Merge branch 'bioconda:master' into master

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,11 +4,40 @@ Describe your pull request here
 
 Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR).
 
+### General instructions
+
 * If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
 * New recipes not directly relevant to the biological sciences need to be submitted to the [conda-forge channel](https://conda-forge.org/docs/) instead of Bioconda.
 * PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the `@BiocondaBot please add label` command.
 * Please post questions [on Gitter](https://gitter.im/bioconda/Lobby) or ping `@bioconda/core` in a comment.
 
+### Instructions for avoiding API, ABI, and CLI breakage issues
+Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
+This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
+If not already present in the meta.yaml, make sure to specify `run_exports` (see [here](https://bioconda.github.io/contributor/linting.html#missing-run-exports) for the rationale and comprehensive explanation).
+Add a `run_exports` section like this:
+
+```yaml
+build:
+  run_exports:
+    - ...
+
+```
+
+with `...` being one of:
+
+| Case                             | run_exports statement                                               |
+| -------------------------------- | ------------------------------------------------------------------- |
+| semantic versioning              | `{{ pin_subpackage("myrecipe", max_pin="x") }}`     |
+| semantic versioning (0.x.x)      | `{{ pin_subpackage("myrecipe", max_pin="x.x") }}`   |
+| known breakage in minor versions | `{{ pin_subpackage("myrecipe", max_pin="x.x") }}` (in such a case, please add a note that shortly mentions your evidence for that) |
+| known breakage in patch versions | `{{ pin_subpackage("myrecipe", max_pin="x.x.x") }}` (in such a case, please add a note that shortly mentions your evidence for that) |
+| calendar versioning              | `{{ pin_subpackage("myrecipe", max_pin=None) }}`    |
+
+while replacing `"myrecipe"` with either `name` if a `name|lower` variable is defined in your recipe or with the lowercase name of the package in quotes.
+
+### Bot commands for PR management
+
 <details>
   <summary>Please use the following BiocondaBot commands:</summary>
 
@@ -29,14 +58,7 @@ Everyone has access to the following BiocondaBot commands, which can be given in
   </tr>
 </table>
 
-For members of the Bioconda project, the following command is also available:
-
-<table>
-  <tr>
-    <td><code>@BiocondaBot please merge</code></td>
-    <td>Upload built packages/containers and merge a PR. <br />Someone must approve a PR first! <br />This reduces CI build time by reusing built artifacts.</td>
-  </tr>
-</table>
+Note that the <code>@BiocondaBot please merge</code> command is now depreciated. Please just squash and merge instead.
 
 Also, the bot watches for comments from non-members that include `@bioconda/<team>` and will automatically re-post them to notify the addressed `<team>`.
 

.github/workflows/Bulk.yml

@@ -10,9 +10,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
-      max-parallel: 13
+      max-parallel: 6
       matrix:
-        runner: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12] #, 13, 14, 15, 16, 17, 18, 19]
+        runner: [0, 1, 2, 3, 4, 5]
     steps:
       - uses: actions/checkout@v3
         with:
@@ -69,7 +69,7 @@ jobs:
           python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")'
           echo '============'
           bioconda-utils build recipes config.yml \
-            --worker-offset ${{ matrix.runner }} --n-workers 13 \
+            --worker-offset ${{ matrix.runner }} --n-workers 6 \
             --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \
             --record-build-failures --skiplist-leafs
           conda clean -y --all

build-fail-blacklist

@@ -1,3 +1,18 @@
+# Currently kills bulk, and dependants 
+recipes/bioconductor-missmethyl
+recipes/bioconductor-conumee
+recipes/r-shazam
+recipes/r-scoper
+recipes/r-dowser
+recipes/bioconductor-chipxpressdata
+recipes/bioconductor-chipxpress
+recipes/bioconductor-meal
+recipes/bioconductor-dmrcate
+recipes/bioconductor-methylgsa
+recipes/bioconductor-champ
+recipes/bioconductor-appreci8r
+recipes/bioconductor-mirsm
+
 # Allegedly requires ancient gatb
 recipes/lordec
 
@@ -17,6 +32,7 @@ recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5
 recipes/bioconductor-mafdb.gnomad.r2.1.grch38
 recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch37
 recipes/bioconductor-snplocs.hsapiens.dbsnp155.grch38
+recipes/bioconductor-trena
 
 # x86_64-conda-linux-gnu-cc: error: unrecognized command-line option '-R'
 recipes/ncbi-util-legacy
@@ -114,7 +130,6 @@ recipes/popscle
 # Maven no longer accepts http connections https://github.com/rdpstaff/ReadSeq/issues/2
 recipes/rdp-readseq
 
