From c8931f7f93a4588a94cf263f62c4b4f24339b9f2 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Mon, 13 Nov 2023 15:30:39 +0100
Subject: [PATCH 01/14] Prepare CHANGES.md for next version

---
 CHANGES.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CHANGES.md b/CHANGES.md
index 7be0ea6..a622c32 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,8 @@
+FragIt v1.X.X Release Notes
+===========================
+
+Updates since  v1.9.0
+
 FragIt v1.9.0 Release Notes
 ===========================
 

From 0d4b40dd7dfa2188c37eb110d2562acb6b54b815 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 16:19:34 +0100
Subject: [PATCH 02/14] Update installation instructions.

---
 ....yml => test_explicit_openbabel_build.yml} |  7 ++--
 README.md                                     | 42 ++++++++++++++-----
 environment.yml                               |  9 ++++
 3 files changed, 44 insertions(+), 14 deletions(-)
 rename .github/workflows/{python-app.yml => test_explicit_openbabel_build.yml} (86%)
 create mode 100644 environment.yml

diff --git a/.github/workflows/python-app.yml b/.github/workflows/test_explicit_openbabel_build.yml
similarity index 86%
rename from .github/workflows/python-app.yml
rename to .github/workflows/test_explicit_openbabel_build.yml
index 3f57d33..e2ff7cc 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/test_explicit_openbabel_build.yml
@@ -1,4 +1,4 @@
-name: FragIt Tests
+name: FragIt with OpenBabel build
 
 on: [push]
 
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
@@ -41,7 +41,6 @@ jobs:
           cd openbabel_build
           sudo make install
 
-      # You can test your matrix by printing the current Python version
-      - name: Display Python version
+      - name: Run Tests
         run: python -m pytest tests/*.py
 
diff --git a/README.md b/README.md
index f45ffd2..5fb25b0 100644
--- a/README.md
+++ b/README.md
@@ -11,23 +11,45 @@ Currently, FragIt supports the [fragment molecular orbital](http://en.wikipedia.
 ## Obtaining FragIt
 
 Since you found this file, it is obvious that you also found the source code. You can obtain the latest version from [github](https://www.github.com/FragIt/fragit-main) where [tagged releases](https://github.com/FragIt/fragit-main/releases) are also available.
+You get the source code by cloning the repository
 
-## Installing FragIt
+    git clone https://github.com/FragIt/fragit-main.git
 
-FragIt is a python library and installation is quite straight forward
+## Installing FragIt in a Conda Environment With Pip
+The easiest installation option is to use Conda.
+We have supplied an `environment.yml` file for you to use.
+Simply run
 
-    python setup.py install
+    cd fragit-main
+    conda env create -f environment.yml
+
+which creates an environment called fragit.
+After activating the `fragit` environment
+
+    conda activate fragit
 
-to install it in the default locations. To install it in a custom location, you can run the following
+you can install fragit using `pip` with the following command
 
-    python setup.py install --prefix=/path/to/custom/installation
+    pip install .
 
-Remember to add the installation paths to your environment variables:
+## Installing FragIt Without Conda
+Without conda, the installation of FragIt becomes slightly more
+tedious and of course system dependent.
+If you have root access, you can install all dependencies using
+the system package manager, but if you don't, then you have to
+install OpenBabel manually
+(Github user [andersx](https://github.com/andersx) [wrote a guide](http://combichem.blogspot.dk/2013/12/compiling-open-babel-with-python.html) to how that is accomplished.)
+Finally, the recommended installation method for FragIt is to use pip again 
 
-    export PATH=/path/to/custom/installation/bin:$PATH
-    export PYTHONPATH=/path/to/custom/installation/lib/python2.7/site-packages:$PYTHONPATH
+    pip install . --user
+
+but it is also possible using the old school approach (deprecated and not recommended)
+
+    python setup.py build
+    python setup.py install
 
-shown here for a python 2.7 installation example.
+remember to make sure that environment variables (`PATH` and `PYTHONPATH` at least!) are
+set up correctly or else FragIt will complain that it cannot find itself.
 
