diff --git a/.github/workflows/ci-dev.yaml b/.github/workflows/ci-dev.yaml deleted file mode 100644 index f451fde..0000000 --- a/.github/workflows/ci-dev.yaml +++ /dev/null @@ -1,12 +0,0 @@ -# Example of workflow trigger for calling workflow (the client). -name: ci-dev -on: - pull_request: - branches: ["dev"] - push: - branches: ["dev"] -jobs: - ci: - uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml@dev - with: - distro: amplicon diff --git a/.github/workflows/ci-q2-fmt.yml b/.github/workflows/ci-q2-fmt.yml new file mode 100644 index 0000000..213fcd9 --- /dev/null +++ b/.github/workflows/ci-q2-fmt.yml @@ -0,0 +1,31 @@ +name: ci-q2-fmt +on: + pull_request: + branches: ["dev"] + push: + branches: ["dev"] +jobs: + ci: + uses: qiime2/distributions/.github/workflows/lib-community-ci.yaml@dev + with: + github-repo: q2-fmt + env-file-name: 2024.10-q2-fmt-environment.yml + lint: + runs-on: ubuntu-latest + steps: + - name: checkout source + uses: actions/checkout@v4 + + - name: install dependencies + run: | + python -m pip install --upgrade pip + pip install -q flake8 + pip install -q https://github.com/qiime2/q2lint/archive/master.zip + + - name: Lint plugin + shell: bash -l {0} + run: | + cd q2-fmt + flake8 + q2lint + diff --git a/.github/workflows/cron-q2-fmt.yml b/.github/workflows/cron-q2-fmt.yml new file mode 100644 index 0000000..b7b5ee4 --- /dev/null +++ b/.github/workflows/cron-q2-fmt.yml @@ -0,0 +1,11 @@ +name: cron-q2-fmt +on: + workflow_dispatch: {} + schedule: + - cron: 0 0 * * SUN +jobs: + ci: + uses: qiime2/distributions/.github/workflows/lib-community-ci.yaml@dev + with: + github-repo: q2-fmt + env-file-name: development-q2-fmt-environment.yml diff --git a/README.md b/README.md index e021793..cdcd992 100644 --- a/README.md +++ b/README.md @@ -8,25 +8,27 @@ ## Installation -Please note that this software is now an alpha release. Initial conda packages are available, but have not been tested in integration against our other plugins yet. For now, create a fresh conda environment for q2-fmt using the following command: +Please note that this software is now an alpha release. Initial conda packages are available, but have not been tested in integration against our other plugins yet. For now, create a fresh conda environment for q2-fmt using the following command: +Note: This is a `Development` install of q2-fmt Mac OS instructions ```bash -wget https://data.qiime2.org/distro/fmt/qiime2-fmt-2023.9-py38-osx-conda.yml -CONDA_SUBDIR=osx-64 conda env create -n qiime2-fmt-2023.9 --file qiime2-fmt-2023.9-py38-osx-conda.yml -conda activate qiime2-fmt-2023.9 -conda config --env --set subdir osx-64 +CONDA_SUBDIR=osx-64 conda env create \ + -n q2-fmt-2024.10 \ + -f https://raw.githubusercontent.com/qiime2/q2-fmt.git/dev/environment-files/2024.10-q2-fmt-environment.yml ``` + Linux instructions ```bash -wget https://data.qiime2.org/distro/fmt/qiime2-fmt-2023.9-py38-linux-conda.yml -conda env create -n qiime2-fmt-2023.9 --file qiime2-fmt-2023.9-py38-linux-conda.yml +conda env create \ + -n q2-fmt-2024.10 \ + -f https://raw.githubusercontent.com/qiime2/q2-fmt.git/dev/environment-files/2024.10-q2-fmt-environment.yml ``` + Then activate your new environment as usual. ```bash -conda activate q2-fmt-2023.9 +conda activate q2-fmt-2024.10 ``` -Please be aware that `q2-fmt` and `q2-stats` will be the only visible plugins in this environment. ## Examples Example data can be generated using the `--example-data` flag on each action diff --git a/environment-files/2024.10-q2-fmt-environment.yml b/environment-files/2024.10-q2-fmt-environment.yml new file mode 100644 index 0000000..caacbf4 --- /dev/null +++ b/environment-files/2024.10-q2-fmt-environment.yml @@ -0,0 +1,10 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.10/amplicon/passed +- conda-forge +- bioconda +dependencies: + - qiime2-amplicon + - pip + - pip: + - q2-fmt@git+https://github.com/qiime2/q2-fmt.git@dev + - frictionless diff --git a/environment-files/development-q2-fmt-environment.yml b/environment-files/development-q2-fmt-environment.yml new file mode 100644 index 0000000..caacbf4 --- /dev/null +++ b/environment-files/development-q2-fmt-environment.yml @@ -0,0 +1,10 @@ +channels: +- https://packages.qiime2.org/qiime2/2024.10/amplicon/passed +- conda-forge +- bioconda +dependencies: + - qiime2-amplicon + - pip + - pip: + - q2-fmt@git+https://github.com/qiime2/q2-fmt.git@dev + - frictionless