-
 # Only specific versions are failing
 recipes/emmix/1.3
 recipes/hyphy/2.3.11
@@ -131,15 +146,20 @@ recipes/panx/1.6.0
 recipes/panx/1.5.0
 recipes/haploclique/1.3.1
 recipes/blast/2.5.0
+
 # Unclear that the following old version is still needed, but the main recipe has an older version?!?
 recipes/mira/4.9.6
+
 # need to fix the download location, the checksum changes everytime
 recipes/osra/2.1.0
 recipes/imfusion/0.3.2
+
 # can't open file setup.py
 recipes/meneco/1.5.2
+
 # Permission denied ESTscan
 recipes/perl-estscan2/2.1
+
 # Source code no longer easily available
 recipes/strip_it/1.0.2
 recipes/shape_it/1.0.1
@@ -156,7 +176,6 @@ recipes/rappas
 recipes/centrifuge
 recipes/nasp
 recipes/mmvc
-recipes/expansionhunter
 recipes/gemma
 recipes/roary
 recipes/deltabs
@@ -345,18 +364,13 @@ recipes/lorikeet-genome
 # rnamoves.c:(.text.RNA2_move_noLP_bpshift+0x1f): undefined reference to `close_bp'
 recipes/kinsimriboswitch
 
-# Package seems to build fine, but then can't be found when uploading for some reason.
-# the built package /home/runner/miniconda/envs/bioconda/conda-bld/noarch/ngscheckmate-1.0.0-py27r42hdfd78af_4.tar.bz2 cannot be found
-recipes/ngscheckmate
-
 # configure: error: R package gtools not found.
 # (even though r-gtools is in host: and run:
 recipes/footprint
 
 # Requests python3, but is written for python2
 recipes/ctat-mutations
 
-
 # Seems to download maven and then have java issues
 recipes/megagta
 
@@ -374,7 +388,6 @@ recipes/frc
 # CMake Error at build-common/cmake/VersionHelper.cmake:11 (list):
 recipes/somatic-sniper
 
-
 # can't find file to patch at input line 3
 recipes/erds
 
@@ -552,7 +565,6 @@ recipes/rnaclust
 
 # Unknown issues
 recipes/lorma
-recipes/microbecensus
 recipes/minialign
 recipes/nspdk
 recipes/dreamtools
@@ -563,8 +575,6 @@ recipes/odose
 # /opt/conda/conda-bld/pash_1531691261758/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- brl/util/textFileUtil (LoadError)
 recipes/pash
 
-
-
 # Uses deprecated POSIX::tmpnam() function, not maintained, partially replaced by estscan 3.0
 recipes/perl-btlib/0.19
 
@@ -659,7 +669,6 @@ recipes/ucsc-pslmap
 recipes/discovar
 
 # source code no longer available at URL
-recipes/r-genometricorr
 recipes/wade
 
 # Requirements pinned down so much that rebuilds are prevented. (Some old deps may only be available on the old pks/free defaults channel.)
@@ -737,14 +746,8 @@ recipes/gvcftools
 recipes/seer
 
 # Can't compile
-recipes/r-boutroslabplottinggeneral
-recipes/r-qorts
-recipes/r-zerone
 recipes/gplas
 
-# Missing tarball
-recipes/r-prestor
-
 # compilation error and dependants
 recipes/mmult
 recipes/bioconductor-hilbertvisgui
@@ -1040,18 +1043,6 @@ recipes/ucsc-wordline
 recipes/ucsc-xmlcat
 recipes/ucsc-xmltosql
 
-# compilation error: https://github.com/tomoyukif/GBScleanR/issues/1
-recipes/bioconductor-gbscleanr
-
-# compilation error: https://github.com/BBCG/epialleleR/issues/1
-recipes/bioconductor-epialleler
-
-# dependency bioconductor-sspa no longer in bioconductor
-recipes/r-metaboanalyst
-
-# needs https://github.com/conda-forge/r-glmnet-feedstock/pull/26
-recipes/bioconductor-omada
-
 # Above v1.0.5 there are licensing restrictions and it cannot be distributed
 # via bioconda. See https://github.com/bioconda/bioconda-recipes/pull/23476.
 recipes/fishtaco
@@ -1087,7 +1078,6 @@ recipes/taxonomy
 # from numba.np.ufunc import _internal
 # SystemError: initialization of _internal failed without raising an exception
 recipes/bbknn
-recipes/gubbins
 
