Main

.github/workflows/docs.yml

@@ -2,9 +2,7 @@ name: docs
 
 on:
   push:
-    branches: [ prod, main, WD, manke ]
   pull_request:
-    branches: [ prod, main, WD, manke ]
 
 defaults:
   run:
@@ -23,6 +21,7 @@ jobs:
       - name: build docs
         run: |
           micromamba activate dissectBCL
+          pip install .
           cd docs
           pip install -r requirements.txt
           make html

.github/workflows/pytest.yml

@@ -4,9 +4,7 @@ name: pytest
 
 on:
   push:
-    branches: [ prod, main, WD, manke, tests ]
   pull_request:
-    branches: [ prod, main, WD, manke, tests ]
 
 defaults:
   run:

README.md

@@ -1,6 +1,6 @@
 [![Documentation Status](https://readthedocs.org/projects/dissectbcl/badge/?version=latest)](https://dissectbcl.readthedocs.io/en/latest/?badge=latest)
-![flake8](https://github.com/maxplanck-ie/dissectBCL/actions/workflows/flake.yml/badge.svg)
-![pytest](https://github.com/maxplanck-ie/dissectBCL/actions/workflows/pytest.yml/badge.svg)
+[![Lint](https://github.com/maxplanck-ie/dissectBCL/actions/workflows/lint.yml/badge.svg)](https://github.com/maxplanck-ie/dissectBCL/actions/workflows/lint.yml)
+![Pytest](https://github.com/maxplanck-ie/dissectBCL/actions/workflows/pytest.yml/badge.svg)
 
 # dissectBCL
 
@@ -12,7 +12,7 @@ Clone this repository, create the environment and pip install
 
  > git clone [email protected]:maxplanck-ie/dissectBCL.git  
  > cd dissectBCL  
- > conda create -f env.yml --name dissectBCL
+ > conda create -f env.yml --name dissectBCL  
  > conda activate dissectBCL  
  > pip install ./  
 
@@ -26,6 +26,10 @@ or
 
  > dissect -c /path/to/config.ini
 
+or
+
+ > dissect -f /path/to/flowcell.ini
+
 ## Docs.
 
 Documentation is available [here](https://dissectbcl.readthedocs.io/en/latest/).

docs/conf.py

@@ -1,5 +1,5 @@
 import sphinx_rtd_theme
-from pbr.version import VersionInfo
+from importlib.metadata import version as versionFetcher
 # Configuration file for the Sphinx documentation builder.
 #
 # For the full list of built-in configuration values, see the documentation:
@@ -11,7 +11,7 @@
 project = 'dissectBCL'
 copyright = '2024'
 author = 'wardDeb'
-release = VersionInfo('dissectBCL').version_string()
+release = versionFetcher("dissectBCL")
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/requirements.txt

@@ -1,3 +1,2 @@
-sphinx==7.2.6
-sphinx_rtd_theme==2.0.0
-pbr==6.0.0
+sphinx>=7.2.6
+sphinx_rtd_theme>=2.0.0

src/tools/emailProjectFinished.py

@@ -175,12 +175,6 @@ def main():
             "our online portal: http://snakequest.ie-freiburg.mpg.de .\n"
             )
 
-    content += (
-        "\nPlease note that sequencing data is no longer deposited "
-        "into Galaxy by default. If you need to access this data in Galaxy, "
-        "please let me know. \n"
-    )
-
     if args.comment:
         content += "\n===\n"
         if os.path.exists(args.comment):