 ## Running FragIt
 
@@ -44,6 +66,6 @@ See the [wiki](https://www.github.com/FragIt/fragit-main/wiki) for more examples
 In order to run FragIt, you *need* the following installed on your system:
 
 * The FragIt source code, look above for information on how to obtain it
-* [Open Babel](http://www.openbabel.org) 2.3 or newer with [python language bindings](http://openbabel.org/docs/dev/Installation/install.html#compile-language-bindings) enabled. Github user [andersx](https://github.com/andersx) [wrote a guide](http://combichem.blogspot.dk/2013/12/compiling-open-babel-with-python.html) to how that is accomplished.
+* [Open Babel](http://www.openbabel.org) 3 or newer with [python language bindings](http://openbabel.org/docs/dev/Installation/install.html#compile-language-bindings) enabled.
 * [Numpy](http://numpy.scipy.org) 1.5 or newer.
 * [Python](http://www.python.org) 3.9 (or later).
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..6262642
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,9 @@
+name: fragit
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python
+  - pytest
+  - numpy
+  - openbabel

From ef31ee2c2afb7d5269e1991737d0c0b15e61c080 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 16:30:12 +0100
Subject: [PATCH 03/14] First attempt at conda based testing

---
 .github/workflows/test_conda.yml | 24 ++++++++++++++++++++++++
 environment.yml                  |  9 +++++++++
 2 files changed, 33 insertions(+)
 create mode 100644 .github/workflows/test_conda.yml
 create mode 100644 environment.yml

diff --git a/.github/workflows/test_conda.yml b/.github/workflows/test_conda.yml
new file mode 100644
index 0000000..9207d68
--- /dev/null
+++ b/.github/workflows/test_conda.yml
@@ -0,0 +1,24 @@
+name: FragIt Conda Tests
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+          activate-environment: fragit
+
+      - name: Run Tests
+        run: python -m pytest tests/*.py
+
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..6262642
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,9 @@
+name: fragit
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python
+  - pytest
+  - numpy
+  - openbabel

From a237abc055702d1c86ae4d0a97fcf527a5456083 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 16:35:04 +0100
Subject: [PATCH 04/14] fixes pytest call

---
 .github/workflows/test_conda.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_conda.yml b/.github/workflows/test_conda.yml
index 9207d68..bd4110c 100644
--- a/.github/workflows/test_conda.yml
+++ b/.github/workflows/test_conda.yml
@@ -20,5 +20,5 @@ jobs:
           activate-environment: fragit
 
       - name: Run Tests
-        run: python -m pytest tests/*.py
+        run: pytest .
 

From 1ddbd1d227d686d45f0981e9c593ac9924cdca96 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 16:42:00 +0100
Subject: [PATCH 05/14] changes the testing with conda.

---
 .github/workflows/test_conda.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test_conda.yml b/.github/workflows/test_conda.yml
index bd4110c..2c2081f 100644
--- a/.github/workflows/test_conda.yml
+++ b/.github/workflows/test_conda.yml
@@ -18,7 +18,9 @@ jobs:
           python-version: ${{ matrix.python-version }}
           auto-activate-base: false
           activate-environment: fragit
-
-      - name: Run Tests
-        run: pytest .
+      - run: |
+          conda info
+          conda list
+      - run:
+          pytest .
 

From 4fc5ffe978ebdf18373cac5ff9863277357b36d4 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 16:50:14 +0100
Subject: [PATCH 06/14] attempt to actually install environment packages

---
 .github/workflows/test_conda.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/test_conda.yml b/.github/workflows/test_conda.yml
index 2c2081f..5234f09 100644
--- a/.github/workflows/test_conda.yml
+++ b/.github/workflows/test_conda.yml
@@ -14,10 +14,9 @@ jobs:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v2
         with:
+          activate-environment: fragit
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
-          auto-activate-base: false
-          activate-environment: fragit
       - run: |
           conda info
           conda list

From 2aa0c4f1fa64b2014166ad483a8ecf8a977b6dea Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 16:54:38 +0100
Subject: [PATCH 07/14] ignore creating custom environment