 # no matching package named `quickersort` found
 recipes/mudskipper

recipes/abismal/meta.yaml

@@ -1,15 +1,15 @@
-{% set version = "3.1.1" %}
+{% set version = "3.2.0" %}
 
 package:
   name: abismal
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
 
 source:
   url: https://github.com/smithlabcode/abismal/releases/download/v{{ version }}/abismal-{{ version }}.tar.gz
-  sha256: 188076f874f5730b4f52e6c1804075f3b9d7b087a02412dfb456aa9ab2b4ae84
+  sha256: 338a21ea32914b8ff457addafb0fe0a750f5cb099e0a9344a9dd7a4d317d2241
 
 requirements:
   build:
@@ -20,9 +20,9 @@ requirements:
     - llvm-openmp  # [osx]
     - libgomp      # [linux]
   host:
-    - zlib
+    - htslib
   run:
-    - zlib
+    - htslib
 
 about:
   home: https://github.com/smithlabcode/abismal

recipes/abromics_galaxy_json_extractor/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "0.4" %}
+{% set version = "0.8" %}
 
 context: {}
 
@@ -8,14 +8,16 @@ package:
 
 source:
   url: https://gitlab.com/ifb-elixirfr/abromics/abromics-galaxy-json-extractor/-/archive/{{ version }}/abromics-galaxy-json-extractor-{{ version }}.tar.gz
-  sha256:  '14bec3067630d8dc67955c587f1e6e8e4232b3913d2bc54ca99b245c190544e8'
+  sha256:  'e356e7bcec23b5a9dc1f4ce59e11c7293c2ddac16d29d0545dd388c641e331c5'
 
 build:
   noarch: python
   number: 0
   script: python -m pip install --no-deps --ignore-installed .
   entry_points:
     - abromics_extract = abromics_galaxy_json_extractor.main:main
+  run_exports:
+    - {{ pin_subpackage('abromics_galaxy_json_extractor', max_pin='x.x') }}
 
 requirements:
   host:

recipes/actc/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "actc" %}
-{% set version = "0.2.0" %}
-{% set sha256 = "44e94104f3a6f6868ce40fcda6d8c1de44e23cfa5bca87690b3e2ab65e31eb13" %}
+{% set version = "0.5.0" %}
+{% set sha256 = "96354e0a7c7981e788ed33aa21cfc7efd115ba92b1494eb57b2a1a811165f049" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  - url: https://github.com/PacificBiosciences/actc/releases/download/{{ version }}/actc
+  - url: https://github.com/PacificBiosciences/actc/releases/download/v{{ version }}/actc
     sha256: {{ sha256 }}
 
 about:
@@ -25,6 +25,8 @@ extra:
 build:
   number: 0
   skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x") }}
 
 test:
   commands:

recipes/agat/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "AGAT" %}
-{% set version = "1.1.0" %}
-{% set sha256 = "38e3df0d0a3817a38e8d824e9d865926c7da6eccc83d583f890faf72e62d7002" %}
+{% set version = "1.2.0" %}
+{% set sha256 = "c812e4b4ca1d27b5b8804025fa5a33f56e9b542948b44885662b2cbb98d06055" %}
 
 package:
   name: "{{ name|lower }}"
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: 0
 
 requirements:
   host:

recipes/agfusion/meta.yaml

@@ -1,5 +1,5 @@
-{% set version = "1.252" %}
-{% set sha256 = "5ac8d27b1e8ece014b8b8138615712ffd3c2f6602dc854d199335986559b7946" %}
+{% set version = "1.4.1" %}
+{% set sha256 = "fd04591d764deeff69978f9d495c3baf854ccfba27366aa0ae4859ad85ca2c60" %}
 
 package:
   name: agfusion
@@ -11,8 +11,10 @@ source:
 
 build:
   noarch: python
-  number: 1
+  number: 0
   script: python -m pip install --no-deps --ignore-installed .
+  run_exports:
+    - {{ pin_subpackage("agfusion", max_pin="x.x") }}
 
 requirements:
   host:
@@ -21,9 +23,9 @@ requirements:
     - setuptools
   run:
     - python
-    - matplotlib >=1.5.0
-    - pandas >=0.18.1
-    - biopython >=1.67
+    - matplotlib-base >=3.6.1
+    - pandas >=1.5.1
+    - biopython >=1.79
     - future >=0.16.0
     - pyensembl >=1.1.0
     - nose2 >=0.6.5

recipes/airr/meta.yaml

@@ -1,19 +1,21 @@
 {% set name = "airr" %}
-{% set version = "1.4.1" %}
+{% set version = "1.5.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 52276f977b31694751f7cc2d56d50843ac7b363883e7daac60130a5abe839ed9
+  sha256: febc0a881bf46b1a9c29ac6a7089dd733ff9120d114585e75dede26403f68d42
 
 build:
   number: 0
   noarch: python
   entry_points:
     - airr-tools=airr.tools:main
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x') }}
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv "
 
 requirements: