissions: read-all
+
+jobs:
+  altdoc:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: quarto-dev/quarto-actions/setup@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+          cache-dependency-path: altdoc/requirements.txt
+
+      - name: Install MkDocs
+        run: |
+          python -m venv .venv_altdoc
+          .venv_altdoc/bin/python -m pip install --requirement altdoc/requirements.txt
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: local::.
+          needs: website
+
+      - name: Build site
+        run: altdoc::render_docs(freeze = FALSE, parallel = FALSE, verbose = TRUE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub Pages
+        if: >-
+          github.event_name != 'pull_request' &&
+          (github.ref == 'refs/heads/main' ||
+          github.ref == 'refs/heads/master' ||
+          startsWith(github.ref, 'refs/tags/'))
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          clean: true
+          clean-exclude: dev
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -15,3 +15,5 @@ immdata-test
 altdoc/freeze.rds
 docs
 wip-*
+annotations.parquet
+metadata.json

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: immundata
 Title: A Unified Data Layer for Large-Scale Single-Cell, Spatial and Bulk Immunomics
-Version: 0.0.5
+Version: 0.1.0
 Authors@R: 
     person("Vadim I.", "Nazarov", , "support@immunomind.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3659-2709"))
@@ -14,18 +14,16 @@ URL: https://immunomind.github.io/docs/, https://github.com/immunomind/immundata
 BugReports: https://github.com/immunomind/immundata/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 Depends: 
     R (>= 4.1.0),
-    dplyr,
-    duckplyr (>= 1.1.0)
+    dplyr (>= 1.2.1),
+    duckplyr (>= 1.2.1)
 Imports:
     checkmate,
     cli,
     dbplyr,
-    ggplot2,
     glue,
-    jsonlite (>= 2.0.0),
+    jsonlite,
     lifecycle,
     R6,
     readr,
@@ -34,8 +32,11 @@ Imports:
     tools,
     utils
 Suggests: 
+    duckdb,
     rmarkdown,
     testthat (>= 3.0.0),
     Seurat
+Config/Needs/website: altdoc
 Config/testthat/edition: 3
 Config/testthat/parallel: true
+Config/roxygen2/version: 8.1.0