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=> requirements}/doc-requirements.txt (84%) rename {configs => requirements}/requirements.txt (76%) diff --git a/.github/workflows.md b/.github/workflows.md deleted file mode 100644 index 184ae21..0000000 --- a/.github/workflows.md +++ /dev/null @@ -1,110 +0,0 @@ -# Workflows - -This file describes some workflows that are used frequently. - -# Testing with pytest - -1. Install pytest package: -```pip install pytest``` - -2. Run pytest: -Windows Powershell: ```python -m pytest``` -Conda Powershell: ```pytest``` -All files of the form ```test_*.py``` in all folders are automatically detected. - -Alternative (to specify a directory and disable warnings): -```python -m pytest -vv tests/ --disable-pytest-warnings``` - - -# Linting with pylint - -1. Install pylint package: -```pip install pylint``` - -2. Run pylint: -Windows Powershell: ```python -m pylint qDNA/**/*.py``` -Conda Powershell: ```pylint qDNA/**/*.py``` - - -# Formatting with black - -1. Install black package: -```pip install black``` - -2. Run black: -```cd .. ``` -Windows Powershell: ```python -m black QuantumDNA``` -Conda Powershell: ````black QuantumDNA``` -reformats all .py files inside the whole project. Alternatively you can apply black to selected folders and files. - - -# Coverage with coveralls.io - -1. Install coverage, coveralls and pytest packages: -```pip install coverage coveralls pytest``` - -2. Run coverage: -Windows Powershell: ```python -m coverage run -m pytest``` -Conda Powershell: ```coverage run -m pytest``` - -The command creates a .coverage file in the working directory. -You can either print the report to the console (```(python -m) coverage report -m```) or save a .html file in the working directory (```(python -m) coverage html```). - -3. Upload report to coveralls.io: - -```$env:COVERALLS_REPO_TOKEN = "secret" ``` -Windows Powershell: ```python -m coveralls``` -Conda Powershell: ```coveralls``` - - -# Documentation on readthedocs.org - -1. Install sphinx package: -```pip install sphinx``` - -2. Start sphinx to automatically create all relevant files: -```sphinx-quickstart``` -Collect all files in the ```docs/``` directory. - -3. Customize documentation: - -* adopt ```docs/index.rst``` -* adopt ```docs/conf.py``` -* if you want to use the sphinx_rtd_theme in conf.py you have to install it first (```pip install sphinx_rtd_theme```) - -4. Create a local html file: -```docs/make.bat html``` -The file is located at ```docs/_build/html/index.html```. - -5. Upload documentation to readthedocs.org: - -* create ```readthedocs.yaml``` -* create ```docs/requirements.txt``` (contains all packages needed to build the documentation) -* make a new commit and push changes to GitHub -* login to readthedocs.org -* refresh and select your GitHub project (repository must be public) -* start "Build-Version" to create the webpage - - -# Publish package on pypi.org - -1. Install setuptools, wheel and twine packages: -```pip install setuptools wheel twine``` - -2. Create source distribution and binary distribution from the setup.py file -```python setup.py sdist bdist_wheel ``` - -Creates a ````dist/``` and ```.egg-info``` directory. - -The package is saved locally in the dist/ directory and can be installed via -```pip install dist/qDNA-0.1.1-py3-none-any.whl``` (from the binary distribution) -```pip install dist/qDNA-0.1.1.tar.gz``` (from the source distribution) - -3. Upload to pypi.org: - -```$env:TWINE_USERNAME="__token__"``` -```$env:TWINE_PASSWORD="secret"``` -Windows Powershell ```python -m twine upload dist/*``` -Conda Powershell ```twine upload dist/*``` - -Uploads sdist and bdist to pypi. \ No newline at end of file diff --git a/.gitignore b/.gitignore index cf2b6d1..5a7f0d0 100644 --- a/.gitignore +++ b/.gitignore @@ -1,25 +1,24 @@ # check which files are ignored: git status --ignored +.venv/ archive/ -docs/my_notebooks/ -docs/figures/my_figures/ -.vscode/ - -development/ -environment_long.yml -.coverage .pre-commit-config.yaml -scripts/info.txt +HOWTO.md +info.txt +main.py +qDNA/data/raw/geometries/ +requirements/pip_freeze.txt -*.egg-info/ +# created by build dist/ build/ -data/raw/geometries -data/raw/test_params -data/processed/ -data/figures/ -data/logging.log - +# created by pytest __pycache__ +.pytest_cache/ + +# created by coverage +*.egg-info/ +.coverage + .ipynb_checkpoints diff --git a/MANIFEST.in b/MANIFEST.in index 0cb0875..b5904c1 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,10 +1,19 @@ +# Include the README, LICENSE, and other documentation files include README.md -include installation.md +include installation.md include LICENSE.txt include CITATION.bib -include qDNA/config.yaml + +# Include requirement files +include requirements/*.txt + +# Include the MANIFEST file itself +include MANIFEST.in + +# Include all .py files +recursive-include qDNA *.py + +# Include specific data files +include qDNA/data/data_paper/*.json +include qDNA/data/figures_paper/*.pdf *.png include qDNA/data/raw/tb_params/*.json -include qDNA/data/figures/doc_paper/*.png -include qDNA/data/figures/doc_paper/*.pdf -include qDNA/data/processed/doc_paper/*.json -include configs/* \ No newline at end of file diff --git a/README.md b/README.md index 4f93977..219a9d9 100644 --- a/README.md +++ b/README.md @@ -103,22 +103,7 @@ The documentation for the [latest release](https://quantumdna.readthedocs.io/en/ ### Tutorials -The code contains some tutorials and demonstrations to better understand and explore the functionalities. -In the [`docs/tutorials`](docs/tutorials) folder you can find the notebook [`0_Paper`](docs/tutorials/0_Paper.ipynb) that contains and reproduces all the figures contained in [D. Herb, M. Rossini and J. Ankerhold, Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence.](https://arxiv.org/abs/2402.16892) - -Additionally, the `QuantumDNA/docs/tutorials` folder contains the following tutorials: - -| Tutorial Name | Description | -|------------------------------------------------------------------------------------------------|----------------------------------------------------------------------| -| [`1_TB_Models`](docs/tutorials/1_TB_Models.ipynb) | Tutorials on predefined and custom tight-binding models. | -| [`2_Data_Visualization`](docs/tutorials/2_Data_Visualization.ipynb) | Tutorial on the predefined plotting routines. | -| [`3_DNA_environment`](docs/tutorials/3_DNA_environment.ipynb) | Tutorial on different ways to treat DNA relaxation and the DNA environment. | -| [`4_Parallelized_Calculations`](docs/tutorials/4_Parallelized_Calculations.ipynb) | Tutorial on how to perform parallelized calculations for several properties. | -| [`Exploration_Notebook`](docs/tutorials/Exploration_Notebook.ipynb) | A place to test the functionality of individual functions isolated from the rest of the code. | - - -These tutorials provide hands-on examples and explanations to help you effectively use the `qDNA` package. ### Graphical user interface diff --git a/configs/dev-requirements.txt b/configs/dev-requirements.txt deleted file mode 100644 index 2369f94..0000000 --- a/configs/dev-requirements.txt +++ /dev/null @@ -1,5 +0,0 @@ -black -pytest -pylint -coverage -coveralls \ No newline at end of file diff --git a/qDNA/data/raw/test_params/Herb2024_relations_between_persons.json b/data/raw/test_params/Herb2024_relations_between_persons.json similarity index 90% rename from qDNA/data/raw/test_params/Herb2024_relations_between_persons.json rename to data/raw/test_params/Herb2024_relations_between_persons.json index e9fcb20..a27a1e1 100644 --- a/qDNA/data/raw/test_params/Herb2024_relations_between_persons.json +++ b/data/raw/test_params/Herb2024_relations_between_persons.json @@ -1 +1 @@ -[{"relation_AliceBob": 5, "relation_AliceCharlie": 3, "relation_AliceEve": -2, "relation_BobAlice": 5, "relation_CharlieAlice": 3, "relation_EveAlice": -2}, {"author": "Herb2024", "subject": "relations_between_persons", "notes": "The parameters describe relations between persons."}] \ No newline at end of file +[{"relation_AliceBob": 5, "relation_AliceCharlie": 3, "relation_AliceEve": -2, "relation_BobAlice": 5, "relation_CharlieAlice": 3, "relation_EveAlice": -2}, {"author": "Herb2024", "subject": "relations_between_persons", "notes": "The parameters describe relations between persons."}] diff --git a/configs/.readthedocs.yaml b/docs/.readthedocs.yaml similarity index 84% rename from configs/.readthedocs.yaml rename to docs/.readthedocs.yaml index 621b092..ce550d5 100644 --- a/configs/.readthedocs.yaml +++ b/docs/.readthedocs.yaml @@ -17,7 +17,7 @@ build: # Build documentation in the "docs/" directory with Sphinx sphinx: - configuration: docs/sphinx_doc/conf.py + configuration: docs/conf.py # Optionally build your docs in additional formats such as PDF and ePub # formats: @@ -29,5 +29,5 @@ sphinx: # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html python: install: - - requirements: configs/requirements.txt - - requirements: configs/doc-requirements.txt \ No newline at end of file + - requirements: requirements/requirements.txt + - requirements: requirements/doc-requirements.txt diff --git a/docs/sphinx_doc/Makefile b/docs/Makefile similarity index 100% rename from docs/sphinx_doc/Makefile rename to docs/Makefile diff --git a/docs/sphinx_doc/_build/doctrees/DNA.doctree b/docs/_build/doctrees/DNA.doctree similarity index 100% rename from docs/sphinx_doc/_build/doctrees/DNA.doctree rename to docs/_build/doctrees/DNA.doctree diff --git a/docs/sphinx_doc/_build/doctrees/DNA.dynamics.doctree b/docs/_build/doctrees/DNA.dynamics.doctree similarity index 100% rename from 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a/docs/sphinx_doc/_build/html/_images/qDNA_logo.png b/docs/_build/html/_images/qDNA_logo.png similarity index 100% rename from docs/sphinx_doc/_build/html/_images/qDNA_logo.png rename to docs/_build/html/_images/qDNA_logo.png diff --git a/docs/sphinx_doc/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html similarity index 98% rename from docs/sphinx_doc/_build/html/_modules/index.html rename to docs/_build/html/_modules/index.html index 77c5352..131adfe 100644 --- a/docs/sphinx_doc/_build/html/_modules/index.html +++ b/docs/_build/html/_modules/index.html @@ -8,11 +8,11 @@ - + - + @@ -21,17 +21,17 @@ - + - +