Merge branch 'master' into jpfeuffer-patch-1

.circleci/config.yml

@@ -11,7 +11,7 @@ version: 2
 jobs:
   autobump:
     machine:
-      image: ubuntu-2004:202201-02
+      image: ubuntu-2204:2024.05.1
     steps:
       - add_ssh_keys:
           fingerprints:

.github/workflows/GithubActionTests.yml

@@ -16,7 +16,9 @@ jobs:
           - long_running_2
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
@@ -27,15 +29,16 @@ jobs:
           wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
           bash install-and-set-up-conda.sh
           eval "$(conda shell.bash hook)"
-          mamba create -n bioconda -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
+          conda create -n bioconda --quiet --yes --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
           conda activate bioconda
+          conda list
           python setup.py install
 
       - name: Build docker container
         run: |
           docker build -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest ./
           docker history quay.io/bioconda/bioconda-utils-build-env-cos7:latest
-          docker run --rm -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest sh -lec 'type -t conda && conda info -a && conda list'
+          docker run --rm -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest sh -lec 'type -t conda && conda info --verbose && conda list'
           docker build -t quay.io/bioconda/bioconda-utils-test-env-cos7:latest -f ./Dockerfile.test ./
 
       - name: Run tests '${{ matrix.py_test_marker }}'
@@ -49,9 +52,11 @@ jobs:
           fi
   test-macosx:
     name: OSX tests
-    runs-on: macos-latest
+    runs-on: macos-13
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
@@ -62,7 +67,8 @@ jobs:
           wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
           bash install-and-set-up-conda.sh
           eval "$(conda shell.bash hook)"
-          mamba create -n bioconda -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
+          conda create -n bioconda --quiet --yes --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
+          conda list
           conda activate bioconda
           python setup.py install
 
@@ -80,7 +86,7 @@ jobs:
     name: autobump test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v4
       - name: set path
         run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
 
@@ -90,8 +96,9 @@ jobs:
           wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
           bash install-and-set-up-conda.sh
           eval "$(conda shell.bash hook)"
-          mamba create -n bioconda -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
+          conda create -n bioconda --quiet --yes --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
           conda activate bioconda
+          conda list
           python setup.py install
 
       - name: Test autobump

.github/workflows/build-image.yml

@@ -24,7 +24,7 @@ jobs:
             image: bioconda-utils-build-env-cos7
             base_image: quay.io/condaforge/linux-anvil-cos7-x86_64
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 

.github/workflows/changevisibility.yml

@@ -10,7 +10,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check Containers and Set Public
         run: |

.github/workflows/conventional-prs.yml

@@ -11,6 +11,6 @@ jobs:
   title-format:
     runs-on: ubuntu-latest
     steps:
-      - uses: amannn/action-semantic-pull-request@v3.4.0
+      - uses: amannn/action-semantic-pull-request@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release-please.yml

@@ -23,7 +23,7 @@ jobs:
     needs: release_please
     if: needs.release_please.outputs.release_created
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

