feat: major ramachandraw-1.0.1 release. (#10)

Co-authored-by: Fabian <fabian.tann@mni.thm.de>

.github/workflows/coveralls.yaml

@@ -0,0 +1,45 @@
+name: ramachandraw
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  coveralls:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.10.13
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+            virtualenvs-create: true
+            virtualenvs-in-project: true
+            installer-parallel: true
+
+      - name: Install dependencies
+        run: poetry install --no-interaction
+
+      - name: Run tests with coverage
+        run: |
+          source .venv/bin/activate
+          pytest --cov=ramachandraw
+          coverage lcov
+
+      - name: Upload coverage to Coveralls
+        uses: coverallsapp/github-action@v2.1.0
+        with:
+          github-token: ${{ secrets.COVERALLS_REPO_TOKEN }}
+          file: coverage.lcov

.gitignore

@@ -1,2 +1,163 @@
-# Project exclude paths
-/venv/
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# MacOS
+.DS_Store

Makefile

@@ -0,0 +1,14 @@
+.PHONY: clean format test all
+
+clean:
+	pyclean .
+	rm -rf .pdb/ obsolete/ .mypy_cache/ .pytest_cache/ .ruff_cache/ htmlcov/ .coverage
+
+format:
+	ruff format ramachandraw/ tests/ scripts/
+	ruff --fix ramachandraw/ tests/ scripts/
+
+test:
+	pytest --cov=ramachandraw --cov-report html
+
+all: clean format test

README.md

@@ -1,94 +1,113 @@
 # Ramachandran plotting tool
-![PyPI](https://img.shields.io/pypi/v/RamachanDraw)
-![PyPI - Downloads](https://img.shields.io/pypi/dm/RamachanDraw)
-![PyPI - License](https://img.shields.io/pypi/l/RamachanDraw)
 
-Draws a Ramachandran plot based on the input PDB file (e.g. 1MBN.pdb). Makes use of a Gaussian KDE (kernel density estimation) to plot the density of favoured torsion angles (φ and ψ).
+[![ramachandraw](https://github.com/alxdrcirilo/ramachandraw/actions/workflows/coveralls.yaml/badge.svg)](https://github.com/alxdrcirilo/ramachandraw/actions/workflows/coveralls.yaml)
+[![coverage](https://coveralls.io/repos/github/alxdrcirilo/ramachandraw/badge.svg?branch=master)](https://coveralls.io/github/alxdrcirilo/ramachandraw?branch=master)
+[![python version](https://img.shields.io/badge/python-3.9|3.10|3.11|3.12-blue)](https://www.python.org/)
+[![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![license: MIT](https://img.shields.io/badge/license-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+![PyPI](https://img.shields.io/pypi/v/ramachandraw)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/ramachandraw)
 
-![](https://raw.githubusercontent.com/alxdrcirilo/RamachanDraw/master/extras/plot.png)
+Draws a [Ramachandran plot](https://en.wikipedia.org/wiki/Ramachandran_plot) based on the input PDB file (e.g. `1mbn.pdb`). Makes use of a Gaussian KDE (kernel density
+estimation) to plot the density of favoured torsion angles (φ and ψ).
+
+Single mode                |  Batch mode
+:-------------------------:|:-------------------------:
+![](https://raw.githubusercontent.com/alxdrcirilo/ramachandraw/master/images/plot_single.png) | ![](https://raw.githubusercontent.com/alxdrcirilo/ramachandraw/master/images/plot_batch.png)
 
 ## Installation
 
 RamachanDraw is hosted on [PyPi](https://pypi.org/project/RamachanDraw/).
 
-```
-pip install RamachanDraw
+```bash
+pip install ramachandraw
 ```
 
 ## Usage
 
 RamachanDraw includes useful functions to effortlessly draw a Ramachandran plot.
 
-### Fetch the PDB file from the online repository
+### Fetch the PDB file
 
-To draw a Ramachandran plot, we need a PDB file. You can use a local PDB file by specifying the path. Alternatively, RamachanDraw conveniently includes a function to automatically fetch and locally store the PDB file for the given PDB id.
+To draw a Ramachandran plot, we need a PDB file. RamachanDraw conveniently includes a function to automatically fetch and locally store the PDB file for the given PDB id.
 
-#### Arguments
+#### Example
 
-```
-fetch(pdb_file)
+```python
+from ramachandraw.utils import fetch_pdb
+
+fetch_pdb(pdb_id, verbose)
 ```
 
-- ```pdb_file (str|list)```: PDB id(s) corresponding to the PDB entry to be downloaded.
-- ```Returns```: path to PDB file.
+- `pdb_id (str|list|tuple)`: PDB id(s) corresponding to the PDB file(s) to be downloaded
+- `verbose (bool)` (*optional*): set the verbosity, defaults to `False`
+- **Returns**: path(s) to PDB file(s)
 
-### Extract φ and ψ angles
+### Extract φ and ψ torsion angles
 
-RamachanDraw extracts the φ and ψ angles from the PDB file by taking advantage of the [Biopython](https://biopython.org/) module.
-Additionally, aminoacid residues that were not drawn on the plot can be extract using the ```return_ignored``` argument.
+RamachanDraw extracts the φ and ψ torsion angles from the PDB file by taking advantage of the [Biopython](https://biopython.org/) module. Additionally, aminoacid residues that were not drawn on the plot can be extract using the `return_ignored` argument.
 
