Pre commit

.codecov.yml

@@ -18,7 +18,7 @@ comment:
   behavior: default
   flags: null
   paths: null
-  
+
 ignore:
   - "pygromos/data/"  # ignore folders and all its contents
   - "pygromos/tests/" # ignore test files

.github/CONTRIBUTING.md

@@ -1,7 +1,7 @@
 # How to contribute
 
 We welcome contributions from external contributors, and this document
-describes how to merge code changes into this pygromos. 
+describes how to merge code changes into this pygromos.
 
 ## Getting Started
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,4 +9,4 @@ Notable points that this PR has either accomplished or will accomplish.
 - [ ] Question1
 
 ## Status
-- [ ] Ready to go
+- [ ] Ready to go

.github/workflows/CI.yaml

@@ -42,8 +42,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
         environment-file:  dev/conda_envs/test_env.yaml
         channels: conda-forge,defaults
-        
-        activate-environment: test
+
+        activate-environment: pygromosTest
         auto-update-conda: true
         auto-activate-base: false
         show-channel-urls: true
@@ -63,12 +63,11 @@ jobs:
       shell: bash -l {0}
 
       run: |
-        pytest -v --color=yes pygromos/tests/ --cov=pygromos --cov-report=xml 
-        
+        pytest -v --color=yes pygromos/tests/ --cov=pygromos --cov-report=xml
+
     - name: CodeCov
       uses: codecov/codecov-action@v1
       with:
         file: ./coverage.xml
         flags: unittests
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
-

.github/workflows/pre-commit.yml

@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main, release3, PyGromosTools_V1]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+    - uses: pre-commit/[email protected]

.pre-commit-config.yaml

@@ -0,0 +1,66 @@
+repos:
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+        args: ["--unsafe"]
+      - id: check-added-large-files
+
+  - repo: https://github.com/psf/black
+    rev: 22.1.0
+    hooks:
+      - id: black
+        name: Fixes formatting
+        language_version: python3
+        args: ["--line-length=120"]
+
+
+  # - repo: https://gitlab.com/pycqa/flake8
+  #   rev: 3.8.4
+  #   hooks:
+  #     - id: flake8
+  #       name: Checks pep8 style
+  #       args: [
+  #         "--max-line-length=120",
+  #         # Ignore imports in init files
+  #         "--per-file-ignores=*/__init__.py:F401,setup.py:E121",
+  #         # ignore long comments (E501), as long lines are formatted by black
+  #         # ignore Whitespace before ':' (E203)
+  #         # ignore Line break occurred before a binary operator (W503)
+  #         "--ignore=E501,E203,W503",
+  #         # needed to not remove * imports (for example in _all_blocks.py)
+  #         "--ignore=F405",
+  #       ]
+
+  # - repo: local
+  #   hooks:
+
+  #     - id: jupyisort
+  #       name: Sorts ipynb imports
+  #       entry: jupytext --pipe-fmt ".py" --pipe "isort - --multi-line=3 --trailing-comma --force-grid-wrap=0 --use-parentheses --line-width=99" --sync
+  #       files: \.ipynb$
+  #       language: python
+
+  #     - id: jupyblack
+  #       name: Fixes ipynb format
+  #       entry: jupytext --pipe-fmt ".py" --pipe "black - --line-length=120" --sync
+  #       files: \.ipynb$
+  #       language: python
+
+  #     - id: nbconvert
+  #       name: Removes ipynb content
+  #       entry: jupyter nbconvert
+  #       args:
+  #         [
+  #           "--ClearOutputPreprocessor.enabled=True",
+  #           "--ClearMetadataPreprocessor.enabled=True",
+  #           "--RegexRemovePreprocessor.enabled=True",
+  #           "--to=notebook",
+  #           "--log-level=ERROR",
+  #           "--inplace",
+  #         ]
+  #       files: \.ipynb$
+  #       language: python

INSTALL.md

@@ -9,7 +9,7 @@ Make sure to have the following packages installed:
 
 ```bash
 #with pip installer:
-pip install <package_name> 
+pip install <package_name>
 #or if you use conda:
 conda install <package_name>
 ```

