diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 300b0b1..4447bd2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -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 diff --git a/copier.yaml b/copier.yaml index b34c5c5..ab158b0 100644 --- a/copier.yaml +++ b/copier.yaml @@ -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 diff --git a/template/{{ package_name }}/.github/workflows/ci.yml b/template/{{ package_name }}/.github/workflows/ci.yml index 0e7ca82..d7eec36 100644 --- a/template/{{ package_name }}/.github/workflows/ci.yml +++ b/template/{{ package_name }}/.github/workflows/ci.yml @@ -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 diff --git a/template/{{ package_name }}/.github/workflows/release-env.yml b/template/{{ package_name }}/.github/workflows/release-env.yml index b11e38b..9a98daa 100644 --- a/template/{{ package_name }}/.github/workflows/release-env.yml +++ b/template/{{ package_name }}/.github/workflows/release-env.yml @@ -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.') @@ -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) @@ -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" diff --git a/template/{{ package_name }}/environment-files/{{ package_name }}-qiime2-{{ target_distro }}-dev.yml b/template/{{ package_name }}/environment-files/{{ package_name }}-rachis-{{ target_distro }}-dev.yml similarity index 96% rename from template/{{ package_name }}/environment-files/{{ package_name }}-qiime2-{{ target_distro }}-dev.yml rename to template/{{ package_name }}/environment-files/{{ package_name }}-rachis-{{ target_distro }}-dev.yml index fe4e2d7..9367a1c 100644 --- a/template/{{ package_name }}/environment-files/{{ package_name }}-qiime2-{{ target_distro }}-dev.yml +++ b/template/{{ package_name }}/environment-files/{{ package_name }}-rachis-{{ target_distro }}-dev.yml @@ -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: diff --git a/template/{{ package_name }}/environment-files/{{ package_name }}-qiime2-{{ target_distro }}-release.yml b/template/{{ package_name }}/environment-files/{{ package_name }}-rachis-{{ target_distro }}-release.yml similarity index 96% rename from template/{{ package_name }}/environment-files/{{ package_name }}-qiime2-{{ target_distro }}-release.yml rename to template/{{ package_name }}/environment-files/{{ package_name }}-rachis-{{ target_distro }}-release.yml index 615eb21..e14fa21 100644 --- a/template/{{ package_name }}/environment-files/{{ package_name }}-qiime2-{{ target_distro }}-release.yml +++ b/template/{{ package_name }}/environment-files/{{ package_name }}-rachis-{{ target_distro }}-release.yml @@ -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: