Merge pull request #2 from bioconda/master

Updating repo to origin

.circleci/config.yml

@@ -300,21 +300,21 @@ workflows:
             branches:
               only:
                 - master
-  # workflow for bulk-updates
-  bioconda-upload-bulk-linux:
-    jobs:
-      - bulk-linux:
-          filters:
-            branches:
-              only:
-                - bulk
-  bioconda-upload-bulk-macos:
-    jobs:
-      - bulk-macos:
-          filters:
-            branches:
-              only:
-                - bulk
+  ## workflow for bulk-updates
+  #bioconda-upload-bulk-linux:
+  #  jobs:
+  #    - bulk-linux:
+  #        filters:
+  #          branches:
+  #            only:
+  #              - bulk
+  #bioconda-upload-bulk-macos:
+  #  jobs:
+  #    - bulk-macos:
+  #        filters:
+  #          branches:
+  #            only:
+  #              - bulk
   # nightly workflow to capture missed recipes
   bioconda-nightly-upload-linux:
      triggers:

.circleci/setup.sh

@@ -23,9 +23,21 @@ git fetch $UPSTREAM_REMOTE
 if ! git diff --quiet HEAD...$UPSTREAM_REMOTE/master -- .circleci/; then
     echo 'Your bioconda-recipes CI configuration is out of date.'
     echo 'Please update it to the latest version of the upstream master branch.'
-    echo 'You can do this, e.g., by running:'
+    echo ''
+    echo 'Have @BiocondaBot attempt to fix this by creating a comment on your PR:'
+    echo ''
+    echo '   @BiocondaBot update'
+    echo ''
+    echo 'Once the update commit has been created, update your local copy of'
+    echo 'your branch:'
+    echo ''
+    echo '  git pull'
+    echo ''
+    echo ''
+    echo 'You can also fix this manually, e.g., by running:'
     echo '  git fetch https://github.com/bioconda/bioconda-recipes.git master'
     echo '  git merge FETCH_HEAD'
+    echo ''
     exit 1
 fi
 git remote remove $UPSTREAM_REMOTE

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,7 +1,19 @@
-Bioconda requires reviews prior to merging pull-requests (PRs). To facilitate this, once your PR is passing tests and ready to be merged, please add the `please review & merge` label so other members of the bioconda community can have a look at your PR and either make suggestions or merge it. Note that if you are not already a member of the bioconda project (meaning that you can't add this label), please ping `@bioconda/core` so that your PR can be reviewed and merged (please note if you'd like to be added to the bioconda project). Please see https://github.com/bioconda/bioconda-recipes/issues/15332 for more details.
+Bioconda requires reviews prior to merging pull-requests (PRs). To facilitate this, once your PR is passing tests and ready to be merged, please add the `please review & merge` label so other members of the bioconda community can have a look at your PR and either make suggestions or merge it.
 
-* [ ] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/guidelines.html).
+* [ ] I have read the [guidelines for bioconda recipes](https://bioconda.github.io/contributor/guidelines.html).
 * [ ] This PR adds a new recipe.
 * [ ] AFAIK, this recipe **is directly relevant to the biological sciences** (otherwise, please submit to the more general purpose [conda-forge channel](https://conda-forge.org/docs/)).
 * [ ] This PR updates an existing recipe.
 * [ ] This PR does something else (explain below).
+
+Everyone has access to the following BiocondaBot commands, which can be given in a comment:
+
+ * `@BiocondaBot please update` will cause the BiocondaBot to merge the master branch into a PR
+ * `@BiocondaBot please add label` will add the `please review & merge` label.
+ * `@BiocondaBot please fetch artifacts` will post links to packages and docker containers built by the CI system. You can use this to test packages locally before merging.
+
+For members of the Bioconda project, the following command is also available:
+
+ * `@BiocondaBot please merge` will cause packages/containers to be uploaded and a PR merged. Someone must approve a PR first! This has the benefit of not wasting CI build time required by manually merging PRs.
+
+If you have questions, please post them in gitter or ping `@bioconda/core` in a comment (if you are not able to directly ping `@bioconda/core` then the bot will repost your comment and enable pinging).

.github/welcome_new_contributor.md

@@ -1,4 +1,4 @@
-Welcome to Bioconda, @{{user}}! Thank you for opening your first pull request! As you're new to Bioconda, please read through our [documentation about contributing recipes](https://bioconda.github.io/contributing.html). If you need help, please ping one of the following teams:
+Welcome to Bioconda, @{{user}}! Thank you for opening your first pull request! As you're new to Bioconda, please read through our [documentation about contributing recipes](https://bioconda.github.io/contributor/guidelines.html). If you need help, please ping one of the following teams:
 
