Merge pull request #31 from KristinaGomoryova/pypi_cleanup

Pypi cleanup

CHANGELOG.md

@@ -6,10 +6,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [0.0.1] - 1900-12-31
+## [0.1.0] - 2024-07-15
 
 ### Added
 
+- function to read the metadata or alkane file in csv/tsv/xls/xlsx format
+- function to process the metadata file: validate file names, derive and rearrange additional metadata columns
+- function to save the processed metadata or alkane dataframe as tsv
+
 ### Removed
 
 ### Changed

CITATION.cff

@@ -13,5 +13,7 @@ repository-code: "https://github.com/RECETOX/rcx-tk"
 keywords:
   - rcx
   - process metadata
+  - alkanes
+  - metabolomics
 message: "If you use this software, please cite it using these metadata."
 license: MIT

README.dev.md

@@ -2,26 +2,31 @@
 
 If you're looking for user documentation, go [here](README.md).
 
-## Development install
+## Package installation
 
-```shell
-# Create a virtual environment, e.g. with
-python -m venv env
+To create a new environment, use the micromamba:
+
+```console
+micromamba create -n rcx-tk poetry
+micromamba activate rcx-tk
+```
+To install all dependencies specified in the `pyproject.toml` file, use poetry:
 
-# activate virtual environment
-source env/bin/activate
+```console
+poetry install
+```
 
-# make sure to have a recent version of pip and setuptools
-python -m pip install --upgrade pip setuptools
+A command line interface was also implemented using Click, so the package can be run by either using python3:
 
-# (from the project root directory)
-# install rcx_tk as an editable package
-python -m pip install --no-cache-dir --editable .
-# install development dependencies
-python -m pip install --no-cache-dir --editable .[dev]
+```console
+python3 -m rcx_tk --method='' <path-to-input-data> <path-to-output-data>
 ```
 
-Afterwards check that the install directory is present in the `PATH` environment variable.
+or using poetry:
+
+```console
+poetry run rcx_tk --method='' <file-path-to-input-data> <file-path-to-output-data>
+```
 
 ## Running the tests
 
@@ -116,9 +121,9 @@ make doctest
 Bumping the version across all files is done with [bump-my-version](https://github.com/callowayproject/bump-my-version), e.g.
 
 ```shell
-bump-my-version bump major  # bumps from e.g. 0.3.2 to 1.0.0
-bump-my-version bump minor  # bumps from e.g. 0.3.2 to 0.4.0
-bump-my-version bump patch  # bumps from e.g. 0.3.2 to 0.3.3
+poetry version major  # bumps from e.g. 0.3.2 to 1.0.0
+poetry version minor  # bumps from e.g. 0.3.2 to 0.4.0
+poetry version patch  # bumps from e.g. 0.3.2 to 0.3.3
 ```
 
 ## Making a release
@@ -145,50 +150,37 @@ In a new terminal:
 # has the state of origin/main branch
 cd $(mktemp -d rcx_tk.XXXXXX)
 git clone [email protected]:RECETOX/rcx-tk .
+```
 
-# make sure to have a recent version of pip and the publishing dependencies
-python -m pip install --upgrade pip
-python -m pip install .[publishing]
-
-# create the source distribution and the wheel
-python -m build
+Create and activate a new environment:
 
-# upload to test pypi instance (requires credentials)
-python -m twine upload --repository testpypi dist/*
+```console
+micromamba create -n rcx-tk-pypi poetry
+micromamba activate rcx-tk-pypi
 ```
 
-Visit
-[https://test.pypi.org/project/rcx_tk](https://test.pypi.org/project/rcx_tk)
-and verify that your package was uploaded successfully. Keep the terminal open, we'll need it later.
+Create an account on PyPI.
 
-In a new terminal, without an activated virtual environment or an env directory:
+In the Account settings, find the API tokens section and click on "Add API token". Copy your token.
 
-```shell
-cd $(mktemp -d rcx_tk-test.XXXXXX)
+Add your API token to Poetry:
 
-# prepare a clean virtual environment and activate it
-python -m venv env
-source env/bin/activate
+```console
+poetry config pypi-token.pypi your-api-token
+```
 
-# make sure to have a recent version of pip and setuptools
-python -m pip install --upgrade pip
+Build your project:
 
-# install from test pypi instance:
-python -m pip -v install --no-cache-dir \
---index-url https://test.pypi.org/simple/ \
---extra-index-url https://pypi.org/simple rcx_tk
+```console
+poetry build
 ```
 
-Check that the package works as it should when installed from pypitest.
-
-Then upload to pypi.org with:
+Publish your package to PyPI:
 
-```shell
-# Back to the first terminal,
-# FINAL STEP: upload to PyPI (requires credentials)
-python -m twine upload dist/*
+```console
+poetry publish
 ```
 
 ### (3/3) GitHub
 
-Don't forget to also make a [release on GitHub](https://github.com/RECETOX/rcx-tk/releases/new). If your repository uses the GitHub-Zenodo integration this will also trigger Zenodo into making a snapshot of your repository and sticking a DOI on it.
+Don't forget to also make a [release on GitHub](https://github.com/RECETOX/rcx-tk/releases/new). If your repository uses the GitHub-Zenodo integration this will also trigger Zenodo into making a snapshot of your repository and sticking a DOI on it.

