updating development documentation

.readthedocs.yaml

@@ -3,7 +3,7 @@
 version: 2
 
 build:
-  os: "ubuntu-22.04"
+  os: "ubuntu-latest"
   tools:
     python: "3.10"
 

docs/develop.rst

@@ -58,9 +58,9 @@ To check for proper documentation build, proper syntax and styling, and pytest o
 
 Before creating a pull request
 
-#. write test cases for the new code.
-#. run :code:`tox` after fixing formatting and syntax with :code:`black` and :code:`flake8`.
-#. create the pull request, if the tox check passes with your local python version.
+#. write test cases for the new code
+#. run :code:`tox` after fixing formatting and syntax with :code:`ruff`
+#. create the pull request, if the tox check passes with your local python version
 
 
 Using Pre-Commit
@@ -84,6 +84,9 @@ all the file using::
 
     pre-commit run --all-files
 
+When the staged files fail the conditions defined in the pre-commit conditions, :code:`ruff` formatting
+will attempt to fix it. After adding the files updated by :code:`ruff`, attempt to commit again. If it fails,
+then the errors have to be manually fixed.
 
 Writing Documentation
 ---------------------
@@ -111,6 +114,8 @@ Accordingly this documentation for developing will have to be changed.
 Making a Release
 ----------------
 
+[No releases made yet. This text is a template.]
+
 #. Update ``CHANGES.rst``: Set the correct version number and ensure that
    all nontrivial, user-visible changes are listed.
 

docs/index.rst

@@ -30,10 +30,20 @@ We recommend installing inside a conda environment to allow easy removal::
     conda activate gaftools-env
     pip install git+https://github.com/marschall-lab/gaftools
 
+If you already have a clone locally, then run::
+
+    git clone https://github.com/marschall-lab/gaftools
+    conda create -n gaftools-env python=3.10
+    conda activate gaftools-env
+    cd gaftools
+    pip install .
+
 To remove gaftools, the conda environment needs to be removed using::
 
     conda env remove -n gaftools-env
 
+gaftools can be used with python>=3.8
+
 
 Requirements
 ------------