CHANGELOG.md

@@ -1,5 +1,238 @@
 # Changelog
 
+### [3.4.1](https://www.github.com/bioconda/bioconda-utils/compare/v3.4.0...v3.4.1) (2024-10-28)
+
+
+### Bug Fixes
+
+* fix image artifact regex to match GitHub Actions filename ([#1013](https://www.github.com/bioconda/bioconda-utils/issues/1013)) ([c1adeea](https://www.github.com/bioconda/bioconda-utils/commit/c1adeeac7125a1483cd3ab57c2dd034a0f6978e3))
+
+## [3.4.0](https://www.github.com/bioconda/bioconda-utils/compare/v3.3.2...v3.4.0) (2024-10-21)
+
+
+### Features
+
+* Update dependencies to latest versions - less complex ([#1011](https://www.github.com/bioconda/bioconda-utils/issues/1011)) ([167f348](https://www.github.com/bioconda/bioconda-utils/commit/167f348724e77384859e54c23b5226f2e67a1975))
+
+### [3.3.2](https://www.github.com/bioconda/bioconda-utils/compare/v3.3.1...v3.3.2) (2024-08-28)
+
+
+### Bug Fixes
+
+* token for CircleCI artifacts ([#1001](https://www.github.com/bioconda/bioconda-utils/issues/1001)) ([a5882cc](https://www.github.com/bioconda/bioconda-utils/commit/a5882cc87c0e451483d19f8bba701496cc058883))
+
+### [3.3.1](https://www.github.com/bioconda/bioconda-utils/compare/v3.3.0...v3.3.1) (2024-06-06)
+
+
+### Bug Fixes
+
+* add missing Arm platforms to skip existing builds ([#999](https://www.github.com/bioconda/bioconda-utils/issues/999)) ([bbc8758](https://www.github.com/bioconda/bioconda-utils/commit/bbc87583db660ccabdbd0d6fc4e14a8e9721551d))
+
+## [3.3.0](https://www.github.com/bioconda/bioconda-utils/compare/v3.2.0...v3.3.0) (2024-06-03)
+
+
+### Features
+
+* Update pinning 2024-05 ([#991](https://www.github.com/bioconda/bioconda-utils/issues/991)) ([d48d6e4](https://www.github.com/bioconda/bioconda-utils/commit/d48d6e4f09046bf4142a63805e1366f655cefd71))
+
+## [3.2.0](https://www.github.com/bioconda/bioconda-utils/compare/v3.1.0...v3.2.0) (2024-06-02)
+
+
+### Features
+
+* Update base-glibc-*-bash images to 3.1 ([#996](https://www.github.com/bioconda/bioconda-utils/issues/996)) ([e7c6ca0](https://www.github.com/bioconda/bioconda-utils/commit/e7c6ca0bf7bf2a0815c694634e45d7dff0aa483a))
+
+
+### Bug Fixes
+
+* Pass pkg_format to container-based build ([#994](https://www.github.com/bioconda/bioconda-utils/issues/994)) ([e3f23ed](https://www.github.com/bioconda/bioconda-utils/commit/e3f23ed70300d97a8f99c5bace7dbba0f559bd19))
+
+## [3.1.0](https://www.github.com/bioconda/bioconda-utils/compare/v3.0.0...v3.1.0) (2024-06-01)
+
+
+### Features
+
+* Update dependencies to latest versions ([#992](https://www.github.com/bioconda/bioconda-utils/issues/992)) ([8c0fe35](https://www.github.com/bioconda/bioconda-utils/commit/8c0fe3548e8087a82050d8cefcfe01e909e61c01))
+
+## [3.0.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.15.1...v3.0.0) (2024-05-17)
+
+
+### ⚠ BREAKING CHANGES
+
+* Separate docs-only requirements (#986)
+* Remove defaults channel dependency (#985)
+
+### Miscellaneous Chores
+
+* Remove defaults channel dependency ([#985](https://www.github.com/bioconda/bioconda-utils/issues/985)) ([eb043dc](https://www.github.com/bioconda/bioconda-utils/commit/eb043dc2649bcdf63c11f19993660b58ec215cb7))
+* Separate docs-only requirements ([#986](https://www.github.com/bioconda/bioconda-utils/issues/986)) ([09d108e](https://www.github.com/bioconda/bioconda-utils/commit/09d108e796cb4fce317c475b7d26bbaea124619c))
+
+### [2.15.1](https://www.github.com/bioconda/bioconda-utils/compare/v2.15.0...v2.15.1) (2024-05-08)
+
+
+### Bug Fixes
+
+* test_package for .tar.bz2 and .conda ([#983](https://www.github.com/bioconda/bioconda-utils/issues/983)) ([c683290](https://www.github.com/bioconda/bioconda-utils/commit/c683290319d4f148644972b6caf626be6d1c6c99))
+
+## [2.15.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.14.0...v2.15.0) (2024-05-03)
+
+
+### Features
+
+* Add support for .conda format ([#981](https://www.github.com/bioconda/bioconda-utils/issues/981)) ([125c9ea](https://www.github.com/bioconda/bioconda-utils/commit/125c9ea5e362b7e5e63dfcbfae995fa3eeb58ce8))
+* choose worker recipes by depth level ([#950](https://www.github.com/bioconda/bioconda-utils/issues/950)) ([4c51ae3](https://www.github.com/bioconda/bioconda-utils/commit/4c51ae31158b0154cf3ed381c4a3ad8b9bff7f14))
+* Update dependencies to latest versions ([#972](https://www.github.com/bioconda/bioconda-utils/issues/972)) ([dc6ca07](https://www.github.com/bioconda/bioconda-utils/commit/dc6ca07a977dfbf7cbc2d25f884dc0333d611116))
+* Use conda/conda-build instead of mamba/conda-mambabuild ([#980](https://www.github.com/bioconda/bioconda-utils/issues/980)) ([17cbc7f](https://www.github.com/bioconda/bioconda-utils/commit/17cbc7fb411864c7c22ff33b40682c0f43e016cc))
