Bulk

.circleci/config.yml

@@ -190,37 +190,37 @@ jobs:
               --git-range $CIRCLE_SHA1~1 $CIRCLE_SHA1 \
               --prelint
 
-  # build, test and upload for bulk branch on linux
-  bulk-linux:
-    <<: *linux
-    steps:
-      - *fail_fork
-      - checkout
-      - *common
-      - *restore_cache
-      - *setup
-      - *save_cache
-      - run:
-          name: Building, testing, and uploading of all unpublished recipes
-          command: |
-            bioconda-utils build recipes config.yml \
-              --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers
+  ## build, test and upload for bulk branch on linux
+  #bulk-linux:
+  #  <<: *linux
+  #  steps:
+  #    - *fail_fork
+  #    - checkout
+  #    - *common
+  #    - *restore_cache
+  #    - *setup
+  #    - *save_cache
+  #    - run:
+  #        name: Building, testing, and uploading of all unpublished recipes
+  #        command: |
+  #          bioconda-utils build recipes config.yml \
+  #            --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers
 
-  # build, test and upload for bulk branch on macos
-  bulk-macos:
-    <<: *macos
-    steps:
-      - *fail_fork
-      - checkout
-      - *common
-      - *restore_cache
-      - *setup
-      - *save_cache
-      - run:
-          name: Building, testing and uploading of all unpublished recipes
-          command: |
-            bioconda-utils build recipes config.yml \
-              --anaconda-upload
+  ## build, test and upload for bulk branch on macos
+  #bulk-macos:
+  #  <<: *macos
+  #  steps:
+  #    - *fail_fork
+  #    - checkout
+  #    - *common
+  #    - *restore_cache
+  #    - *setup
+  #    - *save_cache
+  #    - run:
+  #        name: Building, testing and uploading of all unpublished recipes
+  #        command: |
+  #          bioconda-utils build recipes config.yml \
+  #            --anaconda-upload
 
   # nightly build, test and upload of unpublished recipes on linux
   nightly-upload-linux:
@@ -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:

.github/workflows/Bulk.yml

@@ -0,0 +1,60 @@
+name: Bulk branch
+on:
+  push:
+    branches:
+      - bulk
+jobs:
+  build-linux:
+    name: Bulk Linux Builds
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      max-parallel: 10
+      matrix:
+        runner: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Setup Bioconda-utils
+      uses: bioconda/bioconda-actions/bioconda_recipes_setup/@bulk
+    - name: Debug
+      run: |
+        python -c "import sys; print(sys.platform)"
+    - 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: |
+        bioconda-utils build recipes config.yml \
+          --worker-offset ${{ matrix.runner }} --n-workers 10 \
+          --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers
+  build-osx:
+    name: Bulk OSX Builds
+    runs-on: macOS-latest
+    strategy:
+      fail-fast: false
+      max-parallel: 5
+      matrix:
+        runner: [0, 1, 2, 3, 4]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Setup Bioconda-utils
+      uses: bioconda/bioconda-actions/bioconda_recipes_setup/@bulk
+    - name: Debug
+      run: |
+        python -c "import sys; print(sys.platform)"
+    - 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: |
+        bioconda-utils build recipes config.yml \
+          --worker-offset ${{ matrix.runner }} --n-workers 5 \
+          --anaconda-upload

recipes/simlord/meta.yaml

@@ -8,21 +8,21 @@ source:
 
 build:
   number: 2
+  skip: True  # [py2k]
   entry_points:
     - simlord = simlord.simlord:main
 
 requirements:
   build:
     - {{ compiler('c') }}
   host:
-    - python >=3
+    - python
     - setuptools
     - numpy
     - scipy
     - pysam >=0.8.4
     - cython
     - dinopy
-
   run:
     - python
     - numpy

recipes/srnapipe/meta.yaml

@@ -16,15 +16,15 @@ build:
 
 requirements:
   host:
-    - perl <5.23.0a0
+    - perl
     - perl-getopt-long
     - perl-parallel-forkmanager
     - perl-statistics-r
     - perl-string-random
     - perl-file-copy-recursive
     - perl-math-cdf
   run:
-    - perl <5.23.0a0
+    - perl
     - perl-getopt-long
     - perl-parallel-forkmanager
     - perl-statistics-r

recipes/starfish/meta.yaml

@@ -5,8 +5,8 @@ package:
   version: {{ STARFISH_VERSION }}
 
 source:
-  url: https://github.com/spacetx/starfish/archive/{{ STARFISH_VERSION }}.zip
-  sha256: 6d83167d006e73a4dca486f87a3b049541ef11ea34a967fe22aef3cd88de25f1
+  url: https://github.com/spacetx/starfish/archive/{{ STARFISH_VERSION }}.tar.gz
+  sha256: 1b2625eabc7920754553f7ebd2554c3a98b5d9f7bb51d1713187397b83f6f467
 
 build:
   noarch: python

recipes/vcflatten/meta.yaml

@@ -4,14 +4,13 @@ package:
 
 build:
   noarch: generic
-  number: 2
+  number: 3
 
 source:
   url: https://github.com/downloads/innovativemedicine/vcfimp/vcflatten-0.5.2.zip
   md5: 69864df8a5a228a8fea73e0df5ddf394
 
 requirements:
-  build:
   run:
     - openjdk