Refactor CLI to use Typer

.envrc

@@ -0,0 +1,3 @@
+export TOWER_ACCESS_TOKEN=$(op read "op://Employee/Enterprise Staging Platform/credential" --no-newline)
+export TOWER_WORKSPACE_ID=$(op read "op://Employee/Enterprise Staging Platform/workspace_id" --no-newline)
+export TOWER_API_ENDPOINT=$(op read "op://Employee/Enterprise Staging Platform/hostname" --no-newline)

.github/CONTRIBUTING.md

@@ -29,6 +29,8 @@ conda env create -f environment.yml
 conda activate seqerakit
 ```
 
+Or [install tw-cli from GitHub](https://github.com/seqeralabs/tower-cli?tab=readme-ov-file#getting-started).
+
 You can then install the local repository for development using the `pip -e` command which will install it in place without copying it to your `PYTHONPATH`. Using `--no-deps` will ignore dependencies which have already been installed via Conda. This assumes the current working directory is a clone of this repository.
 
 ```console
@@ -37,6 +39,15 @@ pip install -e . --no-deps
 
 You can then develop the code before committing changes and opening a pull request.
 
+#### uv workflow
+
+1. [Install uv](https://docs.astral.sh/uv/getting-started/installation/)
+2. `uv run seqerakit -h`
+
+##### Publishing
+
+1. [uv publish](https://docs.astral.sh/uv/guides/publish/)
+
 ### pre-commit
 
 We use [pre-commit](https://pre-commit.com/) which runs [Black](https://github.com/psf/black) and [Ruff](https://github.com/astral-sh/ruff) to ensure code consistency during development. Install pre-commit and configure with `pre-commit install` which will now run before every commit ensuring code consistency.

.github/workflows/e2e-testing.yml

@@ -38,21 +38,15 @@ jobs:
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
 
     steps:
-      - name: Check out source-code repository
-        uses: actions/checkout@v3
-
-      - name: Setup Python
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v4
         with:
-          python-version: '3.12'
-
-      - name: Install pip & seqerakit
-        run: |
-          pip install -e .
+          enable-cache: true
+          cache-dependency-glob: 'uv.lock'
 
-      - name: Install Tower CLI v0.9.1
+      - name: Install Tower CLI
         run: |
-          wget https://github.com/seqeralabs/tower-cli/releases/download/v0.9.1/tw-linux-x86_64 \
+          wget https://github.com/seqeralabs/tower-cli/releases/download/v0.10.3/tw-linux-x86_64 \
           && chmod +x tw-linux-x86_64 \
           && sudo mv tw-linux-x86_64 /usr/local/bin/tw
 
@@ -64,7 +58,7 @@ jobs:
           echo $GOOGLE_KEY | base64 -d > $temp_file
           export GOOGLE_KEY=$temp_file
 
-          seqerakit examples/yaml/e2e/*.yml --delete || true
+          uv run seqerakit examples/yaml/e2e/*.yml --delete || true
 
       - name: dryrun
         run: |
@@ -80,7 +74,7 @@ jobs:
           echo $GOOGLE_KEY | base64 -d > $temp_file
           export GOOGLE_KEY=$temp_file
 
-          seqerakit examples/yaml/e2e/*.yml
+          uv run seqerakit examples/yaml/e2e/*.yml
 
       - name: teardown
         if: ( success() || failure() ) && ( github.event_name != 'workflow_dispatch' || inputs.clearup )
@@ -89,4 +83,4 @@ jobs:
           echo $GOOGLE_KEY | base64 -d > $temp_file
           export GOOGLE_KEY=$temp_file
 
-          seqerakit examples/yaml/e2e/*.yml --delete
+          uv runseqerakit examples/yaml/e2e/*.yml --delete

.github/workflows/python-testing.yml

@@ -1,29 +1,22 @@
-name: Lint-and-test
+name: Lint and Test
 
 on: [push]
 
 jobs:
-  lint:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: psf/black@stable
-      - uses: chartboost/ruff-action@v1
+      - uses: actions/setup-python@v4
+      - uses: pre-commit/action@v3.0.1
   test:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: astral-sh/setup-uv@v4
         with:
-          python-version: 3.8
-          cache: 'pip' # caching pip dependencies
-          cache-dependency-path: setup.py
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install pytest
-          pip install pytest-mock
-          pip install -e .
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
       - name: Run tests
         run: |
-          python -m pytest --import-mode=append tests/
+          uv run pytest

.github/workflows/teardown.yml

@@ -26,23 +26,17 @@ jobs:
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
 
     steps:
-      - name: Check out source-code repository
-        uses: actions/checkout@v3
-
-      - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v3
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v4
         with:
-          auto-update-conda: true
-          environment-file: environment.yml
-          python-version: '3.12'
-          mamba-version: '*'
-          channels: conda-forge,bioconda
-          activate-environment: seqerakit
-          use-mamba: true
+          enable-cache: true
+          cache-dependency-glob: 'uv.lock'
 
