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Conda recipe #404

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merged 4 commits into from
Dec 7, 2023
Merged

Conda recipe #404

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c83ad7a
add conda recipe and wrapper script
apriltuesday Nov 28, 2023
c20af12
fix biomart query and conda dependencies
apriltuesday Nov 28, 2023
5066e4a
clean up build.sh
apriltuesday Nov 28, 2023
1f3a405
single source of version for wrapper and setup
apriltuesday Dec 6, 2023
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1 change: 1 addition & 0 deletions bin/cmat/VERSION
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
3.0.6.dev4
2 changes: 1 addition & 1 deletion bin/cmat/cmat
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Expand Up @@ -4,8 +4,8 @@
# ones in Andries Feder's Cladebreaker (https://github.com/andriesfeder/cladebreaker)
# and Robert A. Petit III's Bactopia (https://bactopia.github.io).

VERSION=3.0.6.dev3
CONDA_ENV=$(which cmat | sed 's=bin/cmat==')
VERSION=$(cat "${CONDA_ENV}/bin/VERSION")
CMAT_NF="${CONDA_ENV}/share/cmat-${VERSION}/pipelines"
MAPPINGS_FILE="${CONDA_ENV}/share/cmat-${VERSION}/mappings/latest_mappings.tsv"

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2 changes: 1 addition & 1 deletion conda/meta.yaml
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@@ -1,4 +1,4 @@
{% set version = "3.0.6.dev3" %}
{% set version = "3.0.6.dev4" %}

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Just in case it's a hassle for you to change this manually. Now that we have the version within the file VERSION, would it be handy to have a very simple python script that replaces this bit of version in the meta.yaml, triggered by a GitHub action?

For example, something like the following, summarised by our friend GPT:

import re
version_file_path = 'VERSION'
yaml_file_path = 'meta.yaml'

with open(version_file_path, 'r') as file:
    version = file.read().strip()

with open(yaml_file_path, 'r') as file:
    yaml_content = file.read()

new_yaml_content = re.sub(r'{% set version = ".*" %}', f'{{% set version = "{version}" %}}', yaml_content)

with open(yaml_file_path, 'w') as file:
    file.write(new_yaml_content)

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Again, only if it's less of a hassle to keep in mind that the VERSION is also in the YAML file

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Or actually, rather than modify this YAML file, why not have the other files read the file meta.yaml instead of VERSION? That way, the version exists only in one place. We could use a regex to find the version within this yaml file and extract it instead

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@apriltuesday apriltuesday Dec 7, 2023 •
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I think it's okay for now, but it's something to keep in mind for a future PR (e.g. in #406)... we can decide the direction of information flow (i.e. from VERSION to YAML or vice versa) and how it's triggered there.

package:
name: cmat
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4 changes: 3 additions & 1 deletion setup.py
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Expand Up @@ -6,6 +6,8 @@
# allow setup.py to be run from any path
os.chdir(os.path.normpath(os.path.join(os.path.abspath(__file__), os.pardir)))

version = open(os.path.join(os.path.abspath(os.path.dirname(__file__)), 'bin', 'cmat', 'VERSION')).read().strip()


def get_requires():
requires = []
Expand All @@ -27,7 +29,7 @@ def get_requires():
long_description = fh.read()

setup(name='cmat',
version='3.0.6.dev3',
version=version,
author_email='[email protected]',
url='https://github.com/EBIvariation/CMAT',
packages=find_packages(),
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