-#### Arguments
+#### Example
 
-```
-phi_psi(pdb_file, return_ignored)
+```python
+from ramachandraw.parser import get_phi_psi
+
+phi_psi(pdb_filepath, prune, hide_warnings)
 ```
 
-- ```pdb_file (str)```: PDB id corresponding to the PDB entry to be downloaded.
-- ```return_ignored (bool)```:
-    - ```True``` returns a list of tuple with the format (aminoacid, (phi, psi))
-- ```Returns```: Dictionary with keys as aminoacid residues and values as (phi, psi) angle values.
+- `pdb_id (str|list|tuple)`: PDB filepath(s)
+- `prune (bool)` (*optional*): prunes aminoacids with missing torsion angle(s), defaults to `True`
+- `hide_warnings (bool)` (*optional*): sets the verbosity of the PDB structure parser, defaults to `True`
+- **Returns**: Dictionary with keys as aminoacid residues and values as (φ, ψ) angles.
 
 ### Ramachandran plot
 
 Makes use of the [matplotlib](https://matplotlib.org/) module to draw a highly customizable Ramachandran plot.
 
-#### Arguments
+#### Example
 
-```
-plot(pdb_file, cmap='viridis', alpha=0.75, dpi=100, save=True, show=False, out='plot.png')
+```python
+from ramachandraw.utils import plot
+
+plot(pdb_filepath, cmap="viridis", alpha=0.75, dpi=100, save=True, show=False, filename="plot.png")
 ```
 
-- ```pdb_file (str|list)```: PDB id(s) corresponding to the PDB entry to be downloaded.
-- ```cmap (str)```: colormap to be used (from matplotlib) for the density of the favoured ("allowed") regions; default is <em>viridis</em>.
-- ```alpha (float)```: sets the opacity of the colormap (value between 0-1); default is 0.75.
-- ```dpi (int)```: resolution (<em>dots per inch</em>); default is 100.
-- ```save (bool)```:
-    - ```True```: saves the plot locally; default is True.
-- ```show (bool)```:
-    - ```True```: shows the plot using the Qt5Agg backend; default is False.
-- ```out (str)```: filename to be used in case the plot is saved (i.e. ```save=True```); default is <em>plot.png</em>.
-- ```Returns```: Ramachandran plot (can be saved locally).
+- `pdb_file (str|list|tuple)`: PDB id(s) corresponding to the PDB entry to be downloaded
+- `cmap (str)` (*optional*): colormap to be used (from `matplotlib`) for the density of the favoured ("allowed") regions; default
+  is *viridis*.
+- `alpha (float)` (*optional*): sets the opacity of the colormap (value between 0-1); default is 0.75.
+- `dpi (int)` (*optional*): resolution (in *dots per inch*); default is `100`.
+- `save (bool)` (*optional*):
+  - `True`: saves the plot locally; default is True.
+- `show (bool)` (*optional*):
+  - `True`: shows the plot using the Qt5Agg backend; default is False.
+- `filename (str)` (*optional*): filename to be used in case the plot is saved (i.e. `save=True`); default is `plot.png`.
+- **Returns**: Ramachandran plot (`matplotlib.axes.Axes` object) that can be further customized if needed
 
 ## Example
 
-Herein you will find an example from the PDB id corresponding to the myoglobin entry - [1MBN](https://www.ebi.ac.uk/pdbe/entry/pdb/1mbn/index) - in the Protein Data Bank. 
+Herein you will find an example from the PDB id corresponding to the myoglobin entry: [1MBN](https://www.ebi.ac.uk/pdbe/entry/pdb/1mbn/index) - in the Protein Data Bank.
 
-```
-from RamachanDraw import fetch, phi_psi, plot
+```python
+from ramachandraw.parser import get_phi_psi
+from ramachandraw.utils import fetch_pdb, plot
 
-# PDB id to be downloaded
-PDB_id = '1MBN'
+# PDB id
+pdb_id = "1mbn"
 
-# Drawing the Ramachandran plot
-plot(fetch(PDB_id))
+# Draw the Ramachandran plot
+plot(fetch_pdb(pdb_id))
+
+# Generate a dictionary to store the (phi, psi) torsion angles
+torsion_angles = get_phi_psi(fetch_pdb(pdb_id))
 
-# Generating a dictionary to store the phi and psi angles
-# And returning the ignored aminoacid residues
-phi_psi_dict, ignored_res = phi_psi(fetch(PDB_id), return_ignored=True)
 ```
 
 ## Contributing
-Feedback and constructive criticism is welcome. If necessary, open an issue in the *issues* tab.
+
+Feedback and constructive criticism is welcome. If necessary, open an issue in the [issues](https://github.com/alxdrcirilo/ramachandraw/issues) tab.
 
 ## License
+
 [MIT](https://choosealicense.com/licenses/mit/)