v1.0.0-alpha release (#9)

* Working on new walker and window system.

* Updated README and prepared for release.

* Updated version tag.

* Added shields.

* Added line break.

* Fixed link.

CHANGELOG.md

@@ -10,6 +10,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### ...
 - ...
 
-## [0.0.1]
+## [1.0.0-alpha] - 2021-02-26
 
-[0.0.1] https://github.com/ggirelli/ifpd/releases/tag/v0.0.1  
+[1.0.0-alpha] https://github.com/ggirelli/ifpd/releases/tag/v1.0.0-alpha  

README.md

@@ -1,3 +1,34 @@
 # iFISH Probe Design (II)
 
-Lorem ipsum dolor sit amet, consectetur adipisicing elit. Dolor odit, dolorem, quia eum excepturi unde quis ab, adipisci illum aperiam laborum. Dolore sit perferendis consequatur eum obcaecati et ipsum placeat.
+![](https://img.shields.io/github/license/ggirelli/ifpd2.svg?style=flat)   ![](https://github.com/ggirelli/ifpd2/workflows/Python%20package/badge.svg?branch=main&event=push)  
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/ifpd2) ![PyPI - Format](https://img.shields.io/pypi/format/ifpd2) ![PyPI - Status](https://img.shields.io/pypi/status/ifpd2)  
+![](https://img.shields.io/github/release/ggirelli/ifpd2.svg?style=flat) ![](https://img.shields.io/github/release-date/ggirelli/ifpd2.svg?style=flat) ![](https://img.shields.io/github/languages/code-size/ggirelli/ifpd2.svg?style=flat)  
+![](https://img.shields.io/github/watchers/ggirelli/ifpd2.svg?label=Watch&style=social) ![](https://img.shields.io/github/stars/ggirelli/ifpd2.svg?style=social)
+
+[PyPi](https://pypi.org/project/ifpd2/) | [docs](https://ggirelli.github.io/ifpd2/)
+
+`ifpd2` is a Python3.7+ package containing tools for selection of complementary oligonucleotides to build iFISH probes. It is based on our previous `ifpd` package, but works with a different and more detailed database format, allowing for more precise control on the probe design process. Read the online [documentation](https://ggirelli.github.io/ifpd2/) for more details.
+
+## Requirements
+
+`ifpd2` is fully implemented in Python3.7+, thus you need the corresponding Python version to run it. Check out [here](https://realpython.com/installing-python/) how to install Python+ on your machine if you don't have it yet.
+
+`ifpd2` has been tested with Python 3.7 and 3.8. We recommend installing it using `pipx` (see [below](https://github.com/ggirelli/ifpd2#installation)) to avoid dependency conflicts with other packages. The packages it depends on are listed in our [dependency graph](https://github.com/ggirelli/ifpd2/network/dependencies). We use [`poetry`](https://github.com/python-poetry/poetry) to handle our dependencies.
+
+## Installation
+
+We recommend installing `ifpd2` using [`pipx`](https://github.com/pipxproject/pipx). Check how to install `pipx` [here](https://github.com/pipxproject/pipx#install-pipx) if you don't have it yet!
+
+Once you have `pipx` ready on your system, install the latest stable release of `ifpd2` by running: `pipx install ifpd2`. If you see the stars (✨ 🌟 ✨), then the installation went well!
+
+## Usage
+
+All `ifpd2` commands are accessible via the `ifpd2` keyword on the terminal. For each command, you can access its help page by using the `-h` option. More details on how to run `ifpd2` are available in the online [documentation](https://ggirelli.github.io/ifpd2).
+
+## Contributing
+
+We welcome any contributions to `ifpd2`. In short, we use [`black`](https://github.com/psf/black) to standardize code format. Any code change also needs to pass `mypy` checks. For more details, please refer to our [contribution guidelines](https://github.com/ggirelli/ifpd2/blob/main/CONTRIBUTING.md) if this is your first time contributing! Also, check out our [code of conduct](https://github.com/ggirelli/ifpd2/blob/main/CODE_OF_CONDUCT.md).
+
+## License
+
+`MIT License - Copyright (c) 2021 Gabriele Girelli`

ifpd2/const.py

@@ -3,4 +3,4 @@
 @contact: gigi.ga90@gmail.com
 """
 
-__version__ = "2.0.5"
+__version__ = "1.0.0-alpha"

ifpd2/walker2.py

@@ -0,0 +1,59 @@
+"""
+@author: Gabriele Girelli
+@contact: gigi.ga90@gmail.com
+"""
+
+import logging
+import pandas as pd  # type: ignore
+from typing import Tuple, Union
+
+
+class GenomicWindowSet(object):
+    _window_data: pd.DataFrame = pd.DataFrame(
+        columns=[
+            "set_id",
+            "window_id",
+            "start",
+            "end",
+            "focus_start",
+            "focus_end",
+        ]
+    )
+    _window_id: int = -1
+
+    feature: str  # Chromosome
+    region: Tuple[int, int]
+
+    n_probes: int
+    window_size: int
+    window_shift: float
+
+    # Either in nt (x>1) or fraction of window_size (0<x<=1)
+    focus_size: Union[int, float]
+    # Either in nt (x>1) or fraction of focus_size (0<x<=1)
+    focus_step: Union[int, float]
+
+    _growing: bool = False
+
+    def __init__(self, region: Tuple[int, int]):
+        super(GenomicWindowSet, self).__init__()
+        self.region = region
+        assert self.region[0] <= self.region[1]
+
+    @property
+    def growing(self) -> bool:
+        return self._growing
+
+    @property
+    def reached_last_window(self) -> bool:
+        return (self._window_id + 1) == self._window_data.shape[0]
+
+    def init_windows_for_n_probes(self, n_probes: int) -> None:
+        if 0 < self._window_data.shape[0]:
+            logging.warning("cannot re-initalize windows.")
+            return
+
+    def init_windows_by_size(self, size: int, shift: float) -> None:
+        if 0 < self._window_data.shape[0]:
+            logging.warning("cannot re-initalize windows.")
+            return

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ifpd2"
-version = "0.0.1"
+version = "1.0.0-alpha"
 description = "An iFISH probe design pipeline (II)"
 authors = ["Gabriele Girelli <gigi.ga90@gmail.com>"]
 license = "MIT"