  - `@bioconda/haskel` for Haskell packages
  - `@bioconda/lib` for C/C++ packages

.github/workflows/Bulk.yml

@@ -0,0 +1,102 @@
+name: Bulk branch
+on:
+  push:
+    branches:
+      - bulk
+jobs:
+  build-linux:
+    name: Bulk Linux Builds
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      max-parallel: 15
+      matrix:
+        runner: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14]
+    steps:
+    - uses: actions/checkout@v1
+
+    - name: Fetch common.sh
+      run: |
+        wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh
+
+    - name: Restore cache
+      id: cache
+      uses: actions/cache@v1
+      with:
+        path: /home/runner/miniconda
+        key: ${{ runner.os }}-BULK-${{ hashFiles('**/common.sh') }}
+
+    - name: Setup Bioconda-utils
+      if: steps.cache.outputs.cache-hit != 'true'
+      uses: bioconda/bioconda-actions/bioconda_recipes_setup/@bulk
+
+    - name: Build and upload
+      env:
+        ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
+        QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
+        # Mimic circleci
+        OSTYPE: "linux-gnu"
+        CI: "true"
+      run: |
+        export PATH=/home/runner/miniconda/envs/bioconda/bin:$PATH
+        bioconda-utils build recipes config.yml \
+          --worker-offset ${{ matrix.runner }} --n-workers 15 \
+          --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers
+        conda clean -y --all
+
+  build-osx:
+    name: Bulk OSX Builds
+    runs-on: macOS-latest
+    strategy:
+      fail-fast: false
+      max-parallel: 2
+      matrix:
+        runner: [0, 1]
+    steps:
+    - uses: actions/checkout@v1
+
+    - name: Fetch common.sh
+      run: |
+        wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh
+
+    - name: Restore cache
+      id: cache
+      uses: actions/cache@v1
+      with:
+        path: /Users/runner/miniconda
+        key: ${{ runner.os }}--BULK-${{ hashFiles('**/common.sh') }}
+
+    - name: Setup Bioconda-utils
+      if: steps.cache.outputs.cache-hit != 'true'
+      uses: bioconda/bioconda-actions/bioconda_recipes_setup/@bulk
+
+    - name: OSX stuff
+      run: |
+        # This is taken from conda-forge-ci-setup
+        export PATH=/Users/runner/miniconda/envs/bioconda/bin:/Users/runner/miniconda/condabin:$PATH
+        curl -L -O https://github.com/phracker/MacOSX-SDKs/releases/download/10.13/MacOSX10.9.sdk.tar.xz
+        tar -xf MacOSX10.9.sdk.tar.xz -C /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs
+        # set minimum sdk version to our target
+        plutil -replace MinimumSDKVersion -string 10.9 $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist
+        plutil -replace DTSDKName -string macosx10.9internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist
+        export CONDA_PREFIX="${CONDA_PREFIX:-$(conda info --json | jq -r .root_prefix)}"
+        export CONDA_BUILD_SYSROOT="/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk"
+        mkdir -p ${CONDA_PREFIX}/etc/conda/activate.d
+        echo "export CONDA_BUILD_SYSROOT=\"$CONDA_BUILD_SYSROOT\"" > "${CONDA_PREFIX}/etc/conda/activate.d/bioconda-ci-setup-activate.sh"
+        conda list
+
+    - name: Build and upload
+      env:
+        ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
+        QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
+        # Mimic circleci
+        OSTYPE: "darwin"
+        CI: "true"
+      run: |
+        export PATH=/Users/runner/miniconda/envs/bioconda/bin:$PATH
+        bioconda-utils build recipes config.yml \
+          --worker-offset ${{ matrix.runner }} --n-workers 2 \
+          --anaconda-upload
+        conda clean -y --all

.github/workflows/CommentResponder.yml

@@ -0,0 +1,24 @@
+name: CommentResponder
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  pr_comment:
+    runs-on: ubuntu-latest
+    name: PR comment responder
+    steps:
+    - name: Setup ssh
+      uses: webfactory/[email protected]
+      with:
+        ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
+    - name: Run comment action
+      env:
+        BOT_TOKEN: ${{ secrets.GITHUBTOKEN }}
+        ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
+        QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
+        GITTER_TOKEN: ${{ secrets.GITTER_TOKEN }}
+        CODE_SIGNING_KEY: ${{ secrets.CODE_SIGNING_KEY }}
+        JOB_CONTEXT: ${{ toJson(github) }}
+      uses: bioconda/bioconda-actions/bioconda_recipes_issue_responder/@issue_responder

.gitignore

@@ -20,3 +20,6 @@ cached_bioconductor_tarballs
 
 #People sometimes mistakenly upload their local copy of this file
 .circleci/common.sh
+
+#For people using: pyenv local
+.python-version

CONTRIBUTING.md

@@ -1,3 +1,3 @@
 # Contributing to bioconda
 
-Please visit https://bioconda.github.io/contributing.html for the updated docs.
+Please visit https://bioconda.github.io/contributor/index.html for the updated docs.

GUIDELINES.md

@@ -1,3 +1,3 @@
 # Guidelines for `bioconda` recipes
 
-Please visit https://bioconda.github.io/guidelines.html for the updated guidelines.
+Please visit https://bioconda.github.io/contributor/guidelines.html for the updated guidelines.

README.md

@@ -18,5 +18,5 @@ Please visit https://bioconda.github.io for details.
 
 ## Developer guide
 
-Please visit the new docs at https://bioconda.github.io/contributing.html for details.
+Please visit the new docs at https://bioconda.github.io/contributor/index.html for details.