+
+
+### Bug Fixes
+
+* handle PR list with no items ([#975](https://www.github.com/bioconda/bioconda-utils/issues/975)) ([869577a](https://www.github.com/bioconda/bioconda-utils/commit/869577a76933c2d7bcf386c1179ef454bdc18543))
+* Ignore src_cache for container-built packages ([125c9ea](https://www.github.com/bioconda/bioconda-utils/commit/125c9ea5e362b7e5e63dfcbfae995fa3eeb58ce8))
+* Ignore Zstandard-packed repodata artifact ([125c9ea](https://www.github.com/bioconda/bioconda-utils/commit/125c9ea5e362b7e5e63dfcbfae995fa3eeb58ce8))
+* use circleci api v1.1 to avoid login error ([#982](https://www.github.com/bioconda/bioconda-utils/issues/982)) ([ebafe92](https://www.github.com/bioconda/bioconda-utils/commit/ebafe92ae01dc4a573e861764a4e837bd1321af3))
+
+## [2.14.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.13.2...v2.14.0) (2024-04-01)
+
+
+### Features
+
+* fetch artifacts from GitHub Actions ([#973](https://www.github.com/bioconda/bioconda-utils/issues/973)) ([858e1cf](https://www.github.com/bioconda/bioconda-utils/commit/858e1cfdd4435aca16c9978df5463db845ff9fe3))
+* update deployment target for osx-arm64 ([#967](https://www.github.com/bioconda/bioconda-utils/issues/967)) ([a7c591e](https://www.github.com/bioconda/bioconda-utils/commit/a7c591ea51fdf3308a0075951e8f5efee783c8d1))
+
+### [2.13.2](https://www.github.com/bioconda/bioconda-utils/compare/v2.13.1...v2.13.2) (2024-03-27)
+
+
+### Bug Fixes
+
+* update anaconda-client=1.12 to fix uploads ([#970](https://www.github.com/bioconda/bioconda-utils/issues/970)) ([06dcacc](https://www.github.com/bioconda/bioconda-utils/commit/06dcacca60c17c1a97770e14ae6348ac7acbe9a6))
+
+### [2.13.1](https://www.github.com/bioconda/bioconda-utils/compare/v2.13.0...v2.13.1) (2024-03-27)
+
+
+### Bug Fixes
+
+* detect errors when uploading artifacts ([#968](https://www.github.com/bioconda/bioconda-utils/issues/968)) ([d0a79cd](https://www.github.com/bioconda/bioconda-utils/commit/d0a79cdd5aeed30c4da88e2135329d66b336832f))
+
+## [2.13.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.12.0...v2.13.0) (2024-03-22)
+
+
+### Features
+
+* add osx-arm64 to platform checks ([#965](https://www.github.com/bioconda/bioconda-utils/issues/965)) ([9f6df10](https://www.github.com/bioconda/bioconda-utils/commit/9f6df10bfecd048956acc80e7bb3d57952585529))
+
+## [2.12.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.11.1...v2.12.0) (2024-03-18)
+
+
+### Features
+
+* add support for excluding otherwise-selected recipes ([#962](https://www.github.com/bioconda/bioconda-utils/issues/962)) ([3946732](https://www.github.com/bioconda/bioconda-utils/commit/3946732eb6129f6905e53b62d76287e09d4bef36))
+* bioconductor improvements ([#944](https://www.github.com/bioconda/bioconda-utils/issues/944)) ([b007d34](https://www.github.com/bioconda/bioconda-utils/commit/b007d34e6c723f7f9d6fcb5a6f58e072d4618cdf))
+* Bulk build failure wiki ([#948](https://www.github.com/bioconda/bioconda-utils/issues/948)) ([18f988d](https://www.github.com/bioconda/bioconda-utils/commit/18f988d70966f6f6296170d96cc1ced51ad10392))
+
+
+### Bug Fixes
+
+* Do not emit cython_needs_compiler if compiler("cxx") is set ([#927](https://www.github.com/bioconda/bioconda-utils/issues/927)) ([8255afd](https://www.github.com/bioconda/bioconda-utils/commit/8255afdd9e5c0fd3cb09cb11269f5ff3397c959e))
+
+### [2.11.1](https://www.github.com/bioconda/bioconda-utils/compare/v2.11.0...v2.11.1) (2023-12-13)
+
+
+### Bug Fixes
+
+* add local channel for docker builds ([#945](https://www.github.com/bioconda/bioconda-utils/issues/945)) ([de8ce00](https://www.github.com/bioconda/bioconda-utils/commit/de8ce00d1ccf6a395ff6adce97f71b5c6059500f))
+* Fix version number check in repodata_patches_no_version_bump() ([#946](https://www.github.com/bioconda/bioconda-utils/issues/946)) ([73e69b2](https://www.github.com/bioconda/bioconda-utils/commit/73e69b2f9aabb06f693518b8ee195c7fa897bc76))
+
+## [2.11.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.10.0...v2.11.0) (2023-11-30)
+
+
+### Features
+
+* make GITHUB_TOKEN optional for fetch ([#942](https://www.github.com/bioconda/bioconda-utils/issues/942)) ([c0eab1d](https://www.github.com/bioconda/bioconda-utils/commit/c0eab1d7224d6b13ebe399e7933460249e4e9a58))
+
+## [2.10.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.9.0...v2.10.0) (2023-11-26)
+
+
+### Features
+
+* live logs for mulled build ([#939](https://www.github.com/bioconda/bioconda-utils/issues/939)) ([7f83d7f](https://www.github.com/bioconda/bioconda-utils/commit/7f83d7f66ab81279a5d7c990b9311d493d416d5b))
