Prepare for 0.3.2

CHANGELOG.md

@@ -8,6 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - data/Data.py: Added `update_possible_rt_keys()` and `update_possible_ri_keys()` methods for `Data` class.
 Now users can supply their own identifiers for RT/RI columns (csv files) and identifiers (msp) in their data. [#74](https://github.com/RECETOX/RIAssigner/pull/74)
+- General: Added missing documentation and updated [README](README.md). [#80](https://github.com/RECETOX/RIAssigner/pull/80)
+- setup.py: Added versions for dependencies. [#80](https://github.com/RECETOX/RIAssigner/pull/80)
 ### Changed
 - data/Data.py: Unified default RT/RI column identifiers between `PandasData` and `MatchMSData` classes. [#74](https://github.com/RECETOX/RIAssigner/pull/74)
 - data/MatchMSData.py: `MatchMSData` class now looks up for RT and RI identifiers from within default identifiers list

README.md

@@ -6,18 +6,29 @@
 [![bioconda package](https://img.shields.io/conda/v/bioconda/riassigner)](https://anaconda.org/bioconda/riassigner)
 
 ## Overview
-RIAssigner is a python tool for retention index (RI) computation for GC-MS data developed at [RECETOX](https://www.recetox.muni.cz/en).
+RIAssigner is a python tool for retention index (RI) computation for GC-MS data developed at [RECETOX](https://www.recetox.muni.cz/en) and hosted on [Galaxy](https://umsa.cerit-sc.cz/).
 
-The [retention index](https://goldbook.iupac.org/terms/view/R05360) is a mapping of retention time, making the retention time of compounds on different columns comparable, i.e to compounds might have different retention times on different columns, but a very similar retention index. To compute this index, a set of reference compounds - often an inert alkane series - is analyzed as part of the batch (on the same column). The retention index of the alkanes are fixed (carbon number x 100) and any query compounds can be assigned a retention index depending on its retention time. This can be done via piecewise linear interpolation or other mathematical methods.
+The [retention index](https://goldbook.iupac.org/terms/view/R05360) is a mapping of retention time, making the retention data of compounds comparable, i.e. two compounds might have different retention times in different experiments, but a very similar retention index.
+To compute this index, a set of reference compounds - often an inert alkane series - is analyzed as part of the batch (on the same column).
+The retention index of the alkanes are fixed (carbon number x 100) and any query compounds can be assigned a retention index depending on its retention time.
+This can be done via piece wise linear interpolation or other mathematical methods.
 
 ## Installation
-Installation is currently possible by creating the conda environment with `conda env create -f conda/environment-dev.yml` and then installing the package with `python -m pip install -e .`
 
-Install via [bioconda](https://anaconda.org/bioconda/riassigner) using `conda install -c bioconda riassigner`
+(1) From source by cloning the repository and then installing the package with `pip`.
+```
+git clone https://github.com/RECETOX/RIAssigner.git
+cd RIAssigner
+python -m pip install -e .
+```
+(2) Install via [bioconda](https://anaconda.org/bioconda/riassigner) in your existing evironment.
+```
+conda install -c bioconda riassigner
+```
 
 ## Usage
 RIAssigner can be used to read data from `.msp`, `.csv` and `.tsv` files using [matchms](https://github.com/matchms/matchms) and [pandas](https://pandas.pydata.org/) and to compute the retention indices for the data.
-A reference list of retention indexed compounds (traditionally an Alkane series) with retention times is used to compute the RI for a query dataset of retention time values using the [van Den Dool and Kratz](https://doi.org/10.1016/S0021-9673(01)80947-X) method or by using [cubic spline based interpolation](https://doi.org/10.1021/ac50035a026).
+A reference list of retention indexed compounds (traditionally an Alkane series) with retention times is used to compute the RI for a query dataset of retention time values using the [van Den Dool and Kratz](https://doi.org/10.1016/S0021-9673(01)80947-X) method or by using [cubic spline-based interpolation](https://doi.org/10.1021/ac50035a026).
 ### Example
 ```python
 from RIAssigner.compute import Kovats
@@ -31,11 +42,14 @@ reference = MatchMSData("../tests/data/msp/Alkanes_20210325.msp", "msp", rt_unit
 query.retention_indices = Kovats().compute(query, reference)
 query.write("peaks_with_rt.csv")
 ```
-For more details check out this [notebook](doc/example_usage.ipynb) or try this tool on [Galaxy](https://umsa.cerit-sc.cz/).
+For more details check out this [notebook](doc/example_usage.ipynb).
 
 ## Developer Documentation
 ### Setup
-Create your development environment using the provided [script](conda/environment-dev.yml) via conda to install all required dependencies, including linter and testing frameworks.
+Create your development conda environment using the provided [file](conda/environment-dev.yml) to install all required dependencies, including linter and testing frameworks.
+```
+conda env create -f conda/environment-dev.yml
+```
 
 ### Contributing
 We appreciate contributions - feel free to open an issue on our repository, create your own fork, work on the problem and pose a PR.
@@ -65,13 +79,13 @@ classDiagram
         +read(string filename)
         +write(string filename)
         +retention_times() List~float~
-        +retention_indices() List~int~
+        +retention_indices() List~float~
     }
 
 
     class ComputationMethod{
         <<interface>>
-        +compute(Data query, Data reference) List~int~
+        +compute(Data query, Data reference) List~float~
 
     }
 

RIAssigner/__init__.py

@@ -4,8 +4,6 @@
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
-__author__ = "Helge Hecht"
-__email__ = 'helge.hecht@recetox.muni.cz'
 __all__ = [
     "__version__",
 ]

