Merge branch 'master' into bulk

bioconda · Sep 10, 2024 · 6ca4f03 · 6ca4f03
2 parents 76a8531 + f38fbcf
commit 6ca4f03
Show file tree

Hide file tree

Showing 203 changed files with 13,646 additions and 1,152 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -239,6 +239,52 @@ jobs: # a basic unit of work in a run
               --skiplist-leafs
             conda clean -y --all
 
+  nightly_build:
+    parameters:
+      os:
+        type: executor
+    executor: << parameters.os >>
+    steps:
+      - add_ssh_keys:
+          fingerprints:
+            - 1e:85:74:42:35:5f:c5:a2:35:c2:ec:b7:80:c0:7c:40
+
+      - checkout
+
+      - run:
+          name: Fetch bioconda install script
+          command: wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh
+
+      - run:
+          name: Install bioconda-utils
+          command: |
+            sudo mkdir -p /opt/
+            sudo chmod o+rwx /opt
+            bash install-and-set-up-conda.sh
+
+      - run:
+          name: Setup PATH
+          command:
+            echo 'export PATH=/opt/mambaforge/bin:"$PATH"' >> "$BASH_ENV"
+
+      - run:
+          name: Configure conda
+          command: bash configure-conda.sh
+
+      # For now, do not upload ARM images to biocontainers: --mulled-upload-target biocontainers
+      - run:
+          name: Build and push leftover packages
+          command: |
+            set -e
+            eval "$(conda shell.bash hook)"
+            conda activate bioconda
+            source common.sh
+
+            # build and push all leftover packages
+            bioconda-utils build recipes config.yml \
+                --docker --mulled-test  --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \
+                --anaconda-upload \
+                --prelint --exclude bioconda-repodata-patches
 
 workflows:
   build and test (ARM):
@@ -267,7 +313,6 @@ workflows:
                 - osx-arm64
                 - linux-aarch64
 
-
   Bulk branch (ARM):
     jobs:
       - bulk_build:
@@ -280,3 +325,21 @@ workflows:
                 # - osx-arm64 Bulk is on GitHub Actions
                 - linux-aarch64
               runner: [0, 1, 2, 3, 4, 5]
+
+  Nightly (ARM):
+    triggers:
+      - schedule:
+          cron: "0 0 * * *"
+          filters:
+            branches:
+              only: master
+    jobs:
+      - nightly_build:
+          filters:
+            branches:
+              only: master
+          matrix:
+            parameters:
+              os:
+                # - osx-arm64 Nightly is on GitHub Actions
+                - linux-aarch64
diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
@@ -1,76 +1,17 @@
 name: Nightly Uploader
 on:
   schedule:
-    - cron: '12 2 * * *'
+    - cron: "0 0 * * *"
 jobs:
-  build-linux:
-    name: Linux Upload
+  nightly-osx-arm:
+    name: Nightly OSX-ARM64 Builds
     if: github.repository == 'bioconda/bioconda-recipes'
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      max-parallel: 13
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-
-      - name: set path
-        run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
-
-      - name: Fetch conda install script
-        run: |
-          wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
-
-      - name: Restore cache
-        id: cache
-        uses: actions/cache@v3
-        with:
-          path: /opt/mambaforge
-          key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }}
-
-      - name: Set up bioconda-utils
-        if: steps.cache.outputs.cache-hit != 'true'
-        run: bash install-and-set-up-conda.sh
-
-      # This script can be used to reconfigure conda to use the right channel setup.
-      # This has to be done after the cache is restored, because
-      # the channel setup is not cached as it resides in the home directory.
-      # We could use a system-wide (and therefore cached) channel setup,
-      # but mamba does not support that at the time of implementation
-      # (it ignores settings made with --system).
-      - name: Configure conda
-        run: bash configure-conda.sh
-
-      - name: Build and upload
-        env:
-          QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
-          QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
-          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
-          INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          # Mimic circleci
-          OSTYPE: "linux-gnu"
-          CI: "true"
-        run: |
-          set -ex
-          eval "$(conda shell.bash hook)"
-          conda activate bioconda
-          docker pull quay.io/dpryan79/mulled_container:latest
-          bioconda-utils build recipes config.yml \
-              --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \
-              --prelint
-          docker rmi quay.io/dpryan79/mulled_container:latest
-
-  build-osx:
-    name: OSX Tests
-    if: github.repository == 'bioconda/bioconda-recipes'
-    runs-on: macos-13
+    runs-on: macOS-14 # M1
     strategy:
       fail-fast: false
       max-parallel: 4
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -81,27 +22,13 @@ jobs:
         run: |
           wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
 
