fix: fixed scipy dependency and noxfile cleanup (#47)

* fix: fixed scipy dependency and noxfile cleanup

* fix: add precommit

* fix: make pre-commit pass

* chore: bump version to 1.0.10

* fix: wrong version

.github/workflows/coverage.yml

@@ -5,13 +5,13 @@ jobs:
   coverage:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v1
-      with:
-        python-version: '3.8'
-        architecture: x64
-    - run: pip install nox==2019.11.9
-    - run: pip install poetry==1.0.5
-    - run: nox --sessions tests-3.8 coverage
-      env:
-        CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v1
+        with:
+          python-version: ["3.10", "3.11"]
+          architecture: x64
+      - run: pip install nox==2019.11.9
+      - run: pip install poetry==1.0.5
+      - run: nox --sessions tests-3.8 coverage
+        env:
+          CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}

.github/workflows/tests.yml

@@ -15,14 +15,14 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macOS-latest]
-        python-version: ['3.8']
+        python-version: ["3.10", "3.11"]
     name: Python ${{ matrix.python-version }} OS ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-        architecture: x64
-    - run: pip install nox==2019.11.9
-    - run: pip install poetry==1.0.5
-    - run: nox
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+      - run: pip install nox==2019.11.9
+      - run: pip install poetry==1.0.5
+      - run: nox

.pre-commit-config.yaml

@@ -0,0 +1,52 @@
+exclude: .github
+repos:
+  - repo: local
+    hooks:
+      - id: black
+        name: black
+        entry: black
+        language: system
+        types: [python]
+        require_serial: true
+      - id: check-added-large-files
+        name: Check for added large files
+        entry: check-added-large-files
+        language: system
+      - id: check-toml
+        name: Check Toml
+        entry: check-toml
+        language: system
+        types: [toml]
+      - id: check-yaml
+        name: Check Yaml
+        entry: check-yaml
+        language: system
+        types: [yaml]
+      - id: end-of-file-fixer
+        name: Fix End of Files
+        entry: end-of-file-fixer
+        language: system
+        types: [text]
+        stages: [commit, push, manual]
+      - id: flake8
+        name: flake8
+        entry: flake8
+        language: system
+        types: [python]
+        require_serial: true
+      - id: reorder-python-imports
+        name: Reorder python imports
+        entry: reorder-python-imports
+        language: system
+        types: [python]
+        args: [--application-directories=src]
+      - id: trailing-whitespace
+        name: Trim Trailing Whitespace
+        entry: trailing-whitespace-fixer
+        language: system
+        types: [text]
+        stages: [commit, push, manual]
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.3.0
+    hooks:
+      - id: prettier

CODE_OF_CONDUCT.md

@@ -14,22 +14,22 @@ appearance, race, religion, or sexual identity and orientation.
 Examples of behavior that contributes to creating a positive environment
 include:
 
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery and unwelcome sexual attention or
- advances
-* Trolling, insulting/derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or electronic
- address, without explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
- professional setting
+- The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
 
 ## Our Responsibilities
 

CONTRIBUTING.md

@@ -10,7 +10,7 @@ evaluating changes, and helping you handle your pull requests.
 
 ## Reporting a Bug
 
-A bug is a *demonstratable problem* caused by the code in this repository.
+A bug is a _demonstratable problem_ caused by the code in this repository.
 
 Before opening a bug report:
 
@@ -23,7 +23,6 @@ A good bug report should not leave others needing to chase you up for more
 information. So please try to be as detailed as possible in your report,
 answer at least these questions:
 
-
 1. Which version of `kallisto` are you using? The current version is always
    a subject to change, so be more specific.
 2. What is your environment (your laptop, the cluster of the university)?
@@ -34,46 +33,41 @@ answer at least these questions:
 
 All these details will help people to fix any potential bugs.
 