RIAssigner/__main__.py

@@ -1,5 +1,4 @@
 import sys
-from typing import Tuple
 from RIAssigner.compute.ComputationMethod import ComputationMethod
 import argparse
 

RIAssigner/cli/LoadDataAction.py

@@ -4,10 +4,27 @@
 
 
 class LoadDataAction(argparse.Action):
+    """Method to create a `Data` instance.
+    Inherits from `argparse.Action`.
+    """
     def __init__(self, option_strings, dest, **kwargs):
+        """Constructor
+
+        Args:
+            option_strings (List[str]): See argparse.Action.
+            dest (str): See argparse.Action.
+        """
         super().__init__(option_strings, dest, **kwargs)
 
     def __call__(self, parser, namespace, values, option_string=None):
+        """Overloaded function from `argparse.Action` which is called upon invocation.
+
+        Args:
+            parser (argparse.ArgumentParser): Argument parser with args.
+            namespace: namespace object.
+            values (List[object]): Values passed as parameters to the Action.
+            option_strings (List[str]): See argparse.Action.
+        """
         filename = values[0]
         filetype = values[1]
         rt_unit = values[2]

RIAssigner/compute/ComputationMethod.py

@@ -7,6 +7,15 @@ class ComputationMethod(ABC):
 
     @abstractmethod
     def compute(self, query: Data, reference: Data) -> List[float]:
+        """Abstract method for RI computation
+
+        Args:
+            query (Data): Dataset for which to compute the RI
+            reference (Data): Dataset with retention times & retention index for reference.
+
+        Returns:
+            List[float]: Computed retention indices
+        """
         ...
 
     def _check_data_args(self, query, reference):

RIAssigner/data/Data.py

@@ -16,6 +16,14 @@ class Data(ABC):
 
     @staticmethod
     def is_valid(rt: RetentionTimeType) -> bool:
+        """Determine whether a retention time value is valid
+
+        Args:
+            rt (RetentionTimeType): Value to check for validity.
+
+        Returns:
+            bool: State of validity (True/False).
+        """
         return rt is not None and rt >= 0.0
 
     @classmethod
@@ -55,27 +63,54 @@ def __init__(self, filename: str, filetype: str, rt_unit: str):
 
     @abstractmethod
     def read(self):
+        """Method to initialize internal data storage.
+        """
         ...
 
     @abstractmethod
     def write(self, filename):
+        """Store current content to disk.
+
+        Args:
+            filename (str): Path to output filename.
+        """
         ...
 
     @property
-    def filename(self):
+    def filename(self) -> str:
+        """Getter for filename property.
+
+        Returns:
+            str: Filename of originally loaded data.
+        """
         return self._filename
 
     @property
     @abstractmethod
     def retention_times(self) -> Iterable[RetentionTimeType]:
+        """Getter for `retention_times` property.
+
+        Returns:
+            Iterable[RetentionTimeType]: RT values contained in data.
+        """
         ...
 
     @property
     @abstractmethod
     def retention_indices(self) -> Iterable[RetentionIndexType]:
+        """Getter for `retention_indices` property.
+
+        Returns:
+            Iterable[RetentionIndexType]: RI values stored in data.
+        """
         ...
 
     @retention_indices.setter
     @abstractmethod
     def retention_indices(self, value: Iterable[RetentionIndexType]):
+        """Setter for `retention_indices` variable.
+
+        Args:
+            value (Iterable[RetentionIndexType]): Values to assign to property.
+        """
         ...

RIAssigner/data/MatchMSData.py

@@ -69,6 +69,14 @@ def _sort_spectra_by_rt(self):
         self._spectra.sort(key=lambda spectrum: safe_read_key(spectrum, self._rt_key))
 
     def __eq__(self, o: object) -> bool:
+        """Comparison operator `==`.
+
+        Args:
+            o (object): Object to compare with.
+
+        Returns:
+            bool: State of equality.
+        """
         if not isinstance(o, MatchMSData):
             return False
         other: MatchMSData = o

RIAssigner/data/PandasData.py

@@ -64,6 +64,14 @@ def _sort_by_rt(self):
         self._data.sort_values(by=self._rt_index, axis=0, inplace=True)
 
     def __eq__(self, o: object) -> bool:
+        """Comparison operator `==`.
+
+        Args:
+            o (object): Object to compare with.
+
+        Returns:
+            bool: State of equality.
+        """
         if not isinstance(o, PandasData):
             return False
         other: PandasData = o
@@ -97,4 +105,9 @@ def _ri_from_carbon_numbers(self):
 
     @retention_indices.setter
     def retention_indices(self, values: Iterable[int]):
+        """Setter for `retention_indices` property.
+
+        Args:
+            values (Iterable[int]): Values to assign.
+        """
         self._data[self._ri_index] = values

setup.py

@@ -20,7 +20,8 @@
     long_description=readme,
     long_description_content_type="text/markdown",
     author="Helge Hecht, Maksym Skoryk",
-    author_email="helge.hecht@recetox.muni.cz, 245816@muni.cz",
+    author_email="helge.hecht@recetox.muni.cz, maksym.skoryk@recetox.muni.cz",
+
     maintainer="RECETOX",
     maintainer_email="GalaxyToolsDevelopmentandDeployment@space.muni.cz",
     url="https://github.com/RECETOX/RIAssigner",
@@ -46,10 +47,10 @@
     test_suite="tests",
     python_requires='>=3.7',
     install_requires=[
-        "matchms",
+        "matchms>=0.9.1",
         "numpy",
         "pandas",
-        "pint",
+        "pint>=0.17",
         "scipy"
     ],
     extras_require={