-      - name: Restore cache
-        id: cache
-        uses: actions/cache@v3
-        with:
-          path: /opt/mambaforge
-          key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }}
-
       - name: Set up bioconda-utils
-        if: steps.cache.outputs.cache-hit != 'true'
         run: bash install-and-set-up-conda.sh
 
-      # This script can be used to reconfigure conda to use the right channel setup.
-      # This has to be done after the cache is restored, because
-      # the channel setup is not cached as it resides in the home directory.
-      # We could use a system-wide (and therefore cached) channel setup,
-      # but mamba does not support that at the time of implementation
-      # (it ignores settings made with --system).
       - name: Configure conda
         run: bash configure-conda.sh
 
-      - name: Build and Test
+      - name: Build and push leftover packages
         env:
           QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
           QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
@@ -116,9 +43,11 @@ jobs:
           eval "$(conda shell.bash hook)"
           conda activate bioconda
 
-          # The SDK isn't actually cached, so reinstall it
+          source common.sh
+          # Sets up OSX SDK
           run_conda_forge_build_setup
 
+          # build and push all leftover packages
           bioconda-utils build recipes config.yml \
               --anaconda-upload \
-              --prelint
+              --prelint --exclude bioconda-repodata-patches
diff --git a/recipes/allo/meta.yaml b/recipes/allo/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "allo" %}
-{% set version = "1.1.2" %} 
+{% set version = "1.2.0" %} 
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/b/bio-{{ name }}/bio_allo-{{ version }}.tar.gz
-  sha256: 116390a306d76ae8986762292b51e85de710a36e56d532ae7e3cc4df5796befc
+  sha256: d5ec3b33975743022447ac4cefb9f2b75d188b6f8ece0e8073b636ce6c969f3d
 
 build:
   run_exports:
@@ -24,7 +24,7 @@ requirements:
     - python >=3.10
     - numpy
     - joblib
-    - tensorflow >=2.11
+    - tensorflow >=2.17
     - pysam
 
 test:

diff --git a/recipes/anchorwave/meta.yaml b/recipes/anchorwave/meta.yaml
@@ -1,7 +1,7 @@
 {% set name = "anchorwave" %}
-{% set version = "1.2.3" %}
-{% set tag = "v1.2.3" %}
-{% set sha256 = "1f689c06f9bbc8e1ed64c0addf4aaf5d172a2fea1e55660b8d3f6dfdffe3f157" %}
+{% set version = "1.2.5" %}
+{% set tag = "v1.2.5" %}
+{% set sha256 = "440e233739582f1e3d7a3847a421919b4c426d4f4332f4d812ea4d23b9958cfa" %}
 
 package:
   name: {{ name }}

diff --git a/recipes/anndata2ri/meta.yaml b/recipes/anndata2ri/meta.yaml
@@ -1,20 +1,20 @@
 {% set name = "anndata2ri" %}
-{% set version = "1.3.1" %}
+{% set version = "1.3.2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   noarch: python
   script: "{{ PYTHON }} -m pip install . --no-deps -vvv"
   run_exports:
     - {{ pin_subpackage('anndata2ri', max_pin="x") }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 0e3fa2f81789f682d19ef452fabdb401ec27899db9abe5a78e45e21dcc7caa42
+  sha256: 34a767b16abfac1aacb6edcd394eaf565f53fff6de3e6f47961a3901d3890d93
 
 requirements:
   host:

diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.40.0" %}
+{% set version = "0.41.0" %}
 