+
+
+### Bug Fixes
+
+* specify involucro path when uploading ([#941](https://www.github.com/bioconda/bioconda-utils/issues/941)) ([3086cc0](https://www.github.com/bioconda/bioconda-utils/commit/3086cc083213b9084ba7d0ee5bc12e0d86cebc0b))
+
+
+### Documentation
+
+* run_export -> run_exports plural in help message ([#928](https://www.github.com/bioconda/bioconda-utils/issues/928)) ([2c5d4ad](https://www.github.com/bioconda/bioconda-utils/commit/2c5d4ad754f7bfa17b90495dc602118c7270d4bc))
+
+## [2.9.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.8.0...v2.9.0) (2023-11-05)
+
+
+### Features
+
+* use new container version by default (3.0) ([#935](https://www.github.com/bioconda/bioconda-utils/issues/935)) ([11d53db](https://www.github.com/bioconda/bioconda-utils/commit/11d53dbb18d5edf0a6a546c5a53c6d5e942dfc4a))
+
+## [2.8.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.7.0...v2.8.0) (2023-11-02)
+
+
+### Features
+
+* Enable Live logs and add option to disable ([#930](https://www.github.com/bioconda/bioconda-utils/issues/930)) ([47eaadc](https://www.github.com/bioconda/bioconda-utils/commit/47eaadcd4f0da856733e3fd3170d3451ec9c4b8d))
+
+
+### Bug Fixes
+
+* try locale C.utf8 ([#931](https://www.github.com/bioconda/bioconda-utils/issues/931)) ([584fcdd](https://www.github.com/bioconda/bioconda-utils/commit/584fcddd45854b88cdf4af72df0a1ad5cc3c9fcc))
+
+## [2.7.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.6.0...v2.7.0) (2023-10-14)
+
+
+### Features
+
+* add support to run build for recipes with linux-aarch64 additional-platforms ([#923](https://www.github.com/bioconda/bioconda-utils/issues/923)) ([55671f7](https://www.github.com/bioconda/bioconda-utils/commit/55671f77124065fd09bb7d9c4a856cf0e87e48a4))
+
+## [2.6.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.5.0...v2.6.0) (2023-10-08)
+
+
+### Features
+
+* download aarch64 artifacts from CircleCI ([#921](https://www.github.com/bioconda/bioconda-utils/issues/921)) ([b9cddd4](https://www.github.com/bioconda/bioconda-utils/commit/b9cddd42eb7c45dbbd207cf5d209ea328c02eff1))
+
+## [2.5.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.4.0...v2.5.0) (2023-10-04)
+
+
+### Features
+
+* add special lints for bioconda-repodata-patches recipe ([#855](https://www.github.com/bioconda/bioconda-utils/issues/855)) ([11c9229](https://www.github.com/bioconda/bioconda-utils/commit/11c92296bbc566fcd481ea45c4d55247b4ba154d))
+
+
+### Bug Fixes
+
+* adding "vals" to GithubRelease changes for API and expanded assets ([#912](https://www.github.com/bioconda/bioconda-utils/issues/912)) ([9e0e445](https://www.github.com/bioconda/bioconda-utils/commit/9e0e44581cade8d994a5b923964df060122b7519))
+* Remove htslib build pinning ([#917](https://www.github.com/bioconda/bioconda-utils/issues/917)) ([c7efb92](https://www.github.com/bioconda/bioconda-utils/commit/c7efb9250312abdcfbdc10be60b5a0fa92e52726))
+* Version constraints can start with `!` as well ([#919](https://www.github.com/bioconda/bioconda-utils/issues/919)) ([ee56f6e](https://www.github.com/bioconda/bioconda-utils/commit/ee56f6e1d20aa7c96f150ff79a084faf0521e70b)), closes [#918](https://www.github.com/bioconda/bioconda-utils/issues/918)
+
+
+### Documentation
+
+* try to clarify some confusion with run_exports. ([#914](https://www.github.com/bioconda/bioconda-utils/issues/914)) ([417e7da](https://www.github.com/bioconda/bioconda-utils/commit/417e7da6524c71ac0aafdcd75244bd001de17efd))
+
+## [2.4.0](https://www.github.com/bioconda/bioconda-utils/compare/v2.3.4...v2.4.0) (2023-08-24)
+
+
+### Features
+
+* lint missing run exports ([#908](https://www.github.com/bioconda/bioconda-utils/issues/908)) ([84f5c0c](https://www.github.com/bioconda/bioconda-utils/commit/84f5c0c0b4ec4ba4f1756cbe74da50151efa77a3))
+
+
+### Bug Fixes
+
+* recover --docker-base-image feature ([#906](https://www.github.com/bioconda/bioconda-utils/issues/906)) ([aa08857](https://www.github.com/bioconda/bioconda-utils/commit/aa088572d3721837d08556634961c5c7d86814c1))
+* swaps from github API to expanding the assets ([#907](https://www.github.com/bioconda/bioconda-utils/issues/907)) ([2099a40](https://www.github.com/bioconda/bioconda-utils/commit/2099a405f1b888699eb2026146aa0b4f3f070fb0))
+* use package name instead of folder for build failure list dag check ([#910](https://www.github.com/bioconda/bioconda-utils/issues/910)) ([11fb14f](https://www.github.com/bioconda/bioconda-utils/commit/11fb14fd1a95c05dca96887d0d9935f6954447e2))
+
 ### [2.3.4](https://www.github.com/bioconda/bioconda-utils/compare/v2.3.3...v2.3.4) (2023-07-15)
 