-
 ## Suggesting a New Feature
 
 Feature requests are welcome. But take a moment to find out if your idea fits
 the scope and goals of the project. It is up to you to provide a strong
 argument to convince the project's developers of the benefits of this feature.
 Please provide as much detail and context as possible.
 
-
 ## Implementing a New Feature
 
-
 Contributions are welcome via Github pull requests.
 
-
-- Each pull request should implement *one* feature or fix *one* bug.
+- Each pull request should implement _one_ feature or fix _one_ bug.
   If you want to add or fix more than one thing, submit more than one
   pull request.
 - Do not commit changes to files that are irrelevant to your feature or
-  bugfix (*e.g.* `.gitignore`).
+  bugfix (_e.g._ `.gitignore`).
 - Be willing to accept criticism and work on improving your code.
 - Do not add third-party dependencies, the `kallisto` program should be usable as
   standalone.
 - Make sure the tests run successful on more than
-  your local machine (*e.g.* on cluster of your university).
-  
+  your local machine (_e.g._ on cluster of your university).
+
   Please sign-off your commits
-
-
+
 ### For New Contributors
 
-If you never created a pull request before you can learn how to do this 
+If you never created a pull request before you can learn how to do this
 from [this great tutorial](https://app.egghead.io/courses/how-to-contribute-to-an-open-source-project-on-github)
 
 Don't know where to start?
 You can start by looking through these [help-wanted issues](https://github.com/f3rmion/kallisto/labels/help%20wanted).
 
 ## Sign Your Work
 
-The sign-off is a simple line at the end of the explanation for a commit. All 
+The sign-off is a simple line at the end of the explanation for a commit. All
 commits needs to be signed. Your signature certifies that you wrote the patch or
 otherwise have the right to contribute the material. The rules are pretty simple,
 if you can certify the below (from [developercertificate.org](https://developercertificate.org/)):

README.md

@@ -28,11 +28,10 @@
 
 # Introduction
 
-We developed the `kallisto` program for the efficient and robust calculation of atomic features using molecular geometries either in a ``xmol`` or a ``Turbomole`` format.
-Furthermore, several modelling tools are implemented, e.g., to calculate root-mean squared deviations via quaternions (including rotation matrices), sorting of molecular geometries and many more. All features of ``kallisto`` are described in detail within our [documentation](https://ehjc.gitbook.io/kallisto/) ([GitBook repository](https://github.com/f3rmion/gitbook-kallisto)).
+We developed the `kallisto` program for the efficient and robust calculation of atomic features using molecular geometries either in a `xmol` or a `Turbomole` format.
+Furthermore, several modelling tools are implemented, e.g., to calculate root-mean squared deviations via quaternions (including rotation matrices), sorting of molecular geometries and many more. All features of `kallisto` are described in detail within our [documentation](https://ehjc.gitbook.io/kallisto/) ([GitBook repository](https://github.com/f3rmion/gitbook-kallisto)).
 
-Main dependencies
------------------
+## Main dependencies
 
 ```bash
 click 7.1.2 Composable command line interface toolkit
@@ -43,101 +42,100 @@ scipy 1.6.0 SciPy: Scientific Library for Python
 
 For a list of all dependencies have a look at the pyproject.toml file.
 
-Installation from PyPI
-----------------------
+## Installation from PyPI
+
+To install `kallisto` via `pip` use our published PyPI package
 
-To install ``kallisto`` via `pip` use our published PyPI package
 ```bash
 pip install kallisto
 ```
 
-Installation from Source
-------------------------
+## Installation from Source
+
+Requirements to install `kallisto`from sources:
 
-Requirements to install ``kallisto``from sources:
 - [poetry](https://python-poetry.org/docs/#installation)
 - [pyenv](https://github.com/pyenv/pyenv#installation) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html)
 - python >=3.7
 
-First check that ``poetry`` is running correctly (v1.0.10 at the time of writing)
+First check that `poetry` is running correctly (v1.0.10 at the time of writing)
 
