Merge branch 'release-1.9.1'

.github/workflows/fragit_with_conda.yml

@@ -0,0 +1,29 @@
+name: FragIt with Conda
+
+on: [push]
+
+jobs:
+  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"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: fragit
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+      - name: Conda Information
+        run: |
+          conda info
+          conda list
+      - name: Run Testsuite
+        run:
+          pytest .
+

.github/workflows/python-app.yml → .github/workflows/fragit_with_openbabel_build.yml

@@ -1,14 +1,14 @@
-name: FragIt Tests
+name: FragIt with OpenBabel Build
 
 on: [push]
 
 jobs:
   build:
-
+    name: Testing
     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
-        run: python -m pytest tests/*.py
+      - name: Run Testsuite
+        run: pytest .
 

CHANGES.md

@@ -1,3 +1,22 @@
+FragIt v1.9.1 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
 ===========================
 

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
+s
+## Installing FragIt in a Conda Environment With Pip
+The easiest installation option is to use conda and pip.
+We have supplied an `environment.yml` file for you to use.
+Simply run
 
-FragIt is a python library and installation is quite straight forward
+    cd fragit-main
+    conda env create -f environment.yml
 
-    python setup.py install
+which creates an environment called fragit.
+After activating the `fragit` environment
+
+    conda activate fragit
+
+you can install fragit using `pip` with the following command
 
-to install it in the default locations. To install it in a custom location, you can run the following
+    pip install .
 
-    python setup.py install --prefix=/path/to/custom/installation
+## 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 
 
-Remember to add the installation paths to your environment variables:
+    pip install . --user
 
-    export PATH=/path/to/custom/installation/bin:$PATH
-    export PYTHONPATH=/path/to/custom/installation/lib/python2.7/site-packages:$PYTHONPATH
+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).

environment.yml

@@ -0,0 +1,8 @@
+name: fragit
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - pytest
+  - numpy
+  - openbabel

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.