MANIFEST.in

@@ -3,4 +3,4 @@ include MANIFEST.in
 include versioneer.py
 
 graft pygromos
-global-exclude *.py[cod] __pycache__ *.so
+global-exclude *.py[cod] __pycache__ *.so

README.md

@@ -110,11 +110,11 @@ Content
 # Build gromos System:
   grom_system = Gromos_System(in_cnf_path=cnf_path, in_top_path=top_path,
                               system_name=sys_name, work_folder=root_in_dir)
-             
+
 # Run Emin
   emin_gromos_system, jobID = emin(in_gromos_system=grom_system, project_dir=root_dir,
                           step_name=step_name, submission_system=subSystem())
-      
+
   ```
 
   Run on LSF-Cluster:
@@ -133,12 +133,12 @@ Content
 # Build gromos System:
   grom_system = Gromos_System(in_cnf_path=cnf_path, in_top_path=top_path,
                             system_name=sys_name, work_folder=root_in_dir)
-             
+
 # Run Emin
   sub_system = subSystem(nmpi=4) # allows parallelization
   emin_gromos_system, jobID = emin(in_gromos_system=grom_system, project_dir=root_dir,
                           step_name=step_name, submission_system=sub_system)
-      
+
   ```
 
 * Other utilities:
@@ -164,7 +164,6 @@ see INSTALL.md file for more informations
 Copyright (c) 2020, Benjamin Ries, Marc Lehner, Salome Rieder
 
 ### Acknowledgements
-
-Project based on the 
-[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.3.
 
+Project based on the
+[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.3.

conda_env.yaml

@@ -0,0 +1,30 @@
+name: pygromos
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  # Base depends
+  - python
+  - pip
+  ## Testing
+  - pytest
+  ## Meta
+  - typing
+  - pre-commit
+  - jupyter
+  - tqdm
+  - ipywidgets
+  # Science
+  - mpmath
+  - pandas
+  - pytables
+  - numpy
+  - sympy
+  - scipy
+  ## Chemie
+  - openff-toolkit = 0.10.0
+  - mdtraj
+  - rdkit
+  ## Visualization
+  - matplotlib
+  - nglview

dev/conda_envs/dev_env.yaml

@@ -1,29 +1,36 @@
 name: pygromosDev
 channels:
-  - rdkit
   - conda-forge
   - defaults
 dependencies:
   # Base depends
   - python
   - pip
-  # Testing
+  ## Testing
   - pytest
   - pytest-cov
   - codecov
-  #meta
+  ## Meta
   - typing
+  - pre-commit
+  - jupyter
   - tqdm
   - ipywidgets
-  #science
-  - openff-toolkit
+  ## Documentation
+  - sphinx
+  - m2r
+  - nbsphinx
+  # Science
+  - mpmath
   - pandas
   - pytables
   - numpy
   - sympy
   - scipy
+  ## Chemie
+  - openff-toolkit = 0.10.0
+  - mdtraj
   - rdkit
-  - mpmath
- ##Visualization
+  ## Visualization
   - matplotlib
-  - py3dmol
+  - nglview

dev/conda_envs/test_env.yaml

@@ -1,32 +1,30 @@
-name: test
+name: pygromosTest
 channels:
-  - rdkit
   - conda-forge
   - defaults
 dependencies:
   # Base depends
   - python
   - pip
-  # Testing
+  ## Testing
   - pytest
   - pytest-cov
   - codecov
-  #meta
+  ## Meta
   - typing
-  - tqdm
-  - ipywidgets
-  #science
-  - openff-toolkit = 0.10.0
+  - pre-commit
+  # Science
+  - mpmath
   - pandas
   - pytables
   - numpy
   - sympy
   - scipy
+  ## Chemie
+  - openff-toolkit = 0.10.0
+  - mdtraj
   - rdkit
-  - mpmath
- ##Visualization
+  ## Visualization
   - matplotlib
-  - py3dmol
-
-
-
+  - py3dmol #to be removed! soon after merge of new visualize
+  - nglview

docs/.nojekyll

@@ -1 +0,0 @@
-