From 073a4fd49fa0498aea19508efa13e6609a2bf323 Mon Sep 17 00:00:00 2001
From: Bart Schilperoort <b.schilperoort@gmail.com>
Date: Thu, 24 Nov 2022 13:31:41 +0100
Subject: [PATCH 1/7] Added pypi badge to readme

---
 README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index ee33e733..a173aed9 100644
--- a/README.md
+++ b/README.md
@@ -3,11 +3,12 @@
 
 
 [![github repo badge](https://img.shields.io/badge/github-repo-000.svg?logo=github&labelColor=gray&color=blue)](https://github.com/EcoExtreML/stemmus_scope_processing)
+[![PyPI version](https://badge.fury.io/py/PyStemmusScope.svg)](https://badge.fury.io/py/PyStemmusScope)
 [![build](https://github.com/EcoExtreML/stemmus_scope_processing/actions/workflows/build.yml/badge.svg)](https://github.com/EcoExtreML/stemmus_scope_processing/actions/workflows/build.yml)
+[![Documentation Status](https://readthedocs.org/projects/pystemmusscope/badge/?version=latest)](https://pystemmusscope.readthedocs.io/en/latest/?badge=latest)
 [![fair-software badge](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu)
 [![sonarcloud](https://github.com/EcoExtreML/stemmus_scope_processing/actions/workflows/sonarcloud.yml/badge.svg)](https://github.com/EcoExtreML/stemmus_scope_processing/actions/workflows/sonarcloud.yml)
 [![github license badge](https://img.shields.io/github/license/EcoExtreML/stemmus_scope_processing)](https://github.com/EcoExtreML/stemmus_scope_processing)
-[![Documentation Status](https://readthedocs.org/projects/pystemmusscope/badge/?version=latest)](https://pystemmusscope.readthedocs.io/en/latest/?badge=latest)
 
 <!-- [![RSD](https://img.shields.io/badge/rsd-pystemmusscope-00a3e3.svg)](https://www.research-software.nl/software/pystemmusscope)
 [![workflow pypi badge](https://img.shields.io/pypi/v/pystemmusscope.svg?colorB=blue)](https://pypi.python.org/project/pystemmusscope/)
@@ -60,7 +61,7 @@ conda environment before submitting the the bash script. See
 ### On CRIB
 
 [CRIB](https://crib.utwente.nl/) is the ITC Geospatial Computing Platform. You
-can run the model using `Matlab` or `Octave`. Currently, running the 
+can run the model using `Matlab` or `Octave`. Currently, running the
 exceutable file on CRIB is not supported because MATLAB Runtime can not be
 installed there. See [Install PyStemmusScope](#install-pystemmusscope).
 

From 2c540499654eb981f3133a6cbbdcc4d79126c45c Mon Sep 17 00:00:00 2001
From: Bart Schilperoort <b.schilperoort@gmail.com>
Date: Thu, 24 Nov 2022 13:32:28 +0100
Subject: [PATCH 2/7] Bumped version to 0.1.1, to test pypi GH action

---
 .bumpversion.cfg           | 2 +-
 CITATION.cff               | 2 +-
 PyStemmusScope/__init__.py | 2 +-
 docs/conf.py               | 2 +-
 setup.cfg                  | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 2067d3bd..351bed36 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.0
+current_version = 0.1.1
 
 [comment]
 comment = The contents of this file cannot be merged with that of setup.cfg until https://github.com/c4urself/bump2version/issues/185 is resolved
diff --git a/CITATION.cff b/CITATION.cff
index 11cd1993..58814ba5 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -9,7 +9,7 @@ authors:
     orcid: "https://orcid.org/0000-0000-0000-0000"
 date-released: 20??-MM-DD
 doi: <insert your DOI here>
-version: "0.1.0"
+version: "0.1.1"
 repository-code: "https://github.com/EcoExtreML/stemmus_scope_processing"
 keywords:
   - STEMMUS SCOPE Processing
diff --git a/PyStemmusScope/__init__.py b/PyStemmusScope/__init__.py
index ad06249b..58970fae 100644
--- a/PyStemmusScope/__init__.py
+++ b/PyStemmusScope/__init__.py
@@ -7,4 +7,4 @@
 
 __author__ = "Sarah Alidoost"
 __email__ = "f.alidoost@esciencecenter.nl"
-__version__ = "0.1.0"
+__version__ = "0.1.1"
diff --git a/docs/conf.py b/docs/conf.py
index ae6af940..a76a3031 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -26,7 +26,7 @@
 # built documents.
 #
 # The short X.Y version.
-version = "0.1.0"
+version = "0.1.1"
 # The full version, including alpha/beta/rc tags.
 release = version
 
diff --git a/setup.cfg b/setup.cfg
index c6f9a28b..63bc5057 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -25,7 +25,7 @@ name = PyStemmusScope
 project_urls =
     Bug Tracker = https://github.com/EcoExtreML/stemmus_scope_processing/issues
 url = https://github.com/EcoExtreML/stemmus_scope_processing
-version = 0.1.0
+version = 0.1.1
 
 [options]
 zip_safe = False

From 532e6b5329c8b5cdd22fc22303eb8ca341be4863 Mon Sep 17 00:00:00 2001
From: Bart Schilperoort <b.schilperoort@gmail.com>
Date: Thu, 24 Nov 2022 13:40:43 +0100
Subject: [PATCH 3/7] Updated setup.cfg to have  "python_requires".

