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Update augur: Automatically include requirements from Augur's setup.py
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Reduces the chance of them diverging again in the future (e.g. like the
divergence corrected in bc41202).
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tsibley committed Feb 17, 2021
1 parent 13b981a commit 12c2f39
Showing 1 changed file with 25 additions and 10 deletions.
35 changes: 25 additions & 10 deletions recipes/augur/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
{% set version = "11.1.2" %}
{% set pkg = load_setup_py_data() %}

package:
name: augur
Expand All @@ -9,27 +10,41 @@ source:
sha256: 2a131514c0aa31cabdb24357a116c8f81e79faff4087caed7b81640195056a9c

build:
number: 1
number: 2
noarch: python
entry_points:
- augur = augur.__main__:main
script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv"

requirements:
host:
- python >=3.6
- python {{ pkg.python_requires }}
- pip

run:
- python >=3.6
- bcbio-gff >=0.6.0,<0.7
- biopython >=1.67,<=1.76
- jsonschema >=3.0.0,<4
- packaging >=19.2
- pandas >=1.0.0,<2
- treetime >=0.8,<0.9
- python {{ pkg.python_requires }}

# Requirements declared in Augur's setup.py
{%
set pypi_to_conda = {
"phylo-treetime": "treetime",
}
%}
{% for req in pkg.install_requires %}
{% if ' ' in req %}
{% set name, versions = req.split(maxsplit=1) %}
{% else %}
{% set name, versions = req, '' %}
{% endif %}
- {{ pypi_to_conda[name] | default(name) }} {{versions.replace(' ', '')}}
{% endfor %}

# Extras which will typically be desired in a Conda installation of Augur,
# from PyPI:
- snakemake >=5.4.0
- cvxopt >=1.1.9,<2

# …and non-Python packages.
- mafft
- raxml
- fasttree
Expand All @@ -45,7 +60,7 @@ test:
about:
home: https://github.com/nextstrain/augur
license: AGPL-3.0
summary: 'Process pathogen genome data for the Nextstrain platform'
summary: "{{ pkg.description }}"
license_family: AGPL
license_file: LICENSE.txt

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