Merge pull request #20 from umccr/conda_setup

Conda setup

.bumpversion.cfg

@@ -5,3 +5,15 @@ commit = True
 [bumpversion:file:DESCRIPTION]
 search = Version: {current_version}
 replace = Version: {new_version}
+
+[bumpversion:file:.github/workflows/conda-deploy.yaml]
+search = VERSION: '{current_version}'
+replace = VERSION: '{new_version}'
+
+[bumpversion:file:conda/env/yaml/rportal.yaml]
+search = r-rportal =={current_version}
+replace = r-rportal =={new_version}
+
+[bumpversion:file:conda/recipe/meta.yaml]
+search = version: {current_version}
+replace = version: {new_version}

.github/workflows/conda-deploy.yaml

@@ -0,0 +1,97 @@
+name: conda-docker-docs
+
+on:
+  push:
+    branches:
+      - main
+env:
+  atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
+  recipe_path: conda/recipe
+  env_yaml_path: conda/env/yaml
+  env_lock_path: conda/env/lock
+  VERSION: '0.1.1' # versioned by bump2version
+
+jobs:
+  condarise:
+    # When merging to main and the commit message starts with 'Bump version:'
+    if: "startsWith(github.event.head_commit.message, 'Bump version:')"
+    name: Condarise
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Code checkout
+        uses: actions/checkout@v4
+      - name: Micromamba setup
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ${{ env.env_yaml_path }}/condabuild.yaml
+      - name: 🐍 Conda pkg build and upload
+        run: |
+          conda mambabuild --R 4.3.3 ${recipe_path} -c conda-forge --token ${atoken}
+      - name: 🔒 Conda lock
+        run: |
+          conda-lock lock --file ${env_yaml_path}/rportal.yaml -p linux-64
+          conda-lock render --kind explicit -p linux-64 conda-lock.yml --filename-template 'rportal-{platform}.lock' && rm conda-lock.yml
+          mv rportal-*.lock ${env_lock_path}/
+      - name: 💾 Commit lockfile
+        run: |
+          git status
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          MSG="[bot] Updating conda-lock file (v${VERSION})"
+          git add .
+          git commit -m "${MSG}"
+          git push
+
+      - name: 📥 Pull lock commit
+        id: pull_lock_commit
+        run: |
+          git pull --no-rebase
+          git --no-pager log --decorate=short --pretty=oneline -n3
+          LATEST_COMMIT_HASH="$(git --no-pager log -1 --format='%H')"
+          echo "latest_commit_hash=${LATEST_COMMIT_HASH}" >> $GITHUB_OUTPUT
+      - name: 🔖 Create tag
+        uses: actions/github-script@v7
+        env:
+          LATEST_COMMIT_HASH: ${{ steps.pull_lock_commit.outputs.latest_commit_hash }}
+        with:
+          script: |
+            const the_tag_name = 'refs/tags/v' + process.env.VERSION
+            const the_sha = process.env.LATEST_COMMIT_HASH
+            github.rest.git.createRef({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              ref: the_tag_name,
+              sha: the_sha
+            })
+
+      # work with tag from above
+      - name: Code checkout
+        uses: actions/checkout@v4
+        with:
+          ref: v${{ env.VERSION }}
+      - name: 🏰 QEMU setup
+        uses: docker/setup-qemu-action@v3
+      - name: 🏯 Buildx setup
+        uses: docker/setup-buildx-action@v3
+        with:
+          install: true
+          config-inline: |
+            [worker.oci]
+              max-parallelism = 2
+      - name: 🐙 GitHub CR login
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: 🐳 Docker img build and push
+        uses: docker/build-push-action@v6
+        with:
+          tags: ghcr.io/${{ github.repository }}:${{ env.VERSION }}
+          context: .
+          push: true
+          platforms: linux/amd64

conda/env/lock/README.md

@@ -0,0 +1 @@
+For `conda-lock` see <https://github.com/conda-incubator/conda-lock>

conda/env/yaml/condabuild.yaml

@@ -0,0 +1,10 @@
+name: cbuildenv
+
+channels:
+  - conda-forge
+dependencies:
+  - conda-build
+  - conda-lock
+  - conda-verify
+  - anaconda-client
+  - boa

conda/env/yaml/rportal.yaml

@@ -0,0 +1,9 @@
+name: rportal
+
+channels:
+  - umccr
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - r-rportal ==0.1.1 # versioned by bump2version

conda/recipe/build.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+export DISABLE_AUTOBREW=1
+${R} CMD INSTALL --build . ${R_ARGS}
+
+# Copy CLI to conda bin
+mkdir -p ${PREFIX}/bin
+cp ${SRC_DIR}/inst/scripts/datashare/datashare.R ${PREFIX}/bin
+chmod +x ${PREFIX}/bin/datashare.R

conda/recipe/meta.yaml

@@ -0,0 +1,67 @@
+package:
+  name: r-rportal
+  version: 0.1.1 # bump2version
+
+source:
+  path: ../..
+
+build:
+  number: 0
+  noarch: generic
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+    - git
+  host:
+    - python
+    - boto3
+    - r-base
+    - r-assertthat
+    - r-cli
+    - r-dbi
+    - r-dplyr
+    - umccr::r-dracarys
+    - r-fs
+    - r-glue
+    - r-jsonlite
+    - r-optparse
+    - r-purrr
+    - r-rathena
+    - r-readr
+    - r-rlang
+    - r-tibble
+    - r-tidyr
+
+  run:
+    - python
+    - boto3
+    - r-base
+    - r-assertthat
+    - r-cli
+    - r-dbi
+    - r-dplyr
+    - umccr::r-dracarys
+    - r-fs
+    - r-glue
+    - r-jsonlite
+    - r-optparse
+    - r-purrr
+    - r-rathena
+    - r-readr
+    - r-rlang
+    - r-tibble
+    - r-tidyr
+
+test:
+  commands:
+    - $R -e "library('rportal')"
+    - datashare.R --version
+    - python -c "import boto3"
+
+about:
+  home: https://github.com/umccr/rportal
+  license: MIT
+  summary: UMCCR data portal R functionality