---
 setup.cfg | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.cfg b/setup.cfg
index 63bc5057..36ee1bcb 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -28,6 +28,7 @@ url = https://github.com/EcoExtreML/stemmus_scope_processing
 version = 0.1.1
 
 [options]
+python_requires = >=3.7,<=3.9
 zip_safe = False
 include_package_data = True
 packages = find:

From dbc42501d2ceeb1cd87f3d1cb64c828c7e1d9226 Mon Sep 17 00:00:00 2001
From: Bart Schilperoort <b.schilperoort@gmail.com>
Date: Thu, 24 Nov 2022 13:51:37 +0100
Subject: [PATCH 4/7] See if this works...

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 36ee1bcb..fc0cbe64 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -28,7 +28,7 @@ url = https://github.com/EcoExtreML/stemmus_scope_processing
 version = 0.1.1
 
 [options]
-python_requires = >=3.7,<=3.9
+python_requires = >=3.7,<3.10
 zip_safe = False
 include_package_data = True
 packages = find:

From c748c168a054eb5b1e0504ff64c92e4e8ba43a6a Mon Sep 17 00:00:00 2001
From: Bart Schilperoort <b.schilperoort@gmail.com>
Date: Thu, 24 Nov 2022 13:57:57 +0100
Subject: [PATCH 5/7] Update Python versions in setup.cfg to 3.8, 3.9, 3.10.

---
 setup.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index fc0cbe64..f552e8f5 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -12,9 +12,9 @@ classifiers =
     License :: OSI Approved :: Apache Software License
     Natural Language :: English
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
 description = python modules for running the STEMMUS-SCOPE model
 keywords =
     STEMMUS-SCOPE
@@ -28,7 +28,7 @@ url = https://github.com/EcoExtreML/stemmus_scope_processing
 version = 0.1.1
 
 [options]
-python_requires = >=3.7,<3.10
+python_requires = >=3.8,<3.11
 zip_safe = False
 include_package_data = True
 packages = find:

From 5f86ac9882f7ef9387588f9663cd0aeef3a65f6a Mon Sep 17 00:00:00 2001
From: Bart Schilperoort <b.schilperoort@gmail.com>
Date: Thu, 24 Nov 2022 15:16:39 +0100
Subject: [PATCH 6/7] Specify RTD python version

---
 .readthedocs.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 544d704c..75eabe26 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,4 +1,10 @@
 version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
 python:
   install:
     - method: pip

From 23c01b6c43e1c5caad7cbead743a2a58f0b89ba0 Mon Sep 17 00:00:00 2001
From: Bart Schilperoort <b.schilperoort@gmail.com>
Date: Thu, 24 Nov 2022 16:11:02 +0100
Subject: [PATCH 7/7] Updated citation. Updated readme pip install

---
 CITATION.cff | 13 ++++++++++++-
 README.md    |  5 ++---
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 58814ba5..06b6612c 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -4,10 +4,21 @@ cff-version: "1.1.0"
 title: "PyStemmusScope"
 authors:
   -
+    affiliation: "Netherlands eScience Center"
     family-names: Alidoost
     given-names: Sarah
     orcid: "https://orcid.org/0000-0000-0000-0000"
-date-released: 20??-MM-DD
+  -
+    affiliation: "Netherlands eScience Center"
+    family-names: Schilperoort
+    given-names: Bart
+    orcid: "https://orcid.org/0000-0003-4487-9822"
+  -
+    affiliation: "Netherlands eScience Center"
+    family-names: Liu
+    given-names: Yang
+    orcid: "https://orcid.org/0000-0002-1966-8460"
+date-released: 2022-11-24
 doi: <insert your DOI here>
 version: "0.1.1"
 repository-code: "https://github.com/EcoExtreML/stemmus_scope_processing"
diff --git a/README.md b/README.md
index a173aed9..f0998ebd 100644
--- a/README.md
+++ b/README.md
@@ -75,8 +75,7 @@ Run the commands below in a terminal (On Windows, use `python` instead of
 `python3`):
 
 ```sh
-# will be replaced by `pip install pystemmusscope`
-python3 -m pip install git+https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing.git@main
+python3 -m pip install pystemmusscope
 ```
 
 or
@@ -84,7 +83,7 @@ or
 Open a jupyter notebook and run the code below in a cell:
 
 ```python
-!pip install git+https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing.git@main
+!pip install pystemmusscope
 ```
 
 ### Install jupyterlab