---
 .github/workflows/test_conda.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/test_conda.yml b/.github/workflows/test_conda.yml
index 5234f09..55dd920 100644
--- a/.github/workflows/test_conda.yml
+++ b/.github/workflows/test_conda.yml
@@ -14,7 +14,6 @@ jobs:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: fragit
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
       - run: |

From cd9719814f9f97c5b360f56ed3c5aaccf4217ab3 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 17:00:34 +0100
Subject: [PATCH 08/14] attempt to manually activate test environment

---
 .github/workflows/test_conda.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test_conda.yml b/.github/workflows/test_conda.yml
index 55dd920..e5fae08 100644
--- a/.github/workflows/test_conda.yml
+++ b/.github/workflows/test_conda.yml
@@ -17,8 +17,10 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
       - run: |
+          conda activate test
           conda info
           conda list
       - run:
+          conda activate test
           pytest .
 

From 0ff85ae3674a27f7b9ab48a2bcf72e8effe141b8 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 17:05:11 +0100
Subject: [PATCH 09/14] unclear what environment we are using

---
 .github/workflows/test_conda.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/test_conda.yml b/.github/workflows/test_conda.yml
index e5fae08..7323756 100644
--- a/.github/workflows/test_conda.yml
+++ b/.github/workflows/test_conda.yml
@@ -17,10 +17,9 @@ jobs:
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
       - run: |
-          conda activate test
+          conda env list
           conda info
           conda list
       - run:
-          conda activate test
           pytest .
 

From 12d19777546d2e6a70cbcfa1b2d985f0ed8317d4 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 19:45:21 +0100
Subject: [PATCH 10/14] reworked the .yml file

---
 .github/workflows/test_conda.yml | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/test_conda.yml b/.github/workflows/test_conda.yml
index 7323756..0b03822 100644
--- a/.github/workflows/test_conda.yml
+++ b/.github/workflows/test_conda.yml
@@ -3,23 +3,28 @@ name: FragIt Conda Tests
 on: [push]
 
 jobs:
-  build:
-
+  test:
+    name: Testing
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-
+        python-version: ["3.9"] #, "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v2
         with:
+          activate-environment: fragit
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
-      - run: |
+      - name: Conda Informaiton
+        run: |
           conda env list
           conda info
           conda list
-      - run:
+      - name: Test
+        run:
           pytest .
 

From d6c5a8099d998b6f5f0bec1e6f08e40f8cb841d4 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 19:47:31 +0100
Subject: [PATCH 11/14] remove default python - other packages will include it.

---
 environment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 6262642..a9f0c47 100644
--- a/environment.yml
+++ b/environment.yml
@@ -3,7 +3,6 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python
   - pytest
   - numpy
   - openbabel

From 9b65397593bf040bfd1786bef36da88a70ccd873 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 19:50:49 +0100
Subject: [PATCH 12/14] Conda testing with github action works.

---
 .github/workflows/test_conda.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_conda.yml b/.github/workflows/test_conda.yml
index 0b03822..3400e6e 100644
--- a/.github/workflows/test_conda.yml
+++ b/.github/workflows/test_conda.yml
@@ -11,7 +11,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.9"] #, "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v2

From fe103c84a36300d9780aaa25fcf2a4ac8c0c7649 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Thu, 16 Nov 2023 22:12:27 +0100
Subject: [PATCH 13/14] Updates installation instructions. Fixes #38.

