Merge pull request #800 from maxplanck-ie/dev_adRn

Hopefully, this will solve actual and future issues.

.azure-pipelines/setup.yml

@@ -3,11 +3,11 @@ steps:
 #  inputs:
 #    createCustomEnvironment: true
 #    environmentName: foo
-#    packageSpecs: snakemake fuzzywuzzy mock sphinx sphinx-argparse sphinx_rtd_theme flake8 "python=3.7" pip
+#    packageSpecs: snakemake fuzzywuzzy mock sphinx sphinx-argparse sphinx_rtd_theme flake8 "python=3.9" pip
 #    installOptions: -c conda-forge -c bioconda --quiet
 #    createOptions: -c conda-forge -c bioconda --quiet --yes
 - bash: |
-    conda create -n foo -q --yes --quiet -c conda-forge -c bioconda snakemake=6.2.1 fuzzywuzzy mock sphinx sphinx-argparse sphinx_rtd_theme flake8 coreutils python=3.7
+    conda create -n foo -q --yes --quiet -c conda-forge -c bioconda snakemake=6.2.1 fuzzywuzzy mock sphinx sphinx-argparse sphinx_rtd_theme flake8 coreutils mamba python=3.9
   displayName: Installing dependencies
 - bash: |
     source activate foo

azure-pipelines.yml

@@ -4,11 +4,11 @@ pr:
 jobs:
 - job: 'flake'
   pool:
-    vmImage: 'ubuntu-16.04'
+    vmImage: 'ubuntu-20.04'
   strategy:
     matrix:
-      Python37:
-        python.version: '3.7'
+      Python39:
+        python.version: '3.9'
     maxParallel: 1
 
   steps:
@@ -22,11 +22,11 @@ jobs:
 
 - job: 'CI_tests'
   pool:
-    vmImage: 'ubuntu-16.04'
+    vmImage: 'ubuntu-20.04'
   strategy:
     matrix:
-      Python37:
-        python.version: '3.7'
+      Python39:
+        python.version: '3.9'
     maxParallel: 1
 
   steps:
@@ -40,11 +40,11 @@ jobs:
 
 - job: 'docs'
   pool:
-    vmImage: 'ubuntu-16.04'
+    vmImage: 'ubuntu-20.04'
   strategy:
     matrix:
-      Python37:
-        python.version: '3.7'
+      Python39:
+        python.version: '3.9'
     maxParallel: 1
 
   steps:
@@ -59,21 +59,21 @@ jobs:
 
 - job: 'envs'
   pool:
-    vmImage: 'ubuntu-16.04'
+    vmImage: 'ubuntu-20.04'
   strategy:
     matrix:
-      Python37:
-        python.version: '3.7'
+      Python39:
+        python.version: '3.9'
     maxParallel: 1
 
   steps:
   - bash: echo "##vso[task.prependpath]/usr/share/miniconda/bin"
     displayName: Add conda to PATH
   - template: .azure-pipelines/setup.yml
   - task: UsePythonVersion@0
-    displayName: 'Use Python 3.7'
+    displayName: 'Use Python 3.9'
     inputs:
-      versionSpec: 3.7
+      versionSpec: 3.9
   - bash: |
       source activate foo
       python .azure-pipelines/testCreateEnv.py -d 1
@@ -93,8 +93,8 @@ jobs:
     vmImage: 'macOS-latest'
   strategy:
     matrix:
-      Python37:
-        python.version: '3.7'
+      Python39:
+        python.version: '3.9'
     maxParallel: 1
 
   steps:
@@ -110,9 +110,9 @@ jobs:
     displayName: Fix OSX permissions
   - template: .azure-pipelines/setup.yml
   - task: UsePythonVersion@0
-    displayName: 'Use Python 3.7'
+    displayName: 'Use Python 3.9'
     inputs:
-      versionSpec: 3.7
+      versionSpec: 3.9
   - bash: |
       source activate foo
       sudo -E python .azure-pipelines/testCreateEnv.py -d 1

docs/conf.py

@@ -98,7 +98,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'python'
+# language = 'python'
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:

docs/content/setting_up.rst

@@ -34,7 +34,7 @@ The easiest way to install snakePipes is via our conda channel. The following co
 
 .. code:: bash
 
-    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.4.3
+    conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes
 
 This way, the software used within snakePipes do not conflict with the software pre-installed on your terminal or in your python environment.