 package:
   name: annonars
@@ -12,7 +12,7 @@ build:
 
 source:
   url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 1860e69f89935aa5d5456e55070d4c172cd4b29bdf07ad16b6b4dcf95b4ef7b2
+  sha256: 11cf6d760c9a4f5896c5a6883fda2bd39b734862a6acf6af004704edb0752569
 
 requirements:
   build:

diff --git a/recipes/annotsv/meta.yaml b/recipes/annotsv/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "annotsv" %}
-{% set version = "3.4.2" %}
-{% set sha256 = "a8a06fc60bd4c8fb380598097f644f02ed22051b5b30f4eb42b2474b170fe91d" %}
+{% set version = "3.4.4" %}
+{% set sha256 = "ab7afcdddc1aa1215d3d77cdab74d6db4f24f2c56de9b820a6bbf668f48b1d88" %}
 
 package:
   name: {{ name }}

diff --git a/recipes/argo/meta.yaml b/recipes/argo/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "argo" %}
-{% set version = "0.1.0" %}
+{% set version = "0.1.1" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://github.com/xinehc/argo/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 8dbe2606024c78ca471dea675e4aeaa88140cca0a2f989b2d40081cf6cd62cdc
+  sha256: 9ddc3bea602e3bdcd3518bb3ecd7795b680addaa513eff0fff83e1010ba4e253
 
 build:
   noarch: python

diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "assembly_finder" %}
-{% set version = "0.7.6" %}
+{% set version = "0.7.7" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: aa77170404109f6efcc52aef3bab98d6a24a0c380c18aaba9afba9a6fea7c0ed
+  sha256: 0c6542253464b8ba406aeddc630f5625db74a5e1e07911534be3add0500a1f02
 
 build:
   number: 0

diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "25.3.0" %}
+{% set version = "25.4.0" %}
 
 package:
   name: augur
   version: {{ version }}
 
 source:
   url: https://github.com/nextstrain/augur/releases/download/{{ version }}/nextstrain_augur-{{ version }}.tar.gz
-  sha256: aff6de12fcbdb52f89da7cc6c8a7f1410b1b473882aa824fb3b40e8cea3d5d2a
+  sha256: 935eacb19853e7f6006814d060b5460b3e91501f470a6af88864c512b46b1c6a
 
 build:
   number: 0

diff --git a/recipes/auspice/meta.yaml b/recipes/auspice/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.56.1" %}
+{% set version = "2.57.0" %}
 {% set name = "auspice" %}
 
 package:
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://registry.npmjs.org/{{ name }}/-/{{ name }}-{{ version }}.tgz
-  sha256: d100c0f6cc13ba1f9fe2b7bde5983b0383f523320dcc69a19cf9c86570febf03
+  sha256: b959564d5249334f590081f2d273ae9a775652cb21f9e57175f5a6ba86d43473
 
 build:
   number: 0

diff --git a/recipes/aviary/meta.yaml b/recipes/aviary/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "0.9.1" %}
+{% set version = "0.9.2" %}
 {% set name = "aviary" %}
-{% set sha256 = "51b7096f7e031e0d4cf465249ca6959eda28f66bd8ca24fd5e0989b131a6f9ce" %}
+{% set sha256 = "83e18bbd2abf347ae7e0d83d81d671031a6a98324b01053e79c0d86b989c95ba" %}
 
 package:
   name: aviary

diff --git a/recipes/bcbio-gff/0.6.2/meta.yaml b/recipes/bcbio-gff/0.6.2/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 2
   noarch: python
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
 
@@ -22,7 +22,7 @@ requirements:
   run:
     - python
     - six
-    - biopython
+    - biopython <=1.78
     - bx-python
 
 test:

diff --git a/recipes/bcbio-gff/0.6.4/meta.yaml b/recipes/bcbio-gff/0.6.4/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 2
   noarch: python
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
 
@@ -22,7 +22,7 @@ requirements:
   run:
     - python
     - six
-    - biopython
+    - biopython <=1.78
     - bx-python
 
 test: