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MAINT: env file & distro updates for rachis name change #43

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Merged
lizgehret merged 3 commits into from
Jun 10, 2026
Merged

MAINT: env file & distro updates for rachis name change #43

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6fb6ea7
MAINT: env file & distro updates for rachis name change
lizgehret Jun 10, 2026
826dbd2
update testing CI to accommodate new env file name
lizgehret Jun 10, 2026
46ae9cc
Apply suggestion from @lizgehret
lizgehret Jun 10, 2026
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4 changes: 2 additions & 2 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,8 @@ jobs:
- name: Set up Conda
uses: qiime2-cutlery/setup-miniconda@v3
with:
activate-environment: q2-hello-world-qiime2-tiny-dev
environment-file: q2-hello-world/environment-files/q2-hello-world-qiime2-tiny-dev.yml
activate-environment: q2-hello-world-rachis-tiny-dev
environment-file: q2-hello-world/environment-files/q2-hello-world-rachis-tiny-dev.yml
auto-activate-base: false

- name: Install plugin
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2 changes: 1 addition & 1 deletion copier.yaml
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Expand Up @@ -29,7 +29,7 @@ plugin_short_description:
help: Shorter description, shown when plugin is presented in a list
target_distro:
default: tiny
choices: [tiny, amplicon, metagenome]
choices: [tiny, qiime2, moshpit, pathogenome]
help: Target distribution (if you're not sure, stick with the default).
license:
default: skip-license
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4 changes: 2 additions & 2 deletions template/{{ package_name }}/.github/workflows/ci.yml
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Expand Up @@ -19,8 +19,8 @@ jobs:
- name: Set up Conda
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: {{ package_name }}-qiime2-{{ target_distro }}-dev
environment-file: environment-files/{{ package_name }}-qiime2-{{ target_distro }}-dev.yml
activate-environment: {{ package_name }}-rachis-{{ target_distro }}-dev
environment-file: environment-files/{{ package_name }}-rachis-{{ target_distro }}-dev.yml
auto-activate-base: false

- name: Install plugin
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6 changes: 3 additions & 3 deletions template/{{ package_name }}/.github/workflows/release-env.yml
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Expand Up @@ -76,7 +76,7 @@ jobs:
released_epoch = os.environ['RELEASED_EPOCH']

release_env_path = \
f'environment-files/{pkg_name}-qiime2-{target_distro}-release.yml'
f'environment-files/{pkg_name}-rachis-{target_distro}-release.yml'

if not os.path.exists(release_env_path):
raise Exception(f'{release_env_path} not found.')
Expand Down Expand Up @@ -128,7 +128,7 @@ jobs:
if not updated:
raise ValueError(f'No pip install found for package {pkg_name}.')

new_env_path = f'environment-files/{pkg_name}-qiime2-{target_distro}-{released_epoch}-release-{os.environ['RELEASE_TAG']}.yml'
new_env_path = f'environment-files/{pkg_name}-rachis-{target_distro}-{released_epoch}-release-{os.environ['RELEASE_TAG']}.yml'
with open(new_env_path, 'w') as fh:
yaml.safe_dump(env_data, fh, sort_keys=False)

Expand Down Expand Up @@ -184,7 +184,7 @@ jobs:
run: |
set -e
git checkout automated/release-${{ '{{' }} env.RELEASE_TAG {{ '}}' }}-env-file-updates
ENV_PATH="environment-files/${{ '{{' }} env.PACKAGE_NAME {{ '}}' }}-qiime2-${{ '{{' }} env.TARGET_DISTRO {{ '}}' }}-${{ '{{' }} env.RELEASED_EPOCH {{ '}}' }}-release-${{ '{{' }} env.RELEASE_TAG {{ '}}' }}.yml"
ENV_PATH="environment-files/${{ '{{' }} env.PACKAGE_NAME {{ '}}' }}-rachis-${{ '{{' }} env.TARGET_DISTRO {{ '}}' }}-${{ '{{' }} env.RELEASED_EPOCH {{ '}}' }}-release-${{ '{{' }} env.RELEASE_TAG {{ '}}' }}.yml"

conda env create -n test-release-env -f "$ENV_PATH"

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2 changes: 1 addition & 1 deletion ...ame }}-qiime2-{{ target_distro }}-dev.yml → ...ame }}-rachis-{{ target_distro }}-dev.yml
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Expand Up @@ -3,7 +3,7 @@ channels:
- conda-forge
- bioconda
dependencies:
- qiime2-{{ target_distro }}
- rachis-{{ target_distro }}
# Note 1: Add any additional conda dependencies here.
- pip
- pip:
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2 changes: 1 addition & 1 deletion ...}}-qiime2-{{ target_distro }}-release.yml → ...}}-rachis-{{ target_distro }}-release.yml
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Expand Up @@ -3,7 +3,7 @@ channels:
- conda-forge
- bioconda
dependencies:
- qiime2-{{ target_distro }}
- rachis-{{ target_distro }}
# Note 1: Add any additional conda dependencies here.
- pip
- pip:
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