Also includes github actions updates
---
 .../{test_conda.yml => fragit_with_conda.yml}      |  7 +++----
 ...l_build.yml => fragit_with_openbabel_build.yml} |  8 ++++----
 CHANGES.md                                         | 14 ++++++++++++++
 README.md                                          |  4 ++--
 4 files changed, 23 insertions(+), 10 deletions(-)
 rename .github/workflows/{test_conda.yml => fragit_with_conda.yml} (84%)
 rename .github/workflows/{test_explicit_openbabel_build.yml => fragit_with_openbabel_build.yml} (91%)

diff --git a/.github/workflows/test_conda.yml b/.github/workflows/fragit_with_conda.yml
similarity index 84%
rename from .github/workflows/test_conda.yml
rename to .github/workflows/fragit_with_conda.yml
index 3400e6e..55f671f 100644
--- a/.github/workflows/test_conda.yml
+++ b/.github/workflows/fragit_with_conda.yml
@@ -1,4 +1,4 @@
-name: FragIt Conda Tests
+name: FragIt with Conda
 
 on: [push]
 
@@ -19,12 +19,11 @@ jobs:
           activate-environment: fragit
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
-      - name: Conda Informaiton
+      - name: Conda Information
         run: |
-          conda env list
           conda info
           conda list
-      - name: Test
+      - name: Run Testsuite
         run:
           pytest .
 
diff --git a/.github/workflows/test_explicit_openbabel_build.yml b/.github/workflows/fragit_with_openbabel_build.yml
similarity index 91%
rename from .github/workflows/test_explicit_openbabel_build.yml
rename to .github/workflows/fragit_with_openbabel_build.yml
index e2ff7cc..7c1ee8e 100644
--- a/.github/workflows/test_explicit_openbabel_build.yml
+++ b/.github/workflows/fragit_with_openbabel_build.yml
@@ -1,10 +1,10 @@
-name: FragIt with OpenBabel build
+name: FragIt with OpenBabel Build
 
 on: [push]
 
 jobs:
   build:
-
+    name: Testing
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -41,6 +41,6 @@ jobs:
           cd openbabel_build
           sudo make install
 
-      - name: Run Tests
-        run: python -m pytest tests/*.py
+      - name: Run Testsuite
+        run: pytest .
 
diff --git a/CHANGES.md b/CHANGES.md
index a622c32..d015f45 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,8 +1,22 @@
 FragIt v1.X.X Release Notes
 ===========================
 
+This is a minor improvement release.
+
 Updates since  v1.9.0
 
+  * Documentation on installation is now up to date and
+    is fixed (Issue #38)
+          -- thanks to Anthony Nash for pointing
+             out the obsolete instructions.
+
+    See the README file for updated installation
+    instructions.
+
+  * Github actions now cover both the new installation
+    approach with conda and pip as well as the old
+    school approach with compilation of OpenBabel
+
 FragIt v1.9.0 Release Notes
 ===========================
 
diff --git a/README.md b/README.md
index 5fb25b0..2faa97b 100644
--- a/README.md
+++ b/README.md
@@ -14,9 +14,9 @@ Since you found this file, it is obvious that you also found the source code. Yo
 You get the source code by cloning the repository
 
     git clone https://github.com/FragIt/fragit-main.git
-
+s
 ## Installing FragIt in a Conda Environment With Pip
-The easiest installation option is to use Conda.
+The easiest installation option is to use conda and pip.
 We have supplied an `environment.yml` file for you to use.
 Simply run
 

From 9df822e86ac2d628243841206589f80938971a54 Mon Sep 17 00:00:00 2001
From: Casper Steinmann <casper.steinmann@gmail.com>
Date: Sat, 2 Dec 2023 22:43:21 +0100
Subject: [PATCH 14/14] prepare for fragit 1.9.1 release

---
 CHANGES.md        | 2 +-
 fragit/strings.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index d015f45..4c0a6e8 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,4 +1,4 @@
-FragIt v1.X.X Release Notes
+FragIt v1.9.1 Release Notes
 ===========================
 
 This is a minor improvement release.
diff --git a/fragit/strings.py b/fragit/strings.py
index 2ca9ad9..9f55df4 100644
--- a/fragit/strings.py
+++ b/fragit/strings.py
@@ -2,7 +2,7 @@
 Copyright (C) 2011-2023 Casper Steinmann
 """
 
-version = ("1", "9", "0")
+version = ("1", "9", "1")
 version_str = ".".join(version)
 
 doc_str = """FragIt is a tool to fragment large molecules for use in fragment based quantum chemistry methods.