Merge pull request #9 from cokelaer/dev

Update CI, comments, setup

Author: cokelaer

.github/workflows/main.yml

@@ -38,18 +38,23 @@ jobs:
 
 
     - name: install package itself
+      shell: bash -l {0}
       run: |
-         pip install .
+        which pip
+        pip install .
 
     - name: Install dependencies
+      shell: bash -l {0}
       run: |
         pip install coveralls pytest-cov pytest pytest-xdist
 
     - name: testing
+      shell: bash -l {0}
       run: |
         pytest -v --cov-report term-missing --cov=sequana_pipelines.fastqc
 
     - name: coveralls
+      shell: bash -l {0}
       run: |
         echo $COVERALLS_REPO_TOKEN
         coveralls --service=github

README.rst

@@ -7,7 +7,7 @@
     :alt: JOSS (journal of open source software) DOI
 
 .. image:: https://github.com/sequana/fastqc/actions/workflows/main.yml/badge.svg
-   :target: https://github.com/sequana/fastqc/actions/workflows    
+   :target: https://github.com/sequana/fastqc/actions/workflows/main.yml
 
 
 
@@ -132,6 +132,8 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.6.1     * pin sequana version to 1.4.4 to force usage of new fastqc module
+            to fix falco. Updated config documentation.
 1.6.0     * Fixed falco output error and use singularity containers
 1.5.0     * removed modules completely.
 1.4.2     * simplified pipeline (suppress setup and use existing wrapper)

environment.yml

@@ -1,8 +1,8 @@
 name: sequana_fastqc
 
 channels:
-- bioconda
 - conda-forge
+- bioconda
 - defaults
 - r
 

requirements.txt

@@ -1,2 +1,2 @@
-sequana>=0.12.1
+sequana>=0.14.4
 sequana_pipetools>=0.9.1

sequana_pipelines/fastqc/config.yaml

@@ -21,6 +21,8 @@ input_pattern: '*fastq.gz'
 ##############################################################################
 # general section
 #
+# Choose one of the standard method to perform QC of your fastq data
+#
 # method_choice__ = ['fastqc', 'falco']
 general:
     method_choice: fastqc
@@ -36,6 +38,13 @@ fastqc:
     threads: 4
     resources:
         mem: 8G
+
+##############################################################################
+# Falco section
+#
+# :Parameters:
+#
+# - options: string with any valid FastQC options
 falco:
     options: ''
     threads: 4

setup.py

@@ -5,7 +5,7 @@
 
 _MAJOR               = 1
 _MINOR               = 6
-_MICRO               = 0
+_MICRO               = 1
 version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release              = '%d.%d' % (_MAJOR, _MINOR)
 
@@ -69,7 +69,17 @@ def run(self):
     packages = ["sequana_pipelines.fastqc"],
 
     install_requires = open("requirements.txt").read(),
-
+    extras_require={
+        "testing": [
+            "pytest",
+            "pytest-cov",
+            "pytest-xdist",
+            "pytest-mock",
+            "pytest-timeout",
+            "pytest-runner",
+            "coveralls",
+        ],
+    },
     # This is recursive include of data files
     exclude_package_data = {"": ["__pycache__"]},
     package_data = {