Add publication identifiers to nextstrain recipes, aarch64 to nextcla…

…de2 (#48938)

recipes/augur/meta.yaml

@@ -9,7 +9,7 @@ source:
   sha256: 88ecf208384fff1ba8dee20596c2905a4d27707a39e1e9590d2fef717d29dd5f
 
 build:
-  number: 0
+  number: 1
   noarch: python
   entry_points:
     - augur = augur.__main__:main
@@ -58,6 +58,8 @@ about:
   license_file: LICENSE.txt
 
 extra:
+  identifiers:
+    - doi:10.21105/joss.02906
   recipe-maintainers:
     - huddlej
     - tsibley

recipes/auspice/meta.yaml

@@ -9,7 +9,7 @@ source:
   sha256: 89c620bc790c5e3f28969a253f41e36bf35a13346cb8c6ab55868d9c6ee08714
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage("auspice", max_pin="x.x") }}
 
@@ -42,6 +42,9 @@ about:
   license_family: AGPL
 
 extra:
+  identifiers:
+    # Generic Nextstrain paper, for lack of specific Auspice one
+    - doi:10.1093/bioinformatics/bty407 
   additional-platforms:
     - linux-aarch64
   recipe-maintainers:

recipes/nextclade/meta.yaml

@@ -16,7 +16,7 @@ source:
     sha256: 579f499f7f0f5f2b9d520971ded4e265140859317f083ff8e2879ad74373ec33                                           # [osx and arm64]
 
 build:
-  number: 0
+  number: 1
   binary_relocation: False
   run_exports:
   - {{ pin_compatible(name, max_pin='x') }}
@@ -37,6 +37,8 @@ about:
   dev_url: https://github.com/nextstrain/nextclade
 
 extra:
+  identifiers:
+    - doi:10.21105/joss.03773
   additional-platforms:
     - linux-aarch64
   recipe-maintainers:

recipes/nextclade2/meta.yaml

@@ -6,15 +6,17 @@ package:
   version: "{{ version }}"
 
 source:
-  - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/nextclade-x86_64-unknown-linux-gnu   # [linux64]
+  - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/nextclade-x86_64-unknown-linux-gnu    # [linux64]
     sha256: 1a9a82655830243ffd01937ebb895744ff46ec49f725ef6feff9a3f0e37d90d1                                           # [linux64]
-  - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/nextclade-x86_64-apple-darwin        # [osx and x86_64]
-    sha256: 432f56d2152edda49b8c4a2c3f81d9a5da7419a6cc7c4a3d5205d17d5f834cf6                                           # [osx and x86_64]
-  - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/nextclade-aarch64-apple-darwin       # [arm64]
+  - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/nextclade-x86_64-apple-darwin         # [osx and x86_64]
+    sha256: a5ad4c2ca527929ab8c8b3b2521287488383f78fc1ee3030cbf5af23856b58b0                                           # [osx and x86_64]
+  - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/nextclade-aarch64-apple-darwin        # [arm64]
     sha256: aaac669618d953381428eac3674fe6cb22bef66e7c1ae55552f6a1567f3d3030                                           # [arm64]
+  - url: https://github.com/nextstrain/nextclade/releases/download/{{ version }}/nextclade-aarch64-unknown-linux-gnu   # [aarch64]
+    sha256: e8bf11ba18c40aaad6b91b1a65bd49b304375f77b9273b1a17e75ba32cffbca8                                           # [aarch64]
 
 build:
-  number: 0
+  number: 1
   binary_relocation: False
   run_exports:
   - {{ pin_compatible(name, max_pin='x') }}
@@ -34,6 +36,10 @@ about:
   dev_url: https://github.com/nextstrain/nextclade
 
 extra:
+  identifiers:
+    - doi:10.21105/joss.03773
+  additional-platforms:
+    - linux-aarch64
   recipe-maintainers:
     - corneliusroemer
   skip-lints:

recipes/nextclade2/run_test.sh

@@ -3,6 +3,13 @@
 set -x
 set -e
 
+# Skip if aarch64 on linux
+# Because Nextclade requires glibc >= 2.18 not available yet on aarch64 builder
+if [[ $target_platform == linux-aarch64 ]]; then
+    echo "Skipping test on aarch64"
+    exit 0
+fi
+
 nextclade2 --version
 
 nextclade2 dataset get --name 'sars-cov-2' --output-dir 'data/sars-cov-2'

recipes/nextstrain-cli/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "8.2.0" %}
+{% set version = "8.5.0" %}
 
 package:
   name: nextstrain-cli
   version: {{ version }}
 
 source:
-  url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain-cli-{{ version }}.tar.gz
-  sha256: 9b48dd8f32416d43b5f7db8a4a5ca045913a41a4967a5ae189240cbd67c285a2
+  url: https://pypi.io/packages/source/n/nextstrain-cli/nextstrain_cli-{{ version }}.tar.gz
+  sha256: f5b41b5185560e77f35ce1498ed24dd5ce5561ebd7ca58f434935d8e79f22ac5
 
 build:
   number: 0
@@ -71,3 +71,8 @@ extra:
   recipe-maintainers:
     - tsibley
     - corneliusroemer
+    - genehack
+    - victorlin
+  identifiers:
+    - doi:10.1093/bioinformatics/bty407 
+

recipes/nextstrain/meta.yaml

@@ -4,14 +4,14 @@ package:
 
 build:
   noarch: generic
-  number: 1
+  number: 2
 
 requirements:
   run:
     # Nextstrain components in Conda
     - augur
     - auspice
-    - nextalign
+    - nextclade
     - nextstrain-cli
 
     # Necessary for several of our core builds/tutorials
@@ -23,7 +23,7 @@ test:
   commands:
     - augur --help
     - auspice --help
-    - nextalign --help
+    # - nextclade --help fails on aarch64 due to glibc being too low here
     - nextstrain --help
 
 about:
@@ -45,3 +45,6 @@ extra:
   recipe-maintainers:
     - tsibley
     - huddlej
+  identifiers:
+    - doi:10.1093/bioinformatics/bty407 
+

recipes/treetime/meta.yaml

@@ -11,7 +11,7 @@ source:
 
 build:
   noarch: python
-  number: 0
+  number: 1
   script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . -vvv
   entry_points:
     - treetime = treetime.__main__:main
@@ -46,6 +46,8 @@ about:
   dev_url: https://github.com/neherlab/treetime
 
 extra:
+  identifiers:
+    - doi:10.1093/ve/vex042
   recipe-maintainers:
     - corneliusroemer
     - rneher