Merge pull request #5 from cokelaer/main

Uses click and pyproject

.github/workflows/main.yml

@@ -5,10 +5,11 @@ on:
     branches:
       - main
       - dev
+  workflow_dispatch:
   pull_request:
     branches-ignore: []
   schedule:
-    - cron: '0 0 * * SUN'
+    - cron: '0 0 30 * *'
 
 jobs:
   build-linux:
@@ -29,33 +30,33 @@ jobs:
     - name: checkout git repo
       uses: actions/checkout@v2
 
-    - name: Set up Python 3.X
-      uses: actions/setup-python@v2
+    - name: conda/mamba
+      uses: mamba-org/setup-micromamba@v1
       with:
-        python-version: ${{ matrix.python }}
+          micromamba-version: '1.3.1-0'
+          environment-file: environment.yml
+          create-args: |
+            python=${{ matrix.python }}
+          cache-environment: true
+          cache-downloads: true
 
-    - name: Add conda to system path
+    - name: install package itself
+      shell: bash -el {0}
       run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
+        pip install .
 
-    - name: conda
-      run: |
-          conda install -c conda-forge -c bioconda --quiet -y python=${{ matrix.python }} 
-          conda install -c conda-forge -y ncurses
     - name: Install dependencies
+      shell: bash -el {0}
       run: |
         pip install coveralls pytest-cov pytest pytest-xdist
 
-    - name: install package itself
-      run: |
-         pip install .
-
     - name: testing
+      shell: bash -el {0}
       run: |
         pytest -v --cov-report term-missing --cov=sequana_pipelines.downsampling
 
     - name: coveralls
+      shell: bash -l {0}
       run: |
         echo $COVERALLS_REPO_TOKEN
         coveralls --service=github

.pre-commit-config.yaml

@@ -0,0 +1,33 @@
+
+files: '\.(py|rst|sh)$'
+fail_fast: false
+
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    #-   id: check-executables-have-shebangs
+    -   id: check-ast
+
+-   repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+    -   id: flake8
+        args: ["-j8", "--ignore=E203,E501,W503,E722", "--max-line-length=120", "--exit-zero"]
+
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black
+        args: ["--line-length=120"]
+        exclude: E501
+
+-   repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"] # solves conflicts between black and isort
+

environment.yml

@@ -0,0 +1,13 @@
+name: sequana_downsampling
+
+channels:
+- conda-forge
+- bioconda
+- defaults
+- r
+
+dependencies:
+- pigz
+- pip:
+  - sequana
+

pyproject.toml

@@ -0,0 +1,55 @@
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "sequana-downsampling"
+version = "0.10.0"
+description = "tandem repeat finder pipeline"
+authors = ["Sequana Team"]
+license = "BSD-3"
+repository = "https://github.com/sequana/downsampling"
+readme = "README.rst"
+keywords = ["snakemake", "NGS", "sequana", "fastq", "downsampling"]
+classifiers = [
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Education",
+        "Intended Audience :: End Users/Desktop",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "Operating System :: POSIX :: Linux",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Scientific/Engineering :: Information Analysis",
+]
+
+packages = [
+    {include = "sequana_pipelines"}
+]
+
+
+[tool.poetry.dependencies]
+python = ">=3.8,<4.0"
+sequana = ">=0.16.4"
+sequana_pipetools = ">=0.16.6"
+click-completion = "^0.5.2"
+click = "^8.1.7"
+rich-click = "^1.7.2"
+
+
+
+[tool.poetry.scripts]
+sequana_downsampling = "sequana_pipelines.downsampling.main:main"
+
+
+[tool.poetry.group.dev.dependencies]
+black = "^23.7.0"
+pytest = "^7.4.0"
+mock = "^5.1.0"
+pytest-mock = "^3.11.1"
+pytest-cov = "^4.1.0"
+

sequana_pipelines/downsampling/config.yaml

@@ -7,10 +7,9 @@
 # use it, otherwise use input_samples.
 # ============================================================================
 
-
 input_directory: '.'
 input_pattern: '*.fastq.gz'
-input_readtag: "_R[12]_"
+#input_readtag: "_R[12]_"
 
 
 ##############################################################################
@@ -32,7 +31,3 @@ downsampling:
     input_format: fastq
 
 
-##############################################################################
-#
-#onsuccess:
-#    toclean: " slurm*out downsampling.rules config.yaml stats.txt "

sequana_pipelines/downsampling/downsampling.rules

@@ -11,7 +11,6 @@ snakemake -s downsampling.rules --forceall --stats stats.txt --cores 4
 """
 from sequana_pipetools import PipelineManager
 
-from sequana import sequana_data
 
 # This must be defined before the include
 configfile: "config.yaml"
@@ -24,13 +23,10 @@ else:
 
 
 
-
-
 rule pipeline:
     input: expand("output/{sample}.done", sample=manager.samples)
 
 
-
 if config["downsampling"]['input_format'] == "fastq":
     rule downsampling:
         input:  manager.getrawdata()
@@ -91,4 +87,4 @@ onsuccess:
     shell("mv output/* . && rm -rf output")
 
 onerror:
-    print("An error occurred. See message above.")
+    manager.onerror()