 

Dockerfile

@@ -6,7 +6,7 @@ ARG BASE_IMAGE=quay.io/condaforge/linux-anvil-cos7-x86_64
 FROM ${BASE_IMAGE} as base
 
 # Copy over C.UTF-8 locale from our base image to make it consistently available during build.
-COPY --from=quay.io/bioconda/base-glibc-busybox-bash /usr/lib/locale/C.UTF-8 /usr/lib/locale/C.UTF-8
+COPY --from=quay.io/bioconda/base-glibc-busybox-bash /usr/lib/locale/C.utf8 /usr/lib/locale/C.utf8
 
 # Provide system deps unconditionally until we are able to offer per-recipe installs.
 # (Addresses, e.g., "ImportError: libGL.so.1" in tests directly invoked by conda-build.)
@@ -21,10 +21,12 @@ RUN yum install -y mesa-libGL-devel \
 # This changes root's .condarc which ENTRYPOINT copies to /home/conda/.condarc later.
 RUN . /opt/conda/etc/profile.d/conda.sh && \
     conda config \
-    --add channels defaults \
     --add channels bioconda \
     --add channels conda-forge \
     && \
+    conda config \
+    --remove channels defaults || true \
+    && \
     { conda config --remove repodata_fns current_repodata.json 2> /dev/null || true ; } && \
     conda config --prepend repodata_fns repodata.json && \
     conda config --set channel_priority strict && \
@@ -51,10 +53,10 @@ RUN . /opt/conda/etc/profile.d/conda.sh  && conda activate base && \
     sed -nE \
     '/^conda([><!=~ ].+)?$/p' \
     /opt/bioconda-utils/bioconda_utils-requirements.txt \
-    | xargs -r mamba install --yes && \
-    mamba install --yes --file /opt/bioconda-utils/bioconda_utils-requirements.txt && \
+    | xargs -r conda install --yes && \
+    conda install --yes --file /opt/bioconda-utils/bioconda_utils-requirements.txt && \
     pip install --no-deps --find-links /opt/bioconda-utils bioconda_utils && \
-    mamba clean --yes --index --tarballs && \
+    conda clean --yes --index --tarballs && \
     # Find files that are not already in group "lucky" and change their group and mode.
     find /opt/conda \
     \! -group lucky \