-      - name: Install pip & seqerakit
+      - name: Install Tower CLI v0.9.1
         run: |
-          pip install -e .
+          wget https://github.com/seqeralabs/tower-cli/releases/download/v0.10.3/tw-linux-x86_64 \
+          && chmod +x tw-linux-x86_64 \
+          && sudo mv tw-linux-x86_64 /usr/local/bin/tw
 
       - name: teardown
         run: |
@@ -51,4 +45,4 @@ jobs:
           echo $GOOGLE_KEY | base64 -d > $temp_file
           export GOOGLE_KEY=$temp_file
 
-          seqerakit --delete examples/yaml/seqerakit-e2e.yml
+          uv run seqerakit --delete examples/yaml/seqerakit-e2e.yml

.pre-commit-config.yaml

@@ -14,13 +14,13 @@ repos:
     rev: 'v2.7.1'
     hooks:
       - id: prettier
-  - repo: https://github.com/psf/black
-    rev: 24.10.0
-    hooks:
-      - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.0.272
+    rev: v0.8.3
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.5.9
+    hooks:
+      - id: uv-lock

.python-version

@@ -0,0 +1 @@
+3.12

examples/yaml/datasets/rnaseq_samples.csv

@@ -5,4 +5,4 @@ WT_REP2,s3://ngi-igenomes/test-data/rnaseq/minimal/GSE110004/SRR6357072_1.fastq.
 RAP1_UNINDUCED_REP1,s3://ngi-igenomes/test-data/rnaseq/minimal/GSE110004/SRR6357073_1.fastq.gz,,auto
 RAP1_UNINDUCED_REP2,s3://ngi-igenomes/test-data/rnaseq/minimal/GSE110004/SRR6357074_1.fastq.gz,,reverse
 RAP1_UNINDUCED_REP2,s3://ngi-igenomes/test-data/rnaseq/minimal/GSE110004/SRR6357075_1.fastq.gz,,reverse
-RAP1_IAA_30M_REP1,s3://ngi-igenomes/test-data/rnaseq/minimal/GSE110004/SRR6357076_1.fastq.gz,s3://ngi-igenomes/test-data/rnaseq/minimal/GSE110004/SRR6357076_2.fastq.gz,reverse
+RAP1_IAA_30M_REP1,s3://ngi-igenomes/test-data/rnaseq/minimal/GSE110004/SRR6357076_1.fastq.gz,s3://ngi-igenomes/test-data/rnaseq/minimal/GSE110004/SRR6357076_2.fastq.gz,reverse

examples/yaml/pipelines/nextflow.config

@@ -1 +1 @@
-process.maxRetries = 1
+process.maxRetries = 1

examples/yaml/pipelines/nf_core_rnaseq_params.yml

@@ -1 +1 @@
-outdir: 'az://seqeralabs-showcase/nf-core-rnaseq/results'
+outdir: 'az://seqeralabs-showcase/nf-core-rnaseq/results'

examples/yaml/pipelines/nf_core_viralrecon_illumina_params.yml

@@ -1 +1 @@
-outdir: 'gs://seqeralabs-showcase-eu-north-1/nf-core-viralrecon/illumina/results'
+outdir: 'gs://seqeralabs-showcase-eu-north-1/nf-core-viralrecon/illumina/results'

pyproject.toml

@@ -0,0 +1,56 @@
+[project]
+name = "seqerakit"
+version = "0.4.9"
+description = "Automate creation of Seqera Platform resources"
+readme = "README.md"
+requires-python = ">=3.8,<4"
+keywords = [
+    "nextflow",
+    "bioinformatics",
+    "workflow",
+    "pipeline",
+    "seqera-platform",
+    "seqera",
+]
+authors = [
+  {name = "Esha Joshi", email = "[email protected]"},
+  {name = "Adam Talbot", email = "[email protected]"},
+  {name = "Harshil Patel", email = "[email protected]"},
+]
+# TODO
+maintainers = [
+  {name = "Esha Joshi", email = "[email protected]"},
+]
+# TODO https://pypi.org/classifiers/
+classifiers = [
+    "License :: OSI Approved :: Apache Software License"
+]
+dependencies = [
+    "pyyaml>=6.0.0",
+    "typer>=0.15.1",
+]
+[project.urls]
+Homepage = "https://seqera.io/"
+Documentation = "https://docs.seqera.io/platform/24.2/seqerakit/installation"
+Repository = "https://github.com/seqeralabs/seqera-kit"
+Issues = "https://github.com/seqeralabs/seqera-kit/issues"
+Changelog = "https://github.com/seqeralabs/seqera-kit/releases"
+
+[project.scripts]
+seqerakit = "seqerakit.cli:run"
+
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+packages = ["seqerakit"]
+zip-safe = false
+include-package-data = true
+
+[dependency-groups]
+dev = [
+    "pre-commit>=3.5.0",
+    "pytest-mock>=3.14.0",
+    "pytest>=8.3.4",
+]