README.md

@@ -1,7 +1,5 @@
 ## Badges
 
-(Customize these badges with your own links, and check https://shields.io/ or https://badgen.net/ to see which other badges are available.)
-
 | fair-software.eu recommendations | |
 | :-- | :--  |
 | (1/5) code repository              | [![github repo badge](https://img.shields.io/badge/github-repo-000.svg?logo=github&labelColor=gray&color=blue)](https://github.com/RECETOX/rcx-tk) |
@@ -21,9 +19,16 @@
 
 ## How to use rcx_tk
 
-Tools for internal use
+`rcx-tk` package provides tools to process the metadata or alkane files.
+
+On the input, the user is expected to supply a path to the metadata/alkane file in tsv/csv/xls/xlsx file. The file is then converted to a dataframe which is further processed. The main steps are:
+
+- columns rearrangement
+- validation of the file names
+- validation that the `injectionNumber` column is of integer type
+- derivation of new metadata: `sampleName`, `sequenceIdentifier`, `sampleIdentifier` and `localOrder`
 
-The project setup is documented in [project_setup.md](project_setup.md). Feel free to remove this document (and/or the link to this document) if you don't need it.
+Finally, the processed dataframe is saved into user-defined location.
 
 ## Installation
 
@@ -32,12 +37,23 @@ To install rcx_tk from GitHub repository, do:
 ```console
 git clone [email protected]:RECETOX/rcx-tk.git
 cd rcx-tk
-python -m pip install .
+poetry install
+```
+
+The main functions are process_metadata_file and process_alkane_ri_file.
+
+The tool can be run also using command-line interface, either by the python3 or poetry:
+
+```console
+python3 <path-to-__main.py__> --method='' <path-to-input-data> <path-to-output-data>
 ```
 
+```console
+poetry run rcx_tk --method='' <file-path-to-input-data> <file-path-to-output-data>
+```
 ## Documentation
 
-Include a link to your project's full documentation here.
+The project is documented [here](https://rcx-tk.readthedocs.io/en/latest/?badge=latest).
 
 ## Contributing
 

project_setup.md

@@ -11,9 +11,6 @@ checklist](https://guide.esciencecenter.nl/#/best_practices/checklist).
 
 This repository is set up with Python versions:
 
-- 3.8
-- 3.9
-- 3.10
 - 3.11
 - 3.12
 
@@ -23,19 +20,23 @@ versions.
 
 ## Package management and dependencies
 
-You can use either pip or conda for installing dependencies and package management. This repository does not force you
-to use one or the other, as project requirements differ. For advice on what to use, please check [the relevant section
-of the
-guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=dependencies-and-package-management).
+For installing the dependencies and package management, [micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) and [poetry](https://python-poetry.org/) have been used.
 
-- Runtime dependencies should be added to `pyproject.toml` in the `dependencies` list under `[project]`.
-- Development dependencies should be added to `pyproject.toml` in one of the lists under `[project.optional-dependencies]`.
+The dependencies are listed in the `pyproject.toml` file under the section `[tool.poetry.dependencies]` and `[tool.poetry.group.dev.dependencies]`.
 
 ## Packaging/One command install
 
-You can distribute your code using PyPI.
-[The guide](https://guide.esciencecenter.nl/#/best_practices/language_guides/python?id=building-and-packaging-code) can
-help you decide which tool to use for packaging.
+To create a new environment, use the micromamba:
+
+```console
+micromamba create -n rcx-tk poetry
+micromamba activate rcx-tk
+```
+To install all dependencies specified in the `pyproject.toml` file, use poetry:
+
+```console
+poetry install
+```
 
 ## Testing and code coverage
 
@@ -114,4 +115,4 @@ help you decide which tool to use for packaging.
 ## NOTICE
 
 - List of attributions of this project and Apache-license dependencies
-- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/licensing?id=notice)
+- [Relevant section in the guide](https://guide.esciencecenter.nl/#/best_practices/licensing?id=notice)

pyproject.toml

@@ -2,7 +2,7 @@
 name = "rcx-tk"
 version = "0.1.0"
 description = "This package adjusts and cleans the metadata file provided by a user."
-authors = ["Zargham Ahmad <[email protected]>" ]
+authors = ["Zargham Ahmad <[email protected]>" , "Kristina Gomoryova <[email protected]>"]
 license = "MIT"
 readme = "README.md"
 keywords = ["metadata", "alkanes", "metabolomics"]
@@ -117,17 +117,11 @@ known-first-party = ["rcx_tk"]
 force-single-line = true
 no-lines-before = ["future","standard-library","third-party","first-party","local-folder"]
 
-[[tool.bumpversion.files]]
-filename = "src/rcx_tk/__init__.py"
-
-[[tool.bumpversion.files]]
-filename = "pyproject.toml"
-
-[[tool.bumpversion.files]]
-filename = "CITATION.cff"
-
-[[tool.bumpversion.files]]
-filename = "docs/conf.py"
-
 [tool.poetry.scripts]
 rcx_tk = "rcx_tk.__main__:main"
+
+[tool.poetry_bumpversion.file."src/rcx_tk/__init__.py"]
+[tool.poetry_bumpversion.file."CITATION.cff"]
+[tool.poetry_bumpversion.file."docs/conf.py"]
+[tool.poetry_bumpversion.file."pyproject.toml"]
+