Update tutorials (#5)

.github/workflows/publish.yml → .github/workflows/publish_both.yml

@@ -1,10 +1,7 @@
 name: Quarto Publish
 
 on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
+  workflow_dispatch:
 
 jobs:
   build-deploy:
@@ -19,11 +16,15 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v4
 
-      - name: Install rsync
+      - name: Install rsync and upgrade
         run: |
-          sudo apt-get update
+          sudo apt-get -y update
           sudo apt-get install -y rsync
 
+      # - name: Install alternatives for Python
+      #   run: |
+      #     sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 100
+
       # - name: Install curl
       #   run: |
       #     sudo apt-get install libcurl4-openssl-dev
@@ -43,13 +44,20 @@ jobs:
         run: quarto install tinytex
 
       # - name: Setup Python
-      #   uses: actions/setup-python@v4
+      #   uses: actions/setup-python@v5
       #   with:
-      #     python-version: '3.9'
+      #     python-version: '3.10'
       #     cache: 'pip'
 
+      - name: Test python version
+        run: |
+          python3 --version
+
       - name: Install Python dependencies
-        run: pip install -r requirements.txt
+        run: pip3 install -r requirements.txt
+
+      - name: install geniml
+        run: pip3 install geniml
 
       # - name: Setup R
       #   uses: r-lib/actions/setup-r@v2

.github/workflows/publish_python.yml

@@ -0,0 +1,57 @@
+name: Quarto Publish
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          tinytex: true
+
+      - name: Install Python and Dependencies
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+      - run: pip install -r requirements.txt
+
+      # build SQLite from source, because I need 3.35<=
+      - name: Download SQLite3
+        run: |
+          wget https://www.sqlite.org/2024/sqlite-autoconf-3450300.tar.gz
+          tar -xvf sqlite-autoconf-3450300.tar.gz
+
+      - name: Install SQLite3
+        run: |
+          cd sqlite-autoconf-3450300
+          ./configure
+          make
+          sudo make install
+          export PATH="/usr/local/lib:$PATH"
+          cd ..
+
+      - name: Render
+        uses: quarto-dev/quarto-actions/render@v2
+        with:
+          to: html
+        env:
+          LD_LIBRARY_PATH: /usr/local/lib
+
+      - name: Publish to GH Pages
+        if: github.ref == 'refs/heads/master'
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages # The branch the action should deploy to.
+          render: false

.gitignore

@@ -8,4 +8,5 @@ chapters/zilinois_lung_with_celltypist/
 *whee.h5
 *.tiledb
 *_cache
-*_files
+*_files
+tutorials/cache/*``

README.md

@@ -1,13 +1,23 @@
-## BiocPy tutorial
+## Bioc 2024 workshop tutorial
 
 This is a reproducible Quarto book with reusable snippets. If you're new to Quarto books, you can explore more about them [here](https://quarto.org/docs/books). 
 
 ## Setting Up the Tutorial Locally
 
 To get started locally, follow these steps:
 
-- Install quarto-cli.
-- Install the necessary packages listed in requirements.txt.
+- Install [quarto-cli](https://quarto.org/docs/get-started/).
+- Install the necessary packages listed in [requirements.txt](./requirements.txt) and [rpackages.R](rpackages.R).
+
+```shell
+pip install -r requirements.txt
+Rscript rpackages.R
+```
+
 - Run quarto preview to view the HTML version of the site.
 
+```shell
+qurto preview
+```
+
 Take advantage of GitHub actions, which are available to automatically publish the tutorial book whenever changes are made on the **master** branch.

_quarto.yml

@@ -14,8 +14,9 @@ website:
       - index.qmd
       - section: "Tutorials"
         contents:
+          - tutorials/genomic_ranges.qmd
           - tutorials/annotate_cell_types.qmd
-          - tutorials/sessioninfo
+      - tutorials/sessioninfo.qmd
 
   # navbar:
   #   left:

index.qmd

@@ -1,13 +1,13 @@
 # Welcome
 
 Welcome to our workshop on exploring the data structures and packages 
-available in [BiocPy](https://github.com/biocpy), a project that brings 
-the power of Bioconductor to Python. 
+available in [BiocPy](https://github.com/biocpy), a project that aims 
+to facilitate Bioconductor workflows in Python. 
 
 In this workshop, we will focus on interoperability between R and Python, covering two main topics:
 
 - Reading an RDS file containing `GenomicRanges` and performing downstream range-based analyses.
-- Annotating single-cell RNA-seq data analysis using the [scrnaseq](https://github.com/biocpy/scrnaseq) package.
+- Annotating single-cell RNA-seq data using the [scrnaseq](https://github.com/biocpy/scrnaseq) package.
 
 Attendees will learn how to represent and manipulate their datasets in Python 
 in the same manner as in R/Bioconductor. 
@@ -20,6 +20,8 @@ on [GitHub](https://github.com/BiocPy).
 - [Jayaram Kancherla](https://github.com/jkanche)
 - [Aaron Lun](https://github.com/LTLA)
 
+Always looking for more contributions from the community to improve our packages! Checkout the issues or discussion in our GitHub organization.
+
 ----
 
 ## Other resources
@@ -29,4 +31,4 @@ on [GitHub](https://github.com/BiocPy).
 
 ## Developer notes
 
-This is a reproducible Quarto book with reusable snippets. To learn more about Quarto books visit <https://quarto.org/docs/books>. Check out [Reproduce me](./chapters/sessioninfo.qmd) for more information.
+This is a reproducible Quarto book with reusable snippets. To learn more about Quarto books visit <https://quarto.org/docs/books>. Check out [Session Info](./chapters/sessioninfo.qmd) for more information.

requirements.txt

@@ -2,9 +2,9 @@ biocframe>=0.5.0
 summarizedexperiment>=0.4.3
 singlecellexperiment>=0.4.2
 multiassayexperiment>=0.4.2
-genomicranges
+genomicranges>=0.4.28
 biocutils>=0.1.5
-rds2py>=0.4.0
+rds2py>=0.4.3
 scranpy
 singler>=0.2.0
 numpy
@@ -20,4 +20,4 @@ celldex
 scrnaseq
 anndata
 matplotlib
-scanpy
+geniml

rpackages.R

@@ -1,3 +1,6 @@
 install.packages(c("BiocManager"), repos='http://cran.us.r-project.org')
 library(BiocManager)
-BiocManager::install(c("scRNAseq", "celldex", "SingleR", "scuttle", "reticulate", "rmarkdown", "knitr", "downlit", "xml2", "ggplot2", "edgeR"))
+BiocManager::install(
+    c("scRNAseq", "celldex", "SingleR", "scuttle", "reticulate", 
+    "rmarkdown", "knitr", "downlit", "xml2", "ggplot2", "edgeR", 
+    "AnnotationHub", "TxDb.Hsapiens.UCSC.hg38.refGene"))