 ```bash
 > poetry --version
 Poetry version 1.0.10
 ```
 
-Create a virtual environment (via ``pyenv`` or ``conda``) and activate it. Afterwards, clone the ``kallisto`` project from GitHub and install it using ``poetry``
+Create a virtual environment (via `pyenv` or `conda`) and activate it. Afterwards, clone the `kallisto` project from GitHub and install it using `poetry`
 
 ```bash
 > git clone [email protected]:AstraZeneca/kallisto.git
 > cd kallisto
 > poetry install
 ```
 
-Testing suite
--------------
+## Testing suite
 
-The ``kallisto`` project uses [nox](https://nox.thea.codes/en/stable/tutorial.html#installation) as an automated unit test suite, which is therefore an additional dependency.
+The `kallisto` project uses [nox](https://nox.thea.codes/en/stable/tutorial.html#installation) as an automated unit test suite, which is therefore an additional dependency.
 
 ### Default nox session
 
-The default session includes: linting (lint), type checks (mypy, pytype), and unit tests (tests). 
+The default session includes: linting (lint), type checks (mypy, pytype), and unit tests (tests).
 
 ```bash
 > nox
 ```
 
-When everything runs smoothly through, you are ready to go! After one successful nox run, we can reuse the created virtual environment via the ``-r`` flag.
+When everything runs smoothly through, you are ready to go! After one successful nox run, we can reuse the created virtual environment via the `-r` flag.
 
 ```bash
 > nox -r
 ```
 
-Different unit test sessions are implemented (check the noxfile.py). They can be called separately via the run session ``-rs`` flag.
+Different unit test sessions are implemented (check the noxfile.py). They can be called separately via the run session `-rs` flag.
 
 ### Tests
 
 Run all unit tests that are defined in the /tests directory.
 
-```bash 
+```bash
 > nox -rs tests
 ```
 
 ### Lint
 
-``kallisto`` uses the [flake8](https://flake8.pycqa.org/en/latest/) linter (check the .flake8 config file).
+`kallisto` uses the [flake8](https://flake8.pycqa.org/en/latest/) linter (check the .flake8 config file).
 
 ```bash
 > nox -rs lint
 ```
 
 ### Black
 
-``kallisto`` uses the [black](https://github.com/psf/black) code formatter.
+`kallisto` uses the [black](https://github.com/psf/black) code formatter.
 
-```bash 
+```bash
 > nox -rs black
 ```
 
 ### Safety
 
-``kallisto`` checks the security of dependencies via [safety](https://pyup.io/safety/).
+`kallisto` checks the security of dependencies via [safety](https://pyup.io/safety/).
 
 ```bash
 > nox -rs safety
 ```
 
 ### Mypy
 
-``kallisto`` checks for static types via [mypy](https://github.com/python/mypy) (check the mypy.ini config file).
+`kallisto` checks for static types via [mypy](https://github.com/python/mypy) (check the mypy.ini config file).
 
 ```bash
 > nox -rs mypy
 ```
 
 ### Pytype
 
-``kallisto`` furthermore uses [pytype](https://github.com/google/pytype) for type checks.
+`kallisto` furthermore uses [pytype](https://github.com/google/pytype) for type checks.
 
 ```bash
 > nox -rs pytype
@@ -147,17 +145,15 @@ Run all unit tests that are defined in the /tests directory.
 
 Unit test [coverage](https://coverage.readthedocs.io/en/coverage-5.4/) can be checked as well.
 
-
 ```bash
 > nox -rs coverage
 ```
 
-Reference
----------
+## Reference
 
 Always cite:
 
-Eike Caldeweyher, J. Open Source Softw., *2021*, 6, 3050. DOI: [10.21105/joss.03050](https://doi.org/10.21105/joss.03050)
+Eike Caldeweyher, J. Open Source Softw., _2021_, 6, 3050. DOI: [10.21105/joss.03050](https://doi.org/10.21105/joss.03050)
 
 ```
 @article{Caldeweyher2021,