Commits · 0b075b29f126abbe1685bc2b7d075585f5551d5a · Martin Larralde / peptides.py · GitLab

28 Mar, 2022 40 commits
- Fix path to CSS stylesheets in `docs/conf.py` · 0b075b29
  Martin Larralde authored Oct 23, 2021
  
  0b075b29
- Add a docstring to the `Peptide.__init__` method · c7596a7f
  Martin Larralde authored Oct 23, 2021
  
  c7596a7f
- Fix some documentation styling issues in the CSS · fca128e4
  Martin Larralde authored Oct 23, 2021
  
  fca128e4
- Add missing syntax-highlighting dependencies to `docs/requirements.txt` · 6bf973ae
  Martin Larralde authored Oct 23, 2021
  
  6bf973ae
- Fix build of documentation in ReadTheDocs environment · 4908db59
  Martin Larralde authored Oct 23, 2021
  
  4908db59
- Fix code generation in `setup.py` to work with older Python versions · edc1eafd
  Martin Larralde authored Oct 23, 2021
  
  edc1eafd
- Add `astor` to the documentation dependencies · e16e72fc
  Martin Larralde authored Oct 23, 2021
  
  e16e72fc
- Add Sphinx configuration files to build the project documentation · 4660ba07
  Martin Larralde authored Oct 23, 2021
  
  4660ba07
- Update `setup.py` to generate `array` look-up tables instead of using `dict` tables · 20c405c1
  Martin Larralde authored Oct 23, 2021
  
  20c405c1
- Swap order of `Peptide.hydrophobic_moment` for consistency with profile methods · aacf0521
  Martin Larralde authored Oct 23, 2021
  
  aacf0521
- Add methods to get the occurrences and frequencies of amino acids in a `Peptide` · f93e213b
  Martin Larralde authored Oct 23, 2021
  
  f93e213b
- Update `Peptide.aliphatic_index` to support unknown Leu/Ile residues (code J) · 26d4c118
  Martin Larralde authored Oct 23, 2021
  
  26d4c118
- Update all methods to support unknown amino-acids in input sequences · 8b7cd590
  Martin Larralde authored Oct 23, 2021
  
  8b7cd590
- Add class method to generate a random `Peptide` with fixed AA frequencies · 1a9a544f
  Martin Larralde authored Oct 23, 2021
  
  1a9a544f
- Add documentation and references to all the descriptor methods · 4733137b
  Martin Larralde authored Oct 22, 2021
  
  4733137b
- Add more documentation and references to the methods for physical properties · 3a81853d
  Martin Larralde authored Oct 22, 2021
  
  3a81853d
- Release v0.1.0 · 5ad04a38
  Martin Larralde authored Oct 21, 2021
  
  5ad04a38
- Reformat `peptides/__init__.py` code with `black` · 559d4991
  Martin Larralde authored Oct 21, 2021
  
  559d4991
- Add remaining missing type hints to `peptides/__init__.py` · 629d4dc3
  Martin Larralde authored Oct 21, 2021
  
  629d4dc3
- Implement methods computing several profiles for the whole peptide · 3f236adc
  Martin Larralde authored Oct 21, 2021
  
  3f236adc
- Add a `py.typed` marker file to the `peptides` module · 92748ff9
  Martin Larralde authored Oct 21, 2021
  
  92748ff9
- Add some missing type annotations to `Peptide` methods · fda0dfb7
  Martin Larralde authored Oct 21, 2021
  
  fda0dfb7
- Fix `codegen` command of `setup.py` generating useless tables · 7b3882a3
  Martin Larralde authored Oct 21, 2021
  
  7b3882a3
- Make methods computing multiple descriptors return a dedicated named tuple · 5e53b75b
  Martin Larralde authored Oct 21, 2021
  
  5e53b75b
- Add GitHub Actions workflows to test and publish the package · 0fadb8c1
  Martin Larralde authored Oct 21, 2021
  
  0fadb8c1
- Add `README.md` file with some code examples · 40623207
  Martin Larralde authored Oct 21, 2021
  
  40623207
- Add the `Peptide.descriptors` method to get a dictionary of all descriptors · b61cb6f1
  Martin Larralde authored Oct 21, 2021
  
  b61cb6f1
- Add project files to generate a package distribution · 51d3acc6
  Martin Larralde authored Oct 21, 2021
  
  51d3acc6
- Add example in doctest format for the `Peptide.protfp_descriptors` method · 17afc1d5
  Martin Larralde authored Oct 21, 2021
  
  17afc1d5
- Implement `__len__`, `__getitem__` and `__repr__` magic functions for `Peptide` · 19af244e
  Martin Larralde authored Oct 21, 2021
  
  19af244e
- Implement `Peptide.isoelectric_point` using a naive loop to minimize the charge · 74e6a485
  Martin Larralde authored Oct 21, 2021
  
  74e6a485
- Add correlation and covariance methods to `Peptide` · bb747002
  Martin Larralde authored Oct 21, 2021
  
  bb747002
- Implement `mz`, `mass_shift`, and `molecular_weight` methods for `Peptide` · 5d3d935d
  Martin Larralde authored Oct 20, 2021
  
  5d3d935d
- Add a succinct contribution guide in `CONTRIBUTING.md` · f758ea52
  Martin Larralde authored Oct 20, 2021
  
  f758ea52
- Make `setup.py` generate the data tables out of source · 7630934e
  Martin Larralde authored Oct 20, 2021
  
  7630934e
- Add docstring examples to all currently implemented methods · 62a69a49
  Martin Larralde authored Oct 20, 2021
  
  62a69a49
- Rewrite the `Peptide` properties to use tables from `peptides.data.tables` · 1fffdce3
  Martin Larralde authored Oct 20, 2021
  
  1fffdce3
- Rewrite `setup.py` to generate a single Python file with all data tables · 14be6ac7
  Martin Larralde authored Oct 20, 2021
  
  14be6ac7
- Add data tables extracted from `AAdata.RData` and from the R sources · a1e565bf
  Martin Larralde authored Oct 20, 2021
  
  a1e565bf
- Implement proof-of-concept class providing the same functions as `Peptides` · 7a5019b5
  Martin Larralde authored Oct 20, 2021
  
  7a5019b5